structure=
function
what are some functions of proteins
Transport, Regulation, Structure, Signaling, and Movement
What part of the amino acid determines how the protein is able to fold?
describe primary, secondary, tertiary, and quaternary structures
The R group determines folding.
Primary: principal determinant of overall protein conformation- sequence
Seocondary: more stable arrangements such as alpha and beta - local folding- held together by hydrogen bonds
tertiary: long range folding and more stable 3d structures
quaternary: proteins interact with themselves or other proteins forming the quaternary structure - multimeric
why is the primary sequence important?
the primary aa sequence is the ultimate determinant of final protein structure (and thus function)
which way do proteins go.
in the linear formation of peptide bonds, which is the nonvairant and which is the variable regions? Which is linear, which sticks out?
from amino terminus to carboxyl terminus
- the R groups stick out and these are the variable regions while the
- peptide backbone is nonvariant: consists of amide, alpha carbon, carbonyl C and the oxygen atoms
be able to draw the peptide bond formation btwn 2 amino acids
practice
the peptide bond contributes to protein structure and function through what 3 qualities?
1) peptide bonds are planar and do not allow rotation
2) therefore restrict 3D conformation of proteins
3) because they are planar, they make the R group stick out and they are able to contribute to folding with covalent and non covalent bonding
which carbons in amino acid chain rotate?
the alpha carbons connected to the R group, but the R group may sterically inhibit rotation
why are the R groups important in folding
they contribute to the folding as well as protein function.
- they can also form interactions with other biomolecules in cell membranes
describe an alpha helix? How often are the turns?
where are the bonds formed?
what disrupts formation?
where are the R groups
formed when polypeptide chain twists around on itself in a cylinder
- hydrogen bonds are formed between the BACKBONE- not the R groups as you would think.
- R groups stick out from the central plane
- hydrogen bond occurs between H attached to the Nitrogen and the oxygen of the carbonyl in the next turn.
- bc peptide bonds are planar, there are restrictions in frequency of turns. 4 aa per turn, but really 3.6 bc of interaction btwn a terminus and C terminus so a little shorter turns
- proline is a ring shape making it very rigid so it disrupts formation
describe the beta sheet
what are the 2 types?
comprised of adjacent strands or within the same protein
- parallel: A-C terminus is the same for each strand
- antiparallel: A-C terminus is opposite
- R groups stick out both above and below the plane of the sheet
- H bonds btwn backbone atoms of the strands
describe a beta turn
where are they typically found? (location)
what causes this?
- 4 aa that form a sharp bend and reverse the direction of the polypeptide background
- usually found on the surface of the protein
- caused by proline and glycine : proline has ring and glycine has no side chain therefore give sharp turn
characteristics of the __ determine tertiary structure by ___ interactions
-what are these interactions?
which aa tend to be on the outside/inside
R group determines folding by non covalent interactions (except sulfur is covalent and very strong for tertiary)
- hydrogen bonds, ionic interactions, van der waals forces, and hydrophobic interactions
- polar and charged aa tend to be on the outside and hydrophobic on the inside
what are protein motifs/domains?
how is this?
similar secondary and/or tertiary structures that can be formed from different aa primary sequence but still have similar structure
usually because the qualities of the aa are the same such as replacing a polar aa for another polar aa
describe the 3 protein motifs discussed in class. what is the turning important for?
1) coiled- coil motif:
two proteins with hydrophobic aa on the inside will coil around each other. this also allows proteins to dimerize
-can also have leucine zipper where you see a leucine every 2nd turn or every 7 aa and they are important for transcription factors to bind
- turning is important for stability
2) helix-loop-helix motif where loop region can sometimes bind metals ions like calcium
3) zinc-finger motif (also important for transcription factors)
- cluster of (2) HISTINE and (2) CYSTEINE that bind to zinc.
- sticks out like a finger
* also important for DNA binding. the finger regions make non covalent interactions with base pairs in the major grooves of the DNA helix
how do motifs and domains contribute to protein function?
1) enzymatic activities such as kinase domain for phosphorylation
2) binding to other proteins : like the SH3 domain of sarcoma (scr) protein
3) binding to other ligands like the SH2 domain of scr … SH2 domain is important for binding to phosphorylated tyrosine’s
4) zinc-finger motif contributes to DNA binding
Describe how proteins fold?
-what is the native state?
most proteins can fold without help (spontaneously and rapidly) and will go to most stable conformation or the lowest free energy.
- native conformation is lowest energy
- R groups are key determinant
if a protein needs help with folding, how does it get help?
accessory proteins will help with folding, usually in the rate limiting step for folding:
1) molecular chaperones: bind and stabilize unfolded or partly folded proteins to prevent them from being degraded or aggregated
2) chaperonins: form folding chambers to sequester unfolded proteins and allow them to fold
what protein catalyzes the formation of disulfide bonds
protein disulfide isomerase catalyzes formation of disulfide bonds
- disulfide bond of active site of PDI is readily transferred to a protein by 2 sequential thiol-disulfide reactions
- reduced PDI is generated by this reaction and is returned to an oxidized form by ER resident Ero1 protein (this one is oxidized by molecular oxygen)
why are some of the molecular chaperones known as heat shock proteins
increasing body temp can cause proteins to denature because the increase in thermal energy can disrupt the weak non covalent interactions required to hold proteins together
to avoid this, heat shock proteins are induced by high temperatures and function to protect other proteins from denaturation
how do molecular chaperones work?
- unfolded client protein has exposed hydrophobic residues that are recognized and bound by Hsp 70
- When ATP is bound, HSP 70 ASSUMES OPEN FROM THAT EXPOSES THE HYDROPHOBIC POCKET which can bind to the hydrophobic residue of target protein
- J domain of co=chaperone protein binds to Hsp70, triggering ATP hydrolysis that results in tight binding of Hsp70 to target client protein
- the J domain protein then idssoddciates and another protein NEF causes the release of ADP. Release of ADP causes chaperone to assume closed form and release the client protein
explain the best characterized chaperonin system
GroEl-GroES is the best characterized
- an individual substrate protein molecule binds GroEL via hydrophobic interactions.
- Hydrolysis of ATP changes the strutter of GroEL allowing for substrate encapsulation (enters chamber)
- Ring structure exposes hydrophilic inner will which gives protein a push in clumping of hydrophobic regions
- released by further ATP hydrolysis but if still unfolded then it will be degraded
Describe the structure (what is the motif) of collagen
-3 polypeptide chains wrapped in rope-like coil
-every 3rd reside is GLYCINE (small)
-glycines interact with each other
-proline frequently follows glycine and the 3rd reside can be any other aa
motif: gly-pro-x
(x usually lysine)
-proline and the other residues can be hydroxylated, allowing them to bundle and be more stable
-collagen made of 2 type 1 alpha polypetides and 1 type 2 alpha polypeptide
Describe the brittle bone disease
Called osteogenesis imperfect
- autosomal dominant form (90%)
- mutation of one of the alleles of type I collagen : alpha 1 or alpha 2
- mutation causes reduced stability of the triple helix
-normally
