Transcript Protein Secondary Structure II Lecture 2/24/2003 Principles of Protein Structure Using the Internet • Useful online resource: http://www.cryst.bbk.ac.uk/PPS2/ • Web-based protein course.

Protein Secondary Structure II
Lecture 2/24/2003
Principles of Protein Structure
Using 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 f/y 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
Helices
A repeating spiral, right handed (clockwise twist)
helix
pitch = 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, or
the 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 F and Y 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 f and y angles,
Typically f = -60 º and y = -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 chip
Two types
Parallel
Antiparallel
N
N
C
C
N
C
C
N
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 BetaSheets
beta (b) sheet
• Extended zig-zag
conformation
• Axial distance 3.5 Å
• 2 residues per repeat
• 7 Å pitch