Shapes of polypeptides and proteins

WhatAre theThree-Dimensional Shapes of Polypeptides and Proteins ... 

Acid-Base Properties of Amino Acids Poiypeptides and Proteins Primary Structure of Polypeptides and Proteins Synthesis of Polypeptides 27.6 Three-Dimensional Shapes of Polypeptides and Proteins... 

The properties of polypeptides and proteins are determined to a large extent by the chemistry of the side chain groups, which may be summarized briefly as follows. Glycine in a peptide permits a maximum of conformational mobility. The nine relatively nonpolar amino acids-alanine, valine, leucine, isoleucine, proline, methionine, phenylalanine, tyrosine, and tryptophan-serve as building blocks of characteristic shape. Tyrosine and tryptophan also participate in hydrogen bonding and in aromatic aromatic interactions within proteins. 

Figure 2.21 Characteristic shapes for the CD spectra of some different types of secondary structure conformations found in polypeptides and proteins...

There is also a crucial problem of stereochemistry in the synthesis of polypeptides. Natural proteins consist of L-amino acids, and any racemization at the chiral centers has a profound effect on the structure and biological activity. Altered stereochemistry drastically changes the three-dimensional shape of a polypeptide chain, and this three-dimensional structure is normally essential for the biological function of the polypeptide. 

Biological function in polypeptides and proteins requires a specific three-dimensional shape and arrangement of functional groups, which, in turn, necessitate a definite amino acid sequence. One monkey wrench residue in an otherwise normal protein can completely alter its behavior. For example, sickle-ceU anemia, a potentially lethal condition, is the result of changing a single amino acid in hemoglobin (Section 26-8). The determination of the primary structure of a protein, called amino add or polypeptide sequencing, can help us to understand the protein s mechanism of action. 

The asymmetric unit contains one copy each of the subunits VPl, VP2, VP3, and VP4. VP4 is buried inside the shell and does not reach the surface. The arrangement of VPl, VP2, and VP3 on the surface of the capsid is shown in Figure 16.12a. These three different polypeptide chains build up the virus shell in a way that is analogous to that of the three different conformations A, C, and B of the same polypeptide chain in tomato bushy stunt virus. The viral coat assembles from 12 compact aggregates, or pen tamers, which contain five of each of the coat proteins. The contours of the outward-facing surfaces of the subunits give to each pentamer the shape of a molecular mountain the VPl subunits, which correspond to the A subunits in T = 3 plant viruses, cluster at the peak of the mountain VP2 and VP3 alternate around the foot and VP4 provides the foundation. The amino termini of the five VP3 subunits of the pentamer intertwine around the fivefold axis in the interior of the virion to form a p stmcture that stabilizes the pentamer and in addition interacts with VP4. 

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