Using protein structures to understand disease

what can +ve & -ve charged patches on proteins signify

+ve = electrostatically associated with the plasma membrane

-ve = electrostatically associated with phospholipid heads of membrane

what can we learn by mapping conserved residues

is this residue important for folding

• in hydrophobic core

• at oligomer interface

is this residue important for function

• interactions with small molecules

is it important for both

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how can nonsense & missense mutation affect proteins

nonsense - portions of the protein chain are synthesized, lacks structure that forms the oligomer interface

missense - amino-acid substitution may cause loss of favorable interactions

what is a steric clash

occurs when two atoms in a molecule that aren’t covalently bonded are positioned close to each other, causing their electron clouds to overlap and creating high, repulsive energy.

how can mutations disrupt functionally important oligomeric state

• polar residue in a cluster of non-polar residues

• a charge-altering mutation

how can mutations reduce enzymatic activity

• mutations that change the chemical nature residues that form direct interactions with substrate

• mutations that don’t alter the chemical nature residues that directly interact with the substrate, but change the way the protein chain folds in active site

what are prions

proteinaceous infectious particles, they are misfolded proteins that cause other proteins to misfold leading to death

• caused by fluid-filled holes where neurons have died.

what are some similarities between viruses & prions

• prions & viruses are infectious agents that are not cells

• rely on host cells to provide machinery for replication

describe the mechanism of prions

fibrils are composed of misfolded prions

• β-helix is likely a core structure of protease-resistant fibrils

• the fibrils are thought to cause disease

what is PrP^c

a normal glycosylated cell-surface protein, abundant on surface of nerve cells in the brain

• misfolded form = PrP^Sc

why is it difficult to detect prions

no intrinsic defense mechanism, as they are hosts own proteins

• It is thought that negative selection eliminates B & T cells that recognize PrP^Sc prions because they autoreact against PrP^C

what is the difference between cofactor & coenzyme

cofactor - a small molecule ligand that is tightly bound & remains bound after reaction is complete

coenzyme - a small molecule require for an enzymatic reaction, loosely bound & can dissociate from the enzyme

how can protein-ligand interactions be blocked

blocked through feedback inhibition, enzymes early in the pathway are regulated by the end-products

• competitive inhibitor

• allosteric inhibitor

what is the function of the positive modulator

a molecule that binds to optimize the shape of the conformation of the binding site for the catalytic subunit

what is the equilibrium dissociation constant (K_d)

for P + L ⇌ PL

• K_d = [P][L] / [PL]

low K_d = tight binding or high affinity

high K_d = loose binding or low affinity

what is a binding curve

a measure of the fraction of protein bound against free ligand concentration

• Fraction P bound = [L] / K_d + [L]

• K_d = concentration of free ligand when 50% of protein is bound