Temperature dependent 2nd derivative absorbance spectroscopy of aromatic amino acids as a probe of protein dynamics

Protein Science

Volumn 18, Issue 12, 2009, Pages 2603-2614

  Esfandiary, Reza ^a   Hunjan, Jagtar S ^a   Lushington, Gerald H ^a   Joshi, Sangeeta B ^a   Middaugh, C Russell ^a  

^a UNIVERSITY OF KANSAS   (United States)

Author keywords

Aromatic side chains; Derivative absorbance spectroscopy; Protein dynamics; Solvent dielectric

Indexed keywords

AROMATIC AMINO ACID; PROTEIN; SOLVENT;

ARTICLE; CONFORMATIONAL TRANSITION; MOLECULAR DYNAMICS; PH; PRIORITY JOURNAL; PROTEIN FOLDING; TEMPERATURE DEPENDENCE; METHODOLOGY; TEMPERATURE; ULTRAVIOLET SPECTROPHOTOMETRY;

AMINO ACIDS, AROMATIC; PROTEIN FOLDING; PROTEINS; SOLVENTS; SPECTROPHOTOMETRY, ULTRAVIOLET; TEMPERATURE;

EID: 73149083990     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.264     Document Type: Article

References (30)

1. Beaven GH, Holiday ER (1952) Ultraviolet absorption spectra of proteins and amino acids. Adv Protein Chem 7:319-386.
2. Mach H, Thomson JA, Middaugh CR, Lewis RV (1991) Examination of phenylalanine microenvironments in proteins by second-derivative absorption spectroscopy. Arch Biochem Biophys 287:33-40.
3. Kueltzo LA, Middaugh CR (2005) Ultraviolet absorption spectroscopy. Biotechnology: pharmaceutical aspects (methods for structural analysis of protein pharmaceuticals) 3:1-25.
4. Kueltzo LA, Ersoy B, Ralston JP, Middaugh CR (2003) Derivative absorbance spectroscopy and protein phase diagrams as tools for comprehensive protein characterization: a bGCSF case study. J Pharm Sci 92:1805-1820.
5. Lange R, Balny C (2002) UV-visible derivative spectroscopy under high pressure. Biochim Biophys Acta 1595:80-93.
6. Lucas LH, Ersoy BA, Kueltzo LA, Joshi SB, Brandau DT, Thyagarajapuram N, Peek LJ, Middaugh CR (2006) Probing protein structure and dynamics by second-derivative ultraviolet absorption analysis of cation-π interactions. Protein Sci 15:2228-2243.
7. The Tripos Associates (2007) SYBYL 8.0. St. Louis, MO: The Tripos Associates.
8. Clark M, Cramer RD, III, Van Opdenbosch N (1989) Validation of the general purpose Tripos 5.2 force field. J Comput Chem 10:982-1012.
9. Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity: a rapid access to atomic charges. Tetrahedron 36:3219-3222.
10. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, 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 JP, 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 MS, 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, Revision C.02. Wallingford CT: Gaussian, Inc.
11. Becke AD (1993) Density-functional thermochemistry III. The role of exact exchange. J Chem Phys 98:5648-5652.
12. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B Condens Matter 37:785-789.
13. Ditchfield R, Hehre WJ, Pople JA (1971) Self-consistent molecular-orbital methods IX. Extended Gaussian-type basis for molecular-orbital studies of organic molecules. J Chem Phys 54:724-728.
14. Frisch MJ, Pople JA, Binkley JS (1984) Self-consistent molecular orbital methods 25. Supplementary functions for Gaussian basis sets. J Chem Phys 80:3265-3269.
15. Stratmann RE, Scuseria GE, Frisch MJ (1998) An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules. J Chem Phys 109:8218-8224.
16. Tomasi J, Mennucci B, Cances E (1999) The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level. Theochem 464:211-226.
17. Fernandez DP, Goodwin ARH, Lemmon EW, Sengers JM, Levelt H, Williams RC (1997) A formulation for the static permittivity of water and steam at temperatures from 238 K to 873 K at pressures up to 1200 MPa, including derivatives and Debye-Hueckel coefficients. J Phys Chem Ref Data 26:1125-1166.
18. Lide DR, Kehiaian HV (1994) Handbook of thermophysical and thermochemical data. Boca Raton, FL: CRC Press.
19. Basu S (1964) Theory of solvent effects on molecular electronic spectra. Adv Quantum Chem 1:145-169.
20. Grimme S, Izgorodina EI (2004) Calculation of 0-0 excitation energies of organic molecules by CIS(D) quantum chemical methods. Chem Phys 305:223-230.
21. Anslyn EV, Dougherty DA (2006) Modern physical organic chemistry. Oakland, California: Wilsted & Taylor Publishing Services, pp 1099.
22. Akerlof G (1932) Dielectric constant of some organic solvent-water mixtures atvarious temperatures. J Am Chem Soc 54:4125-4139.
23. Casteel JF, Sears PG (1974) Dielectric constants, viscosities, and related physical properties of 10 liquid sulfoxides and sulfones at several temperatures. J Chem Eng Data 19:196-200.
24. Usacheva TM, Lifanova NV, Zhuravlev VI, Novozhilov AA, Matveev VK (2000) Calculations of the structure parameters of weakly associated liquids: acetonitrile. Zhurnal Fizicheskoi Khimii 74:1962-1966.
25. Ito M (1960) Ultraviolet absorption study of the molecular association of phenols. J Mol Spectrosc 4:125-143.
26. Dwyer JJ, Gittis AG, Karp DA, Lattman EE, Spencer DS, Stites WE, Garcia-Moreno EB (2000) High apparent dielectric constants in the interior of a protein reflect water penetration. Biophys J 79:1610-1620.
27. Eftink MR, Ghiron CA (1976) Exposure of tryptophanyl residues in proteins. Quantitative determination by fluorescence quenching studies. Biochemistry 15:672-680.
28. Turoverov KK, Kuznetsova IM, Zaitsev VN (1985) The environment of the tryptophan residue in Pseudomonas aeruginosa azurin and its fluorescence properties. Biophys Chem 23:79-89.
29. Irie M (1970) Studies on the state of tryptophan residue in ribonuclease T1 and carboxymethyl ribonuclease T1. J Biochem 68:31-37.
30. Rueda M, Ferrer-Costa C, Meyer T, Perez A, Camps J, Hospital A, Gelpi, JL, Orozco M (2007) A consensus view of protein dynamics. Proc Nat Acad Sci USA 104:796-801.