Circular dichroic (CD) spectra of bovine immunosuppressant binding proteins FKBP12 and FKBP25, and cyclophilins (peptidylprolyl isomerases) A (bCyP-18) and B(bCyP-20), the immunophilins which selectively bind the clinically useful immunosuppressants FK506, rapamycin and cyclosporin A, respectively, were analysed using the singular-value-decomposition algorithm augmented by a simplified variable selection method. The differences between the CD-estimated values of alpha-helix, beta-structure and beta-turn and those predicted by the Chou-Fasman algorithm were minimized using the CD data as constraints of an algorithm which utilizes the method of hierarchical updating of quasi-equipotential peptide segments of the Chou-Fasman prediction. The method allows one to correct the Chou-Fasman prediction of secondary structures in globular proteins.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1111/j.1432-1033.1996.00428.x | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
In silico design of potential Mcl-1 peptide-based inhibitors.
J Mol Model
March 2024
Department of Medical Nanotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Daneshgah Street, Tabriz, Iran.
Context: BIM (Bcl-2 interacting mediator of apoptosis)-derived peptides that specifically target over-expressed Mcl-1 (myeloid cell leukemia-1) protein and induce apoptosis are potentially anti-cancer agents. Since the helicity of BIM-derived peptides has a crucial role in their functionality, a range of strategies have been used to increase the helicity including the introduction of unnatural residues and stapling methods that have some drawbacks such as the accumulation in the liver. To avoid these drawbacks, this study aimed to design a more helical peptide by utilizing bioinformatics algorithms and molecular dynamics simulations without exploiting unnatural residues and stapling methods.
View Article and Find Full Text PDF[Prediction and analysis of B cell and T cell epitopes in the spike protein of SARS-CoV-2 by bioinformatics].
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi
January 2023
Ningxia Key Laboratory of Prevention and Control of Common Infectious Diseases, Yinchuan 750003, China. *Corresponding author, E-mail:
Objective To analyze structural features for spike (S) protein of the SARS-CoV-2 and to predict potential B cell and T cell epitopes using bioinformatics. Methods The amino acid sequence of S protein from the NCBI GenBank database was retrieved. Its physicochemical properties were analyzed using ProtParam online program.
View Article and Find Full Text PDFPseAraUbi: predicting arabidopsis ubiquitination sites by incorporating the physico-chemical and structural features.
Plant Mol Biol
September 2022
College of Computer and Information Engineering, Henan Normal University, Xinxiang, 453000, China.
We makes three kinds of important features from Arabidopsis thaliana: protein secondary structure based on the Chou-Fasman parameter, amino acids hydrophobicity and polarity information, and analyze their properties. Ubiquitination modification is an important post-translational modification of proteins, which participates in the regulation of many important life activities in cells. At present, ubiquitination proteomics research is mostly concentrated in animals and yeasts, while relatively few studies have been carried out in plants.
View Article and Find Full Text PDFEpiBuilder: A Tool for Assembling, Searching, and Classifying B-Cell Epitopes.
Bioinform Biol Insights
May 2022
Laboratório de Hemoparasitas e Vetores, Departamento de Produção Animal e Alimentos, Centro de Ciências Agroveterinárias (CAV), Universidade do Estado de Santa Catarina (UDESC), Lages, Brazil.
Epitopes are portions of a protein that are recognized by antibodies. These small amino acid sequences represent a significant breakthrough in a branch of bioinformatics called immunoinformatics. Various software are available for linear B-cell epitope (BCE) prediction such as , , , and ; a well-known BCE predictor is BepiPred-2.
View Article and Find Full Text PDFstructural homology modeling of nif A protein of rhizobial strains in selective legume plants.
J Genet Eng Biotechnol
December 2018
Elyns Group, Hyderabad, India.
Symbiosis is a complex genetic regulatory biological evolution which is highly specific pertaining to plant species and microbial strains. Biological nitrogen fixation in legumes is a functional combination of nodulation by nod genes and regulation by nif, fix genes. Three rhizobial strains (, , and ) that we considered for analysis of nif A are proved to be the best isolates with respect to N fixing for ground nut, chick pea and soya bean (in vitro) out of 47 forest soil samples.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!