Protein Secondary Structure II

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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 f/y 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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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.
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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 a helix.
• Pi helix 4.416 4.4 residues per turn. Not
  seen!!

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The a 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 a helix?) The CO of the nth
residue points towards the N-H of the (N4)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 a helix

• 3.6 amino acids per turn
• Pitch of 5.4 Å
• O(i) to N(i4) hydrogen bonding
• Helix dipole
• Negative f and y angles,
• Typically f -60 º and y -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
  CO 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(i3) hydrogen bonding
• Less stable favorable sidechain packing
• Short often found at the end of a 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/aga
  dir/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 chip
• Two types
• Parallel Antiparallel

N
C
N
C
N
C
N
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 (b) sheet

• Extended zig-zag
• conformation
• Axial distance 3.5 Å
• 2 residues per repeat
• 7 Å pitch