Folding interpenetration in a gliadin model: the role of the characteristic octapeptide motif.

A model of a rheologically relevant protein, omega-gliadin, is proposed and studied in this work by means of molecular dynamics techniques. The model is based on an octapeptide repeat motif that is experimentally described as characteristic of that protein and as constituting it almost entirely. The initial molecular structure consisted of 20 such repeats. It was optimized and the dynamics developed along 980 ps, at dielectric constant epsilon = 80. Remarkable structural features were observed for the model built, such as an elongated twisted tubular overall structure with a peculiar interpenetrating folding pattern, of a very regular character, organized strand formation, topologically segregated sites on the outer surface with an alternate hydrophilic/hydrophobic character and a hydrophilic inner cavity. Dynamics produced significantly more relaxed structures, but was not able to change the main geometric features presented by the original structure. Preliminary attempts of correlating some structural/dynamic aspects observed for the model with features of gliadin rheological behavior are presented.

Molecular dynamics at a cytoplasm/membrane interface of a signal sequence from an E. coli maltoporin.

We used a recently developed software that mimics a cytoplasm/membrane environment, with an interface separating two continuous media of different dielectric constants (1). This software has been designed to allow modelling of different kinds of molecules of biological interest such as proteins and drugs, in each of the isolated continuous media, as well as in their interactions with membrane-like structures, making use of the dielectric discontinuity represented by the interface. In the present study we have applied this program ("THOR") to model a polypeptide sequence corresponding to a 50% active mutant of the signal sequence of the lamB gene product of E. coli, known as maltoporin or lambda receptor (2). The peptide was first submitted to optimization of its molecular geometry followed by molecular dynamics in water (epsilon = 80) until thermalization was achieved. The conformation evolved from a rather extended random conformation to increasingly folded structures. The presence of the dielectric discontinuity induced the movement of the molecule's center of mass from water towards the interface. The entry of the peptide into the lower dielectric constant medium (epsilon = 2) through the interface was paralleled by a decrease in the total potential energy, indicating the affinity of the peptide for the lipid-mimetic phase.

Raman and infrared studies on the conformation of porcine pancreatic and Crotalus durissus terrificus phospholipases A2.

Raman and infrared spectroscopies were used to investigate conformational features of Crotalus durissus terrificus and porcine pancreatic phospholipases A2, as well as the proenzyme of the latter. The results indicate that conformational changes occur for the phospholipase molecules as a consequence of different experimental conditions such as change of physical state, presence of certain ionic species and interaction with a model substrate analog. Amorphous and crystalline solid phospholipase present discrepant conformational features. Conformational transitions were detected for the pancreatic zymogen----phospholipase A2 transformation and different secondary contents were observed for a toxic and a nontoxic form of the phospholipase molecule. All those structural changes have been shown to involve primarily the architecture of the polypeptide backbone rather than the conformation of amino acid residue side-chains. Disulfide bridges have shown consistently a gauche-gauche-gauche geometry which has not been disturbed by any of the experimental conditions employed. The external occurrence of tryptophan residues has been a common feature for the systems assayed, as well as the predominant localization of tyrosine residues in hydrophilic environment, probably at the molecular surface.

Raman and infrared spectra of toxin gamma from the venom of the scorpion Tityus serrulatus.

Toxin gamma is a basic, low-molecular-weight, neurotoxic protein, isolated from the venom of the Brazilian scorpion, Tityus serrulatus. Raman spectra (400-1800 cm-1 region) of this toxin in both the lyophilized state and in 0.1 M acetate buffer (pH 4.5) and the infrared spectrum (700-4000 cm-1 region) of a solid film were investigated. From the vibrational spectra, it can be concluded that the polypeptide backbone of toxin gamma consists of a mixture of the different secondary structures, with predominance of beta-sheet, followed by unordered structure and alpha-helix, with some evidence of beta-turn structures. The four disulfide bridges assume the gauche-gauche-gauche conformation of the CCSSCC fragments. The intensity ratio of the doublet at 853 and 828 cm-1 suggests that four out of the five tyrosine residues are exposed. The three tryptophan residues are exposed on the surface, and the single methionine residue assume the gauche-gauche conformation. Toxin gamma retains full activity in the pH 4.5-7.5 range, but is almost completely inactivated at pH 11.5.