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Resolving mechanistic details of peptide transport across membranes using crystallographic and non-crystallographic structural biology approaches

Grant number: 15/50366-7
Support type:Regular Research Grants
Duration: November 01, 2015 - October 31, 2021
Field of knowledge:Biological Sciences - Biophysics - Molecular Biophysics
Cooperation agreement: BBSRC, UKRI
Principal researcher:Antonio José da Costa Filho
Grantee:Antonio José da Costa Filho
Principal researcher abroad: Anthony Watts
Institution abroad: University of Oxford, England
Home Institution: Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
Associated scholarship(s):20/15032-9 - Expression and purification of GRASPs, BP.TT
20/15135-2 - Biophysical characterization of GRASPs, BP.TT

Abstract

Extending our recent new crystallographic structural models, ESR DEER and MD (Fowler et al., (2015) Structure, 23(2):290- 301 - front cover feature), we now aim to define the reaction coordinates for two peptide transporters from the bacteria Shewanella oniedensis (PepTSo) and from Streptococcus thermophilus (PepTSt). Both the conformational changes associated with discernible Intermediates in the transporter pathway(s), as well as the lipid dependence of the various stages are currently not described, and so will be addressed here using underpinning molecular biology approaches in Oxford and Sao Paulo. The response of the transporter to the proton motive force (pmf) in sealed systems, and the nature of the ligand binding environment, will also be examined, giving new Information about direct coupung of peptide transport to the energetics that drives function, with a view to defining electromechanical coupling within this important drug facilitator. To do this we will: - direct the design of spectroscopic studies of membrane-embedded peptide transporters using currently available, as well as new crystal structural and MD generated models; - use the spectroscopic and functional Information to determine conformational and dynamic details of membrane- embedded transporters, and generate novel detailed molecular models of reaction intermediates; With a final goal of describing the mechanism of action, lipid dependence and conformations of reaction intermediate states of peptide (and other homologues) transporters in molecular and kinetic detail. (AU)

