A simple and novel interpretation of the three-dimensional structure of globular proteins based on quantum-mechanical computations on small model molecules. I

The pseudomolecule method and the structure of globular proteins. II. The example of ribonuclease F1 and T1

The pseudomolecule approach to the structure of globular proteins in which a small number of water molecules are incorporated into the "molecule" is tested again by comparing the ribbon of hydrogen bonds in two proteins, ribonuclease F1 and T1. These two molecules are 59% homologous and have the same backbone conformation both globally and locally. The two ribbons of hydrogen bonds that cover the whole of the backbone are conserved with an accuracy of some 95% providing that allowance is made for the intrusion into one of the pair of such extra factors as the presence of adducts or metal ions, the insertions and the absence of a few water molecules from one of the x-ray data sets. Without these corrections, the conservation of the ribbon is some 85%. There are 35 conserved hydrogen-bonding residues, nearly all of which show many unions to the backbone or interactions with the active site. There are 36 point mutations that involve one or two hydrogen-bonding side chains and nearly all of these have either none or one hydrogen bond to the backbone. These are minor contributors to the ribbon of hydrogen bonds. Of the 71 residues involved in these two categories, all but six fit into the pseudomolecular picture of the structure of globular proteins. The remaining 30 residues almost all contain conserved hydrocarbon side chains that may have a second order effect on the structure through their space filling effects.

In human malaria protective antibodies are directed mainly against the Lys-Glu ion pair within the Lys-Glu-Lys motif of the synthetic vaccine SPf 66

The KEK (Lysine-Glutamic acid-Lysine) motif is frequently found in the primary structure of certain malaria proteins involved in invasion, and plays an important role in the interaction of these proteins with the erythrocyte. This motif is contained in a peptide which forms part of the polymeric synthetic malaria vaccine SPf 66, currently undergoing extensive human trials. Analysis of the antibody titres against the subunit peptides that comprise this vaccine has shown that protection is associated with high titres to the KEK-containing peptide. In this paper we examine the fine recognition of this motif by polyclonal sera from protected vaccinated individuals, demonstrating the critical role played by the interacting ion pair formed between the amino terminal lysine (K) and glutamic acid (E), which act as contact residues for an important proportion of the antibody population directed against this vaccine. This ion pair in the KEK motif constitutes perhaps one of the most important malaria epitopes involved in protection, and could explain the mechanism through which protective immunity is acquired.

Computer analysis of mutations that affect antibody specificity

The mouse hybridoma cell line 40-150 secretes antibodies with high affinity toward the cardiac glycosides digoxin and digitoxin. A spontaneous mutant, 40-150 A2.4, produces an antibody which carries a single residue mutation, Ser----Arg, in its heavy chain (H94) and has an altered specificity. A second-order mutant, 40-150 A2.4 P.10, produces two antibody molecules, one the same as 40-150 A2.4, the other lacking two residues at the N-terminus of its H chain, and having a specificity profile approaching that of 40-150 antibody. The N-terminus and the position H94 are distant from the antigen-binding site of the antibody; thus, the structural basis of the specificity changes was not immediately clear. Approximate structures of the 40-150 antibody and its mutants were constructed in the computer, based on atomic coordinates of the homologous mouse antibody McPC 603. Using the program CONGEN, the torsional space of the polypeptide backbone and side chains around position H94 was uniformly sampled, and the lowest energy conformations were analyzed in detail. The results indicate that when Arg-H94 is substituted for Ser, Arg-H94 can hydrogen bond to side chains of Asp-H101, Arg-L46, and Asp-L55. This results in a change in the surface of the combining site which may account for the affinity changes. Deletion of the two N-terminal residues increases solvent accessibility of Arg-H94. The solvation may cause a hydrogen bond between Arg-H94 and Asp-H101 to be lost, restoring the structure to one similar to that of 40-150.

Salt or ion bridges in biological systems: a study employing quantum and molecular mechanics

Equilibrium geometries and binding energies of model "salt" or "ion" bridge systems have been computed by ab initio quantum chemistry techniques (GAUSSIAN82) and by empirical force field techniques (AMBER2.0). Formate and dimethyl phosphate served as anions in the model compounds while interacting with several organic cations, including methyl ammonium, methyl guanidinium, and divalent metal ion (either Mg2+ or Ca2+) without and with an additional chloride; and a divalent metal ion (either Mg2+ or Ca2+), chloride, and four water molecules of hydration about the metal ion. The majority of the quantum chemical computations were performed using a split-valence basis set. For the model compounds studied we find that the ab initio optimized geometries are in remarkably good agreement with the molecular mechanics geometries. Several calculations were also performed using diffuse fractions. The formate anion binds these model cations more strongly than does dimethyl phosphate, while the organic cation methyl ammonium binds model anions more strongly than does methyl guanidinium. Finally, in model compounds including organic anions, Mg2+ or Ca2+ and four molecules of water, and a chloride anion, we find that the equilibrium structure of the magnesium complex involves a solvent separated ion pair (the magnesium ion is six coordinate), whereas the calcium ion complex remains seven coordinate. Molecular mechanics overestimates binding energies, but the estimates may be close enough to actual binding energies to give useful insight into the details of salt bridges in biological systems.

The rate of equine liver alcohol dehydrogenase denaturation by urea. Dependence on temperature and denaturant concentration

The kinetics of the irreversible urea denaturation of equine liver alcohol dehydrogenase have been studied as a function of temperature and urea concentration. The unfolding of the macromolecule, monitored by means of the phosphorescence properties of a deeply buried tryptophan residue, was found to be strictly a two-state process over the entire temperature range. It is characterized by a steep dependence on urea concentration typical of highly cooperative transitions and below room temperature it possesses large negative activation energies. The reaction is comparatively slow, does not seem to be preceded by a fast phase, and the rate-limiting step does not have the characteristics of proline isomerization. When the data are analyzed in terms of binding equilibria the temperature dependence results from an anomalously large change in heat capacity. Although this is a property of strong hydrophobic interactions in model compounds the slow rates of denaturation are best understood with a model of protein stability which emphasizes the cooperative nature of intramolecular interactions such as hydrogen bonding.