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Molecular Dynamics Simulations of the Bacterial UraA H+-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin

Antreas C. Kalli, Mark S. P. Sansom, Reinhart A. F. Reithmeier, Bert L. de Groot
2015 PLoS Computational Biology  
Simulations were performed in the absence of uracil, and resulted in a closed state of the transporter, due to relative movement of the gate and core domains.  ...  In this study, we have used a multiscale computational methodology to examine the dynamics of UraA and to elucidate its interactions with lipids that resemble its native environment in the bacterial inner  ...  The final atomistic structure of UraA in a bilayer is in a closed state conformation.  ... 
doi:10.1371/journal.pcbi.1004123 pmid:25729859 pmcid:PMC4346270 fatcat:euovfkp4jrbupb4v6xwk7gapey

Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations

George Hedger, Mark S.P. Sansom
2016 Biochimica et Biophysica Acta - Biomembranes  
This demonstrates the power of the molecular dynamics approach in the prediction and characterization of lipid interaction sites on integral membrane proteins.  ...  Molecular dynamics simulations provide a powerful tool for the identification of these sites, complementing advances in membrane protein structural biology and biophysics.  ...  García for simulation structures of β 2 AR used in the table of contents graphic.  ... 
doi:10.1016/j.bbamem.2016.02.037 pmid:26946244 pmcid:PMC5589069 fatcat:n5mv2flpbjg7bp5zukt4btalxa

mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations [article]

Alexandra O. M. Holmes, Adrian Goldman, Antreas C. Kalli
2022 bioRxiv   pre-print
In this work, we use multiscale molecular dynamics simulations to demonstrate for the first time that mPPases form specific anionic lipid interactions at 4 sites at the distal and interfacial regions of  ...  These interactions are conserved in simulations of the mPPases from Thermotoga maritima, Vigna radiata and Clostridium leptum and characterised by interactions with positive residues on helices 1, 2, 3  ...  Acknowledgements This work was funded by a BBSRC DTP fellowship (BB/M011151/1) (to AH). AG was funded by a BBSRC grant BB/T006048/1 and a grant from the Academy of Finland, grant number 1322609.  ... 
doi:10.1101/2022.03.08.483421 fatcat:stbgzvrpbrdpta4csar5s2bl6a

Influence of lipids on protein-mediated transmembrane transport

Elizabeth J. Denning, Oliver Beckstein
2013 Chemistry and Physics of Lipids  
In some cases, a combined approach of molecular and structural biology together with computer simulations has revealed the molecular mechanisms.  ...  We are reviewing the evidence for regulation of these transport processes by interactions with the lipids of the membrane.  ...  Molecular dynamics simulations of LacY in a PE membrane identified a specific salt-bridge between a PE lipid headgroup and the charged residues Asp68 and Lys69 in LacY (Lensink et al., 2010) (Fig.  ... 
doi:10.1016/j.chemphyslip.2013.02.007 pmid:23473882 fatcat:o6e424hr4bfpbp32io2y33hoi4

Emerging Diversity in Lipid–Protein Interactions

Valentina Corradi, Besian I. Sejdiu, Haydee Mesa-Galloso, Haleh Abdizadeh, Sergei Yu. Noskov, Siewert J. Marrink, D. Peter Tieleman
2019 Chemical Reviews  
Computationally, despite important limitations, molecular dynamics simulations with current computer power and theoretical models are now in an excellent position to answer detailed questions about lipid-protein  ...  Membrane lipids interact with proteins in a variety of ways, ranging from providing a stable membrane environment for proteins to being embedded in to detailed roles in complicated and well-regulated protein  ...  In contrast, NapA dimers are stable without cardiolipin, as the glue-like mechanism is provided by an N-terminal segment not present in NhaA. 618 The E. coli UraA/H + symporter couples the uptake of  ... 
doi:10.1021/acs.chemrev.8b00451 pmid:30758191 pmcid:PMC6509647 fatcat:75ypucmcrfhuvintk4tu4jexby

The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes

Douglas B. Kell
2021 Molecules  
if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable  ...  Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological  ...  Conflicts of Interest: The author declares no conflict of interest. Sample Availability: Samples of the compounds are not available from the authors.  ... 
doi:10.3390/molecules26185629 pmid:34577099 pmcid:PMC8470029 fatcat:jf37l2bs45hobbqwuegedg443m