8.29 3D Structure of Proteins

Four levels of protein structure include definition

Primary: Single AA

Secondary: Spatial arrangement of the chain of peptides due to bond angles

Tertiary: Overall 3D arrangement, held via weaker interactions

Quaternary: Arrangement of 2+ polypeptide chains in a 3D complex

Planarity of the peptide bond restricts omega to ____ (____ peptide bond conformation)

180 degrees; trans

Four main secondary structures

Helices, Sheets, Turns, and random coils

phi psi vs omega angles

N-C_a vs C_a-C vs C-N

Peptide chain can rotate around the ___ and __ bonds.

phi and psi

Two principle secondary structural elements in proteins

alpha helix, beta strand (form sheets)

Helix is stabilized by ____ bonds between ____ ___ atoms

hydrogen; main chain

alpha helixes; R groups face where? Space between each turn; left or right handed

Simplest arrangement, max H-bonds, R groups face outwards, 3.6 residues, 5.4 A (0.54 nm); right-handed only

Amount of AAs between H-bonds

n + 4, H of N to O of C

Pauling and Corey (a-keratin)

most simple and elegant arrangement of a peptide chain is a right-handed (N-C) spiral conformation known as the alpha helix

Amino acid that is a helix breaker

proline

3₁₀ residues/turn; 3₁₀ # of atoms

3; 10

alpha residues/turn; alpha # of atoms

3.6; 13

pi residues/turns; pi # of atoms

4.4; 16

Flexible AA in helixes

glycine

Beta conformation; B-strand vs B-sheet

Zigzag, R group extends out of sheet; single protein segment vs several strand stacked together

Antiparallel vs parallel B-sheet

antiparallel has better orientation, straight H-bonds, more common; parallel is diagonal H-bond orientation so weaker and less common

B turns involve ___ amino acid residues in a ____ degree turn connecting segments of antiparallel B-sheets

Type I vs Type II turns

4; 180

Type I has Pro as residue 2

Type II has Gly as residue 3

__ and __ residues hydrogen bond in a beta turn

first and fourth

gamma turns involve ___ amino acid residues in a ___ degree turn and ___ is always the second residue

3; 180; proline

Crossovers are ______ observed in B-turns

rarely

In parallel B-sheets, the strands run in the ___ direction

same

In antiparallel B-sheets, strands run in ____ directions

opposite

Alpha Helix frequency of occurrence of an amino acid residue in secondary structure

Kristin Has Marvelous LACE Q-tips

Beta sheet frequency of occurrence of an amino acid residue in secondary structure

IVY For The Win

Reverse turns frequency of occurrence of an amino acid residue in secondary structure

SPDING

Which AA does not have a possibility of being in a alpha helix, beta sheet, and reverse turn

arginine

Rakmachandran plot

Shows phi and psi angles of each residue in a protein, describes secondary structure

Circular dichroism (CD) spectroscopy

Measures absorption of left-handed vs right handed polarized light

Chromophore

peptide bond

Four types of protein

Fibrous protein: Arranged in long strands or sheets

Globular protein: Spherical or globular shape

Membrane protein: Embedded in hydrophobic lipid membranes

Intrinsically disordered proteins: Lack a stable tertiary structure

alpha keratin, typical orientation of helixes, supertwisted helical orientation, end of each protein is Hydrophobic/philic; Crosslink stabilized by ________ bonds

right-handed, left handed, hydrophobic (A,V,L,I, M, F), disulfide

Collagen; found in __________ tissue; Secondary and Tert/Quart structure

connective tissue; Secondary is left-handed chain (not helix) (Gly, Pro, 4-HyP), right-handed turn of 3 separate polypeptides

Collagen Fibrils: Cross-linked by ________ bonds; Involving ___, _____, or ___

Covalent; Lys, HyLys, or His

Vitamin _ is needed for hydroxylation of ___ and ___ in collagen

C; Pro, Lys

alpha/beta barrel

Series of beta-alpha-beta loops that forms a barrel

Intrinsically disordered proteins; lack _______ structure, often lacks __________ core, high density of _______ residues; helps facilitates a protein to interact with _______ binding partners; can assume different _______

definable; hydrophobic core; charged; multiple; structures

Topography diagram:

Represents secondary structure and relationship among segments

Protein family

similar in primary/tertiary structure

Superfamilies

2+ families that little seq similarity but same major structural motif and function