Molecular Modelling and Computing in Drug Design (DONE) Flashcards
Why is the importance of molecular modelling increasing?
Better hardware and software
Large increase in structural data of proteins and enzymes from x-ray and NMR
Huge increase in sequence data available from projects such as the human genome project
What are the two types of modelling in drug design?
Where the structure of the molecular target (enzyme or protein) is known
Where the structure of the molecular target is not known, but the structure of a number of inhibitors is known
What are the methods for determination of structure of targets?
X-ray crystallography
NMR spectroscopy
Homology modelling
What are the four stages of x-ray crystallography?
Obtain protein
Crystallise protein
Diffraction by x-rays
Mathematical solution of x-ray diffraction pattern to give structure
Describe the resolution of x-ray data
Resolution is expressed in the uncertainty of the position atoms of the structure. It depends on the quality of the crystal and how well it diffracts
A smaller number gives a more accurate structure
>3.5A cannot determine position of main chain
2.5A to 3.5A large structures resolved but loops are uncertain and solvents not seen
2.0 to 2.5 A orientations of side chains are resolved and solvent molecules can be seen
<2.0A confirmations of side chains and solvent molecules are resolved
What are the limitations of x-ray crystal structures?
Requires milligram quantities of proteins
Gives the structure in the solid state whilst most proteins are in solution
Requires few months to solve structure
Generally less successful for receptors
How is NMR used to determine a structure?
Various NMR experiments can be used together to solve the 3D structure of proteins
Uses chemical shifts, various coupling constants and interatomic interactions to determine structure of the protein
Uses nuclear overhauser effects to calculate how close protons are in space
Solves structure in solution which is nearer to the physiological situation
What are the limitations of NMR spectroscopy?
Only applicable to relatively small proteins
Takes a long time to solve the structure as a large number of NMR experiments have to be interpreted
Requires milligrams of protein
What are the definitions of primary, secondary, tertiary and quarternary structure?
Primary- amino acids sequence
Secondary- local architecture of the polypeptide chain
Tertiary- overall topology of the folded polypeptide chain
Quarternary- arrangement of separate subunits into the functional protein
What is homology modelling?
A fast way to predict the structure of a protein based on its gene sequence
Used where the sequence of a protein of unknown structure shows good similarity to the sequence of a homologous protein of known structure
What are the requirements for homology modelling?
Need at least 25% sequence identity (50% for a good model)
Works best for similar classes of protein
Using a template not homologous is possible but the resulting model might not be that accurate
Homologous definition
Proteins that have evolved from a common ancestor
What is the methodology of homology modelling?
Align sequences of reference structure and that of unknown structure
Identification of structurally conserved regions
Construction of SCRs of the target protein using the coordinates from the template
Construction of structurally variable regions of the target protein and optimisation of the final model
What is CASP?
Critical Assessment of protein Structure Prediction
Aims to establish the state of the art in protein structure prediction
