Analysis on conservation of disulphide bonds and their structural features in homologous protein domain families

BMC Structural Biology

Volumn 8, Issue , 2008, Pages

  Thangudu, Ratna R ^a,d   Manoharan, Malini ^b   Srinivasan, N ^c   Cadet, Frédéric ^a   Sowdhamini, R ^b   Offmann, Bernard ^a  

^a UNIVERSITÉ DE LA RÉUNION   (France)

^b TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

^c INDIAN INSTITUTE OF SCIENCE   (India)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; CYTOPLASM PROTEIN; DISULFIDE; CYSTINE; PROTEIN; SOLVENT;

AMINO ACID SEQUENCE; ARTICLE; DISULFIDE BOND; MOLECULAR INTERACTION; MUTATION; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; CHEMISTRY; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY;

CONSERVED SEQUENCE; CYSTINE; DATABASES, PROTEIN; DISULFIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT; SOLVENTS; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 58649113381     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-8-55     Document Type: Article

References (100)

1. The anatomy and taxonomy of protein structure. JS Richardson, Adv Protein Chem 1981 34 167 339 7020376
2. Disulphide bridges in globular proteins. JM Thornton, J Mol Biol 1981 151 2 261 287 7338898
3. Predicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines. A Ceroni P Frasconi A Passerini A Vullo, The Journal of VLSI Signal Processing-Systems for Signal, Image, and Video Technology 2003 35 3 287 295
4. Prediction of the bonding states of cysteines using the support vector machines based on multiple feature vectors and cysteine state sequences. YC Chen YS Lin CJ Lin JK Hwang, Proteins 2004 55 4 1036 1042 15146500
5. Role of evolutionary information in predicting the disulfide-bonding state of cysteine in proteins. P Fariselli P Riccobelli R Casadio, Proteins 1999 36 3 340 346 10409827
6. Different sequence environments of cysteines and half cystines in proteins. Application to predict disulfide forming residues. A Fiser M Cserzo E Tudos I Simon, FEBS Lett 1992 302 2 117 120 1633841
7. Predicting the oxidation state of cysteines by multiple sequence alignment. A Fiser I Simon, Bioinformatics 2000 16 3 251 256 10869018
8. Predicting redox state of cysteines in proteins. A Fiser I Simon, Methods Enzymol 2002 353 10 21 12078485
9. A Two-Stage SVM Architecture for Predicting the Disulfide Bonding State of Cysteines. P Frasconi A Passerini A Vullo, IEEE NNSP International Workshop: special session on signal processing and neural networks for bionformatics: 2002 2002
10. Prediction of disulfide-bonded cysteines in proteomes with a hidden neural network. PL Martelli P Fariselli R Casadio, Proteomics 2004 4 6 1665 1671 15174135
11. Prediction of the disulfide bonding state of cysteines in proteins with hidden neural networks. PL Martelli P Fariselli L Malaguti R Casadio, Protein Eng 2002 15 12 951 953 12601133
12. Prediction of the disulfide-bonding state of cysteines in proteins at 88% accuracy. PL Martelli P Fariselli L Malaguti R Casadio, Protein Sci 2002 11 11 2735 2739 12381855
13. Predicting the disulfide bonding state of cysteines using protein descriptors. MH Mucchielli-Giorgi S Hazout P Tuffery, Proteins 2002 46 3 243 249 11835499
14. Prediction of the disulfide-bonding state of cysteine in proteins. SM Muskal SR Holbrook SH Kim, Protein Eng 1990 3 8 667 672 2217140
15. Learning to discriminate between ligand-bound and disulfide-bound cysteines. A Passerini P Frasconi, Protein Eng Des Sel 2004 17 4 367 373 15166311
16. Prediction of the disulfide-bonding state of cysteines in proteins based on dipeptide composition. JN Song ML Wang WJ Li WB Xu, Biochem Biophys Res Commun 2004 318 1 142 147 15110765
