©cmbi 2001 the amino acids in their natural habitat
TRANSCRIPT
©CMBI 2001
The amino acids in their natural habitat
©CMBI 2001
The amino acids in their natural habitat
Topics:
HydrophobicityHydrogen bonds steer secondary structure
Hydrogen bonds in the helixHelix dipoleHydrogen bonds in strands
Parallel versus anti-parallel strandsTurnsIrregularitiesFolds and structural hierarchy
©CMBI 2002
Hydrogen Bonds
Two electronegative atoms compete for the same hydrogen atom
Hydrogen Bond Donors (D):
Nitrogen e.g. N-H amide in peptide bondOxygen e.g. O-H sidechain of Ser
Hydrogen Bond Acceptors (A):
Oxygen e.g. C=O carbonyl in peptide bond
©CMBI 2002
Hydrogen Bonds (2)
Geometry of Hydrogen Bond D-H …. A:
Distance
H-A 2.5 ÅD-A 3.5 Å
Angle
The ideal hydrogen bond would have an angle of 180° between the lone-pair of the acceptor atom, the polar hydrogen and the donor atom
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The -helix
• hydrogen bond between backbone carbonyl O(i) and hydrogen of N(i+4)• 3.6 residues per turn • right-handed helix
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The -helix
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Helix
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Helix dipole
All peptide units point in the same direction (roughly parallel to the helix axis)
Each peptide bond is a small dipole
The dipoles within the helix are aligned, i.e. all C=O groups point in the same direction and all N-H groups point the other way
The helix becomes a net dipole with +0.5 charge units at the N-terminal and –0.5 at the C-terminal
By convention the dipole points from negative to positive
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Helix dipole
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Helix summary
Hydrophobicity distributionHydrogen bond between O(i) and N(i+4)
Helix dipole
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-strands and -sheets
Backbone adopts an “extended” conformation
Hydrogen bonding between main chain C=O and N-H groups of two or more adjacent -strands forms a -sheet
Adjacent strands can be parallel or anti-parallel
R-groups extend perpendicular to the plane of the H-bonds.
R-groups of neighbouring residues within one -strand point in opposite directions
R-groups of neighbouring residues on adjacent -strands point in the same direction
The strand is twisted
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Residue direction in -sheets
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Antiparallel -sheet
N -> C
C <- N
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Parallel -sheet
N -> C
N -> C
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Mixed -sheet
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Bulge
An irregularity in antiparallel structures
Hydrogen-bonding of two residues from one strand with one residue from the other in antiparallel sheets
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Strand summary
Multiple strands form a sheetHydrophobicity distribution alternatingParallel and anti-parallelHydrogen bond patternsBulges are irregularities
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Turns
Specialized secondary structures that allow for chain reversal without violating conformational probabilities
Nearly one-third of the amino acids in globular proteins are found in turns.
Most turns occur at the surface of the molecule.
©CMBI 2002
Turns
A specific subclass is the -turn, a region of the polypeptide of 4 amino acids (i, i+1, i+2, i+3) having a hydrogen bond from O(i) to N(i+3).
-turns can be classified into several subclasses based on the and angles of residues i+1 and i+2.
Most common turn types: Type I and Type II.
©CMBI 2002
-Turns, Type I & I’
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-Hairpin
•Widespread in globular proteins. •One of the simplest super-secondary structures
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Turn summary
A turn sits between two ‘things’A -turn sits between two -strandsThere are many types of -turn Nearly all -turns contain at least one Gly or Pro
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Classes of Protein Structures
All TopologiesAll Topologies/ Topologies+ Topologies
Categorized and clustered in:CATHSCOPFSSP
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-Topologies
The four-helix bundle
Myohemerythrin
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-Topologies
sandwiches and barrels
Immunoglobulin fold forms a sandwich
Plastocyanin contains barrel
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/ Topologies
/ - mixture of and
unit present in nucleotide binding proteins is named the Rossmann FoldExample: Flavodoxin
/ BarrelExample: TIM triose phosphate isomerase, “TIM-barrel”
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+ Topologies
+ - both and , but located in different domains
Examples:
Ribonuclease HCarbonic AnhydraseSerine protease inhibitor
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Quarternary Structure
Units of tertiary structure aggregate to form homo- or hetero- multimers.
The individual chains are called subunits or monomers.
The subunits (polypeptide chains) may be identical (e.g. TIM dimer) or non-identical (e.g. haemoglobin is a tetramer and contains 2 + 2 subunits).
Summary of Levels of Protein Structure
©George Helmkamp, Jr.