XPyder: A PyMOL plugin to analyze coupled residues and their networks in protein structures.

Journal of Chemical Information and Modeling

Volumn 52, Issue 7, 2012, Pages 1865-1874

  Pasi, Marco ^a,b   Tiberti, Matteo ^a   Arrigoni, Alberto ^a   Papaleo, Elena ^a,c  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b UNIVERSITÉ LYON 1   (France)

^c UNIVERSITY OF COPENHAGEN   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR GRAPHICS; OPEN SOURCE SOFTWARE; OPEN SYSTEMS;

COMMUNICATION ROUTE; CONFORMATIONAL ENSEMBLE; CROSS CORRELATION MATRICES; INTERMOLECULAR INTERACTIONS; PROTEIN DYNAMICS; PROTEIN RESIDUES; PROTEIN STRUCTURES; VERSATILE METHODS;

PROTEINS;

PROTEIN;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; PROTEIN CONFORMATION;

MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; USER-COMPUTER INTERFACE;

EID: 84864205788     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci300213c     Document Type: Article

References (88)

1. Rueda, M.; Ferrer-Costa, C.; Meyer, T.; Perez, A.; Camps, J.; Hospital, A.; Gelpi, J. L.; Orozco, M. A consensus view of protein dynamics Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801 (Pubitemid 46154690)
2. Markwick, P. R. L.; Bouvignies, G.; Salmon, L.; McCammon, J. A.; Nilges, M.; Blackledge, M. Toward a unified representation of protein structural dynamics in solution J. Am. Chem. Soc. 2009, 131, 16968-16975
3. Lindorff-Larsen, K.; Best, R. B.; DePristo, M. A.; Dobson, C. M.; Vendruscolo, M. Simultaneous determination of protein structure and dynamics Nature 2005, 433, 128-132
4. Teilum, K.; Olsen, J. G.; Kragelund, B. B. Functional aspects of protein flexibility Cell. Mol. Life Sci. 2009, 66, 2231-2247
5. Maguid, S.; Fernandez-Alberti, S.; Echave, J. Evolutionary conservation of protein vibrational dynamics Gene 2008, 422, 7-13
6. Marcos, E.; Crehuet, R.; Bahar, I. On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK, the paradigm PLoS Comput. Biol. 2010, 6, 14
7. Hollup, S. M.; Fuglebakk, E.; Taylor, W. R.; Reuter, N. Exploring the factors determining the dynamics of different protein folds Protein Sci. 2011, 20, 197-209
8. Law, A. B.; Fuentes, E. J.; Lee, A. L. Conservation of side-chain dynamics within a protein family J. Am. Chem. Soc. 2009, 131, 6322-6323
9. Maguid, S.; Fernandez-Alberti, S.; Ferrelli, L.; Echave, J. Exploring the common dynamics of homologous proteins. Application to the globin family Biophys. J. 2005, 89, 3-13 (Pubitemid 41098257)
10. Raimondi, F.; Orozco, M.; Fanelli, F. Deciphering the deformation modes associated with function retention and specialization in members of the Ras superfamily Structure 2010, 18, 402-14
11. Angelova, K.; Felline, A.; Lee, M.; Patel, M.; Puett, D.; Fanelli, F. Conserved amino acids participate in the structure networks deputed to intramolecular communication in the lutropin receptor Cell. Mol. Life Sci. 2011, 68, 1227-1239
12. Hongbo, S.; Feng, X.; Hairong, H.; Feifei, W.; Qi, W.; Qiang, H.; Honghai, W. Coevolving residues of (beta/alpha)/sub 8/-barrel proteins play roles in stabilizing active site architecture and coordinating protein dynamics J. Struct. Biol. 2008, 164, 281-92
13. Kornev, A. P.; Taylor, S. S. Defining the conserved internal architecture of a protein kinase Biochim. Biophys. Acta 2010, 1804, 440-444
