Protein Secondary Structure II Lecture 2/24/2003.
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Transcript of Protein Secondary Structure II Lecture 2/24/2003.
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Protein Secondary Structure II
Lecture 2/24/2003
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Principles of Protein StructureUsing the Internet
• Useful online resource:
http://www.cryst.bbk.ac.uk/PPS2/
• Web-based protein course
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Structural hierarchy in proteins
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The Polypeptide Chain
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Peptide Torsion Angles
Torsion angles determine flexibility of backbone structure
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Rammachandran plot for L amino acids
Indicates energetically favorable / backbone rotamers
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Steric hindrance limits backbone flexibility
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Side Chain Conformation
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Sidechain torsion rotamers
• named chi1, chi2, chi3, etc.
e.g. lysine
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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
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Regular Secondary Structure Pauling and Corey
Helix Sheet
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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.
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Examples of helices
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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.
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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!!
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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.
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alpha helix
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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
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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
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Top view along helix axis
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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
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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
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Helical bundle
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Helical propensity
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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
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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.
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Antiparallel beta sheet
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Antiparallel beta sheet side view
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Parallel beta sheet
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Parallel, Antiparallel and Mixed Beta-Sheets
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beta () sheet
• Extended zig-zag
conformation
• Axial distance 3.5 Å
• 2 residues per repeat
• 7 Å pitch