CHM 365 Chapter 4

What are the three main classes of proteins?

globular (aq solution)

fibrous- repeat 2º structure (collagen/keratin)

membrane proteins

What are the type of 2º structures?

a helices and b sheets

What is the most sterically limited and sterically free A.A?

Proline is limited- fixed phi angles

glycine has most freedom to rotate due to having no C(B)

A- Helix

right handed

h-bonds in the backbone

side groups project outside of the helix

core is tightyl packed with van Der Waals contacts between atoms

c=o is nth residue; n-h (n+4)th residue

What are the disruptors of the A-helix?

Proline’s fixed angle and Glycines entropic penalty

What is B-sheets composed of?

B strands with H bonds between adjacent chains

Parallel (needs linker) and Antiparallel

R groups alternate sides within the B strand

What B sheet is more stable?

Antiparallel

Reverse Turns

polypeptide segments with regular secondary structures are joined by reverse turns or B bends

involve 4 A.A and are usually found at the surface of a protein

Type II require Gly at residue 3 while residue 2 is Pro

PII Strand

loose left-handed helix that is stable and the predominant secondary strucutre in the fibrous proteins of the collagen family

Collagen

Triple helix of PII strands in a right-handed twist

H-bonds are interstrand networks

Mainly contains Gly which H-bonds with Pro, and Pro and Hyp provide rigidity

repeating sequence: Gly-X-Y (X=proline and Y=Hyp)

Prolyl hydroxylase

Enzyme that takes proline to hydroxyproline but requires abscorbic acid (Vitamin C)

Keratine

2 Right handed a helix in a L handed twist

Forms 7 pseudorepeat with a and d being NP

coiled coil

goes from dimer to protofilament to microfibril

Propensity

higher propensity for a or B will mean that that configuration will show up more frequently

How do you determine 3º Structure?

X-Ray Crystallography, NMR, Cryo-Electron Microscopy

X-Ray Crystallography

get jello-lke crystal that can form a diffraction pattern to give an e-density map

1 angstrom gives the highest resolution

Cardiotoxin II

antiparallel B sheets

What are the 3º Motiffs?

bab, b hairpin, aa, greek key

What are the B barrels and their respective motifs

B barrel- B hairpin

Jelly Roll barrel- Greek key

a/b barrelR- bab

Rossmann Fold

Has Parallel B sheets with BaBaB unit and is a common nucleotide-binding site in proteins

dinucleotide-binding fold

glyceraldehyde-3-phosphate dehydrogenase binds NAD+

Spatial Organization of Side Chains

HE drives proteins to fold

NP residues are on the interior, while Strongly Ionized Polar Residues (Arg, Lys, Asp, Glu) are on the surface

Uncharged polar residues (Ser, Thr, Asn, Gln) may appear on surface or inside

B turns are on the surface of backbone

exceptions- binding to nonpeptide groups (ligands) or catalytic sites

Cytochrome C

heme group that transfers electrons from compex 3 to 2 in the mitrochondria

Hydropathy

more positive value=more hydrophobic (interior) and vice versa

Ion pairs in Mb

Salt bridges

Electrostatic and usually on the surface

higher number of salt bridges helps to mitigate higher temperatures in thermophiles

Zinc Finger Motif

metal ions like Zn2+ can internally crosslink proteins and stablize structures (nucleic acid binding proteins )

Tetrahedrally coordinated by side chains of Cys, His, and occasionally Asp or Glu

Allysine Crosslinks in Collagen

enzyme lysyl oxidase converts Lys residues into allysine and crosslinks occur between Lys and allysinyl residues or two allysines

as age increases, the number of crosslinks increases (creakiness/stiffness)

What are the advantages of 4º Structure?

decreases translational errors and allows you to replace any damaged subunit

Protomers

indentical units within an oligomer

What are the interactions between subunits in 4º structure?

mainly HE but also intramolecular forces and sometimes disulfide

Hemoglobin

Heterotetramer- a2B2 structure

In RBC and transports O2 from lungs to capillaries

has higher affinity for oxygen when theres a higher partial pressure of O2

F1F0-ATP

Complex 5 (ATP Synthesis)

F0 portion forms water wheel that allows protons to flow through the membrane

f1 is water soluble and contains a trimer of aB protomers where ATP syn occurs

Myoglobin

not rigid and breathes which allows small molecules to diffuse in and out of the protein

has 8 alpha helices with a heme group cofactor in a hydrophobic pocket that’s stabilized by Val and Phe

Has a His ligand that prevents the oxidation of iron

Facilitates oxygen diffusion in muscles

Intrinsically disordered proteins

dont have a set structure

adopt specific structures upon binding to molecules like ions, proteins, or nucleic acids

dsup-binds to protein and protects it

tips- gel like matric that acts as protector from damage

Is native or denatured protein more stable?

native protein is only slightly more stable than denatured

process is reversible (1º is all that is needed for 3-D structure)

What contributes to the stability of Proteins?

mainly HE but also H bonds, salt bridges, and sometimes disulfide bonds

Chaotropic Agents

increase the solubility of NP substances in water (urea and guanidinum ion)

Disrupts the H-bonding cage and decreases the entropic penalty

What can be used to denature proteins?

chaotropic agents, heat, pH, detergents

What reduces disulfide bonds?

BME (mercaptos)

What is the Protein Folding Pathway?

H bonding gives 2º (a and B sheets)→ hydrophobin collapse gives molten globule → 3º (HE)→ 4º (multisubunits)

exergonic (spon) amd typically cotranslational

Leviathan’s Paradox

how long would a protein take to fold in every possible state (forever)

How does protein folding occur (Enthaply/entropy)

progresses from a high energy/entropy state to a low energy/entropy state

Chaperones

Protein Disulfide Isomerase (PDI) can help promate native protein formation

GroEL/ES Molecular Chaperone Structure

ATP is required and it isolates misfolded proteins, which can then refold

PrPc

cellular prions that has three a helices and a short B sheet

PrPsc

scrapie

lower a helix and higher B sheet content and it refolds and aggregates into amyloid fibers

R and T States of Hb

T-Hb/ R-HbO2

when O2 binds, it moves Iron 2 into heme plane, flattening the “pucker” that breaks ion pairs, snapping protein into R state

when pH is low, facilitaes R→ T state

higher pH=higher oxygen affinity

BPG drives adoption of T state (lowers Hb Oxygen affinity) and is expelled during the T→R state because the Hb cavity becomes too small. enhances oxygen relase in tissue

Sickle Cell Anemia

mutation where Val replaces Gly at 6th position of the B chain in Hb

Creates hydrophobic interactions between S tetramers, forming rigid fibers that deform RBC shape'

danger of sickling is greatest when erythrocytes pass through capillaries where deoxygenation occurs (T state that tends to polymerize)

Hydroxyurea

alpha 2 gamma 2 (higher affinity for oxygen than a2B2)

causes R state to be favored so there’s less polymerization (decreasing sickling)