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©CMBI 2001 The amino acids in their natural habitat
©CMBI 2001 The amino acids in their natural habitat Topics: Hydrophobicity Hydrogen bonds steer secondary structure Hydrogen bonds in the helix Helix dipole Hydrogen bonds in strands Parallel versus anti-parallel strands Turns Irregularities Folds and structural hierarchy
©CMBI 2002 Hydrogen Bonds Two electronegative atoms compete for the same hydrogen atom Hydrogen Bond Donors (D): Nitrogene.g. N-H amide in peptide bond Oxygene.g. O-H sidechain of Ser Hydrogen Bond Acceptors (A): Oxygene.g. C=O carbonyl in peptide bond
©CMBI 2002 Hydrogen Bonds (2) Geometry of Hydrogen Bond D-H …. A: Distance H-A 2.5 Å D-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
©CMBI 2002 The -helix hydrogen bond between backbone carbonyl O(i) and hydrogen of N(i+4) 3.6 residues per turn right-handed helix
©CMBI 2002 The -helix
©CMBI 2002 Helix
©CMBI 2002 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
©CMBI 2002 Helix dipole
©CMBI 2002 Helix summary Hydrophobicity distribution Hydrogen bond between O (i) and N (i+4) Helix dipole
©CMBI 2002 -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
©CMBI 2002 Residue direction in -sheets
©CMBI 2002 Antiparallel -sheet N -> C C <- N
©CMBI 2002 Parallel -sheet N -> C
©CMBI 2002 Mixed -sheet
©CMBI 2002 Bulge An irregularity in antiparallel structures Hydrogen-bonding of two residues from one strand with one residue from the other in antiparallel sheets
©CMBI 2002 Strand summary Multiple strands form a sheet Hydrophobicity distribution alternating Parallel and anti-parallel Hydrogen bond patterns Bulges are irregularities
©CMBI 2002 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’
©CMBI 2002 -Hairpin Widespread in globular proteins. One of the simplest super-secondary structures
©CMBI 2002 Turn summary A turn sits between two ‘things’ A -turn sits between two -strands There are many types of -turn Nearly all -turns contain at least one Gly or Pro
©CMBI 2002 Classes of Protein Structures All Topologies All Topologies / Topologies + Topologies Categorized and clustered in: CATH SCOP FSSP
©CMBI 2002 -Topologies The four-helix bundle Myohemerythrin
©CMBI 2002 -Topologies sandwiches and barrels Immunoglobulin fold forms a sandwich Plastocyanin contains barrel
©CMBI 2002 / Topologies / - mixture of and unit present in nucleotide binding proteins is named the Rossmann Fold Example: Flavodoxin / Barrel Example: TIM triose phosphate isomerase, “TIM-barrel”
©CMBI 2002 + Topologies + - both and , but located in different domains Examples: Ribonuclease H Carbonic Anhydrase Serine protease inhibitor
©CMBI 2002 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.
©CMBI 2001 Step 5: The amino acids in their natural habitat.
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