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Scientific publications (15)
(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)
MANSOR BASSO, LUIS GUILHERME; ZERAIK, ANA ELIZA; FELIZATTI, ANA PAULA; COSTA-FILHO, ANTONIO JOSE. Membranotropic and biological activities of the membrane fusion peptides from SARS-CoV spike glycoprotein: The importance of the complete internal fusion peptide domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, v. 1863, n. 11, . (08/57910-0, 15/50366-7, 14/00206-0, 15/18390-5)
THIRUPATHI REDDY, S.; SANTOS MENDES, LUIS FELIPE; FONTANA, NATALIA APARECIDA; COSTA-FILHO, ANTONIO JOSE. Exploring structural aspects of the human Golgi matrix protein GRASP55 in solution. International Journal of Biological Macromolecules, v. 135, p. 481-489, . (16/23863-2, 17/12146-0, 17/24669-8, 15/16812-0, 15/50366-7, 12/20367-3)
BATISTA, MARIANA R. B.; WATTS, ANTHONY; COSTA-FILHO, ANTONIO JOSE. Exploring Conformational Transitions and Free-Energy Profiles of Proton-Coupled Oligopeptide Transporters. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 15, n. 11, p. 6433-6443, . (16/16328-3, 15/50366-7)
REDDY, S. THIRUPATHI; UVERSKY, VLADIMIR N.; COSTA-FILHO, ANTONIO JOSE. Nucleation-dependent amyloid fibrillation of human GRASP55 in aqueous solution. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, v. 49, n. 2, p. 133-143, . (12/20367-3, 17/12146-0, 15/50366-7)
MICHELETTO, MARIANA C.; MENDES, LUIS F. S.; BASSO, LUIS G. M.; FONSECA-MALDONADO, RAQUEL G.; COSTA-FILHO, ANTONIO J.. Lipid membranes and acyl-CoA esters promote opposing effects on acyl-CoA binding protein structure and stability. International Journal of Biological Macromolecules, v. 102, p. 284-293, . (15/50366-7, 14/00206-0, 12/13309-7, 15/18390-5)
FONTANA, N. A.; FONSECA-MALDONADO, R.; MENDES, L. F. S.; MELEIRO, L. P.; COSTA-FILHO, A. J.. The yeast GRASP Grh1 displays a high polypeptide backbone mobility along with an amyloidogenic behavior. SCIENTIFIC REPORTS, v. 8, . (15/18390-5, 16/09676-5, 15/50366-7, 12/13309-7, 12/20367-3, 16/23863-2)
MENDES, LUIS F. S.; BATISTA, MARIANA R. B.; KAVA, EMANUEL; BLEICHER, LUCAS; MICHELETTO, MARIANA C.; COSTA-FILHO, ANTONIO J.. Resurrecting Golgi proteins to grasp Golgi ribbon formation and self-association under stress. International Journal of Biological Macromolecules, v. 194, p. 264-275, . (16/16328-3, 15/16812-0, 15/50366-7, 12/20367-3, 18/13016-6, 17/24669-8)
MENDES, LUIS F. S.; FONTANA, NATALIA A.; REDDY, S. THIRUPATHI; UVERSKY, VLADIMIR N.; COSTA-FILHO, ANTONIO J.. The exquisite structural biophysics of the Golgi Reassembly and Stacking Proteins. International Journal of Biological Macromolecules, v. 164, p. 3632-3644, . (12/20367-3, 15/50366-7, 16/23863-2, 17/24669-8, 17/12146-0)
ALVAREZ, NATALIA; VINA, DIANA; LEITE, CELISNOLIA M.; MENDES, LUIS F. S.; BATISTA, ALZIR A.; ELLENA, JAVIER; COSTA-FILHO, ANTONIO J.; FACCHIN, GIANELLA. Synthesis and structural characterization of a series of ternary copper(II)-L-dipeptide-neocuproine complexes. Study of their cytotoxicity against cancer cells including MDA-MB-231, triple negative breast cancer cells. Journal of Inorganic Biochemistry, v. 203, . (15/50366-7, 17/24669-8)
REDDY, S. THIRUPATHI; UVERSKY, VLADIMIR N.; COSTA-FILHO, ANTONIO J.. Biophysical characterization of intrinsically disordered human Golgi matrix protein GRASP65. International Journal of Biological Macromolecules, v. 162, p. 1982-1993, . (15/50366-7, 17/12146-0, 15/16812-0, 12/20367-3)
MICHELETTO, MARIANA C.; GUIDELLI, EDER J.; COSTA-FILHO, ANTONIO J.. Interaction of Genetically Encoded Photosensitizers with Scintillating Nanoparticles for X-ray Activated Photodynamic Therapy. ACS APPLIED MATERIALS & INTERFACES, v. 13, n. 2, p. 2289-2302, . (12/20367-3, 15/50366-7, 18/13016-6)
MENDES, LUIS F. S.; BASSO, LUIS G. M.; KUMAGAI, PATRICIA S.; FONSECA-MALDONADO, RAQUEL; COSTA-FILHO, ANTONIO J.. Disorder-to-order transitions in the molten globule-like Golgi Reassembly and Stacking Protein. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, v. 1862, n. 4, p. 855-865, . (11/21767-2, 15/50366-7, 12/13309-7, 15/18390-5, 12/20367-3, 14/00206-0)
MENDES, LUIS F. S.; FONTANA, NATALIA A.; OLIVEIRA, CAROLINA G.; FREIRE, MARJORIE C. L. C.; LOPES, JOSE L. S.; MELO, FERNANDO A.; COSTA-FILHO, ANTONIO J.. The GRASP domain in golgi reassembly and stacking proteins: differences and similarities between lower and higher Eukaryotes. FEBS Journal, v. 286, n. 17, p. 3340-3358, . (16/23863-2, 15/50366-7, 12/20367-3, 17/24669-8, 09/53989-4)
MENDES, LUIS FELIPE S.; BATISTA, MARIANA R. B.; JUDGE, PETER J.; WATTS, ANTHONY; REDFIELD, CHRISTINA; COSTA-FILHO, ANTONIO J.. Conformational flexibility of GRASPs and their constituent PDZ subdomains reveals structural basis of their promiscuous interactome. FEBS Journal, v. 287, n. 15, . (12/20367-3, 15/50366-7, 16/09676-5, 17/24669-8)
KAVA, EMANUEL; MENDES, LUIS F. S.; BATISTA, MARIANA R. B.; COSTA-FILHO, ANTONIO J.. Myristoylation and its effects on the human Golgi Reassembly and Stacking Protein 55. Biophysical Chemistry, v. 279, . (15/50366-7, 16/16328-3, 17/24669-8, 12/20367-3)

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