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Current Proteomics

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ISSN (Print): 1570-1646
ISSN (Online): 1875-6247

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Research Article

Analyzing Structural and Functional Characteristics of Collagenase from Bacillus cereus MH19 via in silico Approaches

Author(s): Shihua Chen, Meihu Ma* and Xing Fu

Volume 17, Issue 3, 2020

Page: [200 - 212] Pages: 13

DOI: 10.2174/1570164617666191004165609

Price: $65

Abstract

Background: Collagenase is a type of proteolytic enzyme that specifically hydrolyzes native collagen with a three-dimensional helical structure. The structure and properties of collagenase vary with different sources and types. In addition to the well-characterized Clostridium collagenase, other collagenases are largely unknown. Various gene and protein databases have been widely used to mine novel functional genes in the genome. Gene mining and sequence analysis are effective methods for studying these enzymes.

Objective: The present study aimed to understand the molecular, structural, and functional characteristics of collagenase from Bacillus cereus MH19 using a bioinformatics approach.

Methods: Based on the three-generation sequencing PacBio technique, Sequencing the Bacillus cereus MH19 genome. Function annotation is completed by blasting genes with different databases. Collagenases were investigated based on the physiochemical properties, phylogenetic relation, and domain architecture. The 3D structure model of the selected collagenase has been constructed and verified by SAVES.

Results: There were 5 collagenases in Bacillus cereus MH19 with a molecular weight distribution ranging from 36-110 kDa. The analysis of evolutionary relationship between different collagenases indicating that the BCC000504 and BCC003388 collagenase gene sequences are closer to the typical collagenase genes ColG, ColA, and ColH, followed by BCC003615. The domain and function analysis showed that the collagenases BCC000504 and BCC003388 were similar to the collagenases ColG, ColA and ColH. BCC004271 was similar to BCC004272, and BCC003615 might be quite different from other collagenases. The secondary structure of collagenase was analyzed. The SAVES evaluation indicates that 3D structural modeling of the selected collagenase is acceptable.

Conclusion: This study provides an overview of the molecular, functional, and structural characteristics of collagenase from Bacillus cereus MH19, which helps to understand the bacterial collagenase. The characterization of the collagenase will certainly expand the application range of collagenase.

Keywords: Collagenase, structure, function, Bacillus cereus MH19, computational approaches, protein.

