Structures composing protein domains

Biochimie

Volumn 95, Issue 8, 2013, Pages 1511-1524

  Kubrycht, Jaroslav ^a   Sigler, Karel ^b   Souček, Pavel ^c   Hudeček, Jiří ^a  

^a CHARLES UNIVERSITY   (Czech Republic)

^b INSTITUTE OF MICROBIOLOGY   (Czech Republic)

^c NATIONAL INSTITUTE OF PUBLIC HEALTH   (Czech Republic)

Author keywords

Catalytic; Disordered; Fold; Intradomain; Motif; Repeat

Indexed keywords

COLLAGEN TYPE 1; COLLAGEN TYPE 4; CYCLIC AMP DEPENDENT PROTEIN KINASE; PROTEIN KINASE C; RNA POLYMERASE II; PROTEIN;

ALDOL REACTION; ALLOSTERISM; AMINO ACID SEQUENCE; BINDING SITE; CELL DIFFERENTIATION; CELL PROLIFERATION; COMPLEMENTARITY DETERMINING REGION; CONFORMATIONAL TRANSITION; ELECTROPHILICITY; ENERGY TRANSFER; ENZYME ACTIVE SITE; ENZYME MECHANISM; INTRACELLULAR SIGNALING; ISOMERIZATION; MOLECULAR DOCKING; MOLECULAR RECOGNITION; NUCLEOPHILICITY; PHAGE DISPLAY; PHOSPHOLIPID MEMBRANE; PROTEIN DEPHOSPHORYLATION; PROTEIN DOMAIN; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; REVIEW; SEQUENCE ALIGNMENT; CHEMISTRY; HUMAN; PROTEIN TERTIARY STRUCTURE;

CATALYTIC DOMAIN; HUMANS; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SEQUENCE ALIGNMENT;

EID: 84879686418     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2013.04.001     Document Type: Review

References (244)

