Showing papers by "Bruce Tidor published in 1993"

Probing the roles of residues at the e and g positions of the GCN4 leucine zipper by combinatorial mutagenesis.

Abstract: Combinatorial mutagenesis with an alphabet limited to alanine, glutamic acid, lysine, and threonine was used to probe the role of interactions involving surface residues in stabilizing a short alpha-helical coiled coil. The residues at eight e and g positions in the leucine zipper of the Saccharomyces cerevisiae transcription factor GCN4 were randomized to these four residues in a lambda repressor-leucine zipper fusion protein, resulting in 65,536 possible residue combinations. Roughly three-fourths of these combinations allowed stable coiled-coil formation as assayed by DNA binding by the fusion protein. To understand the basis for the activity differences, functional and non-functional mutants were sequenced and statistical tests were applied to identify structure/function correlations. Helix-forming propensity and favorable intrasubunit and intersubunit charge-charge interactions were positively correlated with activity. These studies suggest that the identities of surface side chains at the e and g positions of coiled coils contribute modestly to stability; by comparison with previous work, however, the e and g positions are far less critical than residues at the a and d positions, which form the hydrophobic core of the dimer interface.

The contribution of cross-links to protein stability: a normal mode analysis of the configurational entropy of the native state.

Abstract: The vibrational entropy of native BPTI, with three disulfide bonds, was determined by use of normal mode calculations and compared with that of folded variants having either one less disulfide bond or lacking a peptide bond at the trypsin-reactive site. Favorable contributions to the free energy of 2.5–5.1 kcal/mol at 300 K were calculated for the reduction of disulfide bonds in the folded state, whereas no favorable contribution was found for the hydrolysis of the peptide bond cleaved by trypsin. This is on the order of the effect of disulfides in the unfolded state. The implications of these results for the stabilization of a folded protein by the introduction of crosslinks are discussed. © 1993 Wiley-Liss, Inc.

Simulated annealing on free energy surfaces by a combined molecular dynamics and Monte Carlo approach

Abstract: A method is presented for sampling coupled potential energy surfaces and selecting the one with the most favorable free energy. Cartesian coordinates and chemical composition are treated as independent variables of the system, and simulated annealing is used to optimize in coordinate and composition spaces to produce a minimum free energy subensemble. Molecular dynamics is used to sample in the Cartesian dimensions, and a Monte Carlo approach is used to sample in the chemical dimensions. The method has been applied to selecting the solute with the most favorable solvation energy for the well-studied system of bromide and chloride