Protein Sectors: Statistical Coupling Analysis versus Conservation

PLoS Computational Biology

Volumn 11, Issue 2, 2015, Pages

  Teşileanu, Tiberiu ^a,b   Colwell, Lucy J ^a,c   Leibler, Stanislas ^a,d  

^a INSTITUTE FOR ADVANCED STUDY   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SPECTRUM ANALYSIS;

BIOCHEMICAL PROPERTIES; COUPLING ANALYSIS; DOMINATING FACTORS; FUNCTIONAL PREDICTIONS; MATRIX; MULTIPLE SEQUENCE ALIGNMENTS; PROTEIN ALIGNMENT; SEQUENCE CONSERVATION;

PROTEINS;

EXPERIMENTAL MODEL; PREDICTION; SEQUENCE ALIGNMENT; SPECTROSCOPY; STATISTICAL MODEL; ALGORITHM; AMINO ACID SEQUENCE; BIOLOGY; CHEMISTRY; CONSERVED SEQUENCE; PDZ DOMAIN; PHYSIOLOGY; PROCEDURES; PROTEIN DOMAIN; SEQUENCE ANALYSIS;

DIHYDROFOLATE REDUCTASE; PROTEIN;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTATIONAL BIOLOGY; CONSERVED SEQUENCE; PDZ DOMAINS; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; TETRAHYDROFOLATE DEHYDROGENASE;

EID: 84944474861     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004091     Document Type: Article

References (35)