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[1]
Watanabe, K. Collagenolytic proteases from bacteria. Appl. Microbiol. Biotechnol., 2004, 63(5), 520-526.
[http://dx.doi.org/10.1007/s00253-003-1442-0] [PMID: 14556041]
[2]
Ozbek, S.; Pertz, O.; Schwager, M.; Lustig, A.; Holstein, T.; Engel, J. Structure/function relationships in the minicollagen of hydra nematocysts. J. Biol. Chem., 2002, 277(51), 49200-49204.
[http://dx.doi.org/10.1074/jbc.M209401200] [PMID: 12368276]
[3]
Kumar, B.; Rani, S. Technical note on the isolation and characterization of collagen from fish waste material. J. Food Sci. Technol., 2017, 54(1), 276-278.
[http://dx.doi.org/10.1007/s13197-016-2443-1] [PMID: 28242926]
[4]
Rani, S. Letter to the editor on isolation, characterization and valorizable applications of fish scale collagen in food and agriculture industries. Biocatal. Agric. Biotechnol., 2016, 7, 279-280.
[http://dx.doi.org/10.1016/j.bcab.2016.08.013]
[5]
Rani, S.; Kumar, B. Characterization of collagen from different discarded fish species of the west coast of the Iberian Peninsula. J. Aquat. Food Prod. Technol., 2017, 26(3), 246-247.
[http://dx.doi.org/10.1080/10498850.2016.1155102]
[6]
Rani, S.; Kumar, B. A Letter to the editor on “nonenzymatic softening mechanism of collagen gel of sea cucumber (Apostichopus japonicus)”. J. Food Process. Preserv., 2016, 40(6), 1153-1153.
[http://dx.doi.org/10.1111/jfpp.12698]
[7]
Zhao, G.Y.; Zhou, M.Y.; Zhao, H.L.; Chen, X.L.; Xie, B.B.; Zhang, X.Y.; He, H.L.; Zhou, B.C.; Zhang, Y.Z. Tenderization effect of cold-adapted collagenolytic protease MCP-01 on beef meat at low temperature and its mechanism. Food Chem., 2012, 134(4), 1738-1744.
[http://dx.doi.org/10.1016/j.foodchem.2012.03.118] [PMID: 23442615]
[8]
Dettmer, A.; Ayub, M.A.Z.; Gutterres, M. Hide unhairing and characterization of commercial enzymes used in leather manufacture. Braz. J. Chem. Eng., 2011, 28(3), 373-380.
[http://dx.doi.org/10.1590/S0104-66322011000300003]
[9]
Swarna, V.K.; Venba, R.; Madhan, B.; Chandrababu, N.K.; Sadulla, S. Studies on the influence of bacterial collagenase in leather dyeing. Dyes Pigments, 2008, 76(2), 338-347.
[http://dx.doi.org/10.1016/j.dyepig.2006.08.043]
[10]
Suphatharaprateep, W.; Cheirsilp, B.; Jongjareonrak, A. Production and properties of two collagenases from bacteria and their application for collagen extraction. N. Biotechnol., 2011, 28(6), 649-655.
[http://dx.doi.org/10.1016/j.nbt.2011.04.003] [PMID: 21549225]
[11]
Takagi, M.; Yoshioka, H.; Wakitani, S. A mass separation of chondrocytes from cartilage tissue utilizing an automatic crushing device. J. Biosci. Bioeng., 2010, 109(1), 73-74.
[http://dx.doi.org/10.1016/j.jbiosc.2009.06.016] [PMID: 20129086]
[12]
Sakai, Y.; Yamato, R.; Onuma, M.; Kikuta, T.; Watanabe, M.; Nakayama, T. Non-antigenic and low allergic gelatin produced by specific digestion with an enzyme-coupled matrix. Biol. Pharm. Bull., 1998, 21(4), 330-334.
[http://dx.doi.org/10.1248/bpb.21.330] [PMID: 9586567]
[13]
Ramundo, J.; Gray, M. Enzymatic wound debridement. J. Wound Ostomy Continence Nurs., 2008, 35(3), 273-280.
[http://dx.doi.org/10.1097/01.WON.0000319125.21854.78] [PMID: 18496083]
[14]
Cemazar, M.; Golzio, M.; Sersa, G.; Escoffre, J.M.; Coer, A.; Vidic, S.; Teissie, J. Hyaluronidase and collagenase increase the transfection efficiency of gene electrotransfer in various murine tumors. Hum. Gene Ther., 2012, 23(1), 128-137.
[http://dx.doi.org/10.1089/hum.2011.073] [PMID: 21797718]
[15]
