alanyl-alanyl-alanyl-alanine and alanylalanine

The absolute free energy--or partition function, equivalently--of a molecule can be estimated computationally using a suitable reference system. Here, we demonstrate a practical method for staging such calculations by growing a molecule based on a series of fragments. Significant computer time is saved by precalculating fragment configurations and interactions for reuse in a variety of molecules. We use such fragment libraries and interaction tables for amino acids and capping groups to estimate free energies for small peptides. Equilibrium ensembles for the molecules are generated at no additional computational cost and are used to check our results by comparison to standard dynamics simulation. We explain how our work can be extended to estimate relative binding affinities.

Topics: Computer Simulation; Dipeptides; Models, Chemical; Oligopeptides; Polymers; Thermodynamics

p6gestibility by proteolytic enzymes of peptides cross-linked by ionizing radiation was investigated. Small peptides of alanine and phenylalanine were chosen as model compounds and aminopeptidases and carboxypeptidases were used as proteolytic enzymes. Peptides exposed to gamma-radiation in aqueous solution were analysed by high-performance liquid chromatography before and after hydrolysis by aminopeptidase M, leucine aminopeptidase, carboxypeptidase A and carboxypeptidase Y. The results obtained clearly demonstrate the different actions of these enzymes on cross-linked aliphatic and aromatic peptides. Peptide bonds of cross-linked dipeptides of alanine were completely resistant to enzymatic hydrolysis whereas the enzymes, except for carboxypeptidase Y, cleaved all peptide bonds of cross-linked peptides of phenylalanine. The actions of the enzymes on these particular compounds are discussed in detail.

Topics: Aminopeptidases; Carboxypeptidases; Carboxypeptidases A; CD13 Antigens; Chromatography, High Pressure Liquid; Cobalt Radioisotopes; Dipeptides; Gamma Rays; Leucyl Aminopeptidase; Oligopeptides; Peptide Hydrolases; Peptides

alpha-Peptide radicals of L-Ala-L-Ala and tetra-L-Ala, formed from reaction with OH radicals, generated in H2O by ionizing radiation, were shown to give peptide dimers. These peptide dimers were separated and isolated by HPLC. On acid hydrolysis, all of the studied peptide dimers yielded alanine and 1,2-diamino-1,2-dimethyl succinic acid, which was characterized by gas chromatography-mass spectrometry as its TMS derivative. The described procedure is also suggested as a suitable method for isolation and characterization of amino acid dimers.

Topics: Cobalt Radioisotopes; Dipeptides; Free Radicals; Gamma Rays; Oligopeptides; Peptides; Solutions; Water

The di-, tri-, and tetrapeptides of L-alanine have been studied in aqueous solution by 13C n.m.r. spectroscopy at 25 and 50 MHz. By using selectively 13C enriched analogs containing either 90% 13C methyl or carbonyl carbons and measurements as a function of pH, assignment of the chemical shifts of the peptides has been made. T1 and NOE measurements of the peptides in their cationic, anionic, and zwitterionic states have been recorded as a function of concentration. The results show considerable segmental motion along the backbone carbons of the peptides, with only small changes occurring in the dynamic motions of the peptides as their charge states are altered. The lack of concentration dependence of the chemical shift and T1 values, as well as the similarity of T1 values for individual peptides in the three charge states, indicate that the peptides do not self-associate in aqueous solution.

Topics: Alanine; Dipeptides; Hydrogen-Ion Concentration; Magnetic Resonance Spectroscopy; Oligopeptides; Protein Conformation; Structure-Activity Relationship