Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops

PLoS Computational Biology

Volumn 10, Issue 9, 2014, Pages

  Invernizzi, Gaetano ^a   Tiberti, Matteo ^a,b   Lambrughi, Matteo ^a,b   Lindorff Larsen, Kresten ^a   Papaleo, Elena ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; GRAPH THEORY; PROTEINS; STRUCTURAL DYNAMICS;

BINDING LOOP; CELL CYCLE REGULATION; COMMUNICATION ROUTE; CONFORMATIONAL CHANGE; DNA-BINDING; DNA-BINDING DOMAIN; EMBRYONIC DEVELOPMENT; LONG-RANGE COMMUNICATIONS; REGULATION DEVELOPMENT; REGULATORY PROCESS;

DNA;

AT RICH INTERACTIVE DOMAIN 3A PROTEIN; CYCLIN DEPENDENT KINASE INHIBITOR 1C; DEAD RINGER LIKE PROTEIN 1; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; ARID3A PROTEIN, HUMAN; DNA; DNA BINDING PROTEIN; PROTEIN BINDING;

ALPHA HELIX; AMINO ACID SUBSTITUTION; ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA BINDING MOTIF; DNA CONFORMATION; DNA HELIX; MOLECULAR DOCKING; NUCLEOTIDE BINDING SITE; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STABILITY; CHEMISTRY; HUMAN; METABOLISM; MOLECULAR DYNAMICS; PROTEIN TERTIARY STRUCTURE;

DNA; DNA-BINDING PROTEINS; HUMANS; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION FACTORS;

EID: 84907572373     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003744     Document Type: Article

References (47)

