Systematic study of anharmonic features in a principal component analysis of gramicidin A

Biophysical Journal

Volumn 98, Issue 3, 2010, Pages 386-395

  Kurylowicz, Martin ^a   Yu, Ching Hsing ^a   Pomès, Régis ^a  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 76249119203     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.10.034     Document Type: Article

References (57)

1. Karplus, M. 1987. Molecular dynamics simulations of proteins. Phys. Today. 40:68-70.
2. Karplus, M., and J. Kuriyan. 2005. Molecular dynamics and protein function. Proc. Natl. Acad. Sci. USA. 102:6679-6685.
3. McCammon, J. A., and S. C. Harvey. 1987. Dynamics of Proteins and Nucleic Acids. Cambridge University Press, New York.
4. Roux, B., and K. Schulten. 2004. Computational studies of membrane channels. Structure. 12:1343-1351.
5. Andersen, O. S., and R. E. Koeppe. 1992. Molecular determinants of channel function. Physiol. Rev. 72:89S-158S.
6. 6. Ketchem, R. R., W. Hu, and T. A. Cross. 1993. High-resolution conformation of gramicidin A in a lipid bilayer by solid-state NMR. Science. 261:1457-1460. (Pubitemid 23334269)
7. Roux, B. 2002. Computational studies of the gramicidin channel. Acc. Chem. Res. 35:366-375.
8. Arseniev, A. S., I. L. Barsukov,YuA Ovchinnikov. 1985.H-NMR study of gramicidin A transmembrane ion channel. Head-to-head righthanded, single-stranded helices. FEBS Lett. 186:168-174.
9. Ketchem, R. R., B. Roux, and T. A. Cross. 1997. High-resolution polypeptide structure in a lamellar phase lipid environment from solid state NMR derived orientational constraints. Structure. 5:1655-1669.
10. Roux, B., and M. Karplus. 1991. Ion transport in a model gramicidin channel. Structure and thermodynamics. Biophys. J. 59:961-981.
11. - translocation along the single-file water chain in the gramicidin. A channel, Biophys. J. 71:19-39.
12. - conduction in the single-file water chain of the gramicidin channel. Biophys. J. 82:2304-2316.
13. Yu, C. H., and R. Pomès. 2003. Functional dynamics of ion channels: modulation of proton movement by conformational switches. J. Am. Chem. Soc. 125:13890-13894.
14. Chiu, S., E. Jakobsson,J. A. McCammon. 1991. Time-correlation analysis of simulated water motion, in flexible and rigid gramicidin, channels. Biophys. J. 60:273-285.
15. Urry, D. W., S. Alonso-Romanowski,R. D. Harris. 1984. Temperature dependence of single channel currents and the peptide libration mechanism for ion transport through the gramicidin A transmembrane channel. J. Memhr. Biol. 81:205-217.
16. 16. Roux, B., and M. Karplus. 1988. The normal modes of the gramicidin-A dimer channel. Biophys. J. 53:297-309. (Pubitemid 18074196)
17. 17. Tian, F., and T. A. Cross. 1999. Cation transport: an example of structural based selectivity. J. Mol. Biol. 285:1993-2003. (Pubitemid 29078166)
18. North, C. L., and T. A. Cross. 1995. Correlations between function and dynamics: time scale coincidence for ion translocation and molecular dynamics in the gramicidin channel backbone. Biochemistry. 34:5883-5895.
19. 15N NMR characterization of polypeptide backbone librations. J. Magn. Reson. B. 107:43-50.
20. + motions in gramicidin A and C. J. Phys. Chem. B. 102:5234-5238.
21. + cation motions in gramicidin A. J. Mol. Struct. 565:213-217.
22. Berendsen, H. J., and S. Hayward. 2000. Collective protein dynamics in relation to function. Curr. Opin. Struct. Biol. 10:165-169.
23. Kitao, A., and N. Go. 1999. Investigating protein dynamics in collective coordinate space. Curr. Opin. Struct. Biol. 9:164-169.
24. García, A. 1992. Large-amplitude nonlinear motions in proteins. Phys. Rev. Lett. 17:2696-2699.
25. 25. Brooks, B., and M. Karplus. 1983. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc. Natl. Acad. Sci. USA. 80:6571-6575. (Pubitemid 14238622)
26. Hayward, S., A. Kitao, and N. Go. 1994. Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis. Protein Sci. 3:936-943.
27. 27. Ma, J. 2005. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure. 13:373-380. (Pubitemid 40342876)
28. Miller, D. W., and D. A. Agard. 1999. Enzyme specificity under dynamic control: a normal mode analysis of α-lytic protease. J. Mol. Biol. 286:267-278.
29. Atilgan, A. R., S. R. Durell,I. Bahar. 2001. Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80:505-515.
