Coarse-Grained Parameterization of Nucleotide Cofactors and Metabolites: Protonation Constants, Partition Coefficients, and Model Topologies

Autor: Manuela M. Pereira, Clement Arnarez, Luís M. P. Lima, Manuel N. Melo, Filipe M. Sousa

Publikováno v: Journal of Chemical Information and Modeling. 61:335-346

Nucleotides are structural units relevant not only in nucleic acids but also as substrates or cofactors in key biochemical reactions. The size- and timescales of such nucleotide-protein interactions fall well within the scope of coarse-grained molecu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2bd4e1fa96f6d208bfdc629a8e8fb91c
https://doi.org/10.1021/acs.jcim.0c01077

Identification of Two New Cholesterol Interaction Sites on the A2A Adenosine Receptor

Autor: Clement Arnarez, Edward Lyman, Eric Rouviere, Lewen Yang

Publikováno v: Biophysical Journal. 113:2415-2424

By mole, cholesterol is the most abundant component of animal cell plasma membranes. Many membrane proteins have been shown to be functionally dependent on cholesterol, several of which have also been shown to bind cholesterol at well-defined locatio

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1c0ed4ebf918668fb6d81d2c130b7af9
https://doi.org/10.1016/j.bpj.2017.09.027

Hysteresis and the Cholesterol Dependent Phase Transition in Binary Lipid Mixtures with the Martini Model

Autor: Clement Arnarez, Edward Lyman, Alexis Webb, Eric Rouviere

Publikováno v: J Phys Chem B

Extensive Martini simulation data, totaling 5 ms, is presented for binary mixtures of dipalmitoylphosphatidylcholine (DPPC) and cholesterol. Using simulation initiated from both gel (s(o)) and liquid-disordered (L(d)) phases, significant and strongly

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::41aa461dd0116c7da9faf44438530124
https://doi.org/10.1021/acs.jpcb.6b09728

Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex

Autor: Xavier Periole, Tomas E. van den Berg, Clement Arnarez, Djurre H. de Jong, Nicoletta Liguori, Siewert J. Marrink

Publikováno v: Journal of Physical Chemistry B, 119(25), 7791-7803. American Chemical Society
de Jong, D H, Liguori, N, van den Berg, T E, Arnarez, C, Periole, X & Marrink, S J 2015, ' Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex ', Journal of Physical Chemistry B, vol. 119, no. 25, pp. 7791-7803 . https://doi.org/10.1021/acs.jpcb.5b00809
The Journal of Physical Chemistry B, 119(25), 7791-7803. AMER CHEMICAL SOC

Electron transfers within and between protein complexes are core processes of the electron transport chains occurring in thylakoid (chloroplast), mitochondrial, and bacterial membranes. These electron transfers involve a number of cofactors. Here we

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4e84f763d0afea616c01f813ceec4391
https://research.vu.nl/en/publications/7d37d658-2c15-4a56-927a-1c45db0b91d2

Lipid organization of the plasma membrane

Autor: Tsjerk A. Wassenaar, Clement Arnarez, Floris J. van Eerden, Siewert J. Marrink, Xavier Periole, Manuel N. Melo, D. Peter Tieleman, Alex H. de Vries, Helgi I. Ingólfsson, Cesar A. Lopez

Publikováno v: Journal of the American Chemical Society, 136(41), 14554-14559. AMER CHEMICAL SOC

The detailed organization of cellular membranes remains rather elusive. Based on large-scale molecular dynamics simulations, we provide a high-resolution view of the lipid organization of a plasma membrane at an unprecedented level of complexity. Our

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4f2bed141f07ef121777782a933f90bf
https://doi.org/10.1021/ja507832e