17. 13C NMR chemical shifts can predict disulfide bond formation. D Sharma K Rajarathnam, J Biomol NMR 2000 18 2 165 171 11101221
18. Prediction of disulfide connectivity in proteins. P Fariselli R Casadio, Bioinformatics 2001 17 10 957 964 11673241
19. Disulfide connectivity prediction using secondary structure information and diresidue frequencies. F Ferre P Clote, Bioinformatics 2005 21 10 2336 2346 15741247
20. DiANNA: a web server for disulfide connectivity prediction. F Ferre P Clote, Nucleic Acids Res 2005 33 Web Server W230 232 15980459
21. Improving disulfide connectivity prediction with sequential distance between oxidized cysteines. CH Tsai BJ Chen CH Chan HL Liu CY Kao, Bioinformatics 2005 21 24 4416 4419 16223789
22. A Recursive Connectionist Approach for Predicting Disulfide Connectivity in Proteins. A Vullo P Frasconi, Proceedings of the 18th ACM Symposium on Applied Computing: 2003 2003 66 71
23. Disulfide connectivity prediction using recursive neural networks and evolutionary information. A Vullo P Frasconi, Bioinformatics 2004 20 5 653 659 15033872
24. Cysteine separations profiles on protein sequences infer disulfide connectivity. E Zhao HL Liu CH Tsai HK Tsai CH Chan CY Kao, Bioinformatics 2005 21 8 1415 1420 15585533
25. Model building of disulfide bonds in proteins with known three-dimensional structure. B Hazes BW Dijkstra, Protein Eng 1988 2 2 119 125 3244694
26. Stereochemical modeling of disulfide bridges. Criteria for introduction into proteins by site-directed mutagenesis. R Sowdhamini N Srinivasan B Shoichet D Santi C Ramakrishnan P Balaram, Protein Eng 1989 3 2 95 103 2594728
27. Molecular recognition in protein families: a database of aligned three-dimensional structures of related proteins. JP Overington ZY Zhu A Sali MS Johnson R Sowdhamini GV Louie TL Blundell, Biochemical Society transactions 1993 21 Pt 3(3) 597 604 8224474
28. Relationship between protein structures and disulfide-bonding patterns. CC Chuang CY Chen JM Yang PC Lyu JK Hwang, Proteins 2003 53 1 1 5 12945044
29. Protein similarities beyond disulphide bridge topology. JM Mas P Aloy MA Marti-Renom B Oliva C Blanco-Aparicio MA Molina R de Llorens E Querol FX Aviles, Journal of Molecular Biology 1998 284 3 541 548 9826496
30. What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioninformatics analysis. VI Abkevich EI Shakhnovich, J Mol Biol 2000 300 4 975 985 10891282
31. The nonconsecutive disulfide bond of Escherichia coli phytase (AppA) renders it dependent on the protein-disulfide isomerase, DsbC. M Berkmen D Boyd J Beckwith, J Biol Chem 2005 280 12 11387 11394 15642731
32. Disulfide bonds and the stability of globular proteins. SF Betz, Protein Sci 1993 2 10 1551 1558 8251931
33. The effects of disulfide bonds on the denatured state of barnase. J Clarke AM Hounslow CJ Bond AR Fersht V Daggett, Protein Sci 2000 9 12 2394 2404 11206061
34. Control of enzyme activity by an engineered disulfide bond. M Matsumura BW Matthews, Science 1989 243 4892 792 794 2916125
35. Stabilization of functional proteins by introduction of multiple disulfide bonds. M Matsumura BW Matthews, Methods Enzymol 1991 202 336 356 1784181
36. Structural evidence for a possible role of reversible disulphide bridge formation in the elasticity of the muscle protein titin. O Mayans J Wuerges S Canela M Gautel M Wilmanns, Structure 2001 9 4 331 340 11525170
37. Disulfide bonds and protein folding. WJ Wedemeyer E Welker M Narayan HA Scheraga, Biochemistry 2000 39 15 4207 4216 10757967
38. Coupling of conformational folding and disulfide-bond reactions in oxidative folding of proteins. E Welker WJ Wedemeyer M Narayan HA Scheraga, Biochemistry 2001 40 31 9059 9064 11478871
