The programme of the event will include lecture-based and practical components.
The lectures will cover the following topics:
1. Structural biology tasks for which the use of synchrotron radiation is most effective
2. Fundamentals of X-ray crystallographic analysis of biopolymers
3. Application of small-angle X-ray scattering to structural biology problems
4. Sample preparation of biopolymers prior to crystallization
5. Application of soft X-ray microscopy to the study of biological objects
6. Tomography of biological objects using synchrotron radiation
7. Fundamentals of coherent diffractive imaging
8. Current status of the SKIF Shared Research Facilities Center and available experimental capabilities
The practical sessions will cover the following topics:
Practical Session 1
PS1. In silico optimization of genetic constructs for heterologous protein expression and crystallization
This session will focus on the in silico optimization of genetic constructs for heterologous protein expression and subsequent crystallization. Participants will become familiar with modern computational tools, including ProteinMPNN, ESMFold, and FoldX, for the rational design of mutations aimed at improving protein solubility and stability. During the practical work, participants will go through the full analysis pipeline: from identifying surface hydrophobic patches to generating, evaluating, and ranking mutant variants. All steps will be carried out in ready-to-use Google Colab notebooks, which will remain available to participants after the session.
Practical Session 2
PS2. Structure solution and refinement of a fluorescent sensor by X-ray crystallography
In this session, participants will become familiar with the main stages of protein crystal structure determination by X-ray crystallography. The practical work will include diffraction data processing, solving the phase problem by molecular replacement, and crystallographic model refinement. All stages will be demonstrated using the structure of a fluorescent sensor and the CCP4 software suite. Participants will gain hands-on experience with DIALS, AIMLESS, MOLREP, REFMAC5, and COOT.
Practical Session 3
PS3. Structural analysis of biomolecules in solution by BioSAXS
This session will focus on primary analysis and key data-processing steps in small-angle X-ray scattering for biological molecules in solution. Participants will work with the ATSAS software package, calculate basic structural parameters, and learn about the main features of the method, sample requirements, and measurement procedures. In the practical part, participants will build three-dimensional models of molecular shape from SAXS data and compare a full-atom structure obtained by molecular modeling with experimental SAXS data. The session will also include an introduction to Maestro Schrödinger and related tools, including VMD, HADDOCK, Desmond, and Gromacs, for protein structure preparation, protein-protein docking, molecular dynamics, and analysis of modeling results.
Practical Session 4
PS4. From projections to a 3D object: fundamentals of synchrotron X-ray tomography data processing
In this workshop, participants will become familiar with the basic pipeline for processing synchrotron X-ray tomography data in biological applications. Using a practical example, they will examine key stages of working with tomographic data: reading projections, image correction and normalization, rotation-center selection, and 3D volume reconstruction. Special attention will be given to how processing parameters affect reconstruction quality and the subsequent interpretation of biological structures. The workshop will help participants understand the logic of moving from raw images to a three-dimensional model of an object.
Practical Session 5
PS5. Molecular docking: assessing the affinity of small molecules to the binding site of a target protein
This practical session will focus on molecular docking of small molecules and assessment of their affinity to the binding site of a target protein. Participants will become familiar with the Maestro environment and discuss the principles of justified target protein selection. The session will cover docking protocol setup, calculations, and analysis of the obtained results. The practical work will allow participants to master a basic workflow for evaluating interactions between small molecules and a protein target.
Practical Session 6
PS6. Macromolecular docking: analysis of protein-protein complexes
This practical session will focus on macromolecular docking, assessment of binding energy parameters, and description of intermolecular interactions in protein-protein complexes. Participants will consider the selection of a target receptor protein and a ligand protein, identification of the putative binding site, and the macromolecular docking procedure. Special attention will be paid to analysis of the calculation results and interpretation of the nature of molecular contacts. The session will introduce participants to approaches used for modeling protein-protein interactions.
Practical Session 7
PS7. Processing primary X-ray crystallography data obtained at the Shanghai Synchrotron Radiation Facility
This session will focus on processing primary X-ray crystallography diffraction data obtained at the Shanghai Synchrotron Radiation Facility. Participants will learn about the specific features of synchrotron diffraction data stored in the special H5 archive format. During the practical work, processing of such data will be demonstrated using XDS. The session will help participants understand the specifics of preparing primary synchrotron data for further structural analysis.
Practical Session 8
PS8. Processing primary BioSAXS data obtained at the Shanghai Synchrotron Radiation Facility
This practical session will focus on processing primary BioSAXS data obtained at the Shanghai Synchrotron Radiation Facility. Participants will examine the processing of experimental data from the combined method of size-exclusion chromatography and small-angle X-ray scattering using ATSAS and RAW. During the session, they will analyze a chromatogram with SAXS data for a multicomponent mixture, separate monomeric components from oligomeric ones, and evaluate their structural characteristics independently. The practical session will introduce participants to the main stages of analyzing complex experimental BioSAXS data.
Practical Session 9
PS9. Segmentation of 3D structures and morphometric analysis of biological objects using HiP-CT data
In this workshop, participants will examine approaches to 3D structure segmentation and quantitative analysis of biological objects based on synchrotron X-ray tomography data, including HiP-CT. The practical part will focus on working with already reconstructed volumes: identifying structures of interest, building masks, 3D visualization, and extracting morphometric characteristics. Methods for analyzing the spatial organization of tissues will also be considered, including assessment of orientation, anisotropy, and the architecture of biological structures. The workshop is intended for participants who are already familiar with the basics of tomographic reconstruction and would like to move from visualization of volumetric data to quantitative biological analysis.
The programme of the School-Conference will also include a welcome dinner, coffee breaks, and an excursion to the SKIF Shared Research Facilities Center.