Conformational analysis of GpA and GpAp in aqueous solution by molecular dynamics and statistical methods

Journal of Molecular Biology

Volumn 283, Issue 4, 1998, Pages 863-882

  Giraldo, Jesús ^a,b   Wodak, Shoshana J ^a   Van Belle, Daniel ^a  

^a 50 B 1050   (Belgium)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Barnase; Conformational families; Dinucleotides; Molecular dynamics; Stacking

Indexed keywords

BARNASE; DINUCLEOTIDE; ENZYME; UNCLASSIFIED DRUG; WATER;

AQUEOUS SOLUTION; ARTICLE; CONFORMATION; DISCRIMINANT ANALYSIS; ENZYME ACTIVITY; HYDROGEN BOND; MOLECULAR DYNAMICS; MULTIPLE REGRESSION; PRIORITY JOURNAL; STATISTICAL ANALYSIS;

BACILLUS AMYLOLIQUEFACIENS;

EID: 0032491566     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2139     Document Type: Article

References (40)

1. Afifi A.A., Clark V. Multiple regression and correlation: examining linear relations between one variable and many variables. Variable selection in regression analysis Discriminant analysis: classifying individuals into populations. Cluster analysis: Empirical grouping of individuals. Computer-Aided Multivariate Analysis. 1984;120-195 Lifetime Learning Publications, Belmont, California. 247-286, 379-411
2. Anderberg M.R. Cluster Analysis for Applications. 1973;Academic Press, Inc, New York
3. Arnott S., Hukins D.W.L. Conservation of conformation in mono- and polynucleotides. Nature. 224:1969;886-888
4. Baudet S., Janin J. Crystal structure of a barnase-d(GpC) complex at 1.9 Å resolution. J. Mol. Biol. 219:1991;123-132
5. Berman H.M., Neidle S., Stodola R.K. Drug-nucleic acid interactions conformational flexibility at the intercalation site. Proc. Natl Acad. Sci. USA. 75:1978;828-832
6. Berman H.M., Olson W.K., Beveridge D.L., Westbrook J., Gelbin A., Demeny T., Hsieh S.-H., Srinivasan A.R., Schneider B. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J. 63:1992;751-759
7. Brooks C.L., Pettitt B.M., Karplus M. Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids. J. Chem. Phys. 83:1985;5897-5908
8. Buckle A.M., Fersht A.R. Subsite binding in an RNase structure of a barnase-tetranucleotide complex at 1.76-Å resolution. Biochemistry. 33:1994;1644-1653
9. Day G.D., Parsonage D., Ebel S., Brown T., Fersht A.R. Barnase has subsites that give rise to large rate enhancements. Biochemistry. 31:1992;6390-6395
10. Delhaise P., van Belle D., Bardiaux M., Alard P., Hamers P., van Cutsem E., Wodak S.J. Analysis of data for computer simulations on macromolecules using the ceram package. J. Mol. Graphics. 3:1985;116-119
11. Frederick C.A., Coll M., Van Der Marel G.A., Van Boom J.H., Wang A.H.-J. Molecular structure of cyclic deoxydiadenylic acid at atomic resolution. Biochemistry. 27:1988;8350-8361
12. Gelbin A., Schneider B., Clowney L., Hsieh S.-H., Olson W.K., Berman H.M. Geometric parameters in nucleic acids sugar and phosphate constituents. J. Am. Chem. Soc. 118:1996;519-529
13. Gilson M.K., Given J.A., Head M.S. A new class of models for computing receptor-ligand binding affinities. Chem. Biol. 4:1997;87-92
14. a NNof catalytic residues in barnase. Proteins: Struct. Funct. Genet. 25:1996;180-194
15. Guillet V., Lapthorn A., Mauguen Y. Three-dimensional structure of a barnase-3′GMP complex at 2.2 Å resolution. FEBS Letters. 330:1993;137-140
16. Jorgensen W.L. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water. J. Am. Chem. Soc. 103:1981;335-340
17. Kitamura K., Wakahara A., Mizuno H., Baba Y., Tomita K. Conformationally "concerted" changes in nucleotide structures. A new description using circular correlation and regression analyses. J. Am. Chem. Soc. 103:1981;3899-3904
18. Lavery R., Hartmann B. Modelling DNA conformational mechanics. Biophys. Chem. 50:1994;33-45
