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Toward molecular models of proton pumping: Challenges, methods and relevant applications

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Toward molecular models of proton pumping: Challenges, methods and relevant applications

Content Provider	Springer Nature Link
Author	Riccardi, Demian Zhu, Xiao Goyal, Puja Yang, Shuo Hou, GuanHua Cui, Qiang
Copyright Year	2011
Abstract	Motivated by several long-lasting mechanistic questions for biomolecular proton pumps, we have engaged in developing hybrid quantum mechanical/molecular mechanical (QM/MM) methods that allow an efficient and reliable description of long-range proton transport in transmembrane proteins. In this review, we briefly discuss several relevant issues: the need to develop a “multi-scale” generalized solvent boundary potential (GSBP) for the analysis of chemical events in large trans-membrane proteins, approaches to validate such a protocol, and the importance of improving the flexibility of QM/MM Hamiltonian. Several recent studies of model and realistic protein systems are also discussed to help put the discussions into context. Collectively, these studies suggest that the QM/MM-GSBP framework based on an approximate density functional theory (SCC-DFTB) as QM holds the promise to strike the proper balance between computational efficiency, accuracy and generality. With additional improvements in the methodology and recent developments by others, especially powerful sampling techniques, this “multi-scale” framework will be able to help unlock the secrets of proton pumps and other biomolecular machines.
Starting Page	3
Ending Page	18
Page Count	16
File Format	PDF
ISSN	16747291
Journal	Science in China Series B: Chemistry
Volume Number	55
Issue Number	1
e-ISSN	18691870
Language	English
Publisher	SP Science China Press
Publisher Date	2011-12-12
Publisher Place	Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	proton pumping QM/MM simulations SCC-DFTB microscopic pK $_{a}$ multi-scale simulations Chemistry/Food Science
Content Type	Text
Resource Type	Article
Subject	Chemistry

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Toward molecular models of proton pumping: Challenges, methods and relevant applications