receptor modelling

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  • Created by: Rscottqub
  • Created on: 05-01-20 18:16
why do we need 3D receptor models?
provide spatial arrangement. provide details of ligand interactions. help understand ligand binding mech. help ligand design. help design selective drugs
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Experimental sources of protein 3D structures (3))
1. Xray crystallography 2. Cryo-electron microscopy 3. NMR- 3 methods to obtain 3D models of proteins
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X ray crystallography is main method to acheive
high resolution
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what can it do
can determine arrangment of atoms within protein crystal
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process of Xray crystal.
Xray beam strikes crystal and diffracted in diff directions- angles and intensities --> 3D picture of e. density inside crystal - e.density can be used to figure out position of atoms and det structure of protein
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Cryo - electron microscopy (cryo-EM)
alternative to xray - initailly thought to be useless as e. microscopes damage tissue but it has been developed
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Now it is used for
structures which cannot be imaged using other techniques - for examples large structures
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Diff between Xray and cryo EM
Xray- xray scattered and diffraction results in structural determination . Cryo - scattered e. pass thru lens which magnifies image to then look at the structure.
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which is easier ?
it is very hard to obtain crystal structures so frozen solution is easier
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NMR
mag fields and radiation applied --> spectra - structure obtained from NMR distances and add. info such as primary seq, bond lengths,bond angles , etc . protein must be dissolved in water
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computational protein 3D structure source
homology modelling
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Homology modelling
computer modelling method- it is sometimes not possible to obtain structure experimentally
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how does it work
makes an atomic model of target protein from AA sew- and an experimental 3D structure
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homology modelling steps (4)
1. Template search & seq allignment 2. 3D model building 3. Energy optimization 4. model validation
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1. template search & seq allignment
primary seq compared between target and template protein
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2. 3D structure building
backbone constructed based on similar regions on template . regions which are not similar are constructed by other proteins
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the 3rd step is called
energy optimization
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4. Model validation
tested experimentally
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Homology is essential fro determination of membrane proteins becuase
they are very difficult to work with
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why are they difficult to work with
Purity - need to be extracted from the membrane . Insoluble in water - long process to obtain Crystal form . outside membrane loses structure
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another computer method is
Ab initio modelling
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Ab initio modelling
constructs atomic resolution model from 1st principles . works for small peptides , cannot be used for large proteins,
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GPCRs
G-protein coupled receptors
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what are GPCRs
membrane proteins which can receive signals
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what % of drugs act on GPCRs
40%
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ubiquitous distribution
they are distrubuted everywhere
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prove to be druggable
binds with high affinity to drugs
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GPCR crystalography
efforts have been unsucessful for last 20 years but now
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solution
replace with soluble protein - helps crystal formation. Restrict helix movements
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what year was a nobel prize won for work in GPCRs
2012
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GPCR technology allows us to
design agonists and antagonists
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once we have a 3D model receptor we can ...
study ligand protein interactions
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we can study these interactions by (2)
1. direct modelling 2. indirect modelling
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direct modelling
study interactions using actual crystal structures in complex with l ligands
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Indirect
use homology model in which the ligand is docked
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molecular docking
computer technique, places ligand into binding site and finds optimal orientation . BUT anything done on compute is theoretical and therefore we need to validate
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2 methods to validate ligand protein complexes ID by docking
1. site directed mutagenisis 2. Ligand structure activity relationships (SARs)
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site directed mutagenesis
AA residues thought to be important for binding are mutated . ligand potency tests against mutated receptor . If potency is lost - the AA residue was important - if no change then not important in and docking pose not right
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Ligand SARs
SARs are derived from ligand analogues with measured activity. They show which parts of the ligand are important for binding and which are not
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modelling of interactions between ligand and receptor help us to understand
potency at a specific receptor . reasons for ligand selectivity . ligand efficacy . design novel drugs
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Card 2

Front

Experimental sources of protein 3D structures (3))

Back

1. Xray crystallography 2. Cryo-electron microscopy 3. NMR- 3 methods to obtain 3D models of proteins

Card 3

Front

X ray crystallography is main method to acheive

Back

Preview of the front of card 3

Card 4

Front

what can it do

Back

Preview of the front of card 4

Card 5

Front

process of Xray crystal.

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