1. T. Pawson, and P. Nash Domains assembly of cell regulatory systems through protein interaction Science 300 2003 445 452
2. C.K. Wang, L. Pan, J. Chen, and M. Zhang Extensions of PDZ domains as important structural and functional elements Protein Cell 1 2010 737 751
3. R.A. Laskowski, F. Gerick, and J.M. Thorton The structural basis of allosteric regulation in proteins FEBS Lett. 583 2009 1692 1698
4. G. Debret, A. Martel, and P. Cuniasse RASMOT-3D PRO: a 3D motif search webserver Nucleic Acids Res. 37 2009 W459 W464
5. J.J. Lacapère, N. Bennett, Y. Dupont, and F. Guillain pH and magnesium dependence of ATP binding to sarcoplasmic reticulum ATPase. Evidence that the catalytic ATP-binding site consists of two domains J. Biol. Chem. 265 1990 348 353
6. X. Ji, W.W. Johnson, M.A. Sesay, L. Dickert, S.M. Prasad, H.L. Ammon, R.N. Armstrong, and G.L. Gilliland Structure and function of the xenobiotic substrate binding site of a glutathione S-transferase as revealed by X-ray crystallographic analysis of product complexes with the diastereomers of 9-(S-glutathionyl)-10-hydroxy-9,10-dihydrophenanthrene Biochemistry 33 1994 1043 1052
7. A. Marsico, K. Scheubert, A. Tuukkanen, A. Henschel, C. Winter, R. Winnenburg, and M. Schroeder MeMotif: a database of linear motifs in alpha-helical transmembrane proteins Nucleic Acids Res. 38 2010 D181 D189
8. H. Dinkel, S. Michael, R.J. Weatheritt, N.E. Davey, K. Van Roey, B. Altenberg, G. Toedt, B. Uyar, M. Seiler, A. Budd, L. Jödicke, M.A. Dammert, C. Schroeter, M. Hammer, T. Schmidt, P. Jehl, C. McGuigan, M. Dymecka, C. Chica, K. Luck, A. Via, A. Chatr-Aryamontri, N. Haslam, G. Grebnev, R.J. Edwards, M.O. Steinmetz, H. Meiselbach, F. Diella, and T.J. Gibson ELM - the database of eukaryotic linear motifs Nucleic Acids Res. 40 2012 D242 D251
9. R.J. Weatheritt, K. Luck, E. Petsalaki, N.E. Davey, and T.J. Gibson The identification of short linear motif-mediated interfaces within the human interactome Bioinformatics 28 2012 976 982
10. J. Kubrycht, K. Sigler, and P. Souček Virtual interactomics of proteins from biochemical standpoint Mol. Biol. Int. 2012 2012 Article ID 976385
11. M. Ohlin, and C.A. Borrebaeck Insertions and deletions in hypervariable loops of antibody heavy chains contribute to molecular diversity Mol. Immunol. 35 1998 233 238
12. P. Wilson, Y.J. Liu, J. Banchereau, J.D. Capra, and V. Pascual Amino acid insertions and deletions contribute to diversify the human Ig repertoire Immunol. Rev. 162 1998 143 151
13. T. Prakash, M. Khandelwal, D. Dasgupta, D. Dash, and S.K. Brahmachari CoPS: comprehensive peptide signature database Bioinformatics 20 2004 2886 2888
14. N. Matsushima, H. Yoshida, Y. Kumaki, M. Kamiya, T. Tanaka, Y. Izumi, and R.H. Kretsinger Flexible structures and ligand interactions of tandem repeats consisting of proline, glycine, asparagine, serine, and/or threonine rich oligopeptides in proteins Curr. Protein Pept. Sci. 9 2008 591 610
15. A.V. Kajava, and A.C. Steven Beta-rolls, beta-helices, and other beta-solenoid proteins Adv. Protein Chem. 73 2006 55 96
16. H.T. Orr, and H.Y. Zoghbi Trinucleotide repeat disorders Annu. Rev. Neurosci. 30 2007 575 621
17. J. Jorda, T. Baudrand, and A.V. Kajava PRDB: Protein Repeat DataBase Proteomics 12 2012 1333 1336
18. D. Sirim, M. Widmann, F. Wagner, and J. Pleiss Prediction and analysis of the modular structure of cytochrome P450 monooxygenases BMC Struct. Biol. 10 2010 Article ID 34
19. I.K. Huang, J. Pei, and N.V. Grishin Defining and predicting structurally conserved regions in protein superfamilies Bioinformatics 29 2013 175 181
20. A. Marchler-Bauer, A.R. Panchenko, B.A. Shoemaker, P.A. Thiessen, L.Y. Geer, and S.H. Bryant CDD: a database of conserved domain alignments with links to domain three-dimensional structure Nucleic Acids Res. 30 2002 281 283
21. N. Hulo, C.J. Sigrist, V. Le Saux, P.S. Langendijk-Genevaux, L. Bordoli, A. Gattiker, E. De Castro, P. Bucher, and A. Bairoch Recent improvements to the PROSITE database Nucleic Acids Res. 32 2004 D134 D137
22. Q.J. Su, L. Lu, S. Saxonov, and D.L. Brutlag eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity Nucleic Acids Res. 33 2005 D178 D182
23. A. Marchler-Bauer, S. Lu, J.B. Anderson, F. Chitsaz, M.K. Derbyshire, C. DeWeese-Scott, J.H. Fong, L.Y. Geer, R.C. Geer, N.R. Gonzales, M. Gwadz, D.I. Hurwitz, J.D. Jackson, Z. Ke, C.J. Lanczycki, F. Lu, G.H. Marchler, M. Mullokandov, M.V. Omelchenko, C.L. Robertson, J.S. Song, N. Thanki, R.A. Yamashita, D. Zhang, N. Zhang, C. Zheng, and S.H. Bryant CDD: a Conserved Domain Database for the functional annotation of proteins Nucleic Acids Res. 39 2011 D225 D229
24. J. Kubrycht, K. Sigler, M. Ruzicka, P. Soucek, J. Borecky, and P. Jezek Ancient phylogenetic beginnings of immunoglobulin hypermutation J. Mol. Evol. 63 2006 691 706
25. S. Ding, S. Zhang, Y. Li, and T. Wang A novel protein structural classes prediction method based on predicted secondary structure Biochimie 94 2012 1166 1171
26. D.P. Klose, B.A. Wallace, and R.W. Janes 2Struc: the secondary structure server Bioinformatics 26 2010 2624 2625
27. P. May, A. Kreuchwig, T. Steinke, and I. Koch PTGL: a database for secondary structure-based protein topologies Nucleic Acids Res. 38 2010 D326 D330
28. E. Faraggi, T. Zhang, Y. Yang, L. Kurgan, and Y. Zhou SPINE X: improving protein secondary structure prediction by multistep learning coupled with prediction of solvent accessible surface area and backbone torsion angles J. Comput. Chem. 33 2012 259 267
29. H.N. Lin, T.Y. Sung, S.Y. Ho, and W.L. Hsu Improving protein secondary structure prediction based on short subsequences with local structure similarity BMC Genomics 11 Suppl. 4 2010 Article ID S4
30. S. Kobs-Conrad, H. Lee, A.M. DiGeorge, and P.T.P. Kaumaya Engineered topographic determinants with αβ, βαβ, βαβα topologies show high affinity binding to native protein antigen (lactate dehydrogenase-C4)* J. Biol. Chem. 268 1993 25285 25295
31. D. van der Spoel, H.J. Vogel, and H.J. Berendsen Molecular dynamics simulations of N-terminal peptides from a nucleotide binding protein Proteins 24 1996 450 466
32. L.G. Laajoki, E. Le Breton, G.K. Shooter, J.C. Wallace, G.L. Francis, J.A. Carver, and M.A. Keniry Secondary structure determination of 15N-labelled human long-[Arg-3]-insulin-like growth factor 1 by multidimensional NMR spectroscopy FEBS Lett. 420 1997 97 102
33. J.C. Horng, V. Moroz, D.J. Rigotti, R. Fairman, and D.P. Raleigh Characterization of large peptide fragments derived from the N-terminal domain of the ribosomal protein L9: definition of the minimum folding motif and characterization of local electrostatic interactions Biochemistry 41 2002 13360 13369