14. Bocahut, A.; Bernad, S.; Sebban, P.; Sacquin-Mora, S. Frontier residues lining globin internal cavities present specific mechanical properties J. Am. Chem. Soc. 2011, 133, 8753-8761
15. Echave, J.; Fernandez, F. M. A perturbative view of protein structural variation Proteins 2010, 78, 173-180
16. Zheng, W. J.; Brooks, B. R.; Thirumalai, D. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 7664-7669
17. Zheng, W.; Brooks, B. R.; Thirumalai, D. Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations Biophys. J. 2007, 93, 2289-2299 (Pubitemid 47511128)
18. Papaleo, E.; Pasi, M.; Riccardi, L.; Sambi, I.; Fantucci, P.; De Gioia, L. Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases FEBS Lett. 2008, 582, 1008-1018
19. Wrabl, J. O.; Gu, J. N.; Liu, T.; Schrank, T. P.; Whitten, S. T.; Hilser, V. J. The role of protein conformational fluctuations in allostery, function, and evolution Biophys. Chem. 2011, 159, 129-141
20. Moorthy, B. S.; Anand, G. S. Multistate allostery in response regulators: Phosphorylation and mutagenesis activate RegA via alternate modes J. Mol. Biol. 2012, 417, 468-487
21. Papaleo, E.; Renzetti, G.; Tiberti, M. Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation PLoS One 2012, 7, e35686
22. Papaleo, E.; Pasi, M.; Tiberti, M.; De Gioia, L. Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: Insights into distal effects induced by the mutations PLoS One 2011, 6, e24214
23. Glembo, T. J.; Farrell, D. W.; Gerek, Z. N.; Thorpe, M. F.; Ozkan, S. B. Collective dynamics differentiates functional divergence in protein evolution PLoS Comput. Biol. 2012, 8, e1002428
24. Dastidar, S. G.; Raghunathan, D.; Nicholson, J.; Hupp, T. R.; Lane, D. P.; Verma, C. S. Chemical states of the N-terminal ″lid″ of MDM2 regulate p53 binding simulations reveal complexities of modulation Cell Cycle 2011, 10, 82-89
25. Lovera, S.; Sutto, L.; Boubeva, R.; Scapozza, L.; Dolker, N.; Gervasio, F. L. The different flexibility of c-Src and c-Abl kinases regulates the accessibility of a druggable inactive conformation J. Am. Chem. Soc. 2012, 134, 2496-2499
26. Karplus, M.; Kuriyan, J. Molecular dynamics and protein function Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 6679-6685 (Pubitemid 40675376)
27. Klepeis, J. L.; Lindorff-Larsen, K.; Dror, R. O.; Shaw, D. E. Long-timescale molecular dynamics simulations of protein structure and function Curr. Op. Struct. Biol. 2009, 19, 120-127
28. Dodson, G. G.; Lane, D. P.; Verma, C. S. Molecular simulations of protein dynamics: New windows on mechanisms in biology Embo Rep. 2008, 9, 144-150 (Pubitemid 351223451)
29. Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; shaw, D. E. Improved side-chain torsion potentials for the Amber ff99SB protein force field Proteins: Struct., Funct., Bioinf. 2010, 78, 1950-1958
30. Lindorff-Larsen, K.; Maragakis, P.; Piana, S.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. Systematic validation of protein force fields against experimental data PLoS One 2012, 7, e32131
31. Boede, C.; Kovacs, I. A.; Szalay, M. S.; Palotai, R.; Korcsmaros, T.; Csermely, P. Network analysis of protein dynamics Febs Lett. 2007, 581, 2776-2782 (Pubitemid 46874391)
