全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...

Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e

DOI: 10.1371/journal.pcbi.1002794

Full-Text   Cite this paper   Add to My Lib

Abstract:

Experimental NMR relaxation studies have shown that peptide binding induces dynamical changes at the side-chain level throughout the second PDZ domain of PTP1e, identifying as such the collection of residues involved in long-range communication. Even though different computational approaches have identified subsets of residues that were qualitatively comparable, no quantitative analysis of the accuracy of these predictions was thus far determined. Here, we show that our information theoretical method produces quantitatively better results with respect to the experimental data than some of these earlier methods. Moreover, it provides a global network perspective on the effect experienced by the different residues involved in the process. We also show that these predictions are consistent within both the human and mouse variants of this domain. Together, these results improve the understanding of intra-protein communication and allostery in PDZ domains, underlining at the same time the necessity of producing similar data sets for further validation of thses kinds of methods.

References

[1]  Ponting CP, Phillips C, Davies KE, Blake DJ (1997) PDZ domains: targeting signalling molecules to sub-membranous sites. BioEssays 19: 469–479. doi: 10.1002/bies.950190606
[2]  Bezprozvanny I, Maximov A (2001) PDZ domains: More than just a glue. Proceedings of the National Academy of Sciences of the United States of America 98: 787–789. doi: 10.1073/pnas.98.3.787
[3]  Fuentes EJ, Der CJ, Lee AL (2004) Ligand-dependent dynamics and intramolecular signaling in a PDZ domain. Journal of molecular biology 335: 1105–1115. doi: 10.1016/j.jmb.2003.11.010
[4]  Gianni S, Walma T, Arcovito A, Calosci N, Bellelli A, et al. (2006) Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering. Structure 14: 1801–1809. doi: 10.1016/j.str.2006.10.010
[5]  Petit CM, Zhang J, Sapienza PJ, Fuentes EJ, Lee AL (2009) Hidden dynamic allostery in a PDZ domain. Proceedings of the National Academy of Sciences of the United States of America 106: 18249–18254. doi: 10.1073/pnas.0904492106
[6]  Peterson FC, Penkert RR, Volkman BF, Prehoda KE (2004) Cdc42 regulates the Par-6 PDZ domain through an allosteric CRIB-PDZ transition. Molecular cell 13: 665–676. doi: 10.1016/s1097-2765(04)00086-3
[7]  van den Berk LC, Landi E, Walma T, Vuister GW, Dente L, et al. (2007) An allosteric intramolecular PDZ-PDZ interaction modulates PTP-BL PDZ2 binding specificity. Biochemistry 46: 13629–13637. doi: 10.1021/bi700954e
[8]  Whitley MJ, Lee AL (2009) Frameworks for understanding long-range intra-protein communication. Current protein & peptide science 10: 116–127. doi: 10.2174/138920309787847563
[9]  Koshland DE (1958) Application of a Theory of Enzyme Specificity to Protein Synthesis. Proceedings of the National Academy of Sciences of the United States of America 44: 98–104. doi: 10.1073/pnas.44.2.98
[10]  Monod J, Wyman J, Changeux JP (1965) On the Nature of Allosteric Transitions: A Plausible Model. Journal of molecular biology 12: 88–118. doi: 10.1016/s0022-2836(65)80285-6
[11]  Tsai CJ, Del Sol A, Nussinov R (2009) Protein allostery, signal transmission and dynamics: a classification scheme of allosteric mechanisms. Molecular bioSystems 5: 207–216. doi: 10.1039/b819720b
[12]  Smock RG, Gierasch LM (2009) Sending signals dynamically. Science 324: 198–203. doi: 10.1126/science.1169377
[13]  Tsai CJ, del Sol A, Nussinov R (2008) Allostery: absence of a change in shape does not imply that allostery is not at play. Journal of molecular biology 378: 1–11. doi: 10.1016/j.jmb.2008.02.034
[14]  Swain JF, Gierasch LM (2006) The changing landscape of protein allostery. Current opinion in structural biology 16: 102–108. doi: 10.1016/j.sbi.2006.01.003
[15]  Gunasekaran K, Ma B, Nussinov R (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57: 433–443. doi: 10.1002/prot.20232
[16]  Hilser VJ (2010) Biochemistry. An ensemble view of allostery. Science 327: 653–654. doi: 10.1126/science.1186121
[17]  Zhang J, Sapienza PJ, Ke H, Chang A, Hengel SR, et al. (2010) Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E. Biochemistry 49: 9280–9291. doi: 10.1021/bi101131f
[18]  Fuentes EJ, Gilmore SA, Mauldin RV, Lee AL (2006) Evaluation of energetic and dynamic coupling networks in a PDZ domain protein. Journal of molecular biology 364: 337–351. doi: 10.1016/j.jmb.2006.08.076
[19]  Law AB, Fuentes EJ, Lee AL (2009) Conservation of side-chain dynamics within a protein family. Journal of the American Chemical Society 131: 6322–6323. doi: 10.1021/ja809915a
