Protein Strucuture

Psi Bonds

Nitrogen bonded alpha C

Phi bonds

Carbonyl C bonded to alpha C

Gly on Ramachandran Chart

R group is a hydrogen, so it allows for my conformations.

Geometry of R alpha helix

There is 3.6 residues per turn and 1.5A raise per residue. The amount it raises 3.6 × 1.5 = 5.4

all alpha fold: Four Helix bundle - Hydrophobic center

E/F Hand (helix loop Helix) - binds to Ca2+

All Beta fold - antiparallel barrel - usually membrane bound to serve as channels

Example of all beta barrel

Retinol Binding protein - inside of

All beta - propeller- active site in the center

Example of a Beta propeller

Nuriminidase is a ligand that cuts the virus off the host cell

A/B

Proteins that contain alternating patterns of beta and alpha folds (often parallel beta folds)

A/B horseshoe (leucine rich). Leucine center stabilizes the structure and bind to microbe origin antigens

ex. of a/b horseshoe

Toll Like Receptors (TLRs). has leucine rich regions to detect antigens

a/b TIM barrel. Common enzyme fold. Triosephosphate isomerase

A/B rossman fold - binds to nucleotide factors

ex. of a/b Rossman fold

dehydrogenase

a + b folds

Folds of proteins that contain both of alpha and beta folds but not alternating. mostly antiparallel folds

a + b SH2 domain used to recognize phosphotyrosine; also a signaling protein

Acetylation

Adds a coch3 to lysine to neutralize the positive charge

Phosporylation

Adds a phosphate group to tyr, thr, and ser. Activates proteins

Methylation

Adds methyl group to K and R to maintain + charge

Ubiquitation

Adds ubiquitin signal protein to a lysine

Glycosylation

Adds a sugar to S, T, N

Lipidation

Adds hydrologic group to C and G. Moves protein to membrane