PyInteraph: A framework for the analysis of interaction networks in structural ensembles of proteins

Journal of Chemical Information and Modeling

Volumn 54, Issue 5, 2014, Pages 1537-1551

  Tiberti, Matteo ^a   Invernizzi, Gaetano ^b   Lambrughi, Matteo ^a   Inbar, Yuval ^c   Schreiber, Gideon ^c   Papaleo, Elena ^b  

^a UNIVERSITY OF MILANO BICOCCA   (Italy)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

GRAPH THEORY; HYDROGEN BONDS; HYDROPHOBICITY; KNOWLEDGE BASED SYSTEMS; MOLECULAR DYNAMICS; OPEN SOURCE SOFTWARE; OPEN SYSTEMS; PROTEINS;

BINARY INTERACTIONS; DIFFERENT CLASS; HYDROPHOBIC INTERACTIONS; INTERACTION ENERGIES; INTERACTION GRAPHS; INTERACTION NETWORKS; INTERMOLECULAR INTERACTIONS; SOFTWARE CAPABILITY;

STRUCTURAL ANALYSIS;

LIGAND; PROTEIN;

BIOLOGY; CHEMICAL PHENOMENA; CHEMISTRY; COMPUTER PROGRAM; HUMAN; HYDROGEN BOND; METABOLISM; MOLECULAR DYNAMICS; PROCEDURES; PROTEIN PROTEIN INTERACTION; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS;

COMPUTATIONAL BIOLOGY; HUMANS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIGANDS; MOLECULAR DYNAMICS SIMULATION; PROTEIN INTERACTION MAPS; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE; THERMODYNAMICS;

EID: 84901593833     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400639r     Document Type: Article

References (73)

