protein folding Flashcards
how does X ray crystallography work? what are the pros and cons?
protein is purified, crystallized, and diffracted so data can be collected to calculate electron density and fit residues into density.
pros: no size limits, well-established
cons: difficult for membrane proteins, cannot see hydrogens (not strong enough electron density)
how does bimolecular NMR work? what are the pros and cons?
Protein is purified and dissolved then NMR data is collected and signals are assigned and structures calculated.
pros: no need to crystallize, can see hydrogens
cons: difficult for insoluble proteins, works best one small proteins
what are intrinsically disordered proteins?
contain protein segments that lack definable structure. , composed of amino acids whose higher concentration forces less-defined structure (Lys, Arg, Glu, and Pro). These disordered regions can conform to many different structures, facilitating interaction with numerous partners.
examples of intrinsically disordered proteins
ion scavengers (generic) and more specifically p27 which binds protein kinases and controls cell division
what is proteostasis?
the continual maintenance of the active set of cellular proteins required under a certain set of conditions. accomplished by coordination of many different pathways
what is denaturation? how to cause it?
loss of structural integrity with accompanying loss of activity. proteins can be denatured by heat/cold, pH extremes, organic solvents, and chaotropic agents (urea and guanidinium hydrochloride
can denatured proteins be refolded? ribonuclease experiment
the ribonuclease experiment concluded that refolding would spontaneously occur with the protein ribonuclease and therefore folding is determined by sequence alone. However, this was kind of a lucky break, not all proteins will spontaneously refold like ribonuclease does.
what are denaturing agents? how do they work?
Urea and guanidinium Cl denature proteins through disrupting favorable non-covalent interactions and increasing entropy through disordering water molecules around protein
what is the path of protein folding? 4 steps
local secondary structures fold first, small sequences in the DNA (~7 residues)
charge interactions and hydrophobic interactions decrease, must be spontaneous so enthalpy low and entropy high
this occurs over long ranges and begins to organize secondary structure elements into motifs
continues until complete domains form and protein is folded properly
motif vs domain?
motif: a similar 3D structure conserved across proteins that serves a similar function. think a helix or b sheets
domain: regions of a protein that serve a specific function and can act independently of the protein
what are chaperones?
proteins that prevent misfolding. the bind to proteins rich in exposed hydrophobic regions and protect from aggregation and aid in folding. they don’t “promote” correct folding, they prevent misfolding
what are chaperonins?
pretty much chaperones but that use ATP
what are amyloid fibrils?
B sheets of partially folded proteins interacts and recruits more proteins to form amyloid fibrils. this can be very problematic and cause large issues
what does prion protein PRP misfolding cause?
Bovine spongiform encephalitis (cattle)
cruetzfeldt-jakob disease (humans)
scrapie (sheep)
chronic wasting (deer)
what is the lock and key model?
proteins have specificity because only certain ligand bind. high specificity can be explained by complementarity of the binding site and the ligand. they can be complementary in size, shape, charge, or hydrophobic/hydrophilic character