Kato, M.; Hattori, Y.; Kubo, M.; Maitani, Y. Collagenase-1 injection improved tumor distribution and gene expression of cationic lipoplex. Int. J. Pharm., 2012, 423(2), 428-434.
[http://dx.doi.org/10.1016/j.ijpharm.2011.12.015] [PMID: 22197775]
[16]
Wu, Z.; Wei, L.X.; Li, J.; Wang, Y.; Ni, D.; Yang, P.; Zhang, Y. Percutaneous treatment of non-contained lumbar disc herniation by injection of oxygen-ozone combined with collagenase. Eur. J. Radiol., 2009, 72(3), 499-504.
[http://dx.doi.org/10.1016/j.ejrad.2008.07.029] [PMID: 18778905]
[17]
Strauss, B.H.; Goldman, L.; Qiang, B.; Nili, N.; Segev, A.; Butany, J.; Sparkes, J.D.; Jackson, Z.S.; Eskandarian, M.R.; Virmani, R. Collagenase plaque digestion for facilitating guide wire crossing in chronic total occlusions. Circulation, 2003, 108(10), 1259-1262.
[http://dx.doi.org/10.1161/01.CIR.0000086320.24172.A1] [PMID: 12939226]
[18]
Bayat, A. Connective tissue diseases: a nonsurgical therapy for Dupuytren disease. Nat. Rev. Rheumatol., 2010, 6(1), 7-8.
[http://dx.doi.org/10.1038/nrrheum.2009.255] [PMID: 20046200]
[19]
Jordan, G.H. The use of intralesional clostridial collagenase injection therapy for Peyronie’s disease: a prospective, single-center, non-placebo-controlled study. J. Sex. Med., 2008, 5(1), 180-187.
[http://dx.doi.org/10.1111/j.1743-6109.2007.00651.x] [PMID: 18173766]
[20]
Thomas, A.; Bayat, A. The emerging role of Clostridium histolyticum collagenase in the treatment of Dupuytren disease. Ther. Clin. Risk Manag., 2010, 6(1), 557-572.
[PMID: 21127696]
[21]
Duarte, A.S.; Correia, A.; Esteves, A.C. Bacterial collagenases - a review. Crit. Rev. Microbiol., 2016, 42(1), 106-126.
[http://dx.doi.org/10.3109/1040841X.2014.904270] [PMID: 24754251]
[22]
Abfalter, C.M.; Schönauer, E.; Ponnuraj, K.; Huemer, M.; Gadermaier, G.; Regl, C.; Briza, P.; Ferreira, F.; Huber, C.G.; Brandstetter, H.; Posselt, G.; Wessler, S. Cloning, purification and characterization of the collagenase ColA expressed by Bacillus cereus ATCC 14579. PLoS One, 2016, 11(9)e0162433
[http://dx.doi.org/10.1371/journal.pone.0162433] [PMID: 27588686]
[23]
de Albuquerque Wanderley, M.C.; Wanderley Duarte Neto, J.M.; Campos Albuquerque, W.W.; de Araújo Viana Marques, D.; de Albuquerque Lima, C.; da Cruz Silvério, S.I.; de Lima Filho, J.L.; Couto Teixeira, J.A.; Porto, A.L.F. Purification and characterization of a collagenase from Penicillium sp. UCP 1286 by polyethylene glycol-phosphate aqueous two-phase system. Protein Expr. Purif., 2017, 133(12), 8-14.
[http://dx.doi.org/10.1016/j.pep.2017.02.010] [PMID: 28242427]
[24]
Wu, Q.; Li, C.; Li, C.; Chen, H.; Shuliang, L. Purification and characterization of a novel collagenase from Bacillus pumilus Col-J. Appl. Biochem. Biotechnol., 2010, 160(1), 129-139.
[http://dx.doi.org/10.1007/s12010-009-8673-1] [PMID: 19475515]
[25]
Okamoto, M.; Yonejima, Y.; Tsujimoto, Y.; Suzuki, Y.; Watanabe, K. A thermostable collagenolytic protease with a very large molecular mass produced by thermophilic Bacillus sp. strain MO-1. J. Appl. Microbiol. Biotechnol., 2001, 57(1-2), 103-108.
[http://dx.doi.org/10.1007/s002530100731] [PMID: 11693905]
[26]
Eckhard, U.; Nüss, D.; Ducka, P.; Schönauer, E.; Brandstetter, H. Crystallization and preliminary X-ray characterization of the catalytic domain of collagenase G from Clostridium histolyticum. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 2008, 64(Pt 5), 419-421.
[http://dx.doi.org/10.1107/S1744309108010476] [PMID: 18453715]
[27]