39. Consequence of the removal of evolutionary conserved disulfide bridges on the structure and function of charybdotoxin and evidence that particular cysteine spacings govern specific disulfide bond formation. E Drakopoulou J Vizzavona J Neyton V Aniort F Bouet H Virelizier A Menez C Vita, Biochemistry 1998 37 5 1292 1301 9477955
40. Coordinated amino acid changes in homologous protein families. D Altschuh T Vernet P Berti D Moras K Nagai, Protein Eng 1988 2 3 193 199 3237684
41. Paired natural cysteine mutation mapping: Aid to constraining models of protein tertiary structure. R Kreisberg V Buchner D Arad, Protein Sci 1995 4 11 2405 2410 8563638
42. SCOP: a structural classification of proteins database for the investigation of sequences and structures. AG Murzin SE Brenner T Hubbard C Chothia, J Mol Biol 1995 247 4 536 540 7723011
43. Response of dynamic structure to removal of a disulfide bond: normal mode refinement of C77A/C95A mutant of human lysozyme. A Kidera K Inaka M Matsushima N Go, Protein Sci 1994 3 1 92 102 8142902
44. Engineered disulfide bonds in staphylococcal nuclease: effects on the stability and conformation of the folded protein. AP Hinck DM Truckses JL Markley, Biochemistry 1996 35 32 10328 10338 8756688
45. Disulphide bonds and protein stability. TE Creighton, Bioessays 1988 8 2 57 63 3282505
46. Theory for the folding and stability of globular proteins. KA Dill, Biochemistry 1985 24 6 1501 1509 3986190
47. Folding of protein fragments. DB Wetlaufer, Adv Protein Chem 1981 34 61 92 6266231
48. The de novo design of protein structures. JS Richardson DC Richardson, Trends Biochem Sci 1989 14 7 304 309 2672455
49. The Disulphide [beta]-Cross: From Cystine Geometry and Clustering to Classification of Small Disulphide-rich Protein Folds. PM Harrison MJE Sternberg, Journal of Molecular Biology 1996 264 3 603 623 8969308
50. New structural motifs on the chymotrypsin fold and their potential roles in complement factor B. H Jing Y Xu M Carson D Moore KJ Macon JE Volanakis SV Narayana, Embo J 2000 19 2 164 173 10637221
51. Human plasminogen catalytic domain undergoes an unusual conformational change upon activation. X Wang S Terzyan J Tang JA Loy X Lin XC Zhang, J Mol Biol 2000 295 4 903 914 10656799
52. The crystal structure of the novel snake venom plasminogen activator TSV-PA: a prototype structure for snake venom serine proteinases. MA Parry U Jacob R Huber A Wisner C Bon W Bode, Structure 1998 6 9 1195 1206 9753698
53. Structure of melanoma inhibitory activity protein, a member of a recently identified family of secreted proteins. JC Lougheed JM Holton T Alber JF Bazan TM Handel, Proc Natl Acad Sci USA 2001 98 10 5515 5520 11331761
54. Escherichia coli alkaline phosphatase fails to acquire disulfide bonds when retained in the cytoplasm. AI Derman J Beckwith, Journal of bacteriology 1991 173 23 7719 7722 1938970
55. Protein disulfide bond formation in prokaryotes. H Kadokura F Katzen J Beckwith, Annual review of biochemistry 2003 72 111 135 12524212
56. The Role of the Thioredoxin and Glutaredoxin Pathways in Reducing Protein Disulfide Bonds in the Escherichia coli Cytoplasm. WA Prinz F Aslund A Holmgren J Beckwith, J Biol Chem 1997 272 25 15661 15667 9188456
57. Structural Basis of the Redox Switch in the OxyR Transcription Factor. H-J Choi S-J Kim P Mukhopadhyay S Cho J-R Woo G Storz S-E Ryu, Cell 2001 105 1 103 113 11301006
58. Chaperone Activity with a Redox Switch. U Jakob W Muse M Eser JCA Bardwell, Cell 1999 96 3 341 352 10025400
59. The crystal structure of adenylosuccinate lyase from Pyrobaculum aerophilum reveals an intracellular protein with three disulfide bonds. EA Toth C Worby JE Dixon ER Goedken S Marqusee TO Yeates, Journal of Molecular Biology 2000 301 2 433 450 10926519
