BIOC40070 Protein Structure and Analysis

Academic Year 2021/2022

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.

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Curricular information is subject to change

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 will cover (7) Introduction to mass spectrometry; Historical developments and overview of the emerging role of mass spectrometry in protein structure characterization (8) mass spectrometry of native proteins and of protein assemblies; Ion mobility mass spectrometry (9) Determination of protein primary sequence using de novo and database-dependent approaches, identifying and mapping protein modifications by tandem mass spectrometry (10) Studying macromolecular assemblies using mass spectrometry: Affinity purification, chemical cross-linking, deuterium exchange mass spectrometry (11) understanding of structural proteomics, chemical proteomics, and functional proteomics and (12) Integrating experimental and computational data to solve complex structural problems.

Student Effort Hours: 
Student Effort Type Hours


Autonomous Student Learning




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 before signing to this module.

Module Requisites and Incompatibles
Not applicable to this module.
Assessment Strategy  
Description Timing Open Book Exam Component Scale Must Pass Component % of Final Grade
Examination: Written essay examination, one compulsory question and one other question from two sections 2 hour End of Trimester Exam No Graded No


Carry forward of passed components
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.
Lecture Offering 1 Week(s) - 1 Fri 10:00 - 10:50
Lecture Offering 1 Week(s) - 2, 3, 4 Fri 10:00 - 10:50
Lecture Offering 1 Week(s) - 1, 2, 3, 4 Mon 09:00 - 09:50
Lecture Offering 1 Week(s) - 1, 2, 3, 4 Wed 09:00 - 09:50