1. Csermely, P.; Korcsmaros, T.; Kiss, H. J. M.; London, G.; Nussinov, R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review Pharmacol. Theor. 2013, 138, 333-408
2. Böde, C.; Kovács, I. A.; Szalay, M. S.; Palotai, R.; Korcsmáros, T.; Csermely, P. Network analysis of protein dynamics FEBS Lett. 2007, 581, 2776-2782
3. Vishveshwara, S.; Ghosh, A.; Hansia, P. Intra and inter-molecular communications through protein structure network Curr. Protein Pept. Sci. 2009, 10, 146-160
4. Atilgan, C.; Okan, O. B.; Atilgan, A. R. Network-based models as tools hinting at nonevident protein functionality Annu. Rev. Biophys. 2012, 41, 205-225
5. Rahat, O.; Alon, U.; Levy, Y.; Schreiber, G. Understanding hydrogen-bond patterns in proteins using network motifs Bioinformatics 2009, 25, 2921-2928
6. Vijayabaskar, M. S.; Vishveshwara, S. Interaction energy based protein structure networks Biophys. J. 2010, 99, 3704-3715
7. Vijayabaskar, M. S.; Vishveshwara, S. Insights into the fold organization of TIM barrel from interaction energy based structure networks PLoS Comput. Biol. 2012, 8, e1002505
8. Scarabelli, G.; Morra, G.; Colombo, G. Predicting interaction sites from the energetics of isolated proteins: a new approach to epitope mapping Biophys. J. 2010, 98, 1966-1975
9. Bhattacharyya, M.; Bhat, C. R.; Vishveshwara, S. An automated approah to network features of protein structure ensembles Protein Sci. 2013, 22, 1399-1416
10. Sengupta, D.; Kundu, S. Role of long- and short-range hydrophobic, hydrophilic and charged residues contact network in protein's structural organization BMC Bioinf. 2012, 13, 142
11. Aftabuddin, M.; Kundu, S. Hydrophobic, hydrophilic and charged amino acid networks within protein Biophys. J. 2007, 93, 225-231
12. Atilgan, A. R.; Akan, P.; Baysal, C. Small-world communication of residues and significance for protein dynamics Biophys. J. 2004, 86, 85-91
13. Vendruscolo, M.; Dokholyan, N.; Paci, E.; Karplus, M. Small-world view of the amino acids that play a key role in protein folding Phys. Rev. E 2002, 65, 1-4
14. Estrada, E. Universitality in protein residue networks Biophys. J. 2010, 98, 890-900
15. 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. U. S. A. 2007, 104, 15711-15716
16. Daily, M. D.; Upadhyaya, T. J.; Gray, J. J. Contact rearrangements form coupled networks from local motions in allosteric proteins Proteins 2008, 71, 455-466
17. Meireles, L.; Gur, M.; Bakan, A.; Bahar, I. Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins Protein Sci. 2011, 20, 1645-1658
18. Martin, A. J. M.; 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
19. Doncheva, N. T.; Klein, K.; Domingues, F. S.; Albrecht, M. Analyzing and visualizing residue networks of protein strucutres Trends Biochem. Sci. 2011, 36, 179-182
20. Vijayabaskar, M. S.; Niranjan, V.; Vishveshwara, S. GraProtStr-Graphs of protein structures: a tool for constructing the graphs and generating graph parameters for protein structures Open Bioinf. J. 2011, 53-58
21. Goncearenco, A.; Mitternacht, S.; Yong, T.; Eisenhaber, B.; Eisenhaber, F.; Berezovsky, I. N. SPACER: server for predicting allosteri communication and effects of regulation Nucleic Acids Res. 2013, 41, W266-W272
22. Boehr, D. D.; Nussinov, R.; Wright, P. E. The role of dynamic conformational ensembles in biomolecular recognition Nat. Chem. Biol. 2009, 5, 789-796
23. Vendruscolo, M. Determination of conformationally heterogeneous states of proteins Curr. Opin. Struct. Biol. 2007, 17, 15-20
24. Barrett, P. J.; Chen, J.; Cho, M.-K.; Kim, J.-H.; Lu, Z.; Mathew, S.; Peng, D.; Song, Y.; Van Horn, W. D.; Zhuang, T.; Sonnichsen, F. D.; Sanders, C. R. The quiet renaissance of protein nuclear magnetic resonance Biochemistry 2013, 1303-1320
25. Manley, G.; Loria, J. P. NMR insights into protein allostery Arch. Biochem. Biophys. 2012, 519, 223-231
26. Tzeng, S.-R.; Kalodimos, C. G. Protein dynamics and allostery: an NMR view Curr. Opin. Struct. Biol. 2011, 21, 62-67
