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CNS & Neurological Disorders - Drug Targets

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Review Article

Comprehensive Perspective Towards the Management of Proteinopathies by Elucidating Protein Misfolding and Aggregation

Author(s): Ishfaq Ahmad Ahanger, Ghulam Md. Ashraf*, Anurag Sharma* and Asimul Islam*

Volume 23, Issue 2, 2024

Published on: 17 April, 2023

Page: [153 - 180] Pages: 28

DOI: 10.2174/1871527322666230306085937

Price: $65

Abstract

Protein misfolding and aggregation is the phenomenon of the generic propensity of proteins, considered as a dark side of the protein world, and its exact mechanism is still not deciphered. Understanding the complexity of protein aggregation is currently the primary apprehension and challenge in biology and medicine due to their association with various debilitating human proteinopathies and neurodegenerative diseases. The mechanism of protein aggregation, associated diseases, and the development of efficient therapeutic strategies against these diseases are very challenging. These diseases are caused by different proteins, each protein with different mechanisms and consisting of various microscopic phases or events. These microscopic steps are functioning on different timescales during aggregation. Here, we highlighted the different features and current trends in protein aggregation. The study thoroughly recapitulates the various factors influencing, possible causes, types of aggregates and aggregation, their different proposed mechanisms, and the methods used to study the aggregation. Additionally, the formation and elimination of misfolded or aggregated proteins in the cell, the role of the ruggedness of the protein folding landscape in protein aggregation, proteinopathies, and the challenges for their prevention are comprehensively elucidated. A holistic understanding of different aspects of aggregation, molecular steps governing the various features of protein quality control, and crucial queries about the modulation of these processes and their interactions with other systems in cellular protein quality control can be considered conducive to comprehending the mechanism, designing effective approaches towards prevention of protein aggregation, rationalizing the etiology and development of novel strategies against therapy and management of the proteinopathies.

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[1]
Dobson CM. Protein misfolding, evolution and disease. Trends Biochem Sci 1999; 24(9): 329-32.
[http://dx.doi.org/10.1016/S0968-0004(99)01445-0] [PMID: 10470028]
[2]
Cohen FE, Kelly JW. Therapeutic approaches to protein-misfolding diseases. Nature 2003; 426(6968): 905-9.
[http://dx.doi.org/10.1038/nature02265] [PMID: 14685252]
[3]
Chiti F, Dobson CM. Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 2006; 75(1): 333-66.
[http://dx.doi.org/10.1146/annurev.biochem.75.101304.123901] [PMID: 16756495]
[4]
Soto C. Unfolding the role of protein misfolding in neurodegenerative diseases. Nat Rev Neurosci 2003; 4(1): 49-60.
[http://dx.doi.org/10.1038/nrn1007] [PMID: 12511861]
[5]
Soto C, Estrada LD. Protein misfolding and neurodegeneration. Arch Neurol 2008; 65(2): 184-9.
[http://dx.doi.org/10.1001/archneurol.2007.56] [PMID: 18268186]
[6]
Soto C. Protein misfolding and disease; protein refolding and therapy. FEBS Lett 2001; 498(2-3): 204-7.
[http://dx.doi.org/10.1016/S0014-5793(01)02486-3] [PMID: 11412858]
[7]
Ahmad S, Kumar V, Ramanand KB, Rao NM. Probing protein stability and proteolytic resistance by loop scanning: A comprehensive mutational analysis. Protein Sci 2012; 21(3): 433-46.
[http://dx.doi.org/10.1002/pro.2029] [PMID: 22246996]
[8]
Mitidieri FE, Wagner JR. Coalescence of o/w emulsions stabilized by whey and isolate soybean proteins. Influence of thermal denaturation, salt addition and competitive interfacial adsorption. Food Res Int 2002; 35(6): 547-57.
[http://dx.doi.org/10.1016/S0963-9969(01)00155-7]
[9]
Sanfelice D, Temussi PA. Cold denaturation as a tool to measure protein stability. Biophys Chem 2016; 208: 4-8.
[http://dx.doi.org/10.1016/j.bpc.2015.05.007] [PMID: 26026885]
[10]
Langer R, Folkman J. Polymers for the sustained release of proteins and other macromolecules. Nature 1976; 263(5580): 797-800.
[http://dx.doi.org/10.1038/263797a0] [PMID: 995197]
[11]
Vendruscolo M, Zurdo J, MacPhee CE, Dobson CM. Protein folding and misfolding: a paradigm of self–assembly and regulation in complex biological systems. Philosophical Transactions of the Royal Society of London Series A: Mathematical. Phy Engin Sci 1807; 2003(361): 1205-22.
[12]
Katchalski-Katzir E. Conformational changes in biological macromolecules. Biorheology 1984; 21(1-2): 57-74.
[http://dx.doi.org/10.3233/BIR-1984-211-211] [PMID: 6466797]
[13]
Apic G, Russell RB. Domain recombination: a workhorse for evolutionary innovation. Sci Signal 2010; 3(139): pe30.
[http://dx.doi.org/10.1126/scisignal.3139pe30] [PMID: 20841565]
[14]
Galburt EA, Pelletier J, Wilson G, Stoddard BL. Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase. Structure 2002; 10(9): 1249-60.
[http://dx.doi.org/10.1016/S0969-2126(02)00835-3] [PMID: 12220496]
[15]
Jalkanen KJ, Elstner M, Suhai S. Amino acids and small peptides as building blocks for proteins: comparative theoretical and spectroscopic studies. J Mol Struct THEOCHEM 2004; 675(1-3): 61-77.
[http://dx.doi.org/10.1016/j.theochem.2003.12.045]
[16]
Privalov PL, Makhatadze GI. Heat capacity of proteins. J Mol Biol 1990; 213(2): 385-91.
[http://dx.doi.org/10.1016/S0022-2836(05)80198-6] [PMID: 2160545]
[17]
Uversky VN. Protein folding revisited. A polypeptide chain at the folding? misfolding? nonfolding cross-roads: which way to go? Cell Mol Life Sci 2003; 60(9): 1852-71.
[http://dx.doi.org/10.1007/s00018-003-3096-6] [PMID: 14523548]
[18]
Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J 1986; 5(4): 823-6.
[http://dx.doi.org/10.1002/j.1460-2075.1986.tb04288.x] [PMID: 3709526]
[19]
Pauling L, Corey RB, Branson HR. The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci 1951; 37(4): 205-11.
[http://dx.doi.org/10.1073/pnas.37.4.205] [PMID: 14816373]
[20]
Kajava AV. Review: proteins with repeated sequence structural prediction and modeling. J Struct Biol 2001; 134(2-3): 132-44.
[http://dx.doi.org/10.1006/jsbi.2000.4328] [PMID: 11551175]
[21]
Kajava AV, Vassart G, Wodak SJ. Modeling of the three-dimensional structure of proteins with the typical leucine rich repeats. Structure 1995; 3(9): 867-77.
[http://dx.doi.org/10.1016/S0969-2126(01)00222-2] [PMID: 8535781]
[22]
O’Brien JS. Cell membranes—composition: structure: Function. J Theor Biol 1967; 15(3): 307-24.
[http://dx.doi.org/10.1016/0022-5193(67)90140-3] [PMID: 5339810]
[23]
Baker D. A surprising simplicity to protein folding. Nature 2000; 405(6782): 39-42.
[http://dx.doi.org/10.1038/35011000] [PMID: 10811210]
[24]
Dobson CM. Protein folding and misfolding. Nature 2003; 426(6968): 884-90.
[http://dx.doi.org/10.1038/nature02261] [PMID: 14685248]
[25]
Dobson CM. Principles of protein folding, misfolding and aggregation. Seminars in cell & developmental biology 2004; 3-16.
[26]
Baker D, Agard DA. Kinetics versus thermodynamics in protein folding. Biochemistry 1994; 33(24): 7505-9.
[http://dx.doi.org/10.1021/bi00190a002] [PMID: 8011615]
[27]
Hill RB, Raleigh DP, Lombardi A, DeGrado WF. De novo design of helical bundles as models for understanding protein folding and function. Acc Chem Res 2000; 33(11): 745-54.
[http://dx.doi.org/10.1021/ar970004h] [PMID: 11087311]
[28]
Wang W, Nema S, Teagarden D. Protein aggregation—Pathways and influencing factors. Int J Pharm 2010; 390(2): 89-99.
[http://dx.doi.org/10.1016/j.ijpharm.2010.02.025] [PMID: 20188160]
[29]
Otzen DE. Protein unfolding in detergents: effect of micelle structure, ionic strength, pH, and temperature. Biophys J 2002; 83(4): 2219-30.
[http://dx.doi.org/10.1016/S0006-3495(02)73982-9] [PMID: 12324439]
[30]
Karantza V, Baxevanis AD, Freire E, Moudrianakis EN. Thermodynamic studies of the core histones: Ionic strength and pH dependence of H2A-H2B dimer stability. Biochemistry 1995; 34(17): 5988-96.
[http://dx.doi.org/10.1021/bi00017a028] [PMID: 7727455]
[31]
Levinthal C. Are there pathways for protein folding? J Chim Phys 1968; 65: 44-5.
[http://dx.doi.org/10.1051/jcp/1968650044]
[32]
Creighton TE. Protein folding. Biochem J 1990; 270(1): 1-16.
[http://dx.doi.org/10.1042/bj2700001] [PMID: 2204340]
[33]
Onuchic JN, Wolynes PG. Theory of protein folding. Curr Opin Struct Biol 2004; 14(1): 70-5.
[http://dx.doi.org/10.1016/j.sbi.2004.01.009] [PMID: 15102452]
[34]
Karplus M, Weaver DL. Protein-folding dynamics. Nature 1976; 260(5550): 404-6.
[http://dx.doi.org/10.1038/260404a0] [PMID: 1256583]
[35]
Gething MJ, Sambrook J. Protein folding in the cell. Nature 1992; 355(6355): 33-45.
[http://dx.doi.org/10.1038/355033a0] [PMID: 1731198]
[36]
Dobson C. Experimental investigation of protein folding and misfolding. Methods 2004; 34(1): 4-14.
[http://dx.doi.org/10.1016/j.ymeth.2004.03.002] [PMID: 15283911]
[37]
Englander SW, Mayne L, Krishna MMG. Protein folding and misfolding: mechanism and principles. Q Rev Biophys 2007; 40(4): 1-41.
[http://dx.doi.org/10.1017/S0033583508004654] [PMID: 18405419]
[38]
Ecroyd H, Carver JA. Unraveling the mysteries of protein folding and misfolding. IUBMB Life 2008; 60(12): 769-74.
[http://dx.doi.org/10.1002/iub.117] [PMID: 18767168]
[39]
Capaldi AP, Kleanthous C, Radford SE. Im7 folding mechanism: misfolding on a path to the native state. Nat Struct Biol 2002; 9(3): 209-16.
[http://dx.doi.org/10.1038/nsb757] [PMID: 11875516]
[40]
Komar AA. A pause for thought along the co-translational folding pathway. Trends Biochem Sci 2009; 34(1): 16-24.