34. J. Soding, and A.N. Lupas More than the sum of their parts: on the evolution of proteins from peptides BioEssays 25 2003 837 846
35. A.F. Angyán, A. Perczel, S. Pongor, and Z. Gáspári Fast protein fold estimation from NMR-derived distance restraints Bioinformatics 24 2008 272 275
36. D.S. Wishart, D. Arndt, M. Berjanskii, P. Tang, J. Zhou, and G. Lin CS23D: a web server for rapid protein structure generation using NMR chemical shifts and sequence data Nucleic Acids Res. 36 2008 W496 W502
37. R.M. Rasia, E. Lescop, J.F. Palatnik, J. Boisbouvier, and B. Brutscher Rapid measurement of residual dipolar couplings for fast fold elucidation of proteins J. Biomol. NMR 51 2011 369 378
38. B.E. Coggins, J.W. Werner-Allen, A. Yan, and P. Zhou Rapid protein global fold determination using ultrasparse sampling, high-dynamic range artifact suppression, and time-shared NOESY J. Am. Chem. Soc. 134 2012 18619 18630
39. I. Sengupta, P.S. Nadaud, J.J. Helmus, C.D. Schwieters, and C.P. Jaroniec Protein fold determined by paramagnetic magic-angle spinning solid-state NMR spectroscopy Nat. Chem. 4 2012 410 417
40. W. Zheng, and S. Doniach Fold recognition aided by constraints from small angle X-ray scattering data Protein Eng. Des. Sel. 18 2005 209 219
41. L. Makowski, D.J. Rodi, S. Mandava, S. Devarapalli, and R.F. Fischetti Characterization of protein fold by wide-angle X-ray solution scattering J. Mol. Biol. 383 2008 731 744
42. R. Khayat, G.C. Lander, and J.E. Johnson An automated procedure for detecting protein folds from sub-nanometer resolution electron density J. Struct. Biol. 170 2010 513 521
43. M. Saha, and M.C. Morais FOLD-EM: automated fold recognition in medium- and low-resolution (4-15 Å) electron density maps Bioinformatics 28 2012 3265 3273
44. R.X. Yan, J.N. Si, C. Wang, and Z. Zhang DescFold: a web server for protein fold recognition BMC Bioinform. 10 2006 Article ID 416
45. Y. Yang, E. Faraggi, H. Zhao, and Y. Zhou Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates Bioinformatics 27 2011 2076 2082
46. B. Vishnepolsky, and M. Pirtskhalava CONTSOR - a new knowledge-based fold recognition potential, based on side chain orientation and contacts between residue terminal groups Protein Sci. 21 2012 134 141
47. Y. Hong, S.V. Chintapalli, K.D. Ko, G. Bhardwaj, Z. Zhang, D. van Rossum, and R.L. Patterson Predicting protein folds with fold-specific PSSM libraries PLoS One 6 2011 e20557
48. A. Dehzangi, and S. Phon-Amnuaisuk Fold prediction problem: the application of new physical and physicochemical-based features Protein Pept. Lett. 18 2011 174 185
49. N. Sibille, and P. Bernadó Structural characterization of intrinsically disordered proteins by the combined use of NMR and SAXS Biochem. Soc. Trans. 40 2012 955 962
50. Z. Dosztányi, B. Mészáros, and I. Simon ANCHOR: web server for predicting protein binding regions in disordered proteins Bioinformatics 25 2009 2745 2746
51. L.P. Kozlowski, and J.M. Bujnicki MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins BMC Bioinform. 13 2012 Article ID 111
52. W.M. Brown, and D.L. Van der Jagt Creating artificial binding pocket boundaries to improve the efficiency of flexible ligand docking J. Chem. Inf. Comput. Sci. 44 2004 1412 1422
53. C. Hetényi, and D. van der Spoel Toward prediction of functional protein pockets using blind docking and pocket search algorithms Protein Sci. 20 2011 880 893
54. F. Yu, L. Lu, L. Du, X. Zhu, A.K. Debnath, and S. Jiang Approaches for identification of HIV-1 entry inhibitors targeting gp41 pocket Viruses 5 2013 127 149
55. Y.F. Chen, K.C. Hsu, S.R. Lin, W.C. Wang, Y.C. Huang, and J.M. Yang SiMMap: a web server for inferring site-moiety map to recognize interaction preferences between protein pockets and compound moieties Nucleic Acids Res. 38 2010 W424 W430
56. C.Y. Wu, Y.C. Chen, and C. Lim A structural-alphabet-based strategy for finding structural motifs across protein families Nucleic Acids Res. 38 2010 e150
57. A.J. Baldwin, and L.E. Kay NMR spectroscopy brings invisible protein states into focus Nat. Chem. Biol. 5 2009 808 814
58. S.C. Gay, A.G. Roberts, and J.R. Halpert Structural features of cytochromes P450 and ligands that affect drug metabolism as revealed by X-ray crystallography and NMR Future Med. Chem. 2 2010 1451 1468
59. L.P. Calle, F.J. Cañada, and J. Jiménez-Barbero Application of NMR methods to the study of the interaction of natural products with biomolecular receptors Nat. Prod. Rep. 28 2011 1118 1125
60. W.T. Franks, A.H. Linden, B. Kunert, B.J. van Rossum, and H. Oschkinat Solid-state magic-angle spinning NMR of membrane proteins and protein-ligand interactions Eur. J. Cell. Biol. 91 2012 340 348
61. M. Hong, Y. Zhang, and F. Hu Membrane protein structure and dynamics from NMR spectroscopy Annu. Rev. Phys. Chem. 63 2012 1 24
62. M. Osawa, K. Takeuchi, T. Ueda, N. Nishida, and I. Shimada Functional dynamics of proteins revealed by solution NMR Curr. Opin. Struct. Biol. 22 2012 660 669
63. R.P. Venkitakrishnan, O. Benard, M. Max, J.L. Markley, and F.M. Assadi-Porter Use of NMR saturation transfer difference spectroscopy to study ligand binding to membrane proteins Methods Mol. Biol. 914 2012 47 63
64. O. Vinogradova, and J. Qin NMR as a unique tool in assessment and complex determination of weak protein-protein interactions Top. Curr. Chem. 326 2012 35 45
65. X. Ding, X. Zhao, and A. Watts G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy Biochem. J. 450 2013 443 457
66. L.F. Murga, Y. Wei, and M.J. Ondrechen Computed protonation properties: unique capabilities for protein functional site prediction Genome Inform. 19 2007 107 118
67. S. Sankararaman, and K. Sjölander INTREPID - INformation-theoretic TREe traversal for Protein functional site Identification Bioinformatics 24 2008 2445 2452
68. S. Somarowthu, and M.J. Ondrechen POOL server: machine learning application for functional site prediction in proteins Bioinformatics 28 2012 2078 2079
69. W. Feng, L. Pan, and M. Zhang Combination of NMR spectroscopy and X-ray crystallography offers unique advantages for elucidation of the structural basis of protein complex assembly Sci. China Life Sci. 54 2011 101 111
70. O. Fisette, P. Lagüe, S. Gagné, and S. Morin Synergistic applications of MD and NMR for the study of biological systems J. Biomed. Biotechnol. 2012 2012 article ID 254208