27. Brüschweiler, S.; Schanda, P.; Kloiber, K.; Brutscher, B.; Kontaxis, G.; Konrat, R.; Tollinger, M. Direct observation of the dynamic process underlying allosteric signal transmission J. Am. Chem. Soc. 2009, 131, 3063-3068
28. Klepeis, J. L.; Lindorff-Larsen, K.; Dror, R. O.; Shaw, D. E. Long-timescale molecular dynamics simulations of protein structure and function Curr. Opin. Struct. Biol. 2009, 19, 120-127
29. Fenwick, R. B.; Esteban-Martín, S.; Salvatella, X. Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles Eur. Biophys. J. 2011, 40, 1339-1355
30. Esteban-Martín, S.; Bryn Fenwick, R.; Salvatella, X. Synergistic use of NMR and MD simulations to study the structural heterogeneity of proteins Wiley Interdiscip. Rev. Comput. Mol. Sci. 2012, 2, 466-478
31. Selvaratnam, R.; Chowdhury, S.; VanSchouwen, B.; Melacini, G. Mapping allostery through the covariance analysis of NMR chemical shifts Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 6133-6138
32. Short, T.; Alzapiedi, L.; Brüschweiler, R.; Snyder, D. A covariance NMR toolbox for MATLAB and OCTAVE J. Magn. Reson. 2011, 209, 75-78
33. Van den Bedem, H.; Bhabha, G.; Yang, K.; Wright, P. E.; Fraser, J. S. Automated identification of functional dynamics contact networks from X-ray crystallography Nat. Methods 2013, 10, 896-902
34. Pandini, A.; Fornili, A.; Fraternali, F.; Kleinjung, J. Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics FASEB J. 2012, 26, 868-881
35. Chiappori, F.; Merelli, I.; Colombo, G.; Milanesi, L.; Morra, G. Molecular mechanism of allosteric communication in Hsp70 revealed by molecular dynamics simulations PLoS Comput. Biol. 2012, 8, e1002844
36. Laine, E.; Auclair, C.; Tchertanov, L. Allosteric communication across the native and mutated KIT receptor tyrosine kinase PLoS Comput. Biol. 2012, 8, e1002661
37. Mariani, S.; Dell'Orco, D.; Felline, A.; Raimondi, F.; Fanelli, F. Network and atomistic simulations unveil the structural determinants of mutations linked to retinal diseases PLoS Comput. Biol. 2013, 9, e1003207
38. Raimondi, F.; Felline, A.; Seeber, M.; Mariani, S.; Fanelli, F. A mixed protein structure network and elastic network model approach to predict the structural communication in biomolecular systems: the PDZ2 domain from tyrosine phosphatase 1E as a case study J. Chem. Theory Comput. 2013, 9, 2504-2518
39. Blacklock, K.; Verkhivker, G. M. Differential modulation of functional dynamics and allosteric interactions in the Hsp90-cochaperone complexes with p23 and Aha1: a computational study PLoS One 2013, 8, e71936
40. Papaleo, E.; Renzetti, G.; Tiberti, M. Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation PLoS One 2012, 7, e35686
41. 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. 2012, 14, 12515-12525
42. Stacklies, W.; Xia, F.; Gräter, F. Dynamic allostery in the methionine repressor revealed by force distribution analysis PLoS Comput. Biol. 2009, 5, e1000574
43. Pandini, A.; Fornili, A.; Fraternali, F.; Kleinjung, J. GSATools: analysis of allosteric communication and functional local motions using a structural alphabet Bioinformatics 2013, 29, 2053-2055
44. 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
45. Michaud-Agrawal, N.; Denning, E. J.; Woolf, T. B.; Beckstein, O. MDAnalysis: a toolkit for the analysis of molecular dynamics simulations J. Comput. Chem. 2011, 2319-2327
46. Potapov, V.; Cohen, M.; Inbar, Y.; Schreiber, G. Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions BMC Bioinf. 2010, 11, 374
47. Cohen, M.; Potapov, V.; Schreiber, G. Four distances between pairs of amino acids provide a precise description of their interaction PLoS Comput. Biol. 2009, 5, e1000470
48. Pasi, M.; Tiberti, M.; Arrigoni, A.; Papaleo, E. xPyder: a PyMOL plugin to analyze coupled residues and their networks in protein structures J. Chem. Inf. Model. 2012, 279, 1-6
49. Cook, B. W.; Shaw, G. S. Architecture of the catalytic HPN motif is conserved in all E2 conjugation enzymes Biochem. J. 2012, 445, 167-174
50. Cañadillas, J. M. P.; Tidow, H.; Freund, S. M. V; Rutherford, T. J.; Ang, H. C.; Fersht, A. R. Solution strucutre of p53 core domain: structural basis for its instability Proc. Natl. Acad. Sci. U. S. A. 2006, 103, 2109-2114
