A practical guide for the computational selection of residues to be experimentally characterized in protein families

Briefings in Bioinformatics

Volumn 13, Issue 3, 2012, Pages 329-336

  Benítez Páez, Alfonso ^a   Cárdenas Brito, Sonia ^a   Gutiérrez, Andrés J ^a  

^a Bioinformatic Analysis Group   (Colombia)

Author keywords

Evolutionary information; Functional divergence; Multiple sequence alignment; Mutagenesis; Protein families; Residue selection

Indexed keywords

AMINO ACID; PROTEIN;

ARTICLE; BIOLOGY; CHEMISTRY; GENETICS; METHODOLOGY; PHYLOGENY; PROTEIN DATABASE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS;

AMINO ACIDS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PHYLOGENY; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 84858667785     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbr052     Document Type: Article

References (52)

1. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-80.
2. Katoh K, Misawa K, Kuma K, et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002;30: 3059-66.
3. Do CB, Mahabhashyam MS, Brudno M, et al. ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res 2005;15:330-40.
4. Notredame C, Higgins DG, Heringa J. T-Coffee: a novel method for fast and accurate multiple sequence alignment. JMol Biol 2000;302:205-17.
5. Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 2004;5:113.
6. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. NucleicAcidsRes 2004; 32:1792-7.
7. Edgar RC, Batzoglou S. Multiple sequence alignment. Curr Opin Struct Biol 2006;16:368-73.
8. Apweiler R, Martin MJ, O'Donovan C, etal. The Universal Protein Resource (UniProt). Nucleic Acids Res 2010;38: D142-8.
9. Benson DA, Karsch-Mizrachi I, Lipman DJ, et al. GenBank. Nucleic Acids Res 2010;38:D46-51.
10. Altschul SF, Gish W, Miller W, et al. Basic local alignment search tool. JMol Biol 1990;215:403-10.
11. Altschul SF, Madden TL, Schaffer AA, etal. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997;25:3389-402.
12. Pei J, Grishin NV. PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics 2007;23:802-08.
13. Pei J, Kim BH, Tang M, et al. PROMALS web server for accurate multiple protein sequence alignments. NucleicAcids Res 2007;35:W649-52.
14. Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89: 10915-9.
15. Finn RD, Mistry J, Tate J, et al. The Pfam protein families database. Nucleic Acids Res 2010;38:D211-22.
16. Clamp M, Cuff J, Searle SM, et al. The Jalview Java alignment editor. Bioinformatics 2004;20:426-7.
17. Waterhouse AM, Procter JB, Martin DM, et al. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 2009;25:1189-91.
18. Galtier N, Gouy M, Gautier C. SEAVIEW and PHYLO_WIN: two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 1996;12: 543-8.
19. Gouy M, Guindon S, Gascuel O. SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol 2010; 27:221-4.
20. Eddy SR. Hidden Markov models. Curr Opin Struct Biol 1996;6:361-5.
21. Schuster-Bockler B, Schultz J, Rahmann S. HMM Logos for visualization of protein families. BMC Bioinformatics 2004;5:7.
22. Dai J, Cheng J. HMMEditor: a visual editing tool for profile hidden Markov model. BMCGenomics 2008;9(Suppl 1):S8.
23. Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol 2009;19:145-55.
24. Pazos F, Valencia A. In silico two-hybrid system for the selection of physically interacting protein pairs. Proteins 2002;47:219-27.
25. Gu X. Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol 1999;16:1664-74.
26. Gu X. Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol 2001;18: 453-64.
27. Gu X. A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol 2006;23:1937-45.
28. Gu X, Vander Velden K. DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. Bioinformatics 2002;18:500-1.
29. Benitez-Paez A, Cardenas-Brito S. Dissection of functional residues in receptor activity-modifying proteins through phylogenetic and statistical analyses. Evol Bioinform Online 2008;4:153-69.
