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

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 18^th and Thursday October 19^th)

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)

Fuente: fap.if.usp.br