30. 30. Bahar, I., and A. J. Rader. 2005. Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol. 15:586-592. (Pubitemid 41393491)
31. Eyal, E., and I. Bahar. 2008. Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network, models. Biophys. J. 94:3424-3435.
32. Tama, F., M. Valle, C. L. Brooks, III. 2003. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proc. Natl. Acad. Sci. USA. 100:9319-9323.
33. Tirion, M. M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 7:1905-1908.
34. Amadei, A., A. B. M. Linssen, and H. J. C. Berendsen. 1993. Essential dynamics of proteins. Proteins. 17:412-425.
35. 35. Garcia, A. E., and G. Hummer. 1999. Conformational dynamics of cytochrome c: correlation, to hydrogen exchange. Proteins. 36:175-191. (Pubitemid 29305087)
36. 36. Hayward, S., and H. J. C. Berendsen. 1998. Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins. 30:144-154. (Pubitemid 28080149)
37. Maisuradze, G. G., and D. M. Leitner. 2006. Principal component analysis of fast-folding λ-repressor mutants. Chem. Phys. Lett. 421:5-10.
38. Mesentean, S., S. Koppole,S. Fischer. 2007. The principal motions involved in the coupling mechanism of the recovery stroke of the myosin motor. J. Mol. Biol. 367:591-602.
39. Camevale, V., S. Raugei,P. Carloni. 2006. Convergent dynamics in the protease enzymatic superfamily. J. Am. Chem. Soc. 128:9766-9772.
40. van Aalten, D. M. F., A. Amadei, H. J. C. Berendsen. 1995. The essential dynamics of thermolysin: confirmation of the hinge-bending motion, and comparison, of simulations in vacuum and water. Proteins.
41. Materese, C. K., C. C. Goldmon, and G. A. Papoian. 2008. Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions. Proc. Natl. Acad. Sci. USA. 105:10659-10664.
42. Maisuradze, G. G., A. Liwo, and H. A. Scheraga. 2009. Principal component analysis for protein folding dynamics.J. Mol. Biol. 385:312-329.
43. Brooks, B. R., R. E. Bruccoleri,M. Karplus. 1983. CHARMMa program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4:187-217.
44. Jorgensen,W. L.,J.Chandrasekhar,M. L. Klein. 1983.Comparison of simple potential functions for simulating water. J. Chem. Phys. 79:926-935.
45. MacKerell, Jr., A. D., D. Bashford, M. Karplus. 1998. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B. 102:3586-3616.
46. Woolf, T. B., and B. Roux. 1994. Molecular-dynamics of the gramicidin channel in a phospholipid membrane. Proc. Natl. Acad. Sci. USA. 91:11631-11635.
47. Ryckaert, J.-P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical, integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
48. Zhang, Y., S. Feller,R. W. Pastor. 1995. Computer simulation of liquid/liquid interfaces. I. Theory and application, to octane/water. J. Chem. Phys. 103:10252-10266.
49. 49. Marrink, S. J., and A. E. Mark. 2001. Effect of undulations on surface tension in simulated bilayers. J. Phys. Chem. B. 105:6122-6127. (Pubitemid 35339078)
50. Hess, B. 2002. Convergence of sampling in protein, simulations. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 65:031910.
51. Faraldo-Gómez, J. D., L. R. Forrest,M. S. Sansom. 2004. Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins. 57:783-791.
52. 52. Grossfield, A., S. E. Feller, and M. C. Pitman. 2007. Convergence of molecular dynamics simulations of membrane proteins. Proteins. 67:31-40. (Pubitemid 46340124)
53. Luchko, T., J. T. Huzil,J. Tuszynski. 2008. Conformational analysis of the carboxy-terminal tails of human β-tubulin isotypes. Biophys. J. 94:1971-1982.
54. Bingham, N. C., N. E. Smith,D. D. Busath. 2003. Molecular dynamics simulations of Trp side-chain, conformational flexibility in the gramicidin A channel. Biopolymers. 71:593-600.
55. Allen, T. W., O. S. Andersen, and B. Roux. 2003. Structure of gramicidin A in a lipid bilayer environment determined using molecular dynamics simulations and solid-state NMR data. J. Am. Chem. Soc. 125:9868-9877.
56. 56. Metzler, R., and J. Klafter. 2004. The restaurant at the end of the random walk: recent developments in the description of anomalous transport by fractional dynamics. J. Phys. A. 37:R161-R208. (Pubitemid 39063557)
57. Maisuradze, G. G., and D. M. Leitner. 2007. Free energy landscape of a biomolecule in dihedral principal component space: sampling convergence and correspondence between structures and minima. Proteins. 67:569-578.