São Paulo School of Advanced Science on Biophysical Methods to Study Biomolecular Interactions


The São Paulo Advanced School of Science on Biophysical Methods to Study Biomolecular Interactions, sediada no Instituto de Fisica da USP, será um marco nas Escolas de formação em Biofísica Molecular de caráter multi e interdisciplinar, sendo um evento inédito no país.

O objetivo da Escola é dar aos alunos uma visão abrangente do estado da arte de técnicas biofísicas experimentais e teóricas no estudo de interações em sistemas biomoleculares.

A programação está dividida em aulas teóricas com práticas experimentais ministradas por especialistas renomados em técnicas de fluorescência, SAXS, EPR, dicroísmo circular, AFM, NMR, DLS, Crio-microscopia e bioinformática.

Além das aulas teóricas, algumas palestras serão proferidas por conferencistas internacionais buscando mostrar um sinergismo entre as técnicas biofísicas na investigação dos mecanismos de ação envolvidos em interações biomoleculares em diferentes sistemas. Os resultados devem gerar impactos científicos e tecnológicos, além da formação abrangente e consolidada de novos recursos humanos.

O programa ainda contempla espaços em que os estudantes expõem e discutem seus projetos de pesquisa: 6 sessões de Casos de Estudo de 1 hora cada e 2 sessões de painéis de 2 horas cada. Com isto, esperamos propiciar um fórum de discussões e novas colaborações durante a Escola.

Finalmente, existem visitas a laboratórios de pesquisa: i) lab de Cristalografia (IFUSP) e de NMR (IQUSP); ii) visita programada de um dia para as facilidades do CNPEM, Campinas (LNLS, LNBio, LNNano).

A Advanced School on Biophysical Methods prevê a presença de 100 estudantes, sendo que 50 serão selecionados de outros paises e25 de outros estados do Brasil. Existe possibilidade de financiamento FAPESP para até 75 estudantes (incluindo passagem aérea e hospedagem).

Ressalta-se que os alunos interessados devem se inscrever através do site (www.fap.if.usp.br/~espcabio), encaminhando um CV resumido, carta de apoio do orientador/supervisor (no caso de pos-doc) indicando os benefícios esperados com a participação na Escola para sua formação e desenvolvimento de seu trabalho.

  • Intituição

    Instituto de Física/IF/USP

  • Área de conhecimento

    Fisiologia

  • Pesquisador Responsável

    Rosangela Itri

  • Nº do Processo FAPESP

    2016/18796-4

  • Período

    16/10/2017 a 27/10/2017

  • Inscrições

    Encerradas

  • Site

    http://www.fap.if.usp.br/~espcabio/

  • Cidade

    São Paulo

  • Palavras-chave

  • Programa Ocultar

    October, 2017 – IF – USP

    Program: First Week

     

    Monday,

    Oct 16th

    Tuesday,

    Oct 17th

    Wednesday, Oct 18th

    Thrusday,

    Oct 19th

    Friday,

    Oct 20th

    7h30-8h15

    Registration

           

    8h15

    Opening

           

    8h30

    L1. Microscopy and Fluorescence Methodologies in Membrane Biophysics

    Manuel Prieto

    L5. Introduction to Cryo-Electron Microscopy, with key application examples

    Jose Maria Carazo

    L9 Biological and biomedical applications of atomic force microscopy

    Nuno Santos

    L11. Introduction to Biomolecular NMR

    Christina Redfield

    L12.Basic Computational approaches in biomolecular simulations: protein folding and protein assembly Yaakov Levy

    10h00

    Coffee Break

    Coffee Break

    Coffee Break

    Coffee Break

    Coffee Break

    10h30

    L2. Membrane SAXS: basic principles and applications

    Rosangela Itri

    L6. SAXS from proteins and protein-membrane interaction

    Leandro Barbosa

    L10. Proteins in membranes: lipid annular region, aggregation and topology by advanced fluorescence methodologies