[http://dx.doi.org/10.1016/j.tibs.2008.10.002] [PMID: 18996013]
[41]
Beaudoin S, Goggin K, Bissonnette C, Grenier C, Roucou X. Aggresomes do not represent a general cellular response to protein misfolding in mammalian cells. BMC Cell Biol 2008; 9(1): 59.
[http://dx.doi.org/10.1186/1471-2121-9-59] [PMID: 18937858]
[42]
Escusa-Toret S, Vonk WIM, Frydman J. Spatial sequestration of misfolded proteins by a dynamic chaperone pathway enhances cellular fitness during stress. Nat Cell Biol 2013; 15(10): 1231-43.
[http://dx.doi.org/10.1038/ncb2838] [PMID: 24036477]
[43]
Bayley H. Protein therapy—delivery guaranteed. Nat Biotechnol 1999; 17(11): 1066-7.
[http://dx.doi.org/10.1038/15050] [PMID: 10545909]
[44]
Chen M, Vonmikecz A. Formation of nucleoplasmic protein aggregates impairs nuclear function in response to SiO nanoparticles. Exp Cell Res 2005; 305(1): 51-62.
[http://dx.doi.org/10.1016/j.yexcr.2004.12.021] [PMID: 15777787]
[45]
Feingold V, Jenkins AB, Kraegen EW. Effect of contact material on vibration-induced insulin aggregation. Diabetologia 1984; 27(3): 373-8.
[http://dx.doi.org/10.1007/BF00304853] [PMID: 6389243]
[46]
Chi EY, Krishnan S, Randolph TW, Carpenter JF. Physical stability of proteins in aqueous solution: mechanism and driving forces in nonnative protein aggregation. Pharm Res 2003; 20(9): 1325-36.
[http://dx.doi.org/10.1023/A:1025771421906] [PMID: 14567625]
[47]
Jucker M, Walker LC. Self-propagation of pathogenic protein aggregates in neurodegenerative diseases. Nature 2013; 501(7465): 45-51.
[http://dx.doi.org/10.1038/nature12481] [PMID: 24005412]
[48]
Sipe JD, Benson MD, Buxbaum JN, et al. Amyloid fibril proteins and amyloidosis: chemical identification and clinical classification International Society of Amyloidosis 2016 Nomenclature Guidelines. Amyloid 2016; 23(4): 209-13.
[http://dx.doi.org/10.1080/13506129.2016.1257986] [PMID: 27884064]
[49]
Goedert M, Spillantini MG, Del Tredici K, Braak H. 100 years of Lewy pathology. Nat Rev Neurol 2013; 9(1): 13-24.
[http://dx.doi.org/10.1038/nrneurol.2012.242] [PMID: 23183883]
[50]
Roos N, Islam MM, Thilsted SH. Small indigenous fish species in bangladesh: contribution to vitamin A, calcium and iron intakes. J Nutr 2003; 133(11) (Suppl. 2): 4021S-6S.
[http://dx.doi.org/10.1093/jn/133.11.4021S] [PMID: 14672305]
[51]
Surguchev A, Surguchov A. Conformational diseases: Looking into the eyes. Brain Res Bull 2010; 81(1): 12-24.
[http://dx.doi.org/10.1016/j.brainresbull.2009.09.015] [PMID: 19808079]
[52]
Prusiner SB. Prion biology and diseases. Cold Spring Harbor Laboratory Press 2004.
[53]
Spinner NB. CADASIL: Notch signaling defect or protein accumulation problem? J Clin Invest 2000; 105(5): 561-2.
[http://dx.doi.org/10.1172/JCI9511] [PMID: 10712425]
[54]
Quinlan RA, Brenner M, Goldman JE, Messing A. GFAP and its role in Alexander disease. Exp Cell Res 2007; 313(10): 2077-87.
[http://dx.doi.org/10.1016/j.yexcr.2007.04.004] [PMID: 17498694]
[55]
Askanas V, Engel WK. Inclusion-body myositis: A myodegenerative conformational disorder associated with A, protein misfolding, and proteasome inhibition. Neurology 2006; 66 (Suppl. 1): S39-48.
[http://dx.doi.org/10.1212/01.wnl.0000192128.13875.1e] [PMID: 16432144]
[56]
Ito D, Suzuki N. Seipinopathy: a novel endoplasmic reticulum stress-associated disease. Brain 2009; 132(1): 8-15.
[http://dx.doi.org/10.1093/brain/awn216] [PMID: 18790819]
[57]
Ecroyd H, Carver JA. Crystallin proteins and amyloid fibrils. Cell Mol Life Sci 2009; 66(1): 62-81.
[http://dx.doi.org/10.1007/s00018-008-8327-4] [PMID: 18810322]
[58]
Marzban L, Park K, Verchere CB. Islet amyloid polypeptide and type 2 diabetes. Exp Gerontol 2003; 38(4): 347-51.
[http://dx.doi.org/10.1016/S0531-5565(03)00004-4] [PMID: 12670620]
[59]
Davies HA, Phelan MM, Wilkinson MC, et al. Oxidative stress alters the morphology and toxicity of aortic medial amyloid. Biophys J 2015; 109(11): 2363-70.
[http://dx.doi.org/10.1016/j.bpj.2015.10.034] [PMID: 26636947]
[60]
Janig E, Stumptner C, Fuchsbichler A, Denk H, Zatloukal K. Interaction of stress proteins with misfolded keratins. Eur J Cell Biol 2005; 84(2-3): 329-39.
[http://dx.doi.org/10.1016/j.ejcb.2004.12.018] [PMID: 15819411]
[61]
Mohammed H, Taylor C, Brown GD, Papachristou EK, Carroll JS, D’Santos CS. Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) for analysis of chromatin complexes. Nat Protoc 2016; 11(2): 316-26.
[http://dx.doi.org/10.1038/nprot.2016.020] [PMID: 26797456]
[62]
Pisal DS, Kosloski MP, Balu-Iyer SV. Delivery of therapeutic proteins. J Pharm Sci 2010; 99(6): 2557-75.
[http://dx.doi.org/10.1002/jps.22054] [PMID: 20049941]
[63]
Dimitrov DS. Therapeutic Proteins. Springer 2012; pp. 1-26.
[64]
Leader B, Baca QJ, Golan DE. Protein therapeutics: a summary and pharmacological classification. Nat Rev Drug Discov 2008; 7(1): 21-39.
[http://dx.doi.org/10.1038/nrd2399] [PMID: 18097458]
[65]
Jao D, Xue Y, Medina J, Hu X. Protein-based drug-delivery materials. Materials (Basel) 2017; 10(5): 517.
[http://dx.doi.org/10.3390/ma10050517] [PMID: 28772877]
[66]
Vuignier K, Schappler J, Veuthey JL, Carrupt PA, Martel S. Drug–protein binding: a critical review of analytical tools. Anal Bioanal Chem 2010; 398(1): 53-66.
[http://dx.doi.org/10.1007/s00216-010-3737-1] [PMID: 20454782]
[67]
Ladisch MR, Kohlmann KL. Recombinant human insulin. Biotechnol Prog 1992; 8(6): 469-78.
[http://dx.doi.org/10.1021/bp00018a001] [PMID: 1369033]
[68]
Chance RE, Frank BH. Research, development, production, and safety of biosynthetic human insulin. Diabetes Care 1993; 16 (Suppl. 3): 133-42.
[http://dx.doi.org/10.2337/diacare.16.3.133] [PMID: 8299470]
[69]
Dingermann T. Recombinant therapeutic proteins: Production platforms and challenges. Biotechnol J 2008; 3(1): 90-7.
[http://dx.doi.org/10.1002/biot.200700214] [PMID: 18041103]
[70]
Shaji J, Patole V. Protein and peptide drug delivery: Oral approaches. Indian J Pharm Sci 2008; 70(3): 269-77.
[http://dx.doi.org/10.4103/0250-474X.42967] [PMID: 20046732]
[71]
Bruno BJ, Miller GD, Lim CS. Basics and recent advances in peptide and protein drug delivery. Ther Deliv 2013; 4(11): 1443-67.
[http://dx.doi.org/10.4155/tde.13.104] [PMID: 24228993]
[72]
Muheem A, Shakeel F, Jahangir MA, et al. A review on the strategies for oral delivery of proteins and peptides and their clinical perspectives. Saudi Pharm J 2016; 24(4): 413-28.
[http://dx.doi.org/10.1016/j.jsps.2014.06.004] [PMID: 27330372]
[73]
Roberts CJ. Therapeutic protein aggregation: mechanisms, design, and control. Trends Biotechnol 2014; 32(7): 372-80.
[http://dx.doi.org/10.1016/j.tibtech.2014.05.005] [PMID: 24908382]
[74]
Lai MC, Topp EM. Solid‐state chemical stability of proteins and peptides. J Pharm Sci 1999; 88(5): 489-500.
[http://dx.doi.org/10.1021/js980374e] [PMID: 10229638]
[75]
Rietveld AWM, Ferreira ST. Kinetics and energetics of subunit dissociation/unfolding of TIM: the importance of oligomerization for conformational persistence and chemical stability of proteins. Biochemistry 1998; 37(3): 933-7.
[http://dx.doi.org/10.1021/bi9721593] [PMID: 9454583]
[76]
Tang Y, Ghirlanda G, Petka WA, Nakajima T, DeGrado WF, Tirrell DA. Fluorinated coiled‐coil proteins prepared in vivo display enhanced thermal and chemical stability. Angew Chem Int Ed 2001; 40(8): 1494-6.
[http://dx.doi.org/10.1002/1521-3773(20010417)40:8<1494:AID-ANIE1494>3.0.CO;2-X]
[77]
Clarkson BR, Schön A, Freire E. Conformational stability and self-association equilibrium in biologics. Drug Discov Today 2016; 21(2): 342-7.
[http://dx.doi.org/10.1016/j.drudis.2015.11.007] [PMID: 26608889]
[78]
Fágáin CÓ. Understanding and increasing protein stability. Biochim Biophys Acta Protein Struct Mol Enzymol 1995; 1252(1): 1-14.
[http://dx.doi.org/10.1016/0167-4838(95)00133-F]
[79]
Shoichet BK, Baase WA, Kuroki R, Matthews BW. A relationship between protein stability and protein function. Proc Natl Acad Sci 1995; 92(2): 452-6.
[http://dx.doi.org/10.1073/pnas.92.2.452] [PMID: 7831309]
[80]
Pace C. Measuring and increasing protein stability. Trends Biotechnol 1990; 8(4): 93-8.
[http://dx.doi.org/10.1016/0167-7799(90)90146-O] [PMID: 1367432]
[81]
Aksel T, Majumdar A, Barrick D. The contribution of entropy, enthalpy, and hydrophobic desolvation to cooperativity in repeat-protein folding. Structure 2011; 19(3): 349-60.
[http://dx.doi.org/10.1016/j.str.2010.12.018] [PMID: 21397186]
[82]
Cooper A, Johnson CM, Lakey JH, Nöllmann M. Heat does not come in different colours: entropy–enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions. Biophys Chem 2001; 93(2-3): 215-30.
