protein secondary structure ii lecture 2/24/2003
TRANSCRIPT
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