A dynamics study of the A-chain of ricin by terahertz vibrational calculation and normal modes analysis

Journal of Molecular Graphics and Modelling

Volumn 27, Issue 5, 2009, Pages 655-663

  Zhang, Hailiang ^a   Zukowski, Eli ^a   Balu, Radhakrishnan ^a   Gregurick, Susan K ^a  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

Author keywords

CHARMM; Depurination mechanism; Normal modes analysis; Ricin A chain; Terahertz spectroscopy

Indexed keywords

FREQUENCY BANDS; SUBSTRATES;

CHARMM; DEPURINATION MECHANISM; NORMAL MODES ANALYSIS; RICIN-A-CHAIN; TERAHERTZ SPECTROSCOPY;

BINDING SITES;

ADENOSINE PHOSPHATE; RICIN;

ARTICLE; CRYSTAL STRUCTURE; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; TERAHERTZ SPECTROSCOPY;

ANIMALS; CYCLIC AMP; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; RICIN; TERAHERTZ SPECTROSCOPY;

EID: 57649181768     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2008.10.005     Document Type: Article

References (57)

1. Korter T.M., Balu R., Campbell M.B., Beard M.C., Gregurick S.K., and Heilweil E.J. Terahertz spectroscopy of solid serine and cysteine. Chem. Phys. Lett. 418 (2006) 65-70
2. Shi Y., and Wang L. Collective vibrational spectra of alpha- and gamma-glycine studied by terahertz and Raman spectroscopy. J. Phys. D: Appl. Phys. 38 (2005) 3741-3745
3. Taday P.F., Bradley I.V., and Arnone D.D. Terahertz pulse spectroscopy of biological materials: L-glutamic acid. J. Biol. Phys. 29 (2003) 109-115
4. Yamamoto K., Tominaga K., Sasakawa H., Tamura A., Murakami H., Ohtake H., and Sarukura N. Terahertz time-domain spectroscopy of amino acids and polypeptides. Biophys. J. 89 (2005) L22-L24
5. Yu B., Zeng F., Yang Y., Xing Q., Chechin A., Xin X., Zeylikovich I., and Alfano R.R. Torsional vibrational modes of tryptophan studied by terahertz time-domain spectroscopy. Biophys. J. 86 (2004) 1649-1654
6. Siegrist K., Buchner C.R., Mandelbaum I., Hight-Walker A.R., Balu R., Gregurick S.K., and Plusquellic D.F. High-resolution terahertz spectroscopy of crystalline trialanine: extreme sensitivity to beta-sheet structure and co-crystallized water. J. Am. Chem. Soc. 128 (2006) 5764-5775
7. Whitmire S.E., Wolpert D., Markelz A.G., Hilebrecht J.R., Galan J., and Brige R.R. Protein flexibility and conformational state: a comparison of collective vibrational modes of wild-type and D96N bacteriorhodopsin. Biophys. J. 85 (2003) 1269-1277
8. Knab J., Chen J.-Y., and Markelz A.G. Hydration dependence of conformational dielectric relaxation of lysozyme. Biophys. J. 90 (2006) 2576-2581
9. Globus T., Bykhovskaia M., Woolard D., and Gelmont B. Sub-millimetre wave absorption spectra of artificial RNA molecules. J. Phys. D: Appl. Phys. 36 (2003) 1314-1322
10. Globus T., Woolard D., Bykhovskaia M., Gelmont B., Werbos L., and Samuels A.C. THz frequency sensing of DNA and related biological materials. Int. J. High Speed Electron. Syst. (IJHSES) 13 (2003) 903-936
11. Li X., Bykhovski A., Gelmont B., Globus T., Woolard D., and Bykhovskaia M. Computational methods for analysis of terahertz spectral signatures of nucleic acids. Nanotechnology 1 (2005) 221-224
12. Woolard D., Globus T., Gelmont B., Bykhovskaia M., Samuels A.C., Cookmeyer D., Hesler J.L., Crowe T.W., Jensen J.O., Jensen J.L., and Loerop W.R. Submillimeter-wave phonon modes in DNA macromolecules. Phys. Rev. E 65 (2002) 051903-051914
13. Barber J., Hooks D.E., Funk D.J., Averitt R.D., Taylor A.J., and Babikov D. Temperature-dependent far-infrared spectra of single crystals of high explosives using terahertz time-domain spectroscopy. J. Phys. Chem. A 109 (2005) 3501-3505