1. Do CB, Katoh K, (2008) Protein multiple sequence alignment. Methods in Molecular Biology 484: 379–413. 18592193
2. Notredame C, (2002) Recent progress in multiple sequence alignment: a survey. Pharmacogenomics 3: 131–144. doi: 10.1517/14622416.3.1.131 11966409
3. Schneider TD, Stormo GD, Gold L, Ehrenfeucht A, (1986) Information content of binding sites on nucleotide sequences. Journal of Molecular Biology 188: 415–431. doi: 10.1016/0022-2836(86)90165-8 3525846
4. Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJE, (1987) Prediction of protein secondary structure and active sites using the alignment of homologous sequences. Journal of Molecular Biology 195: 957–961. doi: 10.1016/0022-2836(87)90501-8 3656439
5. Hollstein M, Sidransky D, Vogelstein B, Harris CC, (1991) p53 Mutations in Human Cancers. Science 253: 49–53. doi: 10.1126/science.1905840 1905840
6. Cargill M, Altshuler D, Ireland J, Sklar P, Ardlie K, et al. (1999) Characterization of singlenucleotide polymorphisms in coding regions of human genes. Nature Genetics 22: 231–238. doi: 10.1038/10290 10391209
7. Ng PC, Henikoff S, (2003) SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Research 31: 3812–3814. doi: 10.1093/nar/gkg509 12824425
8. Russ WP, Lowery DM, Mishra P, Yaffe MB, Ranganathan R, (2005) Natural-like function in artificial WW domains. Nature 437: 579–583. doi: 10.1038/nature03990 16177795
9. Socolich M, Lockless SW, Russ WP, Lee H, Gardner KH, et al. (2005) Evolutionary information for specifying a protein fold. Nature 437: 512–518. doi: 10.1038/nature03991 16177782
10. Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, et al. (2011) Protein 3D Structure Computed from Evolutionary Sequence Variation. PLoS ONE 6: e28766. doi: 10.1371/journal.pone.0028766 22163331
11. Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, et al. (2011) Direct-coupling analysis of residue co-evolution captures native contacts across many protein families. PNAS 108: E1293–E1301. doi: 10.1073/pnas.1111471108 22106262
12. Weigt M, White RA, Szurmant H, Hoch JA, Hwa T, (2009) Identification of direct residue contacts in protein-protein interaction by message passing. PNAS 106: 67–72. doi: 10.1073/pnas.0805923106 19116270
13. Lockless SW, Ranganathan R, (1999) Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families. Science 286: 295–299. doi: 10.1126/science.286.5438.295 10514373
14. Fuentes EJ, Der CJ, Lee AL, (2004) Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. Journal of Molecular Biology 335: 1105–1115. doi: 10.1016/j.jmb.2003.11.010 14698303
15. Peterson FC, Penkert RR, Volkman BF, Prehoda KE, (2004) Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition. Molecular Cell 13: 665–676. doi: 10.1016/S1097-2765(04)00086-3 15023337
16. Süel GM, Lockless SW, Wall MA, Ranganathan R, (2003) Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nature 10: 59–69.
17. Hatley ME, Lockless SW, Gibson SK, Gilman AG, Ranganathan R, (2003) Allosteric determinants in guanine nucleotide-binding proteins. PNAS 100: 14445–14450. doi: 10.1073/pnas.1835919100 14623969
18. Halabi N, Rivoire O, Leibler S, Ranganathan R, (2009) Protein sectors: evolutionary units of three-dimensional structure. Cell 138: 774–786. doi: 10.1016/j.cell.2009.07.038 19703402
19. Ranganathan R, Rivoire O (2012). Note 109: A summary of SCA calculations. Available online at http://systems.swmed.edu/rr_lab/Note109_files/Note109_v3.pdf
20. Smock RG, Rivoire O, Russ WP, Swain JF, Leibler S, et al. (2010) An interdomain sector mediating allostery in Hsp70 molecular chaperones. Molecular Systems Biology 6: 414. doi: 10.1038/msb.2010.65 20865007
21. Bouchaud JP, Potters M (2009) Financial Applications of Random Matrix Theory: a short review. arXiv 0910.1205.
22. Rivoire O, (2013) Elements of Coevolution in Biological Sequences. Physical Review Letters 110: 178102. doi: 10.1103/PhysRevLett.110.178102 23679784
23. Colwell LJ, Brenner MP, Murray AW, (2014) Conservation weighting functions enable covariance analyses to detect functionally important amino acids. PLoS ONE 9: e107723. doi: 10.1371/journal.pone.0107723 25379728
24. Reynolds KA, McLaughlin RN, JrRanganathan R, (2011) Hot spots for allosteric regulation on protein surfaces. Cell 147: 1564–75. doi: 10.1016/j.cell.2011.10.049 22196731
25. McLaughlin RN, JrPoelwijk FJ, Raman A, Gosal WS, Ranganathan R, (2012) The spatial architecture of protein function and adaptation. Nature 491: 138–142. doi: 10.1038/nature11500 23041932
26. Kern D, Zuiderweg ERP, (2003) The role of dynamics in allosteric regulation. Current Opinion in Structural Biology 13: 748–757. doi: 10.1016/j.sbi.2003.10.008 14675554
27. Matoba Y, Sugiyama M, (2003) Atomic resolution structure of prokaryotic phospholipase A2: analysis of internal motion and implication for a catalytic mechanism. Proteins 51: 453–69. doi: 10.1002/prot.10360 12696056
28. Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, et al. (2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature 462: 669–673. doi: 10.1038/nature08615 19956261
29. Dhulesia A, Gsponer J, Vendruscolo M, (2008) Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein. Journal of the American Chemical Society 130: 8931–8939. doi: 10.1021/ja0752080 18558679
30. Remmert M, Biegert A, Hauser A, Söding J, (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods 9: 173–175. doi: 10.1038/nmeth.1818
31. Lee SY, Banerjee A, MacKinnon R, (2009) Two separate interfaces between the voltage sensor and pore are required for the function of voltage-dependent K(+) channels. PLoS Biology 7: 676–686. doi: 10.1371/journal.pbio.1000047
32. Mann HB, Whitney DR, (1947) On a test of whether one of two random variables is stochastically larger than the other. Annals of Mathematical Statistics 18: 50–60. doi: 10.1214/aoms/1177730491
33. Li-Smerin Y, Hackos DH, Swartz KJ, (2000) Alpha-helical structural elements within the voltagesensing domains of a K(+) channel. The Journal of General Physiology 115: 33–49. doi: 10.1085/jgp.115.1.33 10613917
34. Markiewicz P, Kleina LG, Cruz C, Ehret S, Miller JH, (1994) Genetic Studies of the lac Repressor—XIV. Analysis of 4000 Altered Escherichia coli lac Repressors Reveals Essential and Non-essential Residues, as well as “Spacers” which do not Require a Specific Sequence. Journal of Molecular Biology 240: 421–433. doi: 10.1006/jmbi.1994.1458 8046748
35. Mirny LA, Shakhnovich EI, (1999) Universally Conserved Positions in Protein Folds: Reading Evolutionary Signals about Stability, Folding Kinetics and Function. Journal of Molecular Biology 291: 177–196. doi: 10.1006/jmbi.1999.2911 10438614