Abstract
DARPins (designed ankyrin repeat proteins), new kinds of binding proteins, have the potential to overcome the defects of monoclonal antibodies, and hence may become the alternatives to antibodies and generate a novel therapeutic approach. DARPins can be selected to bind any given target proteins with high affinity and specificity. In the process of binding to target proteins, the reason why DARPins have high affinity to target proteins as well as the correlation among sequences, structures, dynamical behaviors and binding to target proteins are still unknown. This paper studied DARPins using the AMBER package with ff03 force field for molecular dynamics simulations, providing a theoretical basis for the research on a new type of protein drug. This shows that the DARPins have more dynamical behaviors regularity after binding to target proteins compared with non-binding DARPins, but the binding to target proteins does not always stabilize the structures of DARPins, and the changes in the regions of β-turn and loop are the most obvious. The changes in hydrogen bonds and hydrophobic interactions have close relationship with the changes in the stability and cross correlation of DARPins.
Keywords: Molecular dynamics simulation DARPins protein drug, dynamical cross correlation stability, binding proteins, monoclonal antibodies, alternatives, AMBER package, theoretical basis, target proteins, β-turn, loop
Current Pharmaceutical Design
Title:Exploring the Relationship between Sequences, Structures, Dynamical Behaviors and Functions of New Type Protein Drugs: DARPins
Volume: 19 Issue: 12
Author(s): Xue Wu, Yue Shi, Pengyu Ren, Deping Wang and Guohui Li
Affiliation:
Keywords: Molecular dynamics simulation DARPins protein drug, dynamical cross correlation stability, binding proteins, monoclonal antibodies, alternatives, AMBER package, theoretical basis, target proteins, β-turn, loop
Abstract: DARPins (designed ankyrin repeat proteins), new kinds of binding proteins, have the potential to overcome the defects of monoclonal antibodies, and hence may become the alternatives to antibodies and generate a novel therapeutic approach. DARPins can be selected to bind any given target proteins with high affinity and specificity. In the process of binding to target proteins, the reason why DARPins have high affinity to target proteins as well as the correlation among sequences, structures, dynamical behaviors and binding to target proteins are still unknown. This paper studied DARPins using the AMBER package with ff03 force field for molecular dynamics simulations, providing a theoretical basis for the research on a new type of protein drug. This shows that the DARPins have more dynamical behaviors regularity after binding to target proteins compared with non-binding DARPins, but the binding to target proteins does not always stabilize the structures of DARPins, and the changes in the regions of β-turn and loop are the most obvious. The changes in hydrogen bonds and hydrophobic interactions have close relationship with the changes in the stability and cross correlation of DARPins.
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Cite this article as:
Wu Xue, Shi Yue, Ren Pengyu, Wang Deping and Li Guohui, Exploring the Relationship between Sequences, Structures, Dynamical Behaviors and Functions of New Type Protein Drugs: DARPins, Current Pharmaceutical Design 2013; 19 (12) . https://dx.doi.org/10.2174/1381612811319120017
DOI https://dx.doi.org/10.2174/1381612811319120017 |
Print ISSN 1381-6128 |
Publisher Name Bentham Science Publisher |
Online ISSN 1873-4286 |
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