Determination and Description of Molecular Structures

Syllabus

1. Why study the structures of molecules. How to describe the geometry of molecules. Basic rules of stereochemistry, their consequences for molecular geometries.

2. Structure-function relationships in biology and chemistry. Formal description of three-dimensional (3D) objects.

3. Stereochemistry of building blocks of biomolecules, amino acids and nucleotides.

4. Structural motifs of secondary structure of proteins, motifs of tertiary structure, classification of protein folds.

5. Structural bioinformatics, relationship between amino acid sequence and protein structure. Methods of comparing sequences and structures.

6. Drug design based on knowledge of 3D structures of target proteins.

7. Structure of nucleic acids. I. Helical conformation.

8. Structure of nucleic acids. II. 3D structures of RNA and DNA molecules.

9. Basics of crystallography, the most important methods for determining 3-D structures of molecules. I. Experimental setup, crystal growth, solution of structures.

10. Basics of crystallography. II. Symmetry, refining. Structural genomics.

11. Comparison of crystallography with other experimental methods such as electron microscopy, nuclear magnetic resonance and other spectral methods.

12. Critical evaluation of computer simulations by quantum chemistry and methods of empirical potential (Monte Carlo, Molecular Dynamics) for the study of 3-D structures.

13. Structural database: search and comparison of molecular structures. Introduction to the use of the three most important databases: CAMBRIDGE STRUCTURAL DATABASE (CSD) for organic molecule structures, PROTEIN DATA BANK (PDB) as the primary archive of experimental biomolecule structures, and NUCLEIC ACID DATABASE (NDB) for nucleic acid-containing crystal structures.

14. Databases in the Internet world: How to find connections that give meaning to things.

Annotation

Structure and stereochemistry of molecules, geometrical description of molecules as 3D objects. Protein structures, domains, folds, bioinformatics.

Drug design based on known 3D protein structures. Structures of nucleic acids, double helices, 3D folds, ribosomal RNA.

Foundations of crystallography, comparison of structures determined by crystallography, NMR spectral techniques, and computer experiments. Structural databases as the main source of molecular 3D structures.