Model-free estimation of the effective correlation time for C–H bond reorientation in amphiphilic bilayers: 1H–13C solid-state NMR and MD simulations

2015 ◽  
Vol 142 (4) ◽  
pp. 044905 ◽  
Author(s):  
Tiago Mendes Ferreira ◽  
O. H. Samuli Ollila ◽  
Roberta Pigliapochi ◽  
Aleksandra P. Dabkowska ◽  
Daniel Topgaard
Keyword(s):  
Solid State ◽  
Correlation Time ◽  
Solid State Nmr ◽  
Md Simulations ◽  
Model Free

Best of Two Worlds? How MD Simulations of Amphiphilic Helical Peptides in Membranes Can Complement Data from Oriented Solid-State NMR

2018 ◽  
Vol 14 (11) ◽  
pp. 6002-6014 ◽  
Author(s):  
Sabine Reißer ◽  
Erik Strandberg ◽  
Thomas Steinbrecher ◽  
Marcus Elstner ◽  
Anne S. Ulrich
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Md Simulations ◽  
Helical Peptides

Irregular structure of the HIV fusion peptide in membranes demonstrated by solid-state NMR and MD simulations

2011 ◽  
Vol 40 (4) ◽  
pp. 529-543 ◽  
Author(s):  
Dorit Grasnick ◽  
Ulrich Sternberg ◽  
Erik Strandberg ◽  
Parvesh Wadhwani ◽  
Anne S. Ulrich
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Md Simulations ◽  
Fusion Peptide ◽  
Irregular Structure

scholarly journals A combination of solid-state NMR and MD simulations reveals the binding mode of a rhomboid protease inhibitor

2021 ◽  
Author(s):  
Claudia Bohg ◽  
Carl Öster ◽  
Tillmann Utesch ◽  
Susanne Bischoff ◽  
Sascha Lange ◽  
...  
Keyword(s):  
Solid State ◽  
Protease Inhibitor ◽  
Solid State Nmr ◽  
Md Simulations ◽  
Binding Mode ◽  
Selective Inhibitors ◽  
Intramembrane Proteolysis ◽  
Rhomboid Protease ◽  
Intramembrane Proteases ◽  
Pharmacological Targets

Intramembrane proteolysis plays a fundamental role in many biological and pathological processes. Intramembrane proteases thus represent promising pharmacological targets, but few selective inhibitors have been identified. This is in contrast...

scholarly journals Ceramide–lipid interactions studied by MD simulations and solid-state NMR

2014 ◽  
Vol 1838 (10) ◽  
pp. 2511-2519 ◽  
Author(s):  
Bercem Dutagaci ◽  
Johanna Becker-Baldus ◽  
José D. Faraldo-Gómez ◽  
Clemens Glaubitz
Keyword(s):  
Solid State ◽  
Solid State Nmr ◽  
Md Simulations ◽  
Lipid Interactions

scholarly journals Model-Free Spectral Density Mapping Applied to Dynamics of Rhodopsin in Solid-State NMR Spectroscopy

2013 ◽  
Vol 104 (2) ◽  
pp. 41a-42a
Author(s):  
Xiaolin Xu ◽  
Andrey V. Struts ◽  
K.J. Mallikarjunaiah ◽  
Michael F. Brown
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Spectral Density ◽  
Solid State Nmr ◽  
Solid State Nmr Spectroscopy ◽  
Density Mapping ◽  
Model Free ◽  
Spectral Density Mapping

scholarly journals Experimental Characterization of the Hepatitis B Virus Capsid Dynamics by Solid-State NMR

2022 ◽  
Vol 8 ◽  
Author(s):  
Alexander A. Malär ◽  
Morgane Callon ◽  
Albert A. Smith ◽  
Shishan Wang ◽  
Lauriane Lecoq ◽  
...  
Keyword(s):  
Hepatitis B Virus ◽  
Solid State ◽  
Hepatitis B ◽  
Solid State Nmr ◽  
Md Simulation ◽  
Core Protein ◽  
Relaxation Times ◽  
Md Simulations ◽  
Blind Spot ◽  
B Virus

Protein plasticity and dynamics are important aspects of their function. Here we use solid-state NMR to experimentally characterize the dynamics of the 3.5 MDa hepatitis B virus (HBV) capsid, assembled from  240 copies of the Cp149 core protein. We measure both T1 and T1ρ relaxation times, which we use to establish detectors on the nanosecond and microsecond timescale. We compare our results to those from a 1 microsecond all-atom Molecular Dynamics (MD) simulation trajectory for the capsid. We show that, for the constituent residues, nanosecond dynamics are faithfully captured by the MD simulation. The calculated values can be used in good approximation for the NMR-non-detected residues, as well as to extrapolate into the range between the nanosecond and microsecond dynamics, where NMR has a blind spot at the current state of technology. Slower motions on the microsecond timescale are difficult to characterize by all-atom MD simulations owing to computational expense, but are readily accessed by NMR. The two methods are, thus, complementary, and a combination thereof can reliably characterize motions covering correlation times up to a few microseconds.

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