51. Invernizzi, G.; Lambrughi, M.; Regonesi, M. E.; Tortora, P.; Papaleo, E. The conformational ensemble of the disordered and aggregation-protective 182-291 region of ataxin-3 Biochim. Biophys. Acta 2013, 1830, 5236-5247
52. Zhang, Z.; Zheng, B.; Wang, Y.; Chen, Y.; 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
53. Harmat, V.; Domokos, K.; Menyhárd, D. K.; Palló, A.; Szeltner, Z.; Szamosi, I.; Beke-Somfai, T.; Náray-Szabó, G.; Polgár, L. Structure and catalysis of acylaminoacyl peptidase: closed and open subunits of a dimer oligopeptidase J. Biol. Chem. 2011, 286, 1987-1998
54. Ghosh, A.; Brinda, K. V.; Vishveshwara, S. Dynamics of lysozyme structure network: probing the process of unfolding Biophys. J. 2007, 92, 2523-2535
55. Dokholyan, N. V.; Shakhnovich, B.; Shakhnovich, E. I. Expanding protein universe and its origin from the biological Big Bang Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 14132-14136
56. Brinda, K. V.; Vishveshwara, S. A network representation of protein structures: implications for protein stability Biophys. J. 2005, 89, 4159-4170
57. Papaleo, E.; Renzetti, G.; Invernizzi, G.; Asgeirsson, B. Dynamics fingerprint and inherent asymmetric flexibility of a cold-adated homodimeric enzyme. A case study of the Vibrio alkaline phosphatase Biochim. Biophys. Acta 2013, 1830, 2970-2980
58. Papaleo, E.; Casiraghi, N.; Arrigoni, A.; Vanoni, M.; Coccetti, P.; De Gioia, L. Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade PLoS One 2012, 7, e40786
59. Cho, Y.; Gorina, S.; Jeffrey, P. D.; Pavletich, N. P. Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations Science 1994, 265, 346-355
60. Hess, B.; Bekker, H.; Berendsen, H.; Fraaije, J. LINCS: a linear constraint solver for molecular simulations J. Comput. Chem. 1997, 18, 1463-1472
61. Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: an N log (N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
62. Munson, M.; Balasubramanian, S.; Fleming, K. G.; Nagi, A. D.; O'Brien, R.; Sturtevant, J. M.; Regan, L. What makes a protein a protein? Hydrophobic core designs that specify stability and structural properties Protein Sci. 1996, 5, 1584-1593
63. Bullock, A. N.; Fersht, A. R. Rescuing the function of mutant p53 Nat. Rev. Cancer 2001, 1, 68-76
64. Ye, Y.; Rape, M. Building ubiquitin chains: E2 enzymes at work Nat. Rev. Mol. Cell Biol. 2009, 10, 755-764
65. Kumar, S.; Nussinov, R. Relationship between ion pair geometries and electrostatic strenghts in proteins Biophys. J. 2002, 83, 1595-1612
66. Kumar, S.; Nussinov, R. Close-range electrostatic interactions in proteins ChemBioChem 2002, 3, 604-617
67. Siddiqui, K. S.; Cavicchioli, R. Cold-adapted enzymes Annu. Rev. Biochem. 2006, 75, 403-433
68. Dyson, H. J.; Wright, P. E. Intrinsically unstructured proteins and their functions Nat. Rev. Mol. Cell Biol. 2005, 6, 197-208
69. Tsai, C. J.; Lin, S. L.; Wolfson, H. J.; Nussinov, R. Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect Protein Sci. 1997, 6, 53-64
70. Narayanan, A.; Jacobson, M. P. Computational studies of protein regulation by post-translational phosphorylation Curr. Opin. Struct. Biol. 2009, 19, 156-163
71. Coccetti, P.; Tripodi, F.; Tedeschi, G.; Nonnis, S.; Marin, O.; Fantinato, S.; Cirulli, C.; Vanoni, M.; Alberghina, L. The CK2 phosphorylation of catalytic domain of Cdc34 modulates its activity at the G1 to S transition in Saccharomyces cerevisiae Cell Cycle 2008, 7, 1391-1401
72. Wei, C.-L.; Wu, Q.; Vega, V. B.; Chiu, K. P.; Ng, P.; Zhang, T.; Shahab, A.; Yong, H. C.; Fu, Y.; Weng, Z.; Liu, J.; Zhao, X. D.; Chew, J.-L.; Lee, Y. L.; Kuznetsov, V. A.; Sung, W.-K.; Miller, L. D.; Lim, B.; Liu, E. T.; Yu, Q.; Ng, H.-H.; Ruan, Y. A global map of p53 transcription-factor binding sites in the human genome Cell 2006, 124, 207-219
73. Pan, Y.; Nussinov, R. Lysine 120 interactions with p53 response elements can allosterically direct p53 organization PLoS Comput. Biol. 2010, 6, e1000878