ArticleWiley interdisciplinary reviews. Computational molecular science
Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation.
Article in Wiley interdisciplinary reviews. Computational molecular science. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 76 citations in OpenAlex.
- Unveiling the Mechanisms of EGCG-p53 Interactions through Molecular Dynamics Simulations.ACS omega · 2024Article
- QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations.Chemical science · 2023Article
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- Anthraquinone and its derivatives as sustainable materials for electrochemical applications - a joint experimental and theoretical investigation of the redox potential in solution.Physical chemistry chemical physics : PCCP · 2022Article
- Transcription Factor Movement and Exercise-Induced Mitochondrial Biogenesis in Human Skeletal Muscle: Current Knowledge and Future Perspectives.International journal of molecular sciences · 2022Review
- The Energy Landscape Perspective: Encoding Structure and Function for Biomolecules.Frontiers in molecular biosciences · 2022Article
- Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins.Methods (San Diego, Calif.) · 2021Article
- Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations.Communications biology · 2021Article
- How to assess the structural dynamics of transcription factors by integrating sparse NMR and EPR constraints with molecular dynamics simulations.Computational and structural biotechnology journal · 2021Review
- Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins.Frontiers in chemistry · 2021Review
- A disordered encounter complex is central to the yeast Abp1p SH3 domain binding pathway.PLoS computational biology · 2020Article
- Protein disorder-to-order transition enhances the nucleosome-binding affinity of H1.Nucleic acids research · 2020Article
- Psi4 1.4: Open-source software for high-throughput quantum chemistry.The Journal of chemical physics · 2020Article
- Impact of electronic polarizability on protein-functional group interactions.Physical chemistry chemical physics : PCCP · 2020Article
- Atomic partial charge predictions for furanoses by random forest regression with atom type symmetry function.RSC advances · 2020Article
- Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding.Protein science : a publication of the Protein Society · 2019Review
- Coupled Binding and Helix Formation Monitored by Synchrotron-Radiation Circular Dichroism.Biophysical journal · 2019Article
- Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications.International journal of molecular sciences · 2019Review
- AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins.The journal of physical chemistry. B · 2018Article
- Machine learning molecular dynamics for the simulation of infrared spectra.Chemical science · 2017Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
Intrinsically disordered proteins (IDPs) are a class of protein that, in the native state, possess no well-defined secondary or tertiary structure, existing instead as dynamic ensembles of conformations. They are biologically important, with approximately 20% of all eukaryotic proteins disordered, and found at the heart of many biochemical networks. To fulfil their biological roles, many IDPs need to bind to proteins and/or nucleic acids. And while unstructured in solution, IDPs typically fold into a well-defined three-dimensional structure upon interaction with a binding partner. The flexibility and structural diversity inherent to IDPs makes this coupled folding and binding difficult to study at atomic resolution by experiment alone, and computer simulation currently offers perhaps the best opportunity to understand this process. But simulation of coupled folding and binding is itself extremely challenging; these molecules are large and highly flexible, and their binding partners, such as DNA or cyclins, are also often large. Therefore, their study requires either or both simplified representations and advanced enhanced sampling schemes. It is not always clear that existing simulation techniques, optimized for studying folded proteins, are well-suited to IDPs. In this article, we examine the progress that has been made in the study of coupled folding and binding using molecular dynamics simulation. We summarise what has been learnt, and examine the state of the art in terms of both methodologies and models. We also consider the lessons to be learnt from advances in other areas of simulation and highlight the issues that remain of be addressed.
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Registered trials
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