Protein secondary structures + some fibrous proteins

Secondary structures result from

alpha and beta helix: result from rotation within the polypeptide backbone

Three bonds that make up a polypeptide

Peptide bond, C-Carbonyl, C-NH

Why can't polypeptide rotate around peptide bonds? How many configs are there?

• peptide bond is very rigid and planar

• as partial double bond characteristics b/c of Nitrogen lone pair and =O double bond (has resonance)

• this gives it a dipole moment

• Trans or Cis configuration

Trans: R-groups are opposite sides of backbone

Cis: R-groups are same side of backbone -> steric clash

Which config is more common in polypeptides cis, or trans? Which amino acid is the one exception?

Trans (cis gives steric clash)

• exception is PROLINE. Trans is STILL favored, but the energy gap is more minimal bc there is steric clash in both configs really

Two angles around an alpha carbon are...

phi (circle with line): C-amide nitrogen

psi (trident): C-Carbonyl

Ramachandran plot

Shows favorable phi-psi angle combinations using alpha carbons from a bunch of residues in a bunch of proteins.

• in the favorable regions where a bunch of residues have these same psi/phi angle patterns, it gives rise to certain motifs like an alpha helix!

3 main "wells" for α-helices, ß-sheets, and left-handed α-helices.

Why are certain psi/phi angles favored vs. unfavored in ramachandran plot?

• more favorable -> form favorable H-bonding interactions around the backbone -> this is made more possible with structures like alpha helix.

• less favorable -> steric crowding of backbone atoms w/ other backbone or side chains

Most residues have similar traditional ramachandran plots. But what are the two exceptions to this?

Glycine - has more favorable regions since small R-group

Proline - has less favorable regions since big R-group

Between which atoms do right-handed alpha helix H-bonds occur?

H-bonding b/w n and n+4 residues -> enthalpy from H-bonding makes it favorable

• can have partial dipole from this H-bonding (positive N term, negative C-term)

Which amino acids ARE GOOD for helices?

Mostly all, but esp small hydrophobic resides like Ala, Leu

Which amino acids CANNOT form helices?

• Proline (steric clash AND no h-bonding donor!)

• glycine (too flexible) - can break helix shape

• bulky AA's

How many residues per turn in an alpha helix, and how many angstroms?

3.6 residues per turn,

5.4 A

How to draw helical world depiction for alpha helix given a amino acid seq.

360/3.6 = 100 degrees between the amino acids, use circle with 0,90,180,270 marked.

Start with first amino acid (N-terminus) at 0. If right handed go clockwise, adding next in the sequence 100 degrees apart each time.

3(10) helix

right handed, tighter turns

• 3 residues per turn, 1 hydrogen bond every 3 amino acids

Beta strands -> sheets

• beta strands are the individual stretched polypeptides

• beta sheets are stacked polypeptides

Beta sheet stabilizing factor

H-bonds between stacked peptide bonds

Arrow and base of beta strands

Arrow = C-term, Base = N-term

Antiparallel vs. parallel B-sheet

• Antiparallel has straighter and stronger H-bonds

• Parallel has weaker, bent H-bonds

Where are R-groups in a beta sheet

They alternate for above and below the backbone

Can B-sheets have emergent property

Yes, can have hydrophobic below backbone and hydrophilic on top for example

Continuous vs. noncontinuous B-sheet?

No other structures between the strands = continuous

Other structures bw strands = discontinuous

Beta turns

Form to reverse backbone direction to allow beta strands to stack/form sheets.

• 180 degree turn -> accomplished over 4 amino acids

• Turn is stabilized by H-bond from carbonyl oxygen (n) and amide proton three residues down (n+3)

Type I vs type II beta turn

• separated by psi/phi angles

• Type 1: favorable to have proline in residue 2

• Type II: favorable to have glycine in position 3

Tertiary vs quarternary structure

Tertiary: folded polypeptide

Quart: multiple polypeptides coming together

Globular vs fibrous proteins

• Globular: chemicals, signaling, transport, hormones

• Fibrous: daily objects and things like hair, nails, fiber

Keratin

Primary: a-b-c-d-e-f-g

• where a and d = NON-polar,

e/g are electrostatic

• 7 amino acid repeating motif

Secondary: alpha helix

Tertiary: Coiled-Coiled stucture - two right-hand alpha helices intertwined in left hand form

-> this causes preference for non-polar residues at positions a and d -> allows the two helices to bury hydrophobic residues inside when they intertwine

-> and e and g will also be opposite each other, favorable electorstatic interactions to hold sturcture together

Quarternary:

• Disulfide bonds bw bundles and adjacent coil-coils to form larger complexes

• Hair = less disulfide, horns = more disulfide

Collagen (skin, connective tissue, bones, teeth)

Primary: Gly-X-Y

• X often proline

Y often 4-hypoxyproline

Secondary:

LEFT handed alpha helix

tighter, 3 aa per turn (proline helps w/ sharp turns)

Tertiary:

• coil coil of THREE polypeptides, right handed intertwining

• Packed very tightly, little room for side chains

Quarternary:

• covalent bonding occurs in diff. ararngement for diff materials like tendons vs skin vs cornea

Silk

Primary: Gly-Ser-Gly-Ala-Gly-Ala

7 aa repeating motif

lots of Gly -> flexible