Development and release of SEQUENCE SLIDER: a multi-side chain evaluator applied to toxinology and phasing

• Grant number: 17/13485-3
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• Start date: September 01, 2017
• End date: August 31, 2018
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Marcos Roberto de Mattos Fontes
• Grantee: Rafael Junqueira Borges
• Supervisor: Isabel Uson
• Host Institution: Instituto de Biociências (IBB). Universidade Estadual Paulista (UNESP). Campus de Botucatu. Botucatu , SP, Brazil
• Institution abroad: Institut de Biologia Molecular de Barcelona (IBMB), Spain
• Associated to the scholarship: 16/24191-8 - Development of methods for crystallographic structure elucidation and structural studies of toxic mechanism of snake venom Phospholipases A2 homologue proteins, BP.PD

Abstract

Most ophidian accidents in Latin America are caused by Bothrops genus snakes. Myonecrosis, which is not efficiently neutralized by antivenom treatment, is one of the consequences of these accidents. Myotoxic phospholipases A2 (PLA2s) and PLA2-like proteins are usually abundant in bothropic venom and one of the main responsible for muscular necrosis. These proteins are myotoxic by breaking membrane integrity by a catalytic and non-catalytic mechanism, being the latter not yet fully known, wherein experiments from other groups as well as our studies are beginning to shed light upon. Usually, these toxins are purified directly from the natural source, extracted venom, and purity is a challenge due to the co-existence of various isoforms. Thus, crystals may contain heterogeneous species not fully characterized. We will address this question by implementing for general use an algorithm, called SEQUENCE SLIDER (SLIDER), to evaluate different sequence possibilities against crystallographic data. We will extend tests on our algorithm to the analysis of all the data of PLA2 and PLA2-like toxins already available in the protein databank and apply SLIDER to unknown crystallographic structures. Furthermore, sequence uncertainty scenario is immediately applicable to phasing program ARCIMBOLDO when dealing with datasets of lower resolution than its usual scope of 2.0 Å. We will develop SLIDER also to enhance partial models in ARCIMBOLDO, usually composed of polyalanine, by incorporation of side chains and extend this phasing method to lower resolutions. Thus, the objectives of this project are to generalize the new algorithms we have developed in the course of my Ph.D. to aid structure solution of challenging datasets in the ARCIMBOLDO and toxinology scope.

Scientific publications

(7)

(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)

RICHARDS, LOGAN S.; MILLAN, CLAUDIA; MIAO, JENNIFER; MARTYNOWYCZ, MICHAEL W.; SAWAYA, MICHAEL R.; GONEN, TAMIR; BORGES, RAFAEL J.; USON, ISABEL; RODRIGUEZ, JOSE A.. Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, n. 8, p. 703-712, AUG 1 2020. (16/24191-8, 17/13485-3)

MEDINA, ANA; TRIVINO, JOSEP; BORGES, RAFAEL J.; MILLAN, CLAUDIA; USON, ISABEL; SAMMITO, MASSIMO D.. ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, n. 3, p. 193-208, MAR 1 2020. (17/13485-3, 16/24191-8)

BORGES, RAFAEL JUNQUEIRA; MEINDL, KATHRIN; TRIVINO, JOSEP; SAMMITO, MASSIMO; MEDINA, ANA; MILLAN, CLAUDIA; ALCORLO, MARTIN; HERMOSO, JUAN A.; FONTES, MARCOS ROBERTO DE MATTOS; USON, ISABEL. SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, n. 3, p. 221-237, MAR 1 2020. (16/24191-8, 17/13485-3)

RICHARDS, LOGAN S.; MILLAN, CLAUDIA; MIAO, JENNIFER; MARTYNOWYCZ, MICHAEL W.; SAWAYA, MICHAEL R.; GONEN, TAMIR; BORGES, RAFAEL J.; USON, ISABEL; RODRIGUEZ, JOSE A.. Fragment-based determination of a proteinase K structure from MicroED data using ARCIMBOLDO_SHREDDER. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, p. 10-pg., 2020-08-01. (16/24191-8, 17/13485-3)

BORGES, RAFAEL JUNQUEIRA; MEINDL, KATHRIN; TRIVINO, JOSEP; SAMMITO, MASSIMO; MEDINA, ANA; MILLAN, CLAUDIA; ALCORLO, MARTIN; HERMOSO, JUAN A.; FONTES, MARCOS ROBERTO DE MATTOS; USON, ISABEL. SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, p. 17-pg., 2020-03-01. (16/24191-8, 17/13485-3)

MEDINA, ANA; TRIVINO, JOSEP; BORGES, RAFAEL J.; MILLAN, CLAUDIA; USON, ISABEL; SAMMITO, MASSIMO D.. ALEPH: a network-oriented approach for the generation of fragment-based libraries and for structure interpretation. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, p. 16-pg., 2020-03-01. (16/24191-8, 17/13485-3)

BOLDRINI-FRANCA, JOHARA; PINHEIRO-JUNIOR, ERNESTO LOPES; PEIGNEUR, STEVE; PUCCA, MANUELA BERTO; CERNI, FELIPE AUGUSTO; BORGES, RAFAEL JUNQUEIRA; COSTA, TASSIA RAFAELLA; IMAI CARONE, SANTE EMMANUEL; DE MATTOS FONTES, MARCOS ROBERTO; SAMPAIO, SUELY VILELA; et al. Beyond hemostasis: a snake venom serine protease with potassium channel blocking and potential antitumor activities. SCIENTIFIC REPORTS, v. 10, n. 1, MAR 11 2020. (15/18432-0, 15/00740-0, 18/14158-9, 16/24191-8, 15/16714-8, 17/13485-3, 11/23236-4, 17/14035-1, 16/04761-4, 14/16182-3, 15/17286-0)