Thermodynamic parameters of the helix-coil transition in polypeptide chains. III. Random copolymers of L-leucine and L-glutamic acid

Conformational Preferences of N-Acetyl-l-leucine-N‘-methylamide. Gas-Phase and Solution Calculations on the Model Dipeptide

A DFT study of N-acetyl-l-leucine-N'-methylamide conformers in the gas phase and in solution was carried out. The theoretical computational analysis revealed 43 different conformations at the B3LYP/6-31G(d) level of theory in the gas phase. In addition, the effects of three solvents (water, acetonitrile, and chloroform) were included in the calculations using the isodensity polarizable continuum model (IPCM) and the Poisson-Boltzmann self-consistent reaction field (PB-SCRF) method. The stability order of the different conformers in solution has been analyzed. The theoretical results were compared with some experimental data (X-ray, IR, and NMR).

Rate of beta-structure formation in polypeptides

An explanation is suggested for why a marginally stable beta-structure folds extremely slowly; it is predicted that even a small increase in stability drastically accelerates beta-folding. According to the theory, this folding is a first-order phase transition, and the rate-limiting step is nucleation. The rate-determining "nucleus" (transition state) is the smallest beta-sheet that is sufficiently large to provide an overall free energy reduction during subsequent folding. If the stability of the beta-structure is low, the nucleus is large and possesses a high free energy due to having a large perimeter. When the net stability of the final beta-structure increases (due to either an increase of the beta-sheet stability or a decrease in stability of the competing structures, e.g., alpha-helices), the size and energy of a nucleus decrease and the rate of folding increases exponentially. This must result in a fast folding of polypeptides enriched by beta-forming residues (e.g., protein chains). The theory is developed for intramolecular beta-structure, but it can also explain the overall features of intermolecular beta-folding; it is applicable both to antiparallel and parallel beta-sheets. The difference in folding of beta-sheets, alpha-helices, and proteins is discussed.

Similarities of protein topologies: evolutionary divergence, functional convergence or principles of folding?

(A)Evolutionary similarities of protein structuresTwo decades have passed from the time that the three dimensional structure of the first globular protein, sperm whale myoglobin, was decoded (Kendrewet al.1960). Its structure, which now looks so simple and habitual, then seemed to be unusually complicated. The decoding of the subsequent proteins, lysozyme (Blakeet al.1965), ribonuclease (Kartha, Bello & Harker, 1967), chymotrypsin (Matthewset al.1967), carboxypeptidase (Lipscombet al.1969) redoubled the feeling of amazement and even of some confusion before the extremely complicated, intricate and, above all, absolutely unlike protein structures. Some consolation against this background was the evident and far-reaching similarity between the three-dimensional structures of myoglobin and hemoglobin subunits (Perutz, Kendrew & Watson, 1965) and an analogous similarity between the structures of chymotrypsin and other serine proteases, elastase (Shotton & Watson, 1970) and trypsin (Stroud, Kay & Dickerson, 1972). However this similarity was easily explained by the far-reaching homology between the primary structures of myoglobin and hemoglobin and between the primary structures of serine proteases.