1. Wilsker D, Probst L, Wain HM, Maltais L, Tucker PW, et al. (2005) Nomenclature of the ARID family of DNA-binding proteins. Genomics 86: 242–251.
2. Patsialou A, Wilsker D, Moran E, (2005) DNA-binding properties of ARID family proteins. Nucleic Acids Res 33: 66–80.
3. Kortschak RD, Tucker PW, Saint R, (2000) ARID proteins come in from the desert. Trends Biochem Sci 25: 294–299.
4. Lin D, Ippolito GC, Zong R-T, Bryant J, Koslovsky J, et al. (2007) Bright/ARID3A contributes to chromatin accessibility of the immunoglobulin heavy chain enhancer. Mol Cancer 6: 23.
5. Huang YJ, Hang D, Lu LJ, Tong L, Gerstein MB, et al. (2008) Targeting the human cancer pathway protein interaction network by structural genomics. Mol Cell Proteomics 7: 2048–2060.
6. Liu G, Huang YJ, Xiao R, Wang D, Acton TB, et al. (2010) Solution NMR structure of the ARID domain of human AT-rich interactive domain-containing protein 3A: a human cancer protein interaction network target. Proteins 78: 2170–2175.
7. Iwahara J, Iwahara M, Daughdrill GW, Ford J, Clubb RT, (2002) The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA. EMBO J 21: 1197–1209.
8. Iwahara J, Clubb RT, (1999) Solution structure of the DNA binding domain from Dead ringer, a sequence-specific AT-rich interaction domain (ARID). EMBO J 18: 6084–6094.
9. Nixon JC, Rajaiya J, Webb CF, (2004) Mutations in the DNA-binding Domain of the Transcription Factor Bright Act as Dominant Negative Proteins and Interfere with Immunoglobulin Transactivation. J Biol Chem 279: 52465–52472.
10. Yao W, Peng Y, Lin D, (2010) The flexible loop L1 of the H3K4 demethylase JARID1B ARID domain has a crucial role in DNA-binding activity. Biochem Biophys Res Commun 396: 323–328.
11. Piana S, Lindorff-Larsen K, Shaw DE, (2011) How robust are protein folding simulatons with respect to force field parametrization? Biophys J 101: 1015.
12. Li D-W, Brüschweiler R, (2012) PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles. J Biomol NMR 54: 257–265.
13. Raimondi F, Seeber M, De Benedetti PG, Fanelli F, (2008) Mechanisms of inter- and intramolecular communication in GPCRs and G proteins. J Am Chem Soc 130: 4310–4325.
14. Ghosh A, Vishveshwara S, (2007) A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis. Proc Natl Acad Sci U S A 104: 15711–15716.
15. Papaleo E, Lindorff-Larsen K, De Gioia L, (2012) Paths of long-range communication in the E2 enzymes of family 3: a molecular dynamics investigation. Phys Chem Chem Phys 14: 12515–12525.
16. Lange OF, Grubmüller H, (2006) Generalized correlation for biomolecular dynamics. Proteins 62: 1053–1061.
17. Brinda KV, Vishveshwara S, (2005) A network representation of protein structures: implications for protein stability. Biophys J 89: 4159–4170.
18. Fanelli F, Felline A, (2011) Dimerization and ligand binding affect the structure network of A(2A) adenosine receptor. Biochim Biophys Acta 1808: 1256–1266.
19. Böde C, Kovács IA, Szalay MS, Palotai R, Korcsmáros T, et al. (2007) Network analysis of protein dynamics. FEBS Lett 581: 2776–2782.
20. Vishveshwara S, Ghosh A, Hansia P, (2009) Intra and inter-molecular communications through protein structure network. Curr Protein Pept Sci 10: 146–160.
21. Ahmad S, Keskin O, Mizuguchi K, Sarai A, Nussinov R, (2010) CCRXP: exploring clusters of conserved residues in protein structures. Nucleic Acids Res 38: W398–401.
22. Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, et al. (2005) The FoldX web server: an online force field. Nucleic Acids Res 33: W382–8.
23. Seeber M, Felline A, Raimondi F, Muff S, Friedman R, et al. (2011) Wordom: a user-friendly program for the analysis of molecular structures, trajectories, and free energy surfaces. J Comput Chem 32: 1183–1194.
24. Angelova K, Felline A, Lee M, Patel M, Puett D, Fanelli F, (2011) Conserved amino acids partecipate in the structure networks deputed to intramolecular communication in the lutropin receptor. Cell Mol Life Sci 68: 1227–1239.
25. Ghosh A, Sakaguchi R, Liu C, Vishveshwara S, Hou Y-M, (2011) Allosteric communication in cysteinyl tRNA synthetase: a network of direct and indirect readout. J Biol Chem 286: 37721–37731.
26. Frappier V, Najmanovich RJ, (2014) A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations. PLoS Comput Biol 10: e1003569.
27. Chennubhotla C, Bahar I, (2006) Markov propagation of allosteric effects in biomolecular systems: application to GroEL-GroES. Mol Syst Biol 2: 36.
28. Del Sol A, Fujihashi H, Amoros D, Nussinov R, (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Mol Syst Biol 2: 2006.0019.
29. Chennubhotla C, Bahar I, (2007) Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol 3: 1716–1726.
30. Pandini A, Fornili A, Fraternali F, Kleinjung J, (2012) Detection of allosteric signal transmission by information-theoretic analysis of protein dynamics. FASEB J 26: 868–881.
31. Papale E, Renzetti G, Tiberti M, (2012) Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl peptidase: a molecular dynamics investigation. PLoS One 7: e35686.
32. Mishra S, Caflisch A, (2011) Dynamics in the active site of Beta-secretase: a network analysis of atomistic simulations. Biochemistry 50: 9328–9339.
33. Buchli B, Waldauer SA, Walser R, Donten ML, Pfister R, et al. (2013) Kinetic response of a photoperturbed allosteric protein. Proc Natl Acad Sci U S A 110: 11725–11730.
34. Zhao L, Li W, Tian P, (2013) Reconciling mediating and slaving roles of water in protein conformational dynamics. PLoS One 8: e60553.
35. Angel TE, Gupta S, Jastzerbska B, Palczewski K, Chance MR, (2009) Structural waters define a functional channel mediating activation of the GPCR, rhodopsin. Proc Natl Acad Sci 106: 14367–14372.
36. Kearney BM, Johnson CW, Roberts DM, Swartz P, Mattos C, (2013) DroP: a water analysis program identifies RAS-GTP specific pathway of communication between membrane interacting regions and active site. J Mol Biol 426: 611–629.
37. Negi SS, Schein CH, Oezguen N, Power TD, Braun W, (2007) InterProSurf: a web server for predicting interacting sites on protein surfaces. Bioinformatics 23: 3397–3399.
38. Hess B, Kutzner C, van der Spoel D, Lindahl E, (2008) GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J Chem Theory Comput 4: 435–447.
39. Jorgesen WL, Chandrasekhar J, Madura JD, Impey RW, Klen ML, (1983) Comparison of simple potential functions for simulating liquid water. J Phys Chem 79: 926.
40. Hess B, Bekker H, Berendsen H, Fraaije J, (1997) LINCS: A linear constraint solver for molecular simulations. J Comput Chem 18: 1463–1472.
41. Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089.
42. Amadei A, Linssen AB, Berendsen HJ, (1993) Essential dynamics of proteins. Proteins 17: 412–425.
43. Amadei A, Ceruso MA, Di Nola A, (1999) On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations. Proteins 36: 419–424.
44. Hess B, (2000) Similarities between principal components of protein dynamics and random diffusion. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 62: 8438–8448.
45. Lange OF, Grubmüller H, (2008) Full correlation analysis of conformational protein dynamics. Proteins 70: 1294–1312.
46. Kannan N, Vishveshwara S, (1999) Identification of side-chain clusters in protein structures by a graph spectral method. J Mol Biol 292: 441–464.
47. Pasi M, Tiberti M, Arrigoni A, Papaleo E, (2012) xPyder: A PyMOL Plugin To Analyze Coupled Residues and Their Networks in Protein Structures. J Chem Inf Model 52: 1865–1874.