We are interested in understanding the molecular machinery of the Dengue Virus. We use computational tools like molecular dynamics simulations to model viral proteins and protein-RNA complexes that are key in different stages of the viral life cycle.
Impact of bound ssRNA length on allostery in the Dengue Virus NS3 helicase
F Amrein, C Sarto, LA Cababie, FL Gonzalez Flecha, SB Kaufman, M Arrar
Nucleic Acids Research 51 (20), 11213-11224 (2023)
Thermodynamic and mechanistic analysis of the functional properties of dengue virus NS3 helicase
JJ Incicco, LA Cababie, C Sarto, NS Adler, F Amrein, E Mikkelsen, M Arrar, SB Kaufman
Biophysical Reviews 15 (4), 591-600 (2023)
Insights into the product release mechanism of dengue virus NS3 helicase
NS Adler, LA Cababie, C Sarto, CN Cavasotto, LG Gebhard, DA Estrin, AV Gamarnik, M Arrar, SB Kaufman
Nucleic Acids Research 50 (12), 6968-6979 (2022)
Atomistic insight into the essential binding event of ACE2-derived peptides to the SARS-CoV-2 spike protein
C Sarto, S Florez-Rueda, M Arrar, CPR Hackenberger, D Lauster, S Di Lella
Biological Chemistry 403 (5-6), 615-624 (2022)
Nucleotide-dependent dynamics of the Dengue NS3 helicase
C Sarto, SB Kaufman, DA Estrin, M Arrar
Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1868 (8), 140441 (2020)
Lessons learned about steered molecular dynamics simulations and free energy calculations
FM Boubeta, RM Contestín García, EN Lorenzo, L Boechi, DA Estrin, M Sued, M Arrar
Chemical biology & drug design 93 (6), 1129-1138
On the accurate estimation of free energies using the Jarzynski equality
M Arrar, FM Boubeta, ME Szretter, M Sued, L Boechi, D Rodriguez
Journal of Computational Chemistry 40 (4), 688-696
F Marsico, O Burastero, LA Defelipe, ED Lopez, M Arrar, AG Turjanski, MA Martí
Biochemical and biophysical research communications 498 (2), 305-312
Understanding the molecular basis of the high oxygen affinity variant human hemoglobin Coimbra
SE Jorge, M Bringas, AA Petruk, M Arrar, MA Marti, MS Skaf, FF Costa, L Capece, MF Sonati, DA Estrin
Archives of biochemistry and biophysics 637, 73-78
J Rinaldi, M Arrar, G Sycz, ML Cerutti, PM Berguer, G Paris, DA Estrín, MA Martí, S Klinke, FA Goldbaum
Journal of Molecular Biology 428 (6), 1165-1179
Accelerated adaptive integration method
JW Kaus, M Arrar, JA McCammon
The Journal of Physical Chemistry B 118 (19), 5109-5118
Inactivating mutation in histone deacetylase 3 stabilizes its active conformation
M Arrar, CAF de Oliveira, J Andrew McCammon
Protein Science 22 (10), 1306-1312
Hydrophobic Effect Drives Oxygen Uptake in Myoglobin via Histidine E7
L Boechi, M Arrar, MA Martí, JS Olson, AE Roitberg, DA Estrin
Journal of Biological Chemistry 288 (9), 6754-6762
M Arrar, CAF de Oliveira, M Fajer, W Sinko, JA McCammon
Journal of chemical theory and computation 9 (1), 18-23
M Arrar, R Turnham, L Pierce, CAF de Oliveira, JA McCammon
Protein Science 22 (1), 83-92
Substrate stereo‐specificity in tryptophan dioxygenase and indoleamine 2, 3‐dioxygenase
L Capece, M Arrar, AE Roitberg, SR Yeh, MA Marti, DA Estrin
Proteins: Structure, Function, and Bioinformatics 78 (14), 2961-2972