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Module Catalogue

CH412-15 Advanced Biophysical Chemistry

Department
Chemistry
Level
Undergraduate Level 4
Module leader
Rebecca Notman
Credit value
15
Module duration
15 weeks
Assessment
30% coursework, 70% exam
Study location
University of Warwick main campus, Coventry

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Introductory description

N/A

Module web page

Module aims

The aim of the module is to describe computational and experimental methods used in physical chemistry and their application to study the structure and dynamics of biological molecules.

The module also aims to provide hands-on experience of performing quantitative analysis of experimental data and practical computational calculations.

The module is divided into three Parts, of which two may be chosen for 15 CATS. These are:

Part 1: Dynamics by NMR
This part module introduces NMR as a technique to study molecular motions and dynamic processes. State-of-the-art methods in solution and solid state will be surveyed. Their theoretical underpinnings and practical experimental implications will be discussed. Module will emphasise applications to study motions in biomolecules.

Part 2: Biomolecular simulation
This part module builds on aspects of theoretical and computational chemistry introduced in the earlier years of the MChem course. A number of methods in molecular simulation and their theoretical foundations will be presented. There will be an emphasis on approaches used to probe biological phenomena and calculations of properties pertinent to biological systems.

Part 3: Structural biology by NMR
This part module describes current use of solution state NMR to understand biomolecular structure and interactions, and builds on materials covered in Years 2 and 3. The focus of the materials covered here is the elucidation of biomolecular structure and ligand-binding properties for biomolecules across a range of sizes. Students will also obtain practical experience of NMR data interpretation in a workshop.

Outline syllabus

This is an indicative module outline only to give an indication of the sort of topics that may be covered. Actual sessions held may differ.

Part 1: Dynamics by NMR

  • Introduction to protein dynamics. Protein energy landscapes. Review of NMR interactions.
  • Motional averaging of anisotropic NMR interactions. Order parameters. Residual dipolar couplings. Fundamental differences between solution and solid-state NMR.
  • Chemical exchange. Approaches to study chemical exchange in fast, intermediate and slow exchange regime. Relaxation dispersion. Invisible states.
  • NMR relaxation and molecular motions. Basics of semi-classical relaxation theory. Correlation function. Spectral density. Model free formalism. Auto-relaxation, cross-relaxation and cross-correlated relaxation. Nuclear Overhauser Effect (NOE). Transverse Relaxation-Optimised Spectroscopy (TROSY).

Part 2: Biomolecular simulation

  • Review of molecular dynamics and Monte Carlo methods.
  • Force fields for biomolecular simulation.
  • Free energy calculations. Thermodynamic integration and perturbation; potentials of mean force.
  • Advanced sampling. Biased sampling methods, replica exchange molecular dynamics.
  • Coarse-graining.
  • Calculated properties. Energetics, structure and dynamics; relationship to experimentally determined quantities.

Part 3: Structural biology by NMR

  • Introduction to structural biology. Structure activity relationships; ligand binding and design; protein-protein interactions; physical chemistry of biomolecular systems. How does NMR contribute to our understanding of biomolecular structure – i.e. what kinds of things can we learn using NMR?
  • Small biomolecules. Homonuclear 2D NMR methods (i.e. TOCSY, NOESY and ROESY); linking data to polypeptide structure (assignment); case studies emphasizing the important biological roles of peptides.
  • Mid-sized proteins. Heteronuclear 2D and 3D NMR methods (e.g. HSQC and hybrid techniques); deuterium exchange; paramagnetic relaxation enhancement.
  • Large proteins. Triple resonance experiments/3D NMR methods; 3D NMR experiments; sensitivity issues; selective labelling and unlabelling methods; TROSY methods.
  • Very large proteins and complexes. Indirect NMR methods for investigating ligand binding. E.g. STD-NMR, DOSY.

Learning outcomes

By the end of the module, students should be able to:

  • Students will be able to describe and evaluate the roles that a selection of experimental and computational methods used in physical chemistry play in solving biological problems.
  • Students will be able to analyse data from experiments involving biological molecules and perform and analyse computational calculations.

Indicative reading list

Part 1: Dynamics by NMR

  • M.H. Levitt, Spin Dynamics.
  • G.S. Rule, Fundamentals of Protein NMR Spectroscopy.

Part 2: Biomolecular simulation

  • A.R. Leach, Molecular Modelling: principles and applications, Longman (1996).
  • M.A. Allen and D.J. Tildesley, Computer Simulation of Liquds, Oxford University Press (2017).
  • A selection of papers from the recent research literature, that may change from year to year, will also be provided.

Part 3: Structural biology by NMR

  • Sanders, J.K.M. and Hunter, B.K., Modern NMR Spectroscopy: A Guide for Chemists.
  • Zerbe, O. and Jurt, S., Applied NMR Spectroscopy for Chemists and Life ScientistsCavanagh, J., Fairbrother, W.J., Palmer, A.G., Rance, M., and Skelton, N.J., Protein NMR Spectroscopy: Principles and Practice.
  • Or any other book on Protein NMR Spectroscopy available from the library.

Subject specific skills

Problem solving
Written communication
Oral communication

Transferable skills

Problem solving
Written communication
Oral communication

Study time

Type Required
Lectures 12 sessions of 1 hour (8%)
Practical classes 5 sessions of 1 hour (3%)
Private study 133 hours (89%)
Total 150 hours

Private study description

N/A

Costs

No further costs have been identified for this module.

You do not need to pass all assessment components to pass the module.

Students can register for this module without taking any assessment.

Assessment group D2
Weighting Study time Eligible for self-certification
Assessment component
Workshop Reports 30% Yes (extension)

2 x workshop reports (15% each)
Reassessment component is the same
Assessment component
Online Examination 70% No

~Platforms - AEP

  • Answerbook Pink (12 page)
  • Periodic Tables
  • Students may use a calculator
Reassessment component is the same
Feedback on assessment

Workshop reports marked by academic staff, written feedback within 20 days. Cohort level exam feedback provided via Moodle.

Past exam papers for CH412

Pre-requisites

To take this module, you must have passed:

Courses

This module is Optional for:

  • Year 1 of TCHA-F1PB MSc in Chemistry with Scientific Writing
  • Year 1 of TCHA-F1PE Postgraduate Taught Scientific Research and Communication
  • UCHA-F110 Undergraduate Master of Chemistry (with Industrial Placement)
    • Year 4 of F110 MChem Chemistry (with Industrial Placement)
    • Year 4 of F112 MChem Chemistry with Medicinal Chemistry with Industrial Placement
  • Year 5 of UCHA-F107 Undergraduate Master of Chemistry (with Intercalated Year)
  • UCHA-F109 Undergraduate Master of Chemistry (with International Placement)
    • Year 4 of F109 MChem Chemistry (with International Placement)
    • Year 4 of F111 MChem Chemistry with Medicinal Chemistry (with International Placement)
  • UCHA-4M Undergraduate Master of Chemistry Variants
    • Year 4 of F105 Chemistry
    • Year 4 of F110 MChem Chemistry (with Industrial Placement)
    • Year 4 of F109 MChem Chemistry (with International Placement)
    • Year 4 of F126 MChem Chemistry with Med Chem (with Prof Exp)
    • Year 4 of F125 MChem Chemistry with Medicinal Chemistry
    • Year 4 of F106 MChem Chemistry with Professional Experience
  • Year 5 of UCHA-F127 Undergraduate Master of Chemistry with Medicinal Chemistry(with Intercalated Year)