PubMed · 2567498
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M J Sternberg, W J Gullick. 1989-06-22. Neu receptor dimerization.. https://doi.org/10.1038/339587a0
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Several neutral solutes, ranging in size from methanol to a tetrasaccharide, stachyose, are shown to stabilize the left-handed Z form of the methylated polynucleotide poly(dG-m5dC). The action of these solutes is consistent with an osmotic stress, that is, with their effect on water chemical potentials coupled to a difference in the number of associated water molecules between the B and Z conformations. The apparent difference in hydration between the two forms is, however, dependent on the particular solute used to probe the reaction. The effect of solutes is not consistent either with a direct binding of solute or with an indirect effect on electrostatics or ion binding through changes in the solution dielectric constant. The interplay of NaCl and neutral solute in modulating the B-Z transition suggests that salt also could be stabilizing the Z form through an osmotic stress.
This paper demonstrates that overall folds of two-layer alpha/beta-proteins and beta-proteins with aligned beta-sheet packings have a number of common features. First of all, there are similar recurrent folding units, the so-called abcd-units, in proteins of both the classes. There are also some larger commonly occurring structures in many representatives of these classes. The fact that these proteins belong to different structural classes and have different functions supports the idea that some physical principles governing the polypeptide chain folding rather than the evolutionary divergence or functional convergence of proteins are the basis of such similarities. The analysis reported here shows that practically all the known protein structures of these classes can be obtained by stepwise addition of secondary structure element to the abcd-units taking into account three simple rules: (1) crossing of connection regions is prohibited; (2) alpha-helices should be packed into the alpha-layer and beta-strands in to the beta-layer of the growing structure; (3) beta alpha beta-units should be folded into right-handed superhelices; three consecutive beta-strands can be folded into the similar right-handed beta beta beta-superhelix if there is at least one additional beta-strand in the layer between the first and third ones. A possible selection of a conformation of a polypeptide chain segment by its protein environment is also discussed.
We present an effective theory for water. Our goal is to formulate an accurate model for the effects of solvation on protein dynamics, without incurring the huge computational cost and the slow temporal evolution typical of molecular dynamics simulations of liquids. We replace the individual water molecules in an all-atom potential with a local dielectric density field, with self-interactions given by the Landau-Ginzburg free energy and external interactions by Lennard-Jones forces at the surface of the protein atoms. We explore conformational space with finite temperature Monte Carlo dynamics, using parallel Langevin and Fourier acceleration algorithms well suited to data-parallel computer architectures such as the Connection Machine. To establish the validity of our approximations, we compare our electrostatic contribution to the solvation energy with the results of Lim, Bashford, and Karplus using a conventional static continuum dielectric cavity model, and the nonelectrostatic contributions with estimates of hydrophobic surface free energy. Our model can also accommodate ionic charges and temperature fluctuations. We propose future investigations extending our effective theory of solvation to include explicit orientational entropy and hydrogen-bonding terms.