Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage.

Autor: Emmanuel E Moutoussamy, Qaiser Waheed, Greta J Binford, Hanif M Khan, Shane M Moran, Anna R Eitel, Matthew H J Cordes, Nathalie Reuter

Publikováno v: PLoS Computational Biology, Vol 18, Iss 2, p e1009871 (2022)

Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present high activity against lip

Externí odkaz: https://doaj.org/article/a50e9a4e541b4ce4a972ecd447bb3e19

Coarse Grained Models: The Martini Force Field

Autor: Hanif M. Khan, D. Peter Tieleman

Publikováno v: Reference Module in Chemistry, Molecular Sciences and Chemical Engineering ISBN: 9780124095472

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::bd7e390340a83a6307aa831946999fad
https://doi.org/10.1016/b978-0-12-821978-2.00087-8

Martini 3

Autor: Vincent Nieto, Valentina Corradi, Siewert J. Marrink, Matti Javanainen, Peter C. Kroon, Ilpo Vattulainen, Hector Martinez-Seara, D. Peter Tieleman, Alex H. de Vries, Jan Domański, Hanif M. Khan, Robert B. Best, Ilias Patmanidis, Sebastian Thallmair, Ignacio Faustino, Xavier Periole, Jonathan Barnoud, Tsjerk A. Wassenaar, Josef Melcr, Nathalie Reuter, Haleh Abdizadeh, Bart M H Bruininks, Paulo C. T. Souza, Fabian Grünewald, Riccardo Alessandri, Luca Monticelli

Publikováno v: Nature Methods, 18, 382-388. Nature Publishing Group
Nature Methods
Souza, P C T, Alessandri, R, Barnoud, J, Thallmair, S, Faustino, I, Grünewald, F, Patmanidis, I, Abdizadeh, H, Bruininks, B M H, Wassenaar, T A, Kroon, P C, Melcr, J, Nieto, V, Corradi, V, Khan, H M, Domański, J, Javanainen, M, Martinez-Seara, H, Reuter, N, Best, R B, Vattulainen, I, Monticelli, L, Periole, X, Tieleman, D P, de Vries, A H & Marrink, S J 2021, ' Martini 3 : a general purpose force field for coarse-grained molecular dynamics ', Nature Methods, vol. 18, no. 4, pp. 382-388 . https://doi.org/10.1038/s41592-021-01098-3

The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 (http://cgmartini.nl), with an improved interaction balance, new bead types and expanded ability to include specific inter

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f1fe1d2646ea2c4aa330b9fd3b0ab46d
https://hdl.handle.net/11370/27f1d65b-ff4d-4290-9fc8-b019e36c5c2e

Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C

Autor: Emmanuel E. Moutoussamy, Hanif M. Khan, Mary F. Roberts, Anne Gershenson, Christophe Chipot, Nathalie Reuter

Publikováno v: Journal of Chemical Information and Modeling

Peripheral membrane proteins (PMPs) bind temporarily to cellular membranes and play important roles in signaling, lipid metabolism, and membrane trafficking. Obtaining accurate membrane-PMP affinities using experimental techniques is more challenging

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::19b3bb9d087a27cdff3b7f391b2b4300
https://hdl.handle.net/11250/3043803

Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage

Autor: Emmanuel E. Moutoussamy, Qaiser Waheed, Greta J. Binford, Hanif M. Khan, Shane M. Moran, Anna R. Eitel, Matthew H. J. Cordes, Nathalie Reuter

Publikováno v: e1009871
PLoS Computational Biology

Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present high activity against lip

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::384f3d8b329207b7b8a0fa2177307221
https://pubmed.ncbi.nlm.nih.gov/35180220