[20]  Kong Y, Karplus M (2009) Signaling pathways of PDZ2 domain: a molecular dynamics interaction correlation analysis. Proteins 74: 145–154. doi: 10.1002/prot.22139
[21]  Gerek ZN, Ozkan SB (2011) Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning. PLoS computational biology 7: e1002154. doi: 10.1371/journal.pcbi.1002154
[22]  Halabi N, Rivoire O, Leibler S, Ranganathan R (2009) Protein sectors: evolutionary units of three-dimensional structure. Cell 138: 774–786. doi: 10.1016/j.cell.2009.07.038
[23]  Kozlov G, Gehring K, Ekiel I (2000) Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptor. Biochemistry 39: 2572–2580. doi: 10.1021/bi991913c
[24]  Kozlov G, Banville D, Gehring K, Ekiel I (2002) Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta2-beta3 loop to PDZ domain-ligand interactions. Journal of molecular biology 320: 813–820. doi: 10.1016/s0022-2836(02)00544-2
[25]  Dhulesia A, Gsponer J, Vendruscolo M (2008) Mapping of two networks of residues that exhibit structural and dynamical changes upon binding in a PDZ domain protein. Journal of the American Chemical Society 130: 8931–8939. doi: 10.1021/ja0752080
[26]  Lenaerts T, Ferkinghoff-Borg J, Stricher F, Serrano L, Schymkowitz JW, et al. (2008) Quantifying information transfer by protein domains: analysis of the Fyn SH2 domain structure. BMC structural biology 8: 43. doi: 10.1186/1472-6807-8-43
[27]  Walma T, Spronk CA, Tessari M, Aelen J, Schepens J, et al. (2002) Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL. Journal of molecular biology 316: 1101–1110. doi: 10.1006/jmbi.2002.5402
[28]  Dubay KH, Bothma JP, Geissler PL (2011) Long-range intra-protein communication can be transmitted by correlated side-chain fluctuations alone. PLoS computational biology 7: e1002168. doi: 10.1371/journal.pcbi.1002168
[29]  Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286: 295–299. doi: 10.1126/science.286.5438.295
[30]  Kozlov G, Banville D, Gehring K, Ekiel I (2002) Solution structure of the PDZ2 domain from cytosolic human phosphatase hPTP1E complexed with a peptide reveals contribution of the beta 2-beta 3 loop to PDZ domain-ligand interactions. Journal of molecular biology 320: 813–820. doi: 10.1016/s0022-2836(02)00544-2
[31]  Kozlov G, Gehring K, Ekiel I (2000) Solution structure of the PDZ2 domain from human phosphatase hPTP1E and its interactions with C-terminal peptides from the Fas receptors. Biochemistry 39: 2572–2580. doi: 10.1021/bi991913c
[32]  Krieger E, Darden T, Nabuurs SB, Finkelstein A, Vriend G (2004) Making optimal use of empirical energy functions: Force-field parameterization in crystal space. Proteins-Structure Function and Bioinformatics 57: 678–683. doi: 10.1002/prot.20251
[33]  Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8: 52–56, 29. doi: 10.1016/0263-7855(90)80070-v
[34]  Guerois R, Nielsen JE, Serrano L (2002) Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. Journal of molecular biology 320: 369–387. doi: 10.1016/s0022-2836(02)00442-4
[35]  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: W382–388. doi: 10.1093/nar/gki387
[36]  Kraskov A, Stogbauer H, Grassberger P (2004) Estimating mutual information. Phys Rev E Stat Nonlin Soft Matter Phys 69: 066138. doi: 10.1103/physreve.83.019903
[37]  Yang Y, Webb GI (2009) Discretization for naive-Bayes learning: managing discretization bias and variance. Machine Learning 74: 39–74. doi: 10.1007/s10994-008-5083-5
[38]  Ben-Dor A, Shamir R, Yakhini Z (1999) Clustering gene expression patterns. Journal of Computational Biology 6: 281–297. doi: 10.1089/106652799318274
[39]  Watts DJ, Strogatz SH (1998) Collective dynamics of ‘small-world’ networks. Nature 393: 440–442. doi: 10.1038/30918
[40]  del Sol A, O'Meara P (2005) Small-world network approach to identify key residues in protein-protein interaction. Proteins 58: 672–682. doi: 10.1002/prot.20348
[41]  del Sol A, Fujihashi H, Amoros D, Nussinov R (2006) Residues crucial for maintaining short paths in network communication mediate signaling in proteins. Molecular systems biology 2: 2006 0019. doi: 10.1038/msb4100063
[42]  Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM (2006) MUSTANG: a multiple structural alignment algorithm. Proteins 64: 559–574. doi: 10.1002/prot.20921
[43]  Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, et al. (2004) UCSF Chimera–a visualization system for exploratory research and analysis. Journal of computational chemistry 25: 1605–1612. doi: 10.1002/jcc.20084
[44]  Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T (2011) Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics 27: 431–432. doi: 10.1093/bioinformatics/btq675

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133