30. Zheng Y, Xu D, Gu X. Functional divergence after gene duplication and sequence-structure relationship: a case study of G-protein alpha subunits. JExpZoolBMolDevEvol 2007; 308:85-96.
31. Zhou H, Gu J, Lamont SJ, et al. Evolutionary analysis for functional divergence of the toll-like receptor gene family and altered functional constraints. J Mol Evol 2007;65: 119-123.
32. Abascal F, Zardoya R, Posada D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 2005; 21:2104-5.
33. Casari G, Sander C, Valencia A. A method to predict functional residues in proteins. Nat Struct Biol 1995;2:171-8.
34. Lichtarge O, Bourne HR, Cohen FE. An evolutionary trace method defines binding surfaces common to protein families. JMol Biol 1996;257:342-58.
35. Pazos F, Rausell A, Valencia A. Phylogeny-independent detection of functional residues. Bioinformatics 2006;22: 1440-8.
36. Rausell A, Juan D, Pazos F, et al. Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc Natl Acad Sci USA 2010;107:1995-2000.
37. Wallace IM, Higgins DG. Supervised multivariate analysis of sequence groups to identify specificity determining residues. BMC Bioinformatics 2007;8:135.
38. Carro A, Tress M, de Juan D, et al. TreeDet: a web server to explore sequence space. Nucleic AcidsRes 2006;34:W110-5.
39. Fornek JL, Gillim-Ross L, Santos C, et al. A singleamino-acid substitution in a polymerase protein of an H5N1 influenza virus is associated with systemic infection and impaired T-cell activation in mice. J Virol 2009;83: 11102-15.
40. Knez J, Bilan PT, Capone JP. A single amino acid substitution in herpes simplex virus type 1 VP16 inhibits binding to the virion host shutoff protein and is incompatible with virus growth. JVirol 2003;77:2892-902.
41. Banerjee M, Balaram H, Balaram P. Structural effects of a dimer interface mutation on catalytic activity of triosephosphate isomerase. The role of conserved residues and complementary mutations. FEBSJ 2009;276:4169-83.
42. Mallam AL, Jackson SE. The dimerization of an alpha/ beta-knotted protein is essential for structure and function. Structure 2007;15:111-22.
43. Osawa T, Ito K, Inanaga H, et al. Conserved cysteine residues of GidA are essential for biogenesis of 5-carboxymethylaminomethyluridine at tRNA anticodon. Structure 2009;17:713-24.
44. Parthiban V, Gromiha MM, Schomburg D. CUPSAT: prediction of protein stability upon point mutations. Nucleic Acids Res 2006;34:W239-42.
45. Melo F, Feytmans E. Novel knowledge-based mean force potential at atomic level. JMol Biol 1997;267:207-22.
46. Melo F, Feytmans E. Assessing protein structures with a non-local atomic interaction energy. J Mol Biol 1998;277: 1141-52.
47. Bujnicki JM, Oudjama Y, Roovers M, etal. Identification of a bifunctional enzyme MnmC involved in the biosynthesis of a hypermodified uridine in the wobble position of tRNA. RNA 2004;10:1236-42.
48. Moukadiri I, Garzón MJ, Benitez-Paez A, et al. Biochemical and functional characterization of domains MnmC1 and MnmC2 of the E. coli MnmC bifunctional enzyme. 23rd tRNAWorkshop, Aveiro, Portugal, 2010.
49. Moukadiri I, Prado S, Piera J, etal. Evolutionarily conserved proteins MnmE and GidA catalyze the formation of two methyluridine derivatives at tRNA wobble positions. Nucleic Acids Res 2009;37:7177-93.
50. Pearson D, Carell T. Assay of both activities of the bifunctional tRNA-modifying enzyme MnmC reveals a kinetic basis for selective full modification of cmnm5s2U to mnm5s2U. Nucleic Acids Res 2011;39:4818-26.
51. Roovers M, Oudjama Y, Kaminska KH, et al. Sequence-structure-function analysis of the bifunctional enzyme MnmC that catalyses the last two steps in the biosynthesis of hypermodified nucleoside mnm5s2U in tRNA. Proteins 2008;71:2076-85.
52. Murakami Y, Jones S. SHARP2: protein-protein interaction predictions using patch analysis. Bioinformatics 2006; 22:1794-5.