L7: Protein structure and function

primary

• raw aa sequence

• written from N to C terminus

• determines how polypeptide folds

• a single mutation can have a huge impact

• determines the type of secondary structure that the backbone will become

secondary

• short regions of the peptide backbone fold into individual 3D structures that compose the tertiary structure

• folding of peptide backbone

tertiary

fully folded, 3D structure of the protein

quaternary

multiple individual proteins combine into a larger structure

multiple sequence alignment

• compares primary sequences of diff proteins

• mutant protein vs wild type

• also compares nucleotide sequences

what does * mean in MSA

indicates that all proteins have the same aa residue at that position

what would V4L mean in MSA

valine at 4th position changed to leucine

sub structures of tertiary

secondary structures

how do tertiary structures form

primary structures fold directly into it

Flt3 structure

• 4 alpha helices bundled together

• 1 beta sheet made of 2 polypeptide backbones

• many linker connecting alpha helices and beta sheets

• 3 disulfide bonds holds linkers together

what holds secondary structures together

H bonds

alpha helix

• single stranded

• right hand helix

• held together by H bonds

how many residue aa per turn in alpha helix

• 3.6

• each aa residue is a 100 degree turn

alpha helix bond pattern

carboxyl o2 of aa(n) forms H bond with N-H group of aa(n+4)

how many H bonds do aa residues in the middle of an alpha helix form

• 2

• one above one below

side chain groups in alpha helix

• point outwards from the center of the helix

• do not interact with other side chain groups in the same helix

• interact with side chains from other secondary structures in the protein

helical wheel

represents the placements of aa in alpha helix

what does the helical wheel show

• once folded into an alpha helix, aa with similar properties end up on the same side of the helix

• polar side together, np together

• polar will interact with water, np will interact with hydrophobic surfaces

amphipathic alpha helix

• have both hydrophobic and hydrophilic surfaces

• 2 helices wrap around each other to minimize aq exposure to hydrophobic surfaces

• form hydrophobic cores

are all alpha helices amphipathic

• no 

• some are completely polar

• some are completely non polar

• depends on the function of the helix

beta sheet

• multiple polypeptide backbones align side by side to form a paper like structure

• appears pleated

1 fold in beta sheet

• 0.7nm per fold

• 2 aa residue per fold

where are the alpha carbons in beta sheets

top edge and bottom edge of folds

where are the side chains in beta sheets

stick up and down in alternating patterns

how peptide backbones in beta sheets held together

• H bonds

• aa residues from adjacent backbones align

• carboxyl oxygen and NH groups form bonds

• bonds alternate

beta sheets irl

• thicker and bumpier

• the bumpy stuff are the side chains

2 ways to align backbones in beta sheets

• parallel

• antiparallel

formation of beta sheets

• regions of peptide backbone that form a beta sheet do not need to be close to each other in the primary sequence

• can be brought closer together in the tertiary structure of the protein

• ex. cysteines come closer to form disulfide bonds

examples of tertiary structures

• purely alpha helix

• mixed alpha helix and beta sheet

• purely beta sheet

protein domains

• local region of the peptide backbone that folds somewhat independently from other regions of the backbone

• each domain belongs to the same backbone

• each domain contains multiple secondary structures

• each domain has its own function

single domain protein

a protein only has 1 domain

how are protein domains connected

linker regions

Translation factor EF-Tu domains

• 3 domains

• domains combine their activities to give the protein its function

seperation of domains

domains can be seperated from each other while retaining its shape and function

domain shuffling

• domains from different proteins can be combined to form a new protein

• has been used to form new proteins from pre exisiting ones

• allows quick formation of new proteins when needed

subunits

individual proteins that make up a quaternary structure

hemoglobin structure

• composed of 2 alpha and 2 beta subunits

• each subunit holds 1 heme molecule

how to quaternary structures form

• each protein in quaternary structures are shaped to fit like locks and keys

• form non-covalent bonds 

• also held by disulfide bonds

homo- (qs)

if all the subunits are the same proteins

hetero- (qs)

if the unit contains atleast 2 diff proteins

monomer (qs)

1 protein by itself

dimer (qs)

2 proteins form a unit

protein count (qs)

• dimer

• trimer

• tetramer

• pentamer

• hexamer

DNA binding proteins structure

• use “fingers” to reach into major grooves of dsDNA to directly contact nitrogenous bases

• bind to their target as a dimer

basic region leucine zipper

• bZIP

• DNA binding protein family

• monomers are made of one, long alpha helix 

• always bind as a dimer

basic region

• contacts target DNA

• fits into a major groove

• some side chains contact bases and bind to specific DNA sequences

• positive side chains contact negatively charged sugar phosphate backbone of dsDNA to increase stability of protein-DNA interaction

leucine zipper structure

• dimerizes 2 monomers

• np side chains (usually leucines) occur at regular intervals

• these face each other to form a hydrophobic core and holds the dimer together by acting as a zipper

• can have polar-polar pairs in the middle

what are protein-protein and protein-DNA interactions based on

2 molecules having a surface that tightly fit onto each other

what determines the shape of protein-protein and protein-DNA interactions

• chemical structure of nucleotides

• aa in macromolecules

• how these structures fold

how do enzymes bind to reagents

• have binding pockets

• aa chains are held at very specific angles to generate these pockets

• peptide bond can contribute too