Affiliation:
1. Departamento de Ciencia y Tecnología Universidad Nacional de Quilmes Bernal Argentina
2. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) Buenos Aires Argentina
3. Department of Information Engineering University of Padova Padova Italy
Abstract
AbstractCoDNaS (http://ufq.unq.edu.ar/codnas/) and CoDNaS‐Q (http://ufq.unq.edu.ar/codnasq) are repositories of proteins with different degrees of conformational diversity. Following the ensemble nature of the native state, conformational diversity represents the structural differences between the conformers in the ensemble. Each entry in CoDNaS and CoDNaS‐Q contains a redundant collection of experimentally determined conformers obtained under different conditions. These conformers represent snapshots of the protein dynamism. While CoDNaS contains examples of conformational diversity at the tertiary level, a recent development, CoDNaS‐Q, contains examples at the quaternary level. In the emerging age of accurate protein structure prediction by machine learning approaches, many questions remain open regarding the characterization of protein dynamism. In this context, most bioinformatics resources take advantage of distinct features derived from protein alignments, however, the complexity and heterogeneity of information makes it difficult to recover reliable biological signatures. Here we present five protocols to explore tertiary and quaternary conformational diversity at the individual protein level as well as for the characterization of the distribution of conformational diversity at the protein family level in a phylogenetic context. These protocols can provide curated protein families with experimentally known conformational diversity, facilitating the exploration of sequence determinants of protein dynamism. © 2023 Wiley Periodicals LLC.Basic Protocol 1: Assessing conformational diversity with CoDNaSAlternate Protocol 1: Assessing conformational diversity at the quaternary level with CoDNaS‐QBasic Protocol 2: Exploring conformational diversity in a protein familyAlternate Protocol 2: Exploring quaternary conformational diversity in a protein familyBasic Protocol 3: Representing conformational diversity in a phylogenetic context
Funder
Universidad Nacional de Quilmes
Consejo Nacional de Investigaciones Científicas y Técnicas
Subject
Medical Laboratory Technology,Health Informatics,General Pharmacology, Toxicology and Pharmaceutics,General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Neuroscience