Nair, R.R.; Boyd, D.D. Expression cloning of novel regulators of 92 kDa type IV collagenase expression. Biochem. Soc. Trans., 2005, 33(Pt 5), 1135-1136.
[http://dx.doi.org/10.1042/BST0331135] [PMID: 16246065]
[28]
Hamdy, H.S. Extracellular collagenase from Rhizoctonia solani: production, purification and characterization. Indian J. Biotechnol., 2008, 7(3), 333-340.
[29]
Tamai, E.; Miyata, S.; Tanaka, H.; Nariya, H.; Suzuki, M.; Matsushita, O.; Hatano, N.; Okabe, A. High-level expression of his-tagged clostridial collagenase in Clostridium perfringens. Appl. Microbiol. Biotechnol., 2008, 80(4), 627-635.
[http://dx.doi.org/10.1007/s00253-008-1592-1] [PMID: 18629492]
[30]
Rainbow, L.; Wilkinson, M.C.; Sargent, P.J.; Hart, C.A.; Winstanley, C. Identification and expression of a Burkholderia pseudomallei collagenase in Escherichia coli. Curr. Microbiol., 2004, 48(4), 300-304.
[http://dx.doi.org/10.1007/s00284-003-4192-4] [PMID: 15057457]
[31]
Lima, C.A.; Rodrigues, P.M.B.; Porto, T.S.; Viana, D.A.; Filho, J.L.L.; Porto, A.L.F.; Cunha, M.G. Cd. Production of a collagenase from Candida albicans URM3622. Biochem. Eng. J., 2009, 43(3), 315-320.
[http://dx.doi.org/10.1016/j.bej.2008.10.014]
[32]
Sakurai, Y.; Inoue, H.; Nishii, W.; Takahashi, T.; Iino, Y.; Yamamoto, M.; Takahashi, K. Purification and characterization of a major collagenase from Streptomyces parvulus. Biosci. Biotechnol. Biochem., 2009, 73(1), 21-28.
[http://dx.doi.org/10.1271/bbb.80357] [PMID: 19129667]
[33]
Matsushita, O.; Yoshihara, K.; Katayama, S.; Minami, J.; Okabe, A. Purification and characterization of Clostridium perfringens 120-kilodalton collagenase and nucleotide sequence of the corresponding gene. J. Bacteriol., 1994, 176(1), 149-156.
[http://dx.doi.org/10.1128/jb.176.1.149-156.1994] [PMID: 8282691]
[34]
Matsushita, O.; Jung, C.M.; Minami, J.; Katayama, S.; Nishi, N.; Okabe, A. A study of the collagen-binding domain of a 116-kDa Clostridium histolyticum collagenase. J. Biol. Chem., 1998, 273(6), 3643-3648.
[http://dx.doi.org/10.1074/jbc.273.6.3643] [PMID: 9452493]
[35]
Matsushita, O.; Jung, C.M.; Katayama, S.; Minami, J.; Takahashi, Y.; Okabe, A. Gene duplication and multiplicity of collagenases in Clostridium histolyticum. J. Bacteriol., 1999, 181(3), 923-933.
[PMID: 9922257]
[36]
Matsushita, O.; Koide, T.; Kobayashi, R.; Nagata, K.; Okabe, A. Substrate recognition by the collagen-binding domain of Clostridium histolyticum class I collagenase. J. Biol. Chem., 2001, 276(12), 8761-8770.
[http://dx.doi.org/10.1074/jbc.M003450200] [PMID: 11121400]
[37]
Matsushita, O.; Okabe, A. Clostridial hydrolytic enzymes degrading extracellular components. Toxicon, 2001, 39(11), 1769-1780.
[http://dx.doi.org/10.1016/S0041-0101(01)00163-5] [PMID: 11595639]
[38]
Oxenoid, K.; Dong, Y.; Cao, C.; Cui, T.; Sancak, Y.; Markhard, A.L.; Grabarek, Z.; Kong, L.; Liu, Z.; Ouyang, B.; Cong, Y.; Mootha, V.K.; Chou, J.J. Architecture of the mitochondrial calcium uniporter. Nature, 2016, 533(7602), 269-273.
[http://dx.doi.org/10.1038/nature17656] [PMID: 27135929]
[39]
Dev, J.; Park, D.; Fu, Q.; Chen, J.; Ha, H.J.; Ghantous, F.; Herrmann, T.; Chang, W.; Liu, Z.; Frey, G.; Seaman, M.S.; Chen, B.; Chou, J.J. Structural basis for membrane anchoring of HIV-1 envelope spike. Science, 2016, 353(6295), 172-175.
[http://dx.doi.org/10.1126/science.aaf7066] [PMID: 27338706]
[40]
Schnell, J.R.; Chou, J.J. Structure and mechanism of the M2 proton channel of influenza A virus. Nature, 2008, 451(7178), 591-595.
[http://dx.doi.org/10.1038/nature06531] [PMID: 18235503]
[41]
