3-D Protein Structure

3-D Protein Structure - Three-Dimensional Structures of...

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Three-Dimensional Structures of Proteins The properties of a protein are largely determined by its three-dimensional structure. Denatured: unfolded protein The peptide group has a rigid, planar structure, which, Pauling pointed out, is a consequence of resonance interactions that give the peptide bond an ~40% double-bond character. Peptide groups, with few exceptions, assume the trans conformation; that in which successive C α atoms are on opposite sides of the peptide bond joining them . The backbone of a protein is a linked-sequence of rigid planar peptide groups . Torsion angles (Dihedral angles): rotation angle about the C α —N bond ( ϕ ) and the C α —C bond ( Ѱ ) of each of the aminoa cid residue; both are defined as 180° when the polypeptide chain is in its planar, fully extended (all-trans) conformation and increases for a clockwise rotation when viewed from C α Staggered conformation: torsion angle=180°, ethane’s most stable arrangement Eclipsed conformation: torsion angle =0° is ethane’s least stable arrangement Energy barrier: the energy difference between the staggered and eclipsed conformations Ramachandran diagram or conformation map: a plot that represents allowed conformations depending on the van der Waals radii chosen to calculate it Only three small regions of the conformational map are physically accessible to a polypeptide chain. Pitch p : the distance the helix rises along its axis per turn p=nd Only one helical polypeptide conformation has simultaneously allowed conformation angles and a favorable hydrogen bonding pattern: the α helix , a particular rigid arrangement of polypeptide chains α helix (3.6 13 helix): it has 3.6 residues per turn and 13 atoms 2.2 7 ribbon: it has 2.2 residues per helical turn and 7 atoms 3 10 helix: it has 3 residues per helical turn and 10 atoms π helix(4.4 16 ): a mildly forbidden conformation; only observed as segments of longer helices because its wide and flat formation results in a axial hole that is too small to admit water molecules but too wide to allow van der Waals association across the helix axis which greatly reduces its stability Polyproline: the most conformationally constrained polypeptide that is unable to assume any common secondary structure due to the conformational constraints imposed by its cyclic pyrrolidine side chains Polyglycine: the least conformationally constrained polypeptide which precipitates from solutiona s a helix whose parameters are almost identical to polyproline
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Three-Dimensional Structures of Proteins In β pleated sheets, a hydrogen bonding occurs between neighboring polypeptide chain. β Pleated sheets come in two varieties: 1) The antiparallel β pleated sheet, in which neighboring hydrogen bonded polypeptide chains run in opposite directions 2) The parallel β pleated sheet, in which they hydrogen bonded chains extend in the same direction Topology: connectivity of the polypeptide strands Regular secondary structures—helices and β sheets—comprise around half of the average globular
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This note was uploaded on 09/19/2011 for the course CHEM 43 taught by Professor Therien during the Fall '09 term at Duke.

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3-D Protein Structure - Three-Dimensional Structures of...

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