BIOC40070 Protein Structure and Analysis

Academic Year 2023/2024

This module, which is a core for the Stage 4 of the BSc degree in Biochemistry and assumes knowledge up to Stage 3 Biochemistry or equivalent, introduces the rationale for and concepts in protein structure, CD spectroscopy, mass spectroscopy and proteomics. The Protein structure part of the course will start by revisiting the importance of the amino acids and their structural properties commonly found in proteins and protein domains. For CD spectroscopic studies, theory of the CD and several examples of CD spectroscopic studies with their importance will be discussed. Standard one dimensional and two dimensional NMR spectroscopic techniques and their pulse sequences will be covered to study the recognition of the amino acids and their spin patterns for protein structural data interpretation and analysis. Advantages and limitations of these techniques for protein structure determination and advanced techniques for structure determination of large proteins that include 3D and 4D NMR measurements will also be covered. Thereafter focus of the lectures to explain protein structure calculations, protein-protein interactions and development of drugs using NMR spectroscopic techniques. Most of the applications will be based on the in-house development of drugs towards diabetes therapy by looking at the ligand receptor interactions and the development of antimicrobial agents using natural sources. Rest of the lectures will cover protein structure analysis based on mass spectroscopic studies and proteomics. Lecture series will start with the basic introduction to mass spectroscopy and developments in this field. Analytical approaches based on mass spectrometry and proteomics are increasingly used to solve structural problems. Principles of mass spectrometry will be reviewed, contrasting 'bottom up' methods (dominant in proteomics) with emerging methods for analyzing intact proteins and protein assemblies. Topics discussed will include de novo and database-dependent protein sequencing, mapping of protein modifications, characterization of protein complexes using tandem mass spectrometry, and structural analysis using cross-linking, deuterium exchange, ion mobility mass spectrometry. Last lectures will cover proteomics, “Life is a relationship between molecules” and the molecular architecture of a 456 component cellular machine. Throughout the lecture course, relevant biological examples will be described for clear understanding of the subject area.