Chapter 4 Protein Structure

Hydrophobic effect

Water makes best H-bonds with itself

Hydrophobic groups aggregate, hiding their entire surface from water, creates a structured solvation layer around the molecule

van der Waals, London dispersion

Attractive force due to induced dipoles in all atoms

Stability and interior of the protein

Hydrogen bonds

N-H and C=O of the peptide bond leads to local regular structures such as beta sheets and alpha helixes

Max in protein structure

Allow polar molecules to transverse interior of protein

Ionic interactions

Long-range strong interactions between permanently charged groups

Salt-bridges especially hydrophobic env strongly stabilize proteins

Disulfide bridge

Mostly in secreted proteins

Not found in reducing environment of cell

The Peptide Bond

Partial double bond

Resonance causes peptide bonds to be?

Less reactive than esters

Rigid and nearly planar

Trans due to steric hinderance

Rotation around peptide bond is?

Not allowed

Phi angle

around alpha carbon: amide nitrogen bond

Psi bond

angle around the alpha carbon: carbonyl carbon bond

Peptide bond is usually?

Trans but proline is cis

Bulky R groups tend to be?

On opposite sides

Secondary structure

Local spatial arrangement of the polypeptide backbone

The alpha helix

Stabilized by H-bonds btw nearby residues

¼ of amino acids in this

The beta sheet

Stabilized by H bonds btw adjacent segments

Could be far away

Random coil

Irregular arrangement of the polypeptide chain

The helical backbone is held together by?

H-bonds btw amide H of one amino acid and carbonyl O four amino acids away, maximizing bonds

Peptide bond has a strong dipole moment in the alpha helix

Negatively charged residues often occur near the positive end of the helix dipole

Not all polypeptide sequences adopt alpha helix structures, instead

Small hydrophobic residues such as Ala and Leu are strong helix formers

Pro acts as a helix breaker

Bc rotation around the N-C alpha bond is impossible

Gly acts as a helix breaker

Bc the tiny R group supports other conformation

Attractive or repulsive interactions between

Side chains 3-4 amino acids away will affect formation

A coiled coil

Side groups packed together only when alpha helices interact at 18 degrees from parallel.

If alpha helices remain parallel, stay in contact for only few residues

Beta sheets are?

Created from the planarity of the peptide bond and tetrahedral geometry of the alpha carbon

Backbone of beta sheet

Held together by H-bonds between the backbone amides in different strands

In a beta sheet?

Side chains protrude from the sheet alternating in up and down direction

In proteins, beta sheets

Tend to twist in a right-handed manner

Parallel Beta sheets

The H-bonded strands run in the same direction

Bent H-bonds (weaker)

Antiparallel Beta sheets

The H-bonded strands run in opposite directions

Linear H-bonds (stronger)

Beta turns

Occur whenever strands in beta sheets change the direction

Stabilized by an H bond from a carbonyl O to amide proton 3 residues down

Tertiary structure

Overall spatial arrnagement of atoms in a proton

Proteins have motifs (folds)

Two classes: fibrous and globular

Weak and strong intrxns btw amino acid side chains, far apart in primary

Strongest influences on protein folding?

Burial of hydrophobic (nonpolar) side chains into the core of the polypeptide”s structure

Delta G is more ___ for nonpolar packing

negative

Some alpha helices have ________ to improve packing of helical bundles

alternating polar and nonpolar amino acids

Hydrophobic interactions

Have no direction

The only way that a polypeptide can transverse the non-aqueous interior of a protein and satisfy H-bond necessity

Forming alpha helices and beta sheets that maximize H-bonds

Require distances and angles

Disulfide bridge is a

Stabilizing covalent bond found in tertiary structure

Not broken by thermal motion

2 SH groups from 2 cysteines are oxidized to form

Disulfide bridges can be between?

Cysteines on same polypeptides or across quaternary structures

more prevalent on extracellular proteins vs intracellular and cyclic peptides

Protein domain properties

Burial of hydrophobic R groups to exclude water

Alpha helices and beta sheets tend to be found in different layers, don’t interact well

Segments adjacent to each other in the amino acid sequence usually stack adjacently

Catalytic sites often where 2 domains meet

Domains are generally

Stable on their own, offer compartmentalization, folding advantage, regulation

Larger than motifs functional

Properties of fibrous proteins

Long and narrow

Structural

Insoluble in water

Repetitive amino acid sequence

Less sensitive to changes in heat, pH

Collagen, myosin, fibrin, actin, keratin, elastin

Properties of globular protein

Rounded

Functional

Soluble in water

Irregular amino acid sequence

More sensitive to changes in heat Ph

Catalase, hemoglobin, insulin, immynoglobulin

Alpha Keratin

Has two parallel strands wrapped to form L-handed coiled coil, hydrophobic packing

Only in mammals

Collagen

Part of the extracellular matrix, stronger than steel

Crosslinked with lys/hydroxylysine

L-handed secondary structure of 3 chains twisted in a superhelical R-handed triple helix

Fibroin

Main protein in silk

Antiparallel Beta sheet structure

Small side chains allow the close packing of sheets

Stabilized by H bonds within sheet and van der Waals between sheets

Myoglobin

Single chain of 153 aa

Stores O2 allows diffusion by contracting muscle

Sickle Cell disease

glutamate → valine in pos 6 of beta chain

Ruptures easily and carries only half of the normal hemoglobin

Thalassemia

Makes abnormal or less hemoglobin due to deletion

Used for solving protein structures

NMR

Circular dichroism

X-ray crystallography

Quaternary structure

Formed by the assembly of individual polypeptides (subunits) into larger FUNCTIONAL cluster

Multimer, oligomer

Allows for proper folding of large complexes that may not fold as a single chain

Quaternary Structure

Transcription/translation in quaternary structure

Use same gene same transcription factors to make subunits

Increase speed of translation

Movement/rotation

Quaternary structure makes possible

Enzyme activity and regulation in quaternary structure

Subunits can cooperate and regulate allosterically

Different enzyme kinetics

Substrate channeling

Proteostais

Maintenance of cellular protein activity is accomplished by the coordination of many different pathways

Denaturation

Loss of proteins structural integrity and activity

Ribonuclease Refolding Experiment

Chris Anfisen

Urea in b-mercaptoethanol fully denatures ribonuclease

When removed the protein refolds and correct disulfide bonds too

Sequence determines the native conformation

Boiling prevented tertiary structure reforming due to hydrophobic aggregation

Proteins fold to the?

Lowest-energy fold

Chaperones

Help proteins refold (prevent misfolding)

Some proteins contain segments that

lack definable structure (disordered regions)

Disordered regions

Can conform to many proteins, facilitating interxn with numerous partner proteins

Amyloidosis

Deposition of fibrils throughout the body