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Structural concepts for molecular interactions (ligand binding (types of…
Structural concepts for molecular interactions
Structure determination methods
X-ray crystallography
Nuclear magnetic resonance
Electron microscopy
ligand binding
types of bonds
hydrogen bonds->specificity
van der Waals
pi interactions
electrostatic/ionic interactions
hydrophobic interactions
complementarity
conformational changes
conformation selectivity
reversability (for enzyme
purpose of structure studies
binding site's location, shape, conformation
visualize the interactions upon binding
reveal ligand and induced changes in prot conformation
drug development
Examples of interactions
prot-metal ions
prot-nucleic acids
bond types
salt bridge: NA phosphate x lys/arg/his.
Distinction ssNA and dsNA
hydrogen bonds: prot x sugar phosphate backbone, prot x NA bases
base stacking interactions: mainly hydrophobic and induced dipole effect. Maintain dsNA structure
prot characteristic
aromatic groups
diverse binding modes for RNA-binding prot
indirect readout for RNA rather than DNA
roles
NA packaging
regulation of genes
catalytic
NA recognition motif
helix-turn-helix
zinc finger
beta-sheet binding motif
prot-prot
