scholarly journals Molecular Dynamics Simulations of Micelle Formation around Dimeric Glycophorin A Transmembrane Helices

2004 ◽  
Vol 87 (2) ◽  
pp. 754-763 ◽  
Author(s):  
Rosemary Braun ◽  
Donald M. Engelman ◽  
Klaus Schulten
2021 ◽  
Author(s):  
Prithvi R. Pandey ◽  
Bartosz Różycki ◽  
Reinhard Lipowsky ◽  
Thomas R. Weikl

AbstractWe investigate the structural and orientational variability of the membrane-embedded T cell receptor (TCR) – CD3 complex in extensive atomistic molecular dynamics simulations based on the recent cryo-EM structure determined by Dong et al. (2019). We find that the TCR extracellular (EC) domain is highly variable in its orientation by attaining tilt angles relative to the membrane normal that range from 15° to 55°. The tilt angle of the TCR EC domain is both coupled to a rotation of the domain and to characteristic changes throughout the TCR – CD3 complex, in particular in the EC interactions of the Cβ FG loop of the TCR, as well as in the orientation of transmembrane helices. The concerted motions of the membrane-embedded TCR – CD3 complex revealed in our simulations provide atomistic insights for force-based models of TCR activation, which involve such structural changes in response to tilt-inducing forces on antigen-bound TCRs.


2016 ◽  
Vol 110 (3) ◽  
pp. 572a
Author(s):  
Sadegh Faramarzi ◽  
Danielle Grodi ◽  
Andrew Philpott ◽  
Michael Block ◽  
Madison Kukura ◽  
...  

2014 ◽  
Vol 10 (5) ◽  
pp. 2165-2175 ◽  
Author(s):  
Benjamin A. Hall ◽  
Khairul Bariyyah Abd Halim ◽  
Amanda Buyan ◽  
Beatrice Emmanouil ◽  
Mark S. P. Sansom

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
George Khelashvili ◽  
Anoop Narayana Pillai ◽  
Joon Lee ◽  
Kalpana Pandey ◽  
Alexander M. Payne ◽  
...  

AbstractMutations in the G protein-coupled receptor (GPCR) rhodopsin are a common cause of autosomal dominant retinitis pigmentosa, a blinding disease. Rhodopsin self-associates in the membrane, and the purified monomeric apo-protein opsin dimerizes in vitro as it transitions from detergent micelles to reconstitute into a lipid bilayer. We previously reported that the retinitis pigmentosa-linked F220C opsin mutant fails to dimerize in vitro, reconstituting as a monomer. Using fluorescence-based assays and molecular dynamics simulations we now report that whereas wild-type and F220C opsin display distinct dimerization propensities in vitro as previously shown, they both dimerize in the plasma membrane of HEK293 cells. Unexpectedly, molecular dynamics simulations show that F220C opsin forms an energetically favored dimer in the membrane when compared with the wild-type protein. The conformation of the F220C dimer is unique, with transmembrane helices 5 and 6 splayed apart, promoting widening of the intracellular vestibule of each protomer and influx of water into the protein interior. FRET experiments with SNAP-tagged wild-type and F220C opsin expressed in HEK293 cells are consistent with this conformational difference. We speculate that the unusual mode of dimerization of F220C opsin in the membrane may have physiological consequences.


eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Prithvi R Pandey ◽  
Bartosz Różycki ◽  
Reinhard Lipowsky ◽  
Thomas R Weikl

We investigate the structural and orientational variability of the membrane-embedded T cell receptor (TCR) - CD3 complex in extensive atomistic molecular dynamics simulations based on the recent cryo-EM structure determined by Dong et al. (2019). We find that the TCR extracellular (EC) domain is highly variable in its orientation by attaining tilt angles relative to the membrane normal that range from 15° to 55°. The tilt angle of the TCR EC domain is both coupled to a rotation of the domain and to characteristic changes throughout the TCR - CD3 complex, in particular in the EC interactions of the C_ FG loop of the TCR, as well as in the orientation of transmembrane helices. The concerted motions of the membrane-embedded TCR - CD3 complex revealed in our simulations provide atomistic insights on conformational changes of the complex in response to tilt-inducing forces on antigen-bound TCRs.


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