19. Louise-May S., Auffinger P., Westhoff E. Calculations of nucleic acid conformations. Curr. Opin. Struct. Biol. 6:1996;289-298
20. Mackerell A.D. Jr, Wiórkiewicz-Kuczera J., Karplus M. An all-atom empirical energy function for the simulation of nucleic acids. J. Am. Chem. Soc. 117:1995;11946-11975
21. McLachlan A.D. Gene duplications in the structural evolution of chymotrypsin. J. Mol. Biol. 128:1979;49-79
22. Meiering E.M., Bycroft M., Lubienski M.J., Fersht A.R. Structure and dynamics of barnase complexed with 3′-GMP studies by NMR spectroscopy. Biochemistry. 32:1993;10975-10987
23. Mossakowska D.E., Nyberg K., Fersht A.R. Kinetic characterization of the recombinant ribonuclease from Bacillus amyloliquefaciens (Barnase) and investigation of key residues in catalysis by site-directed mutagenesis. Biochemistry. 28:1989;3843-3850
24. Norberg J., Nilsson L. Stacking free energy profiles for all 16 natural ribodinucleoside monophosphate in aqueous solution. J. Am. Chem. Soc. 117:1995;10832-10840
25. Norberg J., Nilsson L. Conformational free energy landscape of ApApA from molecular dynamics simulations. J. Phys. Chem. 100:1996;2550-2554
26. Olson W.K., Sussman J.L. How flexible is the furanose ring? 1. A comparison of experimental and theoretical studies. J. Am. Chem.Soc. 104:1982;270-278
27. Pavlovsky A.G., Borisova S.N., Strokopytov B.V., Sanishvili R.G., Vagin A.A., Chepurnova N.K. Metabolism and Enzymology of Nucleic Acids Including Gene Manipulations. 1988;Plenum Press, New York
28. Prévost M., van Belle D., Lippens G., Wodak S.J. Computer simulations of liquid water treatment of long-range interactions. Mol. Phys. 71:1990;587-603
29. Rubin J., Brennan T., Sundaralingam M. Crystal and molecular structure of a naturally occurring dinucleoside monophosphate. Uridylyl-(3′-5′)-adenosine hemihydrate. Conformational "rigidity" of the nucleotide unit and models for polynucleotide chain folding. Biochemistry. 11:1972;3112-3128
30. Rushizky G.W., Greco A.E., Hartley R.W., Sober H.A. Studies on B. subtilis ribonuclease. I. Characterization of enzymatic specificity. Biochemistry. 2:1963;787-793
31. Ryckaert J.P., Cicotti G., Berendsen H.J.C. Numerical integration of the cartesian equations of motion of a system with constraints molecular dynamics of n-alkanes. J. Comp. Phys. 23:1977;327-341
32. Saenger W. Principles of Nucleic Acid Structure. Springer Advanced Text in Chemistry. 1984;Springer-Verlag, New York
33. 31P} fast fourier transform nuclear magnetic resonance methods and conformational energy calculations. J. Am. Chem. Soc. 96:1974;7337-7348
34. 1993;SAS Institute Inc, Cary, USA, NC
35. Seeman N.C., Day R.O., Rich A. Nucleic acid-mutagen interactions crystal structure of adenylyl-3′,5′-uridine plus 9-aminoacridine. Nature. 253:1975;324-326
36. Sevcik J., Dodson E.J., Dodson G.G. Determination and restrained least-squares refinement of the structures of ribonuclease Sa and its complex with 3′-guanylic acid at 1.8 Å resolution. Acta Crystallog. sect. B. 47:1991;240-253
37. Spjøtvoll E., Stoline M.R. An extension of the t-method of multiple comparisons to include the cases with unequal sample size. J. Am. Stat. Assoc. 68:1973;975-978
38. Sundaralingam M. Stereochemistry of nucleic acids and their constituents. IV. Allowed and preferred conformations of nucleosides, nucleoside mono-, di-, tri-, tetraphosphates, nucleic acids and polynucleotides. Biopolymers. 7:1969;821-860
39. Sussman J.L., Seeman N.C., Kim S.-H., Berman H.M. Crystal structure of a naturally occurring dinucleoside phosphate uridylyl 3′,5′-adenosine phosphate models for RNA chain folding. J. Mol. Biol. 66:1972;403-421
40. Yathindra N., Sundaralingam M. Backbone conformations in secondary and tertiary structural units of nucleic acids. Constraint in the phosphodiester conformation. Proc. Natl Acad. Sci. USA. 71:1974;3325-3328