Computer-aided discrimination between active and inactive mutants of the N-terminal domain of the bacteriophage lambda repressor.

Binding of the N-terminal domain of the lambda repressor to DNA is coupled to dimerization. Hydrophobic interactions between helix-5 and helix-5' drive the packing at the dimer interface. We have carried out computations of the conformational energy of packing of the fifth helices (and of the helix-4-loop-helix-5 portions) of variants of the lambda repressor operator binding domain, using an ECEPP/3-based packing algorithm.

Effects on protein structure and function of replacing tryptophan with 5-hydroxytryptophan: single-tryptophan mutants of the N-terminal domain of the bacteriophage lambda repressor.

Conformational energy computations have been carried out on the N-acetyl-N'-methylamide of 5-hydroxytryptophan (5OH-Trp) using ECEPP/3. As observed with tryptophan (Trp), the most preferred conformation about the C alpha-C beta bond of the side chain is g+ or t. This preference is reduced to only the t conformational state when 5-hydroxyTrp is in the middle of a right-handed poly(L-alanine) alpha-helix.

The energy of formation of internal loops in triple-helical collagen polypeptides.

The sequence-dependent local destabilization in the interior of the collagen triple helix has been evaluated by means of conformational energy computations. Using a model poly(Gly-Pro-Pro) triple helix as the reference state, a method was developed for generating local loops, i.e.

Structure of the type I collagen molecule based on conformational energy computations: the triple-stranded helix and the N-terminal telopeptide.

Various studies have implicated a crucial role for the non-helical ends (telopeptides) of the collagen molecule during fibrillogenesis. In this paper, the first extensive conformational analysis of the type I collagen N-terminal telopeptide is reported. The commonly used "build-up" procedure for peptides and proteins has been used, with relevant modifications to take account of all the stereochemical constraints affecting the telopeptide.

The effect of the l-azetidine-2-carboxylic acid residue on protein conformation. IV. Local substitutions in the collagen triple helix.

The properties of collagen are affected by the replacement of Pro by imino acid analogues. The structural effect of the low-level local substitution of L-azetidine-2-carboxylic acid (Aze) has been analyzed by computing the energy of CH3CO-(Gly-Pro-Pro)4-NHCH3 triple helices in which a single residue of one strand has been replaced by Aze. When Aze is in position Y of a (Gly-X-Y) unit, low-energy local deformations are introduced in the triple helix, i.