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Journal ArticleDOI

A Perspective on Enzyme Catalysis

29 Aug 2003-Science (American Association for the Advancement of Science)-Vol. 301, Iss: 5637, pp 1196-1202
TL;DR: A case study for the enzyme dihydrofolate reductase provides evidence for coupled networks of predominantly conserved residues that influence the protein structure and motion that have important implications for the origin and evolution of enzymes, as well as for protein engineering.
Abstract: The seminal hypotheses proposed over the years for enzymatic catalysis are scrutinized. The historical record is explored from both biochemical and theoretical perspectives. Particular attention is given to the impact of molecular motions within the protein on the enzyme's catalytic properties. A case study for the enzyme dihydrofolate reductase provides evidence for coupled networks of predominantly conserved residues that influence the protein structure and motion. Such coupled networks have important implications for the origin and evolution of enzymes, as well as for protein engineering.

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Journal ArticleDOI
12 Dec 2007-Nature
TL;DR: The dream is to 'watch' proteins in action in real time at atomic resolution, which requires addition of a fourth dimension, time, to structural biology so that the positions in space and time of all atoms in a protein can be described in detail.
Abstract: Because proteins are central to cellular function, researchers have sought to uncover the secrets of how these complex macromolecules execute such a fascinating variety of functions. Although static structures are known for many proteins, the functions of proteins are governed ultimately by their dynamic character (or 'personality'). The dream is to 'watch' proteins in action in real time at atomic resolution. This requires addition of a fourth dimension, time, to structural biology so that the positions in space and time of all atoms in a protein can be described in detail.

2,109 citations


Cites background from "A Perspective on Enzyme Catalysis"

  • ...), and they have a minimal effect on the overall rates of biological processe...

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Journal ArticleDOI
TL;DR: In this paper, the authors review quantitative cellulase activity assays using soluble and insoluble substrates, and focus on their advantages and limitations, and hypothesize that continuous culture using insoluble cellulosic substrates could be a powerful selection tool for enriching beneficial cellulase mutants from the large library displayed on the cell surface.

1,495 citations

Journal ArticleDOI
03 Nov 2005-Nature
TL;DR: It is shown that the intrinsic plasticity of the protein is a key characteristic of catalysis, and the pre-existence of collective dynamics in enzymes before catalysis is a common feature of biocatalysts and that proteins have evolved under synergy pressure between structure and dynamics.
Abstract: A unique feature of chemical catalysis mediated by enzymes is that the catalytically reactive atoms are embedded within a folded protein. Although current understanding of enzyme function has been focused on the chemical reactions and static three-dimensional structures, the dynamic nature of proteins has been proposed to have a function in catalysis. The concept of conformational substates has been described; however, the challenge is to unravel the intimate linkage between protein flexibility and enzymatic function. Here we show that the intrinsic plasticity of the protein is a key characteristic of catalysis. The dynamics of the prolyl cis-trans isomerase cyclophilin A (CypA) in its substrate-free state and during catalysis were characterized with NMR relaxation experiments. The characteristic enzyme motions detected during catalysis are already present in the free enzyme with frequencies corresponding to the catalytic turnover rates. This correlation suggests that the protein motions necessary for catalysis are an intrinsic property of the enzyme and may even limit the overall turnover rate. Motion is localized not only to the active site but also to a wider dynamic network. Whereas coupled networks in proteins have been proposed previously, we experimentally measured the collective nature of motions with the use of mutant forms of CypA. We propose that the pre-existence of collective dynamics in enzymes before catalysis is a common feature of biocatalysts and that proteins have evolved under synergistic pressure between structure and dynamics.

1,080 citations


Cites background or result from "A Perspective on Enzyme Catalysis"

  • ...It also implies that the chemical shifts between the two states (Dq),and hence their structural differences, are identical for wild-type CypA and all CypA mutants (scheme (3)); Supplementary Table S2)....

