Functionally important positions can comprise the majority of a protein's architecture

Proteins: Structure, Function and Bioinformatics

Volumn 79, Issue 5, 2011, Pages 1589-1608

  Tungtur, Sudheer ^a   Parente, Daniel J ^a   Swint Kruse, Liskin ^a  

^a UNIVERSITY OF KANSAS SCHOOL OF MEDICINE   (United States)

Author keywords

Bioinformatics; LacI GalR; Protein evolution; Sequence analysis; Specificity determinants; Transcription repressor

Indexed keywords

TISSUE FACTOR PATHWAY INHIBITOR;

'MINER'; ALGORITHM; ARTICLE; COEVOLUTION; CONSURF; ESCHERICHIA COLI; EVOLUTIONARY TRACE ANALYSIS; EXPERIMENTAL STUDY; GENOME ANALYSIS; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SDPPRED; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TEA O;

AMINO ACID SEQUENCE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; LAC REPRESSORS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID;

EID: 79954573471     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22985     Document Type: Article

References (59)

1. Arnaud CH. DNA sequencing forges ahead. Chem Eng News 2009; 87: 16-19.
2. Fischer JD, Mayer CE, Soding J. Prediction of protein functional residues from sequence by probability density estimation. Bioinformatics 2008; 24: 613-620.
3. Dukka Bahadur KC, Livesay DR. Improving position-specific predictions of protein functional sites using phylogenetic motifs. Bioinformatics 2008; 24: 2308-2316.
4. Pei J, Cai W, Kinch LN, Grishin NV. Prediction of functional specificity determinants from protein sequences using log-likelihood ratios. Bioinformatics 2006; 22: 164-171.
5. Pazos F, Rausell A, Valencia A. Phylogeny-independent detection of functional residues. Bioinformatics 2006; 22: 1440-1448.
6. Kalinina OV, Novichkov PS, Mironov AA, Gelfand MS, Rakhmaninova AB. SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res 2004; 32: 424-428.
7. Manning J, Jefferson E, Barton G. The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. BMC Bioinformatics 2008; 9: 51.
8. Lee B, Park K, Kim D. Analysis of the residue-residue coevolution network and the functionally important residues in proteins. Proteins: Struct Funct Bioinformatics 2008; 72: 863-872.
9. Bromberg Y, Yachdav G, Rost B. SNAP predicts effect of mutations on protein function. Bioinformatics 2008; 24: 2397-2398.
10. Kuipers RKP, Joosten H-J, Verwiel E, Paans S, Akerboom J, van der Oost J, Leferink NGH, van Berkel WJH, Vriend G, Schaap PJ. Correlated mutation analyses on super-family alignments reveal functionally important residues. Proteins: Struct Funct Bioinformatics 2009; 76: 608-616.
11. Donald JE, Shakhnovich EI. Predicting specificity-determining residues in two large eukaryotic transcription factor families. Nucl Acids Res 2005; 33: 4455-4465.
12. Ye K, Feenstra AK, Heringa J, Ijzerman AP, Marchiori E. Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting. Bioinformatics 2008; 24: 18-25.
13. Sankararaman S, Sjolander K. INTREPID-Information-theoretic TREe traversal for protein functional site IDentification. Bioinformatics 2008; 24: 2445-2452.
14. Ye K, Vriend G, Ijzerman AP. Tracing evolutionary pressure. Bioinformatics 2008; 24: 908-915.
15. Yip KY, Patel P, Kim PM, Engelman DM, McDermott D, Gerstein M. An integrated system for studying residue coevolution in proteins. Bioinformatics 2008; 24: 290-292.
16. Kalinina OV, Mironov AA, Gelfand MS, Rakhmaninova AB. Automated selection of positions determining functional specificity of proteins by comparative analysis of orthologous groups in protein families. Protein Sci 2004; 13: 443-456.
17. Chakrabarti S, Panchenko AR. Coevolution in defining the functional specificity. Proteins: Struct Funct Bioinformatics 2009; 75: 231-240.
18. Chiu HC, Chang CA, Hu YJ. Prediction of orthologous relationship by functionally important sites. Comput Methods Prog Biomed 2005; 78: 209-222.
19. Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 2005; 33: W299-W302.
20. Ashkenazy H, Erez E, Martz E, Pupko T, Ben-Tal N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res 2010; 38 Suppl: W529-W533.
21. Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996; 257: 342.
22. Morgan DH, Kristensen DM, Mittelman D, Lichtarge O. ET viewer: an application for predicting and visualizing functional sites in protein structures. Bioinformatics 2006; 22: 2049-2050.
23. La D, Sutch B, Livesay DR. Predicting protein functional sites with phylogenetic motifs. Proteins: Struct Funct Bioinformatics 2005; 58: 309-320.
24. Kalinina O, Gelfand M, Russell R. Combining specificity determining and conserved residues improves functional site prediction. BMC Bioinformatics 2009; 10: 174.
25. Rodriguez GJ, Yao R, Lichtarge O, Wensel TG. Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors. Proc Natl Acad Sci 2010; 107: 7787-7792.
26. Zhan H, Swint-Kruse L, Matthews KS. Extrinsic interactions dominate helical propensity in coupled binding and folding of the lactose repressor protein hinge helix. Biochemistry 2006; 45: 5896-5906.
27. Suckow J, Markiewicz P, Kleina LG, Miller J, Kisters-Woike B, Müller-Hill B. Genetic studies of the Lac repressor. XV: 4000 single amino acid substitutions and analysis of the resulting phenotypes on the basis of the protein structure J Mol Biol 1996; 261: 509-523.