32. Csermely, P.; Palotai, R.; Nussinov, R. Induced fit, conformational selection and independent dynamic segments: an extended view of binding events Trends Biochem. Sci. 2010, 35, 539-546
33. Vishveshwara, S.; Ghosh, A.; Hansia, P. Intra and inter-molecular communications through protein structure network Curr. Prot. Pept. Sci. 2009, 10, 146-160
34. Estabrook, R. A.; Luo, J.; Purdy, M. M.; Sharma, V.; Weakliem, P.; Bruice, T. C.; Reich, N. O. Statistical colevolution analysis and molecular dynamics: Identification of amino acid pairs essential for catalysis Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 994-999 (Pubitemid 40170714)
35. Vijayabaskar, M. S.; Vishveshwara, S. Interaction energy based protein structure networks Biophys. J. 2010, 99, 3704-3715
36. Morra, G.; Verkhivker, G.; Colombo, G. Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full-length dimer PLoS Comput. Biol. 2009, 5, e1000323
37. Stacklies, W.; Xia, F.; Grater, F. Dynamic allostery in the methionine repressor revealed by force distribution analysis PLoS Comput. Biol. 2009, 5, e1000574
38. Ghosh, A.; Vishveshwara, S. A study of communication pathways in methionyl-tRNA synthetase by molecular dynamics simulations and structure network analysis Proc. Natl. Acad.Sci. USA. 2007, 104, 15711-15716 (Pubitemid 350035365)
39. Fanelli, F.; Felline, A. Dimerization and ligand binding affect the structure network of A(2A) adenosine receptor Biochim. Biophys. Acta 2011, 1808, 1256-1266
40. Uversky, V. N.; Roman, A.; Oldfield, C. J.; Dunker, A. K. Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs J. Prot. Res. 2006, 5, 1829-1842 (Pubitemid 44232696)
41. Armenta-Medina, D.; Perez-Rueda, E.; Segovia, L. Identification of functional motions in the adenylate kinase (ADK) protein family by computational hybrid approaches Proteins: Struct., Funct., Bioinf. 2011, 79, 1662-1671
42. Ackerman, S. H.; Gatti, D. L. The contribution of coevolving residues to the stability of KDO8P synthase PLoS One 2011, 6, e17459
43. Silvestre-Ryan, J.; Lin, Y. C.; Chu, J. W. "Fluctuograms" reveal the intermittent intra-protein communication in subtilisin Carlsberg and correlate mechanical coupling with co-evolution PLoS Comput. Biol. 2011, 7, e1002023
44. Tsai, C. J.; del Sol, A.; Nussinov, R. Allostery: Absence of a change in shape does not imply that allostery is not at play J. Mol. Biol. 2008, 378, 1-11
45. Gunasekaran, K.; Ma, B. Y.; Nussinov, R. Is allostery an intrinsic property of all dynamic proteins? Proteins: Struct., Funct., Bioinf. 2004, 57, 433-443 (Pubitemid 39390799)
46. Cui, Q.; Karplus, M. Allostery and cooperativity revisited Protein Sci. 2008, 17, 1295-1307
47. Swain, J. F.; Gierasch, L. M. The changing landscape of protein allostery Curr. Op. Struct. Biol. 2006, 16, 102-108 (Pubitemid 43221878)
48. Hunenberger, P. H.; Mark, A. E.; Vangunsteren, W. F. Fluctuation and cross-correlation analysis of protein motions observed in nanosecond molecular dynamics simulations J. Mol. Biol. 1995, 252, 492-503
49. Bhardwaj, N.; Abyzov, A.; Clarke, D.; Shou, C.; Gerstein, M. B. Integration of protein motions with molecular networks reveals different mechanisms for permanent and transient interactions Protein Sci. 2011, 20, 1745-1754
50. Doncheva, N. T.; Klein, K.; Domingues, F. S.; Albrecht, M. Analyzing and visualizing residue networks of protein structures Trends Biochem. Sci. 2011, 36, 179-182
