ArticleThe journal of physical chemistry. B2013
Specific and non-specific protein association in solution: computation of solvent effects and prediction of first-encounter modes for efficient configurational bias Monte Carlo simulations.
Article in The journal of physical chemistry. B, 2013. 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, 22 citations in OpenAlex.
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- Development of R7BP inhibitors through cross-linking coupled mass spectrometry and integrated modeling.Communications biology · 2019Article
- Self-adaptive multiscaling algorithm for efficient simulations of many-protein systems in crowded conditions.Physical chemistry chemical physics : PCCP · 2018Article
- Binding kinetics of ultrasmall gold nanoparticles with proteins.Nanoscale · 2018Article
- Computational study of the inhibitory mechanism of the kinase CDK5 hyperactivity by peptide p5 and derivation of a pharmacophore.Journal of computer-aided molecular design · 2016Article
- Detection and characterization of nonspecific, sparsely populated binding modes in the early stages of complexation.Journal of computational chemistry · 2015Article
- Implicit treatment of solvent dispersion forces in protein simulations.Journal of computational chemistry · 2014Article
- Role of Albumin in the Formation and Stabilization of Nanoparticle Aggregates in Serum Studied by Continuous Photon Correlation Spectroscopy and Multiscale Computer Simulations.The journal of physical chemistry. C, Nanomaterials and interfaces · 2014Article
- Impact of subdomain D1 of the short form S1b of the human prolactin receptor on its inhibitory action on the function of the long form of the receptor induced by prolactin.Biochimica et biophysica acta · 2014Article
- Avidity mechanism of dendrimer-folic acid conjugates.Molecular pharmaceutics · 2014Article
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
Abstract
Weak and ultraweak protein-protein association play a role in molecular recognition and can drive spontaneous self-assembly and aggregation. Such interactions are difficult to detect experimentally, and are a challenge to the force field and sampling technique. A method is proposed to identify low-population protein-protein binding modes in aqueous solution. The method is designed to identify preferential first-encounter complexes from which the final complex(es) at equilibrium evolve. A continuum model is used to represent the effects of the solvent, which accounts for short- and long-range effects of water exclusion and for liquid-structure forces at protein/liquid interfaces. These effects control the behavior of proteins in close proximity and are optimized on the basis of binding enthalpy data and simulations. An algorithm is described to construct a biasing function for self-adaptive configurational-bias Monte Carlo of a set of interacting proteins. The function allows mixing large and local changes in the spatial distribution of proteins, thereby enhancing sampling of relevant microstates. The method is applied to three binary systems. Generalization to multiprotein complexes is discussed.
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Registered trials
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.