71. D.R. Hall, D. Kozakov, and S. Vajda Analysis of protein binding sites by computational solvent mapping Methods Mol. Biol. 819 2012 13 27
72. D. Schneidman-Duhovny, A. Rossi, A. Avila-Sakar, S.J. Kim, J. Velázquez-Muriel, P. Strop, H. Liang, K.A. Krukenberg, M. Liao, H.M. Kim, S. Sobhanifar, V. Dötsch, A. Rajpal, J. Pons, D.A. Agard, Y. Cheng, and A. Sali A method for integrative structure determination of protein-protein complexes Bioinformatics 28 2012 3282 3289
73. J.L. Stark, and R. Powers Application of NMR and molecular docking in structure-based drug discovery Top. Curr. Chem. 326 2012 1 34
74. C.T. Porter, G.J. Bartlett, and J.M. Thornton The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data Nucleic Acids Res. 32 2004 D129 D133
75. S. Mitternacht, and I.N. Berezovsky A geometry-based generic predictor for catalytic and allosteric sites Protein Eng. Des. Sel. 24 2011 405 409
76. D.-B. Borza, and W.T. Morgan Histidine-proline-rich glycoprotein as a plasma pH sensor J. Biol. Chem. 273 1998 5493 5499
77. S.R. Tzeng, and C.G. Kalodimos Protein dynamics and allostery: an NMR view Curr. Opin. Struct. Biol. 21 2011 62 67
78. G. Manley, and J.P. Loria NMR insights into protein allostery Arch. Biochem. Biophys. 519 2012 223 231
79. N.E. Davey, R.J. Edwards, and D.C. Shields Computational identification and analysis of protein short linear motifs Front. Biosci. 15 2010 801 825
80. O. Schilling, and C.M. Overall Proteome-derived, database searchable peptide libraries for identifying protease cleavage sites Nat. Biotechnol. 26 2008 685 694
81. S.A. Shiryaev, A.Y. Savinov, P. Cieplak, B.I. Ratnikov, K. Motamedchaboki, J.W. Smith, and A.Y. Strongin Matrix metalloproteinase proteolysis of the myelin basic protein isoforms is a source of immunogenic peptides in autoimmune multiple sclerosis PLoS One 4 2009 e4952
82. P. Minkiewicz, J. Dziuba, A. Iwaniak, M. Dziuba, and M. Darewicz BIOPEP database and other programs for processing bioactive peptide sequences J. AOAC Int. 91 2008 965 980
83. E.D. Crawford, J.E. Seaman, N. Agard, G.W. Hsu, O. Julien, S. Mahrus, H. Nguyen, K. Shimbo, H.A. Yoshihara, M. Zhuang, R.J. Chalkley, and J.A. Wells The DegraBase: a database of proteolysis in healthy and apoptotic human cells Mol. Cell. Proteomics 12 2013 813 824
84. N. Colaert, D. Maddelein, F. Impens, P. Van Damme, K. Plasman, K. Helsens, N. Hulstaert, J. Vandekerckhove, K. Gevaert, and L. Martens The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events Nucleic Acids Res. 41 2013 D333 D337
85. S. Yoon, J.C. Ebert, E.Y. Chung, G. De Micheli, and R.B. Altman Clustering protein environments for function prediction: finding PROSITE motifs in 3D BMC Bioinform. 8 Suppl. 4 2007 S10
86. W. Hugo, F. Song, Z. Aung, S.K. Ng, and W.K. Sung SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank Bioinformatics 26 2010 1036 1042
87. D.P. Sargeant, M.R. Gryk, M.W. Maciejewski, V. Thapar, V. Kundeti, S. Rajasekaran, P. Romero, K. Dunker, S.C. Li, T. Kaneko, and M.R. Schiller Secondary structure, a missing component of sequence-based minimotif definitions PLoS One 7 2012 e49957
88. M. Akke Conformational dynamics and thermodynamics of protein-ligand binding studied by NMR relaxation Biochem. Soc. Trans. 40 2012 419 423
89. J. Kubrycht, and K. Sigler Animal membrane receptors and adhesive molecules Crit. Rev. Biotechnol. 17 1997 123 147
90. D.T. Chang, T.Y. Chien, and C.Y. Chen seeMotif: exploring and visualizing sequence motifs in 3D structures Nucleic Acids Res. 37 2009 W552 W558
91. J. Ponomarenko, N. Papangelopoulos, D.M. Zajonc, B. Peters, A. Sette, and P.E. Bourne IEDB-3D: structural data within the immune epitope database Nucleic Acids Res. 39 2011 D1164 D1170
92. A. Venkataraman, T.H. Chew, Y.A. Hussein, and M.S. Shamsir A protein short motif search tool using amino acid sequence and their secondary structure assignment Bioinformation 7 2011 304 306
93. M.S. Nawaz, Q.U. Ain, U. Seemab, and S. Rashid MotViz: a tool for sequence motif prediction in parallel to structural visualization and analyses Genomics Proteomics Bioinform. 10 2012 35 43
94. C. Vehlow, H. Stehr, M. Winkelmann, J.M. Duarte, L. Petzold, J. Dinse, and M. Lappe CMView: interactive contact map visualization and analysis Bioinformatics 27 2011 1573 1574
95. Z. Chen, S. Rappert, J. Sun, and A.P. Zeng Integrating molecular dynamics and co-evolutionary analysis for reliable target prediction and deregulation of the allosteric inhibition of aspartokinase for amino acid production J. Biotechnol. 154 2011 248 254
96. A. Godzik, J. Skolnick, and A. Kolinski Regularities in interaction patterns of globular proteins Protein Eng. 6 1993 801 810
97. A. Caprara, R. Carr, S. Istrail, G. Lancia, and B. Walenz 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap J. Comput. Biol. 11 2004 27 52
98. B. Xue, E. Faraggi, and Y. Zhou Predicting residue-residue contact maps by a two-layer, integrated neural-network method Proteins 76 2009 176 183
99. P. Di Lena, P. Fariselli, L. Margara, M. Vassura, and R. Casadio Fast overlapping of protein contact maps by alignment of eigenvectors Bioinformatics 26 2010 2250 2258
100. B. VanSchouwen, R. Selvaratnam, F. Fogolari, and G. Melacini Role of dynamics in the autoinhibition and activation of the exchange protein directly activated by cyclic AMP (EPAC) J. Biol. Chem. 286 2011 42655 42669
101. A.E. Kister, and I. Gefald Finding of residues crucial for supersecondary structure formation Proc. Natl. Acad. Sci. U. S. A. 106 2009 18996 19000
102. C. Blouin, D. Butt, and A.J. Roger Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain Protein Sci. 13 2004 608 616
103. J.T. Welch, W.R. Kearney, and S.J. Franklin Lanthanide-binding helix-turn-helix peptides: solution structure of a designed metallonuclease Proc. Natl. Acad. Sci. U. S. A. 100 2003 3725 3730
104. L.G. Presta, and G.D. Rose Helix signals in proteins Science 240 1988 1632 1641
105. R. Aurora, and G.D. Rose Helix capping Protein Sci. 7 1998 721 738
106. B.M. Hespenheide, and L.A. Kuhn Discovery of a significant, nontopological preference for antiparallel alignment of helices with parallel regions in sheets Protein Sci. 12 2003 1119 1125
107. G.A. Papoian, J. Ulander, M.P. Eastwood, Z. Luthey-Schulten, and P.G. Wolynes Water in protein structure prediction Proc. Natl. Acad. Sci. U. S. A. 101 2004 3352 3357
108. D.G. Fedorov, K. Kitaura, H. Li, J.H. Jensen, and M.S. Gordon The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO) J. Comput. Chem. 27 2006 976 985