[http://dx.doi.org/10.1016/S0301-4622(01)00222-8] [PMID: 11804727]
[83]
Yang AS, Sharp KA, Honig B. Analysis of the heat capacity dependence of protein folding. J Mol Biol 1992; 227(3): 889-900.
[http://dx.doi.org/10.1016/0022-2836(92)90229-D] [PMID: 1404393]
[84]
Livingstone JR, Spolar RS, Record MT Jr. Contribution to the thermodynamics of protein folding from the reduction in water-accessible nonpolar surface area. Biochemistry 1991; 30(17): 4237-44.
[http://dx.doi.org/10.1021/bi00231a019] [PMID: 2021617]
[85]
Luke KA, Higgins CL, Wittung-Stafshede P. Thermodynamic stability and folding of proteins from hyperthermophilic organisms. FEBS J 2007; 274(16): 4023-33.
[http://dx.doi.org/10.1111/j.1742-4658.2007.05955.x] [PMID: 17683332]
[86]
Jaenicke R, Böhm G. The stability of proteins in extreme environments. Curr Opin Struct Biol 1998; 8(6): 738-48.
[http://dx.doi.org/10.1016/S0959-440X(98)80094-8] [PMID: 9914256]
[87]
Manning M, Colón W. Structural basis of protein kinetic stability: resistance to sodium dodecyl sulfate suggests a central role for rigidity and a bias toward β-sheet structure. Biochemistry 2004; 43(35): 11248-54.
[http://dx.doi.org/10.1021/bi0491898] [PMID: 15366934]
[88]
Sanchez-Ruiz JM. Protein kinetic stability. Biophys Chem 2010; 148(1-3): 1-15.
[http://dx.doi.org/10.1016/j.bpc.2010.02.004] [PMID: 20199841]
[89]
Jaswal SS, Sohl JL, Davis JH, Agard DA. Energetic landscape of α-lytic protease optimizes longevity through kinetic stability. Nature 2002; 415(6869): 343-6.
[http://dx.doi.org/10.1038/415343a] [PMID: 11797014]
[90]
Creighton TE. Protein folding: Does diffusion determine the folding rate? Curr Biol 1997; 7(6): R380-3.
[http://dx.doi.org/10.1016/S0960-9822(06)00180-1] [PMID: 9197236]
[91]
Kelch BA, Agard DA. Mesophile versus thermophile: insights into the structural mechanisms of kinetic stability. J Mol Biol 2007; 370(4): 784-95.
[92]
Duy C, Fitter J. Thermostability of irreversible unfolding α-amylases analyzed by unfolding kinetics. J Biol Chem 2005; 280(45): 37360-5.
[http://dx.doi.org/10.1074/jbc.M507530200] [PMID: 16150692]
[93]
Kaushik JK, Ogasahara K, Yutani K. The unusually slow relaxation kinetics of the folding-unfolding of pyrrolidone carboxyl peptidase from a hyperthermophile, Pyrococcus furiosus. J Mol Biol 2002; 316(4): 991-1003.
[http://dx.doi.org/10.1006/jmbi.2001.5355] [PMID: 11884137]
[94]
Porter D, Vollrath F. The role of kinetics of water and amide bonding in protein stability. Soft Matter 2008; 4(2): 328-36.
[http://dx.doi.org/10.1039/B713972A] [PMID: 32907247]
[95]
Colón W, Church J, Sen J, Thibeault J, Trasatti H, Xia K. Biological roles of protein kinetic stability. Biochemistry 2017; 56(47): 6179-86.
[http://dx.doi.org/10.1021/acs.biochem.7b00942] [PMID: 29087706]
[96]
Taverna DM, Goldstein RA. Why are proteins marginally stable? Proteins 2002; 46(1): 105-9.
[http://dx.doi.org/10.1002/prot.10016] [PMID: 11746707]
[97]
Wang Q, Johnson JL, Agar NYR, Agar JN. Protein aggregation and protein instability govern familial amyotrophic lateral sclerosis patient survival. PLoS Biol 2008; 6(7): e170.
[http://dx.doi.org/10.1371/journal.pbio.0060170] [PMID: 18666828]
[98]
Guruprasad K, Reddy BVB, Pandit MW. Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng Des Sel 1990; 4(2): 155-61.
[http://dx.doi.org/10.1093/protein/4.2.155] [PMID: 2075190]
[99]
Idicula-Thomas S, Balaji PV. Understanding the relationship between the primary structure of proteins and its propensity to be soluble on overexpression in Escherichia coli. Protein Sci 2005; 14(3): 582-92.
[http://dx.doi.org/10.1110/ps.041009005] [PMID: 15689506]
[100]
Pekar AH, Frank BH. Conformation of proinsulin. Comparison of insulin and proinsulin self-association at neutral pH. Biochemistry 1972; 11(22): 4013-6.
[http://dx.doi.org/10.1021/bi00772a001] [PMID: 4673642]
[101]
Philo J, Arakawa T. Mechanisms of protein aggregation. Curr Pharm Biotechnol 2009; 10(4): 348-51.
[http://dx.doi.org/10.2174/138920109788488932] [PMID: 19519409]
[102]
Orser, Cindy, Anne Grosset, and Eugene A. Davidson. Detection of conformationally altered proteins and prions. U.S. Patent Application 11/979,226, filed July 17, 2008.
[103]
Siddiqi MK, Alam P, Iqbal T, et al. Elucidating the inhibitory potential of designed peptides against amyloid fibrillation and amyloid associated cytotoxicity. Front Chem 2018; 6: 311.
[104]
A Subirana J. Specific aggregation products of histone fractions (presence of cysteine in F2a1 from echinoderms). FEBS Lett 1971; 16(2): 133-6.
[http://dx.doi.org/10.1016/0014-5793(71)80351-4] [PMID: 11945921]
[105]
Huang L, Lu J, Wroblewski VJ, Beals JM, Riggin RM. In vivo deamidation characterization of monoclonal antibody by LC/MS/MS. Anal Chem 2005; 77(5): 1432-9.
[http://dx.doi.org/10.1021/ac0494174] [PMID: 15732928]
[106]
Adachi K, Asakura T. Nucleation-controlled aggregation of deoxyhemoglobin S. Possible difference in the size of nuclei in different phosphate concentrations. J Biol Chem 1979; 254(16): 7765-71.
[http://dx.doi.org/10.1016/S0021-9258(18)36013-7] [PMID: 468786]
[107]
McCoy BJ. A population balance framework for nucleation, growth, and aggregation. Chem Eng Sci 2002; 57(12): 2279-85.
[http://dx.doi.org/10.1016/S0009-2509(02)00117-3]
[108]
Librizzi F, Rischel C. The kinetic behavior of insulin fibrillation is determined by heterogeneous nucleation pathways. Protein Sci 2005; 14(12): 3129-34.
[http://dx.doi.org/10.1110/ps.051692305] [PMID: 16322584]
[109]
Ferrone F. Analysis of protein aggregation kinetics. Methods Enzymol 1999; 309: 256-74.
[http://dx.doi.org/10.1016/S0076-6879(99)09019-9] [PMID: 10507029]
[110]
Kashchiev D. Protein polymerization into fibrils from the viewpoint of nucleation theory. Biophys J 2015; 109(10): 2126-36.
[http://dx.doi.org/10.1016/j.bpj.2015.10.010] [PMID: 26588571]
[111]
Sharma A, Pasha JM, Deep S. Effect of the sugar and polyol additives on the aggregation kinetics of BSA in the presence of N-cetyl-N,N,N-trimethyl ammonium bromide. J Colloid Interface Sci 2010; 350(1): 240-8.
[http://dx.doi.org/10.1016/j.jcis.2010.06.054] [PMID: 20638070]
[112]
De S, Girigoswami A, Das S. Fluorescence probing of albumin–surfactant interaction. J Colloid Interface Sci 2005; 285(2): 562-73.
[http://dx.doi.org/10.1016/j.jcis.2004.12.022] [PMID: 15837473]
[113]
Gelamo EL, Tabak M. Spectroscopic studies on the interaction of bovine (BSA) and human (HSA) serum albumins with ionic surfactants. Spectrochimica Acta Part a-Molecular and Biomolecular Spectroscopy 2000; 56(11): 2255-71.
[114]
Saha S, Sharma A, Deep S. Differential influence of additives on the various stages of insulin aggregation. RSC Advances 2016; 6(34): 28640-52.
[http://dx.doi.org/10.1039/C5RA27206H]
[115]
Jarrett JT, Lansbury PT Jr. Seeding “one-dimensional crystallization” of amyloid: A pathogenic mechanism in Alzheimer’s disease and scrapie? Cell 1993; 73(6): 1055-8.
[http://dx.doi.org/10.1016/0092-8674(93)90635-4] [PMID: 8513491]
[116]
Dasgupta M, Kishore N. Selective inhibition of aggregation/fibrillation of bovine serum albumin by osmolytes: Mechanistic and energetics insights. PLoS One 2017; 12(2): e0172208.
[http://dx.doi.org/10.1371/journal.pone.0172208] [PMID: 28207877]
[117]
Morris AM, Watzky MA, Finke RG. Protein aggregation kinetics, mechanism, and curve-fitting: A review of the literature. Biochim Biophys Acta Proteins Proteomics 2009; 1794(3): 375-97.
[http://dx.doi.org/10.1016/j.bbapap.2008.10.016] [PMID: 19071235]
[118]
Holm NK, Jespersen SK, Thomassen LV, et al. Aggregation and fibrillation of bovine serum albumin. Biochim Biophys Acta Proteins Proteomics 2007; 1774(9): 1128-38.
[http://dx.doi.org/10.1016/j.bbapap.2007.06.008] [PMID: 17689306]
[119]
Bee JS, Davis M, Freund E, Carpenter JF, Randolph TW. Aggregation of a monoclonal antibody induced by adsorption to stainless steel. Biotechnol Bioeng 2010; 105(1): 121-9.
[http://dx.doi.org/10.1002/bit.22525] [PMID: 19725039]
[120]
Bennett MJ, Schlunegger MP, Eisenberg D. 3D domain swapping: A mechanism for oligomer assembly. Protein Sci 1995; 4(12): 2455-68.
[http://dx.doi.org/10.1002/pro.5560041202] [PMID: 8580836]
[121]
Janowski R, Kozak M, Abrahamson M, Grubb A, Jaskolski M. 3D domain-swapped human cystatin C with amyloidlike intermolecular β-sheets. Proteins 2005; 61(3): 570-8.
[http://dx.doi.org/10.1002/prot.20633] [PMID: 16170782]
[122]
Liu Y, Eisenberg D. 3D domain swapping: As domains continue to swap. Protein Sci 2002; 11(6): 1285-99.
[http://dx.doi.org/10.1110/ps.0201402] [PMID: 12021428]
[123]
Gotte G, Vottariello F, Libonati M. Thermal aggregation of ribonuclease A. A contribution to the understanding of the role of 3D domain swapping in protein aggregation. J Biol Chem 2003; 278(12): 10763-9.
[http://dx.doi.org/10.1074/jbc.M213146200] [PMID: 12533538]
[124]
Jalili-Marandi V. Lok-Fu Pak, Dinavahi V. Real-time simulation of grid-connected wind farms using physical aggregation. IEEE Trans Ind Electron 2010; 57(9): 3010-21.
