ArticleBiophysical journal2013
NMR-based simulation studies of Pf1 coat protein in explicit membranes.
Article in Biophysical journal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 17 citations in OpenAlex.
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- Applications of NMR to membrane proteins.Archives of biochemistry and biophysics · 2017Review
- CHARMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments.The journal of physical chemistry. B · 2017Article
- High quality NMR structures: a new force field with implicit water and membrane solvation for Xplor-NIH.Journal of biomolecular NMR · 2017Article
- Molecular dynamics simulation strategies for protein-micelle complexes.Biochimica et biophysica acta · 2016Article
- NMR Structural Studies of Antimicrobial Peptides: LPcin Analogs.Biophysical journal · 2016Article
- A Practical Implicit Membrane Potential for NMR Structure Calculations of Membrane Proteins.Biophysical journal · 2015Article
- How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?Journal of chemical theory and computation · 2015Article
- Solid-State NMR-Restrained Ensemble Dynamics of a Membrane Protein in Explicit Membranes.Biophysical journal · 2015Article
- Article
- Nanotube array method for studying lipid-induced conformational changes of a membrane protein by solid-state NMR.Biophysical journal · 2015Article
- CHARMM-GUI Membrane Builder toward realistic biological membrane simulations.Journal of computational chemistry · 2014Article
- Structural dynamics and conformational equilibria of SERCA regulatory proteins in membranes by solid-state NMR restrained simulations.Biophysical journal · 2014Article
- A practical implicit solvent potential for NMR structure calculation.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2014Article
- Simplifying solid-state NMR spectra for biophysical studies on membrane proteins: selective targeting of sites and interactions.Biophysical journal · 2014Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
As time- and ensemble-averaged measures, NMR observables contain information about both protein structure and dynamics. This work represents a computational study to extract such information for membrane proteins from orientation-dependent NMR observables: solid-state NMR chemical shift anisotropy and dipolar coupling, and solution NMR residual dipolar coupling. We have performed NMR-restrained molecular dynamics simulations to refine the structure of the membrane-bound form of Pf1 coat protein in explicit lipid bilayers using the recently measured chemical shift anisotropy, dipolar coupling, and residual dipolar coupling data. From the simulations, we have characterized detailed protein-lipid interactions and explored the dynamics. All simulations are stable and the NMR restraints are well satisfied. The C-terminal transmembrane (TM) domain of Pf1 finds its optimal position in the membrane quickly (within 6 ns), illustrating efficient solvation of TM domains in explicit bilayer environments. Such rapid convergence also leads to well-converged interaction patterns between the TM helix and the membrane, which clearly show the interactions of interfacial membrane-anchoring residues with the lipids. For the N-terminal periplasmic helix of Pf1, we identify a stable, albeit dynamic, helix orientation parallel to the membrane surface that satisfies the amphiphatic nature of the helix in an explicit lipid bilayer. Such detailed information cannot be obtained solely from NMR observables. Therefore, the present simulations illustrate the usefulness of NMR-restrained MD refinement of membrane protein structure in explicit membranes.
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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.