28. Meinhardt S, Swint-Kruse L. Experimental identification of specificity determinants in the domain linker of a LacI/GalR protein: bioinformatics-based predictions generate true positives and false negatives. Proteins: Struct Funct Bioinformatics 2008; 73: 941-957.
29. Tungtur S, Egan SM, Swint-Kruse L. Functional consequences of exchanging domains between LacI and PurR are mediated by the intervening linker sequence. Proteins: Struct Funct Bioinformatics 2007; 68: 375-388.
30. Tungtur S, Meinhardt S, Swint-Kruse L. Comparing the functional roles of nonconserved sequence positions in homologous transcription repressors: implications for sequence/function analyses. J Mol Biol 2010; 395: 785-802.
31. Mirny LA, Gelfand MS. Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol 2002; 321: 7-20.
32. Francke C, Kerkhoven R, Wels M, Siezen RJ. A generic approach to identify transcription factor-specific operator motifs; Inferences for LacI-family mediated regulation in Lactobacillus plantarum WCFS1. BMC Genomics 2008; 9: 145.
33. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997; 25: 3389-3402.
34. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947-2948.
35. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41: 95-98.
36. Edgar RC. MUSCLE. Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32: 1792-1797.
37. Shindyalov IN, Bourne PE. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng 1998; 11: 739-747.
38. Hars U, Horlacher R, Boos W, Welte W, Diederichs K. Crystal structure of the effector-binding domain of the trehalose-repressor of Escherichia coli, a member of the LacI family, in its complexes with inducer trehalose-6-phosphate and noninducer trehalose. Protein Sci 1998; 7: 2511-2521.
39. Bell CE, Lewis M. A closer view of the conformation of the Lac repressor bound to operator. Nat Struct Biol 2000; 7: 209-214.
40. Schumacher MA, Glasfeld A, Zalkin H, Brennan RG. The X-ray structure of the PurR-guanine-purF operator complex reveals the contributions of complementary electrostatic surfaces and a water-mediated hydrogen bond to corepressor specificity and binding affinity. J Biol Chem 1997; 272: 22648-22653.
41. Schumacher MA, Allen GS, Diel M, Seidel G, Hillen W, Brennan RG. Structural basis for allosteric control of the transcription regulator CcpA by the phosphoprotein HPr-Ser46-P. Cell 2004; 118: 731-741.
42. La D, Livesay DR. Predicting functional sites with an automated algorithm suitable for heterogeneous datasets. BMC Bioinformatics 2005; 6: 116.
43. La D, Livesay DR. MINER: software for phylogenetic motif identification. Nucleic Acids Res 2005; 33: W267-W270.
44. Fodor AA, Aldrich RW. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. Proteins: Struct Funct Bioinformatics 2004; 56: 211-221.
45. Olmea O, Rost B, Valencia A. Effective use of sequence correlation and conservation in fold recognition. J Mol Biol 1999; 293: 1221-1239.
46. Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins: Struct Funct Bioinformatics 1994; 18: 309-317.
47. Huson DH, Richter DC, Rausch C, Dezulian T, Franz M, Rupp R. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics 2007; 8: 460.
48. Junier T, Zdobnov EM. The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell. Bioinformatics 2010; 26: 1669-1670.
49. Swint-Kruse L, Larson C, Pettitt BM, Matthews KS. Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR. Protein Sci 2002; 11: 778-794.
50. Arvidson DN, Lu F, Faber C, Zalkin H, Brennan RG. The structure of PurR mutant L54M shows an alternative route to DNA kinking. Nat Struct Biol 1998; 5: 436-441.
51. Tretyachenko-Ladokhina V, Cocco MJ, Senear DF. Flexibility and adaptability in binding of E. coli cytidine repressor to different operators suggests a role in differential gene regulation. J Mol Biol 2006; 362: 271-286.
52. Mihalek I, Res I, Lichtarge O. Evolutionary trace Report-Maker: a new type of service for comparative analysis of proteins. Bioinformatics 2006; 22: 1656-1657.
53. Suel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003; 10: 59-69.
54. Zhan H, Taraban M, Trewhella J, Swint-Kruse L. Subdividing repressor function: DNA binding affinity, selectivity, and allostery can be altered by amino acid substitution of nonconserved residues in a LacI/GalR homologue. Biochemistry 2008; 47: 8058-8069.
55. Ishida Y, Kori A, Ishihama A. Participation of regulator AscG of the beta-glucoside utilization operon in regulation of the propionate catabolism operon. J Bacteriol 2009; 191: 6136-6144.
56. Hall BG, Xu L. Nucleotide sequence, function, activation, and evolution of the cryptic asc operon of Escherichia coli K12. Mol Biol Evol 1992; 9: 688-706.
57. Yin Y, Kirsch JF. Identification of functional paralog shift mutations: conversion of Escherichia coli malate dehydrogenase to a lactate dehydrogenase. Proc Natl Acad Sci 2007; 104: 17353-17357.
58. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 2004; 25: 1605-1612.
59. Crooks GE, Hon G, Chandonia J-M, Brenner SE. WebLogo: a sequence logo generator. Genome Res 2004; 14: 1188-1190.