[http://dx.doi.org/10.1109/TIE.2009.2037644]
[125]
Jansen C, Parchi P, Capellari S, et al. Prion protein amyloidosis with divergent phenotype associated with two novel nonsense mutations in PRNP. Acta Neuropathol 2010; 119(2): 189-97.
[http://dx.doi.org/10.1007/s00401-009-0609-x] [PMID: 19911184]
[126]
Sipe JD, Benson MD, Buxbaum JN, Ikeda S-i, Merlini G, Saraiva MJ. Nomenclature 2014: amyloid fibril proteins and clinical classification of the amyloidosis. Taylor & Francis 2014.
[127]
Serpell LC. Alzheimer’s amyloid fibrils: structure and assembly. Biochim Biophys Acta Mol Basis Dis 2000; 1502(1): 16-30.
[http://dx.doi.org/10.1016/S0925-4439(00)00029-6]
[128]
Bashir S, Ahanger IA, Shamsi A, et al. Trehalose restrains the fibril load towards α-lactalbumin aggregation and halts fibrillation in a concentration-dependent manner. Biomolecules 2021; 11(3): 414.
[http://dx.doi.org/10.3390/biom11030414] [PMID: 33799517]
[129]
Münch C, O’Brien J, Bertolotti A. Prion-like propagation of mutant superoxide dismutase-1 misfolding in neuronal cells. Proc Natl Acad Sci 2011; 108(9): 3548-53.
[http://dx.doi.org/10.1073/pnas.1017275108] [PMID: 21321227]
[130]
Ahanger IA, Parray ZA, Nasreen K, et al. Heparin accelerates the protein aggregation via the downhill polymerization mechanism: multi-spectroscopic studies to delineate the implications on proteinopathies. ACS Omega 2021; 6(3): 2328-39.
[http://dx.doi.org/10.1021/acsomega.0c05638] [PMID: 33521471]
[131]
Kraus A, Groveman BR, Caughey B. Prions and the potential transmissibility of protein misfolding diseases. Annu Rev Microbiol 2013; 67(1): 543-64.
[http://dx.doi.org/10.1146/annurev-micro-092412-155735] [PMID: 23808331]
[132]
Ahanger IA, Bashir S, Parray ZA, et al. Rationalizing the role of monosodium glutamate in the protein aggregation through biophysical approaches: potential impact on neurodegeneration. Front Neurosci 2021; 15636454.
[http://dx.doi.org/10.3389/fnins.2021.636454] [PMID: 33746704]
[133]
Coustou-Linares V, Maddelein ML, Bégueret J, Saupe SJ. In vivo aggregation of the HET-s prion protein of the fungus Podospora anserina. Mol Microbiol 2001; 42(5): 1325-35.
[http://dx.doi.org/10.1046/j.1365-2958.2001.02707.x] [PMID: 11886562]
[134]
Cirrito JR, Kang J-E, Lee J, et al. Endocytosis is required for synaptic activity-dependent release of amyloid-β in vivo. Neuron 2008; 58(1): 42-51.
[135]
Stathopulos PB, Rumfeldt JAO, Scholz GA, et al. Cu/Zn superoxide dismutase mutants associated with amyotrophic lateral sclerosis show enhanced formation of aggregates in vitro. Proc Natl Acad Sci 2003; 100(12): 7021-6.
[http://dx.doi.org/10.1073/pnas.1237797100] [PMID: 12773627]
[136]
Nath S, Goodwin J, Engelborghs Y, Pountney DL. Raised calcium promotes α-synuclein aggregate formation. Mol Cell Neurosci 2011; 46(2): 516-26.
[http://dx.doi.org/10.1016/j.mcn.2010.12.004] [PMID: 21145971]
[137]
Olanow CW, Brundin P. Parkinson’s disease and alpha synuclein: is Parkinson’s disease a prion-like disorder? Mov Disord 2013; 28(1): 31-40.
[http://dx.doi.org/10.1002/mds.25373] [PMID: 23390095]
[138]
Frost B, Diamond MI. Prion-like mechanisms in neurodegenerative diseases. Nat Rev Neurosci 2010; 11(3): 155-9.
[http://dx.doi.org/10.1038/nrn2786] [PMID: 20029438]
[139]
Ikenoue T, Lee YH, Kardos J, et al. Heat of supersaturation-limited amyloid burst directly monitored by isothermal titration calorimetry. Proc Natl Acad Sci 2014; 111(18): 6654-9.
[http://dx.doi.org/10.1073/pnas.1322602111] [PMID: 24753579]
[140]
Bramanti E, Ferrari C, Angeli V, Onor M, Synovec RE. Characterization of BSA unfolding and aggregation using a single-capillary viscometer and dynamic surface tension detector. Talanta 2011; 85(5): 2553-61.
[http://dx.doi.org/10.1016/j.talanta.2011.08.009] [PMID: 21962683]
[141]
Liu YF, Oey I, Bremer P, Carne A, Silcock P. Effects of pH, temperature and pulsed electric fields on the turbidity and protein aggregation of ovomucin-depleted egg white. Food Res Int 2017; 91: 161-70.
[http://dx.doi.org/10.1016/j.foodres.2016.12.005] [PMID: 28290320]
[142]
Stabursvik E, Martens H. Thermal denaturation of proteins inPost rigor muscle tissue as studied by differential scanning calorimetry. J Sci Food Agric 1980; 31(10): 1034-42.
[http://dx.doi.org/10.1002/jsfa.2740311010]
[143]
Kunugi S, Tanaka N. Cold denaturation of proteins under high pressure. Biochim Biophys Acta Protein Struct Mol Enzymol 2002; 1595(1-2): 329-44.
[http://dx.doi.org/10.1016/S0167-4838(01)00354-5]
[144]
Ni Y, Wen L, Wang L, Dang Y, Zhou P, Liang L. Effect of temperature, calcium and protein concentration on aggregation of whey protein isolate: Formation of gel-like micro-particles. Int Dairy J 2015; 51: 8-15.
[http://dx.doi.org/10.1016/j.idairyj.2015.07.003]
[145]
Treuheit MJ, Kosky AA, Brems DN. Inverse relationship of protein concentration and aggregation. Pharm Res 2002; 19(4): 511-6.
[http://dx.doi.org/10.1023/A:1015108115452] [PMID: 12033388]
[146]
Fink AL. Protein aggregation: folding aggregates, inclusion bodies and amyloid. Fold Des 1998; 3(1): R9-R23.
[http://dx.doi.org/10.1016/S1359-0278(98)00002-9] [PMID: 9502314]
[147]
Saluja A, Kalonia DS. Nature and consequences of protein–protein interactions in high protein concentration solutions. Int J Pharm 2008; 358(1-2): 1-15.
[http://dx.doi.org/10.1016/j.ijpharm.2008.03.041] [PMID: 18485634]
[148]
Frokjaer S, Otzen DE. Protein drug stability: a formulation challenge. Nat Rev Drug Discov 2005; 4(4): 298-306.
[http://dx.doi.org/10.1038/nrd1695] [PMID: 15803194]
[149]
Blumer JL. Evolution of a new drug formulation: the rationale for high-dose, short-course therapy with azithromycin. Int J Antimicrob Agents 2005; 26 (Suppl. 3): S143-7.
[http://dx.doi.org/10.1016/S0924-8579(05)80320-6] [PMID: 16543075]
[150]
Katayama DS, Nayar R, Chou DK, et al. Effect of buffer species on the thermally induced aggregation of interferon-tau. J Pharm Sci 2006; 95(6): 1212-26.
[http://dx.doi.org/10.1002/jps.20471] [PMID: 16637050]
[151]
Hamada H, Arakawa T, Shiraki K. Effect of additives on protein aggregation. Curr Pharm Biotechnol 2009; 10(4): 400-7.
[http://dx.doi.org/10.2174/138920109788488941] [PMID: 19519415]
[152]
Cavalieri LF, Deutsch JF, Rosenberg BH. The molecular weight and aggregation of DNA. Biophys J 1961; 1(4): 301-15.
[http://dx.doi.org/10.1016/S0006-3495(61)86890-2] [PMID: 19431307]
[153]
Arakawa T, Prestrelski SJ, Kenney WC, Carpenter JF. Factors affecting short-term and long-term stabilities of proteins. Adv Drug Deliv Rev 2001; 46(1-3): 307-26.
[http://dx.doi.org/10.1016/S0169-409X(00)00144-7] [PMID: 11259845]
[154]
Franks F, Franks F. Biophysics and biochemistry at low temperatures. Cambridge University Press Cambridge 1985.
[155]
Timasheff SN. Water as ligand: Preferential binding and exclusion of denaturants in protein unfolding. Biochemistry 1992; 31(41): 9857-64.
[http://dx.doi.org/10.1021/bi00156a001] [PMID: 1390769]
[156]
Arakawa T, Timasheff SN. Stabilization of protein structure by sugars. Biochemistry 1982; 21(25): 6536-44.
[http://dx.doi.org/10.1021/bi00268a033] [PMID: 7150574]
[157]
Cromwell MEM, Hilario E, Jacobson F. Protein aggregation and bioprocessing. AAPS J 2006; 8(3): E572-9.
[http://dx.doi.org/10.1208/aapsj080366] [PMID: 17025275]
[158]
Tsumoto K, Umetsu M, Kumagai I, Ejima D, Philo JS, Arakawa T. Role of arginine in protein refolding, solubilization, and purification. Biotechnol Prog 2004; 20(5): 1301-8.
[http://dx.doi.org/10.1021/bp0498793] [PMID: 15458311]
[159]
Wang W. Protein aggregation and its inhibition in biopharmaceutics. Int J Pharm 2005; 289(1-2): 1-30.
[http://dx.doi.org/10.1016/j.ijpharm.2004.11.014] [PMID: 15652195]
[160]
Tutar Y, Özgür A, Tutar Lt. Role of Protein Aggregation in Neurodegenerative Diseases. Neurodegenerative Diseases In Tech Editors: Uday Kishore. 2013.
[http://dx.doi.org/10.5772/54487]
[161]
Singh J, Udgaonkar JB. Structural effects of multiple pathogenic mutations suggest a model for the initiation of misfolding of the prion protein. Angew Chem Int Ed 2015; 54(26): 7529-33.
[http://dx.doi.org/10.1002/anie.201501011] [PMID: 25959220]
[162]
Jones EM, Surewicz K, Surewicz WK. Role of N-terminal familial mutations in prion protein fibrillization and prion amyloid propagation in vitro. J Biol Chem 2006; 281(12): 8190-6.
[http://dx.doi.org/10.1074/jbc.M513417200] [PMID: 16443601]
[163]
Chiti F, Stefani M, Taddei N, Ramponi G, Dobson CM. Rationalization of the effects of mutations on peptide and protein aggregation rates. Nature 2003; 424(6950): 805-8.
[http://dx.doi.org/10.1038/nature01891] [PMID: 12917692]
[164]
Berke SJS, Paulson HL. Protein aggregation and the ubiquitin proteasome pathway: gaining the upper hand on neurodegeneration. Curr Opin Genet Dev 2003; 13(3): 253-61.
