ArticlePLoS computational biology2016
Similarity in Shape Dictates Signature Intrinsic Dynamics Despite No Functional Conservation in TIM Barrel Enzymes.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes.Chemical reviews · 2024Review
- Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophysical reviews · 2022Review
- Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0.Acta crystallographica. Section D, Structural biology · 2022Review
- A Comparative Evaluation of the Structural and Dynamic Properties of Insect Odorant Binding Proteins.Biomolecules · 2022Article
- Identification of Thermal Conduits That Link the Protein-Water Interface to the Active Site Loop and Catalytic Base in Enolase.Journal of the American Chemical Society · 2021Article
- Hydrogen-Deuterium Exchange within Adenosine Deaminase, a TIM Barrel Hydrolase, Identifies Networks for Thermal Activation of Catalysis.Journal of the American Chemical Society · 2020Article
- Dynamics-function relationship in the catalytic domains of N-terminal acetyltransferases.Computational and structural biotechnology journal · 2020Article
- The role of ligand-gated conformational changes in enzyme catalysis.Biochemical Society transactions · 2019Review
- Shared Signature Dynamics Tempered by Local Fluctuations Enables Fold Adaptability and Specificity.Molecular biology and evolution · 2019Article
- Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members.Journal of chemical information and modeling · 2019Article
- Article
- Comparative Study of Elastic Network Model and Protein Contact Network for Protein Complexes: The Hemoglobin Case.BioMed research international · 2017Article
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2 authors.
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Abstract
The conservation of the intrinsic dynamics of proteins emerges as we attempt to understand the relationship between sequence, structure and functional conservation. We characterise the conservation of such dynamics in a case where the structure is conserved but function differs greatly. The triosephosphate isomerase barrel fold (TBF), renowned for its 8 β-strand-α-helix repeats that close to form a barrel, is one of the most diverse and abundant folds found in known protein structures. Proteins with this fold have diverse enzymatic functions spanning five of six Enzyme Commission classes, and we have picked five different superfamily candidates for our analysis using elastic network models. We find that the overall shape is a large determinant in the similarity of the intrinsic dynamics, regardless of function. In particular, the β-barrel core is highly rigid, while the α-helices that flank the β-strands have greater relative mobility, allowing for the many possibilities for placement of catalytic residues. We find that these elements correlate with each other via the loops that link them, as opposed to being directly correlated. We are also able to analyse the types of motions encoded by the normal mode vectors of the α-helices. We suggest that the global conservation of the intrinsic dynamics in the TBF contributes greatly to its success as an enzymatic scaffold both through evolution and enzyme design.
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