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• W2093612346 abstract "Although proteins are a fundamental unit in biology, the mechanism by which proteins fold into their native state is not well understood. In this work, we explore the assembly of secondary structure units via geometric constraint-based simulations and the effect of refinement of assembled structures using reservoir replica exchange molecular dynamics. Our approach uses two crucial features of these methods: i), geometric simulations speed up the search for nativelike topologies as there are no energy barriers to overcome; and ii), molecular dynamics identifies the low free energy structures and further refines these structures toward the actual native conformation. We use eight α-, β-, and α/β-proteins to test our method. The geometric simulations of our test set result in an average RMSD from native of 3.7 Å and this further reduces to 2.7 Å after refinement. We also explore the question of robustness of assembly for inaccurate (shifted and shortened) secondary structure. We find that the RMSD from native is highly dependent on the accuracy of secondary structure input, and even slightly shifting the location of secondary structure along the amino acid sequence can lead to a rapid decrease in RMSD to native due to incorrect packing." @default.
• W2093612346 created "2016-06-24" @default.
• W2093612346 creator A5002141394 @default.
• W2093612346 creator A5050843177 @default.
• W2093612346 date "2010-03-01" @default.
• W2093612346 modified "2023-10-14" @default.
• W2093612346 title "Union of Geometric Constraint-Based Simulations with Molecular Dynamics for Protein Structure Prediction" @default.
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• W2093612346 doi "https://doi.org/10.1016/j.bpj.2009.11.031" @default.
• W2093612346 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2849074" @default.
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• W2093612346 hasPublicationYear "2010" @default.
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