[http://dx.doi.org/10.1016/S0959-437X(03)00053-4] [PMID: 12787787]
[165]
Invernizzi G, Papaleo E, Sabate R, Ventura S. Protein aggregation: Mechanisms and functional consequences. Int J Biochem Cell Biol 2012; 44(9): 1541-54.
[http://dx.doi.org/10.1016/j.biocel.2012.05.023] [PMID: 22713792]
[166]
Hurle MR, Helms LR, Li L, Chan W, Wetzel R. A role for destabilizing amino acid replacements in light-chain amyloidosis. Proc Natl Acad Sci 1994; 91(12): 5446-50.
[http://dx.doi.org/10.1073/pnas.91.12.5446] [PMID: 8202506]
[167]
Jih KY, Li M, Hwang TC, Bompadre SG. The most common cystic fibrosis-associated mutation destabilizes the dimeric state of the nucleotide-binding domains of CFTR. J Physiol 2011; 589(11): 2719-31.
[http://dx.doi.org/10.1113/jphysiol.2010.202861] [PMID: 21486785]
[168]
Devasagayam TP, Tilak JC, Boloor KK, Sane KS, Ghaskadbi SS, Lele RD. Free radicals and antioxidants in human health: current status and future prospects. J Assoc Physicians India 2004; 52(794804): 794-804.
[PMID: 15909857]
[169]
Sosa Torres M, Saucedo-Vazquez J, Kroneck P. The dark side of dioxygen. Sustaining Life on Planet Earth. Metalloenzymes Mastering Dioxygen and Metal Ions in Life Sciences 2015; 15: 1-12.
[170]
Tyedmers J, Mogk A, Bukau B. Cellular strategies for controlling protein aggregation. Nat Rev Mol Cell Biol 2010; 11(11): 777-88.
[http://dx.doi.org/10.1038/nrm2993] [PMID: 20944667]
[171]
Nilsson MR, Driscoll M, Raleigh DP. Low levels of asparagine deamidation can have a dramatic effect on aggregation of amyloidogenic peptides: Implications for the study of amyloid formation. Protein Sci 2002; 11(2): 342-9.
[http://dx.doi.org/10.1110/ps.48702] [PMID: 11790844]
[172]
Yakhine-Diop SM, Rodríguez-Arribas M, Gómez-Sánchez R, Pizarro-Estrella E, Niso-Santano M, González-Polo RA. Chapter 5-G2019S Mutation of LRRK2 Increases Autophagy via MEK/ERK Pathway. Autophagy: Cancer, Other Pathologies, Inflammation, Immunity, Infection, and Aging. Elsevier 2016; pp. 123-42.
[http://dx.doi.org/10.1016/B978-0-12-802936-7.00005-2]
[173]
Wang J, Farr GW, Zeiss CJ, et al. Progressive aggregation despite chaperone associations of a mutant SOD1-YFP in transgenic mice that develop ALS. Proc Natl Acad Sci 2009; 106(5): 1392-7.
[http://dx.doi.org/10.1073/pnas.0813045106] [PMID: 19171884]
[174]
Münch C, Bertolotti A. Exposure of hydrophobic surfaces initiates aggregation of diverse ALS-causing superoxide dismutase-1 mutants. J Mol Biol 2010; 399(3): 512-25.
[http://dx.doi.org/10.1016/j.jmb.2010.04.019] [PMID: 20399791]
[175]
Gidalevitz T, Ben-Zvi A, Ho KH, Brignull HR, Morimoto RI. Progressive disruption of cellular protein folding in models of polyglutamine diseases. Science 2006; 311(5766): 1471-4.
[http://dx.doi.org/10.1126/science.1124514] [PMID: 16469881]
[176]
Ahanger IA, Sharma A, Islam A. The pathogenesis and complications associated with autism spectrum disorder and Alzheimer’s disease: A comparative study. autism spectrum disorder and Alzheimer’s disease. Springer 2021; p. 43-61.
[177]
Keller JN, Hanni KB, Markesbery WR. Possible involvement of proteasome inhibition in aging: implications for oxidative stress. Mech Ageing Dev 2000; 113(1): 61-70.
[http://dx.doi.org/10.1016/S0047-6374(99)00101-3] [PMID: 10708250]
[178]
Cuervo AM, Dice JF. When lysosomes get old. Exp Gerontol 2000; 35(2): 119-31.
[http://dx.doi.org/10.1016/S0531-5565(00)00075-9] [PMID: 10767573]
[179]
Kikis EA, Gidalevitz T, Morimoto RI. Protein homeostasis in models of aging and age-related conformational disease. Prot Metab Homeost Aging Adv Exper Med Biol 2010; 694: 138-59.
[http://dx.doi.org/10.1007/978-1-4419-7002-2_11]
[180]
Kapon R, Nevo R, Reich Z. Protein energy landscape roughness. Biochem Soc Trans 2008; 36(6): 1404-8.
[http://dx.doi.org/10.1042/BST0361404] [PMID: 19021564]
[181]
Betancourt MR, Onuchic JN. Kinetics of proteinlike models: The energy landscape factors that determine folding. J Chem Phys 1995; 103(2): 773-87.
[http://dx.doi.org/10.1063/1.470109]
[182]
Zhou R, Berne BJ, Germain R. The free energy landscape for β hairpin folding in explicit water. Proc Natl Acad Sci 2001; 98(26): 14931-6.
[http://dx.doi.org/10.1073/pnas.201543998] [PMID: 11752441]
[183]
Veitshans T, Klimov D, Thirumalai D. Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. Fold Des 1997; 2(1): 1-22.
[http://dx.doi.org/10.1016/S1359-0278(97)00002-3] [PMID: 9080195]
[184]
Moulick R, Goluguri RR, Udgaonkar JB. Ruggedness in the free energy landscape dictates misfolding of the prion protein. J Mol Biol 2019; 431(4): 807-24.
[http://dx.doi.org/10.1016/j.jmb.2018.12.009] [PMID: 30611749]
[185]
Porebski BT, Keleher S, Hollins JJ, et al. Smoothing a rugged protein folding landscape by sequence-based redesign. Sci Rep 2016; 6(1): 33958.
[http://dx.doi.org/10.1038/srep33958] [PMID: 27667094]
[186]
Hayashi Y, Aita T, Toyota H, Husimi Y, Urabe I, Yomo T. Experimental rugged fitness landscape in protein sequence space. PLoS One 2006; 1(1): e96.
[http://dx.doi.org/10.1371/journal.pone.0000096] [PMID: 17183728]
[187]
Horwich AL, Weissman JS. Deadly conformations--protein misfolding in prion disease. Cell 1997; 89(4): 499-510.
[http://dx.doi.org/10.1016/S0092-8674(00)80232-9] [PMID: 9160742]
[188]
DeMattos RB, Cirrito JR, Parsadanian M, et al. ApoE and clusterin cooperatively suppress Abeta levels and deposition: evidence that ApoE regulates extracellular Abeta metabolism in vivo. Neuron 2004; 41(2): 193-202.
[http://dx.doi.org/10.1016/S0896-6273(03)00850-X] [PMID: 14741101]
[189]
Yanamandra K, Kfoury N, Jiang H, et al. Anti-tau antibodies that block tau aggregate seeding in vitro markedly decrease pathology and improve cognition in vivo. Neuron 2013; 80(2): 402-14.
[http://dx.doi.org/10.1016/j.neuron.2013.07.046] [PMID: 24075978]
[190]
Cats A, Lafeber GJ, Klein F. Immunoglobulin phagocytosis by granulocytes from sera and synovial fluids in various rheumatoid and nonrheumatoid diseases. Ann Rheum Dis 1975; 34(2): 146-55.
[http://dx.doi.org/10.1136/ard.34.2.146] [PMID: 806270]
[191]
Koo EH, Lansbury PT Jr, Kelly JW. Amyloid diseases: Abnormal protein aggregation in neurodegeneration. Proc Natl Acad Sci 1999; 96(18): 9989-90.
[http://dx.doi.org/10.1073/pnas.96.18.9989] [PMID: 10468546]
[192]
Rajan RS, Illing ME, Bence NF, Kopito RR. Specificity in intracellular protein aggregation and inclusion body formation. Proc Natl Acad Sci 2001; 98(23): 13060-5.
[http://dx.doi.org/10.1073/pnas.181479798] [PMID: 11687604]
[193]
Bennett EJ, Bence NF, Jayakumar R, Kopito RR. Global impairment of the ubiquitin-proteasome system by nuclear or cytoplasmic protein aggregates precedes inclusion body formation. Mol Cell 2005; 17(3): 351-65.
[http://dx.doi.org/10.1016/j.molcel.2004.12.021] [PMID: 15694337]
[194]
Gray A, Scott TFM. Some observations on the intracellular localization of the virus of herpes simplex in the chick embryo liver. J Exp Med 1954; 100(5): 473-84.
[http://dx.doi.org/10.1084/jem.100.5.473] [PMID: 13211908]
[195]
Paik S, Kim S-H, Kim J-H, Yang WI, Lee YC. Russell body gastritis associated with Helicobacter pylori infection: a case report. J Clin Pathol 2006; 59(12): 1316-9.
[http://dx.doi.org/10.1136/jcp.2005.032185] [PMID: 17142575]
[196]
Cambruzzi E, Pêgas KL, Laus FF. Russell body gastritis: case report. J Bras Patol Med Lab 2012; 48(1): 41-4.
[http://dx.doi.org/10.1590/S1676-24442012000100008]
[197]
Crespo R, Koudstaal W, Apetri A. In vitro assay for studying the aggregation of tau protein and drug screening. J Vis Exp 2018; (141): e58570.
[http://dx.doi.org/10.3791/58570] [PMID: 30531722]
[198]
Clark EDB, Schwarz E, Rudolph R. Inhibition of aggregation side reactions during in vitro protein folding. Methods in enzymology. Elsevier 1999; pp. 217-36.
[199]
Kiefhaber T, Rudolph R, Kohler H-H, Buchner J. Protein aggregation in vitro and in vivo: a quantitative model of the kinetic competition between folding and aggregation. Biotechnology 1991; 9(9): 825-9.
[PMID: 1367356]
[200]
Riebesell U, Wolf-Gladrow DA. The relationship between physical aggregation of phytoplankton and particle flux: a numerical model. Deep-Sea Res A, Oceanogr Res Pap 1992; 39(7-8): 1085-102.
[http://dx.doi.org/10.1016/0198-0149(92)90058-2]
[201]
Corezzi S, Fioretto D, Sciortino F. Chemical and physical aggregation of small-functionality particles. Soft Matter 2012; 8(44): 11207-16.
[http://dx.doi.org/10.1039/c2sm26112j]
[202]
Deuflhard P, Huisinga W, Fischer A, Schütte C. Identification of almost invariant aggregates in reversible nearly uncoupled Markov chains. Linear Algebra Appl 2000; 315(1-3): 39-59.
[http://dx.doi.org/10.1016/S0024-3795(00)00095-1]
[203]
Lindquist SL, Kelly JW. Chemical and biological approaches for adapting proteostasis to ameliorate protein misfolding and aggregation diseases: progress and prognosis. Cold Spring Harb Perspect Biol 2011; 3(12): a004507.