Berardi, M.J.; Shih, W.M.; Harrison, S.C.; Chou, J.J. Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching. Nature, 2011, 476(7358), 109-113.
[http://dx.doi.org/10.1038/nature10257] [PMID: 21785437]
[42]
Chou, J.J.; Li, S.; Klee, C.B.; Bax, A. Solution structure of Ca(2+)- calmodulin reveals flexible hand-like properties of its domains. Nat. Struct. Biol., 2001, 8(11), 990-997.
[http://dx.doi.org/10.1038/nsb1101-990] [PMID: 11685248]
[43]
OuYang, B.; Xie, S.; Berardi, M.J.; Zhao, X.; Dev, J.; Yu, W.; Sun, B.; Chou, J.J. Unusual architecture of the p7 channel from hepatitis C virus. Nature, 2013, 498(7455), 521-525.
[http://dx.doi.org/10.1038/nature12283] [PMID: 23739335]
[44]
Fu, Q.; Fu, T-M.; Cruz, A.C.; Sengupta, P.; Thomas, S.K.; Wang, S.; Siegel, R.M.; Wu, H.; Chou, J.J. Structural basis and functional role of intramembrane trimerization of the Fas/CD95 death receptor. Mol. Cell, 2016, 61(4), 602-613.
[http://dx.doi.org/10.1016/j.molcel.2016.01.009] [PMID: 26853147]
[45]
Pal, G.K.; Suresh, P.V. Physico-chemical characteristics and fibril-forming capacity of carp swim bladder collagens and exploration of their potential bioactive peptides by in silico approaches. Int. J. Biol. Macromol., 2017, 101, 304-313.
[http://dx.doi.org/10.1016/j.ijbiomac.2017.03.061] [PMID: 28315441]
[46]
Ghasemi, Y.; Hemmati, S.; Hajighahramani, N.; Negahdaripour, M.; Nezafat, N.; Sadeghian, I.; Rahmatabadi, S. In silico investigation of pullulanase enzymes from various Bacillus species. Curr. Proteomics, 2017, 14(3), 175-185.
[47]
Pooja, K.; Rani, S.; Kanwate, B.; Pal, G.K. Physico-chemical, sensory and toxicity characteristics of dipeptidyl peptidase-IV inhibitory peptides from rice bran-derived globulin using computational approaches. Int. J. Pept. Res. Ther., 2017, 23(3), 1-11.
[http://dx.doi.org/10.1007/s10989-017-9586-4]
[48]
Rani, S.; Pooja, K.; Pal, G.K. Exploration of potential angiotensin converting enzyme inhibitory peptides generated from enzymatic hydrolysis of goat milk proteins. Biocatal. Agric. Biotechnol., 2017, 11, 83-88.
[http://dx.doi.org/10.1016/j.bcab.2017.06.008]
[49]
Pramanik, K.; Ghosh, P.K.; Ray, S.; Sarkar, A.; Mitra, S.; Maiti, T.K. An in silico structural, functional and phylogenetic analysis with three dimensional protein modeling of alkaline phosphatase enzyme of Pseudomonas aeruginosa. J. Genet. Eng. Biotechnol., 2017, 15(2), 527-537.
[http://dx.doi.org/10.1016/j.jgeb.2017.05.003] [PMID: 30647696]
[50]
Pramanik, K.; Soren, T.; Mitra, S.; Maiti, T.K. In silico structural and functional analysis of Mesorhizobium ACC deaminase. Comput. Biol. Chem., 2017, 68(C), 12-21.
[http://dx.doi.org/10.1016/j.compbiolchem.2017.02.005] [PMID: 28214450]
[51]
Rani, S.; Pooja, K. Elucidation of structural and functional characteristics of collagenase from Pseudomonas aeruginosa. Process Biochem., 2018, 64, 116-123.
[http://dx.doi.org/10.1016/j.procbio.2017.09.029]
[52]
Chou, K.C.; Tomasselli, A.G.; Heinrikson, R.L. Prediction of the tertiary structure of a caspase-9/inhibitor complex. FEBS Lett., 2000, 470(3), 249-256.
[http://dx.doi.org/10.1016/S0014-5793(00)01333-8] [PMID: 10745077]
[53]
Chou, K.C. Insights from modelling the 3D structure of the extracellular domain of alpha7 nicotinic acetylcholine receptor. Biochem. Biophys. Res. Commun., 2004, 319(2), 433-438.
[http://dx.doi.org/10.1016/j.bbrc.2004.05.016] [PMID: 15178425]
[54]
Chou, K.C. Coupling interaction between thromboxane A2 receptor and alpha-13 subunit of guanine nucleotide-binding protein. J. Proteome Res., 2005, 4(5), 1681-1686.