51. Doncheva, N. T.; Assenov, Y.; Domingues, F. S.; Albrecht, M. Topological analysis and interactive visualization of biological networks and protein structures Nature Protocols 2012, 7, 670-685
52. Martin, A. J.; Vidotto, M.; Boscariol, F.; Di Domenico, T.; Walsh, I.; Tosatto, S. C. RING: Networking interacting residues, evolutionary information and energetics in protein structures Bioinformatics 2011, 27, 2003-2005
53. Ahmad, S.; Keskin, O.; Mizuguchi, K.; Sarai, A.; Nussinov, R. CCRXP: Exploring clusters of conserved residues in protein structures Nucleic Acids Res. 2010, 38, W398-W401
54. Durrant, J. D.; McCammon, J. A. HBonanza: A computer algorithm for molecular-dynamics-trajectory hydrogen-bond analysis J. Mol. Graph. Modell. 2011, 31, 5-9
55. V., M. S.; Vidya, N.; Saraswathi, V. GraProStr - Graphs of protein structures: A tool for constructing the graphs and generating graph parameters for protein structures Open Bioinf. J. 2011, 5, 53-58
56. Tiberti, M.; Papaleo, E. Dynamic properties of extremophilic subtilisin-like serine-proteases J. Struct. Biol. 2011, 174, 69-83
57. Arrigoni, A.; Grillo, B.; Vitriolo, A.; Gioia, L. D.; Papaleo, E. C-terminal acidic domain of ubiquitin-conjugating enzymes: A multi-functional conserved intrinsically disordered domain in family 3 of E2 enzymes J. Struct. Biol. 2012, 178, 245-259
58. Sanner, M. F. Python: A programming language for software integration and development J. Mol. Graph. Modell. 1999, 17, 57-61 (Pubitemid 30029318)
59. Vehlow, C.; Stehr, H.; Winkelmann, M.; Duarte, J. M.; Petzold, L.; Dinse, J.; Lappe, M. CMView: Interactive contact map visualization and analysis Bioinformatics 2011, 27, 1573-1574
60. Lua, R. C.; Lichtarge, O. PyETV: A PyMOL evolutionary trace viewer to analyze functional site predictions in protein complexes Bioinformatics 2010, 26, 2981-2982
61. Rother, K.; Hildebrand, P. W.; Goede, A.; Gruening, B.; Preissner, R. Voronoia: Analyzing packing in protein structures Nucleic Acids Res. 2009, 37, D393-D395
62. Petrek, M.; Otyepka, M.; Banas, P.; Kosinova, P.; Koca, J.; Damborsky, J. CAVER: A new tool to explore routes from protein clefts, pockets and cavities BMC Bioinf. 2006, 7, 316
63. Hagelueken, G.; Ward, R.; Naismith, J. H.; Schiemann, O. MtsslWizard: In silico spin-labeling and generation of distance distributions in PyMOL Appl. Magn. Reson. 2012, 42, 377-391
64. Dantzer, J.; Moad, C.; Heiland, R.; Mooney, S. MutDB services: Interactive structural analysis of mutation data Nucleic Acids Res. 2005, 33, W311-W314
65. Ordog, R. PyDeT, a PyMOL plug-in for visualizing geometric concepts around proteins Bioinformation 2008, 2, 346-347
66. Bramucci, E.; Paiardini, A.; Bossa, F.; Pascarella, S. PyMod: Sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL Bmc Bioinf. 2012, 13 (Suppl 4) S2
67. Bakan, A.; Meireles, L. M.; Bahar, I. ProDy: Protein dynamics inferred from theory and experiments Bioinformatics 2011, 27, 1575-1577
68. Cabrera, á.; Gil-Redondo, R.; Perona, A.; Gago, F.; Morreale, A. VSDMIP 1.5: An automated structure- and ligand-based virtual screening platform with a PyMOL graphical user interface J. Comput.-Aided Mol. Des. 2011, 25, 813-24
