ArticleThe journal of physical chemistry. B2013
Analysis of 15N-1H NMR relaxation in proteins by a combined experimental and molecular dynamics simulation approach: picosecond-nanosecond dynamics of the Rho GTPase binding domain of plexin-B1 in the dimeric state indicates allosteric pathways.
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 13 papers.
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Who cites it
13 citing papers in PubMed, 29 citations in OpenAlex.
- Predicting NMR Relaxation Using a First-Principles Brownian Dynamics Approach.Journal of chemical theory and computation · 2026Article
- Computational model predicts function of Rho-GTPase binding for plexin receptor GAP activity on Rap1b via dynamic allosteric changes.Protein science : a publication of the Protein Society · 2025Article
- Bootstrap Aggregation for Model Selection in the Model-free Formalism.Magnetic resonance (Gottingen, Germany) · 2021Article
- Conformational Entropy from Restricted Bond-Vector Motion in Proteins: The Symmetry of the Local Restrictions and Relation to NMR Relaxation.The journal of physical chemistry. B · 2020Article
- Molecular Dynamics Simulations Reveal Isoform Specific Contact Dynamics between the Plexin Rho GTPase Binding Domain (RBD) and Small Rho GTPases Rac1 and Rnd1.The journal of physical chemistry. B · 2017Article
- What Mutagenesis Can and Cannot Reveal About Allostery.Biophysical journal · 2016Review
- Local Ordering at Mobile Sites in Proteins from Nuclear Magnetic Resonance Relaxation: The Role of Site Symmetry.The journal of physical chemistry. B · 2016Article
- Protein dynamics in the solid state from 2H NMR line shape analysis: a consistent perspective.The journal of physical chemistry. B · 2015Article
- Information flow and protein dynamics: the interplay between nuclear magnetic resonance spectroscopy and molecular dynamics simulations.Frontiers in plant science · 2015Review
- Article
- Frustration in biomolecules.Quarterly reviews of biophysics · 2014Review
- Structure and dynamics analysis on plexin-B1 Rho GTPase binding domain as a monomer and dimer.The journal of physical chemistry. B · 2014Article
- Cytochrome-P450-cytochrome-b5 interaction in a membrane environment changes 15N chemical shift anisotropy tensors.The journal of physical chemistry. B · 2013Article
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 4 countries.
Funding
Abstract
We investigate picosecond–nanosecond dynamics of the Rho-GTPase Binding Domain (RBD) of plexin-B1, which plays a key role in plexin-mediated cell signaling. Backbone 15N relaxation data of the dimeric RBD are analyzed with the model-free (MF) method, and with the slowly relaxing local structure/molecular dynamics (SRLS-MD) approach. Independent analysis of the MD trajectories, based on the MF paradigm, is also carried out. MF is a widely popular and simple method, SRLS is a general approach, and SRLS-MD is an integrated approach we developed recently. Corresponding parameters from the RBD dimer, a previously studied RBD monomer mutant, and the previously studied complex of the latter with the GTPase Rac1, are compared. The L2, L3, and L4 loops of the plexin-B1 RBD are involved in interactions with other plexin domains, GTPase binding, and RBD dimerization, respectively. Peptide groups in the loops of both the monomeric and dimeric RBD are found to experience weak and moderately asymmetric local ordering centered approximately at the C(i–1)(α)–C(i)(α) axes, and nanosecond backbone motion. Peptide groups in the α-helices and the β-strands of the dimer (the β-strands of the monomer) experience strong and highly asymmetric local ordering centered approximately at the C(i–1)(α)–C(i)(α) axes (N–H bonds). N–H fluctuations occur on the picosecond time scale. An allosteric pathway for GTPase binding, providing new insights into plexin function, is delineated.
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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.