ArticleBMC evolutionary biology2011
Biophysical and structural considerations for protein sequence evolution.
Article in BMC evolutionary biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity.Molecular biology and evolution · 2025Article
- A review of visualisations of protein fold networks and their relationship with sequence and function.Biological reviews of the Cambridge Philosophical Society · 2023Review
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- Characterizing Amino Acid Substitution with Complete Linkage of Sites on a Lineage.Genome biology and evolution · 2021Article
- Ancestral Sequence Reconstruction: From Chemical Paleogenetics to Maximum Likelihood Algorithms and Beyond.Journal of molecular evolution · 2021Article
- Emerging Frontiers in the Study of Molecular Evolution.Journal of molecular evolution · 2020Article
- Characterizing lineage-specific evolution and the processes driving genomic diversification in chordates.BMC evolutionary biology · 2020Article
- The search of sequence variants using a constrained protein evolution simulation approach.Computational and structural biotechnology journal · 2020Article
- ASPEN, a methodology for reconstructing protein evolution with improved accuracy using ensemble models.eLife · 2019Article
- Review
- A new parameter-rich structure-aware mechanistic model for amino acid substitution during evolution.Proteins · 2018Article
- Chaperone-client interactions: Non-specificity engenders multifunctionality.The Journal of biological chemistry · 2017Review
- Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence.Annual review of biophysics · 2017Review
- Accelerated simulation of evolutionary trajectories in origin-fixation models.Journal of the Royal Society, Interface · 2017Article
- Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable.Biology direct · 2016Article
- Selection on protein structure, interaction, and sequence.Protein science : a publication of the Protein Society · 2016Review
- Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes.PLoS biology · 2016Article
- Characterizing selective pressures on the pathway for de novo biosynthesis of pyrimidines in yeast.BMC evolutionary biology · 2015Article
- The utility of protein structure as a predictor of site-wise dN/dS varies widely among HIV-1 proteins.Journal of the Royal Society, Interface · 2015Article
- Maximum-Likelihood Phylogenetic Inference with Selection on Protein Folding Stability.Molecular biology and evolution · 2015Article
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4 authors.
Funding
Abstract
backgroundProtein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field.
resultsHere we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites.
conclusionsSimple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model.
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