60. The intracellular chloride ion channel protein CLIC1 undergoes a redox-controlled structural transition. DR Littler SJ Harrop WD Fairlie LJ Brown GJ Pankhurst S Pankhurst MZ DeMaere TJ Campbell AR Bauskin R Tonini, J Biol Chem 2004 279 10 9298 9305 14613939
61. Crystal structure of the human prion protein reveals a mechanism for oligomerization. KJ Knaus M Morillas W Swietnicki M Malone WK Surewicz VC Yee, Nat Struct Biol 2001 8 9 770 774 11524679
62. Characterisation of human dipeptidyl peptidase IV expressed in Pichia pastoris. A structural and mechanistic comparison between the recombinant human and the purified porcine enzyme. J Bar A Weber T Hoffmann J Stork M Wermann L Wagner S Aust B Gerhartz HU Demuth, Biol Chem 2003 384 12 1553 1563 14719797
63. Crystal structure of mistletoe lectin I from Viscum album. R Krauspenhaar S Eschenburg M Perbandt V Kornilov N Konareva I Mikailova S Stoeva R Wacker T Maier T Singh, Biochem Biophys Res Commun 1999 257 2 418 424 10198229
64. Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies. K Gruber G Klintschar M Hayn A Schlacher W Steiner C Kratky, Biochemistry 1998 37 39 13475 13485 9753433
65. Molecular dynamics simulations of bovine cathepsin B and its complex with CA074. A Yamamoto K Tomoo H Miyagawa Y Takaoka S Sumiya K Kitamura T Ishida, Chem Pharm Bull (Tokyo) 2000 48 4 480 485 10783065
66. An interfacial mechanism and a class of inhibitors inferred from two crystal structures of the Mycobacterium tuberculosis 30 kDa major secretory protein (Antigen 85B), a mycolyl transferase. DH Anderson G Harth MA Horwitz D Eisenberg, J Mol Biol 2001 307 2 671 681 11254389
67. Determination of the gene sequence and the three-dimensional structure at 2.4 angstroms resolution of methanol dehydrogenase from Methylophilus W3A1. Z Xia W Dai Y Zhang SA White GD Boyd FS Mathews, J Mol Biol 1996 259 3 480 501 8676383
68. Calcium-mediated thermostability in the subtilisin superfamily: the crystal structure of Bacillus Ak.1 protease at 1.8 A resolution. CA Smith HS Toogood HM Baker RM Daniel EN Baker, J Mol Biol 1999 294 4 1027 1040 10588904
69. Crystal structures of acutolysin A, a three-disulfide hemorrhagic zinc metalloproteinase from the snake venom of Agkistrodon acutus. W Gong X Zhu S Liu M Teng L Niu, J Mol Biol 1998 283 3 657 668 9784374
70. A Novel Database of Disulfide Patterns and its Application to the Discovery of Distantly Related Homologs. HWT van Vlijmen A Gupta LS Narasimhan J Singh, Journal of Molecular Biology 2004 335 4 1083 1092 14698301
71. Structure of a rat alpha 1-macroglobulin receptor-binding domain dimer. T Xiao DL DeCamp SR Spran, Protein Sci 2000 9 10 1889 1897 11106161
72. Crystal structures of YBHB and YBCL from Escherichia coli, two bacterial homologues to a Raf kinase inhibitor protein. L Serre K Pereira de Jesus C Zelwer N Bureaud F Schoentgen H Benedetti, J Mol Biol 2001 310 3 617 634 11439028
73. A cluster exposed: structure of the Rieske ferredoxin from biphenyl dioxygenase and the redox properties of Rieske Fe-S proteins. CL Colbert MM Couture LD Eltis JT Bolin, Structure 2000 8 12 1267 1278 11188691
74. Interresidue interactions in protein classes. Z Gugolya Z Dosztanyi I Simon, Proteins 1997 27 3 360 366 9094738
75. Stabilization centers in proteins: identification, characterization and predictions. Z Dosztanyi A Fiser I Simon, J Mol Biol 1997 272 4 597 612 9325115
76. Structural patterns in globular proteins. M Levitt C Chothia, Nature 1976 261 5561 552 558 934293
77. Native and modeled disulfide bonds in proteins: knowledge-based approaches toward structure prediction of disulfide-rich polypeptides. RR Thangudu A Vinayagam G Pugalenthi A Manonmani B Offmann R Sowdhamini, Proteins 2005 58 4 866 879 15645448
