Literature DB >> 12653550

Conservation of electrostatic properties within enzyme families and superfamilies.

Dennis R Livesay1, Per Jambeck, Atipat Rojnuckarin, Shankar Subramaniam.   

Abstract

Electrostatic interactions play a key role in enzyme catalytic function. At long range, electrostatics steer the incoming ligand/substrate to the active site, and at short distances, electrostatics provide the specific local interactions for catalysis. In cases in which electrostatics determine enzyme function, orthologs should share the electrostatic properties to maintain function. Often, electrostatic potential maps are employed to depict how conserved surface electrostatics preserve function. We expand on previous efforts to explain conservation of function, using novel electrostatic sequence and structure analyses of four enzyme families and one enzyme superfamily. We show that the spatial charge distribution is conserved within each family and superfamily. Conversely, phylogenetic analysis of key electrostatic residues provide the evolutionary origins of functionality.

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Year:  2003        PMID: 12653550     DOI: 10.1021/bi026918f

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


  22 in total

1.  Differential geometry based solvation model II: Lagrangian formulation.

Authors:  Zhan Chen; Nathan A Baker; G W Wei
Journal:  J Math Biol       Date:  2011-01-30       Impact factor: 2.259

2.  Conferring thermostability to mesophilic proteins through optimized electrostatic surfaces.

Authors:  Michael Torrez; Michael Schultehenrich; Dennis R Livesay
Journal:  Biophys J       Date:  2003-11       Impact factor: 4.033

3.  Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity.

Authors:  Donald J Jacobs; Sargis Dallakyan
Journal:  Biophys J       Date:  2004-11-12       Impact factor: 4.033

4.  The evolutionary origins and catalytic importance of conserved electrostatic networks within TIM-barrel proteins.

Authors:  Dennis R Livesay; David La
Journal:  Protein Sci       Date:  2005-05       Impact factor: 6.725

5.  Redesigning protein pKa values.

Authors:  Barbara Mary Tynan-Connolly; Jens Erik Nielsen
Journal:  Protein Sci       Date:  2006-12-22       Impact factor: 6.725

6.  Computational methods for biomolecular electrostatics.

Authors:  Feng Dong; Brett Olsen; Nathan A Baker
Journal:  Methods Cell Biol       Date:  2008       Impact factor: 1.441

7.  Application of new multi-resolution methods for the comparison of biomolecular electrostatic properties in the absence of global structural similarity.

Authors:  Xiaoyu Zhang; Chandrajit L Bajaj; Bongjune Kwon; Todd J Dolinsky; Jens E Nielsen; Nathan A Baker
Journal:  Multiscale Model Simul       Date:  2006       Impact factor: 1.930

8.  MIBPB: a software package for electrostatic analysis.

Authors:  Duan Chen; Zhan Chen; Changjun Chen; Weihua Geng; Guo-Wei Wei
Journal:  J Comput Chem       Date:  2010-09-15       Impact factor: 3.376

Review 9.  Electrostatic clustering and free energy calculations provide a foundation for protein design and optimization.

Authors:  Ronald D Gorham; Chris A Kieslich; Dimitrios Morikis
Journal:  Ann Biomed Eng       Date:  2010-12-08       Impact factor: 3.934

10.  Kinase peptide specificity: improved determination and relevance to protein phosphorylation.

Authors:  Koichi Fujii; Guozhi Zhu; Yin Liu; John Hallam; Lin Chen; Juan Herrero; Stephen Shaw
Journal:  Proc Natl Acad Sci U S A       Date:  2004-09-08       Impact factor: 11.205

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