ArticlePloS one2010
The combined effects of amino acid substitutions and indels on the evolution of structure within protein families.
Article in PloS one, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 31 citations in OpenAlex.
- Insertion-Deletion Events Are Depleted in Protein Regions with Predicted Secondary Structure.Genome biology and evolution · 2024Article
- Article
- Structural Dynamics Predominantly Determine the Adaptability of Proteins to Amino Acid Deletions.International journal of molecular sciences · 2023Article
- Assessing the Pathogenicity of In-Frame CACNA1F Indel Variants Using Structural Modeling.The Journal of molecular diagnostics : JMD · 2022Article
- Switching an active site helix in dihydrofolate reductase reveals limits to subdomain modularity.Biophysical journal · 2021Article
- Expanded analyses of the functional correlations within structural classifications of glycoside hydrolases.Computational and structural biotechnology journal · 2021Article
- Evolutionary Dynamics of Indels in SARS-CoV-2 Spike Glycoprotein.Evolutionary bioinformatics online · 2021Article
- Contributions of substitutions and indels to the structural variations in ancient protein superfamilies.BMC genomics · 2018Article
- Computational prediction of the tolerance to amino-acid deletion in green-fluorescent protein.PloS one · 2017Article
- Measuring Accelerated Rates of Insertions and Deletions Independent of Rates of Nucleotide Substitution.Journal of molecular evolution · 2016Article
- MSAIndelFR: a scheme for multiple protein sequence alignment using information on indel flanking regions.BMC bioinformatics · 2015Article
- LenVarDB: database of length-variant protein domains.Nucleic acids research · 2014Article
- Different patterns of gene structure divergence following gene duplication in Arabidopsis.BMC genomics · 2013Article
- A stochastic evolutionary model for protein structure alignment and phylogeny.Molecular biology and evolution · 2012Article
- IndelFR: a database of indels in protein structures and their flanking regions.Nucleic acids research · 2012Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn the process of protein evolution, sequence variations within protein families can cause changes in protein structures and functions. However, structures tend to be more conserved than sequences and functions. This leads to an intriguing question: what is the evolutionary mechanism by which sequence variations produce structural changes? To investigate this question, we focused on the most common types of sequence variations: amino acid substitutions and insertions/deletions (indels). Here their combined effects on protein structure evolution within protein families are studied.
resultsSequence-structure correlation analysis on 75 homologous structure families (from SCOP) that contain 20 or more non-redundant structures shows that in most of these families there is, statistically, a bilinear correlation between the amount of substitutions and indels versus the degree of structure variations. Bilinear regression of percent sequence non-identity (PNI) and standardized number of gaps (SNG) versus RMSD was performed. The coefficients from the regression analysis could be used to estimate the structure changes caused by each unit of substitution (structural substitution sensitivity, SSS) and by each unit of indel (structural indel sensitivity, SIDS). An analysis on 52 families with high bilinear fitting multiple correlation coefficients and statistically significant regression coefficients showed that SSS is mainly constrained by disulfide bonds, which almost have no effects on SIDS.
conclusionsStructural changes in homologous protein families could be rationally explained by a bilinear model combining amino acid substitutions and indels. These results may further improve our understanding of the evolutionary mechanisms of protein structures.
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