Improvement and analysis of computational methods for prediction of residual dipolar couplings

Journal of Magnetic Resonance

Volumn 201, Issue 1, 2009, Pages 25-33

  Berlin, Konstantin ^a,b   O'Leary, Dianne P ^b,c   Fushman, David ^a,c  

^a Bldg 142   (United States)

^b NONE   (United States)

^c UNIVERSITY OF MARYLAND   (United States)

Author keywords

Ab initio prediction; Alignment tensor; PALES; Residual dipolar coupling

Indexed keywords

AB INITIO METHOD; AB INITIO PREDICTION; ACCURATE PREDICTION; ALIGNMENT TENSOR; ALIGNMENT TENSORS; BICELLES; COMPUTATIONALLY EFFICIENT; CONVEX HULL; MOLECULAR ALIGNMENT; MOLECULAR SHAPES; NUMERICAL INTEGRATIONS; PALES; PROTEIN SHAPE; RESIDUAL DIPOLAR COUPLING; RESIDUAL DIPOLAR COUPLINGS; UNIFORM SAMPLING;

ALIGNMENT; COUPLINGS;

TENSORS;

BACTERIAL PROTEIN; CARRIER PROTEIN; CYANOVIRIN N; PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; CONFORMATION; FORECASTING; METHODOLOGY; NOSTOC; NUCLEAR MAGNETIC RESONANCE; REPRODUCIBILITY; SIGNAL PROCESSING;

ALGORITHMS; BACTERIAL PROTEINS; CARRIER PROTEINS; FORECASTING; MOLECULAR CONFORMATION; NOSTOC; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; REPRODUCIBILITY OF RESULTS; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 70349748272     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2009.07.028     Document Type: Article

References (39)

