Literature DB >> 18298083

Free-energy landscape of enzyme catalysis.

Stephen J Benkovic1, Gordon G Hammes, Sharon Hammes-Schiffer.   

Abstract

The concept is developed that enzyme mechanisms should be viewed as "catalytic networks" with multiple conformations that occur serially and in parallel in the mechanism. These coupled ensembles of conformations require a multi-dimensional standard free-energy surface that is very "rugged", containing multiple minima and transition states. Experimental and theoretical evidence is presented to support this concept.

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Year:  2008        PMID: 18298083     DOI: 10.1021/bi800049z

Source DB:  PubMed          Journal:  Biochemistry        ISSN: 0006-2960            Impact factor:   3.162


  114 in total

1.  Impact of mutation on proton transfer reactions in ketosteroid isomerase: insights from molecular dynamics simulations.

Authors:  Dhruva K Chakravorty; Sharon Hammes-Schiffer
Journal:  J Am Chem Soc       Date:  2010-06-02       Impact factor: 15.419

2.  Structural and electrostatic asymmetry at the active site in typical and atypical peroxiredoxin dimers.

Authors:  Freddie R Salsbury; Ye Yuan; Michael H Knaggs; Leslie B Poole; Jacquelyn S Fetrow
Journal:  J Phys Chem B       Date:  2012-04-04       Impact factor: 2.991

Review 3.  What history tells us. XXVII. A new life for allostery.

Authors:  Michel Morange
Journal:  J Biosci       Date:  2012-03       Impact factor: 1.826

4.  Good vibrations in enzyme-catalysed reactions.

Authors:  Sam Hay; Nigel S Scrutton
Journal:  Nat Chem       Date:  2012-01-29       Impact factor: 24.427

Review 5.  Single-molecule force spectroscopy approach to enzyme catalysis.

Authors:  Jorge Alegre-Cebollada; Raul Perez-Jimenez; Pallav Kosuri; Julio M Fernandez
Journal:  J Biol Chem       Date:  2010-04-09       Impact factor: 5.157

6.  Nucleotide-dependent conformational change governs specificity and analog discrimination by HIV reverse transcriptase.

Authors:  Matthew W Kellinger; Kenneth A Johnson
Journal:  Proc Natl Acad Sci U S A       Date:  2010-04-12       Impact factor: 11.205

7.  Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease.

Authors:  Fuxiao Xin; Steven Myers; Yong Fuga Li; David N Cooper; Sean D Mooney; Predrag Radivojac
Journal:  Bioinformatics       Date:  2010-06-15       Impact factor: 6.937

8.  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

9.  Computational approach for ranking mutant enzymes according to catalytic reaction rates.

Authors:  Malika Kumarasiri; Gregory A Baker; Alexander V Soudackov; Sharon Hammes-Schiffer
Journal:  J Phys Chem B       Date:  2009-03-19       Impact factor: 2.991

Review 10.  Enzyme (re)design: lessons from natural evolution and computation.

Authors:  John A Gerlt; Patricia C Babbitt
Journal:  Curr Opin Chem Biol       Date:  2009-02-23       Impact factor: 8.822

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