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Analysis of Polypeptide Backbone Bond Angles
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The polypeptide backbone requires a good deal of flexibility in order for a polypeptide to fold up into a globular protein Although side chain flexibility has some effect on protein conformation, the backbone ties the entire chain together and therefore determines or limits the possible shapes that a polypeptide can take Figure 9-6 shows a tripeptide (a three-residue polypeptide) in order to illustrate the features of the polypeptide backbone The backbone consists of a repeating chain of three covalent bonds These bonds are
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FIgure 9-6 A tripeptide is used to illustrate the features of the polypeptide backbone the polypeptide backbone consists of three repeating covalent bonds, two of which (the n-ca and ca-c bonds) allow rotation the third bond (c-n) does not allow rotation the dotted lines indicate the partial double bond character of the c-n bond the two dots next to each nitrogen indicate the otherwise non-bonded nitrogen electrons that spend a portion of their time within the c-n bond
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1 Between the amide nitrogen and the a-carbon (angle of rotation = f) 2 Between the a-carbon and the carbonyl carbon (angle of rotation = c) 3 Between the carbonyl carbon and the amide nitrogen (no rotation) The third bond, the one between the carbonyl carbon and the amide nitrogen, cannot rotate This is because the pair of nonbonded electrons on the nitrogen spends a portion of its time within that bond (so they are not entirely nonbonding once they are part of a peptide chain) This gives the bond somewhat of a double-bond character This in turn prevents free rotation around the bond It also means that the amide nitrogen, the carbonyl carbon, and the carbonyl oxygen must all lie within a plane The other two bonds, however, allow free rotation, and we use the symbols f and c respectively to represent the angle of rotation between these bonds and a plane defined by the carbonyl group and the amide nitrogen The N-Ca and Ca-C bonds themselves allow free rotation; however, other forces come into play to limit the possible values of f and c Obviously all of the forces mentioned above can come into play (electric charge, hydrophobicity, etc), but the two biggest contributors to the limits on f and c are (1) steric hindrances and (2) dipole-dipole interactions from adjacent peptide bonds By taking these two forces into account, it is possible to calculate the potential energy (free energy) associated with every possible pair of f and c values Steric hindrances alone will disallow many values of f and c depending on which amino acid side chains are considered Taking dipole interactions into consideration refines the calculations If we then plot a set of f and c for which the energy is within a particular range, we get a contour diagram that might look similar to Fig 9-7 A f, c contour diagram is also called a ramachandran diagram for the biophysicist G N Ramachandran who invented it
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Common Protein Secondary Structures
There are two very common secondary structural motifs that occur throughout protein structures One is called the alpha helix and the other is called the beta sheet Other structural motifs do occur, but these two are the most common Any given globular protein (tertiary structure) can contain various sections of alpha helix and beta sheet, as well as other structures, along the polypeptide chain This can be seen in Fig 9-2
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FIgure 9-7 An example of what a f, c contour diagram might look like, depending on which amino acid side chains are considered the shaded region shows the values for which f and c result in a negative free energy in other words these values of f and c result in an energetically stable conformation the unshaded regions represent f and c values that are prohibited due to either steric hindrances or an unfavorable (repulsive) dipole interaction
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