Protein structure part II

single polypeptide chains that contain - residues are able to form distinct structural domains

domains are connected by relatively - stretches of the pp chain which act as -, allowing for domains to move about freely and independently of one another

domains often possess unique functions within the protein = -

having domains connected in a single protein permits much more - of its function

>100-200

unstructured, hinges

functional domain

efficient regulation

multidomain proteins arose when DNA sequences that encoded each domain became -, resulting in a new gene = -

joined, domain shuffling

modules are smaller, highly - structural/functional units that readily - into new proteins during evolution via -

conserved, integrate, gene or exon duplication and insertion

duplication of gene

subfunctionalization

neofunctionalization

degeneration/gene loss

cAMP binds reversibly to the - domain, which is present in a diverse range of proteins performing vastly different biological function

cyclic AMP binding

-(three things) binding modules are present in a wide range of proteins, not just a particular protein family

cAMP, ATP, GTP

domains perform - functions in enzymes

ex. glyceraldehyde 3 phosphate dehydrogenase

1st domain binds -

2nd domain binds the - substrate and catalyzes its -, using NAD+ as an -

complementary

NAD+

GAP, oxidation, e- acceptor

domains and modules may be evolutionary -

domains and protein structures are conserved more than -

domains arose and were maintained over evolutionary time because they were able to

• form -

• tolerate amino acid - (three things) without losing stability or function

• support essential biological - or form the basis for - new ones

sinks

AA sequence

• stable protein folding patterns

• deletions, substitutions and insertions

• functions, advantageous

tertiary structure forms from interactions between lengths of amino acids from - of the polypeptide chain

the forces involved in folding a protein into its final tertiary structure are essentially the same as those discussed for secondary structure but in contrast to secondary structure, tertiary structure depends almost entirely on the interactions between -

the polypeptide chain folds, coils, and twists into the native conformation, which represents a stable (-) state for that particular sequence of amino acids

different regions

R groups

low delta G

why do we observe only a few thousand common folding patterns (domains)?

evolution and natural selection, if it aint broke, don’t fix it

• gene duplication and mutations that created advantageous new functions from an already functional and stable protein were selected and maintaned over time

• protein families are evidence of conservation, members perform similar functions and have homologous amino acid sequences and 3D conformations

Levinthal Paradox

protein folding cannot be a random process

the more + a hydropathy value, the more likely a side chain will be found in the - of a protein and vice versa

interior

non-polar residues like Leu, Ile, Met, Val, and Phe occur mostly in the - of proteins

polar residues like Asn, Gln, Ser, Thr, Tyr are usually on the protein -

charged residues like Asp, Glu, Arg, His, Lys are typically found on the -

interior

surface

exterior

a folded protein is - (less/more) energetically favourable

this is due to the - effect

hydrophobic core regions contain non-polar side chains, once protein is folded they do not need to be surrounded by -, those water molecules can go and be -

more

hydrophobic

water cages, chaotic

delta G fold refers to

stability of the final folded state vs stability of the initial unfolded state

delta H fold refers to

difference between amount of energy to break all bonds in the unfolded state vs breaking all bonds in the folded state

T delta S fold

difference in stability associated with molecular motion or freedom

folding is primarily - driven and is a competition between the - of the folded polypeptide vs the - of the bulk water

stabilization forces that to occur during polypeptide folding to produce a favourable enthalpy that tilts energy equation towards - and a -

entropically, reduced entropy, increased entropy

folding, net negative delta G fold

overall, delta G fold is slightly negative, but there is not much -holding a folded polypeptide together

this explains why many proteins can be easily - by increased temperature or detergents that disrupt hydrophobic interactions

net free energy

denatured

Forces that stabilize native protein structure

1. hydrophobic effect

2. VDW

3. H-bonding

4. electrostatic interactions

5. chemical cross-links

hydrophobic effect is a major - to initiate protein folding

driver

because the interiors of native proteins are closely packed, VDW are a major - force of - polypeptides

- proteins do not benefit from VDW because distances between molecules are too -

stabilizing, folded

unfolded, great

H bonds make only a - contribution to overall protein stability during - process

unfolded proteins can also form H bonds with -

H bonds play a key role in determining and refining - though

if protein folded in a way that prevented H bonding, the stabilization energy would be - and the structure would be -

minor, folding

water

folded structure

lost, unstable

association of two ionic residues of opposite charge is called an - or -

75% of charged residues are involved in ion pairs and are located mostly on the protein -

ion pair, salt bridge

surface

disulfide - bonds form within and between polypeptide chains as they fold into their native conformations and/or subunits associate

cytoplasm is a reducing environment, so intracellular proteins do not contain -

covalent

disulfide bonds

cationic metal ions can coordinate several - around them to form discrete domains or motifs

charged a.a. residues

protein denaturation

1. heat

2. pH

3. detergents

4. chaotropic agents

detergents associate with - residues and interfere with - interactions

nonpolar, hydrophobic

chaotropic agents are - or - that increase solubility of - residues in water

ions, small organic molecules, nonpolar

in vivo, chaperones are involved in folding of many proteins to -

ensure correct folding, prevent aggregation, correct misfolded proteins

re-arrangement of non-native disulfide bonds via reduced PDI

de novo formation of disulfide bonds by oxidized PDI

there are 18 human diseases caused by deposition and accumulation of insoluble protein aggregates, collectively called -

amyloids

when enough amyloid accumulates in the affected tissue, normal cellular functions are -, leading to cell - and eventual -

disrupted, death, organ failure

amyloid structures have striking similarities

the likelihood of at least 2 mutant polypeptides aggregating to nucleate the fibril is very low, which presumably explains the long latent period for spontaneous amyloid diseases

gross assemblies of beta sheet structure, which is virtually indestructible

in Alzheimers gamma secretase cleaves APP into AB fragments that can aggregate into - and eventually large fibrils, referred to as -

oligomers, plaques

accumulation of Tau, a - protein, causes - within neuronal cells, which also lead to neuronal cell -

Tau appears to be - by accumulation of AB oligomers

microtubule stabilizing, tangles, death

dysregulated

prions are - versions of WT proteins

misfolded