Evolution: a guide to perturb protein function and networks

被引：22

作者：

Lichtarge, Olivier ^{[1
]}

Wilkins, Angela ^{[1
]}

机构：

[1] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA

来源：

CURRENT OPINION IN STRUCTURAL BIOLOGY | 2010年 / 20卷 / 03期

基金：

美国国家科学基金会;

关键词：

ENZYME FUNCTION; BINDING-SITES; COMPUTATIONAL REDESIGN; FUNCTION PREDICTION; TRACE; IDENTIFICATION; SPECIFICITY; DESIGN; RECEPTOR; RESIDUES;

D O I：

10.1016/j.sbi.2010.04.002

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Protein interactions give rise to networks that control cell fate in health and disease; selective means to probe these interactions are therefore of wide interest. We discuss here Evolutionary Tracing (ET), a comparative method to identify protein functional sites and to guide experiments that selectively block, recode, or mimic their amino acid determinants. These studies suggest, in principle, a scalable approach to perturb individual links in protein networks.

引用

页码：351 / 359

页数：9

共 94 条

[1] A minimal sequence code for switching protein structure and function [J].

Alexander, Patrick A. ;

He, Yanan ;

Chen, Yihong ;

Orban, John ;

Bryan, Philip N. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (50) :21149-21154

[2] EFICAz2: enzyme function inference by a combined approach enhanced by machine learning [J].

Arakaki, Adrian K. ;

Huang, Ying ;

Skolnick, Jeffrey .

BMC BIOINFORMATICS, 2009, 10

[3] Role for the Regulator of G-Protein Signaling Homology Domain of G Protein-Coupled Receptor Kinases 5 and 6 in β2-Adrenergic Receptor and Rhodopsin Phosphorylation [J].

Baameur, Faiza ;

Morgan, Daniel H. ;

Yao, Hui ;

Tran, Tuan M. ;

Hammitt, Richard A. ;

Sabui, Subir ;

McMurray, John S. ;

Lichtarge, Olivier ;

Clark, Richard B. .

MOLECULAR PHARMACOLOGY, 2010, 77 (03) :405-415

[4] Design of protein-ligand binding based on the molecular-mechanics energy model [J].

Boas, F. Edward ;

Harbury, Pehr B. .

JOURNAL OF MOLECULAR BIOLOGY, 2008, 380 (02) :415-424

[5] Specificity versus stability in computational protein design [J].

Bolon, DN ;

Grant, RA ;

Baker, TA ;

Sauer, RT .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2005, 102 (36) :12724-12729

[6] Improved prediction of protein-protein binding sites using a support vector machines approach [J].

Bradford, JR ;

Westhead, DR .

BIOINFORMATICS, 2005, 21 (08) :1487-1494

[7] CHARMM: The Biomolecular Simulation Program [J].

Brooks, B. R. ;

Brooks, C. L., III ;

Mackerell, A. D., Jr. ;

Nilsson, L. ;

Petrella, R. J. ;

Roux, B. ;

Won, Y. ;

Archontis, G. ;

Bartels, C. ;

Boresch, S. ;

Caflisch, A. ;

Caves, L. ;

Cui, Q. ;

Dinner, A. R. ;

Feig, M. ;

Fischer, S. ;

Gao, J. ;

Hodoscek, M. ;

Im, W. ;

Kuczera, K. ;

Lazaridis, T. ;

Ma, J. ;

Ovchinnikov, V. ;

Paci, E. ;

Pastor, R. W. ;

Post, C. B. ;

Pu, J. Z. ;

Schaefer, M. ;

Tidor, B. ;

Venable, R. M. ;

Woodcock, H. L. ;

Wu, X. ;

Yang, W. ;

York, D. M. ;

Karplus, M. .

JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (10) :1545-1614

[8] Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure [J].

Capra, John A. ;

Laskowski, Roman A. ;

Thornton, Janet M. ;

Singh, Mona ;

Funkhouser, Thomas A. .

PLOS COMPUTATIONAL BIOLOGY, 2009, 5 (12)

[9] Functional specificity lies within the properties and evolutionary changes of amino acids [J].

Chakrabarti, Saikat ;

Bryant, Stephen H. ;

Panchenko, Anna R. .

JOURNAL OF MOLECULAR BIOLOGY, 2007, 373 (03) :801-810

[10] Distinguishing structural and functional restraints in evolution in order to identify interaction sites [J].

Chelliah, V ;

Chen, L ;

Blundell, TL ;

Lovell, SC .

JOURNAL OF MOLECULAR BIOLOGY, 2004, 342 (05) :1487-1504

← 1 2 3 4 5 6 7 8 9 10 →