109. H. Li, D.G. Fedorov, T. Nagata, K. Kitaura, J.H. Jensen, and M.S. Gordon Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation J. Comput. Chem. 31 2010 778 790
110. A. Cavalli, and P. Carloni Enzymatic GTP hydrolysis: insights from an ab initio molecular dynamics study J. Am. Chem. Soc. 124 2002 3763 3768
111. E. Krieger, T. Darden, S.B. Nabuurs, A. Finkelstein, and G. Vriend Making optimal use of empirical energy functions: force-field parameterization in crystal space Proteins 57 2004 678 683
112. B.P. Mukhopadhyay, B. Ghosh, H.R. Bairagya, A.K. Bera, and R.K. Roy Conserved water molecular dynamics of the different X-ray structures of rusticyanin: an unique aquation potentiality of the ligand bonded Cu++ center J. Biomol. Struct. Dyn. 24 2007 369 378
113. T. Nakamura, A. Yamaguchi, H. Kondo, H. Watanabe, T. Kurihara, N. Esaki, S. Hirono, and S. Tanaka Roles of K151 and D180 in L-2-haloacid dehalogenase from Pseudomonas sp. YL: analysis by molecular dynamics and ab initio fragment molecular orbital calculations J. Comput. Chem. 30 2009 2625 2634
114. S.B. de Beer, N.P. Vermeulen, and C. Oostenbrink The role of water molecules in computational drug design Curr. Top. Med. Chem. 10 2010 55 66
115. C.-W. Tung, M. Ziehm, A. Kamper, O. Kohlbacher, and S.-Y. Ho POPISK: T-cell reactivity prediction using support vector machines and string kernels BMC Bioinform. 12 2011 Article ID 446
116. M.A. Andrade, C. Perez-Iratxeta, and C.P. Ponting Protein repeats: structures, functions, and evolution J. Struct. Biol. 134 2001 117 131
117. R. Sabarinathan, R. Basu, and K. Sekar ProSTRIP: a method to find similar structural repeats in three-dimensional protein structures Comput. Biol. Chem. 34 2010 126 130
118. P. Bork, and R.F. Doolittle Proposed acquisition of an animal protein domain by bacteria Proc. Natl. Acad. Sci. U. S. A. 89 1992 8990 8994
119. A.A. Terentiev, and N.T. Moldogazieva Cell adhesion proteins and alpha-fetoprotein. Similar structural motifs as prerequisites for common functions Biochemistry (Mosc) 72 2007 920 935
120. M.S. Miettinen, V. Knecht, L. Monticelli, and Z. Ignatova Assessing polyglutamine conformation in the nucleating event by molecular dynamics simulations J. Phys. Chem. B 116 2012 10259 10265
121. F.X. Schmid Prolyl isomerase: enzymatic catalysis of slow protein-folding reactions Annu. Rev. Biophys. Biomol. Struct. 22 1993 123 142
122. J.H. Morse, S. Antohi, K. Kasturi, S. Saito, M. Fotino, M. Humbert, G. Simonneau, R.J. Basst, and C.A. Bona Fine specificity of anti-fibrillin-1 autoantibodies in primary pulmonary hypertension syndrome Scand. J. Immunol. 51 2000 607 611
123. M. Yamazaki, R. Kitamura, S. Kusano, H. Eda, S. Sato, M. Okawa-Takatsuji, S. Aotsuka, and K. Yanagi Elevated immunoglobulin G antibodies to the proline-rich amino-terminal region of Epstein-Barr virus nuclear antigen-2 in sera from patients with systemic connective tissue diseases and from a subgroup of Sjögren's syndrome patients with pulmonary involvements Clin. Exp. Immunol. 139 2005 558 568
124. B. Kemper Structural basis for the role in protein folding of conserved proline-rich regions in cytochromes P450 Toxicol. Appl. Pharmacol. 199 2004 305 315
125. K. Löster, K. Zeilinger, D. Schuppan, and W. Reutter The cysteine-rich region of dipeptidyl peptidase IV (CD 26) is the collagen-binding site Biochem. Biophys. Res. Commun. 217 1995 341 348
126. J. Denault, L. Bissonnette, J. Longpré, G. Charest, P. Lavigne, and R. Leduc Ectodomain shedding of furin: kinetics and role of the cysteine-rich region FEBS Lett. 527 2002 309 314
127. L. Wang, G. Yang, and X. Wu Identification of the role of a cysteine-rich region of PC6B by determining the enzymatic characteristics of its mutants Mol. Biotechnol. 27 2004 15 22
128. G. Thiel, J.A. Sarraj, C. Vinson, L. Stefano, and K. Bach Role of basic region leucine zipper transcription factors cyclic AMP response element binding protein (CREB), CREB2, activating transcription factor 2 and CAAT/enhancer binding protein a in cyclic AMP response element-mediated transcription J. Neurochem. 92 2005 321 336
129. R.S. Kass, J. Kurokawa, S.O. Marx, and A.R. Marks Leucine/isoleucine zipper coordination of ion channel macromolecular signaling complexes in the heart. Roles in inherited arrhythmias Trends Cardiovasc. Med. 13 2003 52 56
130. A.L. Robertson, M.A. Bate, S.G. Androulakis, S.P. Bottomley, and A.M. Buckle PolyQ: a database describing the sequence and domain context of polyglutamine repeats in proteins Nucleic Acids Res. 39 2011 D272 D276
131. C.A. Janeway, and P. Travers Immunobiology. The Immune System in Health and Disease 1994 Garland Publishing New York
132. E.A. James, A.K. Moustakas, D. Berger, L. Huston, G.K. Papadopoulos, and W.W. Kwok Definition of the peptide binding motif within DRB1*1401 restricted epitopes by peptide competition and structural modeling Mol. Immunol. 45 2008 2651 2659
133. H.M. Geysen, T.J. Mason, and S.J. Rodda Cognitive features of continuous antigenic determinants J. Mol. Recognit. 1 1998 32 41
134. J. Van de Water, M.E. Gershwin, P. Leung, A. Ansari, and R.L. Coppel The autoepitope of the 74-kD mitochondrial autoantigen of primary biliary cirrhosis corresponds to the functional site of dihydrolipoamide acetyltransferase J. Exp. Med. 167 1988 1791 1799
135. D.A.D. Parry, L.N. Marekov, P.M. Steinert, and T.A. Smith A role for the 1A and L1 rod domain segments in head domain organization and function of intermediate filaments: structural analysis of trichocyte keratin J. Struct. Biol. 137 2002 97 108
136. E.A. Kabat, T.T. Wu, H.M. Perry, K.S. Gottesman, and C. Foeller Sequences of Proteins of Immunological Interest NIH publication No. 91-3242, Bethesda 1991
137. X.-N. Dong, Y. Xiao, M.P. Dierich, and Y.-H. Chen N- and C-domains of HIV-1 gp41: mutation, structure and functions Immunol. Lett. 75 2001 215 220
138. V. Sivaraman, L. Zhang, E.G. Meissner, J.L. Jeffrey, and L. Su The heptad repeat 2 domain is a major determinant for enhanced human immunodeficiency virus type 1 (HIV-1) fusion and pathogenicity of a highly pathogenic HIV-1 Env J. Virol. 83 2009 11715 11725
139. K. Beck, I. Hunter, and J. Engel Structure and function of laminin: anatomy of a multidomain glycoprotein FASEB J. 4 1990 148 160
140. E. Pang, and K. Lin Yeast protein-protein interaction binding sites: prediction from the motif-motif, motif-domain and domain-domain levels Mol. Biosyst. 6 2010 2164 2173
141. W.L. Jorgensen Rusting of the lock and key model for protein-ligand binding Science 254 1991 954 955
142. S. Chaudhury, and J.J. Gray Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles J. Mol. Biol. 381 2008 1068 1087
