Workshops

Workshops are designed for individuals in the same field, discipline or interests to network and learn the most recent developments and techniques.    As opposed to a session, workshops hold potential for participants to receive some personal attention and the chance to share.  ACA workshops are conducted by individuals who have real experience and passion in the subject under discussion.  While workshops can have different formats, very often our workshops are participatory, i.e. participants are active, both in that they influence the direction of the workshop and also in that they have a chance to practice the techniques, skills, etc. that are under discussion.  There's a good deal of discussion in addition to participation, rather than just a teacher presenting material to be absorbed by attentive students.

The ACA is excited to offer the following workshops at the 2020 Annual Meeting.   Please note that the following schedules, instructor lists and topics are tentative and subject to change.

Sponsors:

Small angle X-ray and neutron scattering (SAXS/SANS, or SAS) has experienced dramatic growth over the past fifteen years within the structural biology community, emerging as an important and versatile analytical technique for the study of the structure and function of biological macromolecules in solution. This workshop is a concise introduction to biological small angle solution scattering, with an emphasis on practical application: knowing how to judge data quality, how to troubleshoot during data collection, the fundamentals of data analysis, and the expectations for a successful experiment and acceptable publication. The workshop includes both lectures and hands-on practical exercises from leading experts. Participants will also learn about aspects of home laboratory data collection, important complementary biophysical techniques for validating your SAXS data, and will be introduced to experiments at national user facilities (synchrotrons and research reactors). Workshop topics include, but are not limited to: 

• The basic principles of SAXS
• Critical sample preparation, data collection, and data evaluation procedures
• Standard model free analysis methods including obtaining the radius of gyration, molecular weight, and P(r) function
• Common model-based analysis including bead model reconstructions
• Hands-on tutorials with several common software packages for data analysis 

The aim of the workshop is to train researchers to use Phenix software for macromolecular structure determination using crystallography and cryo-EM. The attendees will be guided through key stages of structure solution: from obtaining initial atomic models given experimental data (diffraction intensities or 3D reconstruction) to final complete, refined and validated structures. Considering cryo-EM and crystallography, throughout the workshop the tutors will compare and contrast tools and methods available in Phenix to perform these tasks. The attendees will benefit from direct interaction with Phenix developers while learning how to use and get the most out of the software. Also, the attendees will be encouraged to actively participate in the workshop by asking questions about methods and tools being presented and following tutorial exercises. The workshop will have two components. The morning session will introduce the Phenix system and the core algorithms that it uses. The afternoon session will be a hands-on tutorial for researchers. The morning session will begin with a brief general overview of Phenix. Then the new features and algorithms in Phenix will be presented, focusing on cryo-EM and crystallography. These include solving phase problem using MR and SAD, map improvement and manipulations, automated model building and refinement, atomic model and experimental data validation and analysis. During the morning break those attendees that do not already have Phenix installed on their laptop computers will have an opportunity to do so. This process takes about 5 minutes with Linux, Mac OSX, and Windows operating systems. Tutorials will follow in the afternoon. Tutorial exercises will use the material supplied as part of Phenix distribution and will approximately match topics discussed in the morning. The day will conclude with the workshop survey and general discussion.

In this workshop, we will train both new and experienced researchers how to plan, conduct and analyze data for a hydroxyl radical footprinting experiment. The workshop will benefit the structural biology community by enabling the wider use of footprinting as a complementary method to crystallography and other structural methods. Researchers will come away from the workshop with the knowledge and ability to conduct footprinting experiments at both a synchrotron and in the home lab, and how to analyze resulting data to give meaningful information on the macromolecular structure of interest. We will start with a brief history of solvent accessibility methods, their current implementations and the proc/cons of each method. We will then focus three short overview talks on hydroxyl radical methods in particular, showcasing the Fenton reaction, the Fast Protection Oxidative Footprinting (FPOP), and Xray Footprinting with Mass Spectrometry (XFMS). Before the lunch break, we will have a session on practical aspects of sample preparation, including buffer requirements, protein digestion schemes, and sample handling pre- and post- irradiation. In the afternoon session, we will have a series of hands-on tutorials covering all aspects of data collection and analysis. The first tutorial will cover how to identify oxidation reactions for each residue in the mass spectrum. The second will cover the construction of the dose-response plot based on identified oxidations. The third will cover the mapping of the solvent accessibility changes onto known structures, and interpretation of the data.

To fully comprehend material properties and relationships it is necessary to thoroughly investigate the relationships of local structural deviations, which often expands a material’s behavior unexpectedly beyond the understanding of the overall, regular or Bragg structure. Diffuse scattering is the manifestation of such deviations stemming from structural, dynamic or magnetic local arrangements, which can readily be measured with modern neutron diffraction instrumentation capable of capturing and reconstructing full volumes of reciprocal space at modern neutron and X-ray scattering facilities such as the Neutron Spallation Source (SNS), the High Flux Isotope Reactor (HFIR) and the Advanced Photon Source (APS). Contrary to “conventional” or Bragg diffraction techniques, data processing and visualization, as well as data analysis rely on exploiting the information spanning volumes of reciprocal space. Expanding the pair distribution function (PDF) approach to derive a valid model of locally significant variations within the atomic webbing is a critical development to understand how structure influences physical and chemical material properties. For material analysis, improvements and material design, detailed knowledge of the structure details that play a critical role for function and stability are needed. This workshop aims to introduce and provide an overview over new developments in volumetric analysis of 3-dimensional reciprocal space diffraction, starting with data collection and setup, data processing techniques and visualization of reciprocal space volumetric data. It will showcase 3- dimensional PDF of diffuse scattering and give an outlook into computationally intensive structure modeling using high performance computing.

 

Organizers:

Wah Chiu

Gabe Lander

 

Single particle cryo-electron microscopy (cryo-EM) is rapidly becoming the method of choice for structure determination of membrane proteins, large assemblies, and multi-protein complexes. This powerful technique is now capable of resolving biological specimens to better than 2 Angstroms resolution and has been used to solve high-resolution structures of specimens as small as ~50 kilodaltons. Cryo-EM instrumentation is being installed in many universities, and is also available at large multiuser facilities both in the U.S. and worldwide. This workshop, which will be held on Friday, August 7 2020, will introduce scientists with crystallographic backgrounds to the fundamentals of the single particle cryo-EM workflow. The students will also have the opportunity to go through the steps involved in determining a high resolution structure in a hands-on tutorial using a sample dataset.

Lectures will focus on the steps involved in producing a cryo-EM map, from specimen preparation and data collection through to image processing, reconstruction, and modeling. This workshop will benefit those who want to use cryo-EM in the future, or who have recently transitioned into it. We will strive to include up-to-date discussions of cutting-edge methods and technology.