[http://dx.doi.org/10.1101/cshperspect.a004507] [PMID: 21900404]
[204]
Mirzaei H, Regnier F. Protein:protein aggregation induced by protein oxidation. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 873(1): 8-14.
[http://dx.doi.org/10.1016/j.jchromb.2008.04.025] [PMID: 18760979]
[205]
Carter Tyler L. Glycoprotein Ib alpha: An intrinsic promoter of amyloid beta fibrillization. University of Massachusetts Lowell 2011.
[206]
Xie J, Qin M, Cao Y, Wang W. Mechanistic insight of photo-induced aggregation of chicken egg white lysozyme: The interplay between hydrophobic interactions and formation of intermolecular disulfide bonds. Proteins 2011; 79(8): 2505-16.
[http://dx.doi.org/10.1002/prot.23074] [PMID: 21661057]
[207]
Rezaei-Ghaleh N, Ramshini H, Ebrahim-Habibi A, Moosavi-Movahedi AA, Nemat-Gorgani M. Thermal aggregation of α-chymotrypsin: Role of hydrophobic and electrostatic interactions. Biophys Chem 2008; 132(1): 23-32.
[http://dx.doi.org/10.1016/j.bpc.2007.10.001] [PMID: 17964060]
[208]
Berhanu WM, Hansmann UHE. Side-chain hydrophobicity and the stability of Aβ 16-22 aggregates. Protein Sci 2012; 21(12): 1837-48.
[http://dx.doi.org/10.1002/pro.2164] [PMID: 23015407]
[209]
Cloos PAC, Christgau S. Non-enzymatic covalent modifications of proteins: mechanisms, physiological consequences and clinical applications. Matrix Biol 2002; 21(1): 39-52.
[http://dx.doi.org/10.1016/S0945-053X(01)00188-3] [PMID: 11827791]
[210]
Geiger T, Clarke S. Deamidation, isomerization, and racemization at asparaginyl and aspartyl residues in peptides. Succinimide-linked reactions that contribute to protein degradation. J Biol Chem 1987; 262(2): 785-94.
[http://dx.doi.org/10.1016/S0021-9258(19)75855-4] [PMID: 3805008]
[211]
Zhang J, Yip H, Katta V. Identification of isomerization and racemization of aspartate in the Asp–Asp motifs of a therapeutic protein. Anal Biochem 2011; 410(2): 234-43.
[http://dx.doi.org/10.1016/j.ab.2010.11.040] [PMID: 21130067]
[212]
Robbins DC, Cooper SM, Fineberg SE, Mead PM. Antibodies to covalent aggregates of insulin in blood of insulin-using diabetic patients. Diabetes 1987; 36(7): 838-41.
[http://dx.doi.org/10.2337/diab.36.7.838] [PMID: 2438179]
[213]
Chen K, Kazachkov M, Yu PH. Effect of aldehydes derived from oxidative deamination and oxidative stress on β-amyloid aggregation; pathological implications to Alzheimer’s disease. J Neural Transm 2007; 114(6): 835-9.
[http://dx.doi.org/10.1007/s00702-007-0697-5] [PMID: 17401529]
[214]
Wen Hu X, Knight DP, Grant RA. The effect of deamination and/or blocking arginine residues on the molecular assembly of acid-extracted rat tail tendon collagen. Tissue Cell 1996; 28(2): 215-22.
[http://dx.doi.org/10.1016/S0040-8166(96)80009-7] [PMID: 8650674]
[215]
Vijayalakshmi V, Gupta PD. Estradiol-regulated transamidation of keratins by vaginal epithelial cell transglutaminase. Exp Cell Res 1994; 214(1): 358-66.
[http://dx.doi.org/10.1006/excr.1994.1268] [PMID: 7521846]
[216]
Den Engelsman J, Garidel P, Smulders R, et al. Strategies for the assessment of protein aggregates in pharmaceutical biotech product development. Pharm Res 2011; 28: 920-33.
[217]
Li Y, Yan J, Zhang X, Huang K. Disulfide bonds in amyloidogenesis diseases related proteins. Proteins 2013; 81(11): 1862-73.
[http://dx.doi.org/10.1002/prot.24338] [PMID: 23760807]
[218]
Orsi A, Sparvoli F, Ceriotti A. Role of individual disulfide bonds in the structural maturation of a low molecular weight glutenin subunit. J Biol Chem 2001; 276(34): 32322-9.
[http://dx.doi.org/10.1074/jbc.M103833200] [PMID: 11418605]
[219]
Otte J, Zakora M, Qvist KB. Involvement of Disulfide Bonds in Bovine β-Lactoglobulin B Gels Set Thermally at Various pH. J Food Sci 2000; 65(3): 384-9.
[http://dx.doi.org/10.1111/j.1365-2621.2000.tb16012.x]
[220]
McDuffee AT, Senisterra G, Huntley S, et al. Proteins containing non-native disulfide bonds generated by oxidative stress can act as signals for the induction of the heat shock response. J Cell Physiol 1997; 171(2): 143-51.
[http://dx.doi.org/10.1002/(SICI)1097-4652(199705)171:2<143:AID-JCP4>3.0.CO;2-O] [PMID: 9130461]
[221]
Kamberi M, Chung P, Devas R, et al. Analysis of non-covalent aggregation of synthetic hPTH (1–34) by size-exclusion chromatography and the importance of suppression of non-specific interactions for a precise quantitation. J Chromatogr B Analyt Technol Biomed Life Sci 2004; 810(1): 151-5.
[http://dx.doi.org/10.1016/S1570-0232(04)00601-4] [PMID: 15358319]
[222]
Vázquez-Rey M, Lang DA. Aggregates in monoclonal antibody manufacturing processes. Biotechnol Bioeng 2011; 108(7): 1494-508.
[http://dx.doi.org/10.1002/bit.23155] [PMID: 21480193]
[223]
Yang L, Li Y, Hao D, Li L, Peng H, Jin P. Aggregation behavior and non‐covalent functionalization of borofullerenes B 28, B 38, and B 40: A density functional theory investigation. Int J Quantum Chem 2019; 119(14): e25921.
[http://dx.doi.org/10.1002/qua.25921]
[224]
Ravi VK, Goel M, Kotamarthi HC, Ainavarapu SRK, Swaminathan R. Preventing disulfide bond formation weakens non-covalent forces among lysozyme aggregates. PLoS One 2014; 9(2): e87012.
[http://dx.doi.org/10.1371/journal.pone.0087012] [PMID: 24551048]
[225]
Roberts CJ. Protein aggregation and its impact on product quality. Curr Opin Biotechnol 2014; 30: 211-7.
[http://dx.doi.org/10.1016/j.copbio.2014.08.001] [PMID: 25173826]
[226]
Fernández C, Minton AP. Static light scattering from concentrated protein solutions II: experimental test of theory for protein mixtures and weakly self-associating proteins. Biophys J 2009; 96(5): 1992-8.
[http://dx.doi.org/10.1016/j.bpj.2008.11.054] [PMID: 19254559]
[227]
Brange J, Andersen L, Laursen ED, Meyn G, Rasmussen E. Toward understanding insulin fibrillation. J Pharm Sci 1997; 86(5): 517-25.
[http://dx.doi.org/10.1021/js960297s] [PMID: 9145374]
[228]
De Young LR, Dill KA, Fink AL. Aggregation and denaturation of apomyoglobin in aqueous urea solutions. Biochemistry 1993; 32(15): 3877-86.
[http://dx.doi.org/10.1021/bi00066a006] [PMID: 8471600]
[229]
Tennent GA, Lovat LB, Pepys MB. Serum amyloid P component prevents proteolysis of the amyloid fibrils of Alzheimer disease and systemic amyloidosis. Proc Natl Acad Sci 1995; 92(10): 4299-303.
[http://dx.doi.org/10.1073/pnas.92.10.4299] [PMID: 7753801]
[230]
Brummitt RK, Andrews JM, Jordan JL, Fernandez EJ, Roberts CJ. Thermodynamics of amyloid dissociation provide insights into aggregate stability regimes. Biophys Chem 2012; 168-169: 10-8.
[http://dx.doi.org/10.1016/j.bpc.2012.06.001] [PMID: 22750559]
[231]
Wilson S, Smith DB. Separation of the valyl-leucyl- and valyl-glutamyl-polypeptide chains of horse globin by fractional precipitation and column chromatography. Can J Biochem Physiol 1959; 37(3): 405-16.
[http://dx.doi.org/10.1139/o59-042] [PMID: 13638859]
[232]
Jiskoot W, Randolph TW, Volkin DB, et al. Protein instability and immunogenicity: roadblocks to clinical application of injectable protein delivery systems for sustained release. J Pharm Sci 2012; 101(3): 946-54.
[http://dx.doi.org/10.1002/jps.23018] [PMID: 22170395]
[233]
Schrödel A, de Marco A. Characterization of the aggregates formed during recombinant protein expression in bacteria. BMC Biochem 2005; 6(1): 10.
[http://dx.doi.org/10.1186/1471-2091-6-10] [PMID: 15927061]
[234]
Martínez-Alonso M, González-Montalbán N, García-Fruitós E, Villaverde A. The Functional quality of soluble recombinant polypeptides produced in Escherichia coli is defined by a wide conformational spectrum. Appl Environ Microbiol 2008; 74(23): 7431-3.
[http://dx.doi.org/10.1128/AEM.01446-08] [PMID: 18836021]
[235]
Toledo-Rubio V, Vazquez E, Platas G, et al. Protein aggregation and soluble aggregate formation screened by a fast microdialysis assay. SLAS Discov 2010; 15(4): 453-7.
[http://dx.doi.org/10.1177/1087057110363911] [PMID: 20233904]
[236]
Liu J, Song J. A novel nucleolar transcriptional activator ApLLP for long-term memory formation is intrinsically unstructured but functionally active. Biochem Biophys Res Commun 2008; 366(2): 585-91.
[http://dx.doi.org/10.1016/j.bbrc.2007.12.022] [PMID: 18078811]
[237]
Crespo R, Villar-Alvarez E, Taboada P, Rocha FA, Damas AM, Martins PM. Insoluble off-pathway aggregates as crowding agents during amyloid fibril formation. J Phys Chem B 2017; 121(10): 2288-98.
[http://dx.doi.org/10.1021/acs.jpcb.7b01120] [PMID: 28221799]
[238]
Wetzel R. Mutations and off-pathway aggregation of proteins. Trends Biotechnol 1994; 12(5): 193-8.
[http://dx.doi.org/10.1016/0167-7799(94)90082-5] [PMID: 7764903]
[239]
Crespo R, Villar-Alvarez E, Taboada P, Rocha FA, Damas AM, Martins PM. What can the kinetics of amyloid fibril formation tell about off-pathway aggregation? J Biol Chem 2016; 291(4): 2018-32.
[http://dx.doi.org/10.1074/jbc.M115.699348] [PMID: 26601940]
[240]
Pham CLL, Leong SL, Ali FE, et al. Dopamine and the dopamine oxidation product 5,6-dihydroxylindole promote distinct on-pathway and off-pathway aggregation of α-synuclein in a pH-dependent manner. J Mol Biol 2009; 387(3): 771-85.
