Related Experiment Video
Updated: Jul 30, 2025
09:37
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
3.5K
Combining Protein Conformational Diversity and Phylogenetic Information Using CoDNaS and CoDNaS-Q.
Nahuel Escobedo1,2, Alexander Miguel Monzon3, María Silvina Fornasari1,2
1Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina.
Current Protocols
|May 15, 2023
Summary
This study introduces five protocols to analyze protein conformational diversity using the CoDNaS and CoDNaS-Q repositories. These methods explore protein dynamism at both tertiary and quaternary levels, aiding in understanding sequence determinants of protein flexibility.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Protein dynamism is crucial for function, yet challenging to characterize computationally.
- Existing bioinformatics resources often struggle with the complexity of protein structural data.
- CoDNaS and CoDNaS-Q offer experimentally determined protein conformers capturing dynamic states.
Purpose of the Study:
- To present novel protocols for analyzing protein conformational diversity.
- To enable exploration of tertiary and quaternary structural variations.
- To facilitate the study of protein dynamism and its sequence determinants.
Main Methods:
- Utilizing the CoDNaS and CoDNaS-Q databases for protein conformer data.
- Developing protocols for assessing conformational diversity at individual protein and protein family levels.
- Integrating phylogenetic analysis to contextualize conformational diversity.
Main Results:
- Five distinct protocols are provided for exploring protein conformational diversity.
- The protocols allow analysis at both tertiary (CoDNaS) and quaternary (CoDNaS-Q) levels.
- Methods enable characterization of conformational diversity within protein families and phylogenetic contexts.
Conclusions:
- The presented protocols offer a framework for studying protein dynamism.
- These tools facilitate the discovery of sequence-function relationships related to protein flexibility.
- CoDNaS and CoDNaS-Q, coupled with these protocols, enhance the understanding of protein structural ensembles.
Related Concept Videos
02:26Conservation of Protein Domains Over Different Proteins
11.0K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
11.0K
02:51Multi-species Conserved Sequences
4.0K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.0K
02:26Conservation of Protein Domains
3.1K
3.1K
01:57Protein Complexes with Interchangeable Parts
1.9K
1.9K
01:49Conserved Binding Sites
4.3K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.3K
02:05DNA as a Genetic Template
22.2K
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
22.2K