Abstract:
:The relationship between protein dynamics and function is a subject of considerable contemporary interest. Although protein motions are frequently observed during ligand binding and release steps, the contribution of protein motions to the catalysis of bond making/breaking processes is more difficult to probe and verify. Here, we show how the quantum mechanical hydrogen tunneling associated with enzymatic C-H bond cleavage provides a unique window into the necessity of protein dynamics for achieving optimal catalysis. Experimental findings support a hierarchy of thermodynamically equilibrated motions that control the H-donor and -acceptor distance and active-site electrostatics, creating an ensemble of conformations suitable for H-tunneling. A possible extension of this view to methyl transfer and other catalyzed reactions is also presented. The impact of understanding these dynamics on the conceptual framework for enzyme activity, inhibitor/drug design, and biomimetic catalyst design is likely to be substantial.
journal_name
Annu Rev Biochemjournal_title
Annual review of biochemistryauthors
Klinman JP,Kohen Adoi
10.1146/annurev-biochem-051710-133623subject
Has Abstractpub_date
2013-01-01 00:00:00pages
471-96eissn
0066-4154issn
1545-4509journal_volume
82pub_type
杂志文章,评审abstract::I was born in China and would have remained there but for the tumultuous events that led many of my generation to the United States for graduate studies. Norman Davidson introduced me to DNA when I became a postdoctoral fellow in his group at the California Institute of Technology in 1964, and a fortuitous conversatio...
journal_title:Annual review of biochemistry
pub_type: 传,历史文章,杂志文章
doi:10.1146/annurev.biochem.78.030107.090101
更新日期:2009-01-01 00:00:00
abstract::Magic angle spinning (MAS) NMR studies of amyloid and membrane proteins and large macromolecular complexes are an important new approach to structural biology. However, the applicability of these experiments, which are based on (13)C- and (15)N-detected spectra, would be enhanced if the sensitivity were improved. Here...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-060614-034206
更新日期:2015-01-01 00:00:00
abstract::A childhood fascination with animals, plants, and insects was aided and abetted by many giants, beginning with my parents. The Bronx High School of Science and the City College of New York (CCNY) made a solid and priceless grounding in chemistry and biology available free of charge. Abe Mazur at CCNY revealed the wond...
journal_title:Annual review of biochemistry
pub_type: 传,历史文章,杂志文章
doi:10.1146/annurev.biochem.72.081902.140918
更新日期:2003-01-01 00:00:00
abstract::The majority of cellular energy in the form of adenosine triphosphate (ATP) is synthesized by the ubiquitous F(1)F(0) ATP synthase. Power for ATP synthesis derives from an electrochemical proton (or Na(+)) gradient, which drives rotation of membranous F(0) motor components. Efficient rotation not only requires a signi...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.78.081307.104803
更新日期:2009-01-01 00:00:00
abstract::Human immunodeficiency virus type 1 is a complex retrovirus encoding 15 distinct proteins. Substantial progress has been made toward understanding the function of each protein, and three-dimensional structures of many components, including portions of the RNA genome, have been determined. This review describes the fun...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.67.1.1
更新日期:1998-01-01 00:00:00
abstract::Decades of studies have established translation as a multistep, multicomponent process that requires intricate communication to achieve high levels of speed, accuracy, and regulation. A crucial next step in understanding translation is to reveal the functional significance of the large-scale motions implied by static ...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.77.070606.101431
更新日期:2008-01-01 00:00:00
abstract::The existence and function of actin in the nucleus has been hotly debated for forty years. Recently, beta-actin was found to be a component of mammalian SWI/SNF-like BAF chromatin remodeling complexes and still more recently other SWI/SNF-related chromatin remodeling complexes in yeast, flies, and man. Although the fu...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.71.110601.135507
更新日期:2002-01-01 00:00:00
abstract::The lipid A moiety of lipopolysaccharide forms the outer monolayer of the outer membrane of most gram-negative bacteria. Escherichia coli lipid A is synthesized on the cytoplasmic surface of the inner membrane by a conserved pathway of nine constitutive enzymes. Following attachment of the core oligosaccharide, nascen...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.76.010307.145803
更新日期:2007-01-01 00:00:00
abstract::Microtubules are polymers that are essential for, among other functions, cell transport and cell division in all eukaryotes. The regulation of the microtubule system includes transcription of different tubulin isotypes, folding of /¿-tubulin heterodimers, post-translation modification of tubulin, and nucleotide-based ...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.69.1.277
