ArticleeLife2014
Encounter complexes and dimensionality reduction in protein-protein association.
Article in eLife, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
37 citing papers in PubMed.
- Molecular Mechanisms of Interaction of Human Serum Albumin with the CD36 Receptor: Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2026Article
- Highly Optimized Simulation of Atomic Resolution Cell-Like Protein Environment.The journal of physical chemistry. B · 2025Article
- Human CSTF2 RNA Recognition Motif Domain Binds to a U-Rich RNA Sequence through a Multistep Binding Process.Biochemistry · 2024Article
- Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.Journal of molecular biology · 2024Article
- Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data.PLoS computational biology · 2024Article
- Structural principles of peptide-centric chimeric antigen receptor recognition guide therapeutic expansion.Science immunology · 2023Article
- Unexpected dynamics in femtomolar complexes of binding proteins with peptides.Nature communications · 2023Article
- Article
- Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics.Biophysics and physicobiology · 2023Article
- Fast cross-linking by DOPA2 promotes the capturing of a stereospecific protein complex over nonspecific encounter complexes.Biophysics reports · 2022Article
- Docking-based long timescale simulation of cell-size protein systems at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Preferential Regulation of Transient Protein-Protein Interaction by the Macromolecular Crowders.The journal of physical chemistry. B · 2022Article
- Control of Unsaturation inBiochemistry · 2022Article
- Modeling the Dynamics of Protein-Protein Interfaces, How and Why?Molecules (Basel, Switzerland) · 2022Review
- Novel Big Data-Driven Machine Learning Models for Drug Discovery Application.Molecules (Basel, Switzerland) · 2022Article
- PotentBioMed research international · 2022Article
- PP2A is activated by cytochromeComputational and structural biotechnology journal · 2022Article
- Challenges in protein docking.Current opinion in structural biology · 2020Review
- Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin.Biophysical journal · 2020Article
- Model of a Kinetically Driven Crosstalk between Paralogous Protein Encounter Complexes.Biophysical journal · 2019Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors.
Funding
Abstract
An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein-protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles calculated from the docked structures shows that the method captures both specific and non-specific encounter complexes. To explore the energy landscape in the vicinity of the native structure, the nonlinear manifold describing the relative orientation of two solid bodies is projected onto a Euclidean space in which the shape of low energy regions is studied by principal component analysis. Results show that the energy surface is canyon-like, with a smooth funnel within a two dimensional subspace capturing over 75% of the total motion. Thus, proteins tend to associate along preferred pathways, similar to sliding of a protein along DNA in the process of protein-DNA recognition. DOI: http://dx.doi.org/10.7554/eLife.01370.001.
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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.