69. Lill, M. A.; Danielson, M. L. Computer-aided drug design platform using PyMOL J. Comput.-Aided Mol. Des. 2011, 25, 13-19
70. Seeliger, D.; de Groot, B. L. Ligand docking and binding site analysis with PyMOL and Autodock/Vina J. Comput.-Aided Mol. Des. 2010, 24, 417-422
71. Hodis, E.; Schreiber, G.; Rother, K.; Sussman, J. L. eMovie: A storyboard-based tool for making molecular movies Trends Biochem. Sci. 2007, 32, 199-204 (Pubitemid 46694333)
72. Baugh, E. H.; Lyskov, S.; Weitzner, B. D.; Gray, J. J. Real-Time PyMOL visualization for Rosetta and PyRosetta PLoS One 2011, 6, 5
73. Lange, O. F.; Grubmuller, H. Generalized correlation for biomolecular dynamics Proteins: Struct., Funct., Bioinf. 2006, 62, 1053-1061 (Pubitemid 43364168)
74. Camps, J.; Carrillo, O.; Emperador, A.; Orellana, L.; Hospital, A.; Rueda, M.; Cicin-Sain, D.; D'Abramo, M.; Gelpi, J. L.; Orozco, M. FlexServ: An integrated tool for the analysis of protein flexibility Bioinformatics 2009, 25, 1709-1710
75. Cormen, T. H.; Leiserson, C. E.; Rivest, R. L.; Clifford, S. Introduction to Algorithms, 3 rd ed.; 2009; Vol. 1, p 1292.
76. Brinda, K. V.; Vishveshwara, S. A network representation of protein structures: Implications for protein stability Biophys. J. 2005, 89, 4159-4170 (Pubitemid 41725636)
77. D'Amico, S.; Gerday, C.; Feller, G. Temperature adaptation of proteins: Engineering mesophilic-like activity and stability in a cold-adapted alpha-amylase J. Mol. Biol. 2003, 332, 981-988 (Pubitemid 37108792)
78. Zhang, Z. M.; Zheng, B. S.; Wang, Y. P.; Chen, Y. Q.; Manco, G.; Feng, Y. The conserved N-terminal helix of acylpeptide hydrolase from archaeon Aeropyrum pernix K1 is important for its hyperthermophilic activity Biochim. Biophys. Acta 2008, 1784, 1176-1183
79. Oliphant, T. E. Guide to NumPy; Brigham Young University: Provo, UT, 2006.
80. Seeber, M.; Felline, A.; Raimondi, F.; Muff, S.; Friedman, R.; Rao, F.; Caflisch, A.; Fanelli, F. Wordom: A user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces J. Comput. Chem. 2011, 32, 1183-1194
81. Theobald, D. L.; Wuttke, D. S. Accurate structural correlations from maximum likelihood superpositions PLoS Comput. Biol. 2008, 4, e43
82. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22, 2577-2637
83. Michelle, C.; Vourc'h, P.; Mignon, L.; Andres, C. R. What was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor? J. Mol. Evol. 2009, 68, 616-628
84. Papaleo, E.; Lindorff-Larsen, K.; De Gioia, L. Paths of long-range communication in the E2 enzymes of family 3: A molecular dynamics investigation, Phys. Chem. Chem. Phys., DOI: 10.1039/C2CP41224A
85. Chennubhotla, C.; Bahar, I. Signal propagation in proteins and relation to equilibrium fluctuations PLoS Comput. Biol. 2007, 3, 1716-1726 (Pubitemid 47502976)
86. Sacquin-Mora, S.; Lavery, R. Investigating the local flexibility of functional residues in hemoproteins Biophys. J. 2006, 90, 2706-2717
87. Park, K.; Vendruscolo, M.; Domany, E. Toward an energy function for the contact map representation of proteins Proteins: Struct., Funct., Bioinf. 2000, 40, 237-248 (Pubitemid 30413627)
88. Caprara, A.; Carr, R.; Istrail, S.; Lancia, G.; Walenz, B. 1001 optimal PDB structure alignments: Integer programming methods for finding the maximum contact map overlap J. Comput. Biol. 2004, 11, 27-52 (Pubitemid 38429362)