Arrar Group

Welcome

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.

 

Recent Publications

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)

Earlier Publications (before 2019)

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


Multiscale approach to the activation and phosphotransfer mechanism of CpxA histidine kinase reveals a tight coupling between conformational and chemical steps

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


Structural insights into the HWE histidine kinase family: the Brucella blue light-activated histidine kinase domain

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


w-REXAMD: A Hamiltonian replica exchange approach to improve free energy calculations for systems with kinetically trapped conformations

M Arrar, CAF de Oliveira, M Fajer, W Sinko, JA McCammon

Journal of chemical theory and computation 9 (1), 18-23


Structural insight into the separate roles of inositol tetraphosphate and deacetylase‐activating domain in activation of histone deacetylase 3

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