ArticleBiophysical journal2012
Coarse-grained simulations of protein-protein association: an energy landscape perspective.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Classification of protein-protein association rates based on biophysical informatics.BMC bioinformatics · 2021Article
- Understanding the Impacts of Conformational Dynamics on the Regulation of Protein-Protein Association by a Multiscale Simulation Method.Journal of chemical theory and computation · 2020Article
- Using Coarse-Grained Simulations to Characterize the Mechanisms of Protein-Protein Association.Biomolecules · 2020Article
- Article
- A Systematic Test of Receptor Binding Kinetics for Ligands in Tumor Necrosis Factor Superfamily by Computational Simulations.International journal of molecular sciences · 2020Article
- A Multiscale Model for the Self-Assembly of Coat Proteins in Bacteriophage MS2.Journal of chemical information and modeling · 2019Article
- Computational studies of protein-protein dissociation by statistical potential and coarse-grained simulations: a case study on interactions between colicin E9 endonuclease and immunity proteins.Physical chemistry chemical physics : PCCP · 2019Article
- Heterodimer Binding Scaffolds Recognition via the Analysis of Kinetically Hot Residues.Pharmaceuticals (Basel, Switzerland) · 2018Article
- Out-of-Register AβJournal of chemical theory and computation · 2018Article
- A Multiscale Computational Model for Simulating the Kinetics of Protein Complex Assembly.Methods in molecular biology (Clifton, N.J.) · 2018Article
- Predicting Protein-protein Association Rates using Coarse-grained Simulation and Machine Learning.Scientific reports · 2017Article
- Thermodynamics of Hydrophobic Amino Acids in Solution: A Combined Experimental-Computational Study.The journal of physical chemistry letters · 2017Article
- Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking.Journal of structural biology · 2016Article
- Challenges in structural approaches to cell modeling.Journal of molecular biology · 2016Review
- Coupled folding and binding with 2D Window-Exchange Umbrella Sampling.Journal of computational chemistry · 2016Article
- Evaluation of the coarse-grained OPEP force field for protein-protein docking.BMC biophysics · 2016Article
- Conformational frustration in calmodulin-target recognition.Journal of molecular recognition : JMR · 2015Article
- Methods for SAXS-based structure determination of biomolecular complexes.Advanced materials (Deerfield Beach, Fla.) · 2014Article
- Linking 3D and 2D binding kinetics of membrane proteins by multiscale simulations.Protein science : a publication of the Protein Society · 2014Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Understanding protein-protein association is crucial in revealing the molecular basis of many biological processes. Here, we describe a theoretical simulation pipeline to study protein-protein association from an energy landscape perspective. First, a coarse-grained model is implemented and its applications are demonstrated via molecular dynamics simulations for several protein complexes. Second, an enhanced search method is used to efficiently sample a broad range of protein conformations. Third, multiple conformations are identified and clustered from simulation data and further projected on a three-dimensional globe specifying protein orientations and interacting energies. Results from several complexes indicate that the crystal-like conformation is favorable on the energy landscape even if the landscape is relatively rugged with metastable conformations. A closer examination on molecular forces shows that the formation of associated protein complexes can be primarily electrostatics-driven, hydrophobics-driven, or a combination of both in stabilizing specific binding interfaces. Taken together, these results suggest that the coarse-grained simulations and analyses provide an alternative toolset to study protein-protein association occurring in functional biomolecular complexes.
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