Are density functional theory predictions of the Raman spectra accurate enough to distinguish conformational transitions during amyloid formation?

Journal of Molecular Modeling

Volumn 16, Issue 6, 2010, Pages 1093-1101

  Berhanu, Workalemahu Mikre ^a   Mikhailov, Ivan A ^a   Masunov, Artëm E ^a  

^a UNIVERSITY OF CENTRAL FLORIDA   (United States)

Author keywords

Amide vibrational band; Assignment of raman spectra; Densityfunction theory conformational transition; Peptide conformational change; Polyglutamic acid

Indexed keywords

AMYLOID; GLUTAMIC ACID; HEXAPEPTIDE; LYSINE;

ACCURACY; ARTICLE; CONFORMATIONAL TRANSITION; DENSITY FUNCTIONAL THEORY; HYDROGEN BOND; PEPTIDE ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; RAMAN SPECTROMETRY;

AMYLOID; GLUTAMIC ACID; HYDROGEN BONDING; LYSINE; MODELS, MOLECULAR; MOLECULAR STRUCTURE; OLIGOPEPTIDES; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SPECTRUM ANALYSIS, RAMAN; WATER;

EID: 77955096647     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-009-0610-2     Document Type: Article

References (46)

1. Stefani M (2004) Biochim Biophys Acta 1739:5-25
2. Chiti F, Webster P, Taddei N, Clark A, Stefani M, Ramponi G, Dobson CM (1999) Proc Natl Acad Sci USA 96:3590-3594
3. Dobson CM (2001) Philos Trans R Soc Lond B 356:133-145
4. Fandrich M, Fletcher MA, Dobson CM (2001) Nature 410:165-166
5. Jas GS, Eaton WA, Hofrichter J (2001) J Phys Chem B 105:261-272
6. Manas ES, Getahun Z, Wright WW, DeGrado WF, Vanderkooi JM (2000) J Am Chem Soc 122:9883-9890
7. Maji SK, Amsden JJ, Rothschild KJ, Condron MM, Teplow DB (2005) Biochemistry 44:13365-13376
8. Fasman GD (1996) Circular dichroism and the conformational analaysis of biomolecules. Plenum, New York
9. Ozdemir A, Lednev IK, Asher SA (2002) Biochemistry 41:1893-1896
10. McColl IH, Blanch EW, Hecht L, Barron LD (2004) J Am Chem Soc 126:8181-8188
11. Barron LD, Hecht L, Ford SJ, Bell AF, Wilson G (1995) J Mol Struct 349:397-400
12. McColl IH, Blanch EW, Hecht L, Kallenbach NR, Barron LD (2004) J Am Chem Soc 126:5076-5077
13. Zhu FJ, Isaacs NW, Hecht L, Barron LD (2005) Structure 13:1409-1419
14. Spiro T (1987) Biological application of Raman spectroscopy, Vol 1. Raman spectra and the conformation of biological macromolecules. Wiley, New York
15. Chi ZH, Asher SA (1998) J Phys Chem B 102:9595-9602
16. Asher SA, Mikhonin AV, Bykov S (2004) J Am Chem Soc 126:8433-8440
17. Lednev IK, Karnoup AS, Sparrow MC, Asher SA (1999) J Am Chem Soc 121:8074-8086
18. Scheiner S, Kern CW (1977) J Am Chem Soc 99:7042-7050
19. Creighton TE (1993) Proteins: structures and molecular properties. Freeman, New York
20. Baker EN, Hubbard RE (1984) Prog Biophys Mol Biol 44:97-179
21. Bochicchio B, Tamburro AM (2002) Chirality 14:782-792
22. Martino M, Bavoso A, Guantieri V, Coviello A, Tamburro AM (2000) J Mol Struct 519:173-189
23. Mezei M, Fleming PJ, Srinivasan R, Rose GD (2004) Proteins 55:502-507
24. Gnanakaran S, Hochstrasser RM, Garcia AE (2004) Proc Natl Acad Sci USA 101:9229-9234
25. Thanki N, Thornton JM, Goodfellow JM (1988) J Mol Biol 202:637-657
26. Daggett V, Levitt M (1992) J Mol Biol 223:1121-1138
27. Stapley BJ, Creamer TP (1999) Protein Sci 8:587-595
28. Kelly MA, Chellgren BW, Rucker AL, Troutman JM, Fried MG, Miller AF, Creamer TP (2001) Biochemistry 40:14376-14383
29. Adzhubei AA, Sternberg MJE (1993) J Mol Biol 229:472-493
30. Makarov AA, Lobachov VM, Adzhubei IA, Esipova NG (1992) FEBS Lett 306:63-65
31. Makarov AA, Esipova NG, Lobachov VM, Grishkovsky BA, Pankov YA (1984) Biopolymers 23:5-22
32. Hodes ZI, Nemethy G, Scheraga HA (1979) Biopolymers 18:1565-1610
33. Eisenhaber F, Adjhubei AA, Eisenmenger F, Esipova NG (1992) Biofizika 37:62-67
34. Schweitzer-Stenner R (2006) Vib Spectrosc 42:98-117
35. Nielsen OF (2005) In: Jiskoot WCDJA (ed) Methods for structural analysis of protein pharmaceuticals. AAPS, Arlington, pp 167-199
36. Chi ZH, Chen XG, Holtz JSW, Asher SA (1998) Biochemistry 37:2854-2864
37. Diem M (1993) Introduction to modern vibrational spectroscopy. Wiley, New York
38. Herrmann C, Reiher M (2007) First-principles approach to vibrational spectroscopy of biomolecules. In: Reiher M (ed) Atomistic approaches in modern biology: from quantum chemistry to molecular simulations. Springer, Berlin, pp 85-132
39. Deng Z, Polavarapu PL, Ford SJ, Hecht L, Barron LD, Ewig CS, Jalkanen K (1996) J Phys Chem 100:2025-2034
40. Han WG, Jalkanen KJ, Elstner M, Suhai S (1998) J Phys Chem B 102:2587-2602
41. Vaden TD, Gowers SAN, de Boer T, Steill JD, Oomens J, Snoek LC (2008) J Am Chem Soc 130:14640-14650
42. Song SH, Asher SA (1989) J Am Chem Soc 111:4295-4305
43. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA Jr, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, Rev E.01. Gaussian Inc, Wallingford CT
44. Noordik GSJH (2000) J Comput Aided Mol Des 14:123-134
45. Scheiner S (2009) J Phys Chem B 113:10421-10427
46. Wieczorek R, Dannenberg JJ (2004) J Am Chem Soc 126:14198-14205