[http://dx.doi.org/10.1021/pr050145a] [PMID: 16212421]
[55]
Chou, K.C.; Howe, W.J. Prediction of the tertiary structure of the beta-secretase zymogen. Biochem. Biophys. Res. Commun., 2002, 292(3), 702-708.
[http://dx.doi.org/10.1006/bbrc.2002.6686] [PMID: 11922623]
[56]
Chou, K.C. Insights from modeling the tertiary structure of human BACE2. J. Proteome Res., 2004, 3(5), 1069-1072.
[http://dx.doi.org/10.1021/pr049905s] [PMID: 15473697]
[57]
Chou, K.C. Insights from modeling three-dimensional structures of the human potassium and sodium channels. J. Proteome Res., 2004, 3(4), 856-861.
[http://dx.doi.org/10.1021/pr049931q] [PMID: 15359741]
[58]
Chou, K.C. Modeling the tertiary structure of human cathepsin-E. Biochem. Biophys. Res. Commun., 2005, 331(1), 56-60.
[http://dx.doi.org/10.1016/j.bbrc.2005.03.123] [PMID: 15845357]
[59]
Li, X.B.W.; Wang, S.Q.; Xu, W.R.; Wang, R.L.; Chou, K.C. Novel inhibitor design for hemagglutinin against H1N1 influenza virus by core hopping method. PLoS One, 2011, 6(11)e28111
[http://dx.doi.org/10.1371/journal.pone.0028111] [PMID: 22140516]
[60]
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K.C. iSuc-PseOpt: Identifying lysine succinylation sites in proteins by incorporating sequence-coupling effects into pseudo components and optimizing imbalanced training dataset. Anal. Biochem., 2016, 497, 48-56.
[http://dx.doi.org/10.1016/j.ab.2015.12.009] [PMID: 26723495]
[61]
Jia, J.; Zhang, L.; Liu, Z.; Xiao, X.; Chou, K.C. pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC. Bioinformatics, 2016, 32(20), 3133-3141.
[http://dx.doi.org/10.1093/bioinformatics/btw387] [PMID: 27354696]
[62]
Chen, W.; Feng, P.; Yang, H.; Ding, H.; Lin, H.; Chou, K.C. iRNA-3typeA: identifying three types of modification at RNA’s adenosine sites. Mol. Ther. Nucleic Acids, 2018, 11(C), 468-474.
[http://dx.doi.org/10.1016/j.omtn.2018.03.012] [PMID: 29858081]
[63]
Ghauri, A.W.K.; Khan, Y.D.; Rasool, N.; Khan, S.A.; Chou, K.C. pNitro-Tyr-PseAAC: predict nitrotyrosine sites in proteins by incorporating five features into Chou’s general PseAAC. Curr. Pharm. Des., 2018, 24(34), 4034-4043.
[http://dx.doi.org/10.2174/1381612825666181127101039] [PMID: 30479209]
[64]
Qiu, W.R.S.; Sun, B.Q.; Xiao, X.; Xu, Z.C.; Jia, J.H.; Chou, K.C. iKcr-PseEns: Identify lysine crotonylation sites in histone proteins with pseudo components and ensemble classifier. Genomics, 2018, 110(5), 239-246.
[http://dx.doi.org/10.1016/j.ygeno.2017.10.008] [PMID: 29107015]
[65]
Xiao, X.; Min, J.L.; Lin, W.Z.; Liu, Z.; Cheng, X.; Chou, K.C. iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach. J. Biomol. Struct. Dyn., 2015, 33(10), 2221-2233.
[http://dx.doi.org/10.1080/07391102.2014.998710] [PMID: 25513722]
[66]
Feng, P.M.C.; Chen, W.; Lin, H.; Chou, K.C. iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition. Anal. Biochem., 2013, 442(1), 118-125.
[http://dx.doi.org/10.1016/j.ab.2013.05.024] [PMID: 23756733]
[67]
Chen, W.; Feng, P.M.; Deng, E.Z.; Lin, H.; Chou, K.C. iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition. Anal. Biochem., 2014, 462, 76-83.
[http://dx.doi.org/10.1016/j.ab.2014.06.022] [PMID: 25016190]
[68]
Chou, K.C. Advance in predicting subcellular localization of multi-label proteins and its implication for developing multi-target drugs. Curr. Med. Chem., 2019, 26, 1-21.
[http://dx.doi.org/10.2174/0929867326666190507082559] [PMID: 31060481]
[69]
Chou, K.C. Some remarks on protein attribute prediction and pseudo amino acid composition. J. Theor. Biol., 2011, 273(1), 236-247.