    Manuel Prieto

    FAPESP time

    Poster Session

    12h00

    Lunch with teachers

    Lunch with teachers

    Lunch with teachers

    Lunch with teachers

    Lunch w/ teachers

    14h00

    L3. Electron Spin Resonance: Theory and Biophysical Applications

    Antonio Jose da Costa Filho

    L7. Computing cryo-EM maps: The image processing workflow to go from 2D to 3D

    Jose M. Carazo

    Hands-on

    I, II, III, IV and V

    Hands-on

    I, II, III, IV and V

    Hands-on

    II, III, IV, V

    15h30

    Coffee Break

    Coffee Break

         

    15h45

    L4. AFM-based force spectroscopy

    Nuno Santos

    L8. Introduction to Basic Principles of NMR

    Roberto Salinas

    Hands-on

    I, II, III, IV and V

    Hands-on

    I, II, III, IV and V

    Hands-on

    II, III, IV, V

    17h15 – 18h15 *

    Students Case Studies

    L1-L4

    Students Case Studies

    L5-L8

    Students Case Studies

    L9-L10

    Students Case Studies

    L11

    Students Case Studies

    L12

    Program: Second Week

     

    Monday,

    Oct 23rd

    Tuesday,

    Oct 24th

    Wednesday, Oct 25th

    Thrusday,

    Oct 26th

    Friday,

    Oct 27th

    8h15

             

    8h30

    L13. Molecular principles for optimizing protein-DNA interactions

    Yaakov Levy

    L15 Introduction to Molecular Dynamic Simulations of Membranes (Part I)

    Kaline Coutinho

    L17 CD spectroscopy: membrane proteins and drug interactions

    Bonnie Wallace

    Travel to Campinas (CNPEM)

    Talk1. Synergy between NMR, cryo-EM and large- scale MD simulations – an all atom model of a native HIV capside

    Angela M Gronenborn

    10h00

    Coffee Break

    Coffee Break

    Coffee Break

    Coffee Break

    Coffee Break

    10h30

    L14. Introduction to Assignment of Protein NMR Spectra

    Christina Redfield

    L16. CD spectroscopy: basic principles and applications to proteins (including peptides and IDPs)

    Robert Janes

    L18 The effect of post-translational modifications on protein biophysics

    Yaakov Levi

    Visit CNPEM - LNLS – LNBio-LNNano

    Talk2. FRET images applied to living cells

    Manuel Prieto

    12h00

    Lunch with teachers

    Lunch with teachers

    Lunch with teachers

    Lunch at CNPEM

    Lunch with teachers

    14h00

    Hands-on

    III, IV, V and VI

    Hands-on

    III, IV, V and VI

    L19 Introduction to Molecular Dynamic Simulations of Membranes (Part II)

    Kaline Coutinho

    Visit CNPEM - LNLS – LNBio-LNNano

    Talk3 . The effect of post-translational modifications on protein biophysics

    Yaakov Levi

    15h30

       

    Coffee Break

       

    15h45

    Hands-on

    III, IV, V and VI

    Hands-on

    III, IV, V and VI

    Poster Session

    Visit CNPEM - LNLS – LNBio-LNNano

    Talk4 . Exploiting Multiple Spectroscopies to quantify biological signaling in cells

    Anthony Watts

    17h15 – 18h15 *

    Students Case Studies

    L13-L14

    Students Case Studies

    L15-L16

    Poster Session

    Travel back to SP

    Closing Ceremony : Awards

    *Case Studies: some students pre-selected during the registration process (online registration) will present and discuss their results based on the lecturers (themes) given at each day.

    *Lunch with teachers: students will be divided in small groups and have lunch with the teachers to exchange experiences and ideas.

    Hands-On: the students will be split into 5 groups such that each group will attend a specific hands-on per afternoon (from I to V). Further, each student must choose, at least, 3 hands-on.

    Hands-on I: 50 students in the auditorium: Hands-on in cryo Electron Microscopy image processing – Jose Maria Caraso (Wednesday October 18th and Thursday October 19th)

    Electron Microscopy under cryogenic conditions (“cryo EM”) is changing the way we study the three dimensional structure of biological macromolecules, allowing to reach quasi-atomic resolution for flexible samples without the need to grow 3D crystals. The current “resolution revolution” has been made possible thanks to key technological developments in EM instrumentation and on new image processing breakthroughs. Focusing on the latter, at the Instruct Image Processing Center (I2PC) in Madrid (ALBA) we have developed a workflow oriented integrative image processing platform, that we call “Scipion”, that makes very intuitive all image processing steps. During this Demo we will remotely access the I2PC and run Scipion via Web, analyzing the most typical workflow for the analysis of biological macromolecules and some of its main steps, depending on the time allocated to this activity. Attendees will have the opportunity to log-in into a number of Demo accounts running Scipion from the attendee’s own computer through a web browser.

