Peptide bonds: resonance structure. Properties of proteins: Peptide bonds and side chains. Dihedral angles. Peptide bond. Protein physics, Lecture 5

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1 Protein physics, Lecture 5 Peptide bonds: resonance structure Properties of proteins: Peptide bonds and side chains Proteins are linear polymers However, the peptide binds and side chains restrict conformational possibilities How do the peptide backbone and the amino acid side chains influence protein structure? Planarity of the peptide bonds is due to: Partial double bond character Large dipole moment that inhibits rotation Planar Resonance forms of a typical peptide group. The uncharged, single-bonded form (typically ~60%) is shown on the left, whereas the charged, double-bonded form (typically ~40%) is on the right. Peptide bond Dihedral angles Peptide bonds are stiff Rotation around a bond Planarity of bond means that cis and trans forms are possible Trans form is much more common due to less steric hindrance Cis form is most common in Proline residues Compare with bond angle

2 Dihedral angles In general there are 4 dihedral angles involved in describing protein structure Side chain C C N C Backbone and are flexible And account for freedom of protein structure One amino acid O Carbonyl group Peptide bond Planar = 0 or 180 GN Ramachandran ( ) G.N. Ramachandran (1963) used computer models of small polypeptides to systematically vary and with the objective of finding stable conformations For each conformation, the structure was examined for close contacts between atoms Atoms were treated as hard spheres with dimensions corresponding to their van der Waals radii Therefore, and angles which cause spheres to collide correspond to sterically disallowed conformations of the polypeptide backbone Ramachandran plot Plot of vs. The computed angles which are sterically allowed fall on certain regions of plot Dihedral angles C C N C O Protein conformation can be described in terms of the amino acid sequence and dihedral angles: i, i, i for each amino acid residue Flexibilty of the polypetide chain is restricted by Stiff peptide bond Steric hindrance (ie avoiding overlap of atoms) Ramachandran et al Ramachandran plot for glycine Allowed regions are in the 4 corners of the plot Prohibitive contacts are indicated Note that glycine has no side chain and is therefore the most flexible

3 Ramachandran plot for with C Just the crosshatched regions Allowed regions correspond to angles that yield sheet helix Left hand helix Repeating values of and along the chain result in regular structure Experimental Ramachandran plot, distribution from over 80,000 AA residues from high-resolution protein structures (x-ray crystallography) Prediction using potential energy function About 5% of observed conformations fall in forbidden regions Flexibility of peptide bond needs to be taken into account to improve this Deviations of 5 o bond angle; 0.05Å bond length or 12 o torsion angle () increases the potential energy by about 1/kcal/mol each Ramachandran plot for with C Can improve using potential energy function rather than hard sphere model. Protein structure example The structure of cytochrome C shows many segments of helix and the Ramachandran plot shows a tight grouping of, angles near -50,-50 alpha-helix cytochrome C Ramachandran plot

4 Protein structure example Side chain properties Similarly, repetitive values in the region of = -110 to 140 and = +110 to +135 give beta sheets. The structure of plastocyanin is composed mostly of beta sheets; the Ramachandran plot shows values in the 110, +130 region: How do the side chains influence protein structure? Glycine Side chain is just H Increases side chain flexibility (see Ramachandran plot) Can fit chain into small spaces Frequency restricted too much would render chains to flexible and lose 3D shape Alanine beta-sheet plastocyanin Ramachandran plot Has one methyl group as side chain Smallish nonpolar No real preference for inside or surface of protein Very abundant (due to simplicity and availability?) Side chain properties Side chain properties Branched side chains are stiffer Aromatic residues Val, Ile, Leu Reduce possibilities for chain folding Phe, Trp, Tyr, His Contain one methylene group spacer Without this severe steric hinderance Would make chain too stiff Intrinsically fluorescent particularly Trp Polar side chains Cysteine Cys, Ser, Thr, Asn, Gln, Tyr Can form hydrogen bonds Often on surface of protein Has unique property: only side chain with exposed S atom Can form disulfide bond with another Cys further along the chain Used to maintain a given structure of the protein or to respond to oxidation Large non-polar residues Leu, Ile, Phe, Pro, Trp Predominantly found in the interior of the molecule Disulfide bond

5 Side chain properties Proline Back bone is part of the cyclic group Backbone section has a bend Invokes bends in the protein chain or kinks in helices Histidine Side chain has pk value of 6.0 Can be charged or uncharged in the physiological ph range Two readily available states useful as a catalyst Involved in the active site of most enzymes Side chain properties Negative charged side chains Positive charged side chains Asp, Glu Negative charge at physiological ph (lose an H + ) Usually found on protein surface Lys, Arg Positive charge at physiological ph (gain an H + ) Usually found on protein surface Hydrophobicity Folding process of polypetide chain depends on hydrophobicity (non-polarity) of side chains Formation of hydrophobic core is an essential driving force in protein folding

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