更新日期:2000-01-01 00:00:00
abstract::The complexity of even the simplest known life forms makes efforts to synthesize living cells from inanimate components seem like a daunting task. However, recent progress toward the creation of synthetic cells, ranging from simple protocells to artificial cells approaching the complexity of bacteria, suggests that th...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-080411-124036
更新日期:2014-01-01 00:00:00
abstract::Aerobic life is possible because the molecular structure of oxygen (O2) makes direct reaction with most organic materials at ambient temperatures an exceptionally slow process. Of course, these reactions are inherently very favorable, and they occur rapidly with the release of a great deal of energy at high temperatur...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-013118-111529
更新日期:2019-06-20 00:00:00
abstract::Multistep chemical reactions are increasingly seen as important in a growing number of complex biotransformations. Covalently attached prosthetic groups or swinging arms, and their associated protein domains, are essential to the mechanisms of active-site coupling and substrate channeling in a number of the multifunct...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.69.1.961
更新日期:2000-01-01 00:00:00
abstract::Several genes have been identified for monogenic disorders that variably resemble Parkinson's disease. Dominant mutations in the gene encoding alpha-synuclein enhance the propensity of this protein to aggregate. As a consequence, these patients have a widespread disease with protein inclusion bodies in several brain a...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.74.082803.133400
更新日期:2005-01-01 00:00:00
abstract::Proton transfer in the bacterial RC associated with the reduction of the bound QB to the dihydroquinone is an important step in the energetics of photosynthetic bacteria. The binding of two protons by the quinone is associated with the transfer of the second electron to QB at a rate of ca. 10(3) s-1 (pH 7). Mutation o...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.bi.61.070192.004241
更新日期:1992-01-01 00:00:00
abstract::Members of the Rab or ARF/Sar branches of the Ras GTPase superfamily regulate almost every step of intracellular membrane traffic. A rapidly growing body of evidence indicates that these GTPases do not act as lone agents but are networked to one another through a variety of mechanisms to coordinate the individual even...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-052810-093700
更新日期:2012-01-01 00:00:00
abstract::Telomeres are essential for genome stability in all eukaryotes. Changes in telomere functions and the associated chromosomal abnormalities have been implicated in human aging and cancer. Telomeres are composed of repetitive sequences that can be maintained by telomerase, a complex containing a reverse transcriptase (h...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.73.071403.160049
更新日期:2004-01-01 00:00:00
abstract::Clathrin-mediated endocytosis (CME) is the major endocytic pathway in mammalian cells. It is responsible for the uptake of transmembrane receptors and transporters, for remodeling plasma membrane composition in response to environmental changes, and for regulating cell surface signaling. CME occurs via the assembly an...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-062917-012644
更新日期:2018-06-20 00:00:00
abstract::Alterations of chromatin structure have been shown to be crucial for response to cell signaling and for programmed gene expression in development. Posttranslational histone modifications influence changes in chromatin structure both directly and by targeting or activating chromatin-remodeling complexes. Histone modifi...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-061809-175347
更新日期:2011-01-01 00:00:00
abstract::The protein kinase Akt/PKB is activated via a multistep process by a variety of signals. In the early steps of this process, PI-3 kinase-generated D3-phosphorylated phosphoinositides bind the Akt PH domain and induce the translocation of the kinase to the plasma membrane where it co-localizes with phosphoinositide-dep...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.68.1.965
更新日期:1999-01-01 00:00:00
abstract::Histone proteins are subject to a host of posttranslational modifications (PTMs) that modulate chromatin structure and function. Such control is achieved by the direct alteration of the intrinsic physical properties of the chromatin fiber or by regulating the recruitment and activity of a host of trans-acting nuclear ...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-060614-034429
更新日期:2015-01-01 00:00:00
abstract::Early influences led me first to medical school with a view to microbiology, but I felt the lack of a deeper foundation and changed to chemistry, which in turn led me to physics and mathematics. I moved to the University of Cape Town to work on the X-ray crystallography of some small organic compounds. I developed a n...
