Journal
BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS
Volume 1757, Issue 8, Pages 942-968Publisher
ELSEVIER SCIENCE BV
DOI: 10.1016/j.bbabio.2006.06.005
Keywords
electrostatics; electrochemistry; pK(a); E-m; bacteriorhodopsin; simulation; bioenergetics
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Funding
- NCRR NIH HHS [G12 RR003060-245459, RR03060, G12 RR003060] Funding Source: Medline
- NIGMS NIH HHS [R01-GM64540, R01 GM064540] Funding Source: Medline
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A protein structure should provide the information needed to understand its observed properties. Significant progress has been made in developing accurate calculations of acid/base and oxidation/reduction reactions in proteins. Current methods and their strengths and weaknesses are discussed. The distribution and calculated ionization states in a survey of proteins is described, showing that a significant minority of acidic and basic residues are buried in the protein and that most of these remain ionized. The electrochemistry of heme and quinones are considered. Proton transfers in bacteriorhodopsin and coupled electron and proton transfers in photosynthetic reaction centers, 5-coordinate heme binding proteins and cytochrome c oxidase are highlighted as systems where calculations have provided insight into the reaction mechanism. (c) 2006 Published by Elsevier B.V.
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