1. Bax A. Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci. 12 1 (2003) 1-16
2. Tjandra N., and Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science 278 5340 (1997) 1111-1114
3. Tycko R., Blanco F.J., and Ishii Y. Alignment of biopolymers in strained gels: a new way to create detectable dipole-dipole couplings in high-resolution biomolecular NMR. J. Am. Chem. Soc. 122 38 (2000) 9340-9341
4. Sass H., Musco G., Stahl S., Wingfield P., and Grzesiek S. Solution NMR of proteins within polyacrylamide gels: diffusional properties and residual alignment by mechanical stress or embedding of oriented purple membranes. J. Biomol. NMR 18 4 (2000) 303-309
5. Ruckert M., and Otting G. Alignment of biological macromolecules in novel nonionic liquid crystalline media for NMR experiments. J. Am. Chem. Soc. 122 32 (2000) 7793-7797
6. Bewley C., and Clore G. Determination of the relative orientation of the two halves of the domain-swapped dimer of Cyanovirin-N in solution using dipolar couplings and rigid body minimization. J. Am. Chem. Soc. 122 25 (2000) 6009-6016
7. Warren J., and Moore P. Application of dipolar coupling data to the refinement of the solution structure of the Sarcin-Ricin loop RNA. J. Biomol. NMR 20 4 (2001) 311-323
8. Bewley C. Rapid validation of the overall structure of an internal domain-swapped mutant of the anti-HIV protein Cyanovirin-N using residual dipolar couplings. J. Am. Chem. Soc. 123 5 (2001) 1014-1015
9. Azurmendi H., Martin-Pastor M., and Bush C. Conformational studies of Lewis X and Lewis A trisaccharides using NMR residual dipolar couplings. Biopolymers 63 2 (2002) 89-98
10. Bernadó P., Blanchard L., Timmins P., Marion D., Ruigrok R., and Blackledge M. A structural model for unfolded proteins from residual dipolar couplings and small-angle X-ray scattering. Proc. Natl. Acad. Sci. 102 47 (2005) 17002-17007
11. Mukrasch M., Markwick P., Biernat J., von Bergen M., Bernado P., Griesinger C., Mandelkow E., Zweckstetter M., and Blackledge M. Highly populated turn conformations in natively unfolded tau protein identified from residual dipolar couplings and molecular simulation. J. Am. Chem. Soc. 129 16 (2007) 5235-5243
12. Ryabov Y., and Fushman D. Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. J. Am. Chem. Soc. 129 25 (2007) 7894-7902
13. Zweckstetter M., and Bax A. Prediction of sterically induced alignment in a dilute liquid crystalline phase: aid to protein structure determination by NMR. J. Am. Chem. Soc. 122 15 (2000) 3791-3792
14. Zweckstetter M. NMR: prediction of molecular alignment from structure using the PALES software. Nat. Protocols 3 4 (2008) 679-690
15. Eisenhaber F., Lijnzaad P., Argos P., Sander C., and Scharf M. The double cubic lattice method: efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies. J. Comput. Chem. 16 3 (1995) 273-284
16. Fernandes M.X., Bernado P., Pons M., and Garcia de la Torre J. An analytical solution to the problem of the orientation of rigid particles by planar obstacles. Application to membrane systems and to the calculation of dipolar couplings in protein NMR spectroscopy. J. Am. Chem. Soc. 123 48 (2001) 12037-12047
17. Almond A., and Axelsen J. Physical interpretation of residual dipolar couplings in neutral aligned media. J. Am. Chem. Soc. 124 34 (2002) 9986-9987
18. Azurmendi H., and Bush C. Conformational studies of blood group A and blood group B oligosaccharides using NMR residual dipolar couplings. Carbohydr. Res. 337 10 (2002) 905-915
19. Van Loan C.F. Introduction to Scientific Computing: A Matrix-Vector Approach Using MATLAB (1997), Prentice-Hall Inc., Upper Saddle River, NJ, USA
20. Ryabov Y., Geraghty C., Varshney A., and Fushman D. An efficient computational method for predicting rotational diffusion tensors of globular proteins using an ellipsoid representation. J. Am. Chem. Soc. 128 48 (2006) 15432-15444
21. Saupe A., and Englert G. High-resolution nuclear magnetic resonance spectra of orientated molecules. Phys. Rev. Lett. 11 10 (1963) 462-464
22. Murnaghan F. The element of volume of the rotation group. Proc. Natl. Acad. Sci. 36 11 (1950) 670-672
23. Lindstrom P., and Turk G. Fast and memory efficient polygonal simplification. VIS '98: Proceedings of the Conference on Visualization '98 (1998), IEEE Computer Society Press, Los Alamitos, CA, USA 279-286
24. Lindstrom P., and Turk G. Evaluation of memoryless simplification. IEEE Trans. Vis. Comput. Graph. 5 2 (1999) 98-115
25. Varshney A., Brooks Jr. F., and Wright W. Linearly scalable computation of smooth molecular surfaces. IEEE Comput. Graph. Appl. 14 5 (1994) 19-25
26. A. Varshney, F. Brooks Jr., Fast analytical computation of Richard's smooth molecular surface, in: IEEE Visualization'93 Proceedings, 1993, pp. 300-307.
27. Welzl E. Smallest enclosing disks (balls and ellipsoids). New Results and New Trends in Computer Science Vol. 555 (1991), Springer-Verlag 359-370
28. Todd M.J., and Yildirim E.A. On Khachiyan's algorithm for the computation of minimum volume enclosing ellipsoids. Discrete Appl. Math. 155 13 (2007) 1731-1744
29. Cornilescu G., Marquardt J.L., Ottiger M., and Bax A. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J. Am. Chem. Soc. 120 27 (1998) 6836-6837
30. Losonczi J.A., Andrec M., Fischer M.W.F., and Prestegard J.H. Order matrix analysis of residual dipolar couplings using singular value decomposition. J. Magn. Res. 138 2 (1999) 334-342
31. Cai M., Huang Y., Zheng R., Wei S., Ghirlando R., Lee M., Craigie R., Gronenborn A., and Clore G. Solution structure of the cellular factor BAF responsible for protecting retroviral DNA from autointegration. Nat. Struct. Biol. 5 10 (1998) 903-909
32. Kuszewski J., Gronenborn A.M., and Clore G.M. Improving the packing and accuracy of NMR structures with a pseudopotential for the radius of gyration. J. Am. Chem. Soc. 121 10 (1999) 2337-2338
33. Ulmer T.S., Ramirez B.E., Delaglio F., and Bax A. Evaluation of backbone proton positions and dynamics in a small protein by liquid crystal NMR spectroscopy. J. Am. Chem. Soc. 125 30 (2003) 9179-9191
34. Drohat A., Tjandra N., Baldisseri D., and Weber D. The use of dipolar couplings for determining the solution structure of rat apo-S100B (β β). Protein Sci. 8 4 (1999) 800-809
35. Bewley C., Gustafson K., Boyd M., Covell D., Bax A., Clore G., and Gronenborn A. Solution structure of Cyanovirin-N, a potent HIV-inactivating protein. Nat. Struct. Biol. 5 7 (1998) 571-578
36. de Alba E., De Vries L., Farquhar M., and Tjandra N. Solution structure of human GAIP (Gα interacting protein): a regulator of G protein signaling. J. Mol. Biol. 291 4 (1999) 927-939
37. Schwalbe H., Grimshaw S., Spencer A., Buck M., Boyd J., Dobson C., Redfield C., and Smith L. A refined solution structure of hen lysozyme determined using residual dipolar coupling data. Protein Sci. 10 4 (2001) 677-688
38. Jain N.U., Tjioe E., Savidor A., and Boulie J. Redox-dependent structural differences in putidaredoxin derived from homologous structure refinement via residual dipolar couplings. Biochemistry 44 25 (2005) 9067-9078
39. Bax A., Kontaxis G., and Tjandra N. Dipolar couplings in macromolecular structure determination. In: Thomas V.D., James L., and Schmitz U. (Eds). Part B: Nuclear Magnetic Resonance of Biological Macromolecules. Vol. 339 of Methods in Enzymology (2001), Academic Press 127-174