Three-dimensional structures of protein backbones have been predicted using neural networks. A feed forward neural network was trained on a class of functionally, but not structurally, homologous proteins, using backp...
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Three-dimensional structures of protein backbones have been predicted using neural networks. A feed forward neural network was trained on a class of functionally, but not structurally, homologous proteins, using backpropagation learning. The network generated tertiary structure information in the form of binary distance constraints for the C(alpha) atoms in the protein backbone. The binary distance between two C(alpha) atoms was 0 if the distance between them was less than a certain threshold distance, and 1 otherwise. The distance constraints predicted by the trained neural network were utilized to generate a folded conformation of the protein backbone, using a steepest descent minimization approach.
The assumption that homologous segments in different proteins may share a similar conformation is applied to the prediction of secondarystructures in proteins. Sequences homologous to a target protein are searched, w...
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The assumption that homologous segments in different proteins may share a similar conformation is applied to the prediction of secondarystructures in proteins. Sequences homologous to a target protein are searched, without allowing any gap, and compared against a number of reference proteins of known three-dimensional structure, and then a conformational state (.alpha., .beta. or coil) for each residue of the protein is predicted by looking at the secondarystructure of corresponding homologous segments. This prediction is done in a statistical rather than deterministic way, by assigning the most probable conformation state among homologous data to each residue site of a target protein. A test application for 22 sample proteins yields 60% correctness on the average, a better value in comparison with two other existing methods. Joint prediction combining three methods into one is shown to increase the reliability up to 70%, when only the regions identically predicted with the three methods are taken into account. Application of the present method to 10 proteins of unknown structure is demonstrated.
secondarystructures of leucocyte alpha 1- and alpha 2-interferons and of fibroblast beta-interferon are calculated using the molecular theory of proteinsecondarystructures. The common secondarystructure calculated...
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secondarystructures of leucocyte alpha 1- and alpha 2-interferons and of fibroblast beta-interferon are calculated using the molecular theory of proteinsecondarystructures. The common secondarystructure calculated for alpha- and beta-interferons is used to predict the three-dimensional structures of fragments 1-110 and 111-166 of the chains (which are supposed to be quasi-independent domains). The predicted structure of the active domain I (1-110) is an 'up-and-down' tetrahelical complex (in which the second helix is shorter than the others and can be absent in alpha 1-interferon) similar to the mirror image of myohaemoerythrin. The predicted structure of domain II (111-166) is either a three-stranded beta-sheet screened from one side by two alpha-helices or a three-helical complex (similar to that in the N-domain of papain), the first structure being more consistent with the circular dichroism data of alpha-interferon and its C-end fragment.
A hydrophobic 24-residue polypeptide that could potentially form a four-stranded antiparallel β-pleated sheet and bind the insecticide DDT was designed and synthesized. The synthetic peptide aggregated in 1 M acetic ...
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A hydrophobic 24-residue polypeptide that could potentially form a four-stranded antiparallel β-pleated sheet and bind the insecticide DDT was designed and synthesized. The synthetic peptide aggregated in 1 M acetic acid but was monomeric in aqueous 50% ethanol. In the latter solvent the 24-residue polypeptide and DDT formed a complex with an apparent dissociation constant of ≈2 × 10 −5 M. The DDT binding of an analogue of this peptide possessing the same amino acid residues in a random sequence was more than 2 orders of magnitude and that of bovine serum albumin at least 3 orders of magnitude weaker. The designed polypeptide could be crystallized.
A DEC-SYSTEM 10 FORTRAN computer program to carry out secondarystructureprediction of proteins, according to the algorithm of Chou and Fasman is described. Program results are compared with predictions made by Chou ...
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A DEC-SYSTEM 10 FORTRAN computer program to carry out secondarystructureprediction of proteins, according to the algorithm of Chou and Fasman is described. Program results are compared with predictions made by Chou and Fasman.
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