Insights into protein sequence and structure-derived features mediating 3D domain swapping mechanism using support vector machine based approach

Bioinformatics and Biology Insights

Volumn 4, Issue , 2010, Pages 33-42

  Shameer, Khader ^a   Pugalenthi, Ganesan ^b   Kandaswamy, Krishna Kumar ^c   Suganthan, Ponnuthurai N ^b   Archunan, Govindaraju ^d   Sowdhamini, Ramanathan ^a  

^a TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^c UNIVERSITY OF LÜBECK   (Germany)

^d BHARATHIDASAN UNIVERSITY   (India)

Author keywords

3D domain swapping; Domain swap; Feature selection; Machine learning; SVM

Indexed keywords

OLIGOMER; PROTEIN; PROTEIN SUBUNIT; AMINO ACID; BINDING PROTEIN;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; PREDICTION; PROTEIN AGGREGATION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; SUPPORT VECTOR MACHINE; ANTIGEN BINDING; DEGENERATIVE DISEASE; PRION; PROTEIN BINDING; PROTEIN MISFOLDING; THREE DIMENSIONAL IMAGING;

EID: 77955242486     PISSN: None     EISSN: 11779322     Source Type: Journal    
DOI: 10.4137/bbi.s4464     Document Type: Article

References (65)

1. Almassy RJ, Janson CA, Hamlin R, Xuong NH, Eisenberg D. Novel subunitsubunit interactions in the structure of glutamine synthetase. Nature. 1986;323:304-9.
2. Anfinsen CB. The formation and stabilization of protein structure. Biochem J. 1972;128: 737-49.
3. Bennett MJ, Choe S, Eisenberg D. Domain swapping: entangling alliances between proteins. Proc Natl Acad Sci U S A. 1994;91:3127-31.
4. Parge HE, Arvai AS, Murtari DJ, Reed SI. Tainer JA. Human CksHs2 atomic structure: a role for its hexameric assembly in cell cycle control. Science. 1993;262:387-95.
5. Bennett MJ, Schlunegger MP, Eisenberg D. IIID domain swapping: a mechanism for oligomer assembly. Protein Sci. 1995;4:2455-68.
6. Liu Y, Eisenberg D. 3D domain swapping: as domains continue to swap. Protein Sci. 2002;11:1285-99.
7. Bennett MJ, Sawaya MR, Eisenberg D. Deposition diseases and 3D domain swapping. Structure. 2006;14:811-24.
8. Khare SD, Dokholyan NV. Molecular mechanisms of polypeptide aggregation in human diseases. Curr Protein Pept Sci. 2007;8:573-9.
9. Bennett MJ, Eisenberg D. The evolving role of 3D domain swapping in proteins. Structure. 2004;12:1339-41.
10. Gronenborn AM. Protein acrobatics in pairs-dimerization via domain swapping. Curr Opin Struct Biol. 2009;19:39-49
11. Jaskolski M. 3D domain swapping, protein oligomerization, and amyloid formation. Acta Biochim Pol. 2001;48:807-27.
12. Nagradova NK. Three-dimensional domain swapping in homooligomeric proteins and its functional significance. Biochemistry (Mosc). 2002;67: 839-49.
13. Newcomer ME. Protein folding and three-dimensional domain swapping: a strained relationship? Curr Opin Struct Biol. 2002;12:48-53.
14. Guo Z, Eisenberg D. Runaway domain swapping in amyloid-like fibrils of T7 endonuclease I. Proc Natl Acad Sci U S A. 2006;103:8042-7.
15. Pelosi P. Odorant-binding proteins. Crit Rev Biochem Mol Biol. 1994;29: 199-228.
16. Ramoni R, et al. Control of domain swapping in bovine odorant-binding protein. Biochem J. 2002;365:739-48.
17. Liu Y, Hart PJ, Schlunegger MP, Eisenberg D. The crystal structure of a 3D domain-swapped dimer of RNase A at a 2.1-A resolution. Proc Natl Acad Sci U S A. 1998;95:3437-42.
18. Zegers I, Deswarte J, Wyns L. Trimeric domain-swapped barnase. Proc Natl Acad Sci U S A. 1999;96:818-22.
19. Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25-9.
20. Berman H, Henrick K, Nakamura H, Markley JL. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 2007;35:D301-3.
21. DeLano WL. The PyMOL Molecular Graphics System. 2002.
22. Bernstein HJ. Recent changes to RasMol, recombining the variants. Trends Biochem Sci. 2000;25:453-5.
