BIOCHEMISTRY 3 (Advanced Topics in Protein Science) - SHB4004

Assessment 1: In-Class Test

In-Class Test

Assessment 1: Exam

Exam

Assessment 2: Written Assignment

Written assignment based on molecular modelling

Written assignment

The module starts with the basic definitions of the transcriptome, proteome and metabolome. There is then an overview of protein structure and how this is related to function. Protein super secondary structure is discussed alongside various computational methods for secondary structure prediction (including alpha helix, beta strand, Coil-Coil, and disordered regions). This is followed by a description of domain classification schemes (SCOP &amp; CATH).
The concept of a priori protein structure prediction is introduced at a basic level. The computational challenge of finding the global energy minimum is described alongside attempts to simply the problem.
The importance of membrane proteins in biology is illustrated with examples of bacterial, eukaryotic and mitochondrial proteins. Included in this are details of conformational change, control of protein activity and protein-lipid interactions.
The use of X-ray crystallography, Cryo-EM, NMR and mass spectroscopy to solve chemical and macromolecular structures will be described, together with the use of this data in computational research.
Structural databases (The Protein Databank) and molecular modelling software will be used to explore the 3D structure of proteins and molecular interactions of macromolecules and small compounds (e.g. enzyme-inhibitor complexes).
Students will gain hands on experience of X-ray refinement using the widely used program COOT. Students will rebuild and optimise a model to maximise the fit to real experimental data.
Structure will be related to protein function in areas such as metabolic regulation in diabetes and cancer.

School of Applied Sciences

<a href="https://library.hud.ac.uk/readinglists/SHB4004">https://library.hud.ac.uk/readinglists/SHB4004</a>

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Biomedical & Life Sciences

SHB4004 - BIOCHEMISTRY 3 (Advanced Topics in Protein Science)

BIOCHEMISTRY 3 (Advanced Topics in Protein Science)

Describe various computational structure prediction methods, highlighting any limitations.

understand how computational methods may be used to predict protein structure and domains.

Run stereochemical checks (bond distance/angles) to validate a protein structure.

understand how protein structure determines function.

Understand how small molecules interact with proteins and how the study of enzyme structure is crucial for the development of pharmaceuticals.

Generate publication quality images of proteins from the Protein Databank, highlighting important features such as bound ligands.

Open and manipulate protein structure coordinate files in appropriate software.

Open X-ray data files in appropriate software and refine a protein structure against this data.

Run and interpret online secondary structure prediction algorithms.

Give examples of protein conformational change.

compare and contrast techniques for studying protein structure (both experimental and in silico).

Understand the importance of membrane proteins and the practical challenges involved with this special group of proteins.