ArticleProceedings of the National Academy of Sciences of the United States of America2006
Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 135 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
135 citing papers in PubMed.
- Role of Hsp70 chaperone in client-protein folding elucidated by Markov state modeling and NMR restraint-assisted molecular dynamics simulations.Biophysical journal · 2026Article
- SMC complex unidirectionally translocates DNA by coupling segment capture with an asymmetric kleisin path.eLife · 2026Article
- Isolation, Purification, Identification, and In Vitro ACE Inhibitory Activity of Tyrosine-Arginine Dipeptide From Red Millet Huangjiu.Food science & nutrition · 2026Article
- Allosteric regulation of enzymatic catalysis by molecular crowding.Communications chemistry · 2026Article
- Tracking the protein conformational motions driving HIV-1 membrane fusion.Scientific reports · 2026Article
- Unbiased Enhanced Sampling in Molecular Dynamics via Simultaneously Accelerating Diffusion in Multiple Low-Dimensional Collective Variable Spaces.Journal of chemical theory and computation · 2025Article
- Article
- The ATPase asymmetry: Novel computational insight into coupling diverse FBiophysical journal · 2025Article
- MEF-AlloSite: an accurate and robust Multimodel Ensemble Feature selection for the Allosteric Site identification model.Journal of cheminformatics · 2024Article
- GENESIS 2.1: High-Performance Molecular Dynamics Software for Enhanced Sampling and Free-Energy Calculations for Atomistic, Coarse-Grained, and Quantum Mechanics/Molecular Mechanics Models.The journal of physical chemistry. B · 2024Article
- Article
- Identification of Residues Potentially Involved in Optical Shifts in the Water-Soluble ChlorophyllThe journal of physical chemistry. B · 2024Article
- Multi-Journal of chemical theory and computation · 2024Article
- How aberrant N-glycosylation can alter protein functionality and ligand binding: An atomistic view.Structure (London, England : 1993) · 2023Article
- Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models.Biophysical reviews · 2023Review
- FBiophysical journal · 2023Article
- How a single mutation alters the protein structure: a simulation investigation on protein tyrosine phosphatase SHP2.RSC advances · 2023Article
- Design of novel cyanovirin-N variants by modulation of binding dynamics through distal mutations.eLife · 2022Article
- Nucleosome breathing facilitates cooperative binding of pluripotency factors Sox2 and Oct4 to DNA.Biophysical journal · 2022Article
- Role of Repeated Conformational Transitions in Substrate Binding of Adenylate Kinase.The journal of physical chemistry. B · 2022Article
75 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Biomolecules often undergo large-amplitude motions when they bind or release other molecules. Unlike macroscopic machines, these biomolecular machines can partially disassemble (unfold) and then reassemble (fold) during such transitions. Here we put forward a minimal structure-based model, the "multiple-basin model," that can directly be used for molecular dynamics simulation of even very large biomolecular systems so long as the endpoints of the conformational change are known. We investigate the model by simulating large-scale motions of four proteins: glutamine-binding protein, S100A6, dihydrofolate reductase, and HIV-1 protease. The mechanisms of conformational transition depend on the protein basin topologies and change with temperature near the folding transition. The conformational transition rate varies linearly with driving force over a fairly large range. This linearity appears to be a consequence of partial unfolding during the conformational transition.
Indexed as
Identifiers
What OpenQuestion holds
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.