ArticlePLoS computational biology2013
Thermal adaptation of conformational dynamics in ribonuclease H.
Article in PLoS computational biology, 2013. 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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Who cites it
15 citing papers in PubMed.
- Parsing Dynamics of Protein Backbone NH and Side-Chain Methyl Groups using Molecular Dynamics Simulations.Journal of chemical theory and computation · 2024Article
- Comparisons of Ribonuclease HI Homologs and Mutants Uncover a Multistate Model for Substrate Recognition.Journal of the American Chemical Society · 2022Article
- The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes.Frontiers in molecular biosciences · 2022Article
- Quantifying the Relationship between Conformational Dynamics and Enzymatic Activity in Ribonuclease HI Homologues.Biochemistry · 2020Article
- Detection of chemical exchange in methyl groups of macromolecules.Journal of biomolecular NMR · 2019Article
- Slow conformational exchange and overall rocking motion in ubiquitin protein crystals.Nature communications · 2017Article
- Thermostability of Enzymes from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2016Article
- Predicting protein thermal stability changes upon point mutations using statistical potentials: Introducing HoTMuSiC.Scientific reports · 2016Article
- Early Folding Events, Local Interactions, and Conservation of Protein Backbone Rigidity.Biophysical journal · 2016Article
- Conformational preferences underlying reduced activity of a thermophilic ribonuclease H.Journal of molecular biology · 2015Article
- Enzyme dynamics from NMR spectroscopy.Accounts of chemical research · 2015Review
- Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins.Journal of biomolecular NMR · 2015Article
- Protein dynamics control the progression and efficiency of the catalytic reaction cycle of the Escherichia coli DNA-repair enzyme AlkB.The Journal of biological chemistry · 2014Article
- Chemical exchange in biomacromolecules: past, present, and future.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2014Review
- Evidence from molecular dynamics simulations of conformational preorganization in the ribonuclease H active site.F1000Research · 2014Article
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Authors and funding
3 authors.
Funding
Abstract
The relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize. The study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functional aspects of conformational dynamics. In particular, ribonuclease HI (RNase H), an 18 kD globular protein that hydrolyzes the RNA strand of RNA:DNA hybrid substrates, has been extensively studied by NMR spectroscopy to characterize the differences in dynamics between homologs from the mesophilic organism E. coli and the thermophilic organism T. thermophilus. Herein, molecular dynamics simulations are reported for five homologous RNase H proteins of varying thermostabilities and enzymatic activities from organisms of markedly different preferred growth temperatures. For the E. coli and T. thermophilus proteins, strong agreement is obtained between simulated and experimental values for NMR order parameters and for dynamically averaged chemical shifts, suggesting that these simulations can be a productive platform for predicting the effects of individual amino acid residues on dynamic behavior. Analyses of the simulations reveal that a single residue differentiates between two different and otherwise conserved dynamic processes in a region of the protein known to form part of the substrate-binding interface. Additional key residues within these two categories are identified through the temperature-dependence of these conformational processes.
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