Prof. Fernando Barroso Da Silva - University of São Paulo, Brazil
Host: Andrey Brukhno, Computational Chemistry, SCD
Thursday 2nd December at 14:00-15:00
Prof. Dr. Fernando Barroso da Silva obtained his Ph.D. degree in Theoretical Chemistry at University of Lund (LU), Sweden. At USP (University of São Paulo), he carried out research on fundamental forces in Molecular Biophysics (particularly protein electrostatics), structural Bioinformatics and Computational Virology/Immunology. Biomolecular interactions and data-driven science are his central research topics in all his projects. He is currently researching with three significant aims: a) methodological development of computational tools, methods and simulation software for (bio)molecular systems; b) investigations of generic aspects of ionic strength and proton effects in the stability, structure and function of biological macromolecules in solution; c) application of this technology to functionally interesting systems (e.g., viral and food proteins, antibody development, biomaterials, and protein-RNA interactions). He is the Head of the Laboratory of Computational Biophysical Chemistry (BPC) where he also applies his innovative technology to offer a rational approach to the discovery of therapeutic agents, biomarkers and their controlled release. He is a frequent visiting researcher/professor at Universities from different countries (Sweden, USA, France and Ireland) working also to promote the scientific partnership with them.
Development and applications of bioinformatic methods with a biophysical approach: from food, biomaterials to virus and antibody design
A vast class of biomolecular engineering problems at the present including the understanding, diagnosis and treatment of diseases; developments in the pharmaceutical and food industries; design of new (bio)functionalized materials and processes of bioseparation in general relies on a better knowledge of the fundamental physical interactions responsible for the formation and stability of molecular complexes. pH is a key physical chemical parameter for many of them that is also related to the macromolecular complexation even "on the wrong side of the pI". At our lab, our focus has been on the development of coarse-grained descriptions that could result in a good compromise between the proper modelling of the constant-pH physics and the simulation time. In this talk, I will review the main aspects of the peculiar attraction behind like-charge macromolecules, the constant-pH simulation models devised for different biomolecular applications, and how we have been using these tools together with other structural bioinformatic methods to better understand spidroins, viruses and designing therapeutic agents.
Key-papers:
[1] Giron, C. C.; Laaksonen, A.; Barroso da Silva, F.L Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants, Front. Med. Technol., v. 3, article 694347, 2021. (DOI:10.3389/fmedt.2021.694347).
[2] Poveda-Cuevas, S. A.; Barroso da Silva, F.L; Etchebest, C.; How the Strain Origin of Zika Virus NS1 Protein Impacts Its Dynamics and Implications to Their Differential Virulence, J. Chemical Information and Modeling, v. 61, pp. 1516-1530, 2021.
[3] Giron, C. C.; Laaksonen, A.; Barroso da Silva, F.L On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2, Virus Research, May 13;198021, 2020. (DOI:10.1016/j.virusres.2020.198021).
[4] Poveda-Cuevas, S. A.; Etchebest, C.; Barroso da Silva, F.L. On the identification of electrostatic epitopes in flavivirus by computer simulations: The PROCEEDpKa Method, J. Chemical Information and Modeling, v. 60, pp. 944-963, 2020.
[5] Barroso da Silva, F.L.; Carloni, P.; Cheung, D.; Cottone, G.; Donnini, S.; Foegeding, E.A.; Gulzar, M.; Jacquier, J.C.; Lobaskin, V.; MacKernan, D.; Naveh, Z.M.H.; Radhakrishnan, R.; Santiso, E., Understanding and Controlling Food Protein Folding and Aggregation and Taste: perspectives from experiment and simulation, Annual Review of Food Science and Technology, v. 11, pp. 365-387, 2020.
[6] Barroso da Silva, F.L.; Derreumaux, P.; Pasquali, S.; Dias, L.G. Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the Major Ampullate Spidroin. Soft Matter, v. 12, pp. 5600-5612, 2016.
