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• Lysing E.coli cells with Emulsiflex
• Introduction to modern chromatography systems
• Running ion-exchange chromatography in AKTA
• His-tag purfication using gravity flow
• Gel filtration - determining protein concentration

• Crystallisation robotics: Operation of the PHOENIX (Art Robbins Instruments Inc.) nano-litre dispensing crystallisation platform and the FREEDOM EVO 100 (Tecan Group Ltd) liquid dispensing system.
• Manual set-up of the hanging-drop vapour diffusion crystallization trials.
• What is in my drop? Crystallisation trails analysis, precipitate classification and identification of promising crystallization conditions. Operation of crystallisation plates hotel/imager system (ROCK IMAGER-500 by Formulatrix Inc.).

• Cryocrystallographic crystal mounting techniques for the X-ray diffraction data collection experiments.
• Diffraction data collection and analysis using an in-house X-ray radiation source (ICARUS – the PROTEUM X8 X-ray diffraction system by Bruker-AXS)
• Looking at the electron density maps: Introduction to the protein crystal structure model building using crystallographic graphics software package Coot.

• Sample preparation for NMR
• How to setup a simple 1D NMR experiment for biomolecular NMR
• Basic information from a 1D experiment: what does it say about my sample?
• How we can study larger proteins: 2D methods
• Beyond 2D NMR: towards more comprehensive studies

• Viewing and finding signals in 2D and 3D NMR spectra
• Understanding the spectra from common NMR experiments
• Basic protein sequence assignment
• Deriving structural information from spectra

• Introduction and description of the experiments to be carried out throughout the day.
• Tour of the proteomics labs.
• Demonstration of an enzymatic protein and the precautions required to reduce keratin contamination  within target samples.
• Overview of the different types of mass spectrometers used for proteomic experiments.
• Real time LC-MS/MS experiment of a 48 protein tryptic digest with explanation of progress at each stage of the experiment.
• Analysis and explanation of intact protein mass spectrometry for the determination of accurate molecular weight measurements of proteins.
• Demonstration of non-covalent interaction mass spectrometry and how such interactions can be measured in the gas-phase.
• Mascot database searching of the output data from the 48 protein digest experiment.
• Analysis of the Mascot output data for the assessment of significant protein identifications and possible post-translational modifications.

• Introduction to multivariate statistics using PCA (principal component analysis) and supervised extensions of this approach.
• We will look at two datasets – one a study of diets across Europe and the other on metabolomics.

• How to run pH scouting experiments for immobilisation
• Immobilise a ligand onto a Chip via amine coupling
• Inject an analyte and run a kinetic experiment
• Analyse kinetic data

• Isothermal Titration Calorimetry (ITC) is used to characterise the interaction of macromolecules with each other and with small molecules
• ITC allows accurate measurement of binding constant, stoichiometry, enthalpy and entropy of binding:  a complete energetic picture of binding
• The practical will address the physical basis of the technique and the use of the small-volume ITC instrument
• The binding of a short peptide and a nucleotide to a protein involved in homologous recombination will be measured and the data analysed

• Finding template structures for modelling using FUGUE
• Making sequence-structure alignments
• Generating model protein structures using MODELLER
• Assessment of model accuracy and its relation to sequence similarity

This session will use the Pymol package and will demonstrate how to:

• download structure coordinates
• prepare quick high quality structure figures
• display electron density on an X-ray crystal structure
• display an ensemble of NMR solution structures
• measure distances and angles
• overlay two similar structures
• display the electrostatic surface of a protein
• illustrate a ligand binding pocket
• show hydrogen bonds
• colour a structure to show trends in different properties
• basic atom selection commands

• This practical is aimed at students with no previous experience of using Linux/MacOSX/Unix via the command line
• We will look at a few commonly used types of sequence analysis and students may investigate some points mentioned in Tim Stevens' lecture
• Students should gain the confidence to explore software options more fully, to attend more advanced courses and to think about how they might use bioinformatics and other computing in their project

• Extraction of quantitative information from a microarray image
• Normalisation and quality control
• Identification of differentially-expressed gene
• Clustering and other approaches to high-level analysis

• Theoretical aspects of RNA extraction, RNA quality, reverse transcription, primer design and real time PCR.
• Hands on real time PCR set up and analysis.