[http://dx.doi.org/10.1016/j.jtbi.2010.12.024] [PMID: 21168420]
[70]
Xie, H.L.; Fu, L.; Nie, X.D. Using ensemble SVM to identify human GPCRs N-linked glycosylation sites based on the general form of Chou’s PseAAC. Protein Eng. Des. Sel., 2013, 26(11), 735-742.
[http://dx.doi.org/10.1093/protein/gzt042] [PMID: 24048266]
[71]
Xu, Y.; Ding, J.; Wu, L.Y.; Chou, K.C. iSNO-PseAAC: predict cysteine S-nitrosylation sites in proteins by incorporating position specific amino acid propensity into pseudo amino acid composition. PLoS One, 2013, 8(2)e55844
[http://dx.doi.org/10.1371/journal.pone.0055844] [PMID: 23409062]
[72]
Xu, Y.; Shao, X.J.; Wu, L.Y.; Deng, N.Y.; Chou, K.C. iSNO-AAPair: incorporating amino acid pairwise coupling into PseAAC for predicting cysteine S-nitrosylation sites in proteins. PeerJ, 2013, 1e171
[73]
Jia, C.; Lin, X.; Wang, Z. Prediction of protein S-nitrosylation sites based on adapted normal distribution bi-profile Bayes and Chou’s pseudo amino acid composition. Int. J. Mol. Sci., 2014, 15(6), 10410-10423.
[http://dx.doi.org/10.3390/ijms150610410] [PMID: 24918295]
[74]
Qiu, W.R.; Xiao, X.; Lin, W.Z.; Chou, K.C. iMethyl-PseAAC: identification of protein methylation sites via a pseudo amino acid composition approach. BioMed Res. Int., 2014, 2014(12)947416
[http://dx.doi.org/10.1155/2014/947416] [PMID: 24977164]
[75]
Xu, Y.; Wen, X.; Shao, X.J.; Deng, N.Y.; Chou, K.C. iHyd-PseAAC: predicting hydroxyproline and hydroxylysine in proteins by incorporating dipeptide position-specific propensity into pseudo amino acid composition. Int. J. Mol. Sci., 2014, 15(5), 7594-7610.
[http://dx.doi.org/10.3390/ijms15057594] [PMID: 24857907]
[76]
Xu, Y.; Wen, X.; Wen, L.S.; Wu, L.Y.; Deng, N.Y.; Chou, K.C.; Albert, V.R. iNitro-Tyr: prediction of nitrotyrosine sites in proteins with general pseudo amino acid composition. PLoS One, 2014, 9(8)e105018
[http://dx.doi.org/10.1371/journal.pone.0105018] [PMID: 25121969]
[77]
Jia, J.; Liu, Z.; Xiao, X.; Liu, B.; Chou, K.C. iPPI-Esml: an ensemble classifier for identifying the interactions of proteins by incorporating their physicochemical properties and wavelet transforms into PseAAC. J. Theor. Biol., 2015, 377, 47-56.
[http://dx.doi.org/10.1016/j.jtbi.2015.04.011] [PMID: 25908206]
[78]
Liu, Z.; Xiao, X.; Qiu, W-R.; Chou, K.C. iDNA-Methyl: identifying DNA methylation sites via pseudo trinucleotide composition. Anal. Biochem., 2015, 474, 69-77.
[http://dx.doi.org/10.1016/j.ab.2014.12.009] [PMID: 25596338]
[79]
Chen, W.; Feng, P-M.; Lin, H.; Chou, K.C. iRSpot-PseDNC: identify recombination spots with pseudo dinucleotide composition. Nucleic Acids Res., 2013, 41(6)e68
[http://dx.doi.org/10.1093/nar/gks1450] [PMID: 23303794]
[80]
Lin, H.; Deng, E.Z.; Ding, H.; Chen, W.; Chou, K.C. iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition. Nucleic Acids Res., 2014, 42(21), 12961-12972.
[http://dx.doi.org/10.1093/nar/gku1019] [PMID: 25361964]
[81]
Chou, K.C. Prediction of protein cellular attributes using pseudo-amino acid composition. Proteins, 2001, 43(3), 246-255.
[http://dx.doi.org/10.1002/prot.1035] [PMID: 11288174]
[82]
Chen, W.; Lei, T-Y.; Jin, D.C.; Lin, H.; Chou, K.C. PseKNC: a flexible web server for generating pseudo K-tuple nucleotide composition. Anal. Biochem., 2014, 456(1), 53-60.
[http://dx.doi.org/10.1016/j.ab.2014.04.001] [PMID: 24732113]
[83]
Chou, K.C. Impacts of bioinformatics to medicinal chemistry. Med. Chem., 2015, 11(3), 218-234.