78. MODIP revisited: re-evaluation and refinement of an automated procedure for modeling of disulfide bonds in proteins. VS Dani C Ramakrishnan R Varadarajan, Protein Eng 2003 16 3 187 193 12702798
79. Evolutionary plasticity of protein families: coupling between sequence and structure variation. AR Panchenko YI Wolf LA Panchenko T Madej, Proteins 2005 61 3 535 544 16184609
80. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. CA Wilson J Kreychman M Gerstein, J Mol Biol 2000 297 1 233 249 10704319
81. Using a library of structural templates to recognise catalytic sites and explore their evolution in homologous families. JW Torrance GJ Bartlett CT Porter JM Thornton, J Mol Biol 2005 347 3 565 581 15755451
82. Intra-A chain disulfide bond (A6-11) of insulin is essential for displaying its activity. Y Dai JG Tang, Biochem Mol Biol Int 1994 33 6 1049 1053 7804129
83. Structural effects induced by removal of a disulfide-bridge: the X-ray structure of the C30A/C51A mutant of basic pancreatic trypsin inhibitor at 1.6 A. C Eigenbrot M Randal AA Kossiakoff, Protein Eng 1990 3 7 591 598 1699222
84. Effect of the intermolecular disulfide bond on the conformation and stability of glial cell line-derived neurotrophic factor. T Li H Yamane T Arakawa LO Narhi J Philo, Protein Eng 2002 15 1 59 64 11842239
85. The genealogy of some recently evolved vertebrate proteins. RF Doolittle, Trends in Biochemical Sciences 1985 10 6 233 237
86. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. P Mallick DR Boutz D Eisenberg TO Yeates, Proc Natl Acad Sci USA 2002 99 15 9679 9684 12107280
87. Reconsideration of an early dogma, saying "there is no evidence for disulfide bonds in proteins from archaea". R Ladenstein B Ren, Extremophiles 2008 12 1 29 38 17508126
88. Discrimination of intracellular and extracellular proteins using amino acid composition and residue-pair frequencies. H Nakashima K Nishikawa, J Mol Biol 1994 238 1 54 61 8145256
89. Classification of proteins into groups based on amino acid composition and other characters. II. Grouping into four types. K Nishikawa Y Kubota T Ooi, Journal of biochemistry 1983 94 3 997 1007 6643433
90. Analycys: a database for conservation and conformation of disulphide bonds in homologous protein domains. RR Thangudu P Sharma N Srinivasan B Offmann, Proteins 2007 67 2 255 261 17285632
91. The Protein Data Bank. HM Berman J Westbrook Z Feng G Gilliland TN Bhat H Weissig IN Shindyalov PE Bourne, Nucleic Acids Res 2000 28 1 235 242 10592235
92. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. O Emanuelsson H Nielsen S Brunak G von Heijne, J Mol Biol 2000 300 4 1005 1016 10891285
93. PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. K Nakai P Horton, Trends Biochem Sci 1999 24 1 34 36 10087920
94. Support vector machine approach for protein subcellular localization prediction. S Hua Z Sun, Bioinformatics 2001 17 8 721 728 11524373
95. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. RB Russell GJ Barton, Proteins 1992 14 2 309 323 1409577
96. A method to determine heavy-atom positions for virus structures. P Argos MG Rossmann, Acta Crystallographica 1976 B32 2975 2979
97. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. W Kabsch C Sander, Biopolymers 1983 22 12 2577 2637 6667333
98. The interpretation of protein structures: estimation of static accessibility. B Lee FM Richards, J Mol Biol 1971 55 3 379 400 5551392
99. Naccess V2.1.1, Atomic solvent accessible area calculations. SJ Hubbard JM Thornton, Department of biochemistry and molecular biology University college London 1993
100. DPX: for the analysis of the protein core. A Pintar O Carugo S Pongor, Bioinformatics 2003 19 2 313 314 12538266