143. M. Daëron, S. Jaeger, L. Du Pasquier, and E. Vivier Immunoreceptor tyrosine-based inhibition motifs: a quest in the past and future Immunol. Rev. 224 2008 11 43
144. D.T. Moore, B.W. Berger, and W.F. DeGrado Protein-protein interactions in the membrane: sequence, structural, and biological motifs Structure 16 2008 991 1001
145. K.N. Pandey Functional roles of short sequence motifs in the endocytosis of membrane receptors Front. Biosci. 14 2009 5339 5360
146. X. Ren, and J.H. Hurley Proline-rich regions and motifs in trafficking: from ESCRT interaction to viral exploitation Traffic 12 2011 1282 1290
147. B. Eisenhaber, and F. Eisenhaber Prediction of posttranslational modification of proteins from their amino acid sequence Methods Mol. Biol. 609 2010 365 384
148. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P. Walter Molecular Biology of the Cell fifth ed. 2008 Garland Science New York
149. D.J. Leahy, I. Aukhil, and H.P. Erickson 2.0 Å crystal structure of a four-domain segment of human fibronectin encompassing the RGD loop and synergy region Cell 84 1996 155 164
150. E. Koivunen, B. Wang, and E. Ruoslahti Isolation of a highly specific ligand for the alpha 5 beta 1 integrin from a phage display library J. Cell. Biol. 124 1994 373 380
151. N. Fernandez-Fuentes, B. Oliva, and A. Fiser A supersecondary structure library and search algorithm for modeling loops in protein structures Nucleic Acids Res. 34 2006 2085 2097
152. H.M. Strauss, and S. Keller Pharmacological interference with protein-protein interactions mediated by coiled-coil motifs Handb. Exp. Pharmacol. 186 2008 461 482
153. B. Apostolovic, M. Danial, and H.A. Klok Coiled coils: attractive protein folding motifs for the fabrication of self-assembled, responsive and bioactive materials Chem. Soc. Rev. 39 2010 3541 3575
154. B. Mészáros, P. Tompa, I. Simon, and Z. Dosztányi Molecular principles of the interactions of disordered proteins J. Mol. Biol. 372 2007 549 561
155. B. Mészáros, I. Simon, and Z. Dosztányi Prediction of protein binding regions in disordered proteins PLoS Comput. Biol. 5 2009 e1000376
156. B. Mészáros, I. Simon, and Z. Dosztányi The expanding view of protein-protein interactions: complexes involving intrinsically disordered proteins Phys. Biol. 8 2011 Article ID 035003
157. R. Nussinov, A.R. Panchenko, and T. Przytycka Physics approaches to protein interactions and gene regulation Phys. Biol. 8 2011 Article ID 030301
158. C.J. Oldfield, J. Meng, J.Y. Yang, M.Q. Yang, V.N. Uversky, and A.K. Dunker Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners BMC Genomics 9 Suppl. 1 2008 S1
159. R. Dawson, L. Müller, A. Dehner, C. Klein, H. Kessler, and J. Buchner The N-terminal domain of p53 is natively unfolded J. Mol. Biol. 332 2003 1131 1141
160. P.H. Kussie, S. Gorina, V. Marechal, B. Elenbaas, J. Moreau, A.J. Levine, and N.P. Pavletich Structure of the MDM2 oncoprotein bound to the p53 tumor suppressor transactivation domain Science 274 1996 948 953
161. S. Krishnamurthy, M.A. Ghazy, C. Moore, and M. Hampsey Functional interaction of the Ess1 prolyl isomerase with components of the RNA polymerase II initiation and termination machineries Mol. Cell. Biol. 29 2009 2925 2934
162. S. Yuzawa, M. Yokochi, H. Hatanaka, K. Ogura, M. Kataoka, K. Miura, V. Mandiyan, J. Schlessinger, and F. Inagaki Solution structure of Grb2 reveals extensive flexibility necessary for target recognition J. Mol. Biol. 306 2001 527 537
163. S. Casares, E. Ab, H. Eshuis, O. Lopez-Mayorga, N.A. van Nuland, and F. Conejero-Lara The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: understanding the determinants of binding affinity by comparison with Abl-SH3 BMC Struct. Biol. 7 2007 Article ID 22
164. J.M. Martín-García, I. Luque, P.L. Mateo, J. Ruiz-Sanz, and A. Cámara-Artigas Crystallographic structure of the SH3 domain of the human c-Yes tyrosine kinase: loop flexibility and amyloid aggregation FEBS Lett. 581 2007 1701 1706
165. E. Polverini, G. Rangaraj, D.S. Libich, J.M. Boggs, and G. Harauz Binding of the proline-rich segment of myelin basic protein to SH3 domains: spectroscopic, microarray, and modeling studies of ligand conformation and effects of posttranslational modifications Biochemistry 47 2008 267 282
166. A.M. Candel, N.A. van Nuland, F.M. Martin-Sierra, J.C. Martinez, and F. Conejero-Lara Analysis of the thermodynamics of binding of an SH3 domain to proline-rich peptides using a chimeric fusion protein J. Mol. Biol. 377 2008 117 135
167. J. Kubrycht, J. Borecký, and K. Sigler Sequence similarities of protein kinase peptide substrates and inhibitors: comparison of their primary structures with immunoglobulin repeats Folia Microbiol. 47 2002 319 358
168. J. Kubrycht, J. Borecký, P. Soucek, and P. Jezek Sequence similarities of protein kinase substrates and inhibitors with immunoglobulins and model immunoglobulin homologue: cell adhesion molecule from the living fossil sponge Geodia cydonium. Mapping of coherent database similarities and implications for evolution of CDR1 and hypermutation Folia Microbiol. 49 2004 219 246
169. N. Page, N. Schall, J.-M. Strub, M. Quinternet, O. Chaloin, M. Décossas, M.T. Cung, A. Van Dorsselaer, J.-P. Briand, and S. Muller The spliceosomal phosphopeptide P140 controls the lupus disease by interacting with the HSC70 protein and via a mechanism mediated by gamma delta T cells PLoS One 4 2009 e5273
170. J.J. Devlin, L.C. Panganiban, and P.E. Devlin Random peptide libraries: a source of specific protein binding molecules Science 249 1990 404 406
171. R. Schmitz, G. Baumann, and H. Gram Catalytic specificity of phosphotyrosine kinases Blk, Lyn, c-Src and Syk as assessed by phage display J. Mol. Biol. 260 1996 664 677
172. F. Fack, B. Hügle-Dörr, D. Song, I. Queitsch, G. Petersen, and E.K. Bautz Epitope mapping by phage display: random versus gene-fragment libraries J. Immunol. Methods 206 1997 43 52
173. M. Blüthner, C. Schäfer, C. Schneider, and F.A. Bautz Identification of major linear epitopes on the sp100 nuclear PBC autoantigen by the gene-fragment phage-display technology Autoimmunity 29 1999 33 42
174. S. Mandava, L. Makowski, S. Devarapalli, J. Uzubell, and D.J. Rodi RELIC-a bioinformatics server for combinatorial peptide analysis and identification of protein-ligand interaction sites Proteomics 4 2004 1439 1460
175. Y.X. Huang, Y.L. Bao, S.Y. Guo, Y. Wang, C.G. Zhou, and Y.X. Li Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis BMC Bioinform. 9 2008 Article ID 538
