Protein Secondary Structure II

Lecture 2/24/2003

Principles of Protein StructureUsing the Internet

• Useful online resource:

http://www.cryst.bbk.ac.uk/PPS2/

• Web-based protein course

Structural hierarchy in proteins

The Polypeptide Chain

Peptide Torsion Angles

Torsion angles determine flexibility of backbone structure

Rammachandran plot for L amino acids

Indicates energetically favorable / backbone rotamers

Steric hindrance limits backbone flexibility

Side Chain Conformation

Sidechain torsion rotamers

• named chi1, chi2, chi3, etc.

e.g. lysine

chi1 angle is restricted

• Due to steric hindrance between the gamma side chain atom(s) and the main chain

• The different conformations referred to as gauche(+), trans and gauche(-)

• gauche(+) most common

Regular Secondary Structure Pauling and Corey

Helix Sheet

HelicesA repeating spiral, right handed (clockwise twist)

helixpitch = p

Number of repeating units per turn = n

d = p/n = Rise per repeating unit

Fingers of a right - hand.

Several types , 2.27 ribbon, 310 , helicies, orthe most common is the helix.

Examples of helices

The Nm nomenclature for helices

N = the number of repeating units per turn

M = the number of atoms that complete the cyclic system that is enclosed by the hydrogen bond.

The 2.27 Ribbon

•Atom (1) -O- hydrogen bonds to the 7th atom in the chain with an N = 2.2 (2.2 residues per turn)

3.010 helix

•Atom (1) -O- hydrogen bonds to the 10th residue in the chain with an N= 3.

•Pitch = 6.0 Å occasionally observed but torsion angles are slightly forbidden. Seen as a single turn at the end of an helix.

•Pi helix 4.416 4.4 residues per turn. Not seen!!

The helix

The most favorable and angles with little steric hindrance.

Forms repeated hydrogen bonds.

N = 3.6 residues per turn

P = 5.4 Å ( What is the d for an helix?)

The C=O of the nth residue points towards the N-H of the (N+4)th residue.

The N H O hydrogen bond is 2.8 Å and the atoms are 180o in plane. This is almost optimal with favorable Van der Waals interactions within the helix.

alpha helix

Properties of the helix

• 3.6 amino acids per turn

• Pitch of 5.4 Å

• O(i) to N(i+4) hydrogen bonding

• Helix dipole

• Negative and angles,

• Typically = -60 º and = -50 º

Distortions of alpha-helices

• The packing of buried helices against other secondary structure elements in the core of the protein.

• Proline residues induce distortions of around 20 degrees in the direction of the helix axis. (causes two H-bonds in the helix to be broken)

• Solvent. Exposed helices are often bent away from the solvent region. This is because the exposed C=O groups tend to point towards solvent to maximize their H-bonding capacity

Top view along helix axis

310 helix

• Three residues per turn

• O(i) to N(i+3) hydrogen bonding

• Less stable & favorable sidechain packing

• Short & often found at the end of helices

Proline helix

Left handed helix

3.0 residues per turn

pitch = 9.4 Å

No hydrogen bonding in the backbone but helix still forms.

Poly glycine also forms this type of helix

Collagen: high in Gly-Pro residues has this type of helical structure

Helical bundle

Helical propensity

Peptide helicity prediction

• AGADIR

http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html

Agadir predicts the helical behaviour of monomeric peptides

It only considers short range interactions

Beta sheets

•Hydrogen bonding between adjacent peptide chains.•Almost fully extended but have a buckle or a pleat.

Much like a Ruffles potato chipTwo types

Parallel Antiparallel

NN

C

C

N

NC

C

7.0 Å between pleats on the sheet

Widely found pleated sheets exhibit a right-handed twist, seen in many globular proteins.

Antiparallel beta sheet

Antiparallel beta sheet side view

Parallel beta sheet

Parallel, Antiparallel and Mixed Beta-Sheets

beta () sheet

• Extended zig-zag

conformation

• Axial distance 3.5 Å

• 2 residues per repeat

• 7 Å pitch