PubMed · 6554105
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J M Morse, A Conrad. 1983. Putting research into practice.. https://pubmed.ncbi.nlm.nih.gov/6554105/
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We investigate the role that local conformational tendencies can have in guiding the folding of helical proteins, using simple statistical mechanical models. The theory provides a synthesis of classical models of the helix-coil transition in polymers with an approximate treatment of the effects of excluded volume, confinement, and packing alignment of the helices based on a free energy function. The theory studies the consequences of signals encoded locally in the sequence as stabilization energies associated with three types of local structure: native helical conformations, native non-helical conformations, and native helix caps or start-stop signals. The role of randomness in the energies of conformations due to tertiary interactions is also studied vis-à-vis the difficulty of conformational search. The thermal behavior of the model is presented for realistic values of the conformational signal energies, which can be estimated from experimental studies on peptide fragments. Estimates are made for the relative contribution of local signals and specific tertiary interactions to the folding stability gap.
Earlier studies [P.J. Westervelt, J. Acoust. Soc. Am. 29, 199-203, 934-935 (1957)] of the mutual nonlinear interaction of two plane waves of sound with each other are extended to include the viscous effect. The viscous effect is considered both from the equations of motion and the equation of state of the medium. An analytical solution to the lowest-order scattering process is obtained if the viscous effect of second order and higher can be neglected.
As the three-dimensional structures of more and more proteins are determined by experiment, discovering substantially novel folding motifs becomes ever rarer. The natural question is how many motifs are there and how many have already been found? In order to answer this in at least one plausible and well-defined sense, we have chosen a quantitative measure of conformational similarity, rho (based on optimal rigid body superposition), and a means of generating all possible three-dimensional chain conformations using the discrete cosine transform. How many different folding motifs there are then depends on the specified cutoff in rho and on the flexibility allowed for the model polypeptide chain. For single chain proteins having no more than about 170 residues and which are not beta-barrels, there are only about 128 motifs that differ by rho > 1.0 (an extremely vague level of similarity), of which so far only 100 have been seen experimentally. The remaining 28 can be viewed as very low-resolution models of either undiscovered novel folds or violations of unknown principles of protein folding.