[http://dx.doi.org/10.1016/j.jmb.2009.02.007] [PMID: 19361420]
[241]
Pellarin R, Caflisch A. Interpreting the aggregation kinetics of amyloid peptides. J Mol Biol 2006; 360(4): 882-92.
[http://dx.doi.org/10.1016/j.jmb.2006.05.033] [PMID: 16797587]
[242]
Sipe JD, Cohen AS. Review: history of the amyloid fibril. J Struct Biol 2000; 130(2-3): 88-98.
[http://dx.doi.org/10.1006/jsbi.2000.4221] [PMID: 10940217]
[243]
Ghetti B, Piccardo P, Frangione B, et al. Prion protein amyloidosis. Brain Pathol 1996; 6(2): 127-45.
[http://dx.doi.org/10.1111/j.1750-3639.1996.tb00796.x] [PMID: 8737929]
[244]
Bousset L, Thomson NH, Radford SE, Melki R. The yeast prion Ure2p retains its native α-helical conformation upon assembly into protein fibrils in vitro. EMBO J 2002; 21(12): 2903-11.
[http://dx.doi.org/10.1093/emboj/cdf303] [PMID: 12065404]
[245]
Rousseau F, Schymkowitz JWH, Wilkinson HR, Itzhaki LS. Three-dimensional domain swapping in p13suc1 occurs in the unfolded state and is controlled by conserved proline residues. Proc Natl Acad Sci 2001; 98(10): 5596-601.
[http://dx.doi.org/10.1073/pnas.101542098] [PMID: 11344301]
[246]
Soldi G, Bemporad F, Torrassa S, et al. Amyloid formation of a protein in the absence of initial unfolding and destabilization of the native state. Biophys J 2005; 89(6): 4234-44.
[http://dx.doi.org/10.1529/biophysj.105.067538] [PMID: 16169977]
[247]
Marcon G, Plakoutsi G, Canale C, et al. Amyloid formation from HypF-N under conditions in which the protein is initially in its native state. J Mol Biol 2005; 347(2): 323-35.
[http://dx.doi.org/10.1016/j.jmb.2005.01.034] [PMID: 15740744]
[248]
Ruysschaert JM, Raussens V. ATR-FTIR analysis of amyloid proteins. Peptide Self-Assembly. Methods Protoc 2018; 69-81.
[http://dx.doi.org/10.1007/978-1-4939-7816-8]
[249]
Sunde M, Blake C. The structure of amyloid fibrils by electron microscopy and X-ray diffraction. Advances in protein chemistry. Elsevier 1997; pp. 123-59.
[250]
Sunde M, Serpell LC, Bartlam M, Fraser PE, Pepys MB, Blake CCF. Common core structure of amyloid fibrils by synchrotron Xray diffraction 1 1Edited by F. E. Cohen. J Mol Biol 1997; 273(3): 729-39.
[http://dx.doi.org/10.1006/jmbi.1997.1348] [PMID: 9356260]
[251]
Cobb NJ, Sönnichsen FD, Mchaourab H, Surewicz WK. Molecular architecture of human prion protein amyloid: A parallel, in-register β-structure. Proc Natl Acad Sci 2007; 104(48): 18946-51.
[http://dx.doi.org/10.1073/pnas.0706522104] [PMID: 18025469]
[252]
Krebs MRH, Morozova-Roche LA, Daniel K, Robinson CV, Dobson CM. Observation of sequence specificity in the seeding of protein amyloid fibrils. Protein Sci 2004; 13(7): 1933-8.
[http://dx.doi.org/10.1110/ps.04707004] [PMID: 15215533]
[253]
Ogomori K, Kitamoto T, Tateishi J, Sato Y, Suetsugu M, Abe M. Beta-protein amyloid is widely distributed in the central nervous system of patients with Alzheimer’s disease. Am J Pathol 1989; 134(2): 243-51.
[PMID: 2464938]
[254]
Westermark P, Benson MD, Buxbaum JN, et al. A primer of amyloid nomenclature. Amyloid 2007; 14(3): 179-83.
[http://dx.doi.org/10.1080/13506120701460923] [PMID: 17701465]
[255]
Adamcik J, Mezzenga R. Amyloid polymorphism in the protein folding and aggregation energy landscape. Angew Chem Int Ed 2018; 57(28): 8370-82.
[http://dx.doi.org/10.1002/anie.201713416] [PMID: 29446868]
[256]
Greenwald J, Riek R. Biology of amyloid: structure, function, and regulation. Structure 2010; 18(10): 1244-60.
[http://dx.doi.org/10.1016/j.str.2010.08.009] [PMID: 20947013]
[257]
Agbas Abdulbaki. Trends of protein aggregation in neurodegenerative diseases. Neurochemical basis of brain function and dysfunction. IntechOpen ISBN:183880000X 2018.
[http://dx.doi.org/10.5772/intechopen.81224]
[258]
Ghahghaei A, Divsalar A, Faridi N. The effects of molecular crowding on the amyloid fibril formation of α-lactalbumin and the chaperone action of α-casein. Protein J 2010; 29(4): 257-64.
[http://dx.doi.org/10.1007/s10930-010-9247-3] [PMID: 20496103]
[259]
Wilson MR, Yerbury JJ, Poon S. Potential roles of abundant extracellular chaperones in the control of amyloid formation and toxicity. Mol Biosyst 2008; 4(1): 42-52.
[http://dx.doi.org/10.1039/B712728F] [PMID: 18075673]
[260]
Stoppini M, Bellotti V. Systemic amyloidosis: lessons from β2-microglobulin. J Biol Chem 2015; 290(16): 9951-8.
[http://dx.doi.org/10.1074/jbc.R115.639799] [PMID: 25750126]
[261]
Yoshimura Y, Lin Y, Yagi H, et al. Distinguishing crystal-like amyloid fibrils and glass-like amorphous aggregates from their kinetics of formation. Proc Natl Acad Sci 2012; 109(36): 14446-51.
[http://dx.doi.org/10.1073/pnas.1208228109] [PMID: 22908252]
[262]
Sipe JD, Benson MD, Buxbaum JN, et al. Amyloid fibril protein nomenclature: 2010 recommendations from the nomenclature committee of the International Society of Amyloidosis. Amyloid 2010; 17(3-4): 101-4.
[http://dx.doi.org/10.3109/13506129.2010.526812] [PMID: 21039326]
[263]
Dispenzieri A, Gertz MA, Buadi F. What do I need to know about immunoglobulin light chain (AL) amyloidosis? Blood Rev 2012; 26(4): 137-54.
[264]
Canichella M, Serrao A, Annechini G, D’Elia GM, De Luca ML, Pulsoni A. Long-term response to daratumumab in a patient with advanced immunoglobulin light-chain (AL) amyloidosis with organ damage. Ann Hematol 2019; 98(4): 1047-8.
[http://dx.doi.org/10.1007/s00277-018-3566-4] [PMID: 30488327]
[265]
Muchtar E, Therneau TM, Larson DR, et al. Comparative analysis of staging systems in AL amyloidosis. Leukemia 2019; 33(3): 811-4.
[http://dx.doi.org/10.1038/s41375-018-0370-z] [PMID: 30675009]
[266]
Wang ST, Wang QP, Li J, Zhang T, Zhang L, Mao YY. Amyloidosis secondary to intrapulmonary Castleman disease mimicking pulmonary hyalinizing granuloma-like clinical features. Medicine 2019; 98(14): e15039.
[http://dx.doi.org/10.1097/MD.0000000000015039] [PMID: 30946344]
[267]
Ando Y, Coelho T, Berk JL, et al. Guideline of transthyretin-related hereditary amyloidosis for clinicians. Orphanet J Rare Dis 2013; 8(1): 31.
[http://dx.doi.org/10.1186/1750-1172-8-31] [PMID: 23425518]
[268]
Benson MD. The hereditary amyloidoses. Best Pract Res Clin Rheumatol 2003; 17(6): 909-27.
[http://dx.doi.org/10.1016/j.berh.2003.09.001] [PMID: 15123043]
[269]
Benson MD, Uemichi T. Transthyretin amyloidosis. Amyloid 1996; 3(1): 44-56.
[http://dx.doi.org/10.3109/13506129609014354]
[270]
Koch KM. Dialysis-related amyloidosis. Kidney Int 1992; 41(5): 1416-29.
[http://dx.doi.org/10.1038/ki.1992.207] [PMID: 1614057]
[271]
Küchle C, Fricke H, Held E, Schiffl H. High-flux hemodialysis postpones clinical manifestation of dialysis-related amyloidosis. Am J Nephrol 1996; 16(6): 484-8.
[http://dx.doi.org/10.1159/000169048] [PMID: 8955759]
[272]
Kiss E, Keusch G, Zanetti M, et al. Dialysis-related amyloidosis revisited. AJR Am J Roentgenol 2005; 185(6): 1460-7.
[http://dx.doi.org/10.2214/AJR.04.1309] [PMID: 16303998]
[273]
Pinney JH, Whelan CJ, Petrie A, et al. Senile systemic amyloidosis: clinical features at presentation and outcome. J Am Heart Assoc 2013; 2(2): e000098.
[http://dx.doi.org/10.1161/JAHA.113.000098] [PMID: 23608605]
[274]
Hamidi Asl K, Liepnieks JJ, Nakamura M, Benson MD. Organ-specific (localized) synthesis of Ig light chain amyloid. J Immunol 1999; 162(9): 5556-60.
[http://dx.doi.org/10.4049/jimmunol.162.9.5556] [PMID: 10228037]
[275]
Westermark P, Wilander E, Westermark GT, Johnson KH. Islet amyloid polypeptide-like immunoreactivity in the islet B cells of Type 2 (non-insulin-dependent) diabetic and non-diabetic individuals. Diabetologia 1987; 30(11): 887-92.
[http://dx.doi.org/10.1007/BF00274799] [PMID: 3328723]
[276]
Goltzman D, Huang SN, Browne C, Solomon S. Adrenocorticotropin and calcitonin in medullary thyroid carcinoma: frequency of occurrence and localization in the same cell type by immunocytochemistry. J Clin Endocrinol Metab 1979; 49(3): 364-9.
[http://dx.doi.org/10.1210/jcem-49-3-364] [PMID: 224074]
[277]
Louros NN, Iconomidou VA, Tsiolaki PL, et al. An N-terminal pro-atrial natriuretic peptide (NT-proANP) ‘aggregation-prone’ segment involved in isolated atrial amyloidosis. FEBS Lett 2014; 588(1): 52-7.
[http://dx.doi.org/10.1016/j.febslet.2013.10.049] [PMID: 24220659]
[278]
Voigt C, Saeger W, Gerigk C, Lüdecke DK. Amyloid in pituitary adenomas. Pathol Res Pract 1988; 183(5): 555-7.
[http://dx.doi.org/10.1016/S0344-0338(88)80008-6] [PMID: 3237543]
[279]
Hashimoto K, Ito K, Taniguchi Y, Yang F, Youngberg G. Keratin in cutaneous amyloidoses. Clin Dermatol 1990; 8(2): 55-65.
