ABSTRACT
A procedure is described for estimating the probabilities for the backbone phi-psi angles of a protein molecule from the data base of known protein structures. The procedure is basically an adaptation of a published secondary structure prediction scheme, applied to the phi-psi angle bins rather than to the secondary types. The phi-psi angle probabilities estimated this way include all effects of local sequence and are "context sensitive" in that the probabilities for a given residue type depend on its position along the sequence. These probabilities can be used to predict the three-dimensional structure of short polypeptides that are stabilized mainly by local interactions only and to predict the protein folding initiation sites, with moderate to good success rates in each case. They are also potentially useful for efficient sampling in a Monte Carlo scheme of protein tertiary structure prediction methods.
Subject(s)
Protein Conformation , Amino Acid Sequence , Animals , Computer Simulation , Humans , Molecular Sequence Data , Monte Carlo Method , Peptides/chemistry , Probability , ThermodynamicsABSTRACT
A stereochemical simulation of the formation of ionic bridges between adjacent peptide groups along the polypeptide chain has been made. Such ionic bridges constrain the amino-acid residues into eight conformations. It is shown that the path of any protein-chain fragment 10-15 residues long can be approximated well by these conformations. This suggests that the conformations dictated by the ionic bridges can be used as blocks in the formation of the spatial protein structure.
Subject(s)
Models, Molecular , Proteins/chemistry , Trypsin Inhibitors/chemistry , Amino Acid Sequence , Animals , Cattle , Ions , Molecular Sequence Data , Protein ConformationSubject(s)
Peptides/chemistry , Amino Acid Sequence , Cations , Molecular Sequence Data , Protein Conformation , StereoisomerismABSTRACT
A panel of 4 monoclonal antibodies and 7 polyclonal antisera against NAD-dependent formate dehydrogenase from methylotrophic bacterium Pseudomonas sp. 101 has been obtained. The reactivity of the 37 overlapping proteolytic peptides with the monoclonal antibodies and polyclonal antisera has been studied with ELISA test. The data obtained were interpreted residing on the structural model of the formate dehydrogenase at 3 A resolution. The immunodominant regions in the formate dehydrogenase molecule and the epitopes for the monoclonal antibodies were elucidated.
