Ramachandran Principle and Alpha Helices

What do peptide bonds link amino acids through

dehydration

what are the implications for secondary structure because of peptide bonds

• each peptide group in a polypeptide chain has a H-bond donor and acceptor, allowing for internal backbone-backbone H-bonding

• rotation cannot occur around the peptide bond, limiting secondary structure conformations (only three forms of secondary structure)

what prevents rotation in relation to the peptide bond

the partial double-bond of the peptide bond

Expand on why the partial double bond prevents rotation

• the resonance where the peptide bond has the double bond character is around 40%

• because of the partial double-bond character, there is no rotation around the C-N bond

• in a polypeptide backbone, the repeating N-Calpha-C units of the amino acid residues are a series of planar peptide groups

rotation of the polypeptide backbone can only occur across __ bonds

two

What are the two backbone bonds about which rotation is permitted in a polypeptide chain

Phi and Psi

which rotation around phi and psi is defined as clock wise when looking in either direction from the alpha carbon

positive 

what limits the possible angles of phi and psi

steric clash

what do the psi and phi angles dictate

secondary structure conformation

what do Ramachandran plots show

the combination of phi and psi that create different secondary structures

What does each region of a Ramachandran plot represent and what do they correspond to

Shaded areas: combinations found in proteins

white regions: angles not allowed due to steric clash

regions corresponding to specific secondary structures are labeled 

every ____ in the protein yields a ___ on the plot

amino acid

point

what further defines secondary structure

Hydrogen bonding in the polypeptide chain

What does each peptide group have and what do polypeptide chains have a great capacity for

Each peptide group has both a H-bond donor and acceptor

The polypeptide chain has great capacity to form hydrogen bond with itself

Protein folding is ____ by the ___ effect

nucleated

hydrophobic

Explain how water and polypeptides interact

• for an unfolding polypeptide in solution, the peptide groups and polar side chains are hydration (H-bonded to water)

• water is a poor solvent for the nonpolar side chains of a polypeptide chain

• in water, there is a strong tendency for the polypeptide chain to bury the nonpolar side chains via the hydrophobic effect

what does hydrogen bonding stabilize in the hydrophobic core

stabilizes the N-H and C=O peptide groups

Explain the stabilization of N-H and C=O groups by hydrogen bonding

• many polar C=O and N-H groups of peptide bonds connecting hydrophobic residues are dragged into protein core, breaking many H-bonds to water

• these broken H-bonds must be replaced by internal H-bonds, otherwise the energetic cost would be prohibitive

• most peptide N-H and C=O groups H-bond with other peptide groups or R-groups

Secondary structures preserve ___ bonding of peptide ___ and ___ groups while satisfying ___ and ___

• hydrogen

• C=O

• N-H

• Phi

• Psi

What creates the backbone for tertiary structures

secondary structures

what does the polypeptide backbone serve as when there are no sidechains

serves as a semi-flexible platform for the sidechains

When a tripeptide becomes a tertiary structure, what do the sidechains form and what must they do

form knobs that must fit in holes to achieve tight packing seen in proteins

what color represents beta carbons

dark grey

what do secondary structures provide during protein folding

provide scaffolds for knobs in holes packing during protein folding

what defines the alpha helix

peptide torsion angles

list the 4 basic features of the alpha helix

• a helix is a spiral with a constant radius

• right-handed helix with 3.6 amino acid residues per turn

• carbonyl groups point toward the C-terminus

• there are minimal gaps inside the helix, since efficient packing of the main-chain atoms takes up 99% of the core

what stabilizes the alpha helix

hydrogen bonds

How are the C=O and N-H groups positioned on an alpha helix

every C=O group is in position for hydrogen bonding with the N-H group four residues away

Each amino acid ___ in the helix is involved in ___ hydrogen bonds (except for the ___ at the ___)

• residue

• two

• residues

• ends

the hydrogen bonds in the alpha helix are nearly ___ to the___ axis

• parallel

• helix 

The hydrogen bond geometry in alpha helices is not perfect, as the peptide N-H is ___ directed precisely towards the ___ electrons of the ___atom

• NOT

• lone-pair

• oxygen

What provides H-bonds for the residues at the end of the alpha helix

helix capping

Explain what you would see in the N-terminal view

the four amide groups at this end of the helix lack H-bonding partners within the helix

explain what you would see in the C-terminal view

the four carbonyl groups at this end also lack H-bonding partners 

Why can some of the orphan peptide groups at the end of the alpha helix form hydrogen bonds to the solvent

since alpha helices often run through the protein molecule from one side to the other

if the ends of the alpha helices do not bond to a solvent, where do they bond

they will form hydrogen bonds with side chains at or near the ends of the helix

what color is beta carbons

magenta

what direction to the Beta carbons of the side chains pint

away from the axis of the alpha helix

how are alpha helices often stabilized

by non-covalent interactions between residues that are 4 apart

what is △△Gº

the difference in free energy change relative to alanine for the amino acid to form an alpha helix

amino acids vary in ___ to form alpha helices

propensity

list the three amino acids that are problematic to include in an alpha helix

Proline, Cysteine, Glycine

List the 5 things that influence alpha helix stability

• H-bonds every 4th amino acid

• Helix capping

• interaction between sidechains that are 4 residues away

  • attraction (different charges, other non-covalent interactions)

  • repulsion (like charges)

• Adjacent bulky sidechains cause instability 

• Gly, Pro can “break” a helix (but not always)

what is an amphipathic helix, where are they found

• an alpha helix with both hydrophobic and hydrophilic amino acid residues arranged in such a way as to create two faces on opposite sides of the helix, one face being hydrophobic and the other hydrophilic

• found near the surface of water-soluble globular proteins, while hydrophobic helices are on the inside 

where will nonpolar and polar side chains be found

on the side of the helix facing that interior, whereas the polar side chains will be on the other solvent side

in an amphipathic alpha helix, hydrophobic and hydrophilic residues are on ___ sides

opposite

does an alpha helix have a small or large dipole moment, why

large, bc the N-terminal end of the helix is more positive than the C-terminal end

How does the alpha helix dipole moment function in the KcsA channel

• allows for K+ efflux from inside the cell

• 4 subunits and 8 total transmembrane helices (TM1 and TM2)

• each subunit also contains a shorter alpha helix, called the “pore helix”

• each pore helix dipole points directly at the central aqueous cavity, creating a negative ‘well’ that attracts a cation into the channel