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Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

Content Provider	PubMed Central
Author	Lei, Hongxing Wu, Chun Wang, Zhi-xiang Zhou, Yaoqi Duan, Yong
Copyright Year	2008
Abstract	Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 Å C α root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 Å C α RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II∕III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0 Å C α RMSD away from the experimentally determined structure.
Related Links	http://dx.doi.org/10.1063/1.2937135
Starting Page	235105
File Format	PDF
ISSN	00219606
e-ISSN	10897690
Journal	The Journal of Chemical Physics
Issue Number	23
Volume Number	128
Language	English
Publisher	American Institute of Physics
Publisher Date	2008-01-01
Access Restriction	Open
Rights Holder	American Institute of Physics
Subject Keyword	Physical and Theoretical Chemistry Physics and Astronomy(all) Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Physics and Astronomy Medicine Physical and Theoretical Chemistry

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