23. Pugalenthi G, Archunan G, Sowdhamini R. DIAL: a web-based server for the automatic identification of structural domains in proteins. Nucleic Acids Res. 2005;33:W130-2.
24. Laskowski RA. Enhancing the functional annotation of PDB structures in PDBsum using key figures extracted from the literature. Bioinformatics. 2007;23;1824-7.
25. Henrick K, Thornton JM. PQS: a protein quaternary structure file server. Trends Biochem Sci. 1998;23:358-61.
26. Andreeva A, et al. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2008;36:D419-25.
27. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:1658-9.
28. Pugalenthi G, Tang K, Suganthan PN, Archunan G, Sowdhamini R. A machine learning approach for the identification of odorant binding proteins from sequence-derived properties. BMC Bioinformatics. 2007; 8:351.
29. Pugalenthi G, Kumar KK, Suganthan PN, Gangal R. Identification of catalytic residues from protein structure using support vector machine with sequence and structural features. Biochem Biophys Res Commun. 2008;367;630-4.
30. Mizuguchi K, Deane CM, Blundell TL, Johnson MS, Overington JP. JOY: protein sequence-structure representation and analysis. Bioinformatics. 1998;14:617-23.
31. Kawashima S, et al. AAindex: amino acid index database, progress report 2008. Nucleic Acids Res. 2008;36:D202-5.
32. Bulka B, desJardins M, Freeland SJ. An interactive visualization tool to explore the biophysical properties of amino acids and their contribution to substitution matrices. BMC Bioinformatics. 2006;7:329.
33. Vapnik V. The Nature of Statistical Learning Theory, (Springer, NY, 1995). 34. Muller KR. An introduction to kernel-based learning algorithms. IEEE Transactions in Neural Network. 2001;2:181-201.
34. Chou KC, Cai YD. Using functional domain composition and support vector machines for prediction of protein subcellular location. J Biol Chem. 2002;277:45765-9.
35. Ding YS, Zhang TL, Chou KC. Prediction of protein structure classes with pseudo amino acid composition and fuzzy support vector machine network. Protein Pept Lett. 2007;14:811-5.
36. Du QS, Wei YT, Pang ZW, Chou KC, Huang RB. Predicting the affinity of epitope-peptides with class I MHC molecule HLA-A*0201: an application of amino acid-based peptide prediction. Protein Eng Des Sel. 2007;20: 417-23
37. Frank E, Hall M, Trigg L, Holmes G, Witten IH. Data mining in bioinformatics using Weka. Bioinformatics. 2004;20:2479-81.
38. Ahuja U, Rozhkova A, Glockshuber R, Thony-Meyer L, Einsle O. Helix swapping leads to dimerization of the N-terminal domain of the c-type cytochrome maturation protein CcmH from Escherichia coli. FEBS Lett. 2008;582:2779-86.
39. Alcantara EH, Kim DH, Do SI, Lee SS. Bi-functional activities of chimeric lysozymes constructed by domain swapping between bacteriophage T7 and K11 lysozymes. J Biochem Mol Biol. 2007;40:539-46.
40. Andjelkovic M, Maira SM, Cron P, Parker PJ, Hemmings BA. Domain swapping used to investigate the mechanism of protein kinase B regulation by 3-phosphoinositide-dependent protein kinase 1 and Ser473 kinase. Mol Cell Biol. 1999;19:5061-72.
41. Aravind P, Suman SK, Mishra A, Sharma Y, Sankaranarayanan R. Threedimensional domain swapping in nitrollin, a single-domain betagammacrystallin from Nitrosospira multiformis, controls protein conformation and stability but not dimerization. J Mol Biol. 2009;385:163-77.
42. Back K, Chappell J. Identifying functional domains within terpene cyclases using a domain-swapping strategy. Proc Natl Acad Sci U S A. 1996;93: 6841-5.
43. Back K, et al. Cloning of a sesquiterpene cyclase and its functional expression by domain swapping strategy. Mol Cells. 2000;10:220-5.
