Literature DB >> 18779576

On the relationship between folding and chemical landscapes in enzyme catalysis.

Maite Roca1, Benjamin Messer, Donald Hilvert, Arieh Warshel.   

Abstract

Elucidating the relationship between the folding landscape of enzymes and their catalytic power has been one of the challenges of modern enzymology. The present work explores this issue by using a simplified folding model to generate the free-energy landscape of an enzyme and then to evaluate the activation barriers for the chemical step in different regions of the landscape. This approach is used to investigate the recent finding that an engineered monomeric chorismate mutase exhibits catalytic efficiency similar to the naturally occurring dimer even though it exhibits the properties of an intrinsically disordered molten globule. It is found that the monomer becomes more confined than its native-like counterpart upon ligand binding but still retains a wider catalytic region. Although the overall rate acceleration is still determined by reduction of the reorganization energy, the detailed contribution of different barriers yields a more complex picture for the chemical process than that of a single path. This work provides insight into the relationship between folding landscapes and catalysis. The computational approach used here may also provide a powerful strategy for modeling single-molecule experiments and designing enzymes.

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Year:  2008        PMID: 18779576      PMCID: PMC2544547          DOI: 10.1073/pnas.0803405105

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  23 in total

1.  Transition-state structure as a unifying basis in protein-folding mechanisms: contact order, chain topology, stability, and the extended nucleus mechanism.

Authors:  A R Fersht
Journal:  Proc Natl Acad Sci U S A       Date:  2000-02-15       Impact factor: 11.205

Review 2.  Electrostatic basis for enzyme catalysis.

Authors:  Arieh Warshel; Pankaz K Sharma; Mitsunori Kato; Yun Xiang; Hanbin Liu; Mats H M Olsson
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

3.  Exploring the role of large conformational changes in the fidelity of DNA polymerase beta.

Authors:  Yun Xiang; Myron F Goodman; William A Beard; Samuel H Wilson; Arieh Warshel
Journal:  Proteins       Date:  2008-01-01

4.  Predicting drug-resistant mutations of HIV protease.

Authors:  Hiroshi Ishikita; Arieh Warshel
Journal:  Angew Chem Int Ed Engl       Date:  2008       Impact factor: 15.336

5.  Structure and dynamics of a molten globular enzyme.

Authors:  Konstantin Pervushin; Katherina Vamvaca; Beat Vögeli; Donald Hilvert
Journal:  Nat Struct Mol Biol       Date:  2007-11-11       Impact factor: 15.369

6.  Two-dimensional reaction free energy surfaces of catalytic reaction: effects of protein conformational dynamics on enzyme catalysis.

Authors:  Wei Min; X Sunney Xie; Biman Bagchi
Journal:  J Phys Chem B       Date:  2007-12-18       Impact factor: 2.991

7.  An interpretation of fluctuations in enzyme catalysis rate, spectral diffusion, and radiative component of lifetimes in terms of electric field fluctuations.

Authors:  Meher K Prakash; R A Marcus
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-02       Impact factor: 11.205

Review 8.  Free-energy landscape of enzyme catalysis.

Authors:  Stephen J Benkovic; Gordon G Hammes; Sharon Hammes-Schiffer
Journal:  Biochemistry       Date:  2008-02-26       Impact factor: 3.162

9.  The catalytic effect of dihydrofolate reductase and its mutants is determined by reorganization energies.

Authors:  Hanbin Liu; Arieh Warshel
Journal:  Biochemistry       Date:  2007-05-01       Impact factor: 3.162

10.  On the relationship between thermal stability and catalytic power of enzymes.

Authors:  Maite Roca; Hanbin Liu; Benjamin Messer; Arieh Warshel
Journal:  Biochemistry       Date:  2007-12-01       Impact factor: 3.162

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  28 in total

1.  Impact of oxidation on protein therapeutics: conformational dynamics of intact and oxidized acid-β-glucocerebrosidase at near-physiological pH.

Authors:  Cedric E Bobst; John J Thomas; Paul A Salinas; Philip Savickas; Igor A Kaltashov
Journal:  Protein Sci       Date:  2010-12       Impact factor: 6.725

2.  An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling.

Authors:  Shina C L Kamerlin; Arieh Warshel
Journal:  J Phys Org Chem       Date:  2010-07       Impact factor: 2.391

3.  Simulating the electrostatic guidance of the vectorial translocations in hexameric helicases and translocases.

Authors:  Hanbin Liu; Yemin Shi; Xiaojiang S Chen; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2009-04-21       Impact factor: 11.205

4.  Molecular dynamics simulation of the last step of a catalytic cycle: product release from the active site of the enzyme chorismate mutase from Mycobacterium tuberculosis.

Authors:  Alexandra Choutko; Wilfred F van Gunsteren
Journal:  Protein Sci       Date:  2012-11       Impact factor: 6.725

5.  A 21st century revisionist's view at a turning point in enzymology.

Authors:  Zachary D Nagel; Judith P Klinman
Journal:  Nat Chem Biol       Date:  2009-08       Impact factor: 15.040

6.  Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm.

Authors:  Garegin A Papoian
Journal:  Proc Natl Acad Sci U S A       Date:  2008-09-17       Impact factor: 11.205

7.  Enzyme millisecond conformational dynamics do not catalyze the chemical step.

Authors:  Andrei V Pisliakov; Jie Cao; Shina C L Kamerlin; Arieh Warshel
Journal:  Proc Natl Acad Sci U S A       Date:  2009-09-25       Impact factor: 11.205

Review 8.  NMR spectroscopy brings invisible protein states into focus.

Authors:  Andrew J Baldwin; Lewis E Kay
Journal:  Nat Chem Biol       Date:  2009-11       Impact factor: 15.040

9.  Multiscale simulations of protein landscapes: using coarse-grained models as reference potentials to full explicit models.

Authors:  Benjamin M Messer; Maite Roca; Zhen T Chu; Spyridon Vicatos; Alexandra Vardi Kilshtain; Arieh Warshel
Journal:  Proteins       Date:  2010-04

10.  Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis.

Authors:  Moitrayee Bhattacharyya; Saraswathi Vishveshwara
Journal:  BMC Struct Biol       Date:  2010-08-12
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