176. W.H. Chen, P.P. Sun, L. Lu, W.W. Guo, Y.X. Huang, and Z.Q. Ma MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries BMC Bioinform. 12 2011 Article ID 199
177. J. Huang, B. Ru, and P. Dai Bioinformatics resources and tools for phage display Molecules 16 2011 694 709
178. J. Huang, B. Ru, P. Zhu, F. Nie, J. Yang, X. Wang, P. Dai, H. Lin, F.-B. Guo, and N. Rao MimoDB 2.0: a mimotope database and beyond Nucleic Acids Res. 40 Database issue 2012 D271 D277
179. R.A. Johanson, A.R. Shaw, and M. Schlamowitz Evidence that the CH2 domain of IgG contains the recognition unit for binding by the fetal rabbit yolk sac membrane receptor J. Immunol. 126 1981 194 199
180. T. Thomsen, J.B. Moeller, A. Schlosser, G.L. Sorensen, S.K. Moestrup, N. Palaniyar, R. Wallis, J. Mollenhauer, and U. Holmskov The recognition unit of FIBCD1 organizes into a noncovalently linked tetrameric structure and uses a hydrophobic funnel (S1) for acetyl group recognition J. Biol. Chem. 285 2010 1229 1238
181. C. Gaboriaud, L. Gregory-Pauron, F. Teillet, N.M. Thielens, I. Bally, and G.J. Arlaud Structure and properties of the Ca(2+)-binding CUB domain, a widespread ligand-recognition unit involved in major biological functions Biochem. J. 439 2011 185 193
182. X. Qiu, J.S. Culp, A.G. DiLella, B. Hellmig, S.S. Hoog, C.A. Janson, W.W. Smith, and S.S. Abdel-Meguid Unique fold and active site in cytomegalovirus protease Nature 383 1996 275 279
183. T.M. Penning 3 Alpha-hydroxysteroid dehydrogenase: three dimensional structure and gene regulation J. Endocrinol. 150 Suppl. 1996 S175 S187
184. C. Cheng, P. Kussie, N. Pavletich, and S. Shuman Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases Cell 92 1998 841 850
185. P. Iengar, and C. Ramakrishnan Knowledge-based modeling of the serine protease triad into non-proteases Protein Eng. 12 1999 649 656
186. D. Hyndman, D.R. Bauman, V.V. Heredia, and T.M. Penning The aldo-keto reductase superfamily homepage Chem. Biol. Interact. 143/144 2003 621 631
187. U. Oppermann, C. Filling, M. Hult, N. Shafqat, X. Wua, M. Lindh, J. Shafqat, E. Nordling, Y. Kallberg, B. Persson, and H. Jornvall Short-chain dehydrogenases/reductases (SDR): the 2002 update Chem. Biol. Int. 143/144 2003 247 253
188. K. Vanommeslaeghe, F. De Proft, S. Loverix, D. Tourwé, and P. Geerlings Theoretical study revealing the functioning of a novel combination of catalytic motifs in histone deacetylase Bioorg. Med. Chem. 13 2005 3987 3992
189. E. Chovancová, J. Kosinski, J.M. Bujnicki, and J. Damborský Phylogenetic analysis of haloalkane dehalogenases Proteins 67 2007 305 316
190. R.G. Pearson Hard and soft acids and bases J. Am. Chem. Soc. 85 1963 3533 3539
191. R.G. Pearson Hard and soft acids and bases, HSAB, part 1: fundamental principles J. Chem. Educ. 45 1968 581 586
192. R.G. Pearson Hard and soft acids and bases, HSAB, part II: underlying theories J. Chem. Educ. 45 1968 643 648
193. A. Kotyk, and J. Horák Enzyme Kinetics 1977 Academia Prague
194. M. Meyer, G. Wohlfahrt, J. Knäblein, and D. Schomburg Aspects of the mechanism of catalysis of glucose oxidase: a docking, molecular mechanics and quantum chemical study J. Comput. Aided. Mol. Des. 12 1998 425 440
195. R.J.T. Houk, A. Monzingo, and E.V. Anslyn Electrophilic coordination catalysis: a summary of previous thought and a new angle of analysis Acc. Chem. Res. 41 2008 401 410
196. Z. Ke, S. Wang, D. Xie, and Y. Zhang Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4 J. Phys. Chem. B 113 2009 16705 16710
197. 5Arg catalytic motif in phosphoester hydrolysis Biochemistry 33 1994 15266 15270
198. C. Zhang, D. Zhou, S. Zheng, L. Liu, S. Tao, L. Yang, S. Hu, and Q. Feng A chymotrypsin-like serine protease cDNA involved in food protein digestion in the common cutworm, Spodoptera litura: cloning, characterization, developmental and induced expression patterns, and localization J. Insect Physiol. 56 2010 788 799
199. B. He, G. Cai, Y. Ni, Y. Li, H. Zong, and L. He Characterization and expression of a novel cystatin gene from Schistosoma japonicum Mol. Cell. Probes 25 2011 86 193
200. S. Hitaoka, M. Harada, T. Yoshida, and H. Chuman Correlation analyses on binding affinity of sialic acid analogues with influenza virus neuraminidase-1 using ab initio MO calculations on their complex structures J. Chem. Inf. Model. 50 2010 1796 1805
201. F. Tanaka, and C.F. Barbas A modular assembly strategy for improving the substrate specificity of small catalytic peptides J. Am. Chem. Soc. 124 2002 3510 3511
202. S. Ha, D. Walker, Y. Shi, and S. Walker The 1.9 Å crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis Protein Sci. 9 2000 1045 1052
203. G. Sanli, J.I. Dudley, and M. Blaber Structural biology of the aldo-keto reductase family of enzymes: catalysis and cofactor binding Cell. Biochem. Biophys. 38 2003 79 101
204. D. Koesling, M. Russwurm, E. Mergia, F. Mullershausen, and A. Friebe Nitric oxide-sensitive guanylyl cyclase: structure and regulation Neurochem. Int. 45 2004 813 819
205. A. Roeben, J.M. Plitzko, R. Körner, U.M. Böttcher, K. Siegers, M. Hayer-Hartl, and A. Bracher Structural basis for subunit assembly in UDP-glucose pyrophosphorylase from Saccharomyces cerevisiae J. Mol. Biol. 364 2006 551 560
206. H.M. Jackson, T. Kawahara, Y. Nisimoto, S.M. Smith, and J.D. Lambeth Nox4 B-loop creates an interface between the transmembrane and dehydrogenase domains J. Biol. Chem. 285 2010 10281 10290
207. V. Mishra, A. Kumar, V. Ali, T. Nozaki, K.Y. Zhang, and V. Bhakuni Glu-108 is essential for subunit assembly and dimer stability of D-phosphoglycerate dehydrogenase from Entamoeba histolytica Mol. Biochem. Parasitol. 181 2012 117 124
208. B.K. Ho, and D.A. Agard Probing the flexibility of large conformational changes in protein structures through local perturbations PLoS Comput. Biol. 5 2009 e1000343
209. N. Selevsek, S. Rival, A. Tholey, E. Heinzle, U. Heinz, L. Hemmingsen, and H.W. Adolph Zinc ion-induced domain organization in metallo-beta-lactamases: a flexible zinc arm for rapid metal ion transfer? J. Biol. Chem. 284 2009 16419 16431
210. A.G. Roberts, M.J. Cheesman, A. Primak, M.K. Bowman, W.M. Atkins, and A.E. Rettie Intramolecular heme ligation of the cytochrome P450 2C9 R108H mutant demonstrates pronounced conformational flexibility of the B-C loop region: implications for substrate binding Biochemistry 49 2010 8700 8708
211. H. Cha, E. Kopetzki, R. Huber, M. Lanzendörfer, and H. Brandstetter Structural basis of the adaptive molecular recognition by MMP9 J. Mol. Biol. 320 2002 1065 1079
