Hydrogen tunneling links protein dynamics to enzyme catalysis.

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 Biochem

authors

Klinman JP,Kohen A

doi

10.1146/annurev-biochem-051710-133623

subject

Has Abstract

pub_date

2013-01-01 00:00:00

pages

471-96

eissn

0066-4154

issn

1545-4509

journal_volume

82

pub_type

杂志文章,评审
  • A journey in the world of DNA rings and beyond.

    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

    authors: Wang JC

    更新日期:2009-01-01 00:00:00

  • Magic angle spinning NMR of proteins: high-frequency dynamic nuclear polarization and (1)H detection.

    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

    authors: Su Y,Andreas L,Griffin RG

    更新日期:2015-01-01 00:00:00

  • With the help of giants.

    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

    authors: Fridovich I

    更新日期:2003-01-01 00:00:00

  • Essentials for ATP synthesis by F1F0 ATP synthases.

    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

    authors: von Ballmoos C,Wiedenmann A,Dimroth P

    更新日期:2009-01-01 00:00:00

  • HIV-1: fifteen proteins and an RNA.

    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

    authors: Frankel AD,Young JA

    更新日期:1998-01-01 00:00:00

  • Translation at the single-molecule level.

    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

    authors: Marshall RA,Aitken CE,Dorywalska M,Puglisi JD

    更新日期:2008-01-01 00:00:00

  • Nuclear actin and actin-related proteins in chromatin remodeling.

    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

    authors: Olave IA,Reck-Peterson SL,Crabtree GR

    更新日期:2002-01-01 00:00:00

  • Lipid A modification systems in gram-negative bacteria.

    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

    authors: Raetz CR,Reynolds CM,Trent MS,Bishop RE

    更新日期:2007-01-01 00:00:00

  • Structural insights into microtubule function.

    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

    authors: Nogales E

    更新日期:2000-01-01 00:00:00

  • Progress toward synthetic cells.

    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

    authors: Blain JC,Szostak JW

    更新日期:2014-01-01 00:00:00

  • Soluble Methane Monooxygenase.

    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

    authors: Banerjee R,Jones JC,Lipscomb JD

    更新日期:2019-06-20 00:00:00

  • Swinging arms and swinging domains in multifunctional enzymes: catalytic machines for multistep reactions.

    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

    authors: Perham RN

    更新日期:2000-01-01 00:00:00

  • The biochemistry of Parkinson's disease.

    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

    authors: Cookson MR

    更新日期:2005-01-01 00:00:00

  • Proton transfer in reaction centers from photosynthetic bacteria.

    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

    authors: Okamura MY,Feher G

    更新日期:1992-01-01 00:00:00

  • GTPase networks in membrane traffic.

    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

    authors: Mizuno-Yamasaki E,Rivera-Molina F,Novick P

    更新日期:2012-01-01 00:00:00

  • Regulation of telomerase by telomeric proteins.

    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

    authors: Smogorzewska A,de Lange T

    更新日期:2004-01-01 00:00:00

  • Regulation of Clathrin-Mediated Endocytosis.

    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

    authors: Mettlen M,Chen PH,Srinivasan S,Danuser G,Schmid SL

    更新日期:2018-06-20 00:00:00

  • Signals and combinatorial functions of histone modifications.

    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

    authors: Suganuma T,Workman JL

    更新日期:2011-01-01 00:00:00

  • AKT/PKB and other D3 phosphoinositide-regulated kinases: kinase activation by phosphoinositide-dependent phosphorylation.

    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

    authors: Chan TO,Rittenhouse SE,Tsichlis PN

    更新日期:1999-01-01 00:00:00

  • Application of the protein semisynthesis strategy to the generation of modified chromatin.

    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

    authors: Holt M,Muir T

    更新日期:2015-01-01 00:00:00

  • From virus structure to chromatin: X-ray diffraction to three-dimensional electron microscopy.

    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

    authors: Klug A

    更新日期:2010-01-01 00:00:00

  • From chemistry to biochemistry to catalysis to movement.

    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

    authors: Jencks WP

    更新日期:1997-01-01 00:00:00

  • Protein folding and modification in the mammalian endoplasmic reticulum.

    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

    authors: Braakman I,Bulleid NJ

    更新日期:2011-01-01 00:00:00

  • Using protein folding rates to test protein folding theories.

    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

    authors: Gillespie B,Plaxco KW

    更新日期:2004-01-01 00:00:00

  • D-amino acids in animal peptides.

    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

    authors: Kreil G

    更新日期:1997-01-01 00:00:00

  • Principles of Protein Stability and Their Application in Computational Design.

    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

    authors: Goldenzweig A,Fleishman SJ

    更新日期:2018-06-20 00:00:00

  • Nucleocytoplasmic transport: the soluble phase.

    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

    authors: Mattaj IW,Englmeier L

    更新日期:1998-01-01 00:00:00

  • DNA mismatch repair.

    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

    authors: Kunkel TA,Erie DA

    更新日期:2005-01-01 00:00:00

  • Long-distance electron transfer through DNA.

    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

    authors: Giese B

    更新日期:2002-01-01 00:00:00

  • Mechanics and Single-Molecule Interrogation of DNA Recombination.

    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

    authors: Bell JC,Kowalczykowski SC

    更新日期:2016-06-02 00:00:00