Literature DB >> 10902152

Enzyme evolution explained (sort of).

A M Dean1, G B Golding.   

Abstract

Sites in proteins evolve at markedly different rates; some are highly conserved, others change rapidly. We have developed a maximum likelihood method to identify regions of a protein that evolve rapidly or slowly relative to the remaining structure. We also show that solvent accessibility and distance from the catalytic site are major determinants of evolutionary rate in eubacterial isocitrate dehydrogenases. These two variables account for most of the rate heterogeneity not ascribable to stochastic effects.

Mesh:

Substances:

Year:  2000        PMID: 10902152     DOI: 10.1142/9789814447331_0002

Source DB:  PubMed          Journal:  Pac Symp Biocomput        ISSN: 2335-6928


  11 in total

1.  Inference of functional regions in proteins by quantification of evolutionary constraints.

Authors:  Alexander L Simon; Eric A Stone; Arend Sidow
Journal:  Proc Natl Acad Sci U S A       Date:  2002-03-05       Impact factor: 11.205

2.  Inferring functional constraints and divergence in protein families using 3D mapping of phylogenetic information.

Authors:  Christian Blouin; Yan Boucher; Andrew J Roger
Journal:  Nucleic Acids Res       Date:  2003-01-15       Impact factor: 16.971

Review 3.  Genomic biodiversity, phylogenetics and coevolution in proteins.

Authors:  David D Pollock
Journal:  Appl Bioinformatics       Date:  2002

4.  Context dependence and coevolution among amino acid residues in proteins.

Authors:  Zhengyuan O Wang; David D Pollock
Journal:  Methods Enzymol       Date:  2005       Impact factor: 1.600

5.  Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account.

Authors:  Itay Mayrose; Amir Mitchell; Tal Pupko
Journal:  J Mol Evol       Date:  2005-03       Impact factor: 2.395

6.  Testing for spatial clustering of amino acid replacements within protein tertiary structure.

Authors:  Jiaye Yu; Jeffrey L Thorne
Journal:  J Mol Evol       Date:  2006-04-25       Impact factor: 2.395

7.  Association of putative concave protein-binding sites with the fluctuation behavior of residues.

Authors:  Asli Ertekin; Ruth Nussinov; Turkan Haliloglu
Journal:  Protein Sci       Date:  2006-10       Impact factor: 6.725

8.  Concentration of specific amino acids at the catalytic/active centers of highly-conserved "housekeeping" enzymes of central metabolism in archaea, bacteria and Eukaryota: is there a widely conserved chemical signal of prebiotic assembly?

Authors:  J Dennis Pollack; Xueliang Pan; Dennis K Pearl
Journal:  Orig Life Evol Biosph       Date:  2010-01-13       Impact factor: 1.950

9.  In silico identification of functional protein interfaces.

Authors:  Rachel E Bell; Nir Ben-Tal
Journal:  Comp Funct Genomics       Date:  2003

10.  Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures.

Authors:  Yi-Fei Huang; G Brian Golding
Journal:  PLoS Comput Biol       Date:  2014-01-16       Impact factor: 4.475

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