Methods of peptide conformation studies

• Autorzy: Bierzynski A.
• Języki publikacji: EN

Abstrakty

EN

In solution most of the peptides assume multiple flexible conformations. Determina­tion of the dominant conformers and evaluation of their populations is the aim of pep- tide conformation studies, in which theoretical and experimental methods play com­plementary roles. Molecular dynamics or Monte Carlo methods are quite effective in searching the conformational space accessible to a peptide but they are not able to es­timate, precisely enough, the populations of various conformations. Therefore, they must be supplemented by experimental data. In this paper, a short review of the experimental methods, most widely used in pep­tide conformational studies, is presented. Among them NMR plays the leading role. Valuable information is also obtained from hydrogen exchange, fluorescence reso­nance energy transfer, and circular dichroism measurements. The advantages and shortcomings of these methods are discussed.

Słowa kluczowe

EN

fluorescence resonance energy transfer; hydrogen exchange; peptide conformation; circular dichroism

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2001
• Tom: 48
• Numer: 4
• Opis fizyczny: p.1091-1099,fig.

Twórcy

autor

Bierzynski A.

• Polish Academy of Sciences, A.Pawinskiego 5A, 02-106 Warsaw, Poland

Bibliografia

• 1.Dyson, H.J. & Wright, P.E. (1993) Peptide conformation and protein folding. Curr. Opin. Struct. Biol. 3, 60-65.
• 2.Pauling, L., Corey, R.B. & Branson, H.R. (1951) The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. U.S.A. 37, 205-211.
• 3.Pauling, L. & Corey, R.B. (1951) Configurations of polypeptide chains with favoured orientations around single bonds: Two new pleated sheets. Proc. Natl. Acad. Sci. U.S.A. 37, 729-740.
• 4.Chakrabartty, A. & Baldwin, R.L. (1995) Stability of alpha-helice. Adv. Protein Chem. 46, 141-176.
• 5.Soto, C. (2001) Protein misfolding and disease; protein refolding therapy. FEBSLett. 498, 204-207.
• 6.Serpell, L.C. (2000) Alzheimer's amyloid fibrils: structure and assembly. Biochim. Biophys. Acta 1502, 16-30.
• 7.Ripka, A.S. & Rich, D.H. (1998) Peptomimetic design. Curr. Opin. Chem. Biol. 2(4), 441-452.
• 8.Bierzynski, A. (1988) Deprotonation of Glu9 destabilizes the alpha-helix in C-peptide of RNase A. Int. J. Pept Protein Res. 32, 256-261.
• 9.Dyson, H.J., Rance, M., Houghten, R.A., Lerner, R.A. & Wright, P.E. (1988) Folding of immunogenic peptide fragments of proteins in water solution. I. Sequence requirements for the formation of a reverse turn. J. Mol. Biol. 201, 161-200.
• 10.Siedlecka, M., Goch, G., Ejchart, A., Sticht, H. & Bierzynski, A. (1999) alpha-Helix nucleation by a calcium-binding peptide loop. Proc. Natl. Acad. Sci. U.S.A. 96, 903-908.
• 11.Lakowicz, J.R. & Eis, P.S. (1993) Time-resolved energy transfer measurements of donor-acceptor distance distributions and intramolecular flexibility of a CCHH zinc finger peptide. Biochemistry 32, 7981-7993.
• 12.Groth, M., Malicka, J., Rodziewicz-Motowidlo, S., Czaplewski, C., Klaudel, L., Wiczk, W. & Liwo, A. (2001) Determination of conformational equilibrium of peptides in solution by NMR spectroscopy and theoretical conformational analysis: Application to the calibration of mean-field solvation models. Biopolymers 60, 79-95.
• 13.Groth, M., Malicka, J., Czaplewski, C., Oldziej, S., Lankiewicz, L., Wiczk, W. & Liwo, A. (1999) Maximum entropy approach to the determination of solution conformation of flexible polypeptides by global conformation analysis and NMR spectroscopy — Application to DNS1-c-[D-A2bu2, Trp4, Leu5]enkephalin and DNS 1-c-[D-A2bu2, Trp4, D-Leu5]enkephalin. J. Biomol. NMR 15, 315-330.
• 14. Sidor, M., Wojcik, J., Pawlak, D. & Izdebski, J. (1999) Conformational analysis of a novel cyclic enkephalin analogue using NMR and EDMC calculations. Acta Biochim. Polon. 46, 641-650.
• 15.Pawlak, D., Oleszczuk, M., Wojcik, J., Pachulska, M., Chung, N.N., Schiller, P.W. & Izdebski, J. (2001) Higly potent side-chain to side-chain cyclized enkephalin analogues containing a carbonyl bridge: Synthesis, biology and conformation. J. Pept. Sci. 7, 128-140.
