Helix-coil stability constants for the naturally occurring amino acids in water. 19. Isoleucine parameters from random poly[(hydroxypropyl)glutamine-co-L-isoleucine]

A molecular thermodynamic approach to predict the secondary structure of homopolypeptides in aqueous systems

Under physiological conditions, many polypeptide chains spontaneously fold into discrete and tightly packed three-dimensional structures. The folded polypeptide chain conformation is believed to represent a minimum Gibbs energy of the system, governed by the weak interactions that operate between the amino acid residues and between the residues and the solvent. A semiempirical molecular thermodynamic model is proposed to represent the Gibbs energy of folding of aqueous homopolypeptide systems. The model takes into consideration both the entropy contribution and the enthalpy contribution of folding homopolypeptide chains in aqueous solutions. The entropy contribution is derived from the Flory-Huggins expression for the entropy of mixing. It accounts for the entropy loss in folding a random-coiled polypeptide chain into a specific polypeptide conformation. The enthalpy contribution is derived from a molecular segment-based Non-Random Two Liquid (NRTL) local composition model [H. Renon and J. M. Prausnitz (1968) AIChE J., Vol. 14, pp. 135-142; C.-C. Chen and L. B. Evans (1986) AIChE J., Vol. 32, pp. 444-454], which takes into consideration of the residue-residue, residue-solvent, and solvent-solvent binary physical interactions along with the local compositions of amino acid residues in aqueous homopolypeptides. The UNIFAC group contribution method [A. Fredenslund, R. L. Jones, and J. M. Prausnitz (1975) AIChE J., 21, 1086-1099; A. Fredenslund, J. Gmehling, and P. Rasmussen (1977) Vapor-Liquid Equilibrium Using UNIFAC, Elsevier Scientific Publishing Company, Amsterdam], developed originally to estimate the excess Gibbs energy of solutions of small molecules, was used to estimate the NRTL binary interaction parameters. The model yields a hydrophobicity scale for the 20 amino acid side chains, which compares favorably with established scales [Y. Nozaki and C. Tanford (1971) Journal of Biological Chemistry, Vol. 46, pp. 2211-2217; E. B. Leodidis and T. A. Hatton (1990) Journal of Physical Chemistry, Vol. 94, pp. 6411-6420]. In addition, the model generates qualitatively correct thermodynamic constants and it accurately predicts thermodynamically favorable folding of a number of aqueous homopolypeptides from random-coiled states into alpha-helices. The model further facilitates estimation of the Zimm-Bragg helix growth parameter s and the nucleation parameter sigma for amino acid residues [B. H. Zimm and J. K. Bragg (1959) Journal of Chemical Physics, Vol. 31, pp. 526-535]. The calculated values of the two parameters fall into the ranges suggested by Zimm and Bragg.

Influence of L-cystinyl side-chain configurations on the melting of crosslinked alpha-tropomyosin dimers

The experimental melting profile reported by Holtzer, M.E., Holtzer, A. and Skolnick, J. (Macromolecules 16 (1983) 173-180) for the rabbit alpha-tropomyosin dimer crosslinked at cysteine residue 190 has been analyzed using matrix methods. The configuration partition function employed includes a term arising from interactions at the crosslink site. This term, denoted by omega, is found to be smaller than 1, implying that events at the crosslink site resist helix formation by dimer. A theoretical analysis of the conformational restrictions imposed on the crosslink provides a satisfactory estimate of omega at high temperatures. Agreement deteriorates at lower temperatures, perhaps as a consequence of difficulty in establishing a reliable value for omega from analysis of the low-temperature circular dichroism data.

Helix formation upon acidification of protein-dodecyl sulfate complexes

The pH dependence of circular dichroism spectra has been studied for dodecyl sulfate complexes formed by 25 proteins and for a random copolypeptide of glutamic acid and alanine. The pH range covered is that in which titration of side-chain carboxyl groups is to be expected. Circular dichroism spectra signify an increase in helical content upon acidification, although in many cases the increase is quite small. For all but three of the proteins studied, the spectral changes are in reasonable agreement with those expected because helix propagation by glutamyl and aspartyl residues is enhanced when the state of the side-chain carboxyl changes from COO- to COOH. This simple explanation seriously underestimates conformational changes reported for gastrin, Kunitz trypsin inhibitor and tropomyosin. Changes in charge density appear to play an important role in these proteins.