Investigating dynamic and energetic determinants of protein nucleic acid recognition: Analysis of the zinc finger zif268-DNA complexes

BMC Structural Biology

Volumn 10, Issue , 2010, Pages

  Torella, Rubben ^a   Moroni, Elisabetta ^a,b   Caselle, Michele ^b   Morra, Giulia ^a   Colombo, Giorgio ^a  

^a CNR   (Italy)

^b UNIVERSITY OF TURIN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID; UNCLASSIFIED DRUG; ZIF268 PROTEIN; ZINC FINGER PROTEIN; DNA; DNA BINDING PROTEIN; EARLY GROWTH RESPONSE FACTOR 1;

AMINO ACID SEQUENCE; ARTICLE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA SEQUENCE; MOLECULAR DYNAMICS; POINT MUTATION; PROTEIN CONFORMATION; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ENZYME SPECIFICITY; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; BASE SEQUENCE; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; DNA; DNA-BINDING PROTEINS; EARLY GROWTH RESPONSE PROTEIN 1; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY; ZINC FINGERS;

EID: 78549243769     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-10-42     Document Type: Article

References (53)

1. Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. MF Berger AA Philippakis AM Qureshi FH He PW Estep III ML Bulyk, Nature Biotech 2006 23 1429 1435 10.1038/nbt1246 (Pubitemid 44722107)
2. Sequence specific recognition of double helical nucleic acids by proteins. NC Seaman JM Rosenberg A Rich, Proc Natl Acad Sci USA 1976 73 804 808 10.1073/pnas.73.3.804 1062791
3. Molecular dynamics simulations of nucleic acid-protein complexes. AD MacKerell L Nilsson, Curr Op Struct Biol 2008 18 2 194 199
4. Comparing native and irradiated E. coli lactose repressor-operator complex by molecular dynamics simulation. S Aci-Seche N Garnier S Goffinont D Ganest M Spotheim-Maurizot M Genest, Eur Biophys J with Biophis Lett 2010 39 10 1375 1384
5. Wrapped around models for Lac Operon Complex. G La Penna A Perico, Biophys J 2010 98 12 2964 2973 10.1016/j.bpj.2010.03.024 20550909
6. Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the preorganization of specificity determinant side chains. AN Temiz PV Benos CJ Camacho, NAR 2010 38 7 2134 2144 10.1093/nar/gkp1132 20047959
7. Binding of the Bacteriophage P22 N-Peptide to the boxB RNA Motif Studied by Molecular Dynamics Simulations. RP Bahadur S Kannan M Zacharias, Biophys J 2009 97 12 3139 3149 10.1016/j.bpj.2009.09.035 20006951
8. Experimental snapshots of a protein-dna binding landscape. IE Sanchez DU Ferreiro M Dellarole G de Prat-Gray, Proc Natl Acad Sci USA 2010 107 17 7751 7756 10.1073/pnas.0911734107 20375284
9. Protein sliding along DNA: dynamics and structural characterization. O Givaty Y Levy, J Mol Biol 2009 385 4 1087 1097 10.1016/j.jmb.2008.11.016 19059266
10. Water-mediated interactions between DNA and PhoB DNA-binding/ transactivation domain: NMR-restrained molecular dynamics in explicit water environment. T Yamane H Okamura M Ikeguchi Y Nishimura A Kidera, Proteins 2008 71 4 1970 1983 10.1002/prot.21874 18186481
11. Thermodynamic profiling of HIV RREIIB RNA-Zinc Finger Interactions. SH Mishra AM Spring MW Germann, J Mol Biol 2009 393 2 369 382 10.1016/j.jmb.2009. 07.066 19646998
12. Relaxation dynamics of nucleosomal DNA. SY Ponomarev V Putkaradze TC Bishop, PhysChemChemPhys 2009 11 45 10633 10643
13. Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics Simulations. P Singhal B Jayaram SB Dixit DL Beveridgey, Biophys J 2008 94 11 4173 4183 10.1529/biophysj.107.116392 18326660
14. Molecular dynamics simulations of DNA using the generalized born solvation model: Quantitative comparisons with explicit solvation results. ZA Sands CA Laughton, J Phys Chem B 2004 108 28 10113 10119 10.1021/jp048757q
