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BIOC40070

Academic Year 2025/2026

Protein Structure and Analysis (BIOC40070)

Subject:
Biochemistry
College:
Science
School:
Biomolecular & Biomed Science
Level:
4 (Masters)
Credits:
5
Module Coordinator:
Assoc Professor Chandralal Hewage
Trimester:
Autumn
Mode of Delivery:
Blended
Internship Module:
No
How will I be graded?
Letter grades

Curricular information is subject to change.

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, proteomics, x-ray crystallography and cryo-electron microscopy.
Lecture 1-6:
Protein structure analysis based on NMR and CD spectroscopic methods
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.
Lecture 1: Protein structure and various conformations
Lecture 2: Importance of sample preparation and various techniques for data collection
Lecture 3: COSY, TOCSY for resonance identification
Lecture 4: NOESY, XD NMR and protein structure characterization
Lecture 5: Molecular modelling and NMR applications
Lecture 6: CD spectroscopy and applications
Lecture 7-10:
Protein structure analysis based on mass spectroscopic studies and proteomics.
7. Mass Spectrometry Basics (MS basics; Ionization methods; Instrument architecture; Measuring instrument performance; Tandem MS & protein sequencing; LCMS; Protein modifications)
8. Advanced Structural Biology Techniques (Intact protein MS; MS of protein complexes; Ion mobility MS; Chemical Proteomics; Crosslink-MS, Hydrogen Exchange MS; SAXS; Cryo-EM tomography; Molecular Modelling, Bayesian analysis; AI, AlphaFold; Ensemble structural models
9. Protein Interactions & Macromolecular Assemblies (Molecular basis for protein interactions; Protein complexes and protein pathways; Purification & techniques for studying protein interactions; Insights into human disease from protein complexes & networks)
10. Group Presentations: In the final class, teams of students will present examples from the literature of protein structure/function examples that they find interesting; alternatively they can explain a panel from a paper highlighting the structure of a major macromolecular assembly
Lecture 11-12:
Protein structure analysis based on X-ray crystallography and cryo-electron microscopy
The purpose of these lectures are to teach the students about the use of x-ray crystallography and cryo-electron microscopy in macromolecular structural biology. Students will learn about the history, key discoveries and milestones, theory and methods of x-ray crystallography and cryo-electron microscopy (cryo-EM). The lectures will also cover the use of structural biology to understand macromolecular mechanisms and functions and in drug discovery and design.  
Lecture11: X-ray crystallography in macromolecular structural biology. 
Lecture 12: Cryo-electron microscopy in macromolecular structural biology.

About this Module

Learning Outcomes:

On completion of the protein structure part of this module students should be able to: (1) Explain the fundamentals of CD spectroscopy (2) Explain the applications of CD spectroscopy with several examples (3) Explain the importance of amino acids for formation of protein structural features commonly found in proteins (4) Explain the important structural features of the polypeptide structure (5) Explain the one dimensional and two dimensional NMR techniques for polypeptide structure determination and discuss the advanced pulse sequences and their importance to protein structure determination (6) Discuss the strategies of protein structure determination by NMR spectroscopy and explain the biophysical studies, protein-protein interactions, limitations of NMR. Protein structure analysis (7-10): Students gain an understanding of the importance of molecular assemblies and protein networks in the cell during health and disease, and how protein structure contributes to these activities at functional level. Students will also gain experience at presenting detailed structural biology analyses to their peers. X-ray and cryo-EM (11-12): Students gain an understanding of the macromolecular mechanisms and functions and in drug discovery and design.  

Student Effort Hours:
Student Effort Type Hours
Lectures

12
Tutorial

2
Autonomous Student Learning

90
Total

104

Approaches to Teaching and Learning:
This modules uses analytical skills by understanding the methods and techniques used in physical biochemistry. Students are encouraged to read state-of-the-art research papers which will improve their problem solving skills.

Requirements, Exclusions and Recommendations
Learning Recommendations:

It is anricipated that students will have a good understanding basic NMR spectroscopy and other analytical techniques such as Mass, proteomics before signing to this module.


Module Requisites and Incompatibles
Pre-requisite:
BIOC30090 - Proteins and Enzymes

Incompatibles:
BIOC40270 - Structural Biochemistry


 

Assessment Strategy
Description Timing Component Scale Must Pass Component % of Final Grade In Module Component Repeat Offered
Exam (In-person): End trimester exam: Exam covers all aspects of teaching. End of trimester
Duration:
2 hr(s)
 Standard conversion grade scale 40% No
100
 No

Carry forward of passed components
No
 

Resit In Terminal Exam
Spring Yes - 2 Hour
Please see Student Jargon Buster for more information about remediation types and timing. 

Feedback Strategy/Strategies

• Feedback individually to students, post-assessment

How will my Feedback be Delivered?

Students are encouraged to read literature and published articles related to the course material which will be discussed in great detail. This will allow the students to be competent in structural biology techniques. This will further enhance the thinking and writing skills.

Name Role
Assoc Professor Gerard Cagney Lecturer / Co-Lecturer

Timetabling information is displayed only for guidance purposes, relates to the current Academic Year only and is subject to change.
Autumn Lecture Offering 1 Week(s) - 1, 2, 3, 4 Fri 10:00 - 10:50
Autumn Lecture Offering 1 Week(s) - 1 Mon 09:00 - 09:50
Autumn Lecture Offering 1 Week(s) - 2, 3, 4 Mon 09:00 - 09:50
Autumn Lecture Offering 1 Week(s) - 1, 2, 3, 4 Wed 09:00 - 09:50
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