44. Bakker RA, et al. Domain swapping in the human histamine H1 receptor. J Pharmacol Exp Ther. 2004;311:131-8.
45. Balciunas D, Ronne H. Evidence of domain swapping within the jumonji family of transcription factors. Trends Biochem Sci. 2000;25:274-6.
46. Chan YH, Cheng CH, Chan KM. Study of goldfish (Carassius auratus) growth hormone structure-function relationship by domain swapping. Comp Biochem Physiol B Biochem Mol Biol. 2007;146:384-94.
47. Chintakayala K, et al. Domain swapping reveals that the C- and N-terminal domains of DnaG and DnaB, respectively, are functional homologues. Mol Microbiol. 2007;63:1629-39.
48. Cho SS, Levy Y, Onuchic JN, Wolynes PG. Overcoming residual frustration in domain-swapping: the roles of disulfide bonds in dimerization and aggregation. Phys Biol. 2005;2:S44-S55.
49. Alonso DO, Alm E, Daggett V. Characterization of the unfolding pathway of the cell-cycle protein p13 suc1 by molecular dynamics simulations: implications for domain swapping. Structure. 2000;8:101-10.
50. Esposito L, Daggett V. Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations. Biochemistry. 2005;44: 3358-68.
51. Lin YM, et al. Molecular dynamics simulations to investigate the domain swapping mechanism of human cystatin C. Biotechnol Prog. 2007;23: 577-84.
52. Liu HL, et al. Molecular dynamics simulations of human cystatin C and its L68Q varient to investigate the domain swapping mechanism. J Biomol Struct Dyn. 2007;25:135-44.
53. Chahine J, Cheung MS. Computational studies of the reversible domain swapping of p13 suc1. Biophys J. 2005;89:2693-700.
54. Cozza G, Moro S, Gotte G. Elucidation of the ribonuclease A aggregation process mediated by 3D domain swapping: a computational approach reveals possible new multimeric structures. Biopolymers. 2008;89:26-39.
55. Gouldson PR, et al. Dimerization and domain swapping in G-proteincoupled receptors: a computational study. Neuropsychopharmacology. 2000;23:S60-S77.
56. Murray AJ, Head JG, Barker JJ, Brady RL. Engineering an intertwined form of CD2 for stability and assembly. Nat Struct Biol. 1998;5:778-82.
57. Liu S, et al Crystal structures of 2-methylisocitrate lyase in complex with product and with isocitrate inhibitor provide insight into lyase substrate specificity, catalysis and evolution. Biochemistry. 2005;44: 2949-62.
58. Ireton GC, McDermott G, Black ME, Stoddard BL. The structure of Escherichia coli cytosine deaminase. J Mol Biol. 2002;315:687-97.
59. Vitagliano L, et al. Binding of a substrate analog to a domain swapping protein: X-ray structure of the complex of bovine seminal ribonuclease with uridylyl(2',5')adenosine. Protein Sci. 1998;7:1691-9.
60. Argiriadi MA, et al. Binding of alkylurea inhibitors to epoxide hydrolase implicates active site tyrosines in substrate activation. J Biol Chem. 2000;275:15265-70.
61. Peneff C, Mengin-Lecreulx D, Bourne Y. The crystal structures of Apo and complexed Saccharomyces cerevisiae GNA1 shed light on the catalytic mechanism of an amino-sugar N-acetyltransferase. J Biol Chem. 2001; 276:16328-34.
62. Botos I, et al. Structures of the complexes of a potent anti-HIV protein cyanovirin-N and high mannose oligosaccharides. J Biol Chem. 2002;277:34336-42.
63. Cameron AD, Olin B, Ridderstrom M, Mannervik B, Jones TA. Crystal structure of human glyoxalase I-evidence for gene duplication and 3D domain swapping. EMBO J. 1997;16:3386-95.
64. Bennett MJ, Choe S, Eisenberg D. Refined structure of dimeric diphtheria toxin at 2.0 A resolution. Protein Sci. 1994;3:1444-63.
65. Roosild TP, Miller S, Booth IR, Choe S. A mechanism of regulating transmembrane potassium flux through a ligand-mediated conformational switch. Cell. 2002;109:781-91.