14. Federici J.F., Schulkin B., Huang F., Gary D., Barat R., Oliveira F., and Zimdars D. THz imaging and sensing for security applications-explosives, weapons and drugs. Semicond. Sci. Technol. 20 (2005) S266-S280
15. Shen Y.C., Lo T., Taday P.F., Cole B.E., Tribe W.R., and Kemp M.C. Detection and identification of explosives using terahertz pulsed spectroscopic imaging. Appl. Phys. Lett. 86 (2005) 24116-24118
16. Schmuttenmaer C.A. Exploring dynamics in the far-infrared with terahertz spectroscopy. Chem. Rev. 104 (2004) 1759-1779
17. Siegel P.H. Terahertz technology in biology and medicine. IEEE Trans. Microwave Theory Tech. 52 (2004) 2438-2447
18. Balu R., Zhang H., Zukowski E., Chen J.-Y., Markelz A.G., and Gregurick S.K. Terahertz spectroscopy of bacteriorhodopsin and rhodopsin; similarities and differences. Biophys. J. 94 (2008) 3217-3226
19. Chen J.-Y., Knab J., Cerne J., and Markelz A.G. Large oxidation dependence observed in terahertz dielectric response for cytochrome c. Phys. Rev. E 72 (2005) 040901
20. Chen J.-Y., Knab J., Ye S., He Y., and Markelz A.G. Terahertz dielectric assay of solution phase protein binding. Appl. Phys. Lett. 90 (2007) 243901
21. Markelz A.G., Knab J., Chen J.-Y., and He Y. Protein dynamical transition in terahertz dielectric response. Chem. Phys. Lett. 442 (2007) 413-417
22. Markelz A.G., Whitmire S.E., Hillebrecht J., and Birge R. THz time domain spectroscopy of biomolecular conformational modes. Phys. Med. Biol. 47 (2002) 3797-3805
23. Castro-Camus E., and Johnston M.B. Conformational changes of photoactive yellow protein monitored by terahertz spectroscopy. Chem. Phys. Lett. 455 (2008) 289-292
24. Yoneyama H., Yamashita M., Kasai S., Kawase K., Ueno R., Ito H., and Ouchi T. Terahertz spectroscopy of native-conformation and thermally denatured bovine serum albumin (BSA). Phys. Med. Biol. 53 (2008) 3543-3549
25. Jaaskelainen S., Verma C.S., Hubbard R., Linko P., and Caves L.S.D. Conformational change in the activation of lipase: an analysis in terms of low-frequency normal modes. Protein Sci. 7 (1998) 1359-1367
26. Markelz A.G., Roitberg A., and Heilweil E.J. Pulsed terahertz spectroscopy of DNA, bovine serum albumin and collagen between 0.1 and 2.0 THz. Chem. Phys. Lett. 320 (2000) 42-48
27. Tama F., Gadea F.X., Marques O., and Sanejouand Y.-H. Building-block approach for determining low-frequency normal modes of macromolecules. Proteins Struct. Funct. Genet. 41 (2000) 1-7
28. Tama F., and Sanejouand Y.-H. Conformational change of proteins arising from normal mode calculations. Protein Eng. 14 (2001) 1-6
29. Alexandrov V., Lehnert U., Echols N., Milburn D., Engelman D., and Gerstein M. Normal modes for predicting protein motions: a comprehensive database assessment and associated web tool. Protein Sci. 14 (2005) 633-643
30. Amadei A., Linnsen A.B.M., and Berendsen H.J.C. Essential dynamics of proteins. Proteins Struct. Funct. Genet. 17 (1993) 412-425
31. Brooks B.R., and Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. PNAS 80 (1983) 6571-6575
32. Ichiye T., and Karplus M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations. Proteins Struct. Funct. Genet. 11 (1991) 205-217
33. Ma J. Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. Structure 13 (2005) 373-380
34. Katzin B.J., Collins E.J., and Robertus J.D. Structure of ricin A-chain at 2.5 Å. Proteins 10 (1991) 251-259
