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BioMolecular Simulation

MEMBERS

  • Sergio Pantano, PhD (Head)
  • Matías Machado, PhD (Staff Member)
  • Astrid Brandner, MSc (Staff Member)
  • Steffano Silva (Undergraduate Student)
  • Carlos Cruz (Short term Visitor )

RESEARCH

The Group of BioMolecular Simulations develops and applies cutting-edge modeling and simulation methods to the study of problems of biomedical relevance.

We develop and maintain a general-purposes Coarse-Grained (CG) force field for biomolecular systems, for which we coined the name SIRAH©. The force field currently includes parameters for simulating aqueous solvent and simple electrolytes; single/double stranded DNA and proteins at Coarse Grained and multiresolution level. A substantial effort has been devoted to make the implementation of SIRAH© user-friendly and straightforward in popular simulation packages. As a result, tarballs for using SIRAH© on Amber and Gromacs (the two most popular molecular dynamics simulation packages) along with step-by-step tutorials and scripts for analysis and visualization were made available from our web site (www.sirahff.com).

Latest developments include:

  • Parameters for phospholipids (In collaboration with E. Frigini and R. Porasso, Universidad Nacional de San Luis, Argentina)
  • Supra molecular water models for multiresolution simulations. These are applied to the study of entire viral capsids (In collaboration with D. Guerin and M. Costabel).

PUBLICATIONS

(Only latest 3 years listed)
– Machado MR and Pantano S. SIRAH Tools: mapping, backmapping and visualization of coarse-grained models. Bioinformatics, 2016, 1-3.

– Machado MR and Pantano S. Exploring LacI−DNA Dynamics by Multiscale Simulations Using the SIRAH force field. JCTC, 2015, 11:5012.

– Jäger AV, De Gaudenzi JG, Mild JG, Cormack BM, Pantano S, Altschuler DL, Edreira MM. Identification of novel cyclic nucleotide binding proteins in Trypanosoma cruzi. Mol Biochem Parasitol. 2015, 198:104.

– Darré L, Machado MR, Brandner AF, Ferreira S, Gonzalez HC, Pantano S. SIRAH: a structurally unbiased coarse-grained force field for proteins with aqueous solvation and long-range electrostatics. JCTC, 2015, 11:723.

– Morande PE, Borge M, Abreu C, Galletti J, Zanetti SR, Nannini P, Bezares RF, Pantano S, Dighiero G, Oppezzo P, Gamberale R, Giordano M. Surface localization of high-mobility group nucleosome-binding protein 2 (HMGN2) on leukemic B cells from chronic lymphocytic leukemia patients is related to secondary autoimmune hemolytic anemia. Leuk Lymphoma. 2015. Jan 21:1-8.

– Sanguinetti M, Amillis S, Pantano S, Scazzocchio C and Ramón A. Modeling and mutational analysis of Aspergillus nidulans UreA, a member of the subfamily of urea/H+ transporters in fungi and plants. Open Biology, 2014, 4:140070

– Zecchin A, Pattarini L, Gutierrez MI, Mano M, Mai A, Valente S, Myers MP, Pantano S, and Giacca M. Reversible acetylation regulates vascular endothelial growth factor receptor-2 activity. Journal of Molecular Cell Biology, 2014, 6:116.

– Gonzalez HC, Darré, L. Pantano, S. Transferable Mixing of Atomistic and Coarse-Grain Water Models. J. Phys. Chem. B, 2013, 117 :14438.

– Pantano S, Montecucco C. The Blockade of the Neurotransmitter Release Apparatus by Botulinum Neurotoxins. Cell. Mol. Life Sci. 2013, DOI:10.1007/s00018-013-1380-7.

– Megighian A, Zordan M, Pantano S, Scorzeto M, Rigoni M, Zanini D, Rossetto O, Montecucco C. Evidence for a radial SNARE super-complex mediating neurotransmitter release at the Drosophila neuromuscular junction. J. Cell. Sci., 2013, 136: 3134.

– Almeida RS, Loss O, Colabardini AC, Brown NA, Bignell E, Savoldi M, Pantano S, Goldman MH, Arst HN Jr, Goldman GH. Genetic Bypass of Aspergillus nidulans crzA Function in Calcium Homeostasis. G3 (Bethesda), 2013, 3:1129.

CONTACT

Sergio Pantano, PhD.
Tel: +598 2 5220910 Int 156
e-mail: spantano “at” pasteur.edu.uy