[http://dx.doi.org/10.2174/1573406411666141229162834] [PMID: 25548930]
[84]
Koteswara Reddy, G.; Nagamalleswara Rao, K.; Yarrakula, K. Insights into structure and function of 30S ribosomal protein S2 (30S2) in Chlamydophila pneumoniae: a potent target of pneumonia. Comput. Biol. Chem., 2017, 66, 11-20.
[http://dx.doi.org/10.1016/j.compbiolchem.2016.10.014] [PMID: 27866051]
[85]
Thompson, J.D.; Gibson, T.J.; Higgins, D.G. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinform., 2002, Chapter 2: Unit 2.3.
[http://dx.doi.org/10.1002/0471250953.bi0203s00] [PMID: 18792934]
[86]
Bateman, A.; Birney, E.; Durbin, R.; Eddy, S.R.; Howe, K.L.; Sonnhammer, E.L.L. The Pfam protein families database. Nucleic Acids Res., 2008, 32(1), D138.
[87]
Bateman, A.; Coin, L.; Durbin, R.; Finn, R.D.; Hollich, V.; Griffiths-Jones, S.; Khanna, A.; Marshall, M.; Moxon, S.; Sonnhammer, E.L.; Studholme, D.J.; Yeats, C.; Eddy, S.R. The Pfam protein families database. Nucleic Acids Res., 2004, 32(Database issue), D138-D141.
[http://dx.doi.org/10.1093/nar/gkh121] [PMID: 14681378]
[88]
Buchan, D.W.A.; Federico, M.; Nugent, T.C.O.; Kevin, B.; Jones, D.T. Scalable web services for the PSIPRED protein analysis workbench. Nucleic Acids Res., 2013, 42, 349-357.
[http://dx.doi.org/10.1093/nar/gkt381]
[89]
Marco, B.; Stefan, B.; Andrew, W.; Konstantin, A.; Gabriel, S.; Tobias, S.; Florian, K.; Tiziano Gallo, C.; Martino, B.; Lorenza, B. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res., 2014, 42, 252-258.
[90]
Van Wart, H.E.; Steinbrink, D.R. A continuous spectrophotometric assay for Clostridium histolyticum collagenase. Anal. Biochem., 1981, 113(2), 356-365.
[http://dx.doi.org/10.1016/0003-2697(81)90089-0] [PMID: 6269461]
[91]
Eckhard, U.; Schönauer, E.; Brandstetter, H. Structural basis for activity regulation and substrate preference of clostridial collagenases G, H, and T. J. Biol. Chem., 2013, 288(28), 20184-20194.
[http://dx.doi.org/10.1074/jbc.M112.448548] [PMID: 23703618]
[92]
Eckhard, U.; Schönauer, E.; Nüss, D.; Brandstetter, H. Structure of collagenase G reveals a chew-and-digest mechanism of bacterial collagenolysis. Nat. Struct. Mol. Biol., 2011, 18(10), 1109-1114.
[http://dx.doi.org/10.1038/nsmb.2127] [PMID: 21947205]
[93]
Wlodawer, A.; Li, M.; Gustchina, A.; Oyama, H.; Dunn, B.M.; Oda, K. Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases. Acta Biochim. Pol., 2003, 50(1), 81-102.
[PMID: 12673349]
[94]
Kato, T.; Takahashi, N.; Kuramitsu, H.K. Sequence analysis and characterization of the Porphyromonas gingivalis prtC gene, which expresses a novel collagenase activity. J. Bacteriol., 1992, 174(12), 3889-3895.
[http://dx.doi.org/10.1128/jb.174.12.3889-3895.1992] [PMID: 1317840]
[95]
Lüthy, R.; Bowie, J.U.; Eisenberg, D. Assessment of protein models with three-dimensional profiles. Nature, 1992, 356(6364), 83-85.
[http://dx.doi.org/10.1038/356083a0] [PMID: 1538787]
[96]
Colovos, C.; Yeates, T.O. Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci., 1993, 2(9), 1511-1519.
[http://dx.doi.org/10.1002/pro.5560020916] [PMID: 8401235]
[97]
Pontius, J.; Richelle, J.; Wodak, S.J. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J. Mol. Biol., 1996, 264(1), 121-136.
[http://dx.doi.org/10.1006/jmbi.1996.0628] [PMID: 8950272]
[98]
Laskowski, R.A.; Macarthur, M.W.; Moss, D.S.; Thornton, J.M. PROCHECK - a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 1993, 26, 283-291.
[http://dx.doi.org/10.1107/S0021889892009944]

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