35. Rutenber E., Katzin B.J., Ernst S.R., Collins E.J., Misna D., Ready M.P., and Robertus J.D. Crystallographic refinement of ricin at 2.5 Å. Proteins 10 (1991) 240-250
36. Weston S.A., Tucker A.D., Thatcher D.R., Derbyshire D.J., and Pauptit R.A. X-ray structure of recombinant ricin A-chain at 1.8 A resolution. J. Mol. Biol. 244 (1994) 410-422
37. Olson M.A. Ricin A-Chain structural determinant for binding substrate analogues: a molecular dynamics simulation analysis. Proteins Struct. Funct. Genet. 27 (1997) 80-95
38. Lord J.M., Roberts L.M., and Robertus J.D. Ricin: structure, mode of action, and some current applications. FASEB J. 8 (1994) 201-208
39. Monzingo A.F., and Robertus J.D. X-ray analysis of substrate analogs in the ricin. J. Mol. Biol. 227 (1992) 1136-1145
40. Ready M.P., Kim Y., and Robertus J.D. Site directed mutagenesis of ricin A chain and implications for the mechanism of action. Proteins Struct. Funct. Genet. 10 (1991) 270-278
41. Mentch F., Parkin D.W., and Schramm V.L. Transition-state structures for N-glycoside hydrolysis of AMP by acid and by AMP nucleosidase in the presence and absence of allosteric activator. Biochemistry 26 (1987) 921-930
42. Endo Y., Gluck A., and Wool I.G. Ribosomal RNA identity elements for ricin A-chain recognition and catalysis. J. Mol. Biol. 221 (1991) 193-207
43. Correll C.C., Munishkin A., Chan Y.L., Ren Z., Wool I.G., and Steitz T.A. Crystal structure of the ribosomal RNA domain essential for binding elongation factors. PNAS 95 (1998) 13436-13441
44. Heus H.A., and Pardi A. Structure features that give rise to the unusual stability of RNA hairpins containing GNRA loops. Science 253 (1991) 191-194
45. Brooks B.R., Janezic D., and Karplus M. Harmonic analysis of large systems. J. Comp. Chem. 16 (1995) 1522-1542
46. Hayward S., Kitao A., and Go N. Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis. Protein Sci. 3 (1994) 936-943
47. Day P.J., Ernst S.R., Frankel A.E., Monzingo A.F., Pascal J.M., Molina-Svinth M.C., and Robertus J.D. Structure and activity of an active site substitution of ricin A chain. Biochemistry 35 (1996) 11098-11103
48. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4 (1983) 187-217
49. Day G.M., Zeitler J.A., Jones W., Rades T., and Taday P.F. J. Phys. Chem. B 110 (2006) 447-456
50. Sanejouand Y.-H. Normal-mode analysis suggests important flexibility between the two N-terminal domains of CD4 and supports the hypothesis of a conformational change in CD4 upon HIV binding. Protein Eng. 9 (1996) 671-677
51. Wilson Jr. E.B., Decius J.C., and Cross P.C. Molecular Vibrations: The Theory of Infrared and Raman vibrational spectra (1955), McGraw-Hill, New York
52. Harrison W. Variational calculation of the normal modes of a large macromolecule: methods and some initial results. Biopolymers 23 (1984) 2943-2949
53. Brooks B.R., and Karplus M. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. PNAS 82 (1985) 4995-4999
54. Marques O., and Sanejouand Y.-H. Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins Struct. Funct. Genet. 23 (1995) 557-560
55. Thomas A., Hinsen K., Field M.J., and Perahia D. Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study. Proteins Struct. Funct. 34 (1999) 96-112
56. Humphrey W., Dalke A., and Schulten K. VMD-visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
57. Jung J.O., and Gerber R.B. Vibrational wave functions and energy levels of large anharmonic clusters: a vibrational SCF study of (Ar)13. J. Chem. Phys. 105 (1996) 10682-10689