Hydrogen Bonds: Simple after All?

被引:233
作者
Herschlag, Daniel [1 ,2 ,3 ,4 ]
Pinney, Margaux M. [1 ]
机构
[1] Stanford Univ, Dept Biochem, Stanford, CA 94305 USA
[2] Stanford Univ, Dept Chem, Stanford, CA 94305 USA
[3] Stanford Univ, Dept Chem Engn, Stanford, CA 94305 USA
[4] Stanford Univ, Stanford ChEM H, Stanford, CA 94305 USA
基金
美国国家科学基金会;
关键词
CYCLOTRON RESONANCE DETERMINATION; ISOMERASE OXYANION HOLE; RAY-STRUCTURE ANALYSES; ENZYME ACTIVE-SITE; KETOSTEROID ISOMERASE; GAS-PHASE; NMR-SPECTROSCOPY; SERINE PROTEASES; ELECTRIC-FIELDS; CATALYTIC TRIAD;
D O I
10.1021/acs.biochem.8b00217
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Hydrogen bonds play integral roles in biological structure, function, and conformational dynamics and are fundamental to life as it has evolved on Earth. However, our understanding of these fundamental and ubiquitous interactions has seemed fractured and incomplete, and it has been difficult to extract generalities and principles about hydrogen bonds despite thousands of papers published on this topic, perhaps in part because of the expanse of this subject and the density of studies. Fortunately, recent hydrogen bond proposals, discussions, and debates have stimulated new tests and models and have led to a remarkably simple picture of the structure of hydrogen bonds. This knowledge also provides clarity concerning hydrogen bond energetics, limiting and simplifying the factors that need be considered. Herein we recount the advances that have led to this simpler view of hydrogen bond structure, dynamics, and energetics. A quantitative predictive model for hydrogen bond length can now be broadly and deeply applied to evaluate current proposals and to uncover structural features of proteins, their conformational restraints, and their correlated motions. In contrast, a quantitative energetic description of molecular recognition and catalysis by proteins remains an important ongoing challenge, although our improved understanding of hydrogen bonds may aid in testing predictions from current and future models. We close by codifying our current state of understanding into five "Rules for Hydrogen Bonding" that may provide a foundation for understanding and teaching about these vital interactions and for building toward a deeper understanding of hydrogen bond energetics.
引用
收藏
页码:3338 / 3352
页数:15
相关论文
共 128 条
[1]   Identification of Hydroxyl Protons, Determination of Their Exchange Dynamics, and Characterization of Hydrogen Bonding in a Microcrystallin Protein [J].
Agarwal, Vipin ;
Linser, Rasmus ;
Fink, Uwe ;
Faelber, Katja ;
Reif, Bernd .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2010, 132 (09) :3187-3195
[2]   A SYSTEMATIC STUDY OF COORDINATE PRECISION IN X-RAY STRUCTURE ANALYSES .2. PREDICTIVE ESTIMATES OF ESDS FOR THE GENERAL-ATOM CASE [J].
ALLEN, FH ;
COLE, JC ;
HOWARD, JAK .
ACTA CRYSTALLOGRAPHICA SECTION A, 1995, 51 :112-121
[3]   A SYSTEMATIC STUDY OF COORDINATE PRECISION IN X-RAY STRUCTURE ANALYSES .1. DESCRIPTIVE STATISTICS AND PREDICTIVE ESTIMATES OF ESDS FOR C ATOMS [J].
ALLEN, FH ;
COLE, JC ;
HOWARD, JAK .
ACTA CRYSTALLOGRAPHICA SECTION A, 1995, 51 :95-111
[4]   A cartography of the van der Waals territories [J].
Alvarez, Santiago .
DALTON TRANSACTIONS, 2013, 42 (24) :8617-8636
[5]  
[Anonymous], 1997, HYDROGEN BONDING THE
[6]   A low-barrier hydrogen bond in the catalytic triad of serine proteases? Theory versus experiment [J].
Ash, EL ;
Sudmeier, JL ;
DeFabo, EC ;
Bachovchin, WW .
SCIENCE, 1997, 278 (5340) :1128-1132
[7]   Van der Waals radii of elements [J].
Batsanov, SS .
INORGANIC MATERIALS, 2001, 37 (09) :871-885
[8]   DETERMINATION OF STABILITY CONSTANTS OF HYDROGEN AND ALUMINUM FLUORIDES WITH A FLUORIDE-SELECTIVE ELECTRODE [J].
BAUMANN, EW .
JOURNAL OF INORGANIC & NUCLEAR CHEMISTRY, 1969, 31 (10) :3155-&
[9]  
Berg J.M., 2002, Oxidative Phosphorylation, V5
[10]   Keep on Moving: Discovering and Perturbing the Conformational Dynamics of Enzymes [J].
Bhabha, Gira ;
Biel, Justin T. ;
Fraser, James S. .
ACCOUNTS OF CHEMICAL RESEARCH, 2015, 48 (02) :423-430