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  • ...It is also noteworthy that the calculated chemical-shift differences (equation (1)) between Emajor and Eminor (qEmajor 2 qEminor; scheme (3)) are similar to those between EScis and EStrans (qEScis 2 qEStrans; scheme (2)) for residues remote from the substrate, suggesting that the cis substrate binds Emajor to form EScis, whereas the trans substrate binds Eminor to form EStrans....

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Journal ArticleDOI
09 Jan 2004-Science
TL;DR: A framework for understanding the effects of lowering of the activation free energy and changes in the generalized transmission coefficient on enzyme catalysis is presented, and the contributions of the different factors are identified and quantified by computer simulations.
Abstract: Advances in transition state theory and computer simulations are providing new insights into the sources of enzyme catalysis. Both lowering of the activation free energy and changes in the generalized transmission coefficient (recrossing of the transition state, tunneling, and nonequilibrium contributions) can play a role. A framework for understanding these effects is presented, and the contributions of the different factors, as illustrated by specific enzymes, are identified and quantified by computer simulations. The resulting understanding of enzyme catalysis is used to comment on alternative proposals of how enzymes work.

1,003 citations

Journal ArticleDOI
TL;DR: Efficient sampling of mutations likely to affect enzyme function has been conducted both experimentally and computationally, with remarkable improvements in substrate selectivity and specificity and in the de novo design of enzyme activities within scaffolds of known structure.

844 citations

References
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Journal ArticleDOI
TL;DR: In this paper, the electron transfer reactions between ions and molecules in solution have been the subject of considerable experimental study during the past three decades, including charge transfer, photoelectric emission spectra, chemiluminescent electron transfer, and electron transfer through frozen media.

7,155 citations

Journal ArticleDOI
TL;DR: Electrostatic stabilization is an important factor in increasing the rate of the reaction step that leads to the formation of the carbonium ion intermediate, found in the cleavage of a glycosidic bond by lysozyme.

3,951 citations

Journal ArticleDOI
02 Aug 1996-Science
TL;DR: An exhaustive all-on-all shape comparison provides a map of physical attractor regions in the abstract shape space of proteins, with implications for the processes of protein folding and evolution.
Abstract: The comparison of the three-dimensional shapes of protein molecules poses a complex algorithmic problem. Its solution provides biologists with computational tools to organize the rapidly growing set of thousands of known protein shapes, to identify new types of protein architecture, and to discover unexpected evolutionary relations, reaching back billions of years, between protein molecules. Protein shape comparison also improves tools for identifying gene functions in genome databases by defining the essential sequence-structure features of a protein family. Finally, an exhaustive all-on-all shape comparison provides a map of physical attractor regions in the abstract shape space of proteins, with implications for the processes of protein folding and evolution.

1,551 citations

Journal ArticleDOI
22 May 1965-Nature
TL;DR: Structure of Hen Egg-White Lysozyme: A Three-dimensional Fourier Synthesis at 2 A Resolution as mentioned in this paper, 3D Fourier synthesis at 2 a resolution.
Abstract: Structure of Hen Egg-White Lysozyme: A Three-dimensional Fourier Synthesis at 2 A Resolution

1,494 citations

Journal ArticleDOI
TL;DR: In this paper, a qualitative discussion of electron transfer, its time and distance scales, energy curves, and basic parabolic energy models are introduced to define the electron transfer process, and some of the important, challenging, and problematic issues in contemporary electron transfer research are discussed.
Abstract: This is an overview of some of the important, challenging, and problematic issues in contemporary electron transfer research. After a qualitative discussion of electron transfer, its time and distance scales, energy curves, and basic parabolic energy models are introduced to define the electron transfer process. Application of transition state theory leads to the standard Marcus formulation of electron transfer rate constants. Electron transfer in solution is coupled to solvent polarization effects, and relaxation processes can contribute to and even control electron transfer. The inverted region, in which electron transfer rate constants decrease with increasing exoergicity, is one of the most striking phenomena in electron transfer chemistry. It is predicted by both semiclassical and quantum mechanical models, with the latter appropriate if there are coupled high- or medium-frequency vibrations. The intramolecular reorganizational energy has different contributions from different vibrational modes, whic...

1,413 citations