ArticleBiophysical journal2011
A direct coupling between global and internal motions in a single domain protein? MD investigation of extreme scenarios.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
6 citing papers in PubMed, 12 citations in OpenAlex.
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Dissociation of a Dynamic Protein Complex Studied by All-Atom Molecular Simulations.Biophysical journal · 2016Article
- Structure and dynamics analysis on plexin-B1 Rho GTPase binding domain as a monomer and dimer.The journal of physical chemistry. B · 2014Article
- Molecular simulations of a dynamic protein complex: role of salt-bridges and polar interactions in configurational transitions.Biophysical journal · 2013Article
- 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.The journal of physical chemistry. B · 2013Article
- Crowding induces differences in the diffusion of thermophilic and mesophilic proteins: a new look at neutron scattering results.Biophysical journal · 2011Article
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
Proteins are not rigid molecules, but exhibit internal motions on timescales ranging from femto- to milliseconds and beyond. In solution, proteins also experience global translational and rotational motions, sometimes on timescales comparable to those of the internal fluctuations. The possibility that internal and global motions may be directly coupled has intriguing implications, given that enzymes and cell signaling proteins typically associate with binding partners and cellular scaffolds. Such processes alter their global motion and may affect protein function. Here, we present molecular dynamics simulations of extreme case scenarios to examine whether a possible relationship exists. In our model protein, a ubiquitin-like RhoGTPase binding domain of plexin-B1, we removed either internal or global motions. Comparisons with unrestrained simulations show that internal and global motions are not appreciably coupled in this single-domain protein. This lack of coupling is consistent with the observation that the dynamics of water around the protein, which is thought to permit, if not stimulate, internal dynamics, is also largely independent of global motion. We discuss implications of these results for the structure and function of proteins.
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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.