Module Details

The information contained in this module specification was correct at the time of publication but may be subject to change, either during the session because of unforeseen circumstances, or following review of the module at the end of the session. Queries about the module should be directed to the member of staff with responsibility for the module.
Title PROTEIN STRUCTURE AND DYNAMICS
Code CHEM452
Coordinator Dr M Volk
Chemistry
M.Volk@liverpool.ac.uk
Year CATS Level Semester CATS Value
Session 2018-19 Level 7 FHEQ Second Semester 7.5

Pre-requisites before taking this module (or general academic requirements):

Completion of year 2 of an MChem Chemistry programme or equivalent or, for PGT students, completion of BSc (Hons) Chemistry.  

Aims

The aim of this module is to discuss the application of basic physical chemistry concepts for describing protein structure and dynamics and to show how advanced physical chemistry methods are used for investigating these important aspects of proteins.


Learning Outcomes

Ability to discuss the importance of protein structure and dynamics for understanding biological processes.

Ability to describe the experimental methods that are used to study structure, folding and fast dynamics of proteins.

Ability to discuss the physical chemistry principles underlying these methods and apply the basic equations needed for the analysis of such data.

Ability to describe and discuss some of the theoretical methods that are used to predict protein structure and and model protein folding/dynamics.

Ability to analyse PDB-structure files and create meaningful graphical representations from these files.


Teaching and Learning Strategies

Lecture -

Seminar -

Literature Seminar

Tutorial -

Laboratory Work -

VMD-workshop


Syllabus

This lecture course deals with topics at the interface between physical chemistry and biology, which is of increasing importance as physical chemical methods and ideas are being applied to understanding biological processes. The course is split into three sections. Section A deals with protein structure determination, Section B discusses protein folding, and Section C briefly outlines the importance of fast protein dynamics.

A Protein Structure

  • Protein structure classification: Primary, secondary, tertiary, quaternary
  • Ramachandran plot
  • Secondary structural elements: alpha-helix, beta-sheets, turns, others
  • Importance of 3D structure for function
  • Methods for protein structure determination: diffraction methods, NMR, CD, FTIR/Raman
  • Protein data bank
  • Physical chemistry background: protein crystallisation, diffraction of X-rays electrons and neutrons, 2D-NMR, dipole interactions, electronic and vibrational spectroscopies
  • Methods of protein structure prediction: Molecular Dynamics calculations, Zimm-Bragg statistical mechanics model of helix formation

B Protein Folding

  • Forces relevant for protein folding; hydrophobic interaction and its thermodynamic consequence: cold- and heat denaturation
  • DSC (Differential Scanning Calorimetry) for determination of thermodynamic parameters of folding
  • Levinthal paradoxon
  • Basic models of protein folding
  • Observing the folding process - initialisation methods:
    rapid mixing, photochemical methods, temperature and pH jumps
  • Observing the folding process - detect ion:
    Fluorescence (Förster transfer, FRET, spectral shifts), UV/vis-absorbance, CD, FTIR/Raman, NMR, H/D-exchange
  • Folding kinetics analysis: Chevron plot, Phi-value analysis
C Protein Dynamics
  • Examples and timescales of protein dynamics - femtoseconds to minutes
  • Examples of methods for investigating fast protein dynamics: H/D-exchange and Molecular Dynamics

Recommended Texts

Reading lists are managed at readinglists.liverpool.ac.uk. Click here to access the reading lists for this module.
Explanation of Reading List:

Teaching Schedule

  Lectures Seminars Tutorials Lab Practicals Fieldwork Placement Other TOTAL
Study Hours 14

1

2

2

    19
Timetable (if known)   Literature Seminar
 
  VMD-workshop
 
     
Private Study 56
TOTAL HOURS 75

Assessment

EXAM Duration Timing
(Semester)
% of
final
mark
Resit/resubmission
opportunity
Penalty for late
submission
Notes
Unseen Written Exam  2 hours  Semester 2  90  No reassessment opportunity  Standard UoL penalty applies  Assessment 2 There is no reassessment opportunity, Notes (applying to all assessments) Assessed Tasks for VMD-workshop not marked anonymously, since submitted electronically via Vital. Marking is done to very detailed marking scheme. Written paper: August resit for PGT students if applicable. Integrated Master's students resit at the next normal opportunity.  
CONTINUOUS Duration Timing
(Semester)
% of
final
mark
Resit/resubmission
opportunity
Penalty for late
submission
Notes
Practical Assessment  5 hours  Semester 2  10  No reassessment opportunity  Standard UoL penalty applies  Assessment 1 There is no reassessment opportunity,