• 16.Wojcik, J., Goral, J., Pawlowski, K. & Bierzynski, A. (1997) Isolated calcium-binding loops of EF-hand proteins can dimerize to form a native-like structure. Biochemistry 36, 680-687.
• 17.Jaravine, V.A., Alexandrescu, A.T. & Grzesiek, S. (2001) Observation of the closing of individual hydrogen bonds during TFE-induced helix formation in a peptide. Protein Sci. 10, 943-950.
• 18.Cordier, F. & Grzesiek, S. (1999) Direct observation of hydrogen bonds in proteins by interresidue 3hJNC' scalar couplings. J. Am. Chem. Soc. 121, 1601-1602.
• 19.Cornilescu, G., Hu, J.S. & Bax, A. (1999) Identification of the hydrogen bonding network in a protein by scalar couplings. J. Am. Chem. Soc. 121, 2949-2950.
• 20.Bai, Y., Milne, J.S., Mayne, L. & Englander, S.W. (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17, 75-86.
• 21.Connelly, G.P., Bai, Y., Jeng, M.-F. & Englander, S.W. (1993) Isotope effects in peptide group hydrogen exchange. Proteins 17, 87-92.
• 22.Wojcik, J., Ruszczynska, K., Zhukov, I. & Ejchart, A. (1999) NMR measurements of proton exchange between solvent and peptides and proteins. Acta Biochim. Polon. 46, 651- 663.
• 23.Wagner, D.S., Milton, L.G., Yan, Y., Erickson, B.W. & Anderegg, R.J. (1994) Deuterium exchange of alpha-helices and beta-sheets as monitored by electrospray ionization mass spectrometry. Protein Sci. 3, 1305-1314.
• 24.Donward, K.M. (1997) Characterization of the conformations of antigenic peptides of protein lactate dehydrogenase (LDH-C4) by electrospray ionization spectroscopy. Rapid Commun. Mass Spectrom. 11, 1853-1858.
• 25.Buijs, J., Hakansson, K., Hagman, C., Hakansson, P. & Oscarsson, S. (2000) A new method for the accurate determination of the isotopic state of single amide hydrogens within peptides using Fourier transform ion cyclotron resonance mass spectrometry. Rapid Commun. Mass Spectrom. 14, 1751-1756.
• 26.Forster, T. (1965) Delocalized excitation and excitation transfer; in Modern Quantum Chemistry (Sinanoglu, O., ed.) vol. 3, Academic Press, New York.
• 27.Lankiewicz, L., Malicka, J. & Wiczk, W. (1997) Fluorescence resonance energy transfer in studies of inter-chromophoric distances in biomolecules. Acta Biochim. Polon. 44, 477-490.
• 28.Gryczynski, I., Wiczk, W., Johnson, M.L., Cheung, H.C., Wang, C. & Lakowicz, J.R. (1988) Resolution of the end-to-end distance distribution of flexible molecules using quenching-induced variations of the Forster distance for fluorescence energy transfer. Biophys. J. 54, 577-586.
• 29.Gryczynski, I., Wiczk, W., Johnson, M.L. & Lakowicz, J.R. (1988) End-to-end distance distributions of flexible molecules from steady state fluorescence energy transfer and quenching-induced changes in the Forser distance. Chem. Phys. Lett. 145, 439-446.
• 30.Lakowicz, J.R., Gryczynski, I., Kusba, J., Wiczk, W., Szmacinski, H. & Johnson, M.L. (1994) Site-to-site diffusion in proteins as observed by energy transfer and frequency-domain fluorometry. Photochem. Photobiol. 59, 16-29.
• 31.Greenfield, N.J. (1996) Methods to estimate the conformation of proteins and polypeptides from circular dichroism data. Anal. Biochem. 235, 1-10.
• 32.Gans, P.J., Lyu, P.C., Manning, M.C., Woody, R.W. & Kallenbach, N.R. (1991) The helix-coil transition in heterogeneous peptides with specific side-chain interactions: Theory and comparison with CD spectral data. Biopolymers 31, 1605-1614.
• 33.Rohl, C.A. & Baldwin, R.L. (1997) Comparison of NH exchange and circular dichroism as techniques for measuring the parameters of the helix-coil transition in peptides. Biochemistry 36, 8435-8442.
• 34.Malicka, J., Groth, M., Czaplewski, C., Liwo, A. & Wiczk, W. (1999) Fluorescence decay time distribution analysis of cyclic enkephalin analogues. Influence of the sovents and configuration of amino acids in position 2 and 3 on changes in conformation. Acta Biochim. Polon. 46, 615-629.
• 35.Greenfield, N. & Fasman, G.D. (1969) Computed circular dichroism spectra for the evaluation of protein conformation. Biochemistry 8, 4108.