ArticlePloS one2011
Discovering conformational sub-states relevant to protein function.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 74 citations in OpenAlex.
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- Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome.Genome medicine · 2022Article
- Why are large conformational changes well described by harmonic normal modes?Biophysical journal · 2021Article
- Compost Samples from Different Temperature Zones as a Model to Study Co-occurrence of Thermophilic and Psychrophilic Bacterial Population: a Metagenomics Approach.Current microbiology · 2021Article
- Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Simulations.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Protein Conformational States-A First Principles Bayesian Method.Entropy (Basel, Switzerland) · 2020Article
- Enzyme dynamics: Looking beyond a single structure.ChemCatChem · 2020Article
- Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain.Biomolecules · 2020Article
- Entropy-Based Strategies for Rapid Pre-Processing and Classification of Time Series Data from Single-Molecule Force Experiments.Entropy (Basel, Switzerland) · 2020Article
- Conformational perturbation, allosteric modulation of cellular signaling pathways, and disease in P23H rhodopsin.Scientific reports · 2020Article
- A Biophysical Perspective on Enzyme Catalysis.Biochemistry · 2019Article
- Deep clustering of protein folding simulations.BMC bioinformatics · 2018Article
- Modulating Enzyme Activity by Altering Protein Dynamics with Solvent.Biochemistry · 2018Article
- ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations.Biophysical journal · 2018Article
- Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily.Structure (London, England : 1993) · 2018Article
- Dynamics based clustering of globin family members.PloS one · 2018Article
- Small Angle Neutron Scattering Studies of R67 Dihydrofolate Reductase, a Tetrameric Protein with Intrinsically Disordered N-Termini.Biochemistry · 2017Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundInternal motions enable proteins to explore a range of conformations, even in the vicinity of native state. The role of conformational fluctuations in the designated function of a protein is widely debated. Emerging evidence suggests that sub-groups within the range of conformations (or sub-states) contain properties that may be functionally relevant. However, low populations in these sub-states and the transient nature of conformational transitions between these sub-states present significant challenges for their identification and characterization. METHODS AND
findingsTo overcome these challenges we have developed a new computational technique, quasi-anharmonic analysis (QAA). QAA utilizes higher-order statistics of protein motions to identify sub-states in the conformational landscape. Further, the focus on anharmonicity allows identification of conformational fluctuations that enable transitions between sub-states. QAA applied to equilibrium simulations of human ubiquitin and T4 lysozyme reveals functionally relevant sub-states and protein motions involved in molecular recognition. In combination with a reaction pathway sampling method, QAA characterizes conformational sub-states associated with cis/trans peptidyl-prolyl isomerization catalyzed by the enzyme cyclophilin A. In these three proteins, QAA allows identification of conformational sub-states, with critical structural and dynamical features relevant to protein function.
conclusionsOverall, QAA provides a novel framework to intuitively understand the biophysical basis of conformational diversity and its relevance to protein function.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.