    Hands-on II: 10 students in the Crystallography lab (IFUSP) and class room: Hands-on Characterization of colloidal systems based on laser Scattering techniques: DLS and NTA – Dra Lígia Nunes de Morais Ribeiro (IB-Unicamp)

    Colloidal systems are heterogeneous and composed of a dispersed particulate phase in a non-miscible solution. They are widely applied in healthy, food and environmental fields, but they can be difficult to characterize due to their intrinsic dynamism. The light scattering approaches are the most employed techniques for evaluating the nanoparticles size distributions in colloids based on their Brownian motion. Dynamic light scattering (DLS) is the most used method for the measure of size distribution and Zeta potential by the intensity correlation function of the scattered light by the nanoparticles. Nanotracking analysis (NTA) is an innovator real-time technique that is changing the way to characterize nanoparticles in suspension. It comprises a laser source plus microscope (20x), charge-coupled device (CCD) camera and analytical software, providing individual measure of the dispersed nanoparticles. It also allows for the determination of the number of particles in suspension (concentration) by the “particle-by-particle” approach. Both techniques work in the 1-1000 nm range, at very diluted samples. In this hands-on, monodisperse and polydisperse samples will be measured, and the attendees will be trained to operate, understand and discuss the results obtained from both techniques, focusing in the suitable data quality parameters. Such information helps to understand the molecular interaction between their components: drug-carrier, RNA-exosome, and many others application, such as treatment monitoring and diagnosis.

    Hands-on III: 20 students in a class room: EPR data analysis – Antonio Jose da Costa Filho (FFCLRP-USP)

    EPR results from lipid model membranes containing spin-labeled lipids at different temperatures will be investigated. The molecular dynamics and ordering of the lipids will be analyzed as a function of the depth within the bilayer. The spectral analyses will be based on semi-empirical approaches as well as simulations using specific softwares.

    Hands-on IV: 10 students in a Crystallography lab (IFUSP) and class room: SAXS of proteins and membranes: measurement and analysis – Rosangela Itri and Leandro Barbosa (IFUSP)

    Samples of lipid model membranes in the presence of proteins will be measured at SAXS set-up (NanoStar) (IFUSP). The basic structural parameters as radius of gyration, shape and maximum dimension of the scattering objects will be retrieved from the SAXS curves as well as modelling using specific softwares will be done.

    Hands-on V: 10 students in the NMR facility (IQUSP) and class room: NMR: measurement and data analysis – Roberto Salinas (IQUSP) and Eneida de Paula (IB-Unicamp)

    Visit to the NMR facility; acquisition of 1D and 2D NMR spectra of proteins in water and small molecules; a short A short tutorial on the analysis of NMR titration to study protein-ligand interaction will be offered with the possibility for students to carry out data analysis using their own laptop computers. In this case students will be requested to install the specific NMR softwares in their laptops prior to the realization of the course. There will no time available for software installation.

    Hands-on VI: 20 students in a classroom: CD spectroscopy on Data Processing and Methods of Analysis – Bonnie Wallace (Birkbeck College), Robert W James (Un. London) and Jose Luiz Lopes (IFUSP)

    In this practice, students will remotely access the Protein CD Data Base (PCDDB) developed by profs. Bonnie Wallace and Robert W James and will perform a complete analysis of the secondary structure of an “unknown” folded protein and thermally unfolded.

    Poster Session: there will be two posters sections dedicated to the students presentation.

    Visit to CNPEM: the students will have the opportunity to know the facilities of the Brazilian National Lab: LNLS (in special the SAXS and IR beam lines), LNBIO (NMR facility) and LNNano (Cryo-TEM and negative stain microscopy)