212. C.M. Overall Molecular determinants of metalloproteinase substrate specificity: matrix metalloproteinase substrate binding domains, modules, and exosites Mol. Biotechnol. 22 2002 51 86
213. I.B. Rogozin, and M. Diaz Cutting edge: DGYW/WRCH is a better predictor of mutability at G: C bases in Ig hypermutation than the widely accepted RGYW/WRCY motif and probably reflects a two-step activation-induced cytidine deaminase-triggered process J. Immunol. 172 2004 3382 3384
214. M.L. Duquette, P. Pham, M.F. Goodman, and N. Maizels AID binds to transcription-induced structures in c-MYC that map to regions associated with translocation and hypermutation Oncogene 24 2005 5791 5798
215. K.A. Denessiouk, A.I. Denesyuk, J.V. Lehtonen, T. Korpela, and M.S. Johnson Common structural elements in the architecture of the cofactor-binding domains in unrelated families of pyridoxal phosphate-dependent enzymes Proteins 35 1999 250 261
216. C.-J. Tsai, A. del Sol, and R. Nussinov Allostery: absence of a change in shape does not imply that allostery is not at play J. Mol. Biol. 378 2008 1 11
217. A. Pandini, A. Fornili, F. Fraternali, and J. Kleinjung Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics FASEB J. 26 2012 868 881
218. J.P. Duneau, N. Garnier, and M. Genest Insight into signal transduction: structural alterations in transmembrane helices probed by multi-1 ns molecular dynamics simulations J. Biomol. Struct. Dyn. 15 1997 555 572
219. J. Seco, C. Ferrer-Costa, J.M. Campanera, R. Soliva, and X. Barril Allosteric regulation of PKCθ: understanding multistep phosphorylation and priming by ligands in AGC kinases Proteins 80 2012 269 280
220. A.P. Kornev, N.M. Haste, S.S. Taylor, and L.F. Ten Eyck Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism Proc. Natl. Acad. Sci. U. S. A. 103 2006 17783 17788
221. A.P. Kornev, S.S. Taylor, and L.F. Ten Eyck A helix scaffold for the assembly of active protein kinases Proc. Natl. Acad. Sci. U. S. A. 105 2008 14377 14382
222. R.E. Joseph, Q. Xie, and A.H. Andreotti Identification of an allosteric signaling network within Tec family kinases J. Mol. Biol. 403 2010 231 242
223. A. Bahr, J.D. Thompson, J.C. Thierry, and O. Poch BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations Nucleic Acids Res. 29 2001 323 326
224. M.K. Kalita, G. Ramasamy, S. Duraisamy, V.S. Chauhan, and D. Gupta ProtRepeatsDB: a database of amino acid repeats in genomes BMC Bioinform. 7 2006 Article ID 336
225. D.P. Depledge, R.P. Lower, and D.F. Smith RepSeq-a database of amino acid repeats present in lower eukaryotic pathogens BMC Bioinform. 8 2007 Article ID 122
226. T. Wei, J. Gong, F. Jamitzky, W.M. Heckl, R.W. Stark, and S.C. Rössle LRRML: a conformational database and an XML description of leucine-rich repeats (LRRs) BMC Struct. Biol. 8 2008 Article ID 47
227. V. Offord, T.J. Coffey, and D. Werling LRRfinder: a web application for the identification of leucine-rich repeats and an integrative Toll-like receptor database Dev. Comp. Immunol. 34 2010 1035 1041
228. P.P. Kuksa, and V. Pavlovic Efficient motif finding algorithms for large-alphabet inputs BMC Bioinform. 11 2010 Article ID S1
229. D.M. Standley, R. Yamashita, A.R. Kinjo, H. Toh, and H. Nakamura SeSAW: balancing sequence and structural information in protein functional mapping Bioinformatics 26 2010 1258 1259
230. A.S. Konagurthu, J.C. Whisstock, P.J. Stuckey, and A.M. Lesk MUSTANG: a multiple structural alignment algorithm Proteins 64 2006 559 574
231. C. Micheletti, and H. Orland MISTRAL: a tool for energy-based multiple structural alignment of proteins Bioinformatics 25 2009 2663 2669
232. A.S. Konagurthu, C.F. Reboul, J.W. Schmidberger, J.A. Irving, A.M. Lesk, P.J. Stuckey, J.C. Whisstock, and A.M. Buckle MUSTANG-MR structural sieving server: applications in protein structural analysis and crystallography PLoS One 5 2010 e10048
233. W.Y. Siu, N. Mamoulis, S.M. Yiu, and H.L. Chan A data-mining approach for multiple structural alignment of proteins Bioinformation 4 2010 366 370
234. D. Allorge, D. Bréant, J. Harlow, J. Chowdry, J.M. Lo-Guidice, D. Chevalier, C. Cauffiez, M. Lhermitte, F.E. Blaney, G.T. Tucker, F. Broly, and S.W. Ellis Functional analysis of CYP2D6.31 variant: homology modeling suggests possible disruption of redox partner interaction by Arg440His substitution Proteins 59 2005 339 346
235. Y.H. Zhou, Q.C. Zheng, Z.S. Li, Y. Zhang, M. Sun, C.C. Sun, D. Si, L. Cai, Y. Guo, and H. Zhou On the human CYP2C9*13 variant activity reduction: a molecular dynamics simulation and docking study Biochimie 88 2006 1457 1465
236. H. Banu, N. Renuka, and G. Vasanthakumar Reduced catalytic activity of human CYP2C9 natural alleles for gliclazide: molecular dynamics simulation and docking studies Biochimie 93 2011 1028 1036
237. Y. Zhou, S. Wang, and Y. Zhang Catalytic reaction mechanism of acetylcholinesterase determined by Born-Oppenheimer ab initio QM/MM molecular dynamics simulations J. Phys. Chem. B 114 2010 8817 8825
238. P.R. Markwick, and J.A. McCammon Studying functional dynamics in bio-molecules using accelerated molecular dynamics Phys. Chem. Chem. Phys. 13 2011 20053 20065
239. J. Yang Molecular modeling of human hepatocyte PKA (cAMP-dependent protein kinase type-II) and its structure analysis Protein Pept. Lett. 17 2010 646 659
240. A.P. Eichenberger, L.J. Smith, and V.F. van Gunsteren Ester-linked hen egg white lysozyme shows a compact fold in a molecular dynamics simulation - possible causes and sensitivity of experimentally observable quantities to structural changes maintaining this compact fold FEBS J. 279 2012 299 315
241. H. Vankayalapati, D.J. Bearss, J.W. Saldanha, R.M. Muñoz, S. Rojanala, D.D. Von Hoff, and D. Mahadevan Targeting aurora2 kinase in oncogenesis: a structural bioinformatics approach to target validation and rational drug design Mol. Cancer Ther. 2 2003 283 294
242. J. Caballero, J.H. Alzate-Morales, and A. Vergara-Jaque Investigation of the differences in activity between hydroxycycloalkyl N1 substituted pyrazole derivatives as inhibitors of B-Raf kinase by using docking, molecular dynamics, QM/MM, and fragment-based de novo design: study of binding mode of diastereomer compounds J. Chem. Inf. Model. 51 2011 2920 2931
243. J.D. Durrant, and J.A. McCammon Molecular dynamics simulations and drug discovery BMC Biol. 9 2011 Article ID 71
244. R.E. Amaro, A. Sethi, R.S. Myers, V.J. Davisson, and Z.A. Luthey-Schulten A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase Biochemistry 46 2007 2156 2173