[http://dx.doi.org/10.1016/0738-081X(90)90088-I] [PMID: 1699647]
[280]
Westermark GT, Westermark P. Localized amyloids important in diseases outside the brain - lessons from the islets of Langerhans and the thoracic aorta. FEBS J 2011; 278(20): 3918-29.
[http://dx.doi.org/10.1111/j.1742-4658.2011.08298.x] [PMID: 21834879]
[281]
Claessen D, Rink R, de Jong W, et al. A novel class of secreted hydrophobic proteins is involved in aerial hyphae formation in Streptomyces coelicolor by forming amyloid-like fibrils. Genes Dev 2003; 17(14): 1714-26.
[http://dx.doi.org/10.1101/gad.264303] [PMID: 12832396]
[282]
Fowler DM, Koulov AV, Balch WE, Kelly JW. Functional amyloid – from bacteria to humans. Trends Biochem Sci 2007; 32(5): 217-24.
[http://dx.doi.org/10.1016/j.tibs.2007.03.003] [PMID: 17412596]
[283]
Smith JF, Knowles TPJ, Dobson CM, MacPhee CE, Welland ME. Characterization of the nanoscale properties of individual amyloid fibrils. Proc Natl Acad Sci 2006; 103(43): 15806-11.
[http://dx.doi.org/10.1073/pnas.0604035103] [PMID: 17038504]
[284]
Otzen D, Nielsen PH. We find them here, we find them there: Functional bacterial amyloid. Cell Mol Life Sci 2008; 65(6): 910-27.
[http://dx.doi.org/10.1007/s00018-007-7404-4] [PMID: 18034321]
[285]
Carulla N, Zhou M, Arimon M, et al. Experimental characterization of disordered and ordered aggregates populated during the process of amyloid fibril formation. Proc Natl Acad Sci 2009; 106(19): 7828-33.
[http://dx.doi.org/10.1073/pnas.0812227106] [PMID: 19416886]
[286]
Chiti F, Calamai M, Taddei N, Stefani M, Ramponi G, Dobson CM. Studies of the aggregation of mutant proteins in vitro provide insights into the genetics of amyloid diseases. Proc Natl Acad Sci 2002; 99 (Suppl. 4): 16419-26.
[http://dx.doi.org/10.1073/pnas.212527999] [PMID: 12374855]
[287]
Chiti F, Taddei N, Baroni F, et al. Kinetic partitioning of protein folding and aggregation. Nat Struct Biol 2002; 9(2): 137-43.
[http://dx.doi.org/10.1038/nsb752] [PMID: 11799398]
[288]
Melki R. How the shapes of seeds can influence pathology. Neurobiol Dis 2018; 109(Pt B): 201-8.
[http://dx.doi.org/10.1016/j.nbd.2017.03.011] [PMID: 28363800]
[289]
Chaudhuri TK, Paul S. Protein-misfolding diseases and chaperone-based therapeutic approaches. FEBS J 2006; 273(7): 1331-49.
[http://dx.doi.org/10.1111/j.1742-4658.2006.05181.x] [PMID: 16689923]
[290]
Butterfield DA, Di Domenico F, Swomley AM, Head E, Perluigi M. Redox proteomics analysis to decipher the neurobiology of Alzheimer-like neurodegeneration: overlaps in Down’s syndrome and Alzheimer’s disease brain. Biochem J 2014; 463(2): 177-89.
[http://dx.doi.org/10.1042/BJ20140772] [PMID: 25242166]
[291]
Dunker AK, Obradovic Z. The protein trinity—linking function and disorder. Nat Biotechnol 2001; 19(9): 805-6.
[http://dx.doi.org/10.1038/nbt0901-805] [PMID: 11533628]
[292]
Uversky VN. Intrinsically disordered proteins from A to Z. Int J Biochem Cell Biol 2011; 43(8): 1090-103.
[http://dx.doi.org/10.1016/j.biocel.2011.04.001] [PMID: 21501695]
[293]
Uversky VN. Intrinsically disordered proteins and their (disordered) proteomes in neurodegenerative disorders. Front Aging Neurosci 2015; 7: 18.
[http://dx.doi.org/10.3389/fnagi.2015.00018] [PMID: 25784874]
[294]
King OD, Gitler AD, Shorter J. The tip of the iceberg: RNA-binding proteins with prion-like domains in neurodegenerative disease. Brain Res 2012; 1462: 61-80.
[http://dx.doi.org/10.1016/j.brainres.2012.01.016] [PMID: 22445064]
[295]
Hegde RS, Mastrianni JA, Scott MR, et al. A transmembrane form of the prion protein in neurodegenerative disease. Science 1998; 279(5352): 827-34.
[http://dx.doi.org/10.1126/science.279.5352.827] [PMID: 9452375]
[296]
Riesner D. Biochemistry and structure of PrPC and PrPSc. Br Med Bull 2003; 66(1): 21-33.
[http://dx.doi.org/10.1093/bmb/66.1.21] [PMID: 14522846]
[297]
Pan KM, Baldwin M, Nguyen J, et al. Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins. Proc Natl Acad Sci 1993; 90(23): 10962-6.
[http://dx.doi.org/10.1073/pnas.90.23.10962] [PMID: 7902575]
[298]
Grune T, Jung T, Merker K, Davies KJA. Decreased proteolysis caused by protein aggregates, inclusion bodies, plaques, lipofuscin, ceroid, and ‘aggresomes’ during oxidative stress, aging, and disease. Int J Biochem Cell Biol 2004; 36(12): 2519-30.
[http://dx.doi.org/10.1016/j.biocel.2004.04.020] [PMID: 15325589]
[299]
Krebs MRH, MacPhee CE, Miller AF, Dunlop IE, Dobson CM, Donald AM. The formation of spherulites by amyloid fibrils of bovine insulin. Proc Natl Acad Sci 2004; 101(40): 14420-4.
[http://dx.doi.org/10.1073/pnas.0405933101] [PMID: 15381766]
[300]
House E, Mold M, Collingwood J, Baldwin A, Goodwin S, Exley C. Copper abolishes the β-sheet secondary structure of preformed amyloid fibrils of amyloid-β(42). J Alzheimers Dis 2009; 18(4): 811-7.
[http://dx.doi.org/10.3233/JAD-2009-1235] [PMID: 19749401]
[301]
Chennamsetty N, Helk B, Trout B, Kayser V, Voynov V. Novartis AG and Massachusetts Institute of Technology, 2018. Methods to identify macromolecule binding and aggregation prone regions in proteins and uses therefor. U.S. Patent 9,922,164.
[302]
Agrawal NJ, Kumar S, Wang X, Helk B, Singh SK, Trout BL. Aggregation in protein-based biotherapeutics: computational studies and tools to identify aggregation-prone regions. J Pharm Sci 2011; 100(12): 5081-95.
[http://dx.doi.org/10.1002/jps.22705] [PMID: 21789769]
[303]
Pawar AP, DuBay KF, Zurdo J, Chiti F, Vendruscolo M, Dobson CM. Prediction of “aggregation-prone” and “aggregation-susceptible” regions in proteins associated with neurodegenerative diseases. J Mol Biol 2005; 350(2): 379-92.
[http://dx.doi.org/10.1016/j.jmb.2005.04.016] [PMID: 15925383]
[304]
Cellmer T, Bratko D, Prausnitz JM, Blanch HW. Protein aggregation in silico. Trends Biotechnol 2007; 25(6): 254-61.
[http://dx.doi.org/10.1016/j.tibtech.2007.03.011] [PMID: 17433843]
[305]
Gsponer J, Vendruscolo M. Theoretical approaches to protein aggregation. Protein Pept Lett 2006; 13(3): 287-93.
[http://dx.doi.org/10.2174/092986606775338407] [PMID: 16515457]
[306]
Hashimoto M, Rockenstein E, Crews L, Masliah E. Role of protein aggregation in mitochondrial dysfunction and neurodegeneration in Alzheimer’s and Parkinson’s diseases. Neuromolecular Med 2003; 4(1-2): 21-36.
[http://dx.doi.org/10.1385/NMM:4:1-2:21] [PMID: 14528050]
[307]
Frank E. Effect of Alzheimer’s disease on communication function. J S C Med Assoc 1994; 90(9): 417-23.
[308]
Tulisiak CT, Mercado G, Peelaerts W, Brundin L, Brundin P. Can infections trigger alpha-synucleinopathies? Prog Mol Biol Transl Sci 2019; 168: 299-322.
[http://dx.doi.org/10.1016/bs.pmbts.2019.06.002] [PMID: 31699323]
[309]
Jankovic J. Parkinson’s disease: clinical features and diagnosis. J Neurol Neurosurg Psychiatry 2008; 79(4): 368-76.
[http://dx.doi.org/10.1136/jnnp.2007.131045] [PMID: 18344392]
[310]
D’Aguanno V, Ralli M, Artico M, et al. Systemic amyloidosis: a contemporary overview. Clin Rev Allergy Immunol 2020; 59(3): 304-22.
[http://dx.doi.org/10.1007/s12016-019-08759-4] [PMID: 31376044]
[311]
Merlini G. CyBorD: stellar response rates in AL amyloidosis. Blood 2012; 119(19): 4343-5.
[http://dx.doi.org/10.1182/blood-2012-03-413112] [PMID: 22577156]
[312]
Abyadeh M, Gupta V, Gupta V, et al. Comparative analysis of aducanumab, zagotenemab and pioglitazone as targeted treatment strategies for Alzheimer’s disease. Aging Dis 2021; 12(8): 1964-76.
[http://dx.doi.org/10.14336/AD.2021.0719] [PMID: 34881080]
[313]
Dispenzieri A, Kyle R, Lacy M, Jaffe AS, Therneau TM, Zeldenrust S. Serum cardiac troponins and N-terminal pro-brain natriuretic peptide: a staging system for primary systemic amyloidosis.Amyloid and Amyloidosis. CRC Press 2004; pp. 67-9.
[314]
Brooks DJ. Imaging approaches to Parkinson disease. J Nucl Med 2010; 51(4): 596-609.
[http://dx.doi.org/10.2967/jnumed.108.059998] [PMID: 20351351]
[315]
Suwijn SR, van Boheemen CJM, de Haan RJ, Tissingh G, Booij J, de Bie RMA. The diagnostic accuracy of dopamine transporter SPECT imaging to detect nigrostriatal cell loss in patients with Parkinson’s disease or clinically uncertain parkinsonism: a systematic review. EJNMMI Res 2015; 5(1): 12.
[http://dx.doi.org/10.1186/s13550-015-0087-1] [PMID: 25853018]
[316]
Parray ZA, Naqvi AAT, Ahanger IA, et al. Measuring structural changes in cytochrome c under crowded conditions using in vitro and in silico approaches. Polymers 2022; 14(22): 4808.
[http://dx.doi.org/10.3390/polym14224808] [PMID: 36432935]
[317]
Ahanger IA, Parray ZA, Raina N, et al. Counteraction of the cetyltrimethylammonium bromide-induced protein aggregation by heparin: Potential impact on protein aggregation and neurodegenerative diseases using biophysical approaches. J Mol Struct 2023; 1276: 134714.

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