Molecular mechanisms of electrostatic origin responsible for protein complexation

• Grant number: 15/16116-3
• Support Opportunities: Regular Research Grants
• Start date: June 01, 2016
• End date: November 30, 2018
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Fernando Luis Barroso da Silva
• Grantee: Fernando Luis Barroso da Silva
• Host Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil

Abstract

Electrostatic interactions in and between biomolecules play an important role in the understanding and the control of the behaviour of proteins and mixtures of biopolymers, including several systems of considerable relevance both in the life sciences and in (bio)technology. In this research proposal, we intend to evaluate the effect of the charge regulation mechanism in the increase of electrostatic interactions responsible for the complexation of proteins with nucleic acids. For this purpose, it is necessary the development of new mesoscopic models and computational tools. The main systems to be studied will be the complex regulatory 7SK, which is a prototype of the regulating activity of non-coding RNAs in gene expression, and due its high electrical charge, it should enhance the effects of the charge regulation mechanism. Our basic working tool is the Statistical Mechanics (molecular simulations). The main outcome will be the free energy of interactions (and its derivatives). The modelling systems is based on continuous models previously developed by us, whose effective Hamiltonian will be solved by Monte Carlo simulations together with thermodynamic perturbation techniques and algorithms that will be developed to facilitate the sampling of the phase space. These calculations will be complemented by molecular dynamics simulations. We also intend to review here methodological aspects, to improve and develop new computational tools. (AU)

Scientific publications

(18)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BARROSO DA SILVA, FERNANDO LUIS; DERREUMAUX, PHILIPPE; PASQUALI, SAMUELA. Protein-RNA complexation driven by the charge regulation mechanism. Biochemical and Biophysical Research Communications, v. 498, n. 2, SI, p. 264-273, MAR 29 2018. (15/16116-3)

POVEDA-CUEVAS, SERGIO A.; BARROSO DA SILVA, FERNANDO LUIS; ETCHEBEST, CATHERINE. How the Strain Origin of Zika Virus NS1 Protein Impacts Its Dynamics and Implications to Their Differential Virulence. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 61, n. 3, p. 1516-1530, MAR 22 2021. (15/16116-3, 20/07158-2)

POVEDA-CUEVAS, SERGIO A.; ETCHEBEST, CATHERINE; BARROSO DA SILVA, FERNANDO L.. Identification of Electrostatic Epitopes in Flavivirus by Computer Simulations: The PROCEEDpKa Method. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 60, n. 2, p. 944-963, FEB 2020. (19/06139-7, 15/16116-3)

BARROSO DA SILVA, FERNANDO LUIS; STERPONE, FABIO; DERREUMAUX, PHILIPPE. OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 15, n. 6, p. 3875-3888, JUN 2019. (15/16116-3)

PASQUALI, S.; FREZZA, E.; BARROSO DA SILVA, F. L.. Coarse-grained dynamic RNA titration simulations. INTERFACE FOCUS, v. 9, n. 3, JUN 6 2019. (15/16116-3)

BARROSO DA SILVA, FERNANDO LUIS; DERREUMAUX, PHILIPPE; PASQUALI, SAMUELA. Fast coarse-grained model for RNA titration. Journal of Chemical Physics, v. 146, n. 3, JAN 21 2017. (15/16116-3)

POVEDA-CUEVAS, SERGIO A.; ETCHEBEST, CATHERINE; BARROSO DA SILVA, FERNANDO L.. Insights into the ZIKV NS1 Virology from Different Strains through a Fine Analysis of Physicochemical Properties. ACS OMEGA, v. 3, n. 11, p. 16212-16229, NOV 2018. (15/16116-3)

BARROSO DA SILVA, FERNANDO LUIS; MACKERNAN, DONAL. Benchmarking a Fast Proton Titration Scheme in Implicit Solvent for Biomolecular Simulations. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 13, n. 6, p. 2915-2929, JUN 2017. (15/16116-3)

CARVALHO, PATRICIA P. D.; ALVES, NELSON A.. Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, v. 40, n. 22, p. 10-pg., 2022-01-01. (15/16116-3)

BARROSO DA SILVA, FERNANDO LUIS; DERREUMAUX, PHILIPPE; PASQUALI, SAMUELA. Protein-RNA complexation driven by the charge regulation mechanism. Biochemical and Biophysical Research Communications, v. 498, n. 2, p. 10-pg., 2018-03-29. (15/16116-3)

MONTELLANO DURAN, NATALIA; SPELZINI, DARIO; WAYLLACE, NATAEL; BOERIS, VALERIA; BARROSO DA SILVA, FERNANDO L.. A combined experimental and molecular simulation study of factors influencing interaction of quinoa proteins-carrageenan. International Journal of Biological Macromolecules, v. 107, n. A, p. 949-956, FEB 2018. (15/16116-3)

FRIGORI, RAFAEL B.; BARROSO DA SILVA, FERNANDO L.; CARVALHO, PATRICIA P. D.; ALVES, NELSON A.. Occurrence of Biased Conformations as Precursors of Assembly States in Fibril Elongation of Amyloid-beta Fibril Variants: An In Silico Study. Journal of Physical Chemistry B, v. 124, n. 14, p. 2798-2805, APR 9 2020. (15/16116-3, 16/04176-4)

CARVALHO, PATRICIA P. D.; ALVES, NELSON A.. Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, AUG 2021. (15/16116-3)

MENDONCA, DEBORAH C.; MACEDO, JOCI N.; GUIMARAES, SAMUEL L.; BARROSO DA SILVA, FERNANDO L.; CASSAGO, ALEXANDRE; GARRATT, RICHARD C.; PORTUGAL, RODRIGO V.; ARAUJO, ANA P. U.. A revised order of subunits in mammalian septin complexes. CYTOSKELETON, v. 76, n. 9-10, p. 457-466, SEP 2019. (15/16116-3, 14/15546-1, 17/15340-2)

GIRON, CAROLINA CORREA; LAAKSONEN, AATTO; BARROSO DA SILVA, FERNANDO 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, v. 285, AUG 2020. (15/16116-3)

CUEVAS, SERGIO ALEJANDRO POVEDA; DA SILVA, FERNANDO L. BARROSO; ETCHEBEST, CATHERINE. NS1 from Two Zika Virus Strains Differently Interact with a Membrane: Insights to Understand Their Differential Virulence. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. N/A, p. 15-pg., 2023-02-13. (20/07158-2, 15/16116-3)

MONTELLANO DURAN, NATALIA; SPELZINI, DARIO; WAYLLACE, NATAEL; BOERIS, VALERIA; BARROSO DA SILVA, FERNANDO L.. A combined experimental and molecular simulation study of factors influencing interaction of quinoa proteins-carrageenan. International Journal of Biological Macromolecules, v. 107, p. 8-pg., 2018-02-01. (15/16116-3)

BARROSO DA SILVA, FERNANDO LUIS; CARLONI, PAOLO; CHEUNG, DAVID; COTTONE, GRAZIA; DONNINI, SERENA; FOEGEDING, E. ALLEN; GULZAR, MUHAMMAD; JACQUIER, JEAN CHRISTOPHE; LOBASKIN, VLADIMIR; MACKERNAN, DONAL; et al. Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations. ANNUAL REVIEW OF FOOD SCIENCE AND TECHNOLOGY, VOL 11, v. 11, p. 23-pg., 2020-01-01. (15/16116-3, 19/06139-7)