journal_title:Annual review of biochemistry
pub_type: 传,历史文章,杂志文章
doi:10.1146/annurev.biochem.79.091407.093947
更新日期:2010-01-01 00:00:00
abstract::Mechanisms of chemical reaction can often be predicted by determining the dependence of the lifetime of reaction intermediates on the structure of the reactants. When there is no lifetime in the presence of another reactant or catalyst the reaction proceeds through an enforced concerted mechanism. Noncovalent binding ...
journal_title:Annual review of biochemistry
pub_type: 传,历史文章,杂志文章
doi:10.1146/annurev.biochem.66.1.1
更新日期:1997-01-01 00:00:00
abstract::Analysis of the human genome reveals that approximately a third of all open reading frames code for proteins that enter the endoplasmic reticulum (ER), demonstrating the importance of this organelle for global protein maturation. The path taken by a polypeptide through the secretory pathway starts with its translocati...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-062209-093836
更新日期:2011-01-01 00:00:00
abstract::The fastest simple, kinetically two-state protein folds a million times more rapidly than the slowest. Here we review many recent theories of protein folding kinetics in terms of their ability to qualitatively rationalize, if not quantitatively predict, this fundamental experimental observation. ...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.73.011303.073904
更新日期:2004-01-01 00:00:00
abstract::D-amino acids have been detected in a variety of peptides synthesized by animal cells. These include opiate and antimicrobial peptides from amphibian skin, neuropeptides from snail ganglia, a hormone from crustaceans, and a constituent of a spider venom. cDNA cloning has shown that at those positions where a D-amino a...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.66.1.337
更新日期:1997-01-01 00:00:00
abstract::Proteins are increasingly used in basic and applied biomedical research. Many proteins, however, are only marginally stable and can be expressed in limited amounts, thus hampering research and applications. Research has revealed the thermodynamic, cellular, and evolutionary principles and mechanisms that underlie marg...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-062917-012102
更新日期:2018-06-20 00:00:00
abstract::Active transport between the nucleus and cytoplasm involves primarily three classes of macromolecules: substrates, adaptors, and receptors. Some transport substrates bind directly to an import or an export receptor while others require one or more adaptors to mediate formation of a receptor-substrate complex. Once ass...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.67.1.265
更新日期:1998-01-01 00:00:00
abstract::DNA mismatch repair (MMR) is an evolutionarily conserved process that corrects mismatches generated during DNA replication and escape proofreading. MMR proteins also participate in many other DNA transactions, such that inactivation of MMR can have wide-ranging biological consequences, which can be either beneficial o...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.74.082803.133243
更新日期:2005-01-01 00:00:00
abstract::DNA molecules are able to transport electrons over long distances. In most experiments the process is stimulated by the oxidation of guanines (G), which generates guanine radical cations. The electron transport through DNA occurs in a multistep hopping mechanism with all Gs as carriers of the positive charge. The rate...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev.biochem.71.083101.134037
更新日期:2002-01-01 00:00:00
abstract::The repair of DNA by homologous recombination is an essential, efficient, and high-fidelity process that mends DNA lesions formed during cellular metabolism; these lesions include double-stranded DNA breaks, daughter-strand gaps, and DNA cross-links. Genetic defects in the homologous recombination pathway undermine ge...
journal_title:Annual review of biochemistry
pub_type: 杂志文章,评审
doi:10.1146/annurev-biochem-060614-034352
更新日期:2016-06-02 00:00:00