15. Tethered-Hopping Model for Protein-DNA Binding and Unbinding Based on Sox2-Oct1-Hoxb1 Ternary Complex Simulations. P Lian LA Liu YX Shi YX Bu DQ Wei, Biophys J 2010 98 7 1285 1293 10.1016/j.bpj.2009.12.4274 20371328
16. Simulation of DNA double-strand dissociation and formation during replica-exchange molecular dynamics simulations. S Kannan M Zacharias, PhysChemChemPhys 2009 11 45 10589 10595
17. Analyzing protein-DNA recognition mechanisms. G Paillard R Lavery, Structure 2004 12 113 122 10.1016/j.str.2003.11.022 14725771
18. The role of DNA shape in protein-DNA recognition. R Rohs SM West A Sosinsky P Liu RS Mann B Honig, Nature 2009 461 7268 1248 10.1038/nature08473 19865164
19. Simulation and modeling of nucleic acid structure, dynamics and interactions. TEI Cheatham, Curr Op Struct Biol 2004 14 360 367 10.1016/j.sbi.2004.05.001 (Pubitemid 38749065)
20. NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex. V Tsui I Radhakrishnan PE Wright DA Case, J Mol Biol 2000 302 1101 1117 10.1006/jmbi.2000.4108 11183777
21. Extracting the casuality of correlated motions from molecular dynamics simulations. H Kamberaj A van der Vaart, Biophys J 2009 97 1747 1755 10.1016/j.bpj.2009.07.019 19751680
22. Are many body effects important in protein folding? A van der Vaart BD Bursulaya CLI Brooks KMMJ Merz, J Phys Chem B 2000 104 9554 9563 10.1021/jp001193f
23. Molecular dynamics simulation of the Escherichia coli NikR protein: Equilibrium conformational fluctuations reveal interdomain allosteric communication pathways. MJ Bradley PT Chivers NA Baker, J Mol Biol 2008 378 5 1155 1173 10.1016/j.jmb.2008.03.010 18433769
24. Zinc Finger Phage: Affinity selection of fingers with new DNA-binding specificities. EJ Rebar CO Pabo, Science 1994 263 671 673 10.1126/science. 8303274 8303274
25. High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. M Elrod-Erickson TE Benson CO Pabo, Structure 1998 6 451 464 10.1016/S0969-2126(98)00047-1 9562555
26. Diversity in DNA recognition by p53 revealed by crystal structures with Hoogsteen base pairs. M Kitayner H Rozenberg R Rohs O Suad D Rabinovich B Honig Z Shakked, Nat Struct Mol Biol 2010 17 4 423 10.1038/nsmb.1800 20364130
27. Transactivation of the EGR1 gene contributes to mutant p53 gain of function. L Weisz A Zalcenstein P Stambolsky Y Cohen N Goldfinger M Oren V Rotter, Cancer Res 2004 64 22 8318 8327 10.1158/0008-5472.CAN-04-1145 15548700
28. PTEN expression elicted by EGR-1 transcriptio factor in calyucin A-induced apoptotic cells. H Okamura K Yoshida H Morimoto T Haneji, J Cell Biochem 2005 94 1 117 125 10.1002/jcb.20283 15517593
29. Essential dynamics of proteins. A Amadei ABM Linssen HJC Berendsen, Proteins: Struct, Funct, and Gen 1993 17 412 425 10.1002/prot.340170408 (Pubitemid 23358549)
30. Large-amplitude nonlinear motions in proteins. A García, Phys Rev Lett 1992 66 2696 2699 10.1103/PhysRevLett.68.2696
31. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. J Schlitter, Chem Phys Lett 1993 215 6 617 621 10.1016/0009-2614(93)89366-P
32. A Free Energy Pathway for the Interaction of the SRY Protein with Its Binding Site on DNA from Atomistic Simulations. B Bouvier R Lavery, J Am Chem Soc 2009 131 29 9864 10.1021/ja901761a 19580270
33. Relationship between energy distribution and fold stability: Insights from molecular dynamics simulations of native and mutant proteins. G Morra G Colombo, Proteins: Structure, Function and Bioinformatics 2008 72 2 660 672 10.1002/prot.21963 (Pubitemid 351928520)
34. Determinants of protein stability and folding: Comparative analysis of beta-lactoglobulins and liver basic fatty acid binding protein. L Ragona G Colombo M Catalano H Molinari, Proteins: Structure, Function and Bioinformatics 2005 61 2 366 376 10.1002/prot.20493 (Pubitemid 41429144)
