ArticleBiophysical journal2011
Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables.
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 14 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
14 citing papers in PubMed.
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Structural determination of virus protein U from HIV-1 by NMR in membrane environments.Biochimica et biophysica acta · 2015Article
- Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.PLoS computational biology · 2015Article
- Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes.Biophysical journal · 2015Article
- Combining experiments and simulations using the maximum entropy principle.PLoS computational biology · 2014Review
- Ensemble-based interpretations of NMR structural data to describe protein internal dynamics.Molecules (Basel, Switzerland) · 2013Review
- NMR-based simulation studies of Pf1 coat protein in explicit membranes.Biophysical journal · 2013Article
- Structural refinement from restrained-ensemble simulations based on EPR/DEER data: application to T4 lysozyme.The journal of physical chemistry. B · 2013Article
- Restrained-ensemble molecular dynamics simulations based on distance histograms from double electron-electron resonance spectroscopy.The journal of physical chemistry. B · 2013Article
- Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An implicit membrane model with a dynamically varying bilayer thickness.Journal of chemical theory and computation · 2013Article
- On the statistical equivalence of restrained-ensemble simulations with the maximum entropy method.The Journal of chemical physics · 2013Article
- Comparative analysis of the orientation of transmembrane peptides using solid-state (2)H- and (15)N-NMR: mobility matters.European biophysics journal : EBJ · 2012Article
- Influence of hydrophobic mismatch on structures and dynamics of gramicidin a and lipid bilayers.Biophysical journal · 2012Article
- Solid-state NMR ensemble dynamics as a mediator between experiment and simulation.Biophysical journal · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As the major component of membrane proteins, transmembrane helices embedded in anisotropic bilayer environments adopt preferential orientations that are characteristic or related to their functional states. Recent developments in solid-state nuclear magnetic resonance (SSNMR) spectroscopy have made it possible to measure NMR observables that can be used to determine such orientations in a native bilayer environment. A quasistatic single conformer model is frequently used to interpret the SSNMR observables, but important motional information can be missing or misinterpreted in the model. In this work, we have investigated the orientation of the single-pass transmembrane domain of viral protein "u" (VpuTM) from HIV-1 by determining an ensemble of structures using multiple conformer models based on the SSNMR ensemble dynamics technique. The resulting structure ensemble shows significantly larger orientational fluctuations while the ensemble-averaged orientation is compatible with the orientation based on the quasistatic model. This observation is further corroborated by comparison with the VpuTM orientation from comparative molecular dynamics simulations in explicit bilayer membranes. SSNMR ensemble dynamics not only reveals the importance of transmembrane helix dynamics in interpretation of SSNMR observables, but also provides a means to simultaneously extract both transmembrane helix orientation and dynamics information from the SSNMR measurements.
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.