35. Similar folds with different stabilization mechanisms: the cases of Prion and Doppel proteins. S Colacino G Tiana G Colombo, BMC Struct Biol 2006 6 17 16857062
36. Understanding the determinants of stability and folding of small globular proteins from their energetics. G Tiana F Simona GMS De Mori RA Broglia G Colombo, Protein Science 2004 13 1 113 124 10.1110/ps.03223804 14691227
37. Selecting sequences that fold into a defined 3 D structure: A new approach for protein design based on molecular dynamics and energetics. G Morra C Baragli G Colombo, Biophys Chem 2010 146 32 76 84 10.1016/j.bpc.2009.10.007 19926206
38. Predicting interaction sited from the energetics of isolated proteins: a new approach to epitope mapping. G Scarabelli G Morra G Colombo, Biophys J 2010 98 9 1966 1975 10.1016/j.bpj.2010.01.014 20441761
39. Computational Study of the Resistance Shown by the Subtype B/HIV-1 Protease to Currently Known Inhibitors. A Genoni G Morra KMM Merz G Colombo, Biochemistry 2010 49 19 4283 4295 10.1021/bi100569u 20415450
40. Diffusion driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. OG Berg RB Winter PH von Hippel, Biochemistry 1981 20 6929 6948 10.1021/bi00527a028 7317363
41. How do site-specific DNA-binding proteins find their targets? SE Halford JF Marko, Nucleic Acid Res 2004 32 3040 3052 10.1093/nar/gkh624 15178741
42. Modeling signal propagation mechanisms and ligand-based conformational dynamics of the Hsp90 molecular chaperone full length dimer. G Morra GM Verkhivker G Colombo, PLOS Comp Biol 2009 5 3 1000323 10.1371/journal.pcbi. 1000323
43. Dynamics-Based Discovery of Allosteric Inhibitors: Selection of New Ligands for the C-terminal Domain of Hsp90. G Morra MAC Neves CJ Plescia S Tsutsumi L Neckers G Verkhivker DC Altieri G Colombo, J Chem Theory and Computation 2010 6 9 2978 2989 10.1021/ct100334n
44. Cooperative DNA-Binding and sequence-recognition mechanisms of aristaless and clawless. K Miyazono Y Zhi Y Takamura K Nagata K Saigo T Kojima M Tanokura, EMBO J 2010 29 1613 1623 10.1038/emboj.2010.53 20389279
45. Specificity by design. CO Pabo, Nat Biotech 2006 24 8 954 955 10.1038/nbt0806-954 (Pubitemid 44215388)
46. AMBER 9. DA Case TA Darden TEI Cheatham CL Simmerling J Wang RE Duke R Luo KM Merz DA Pearlman M Crowley RC Walker W Zhang B Wang S Hayik A Roitberg G Seabra KF Wong F Paesani X Wu S Brozell V Tsui H Gohlke L Yang C Tan J Mongan V Hornak G Cui P Beroza DH Mathews C Schafmeister WS Ross PA Kollman, University of California 2006
47. Comparison of simple potential functions for simulating liquid water. WL Jorgensen J Chandrasekhar J Madura RW Impey ML Klein, J Chem Phys 1983 79 926 935 10.1063/1.445869
48. Particle mesh Ewald: An N-log(N) method for Ewald sums in large systems. T Darden D York L Pedersen, J Chem Phys 1993 98 10089-10092
49. Molecular dynamics with coupling to an external bath. HJC Berendsen JPM Postma WFv Gunsteren AD Nola JR Haak, J Chem Phys 1984 81 3684 3690 10.1063/1.448118
50. Inhibition of carbonic anhydrase. KMMJ Merz MA Murcko PA Kollman, J Am Chem Soc 1991 113 12 4484 4490 10.1021/ja00012a017
51. Essential dynamics of proteins. A Amadei ABM Linssen HJC Berendsen, Proteins: Struct Funct Genet 1993 17 412 425 10.1002/prot.340170408 (Pubitemid 23358549)
52. Coupling between global dynamics and signal transduction pathways: a mechanism of allostery for chaperonin GroEL. C Chennubhotla Z Yang I Bahar, Mol BioSyst 2008 4 287 292 10.1039/b717819k 18354781
53. Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. WC Still A Tempczyk RC Hawley T Hendrickson, J Am Chem Soc 1990 112 6127 6129 10.1021/ja00172a038