Extended polypeptide chain structures

The secondary and tertiary structures of myoglobin and ribonuclease A illustrate the importance of packing in tertiary structures. Secondary structures pack closely to one another and also intercalate with (insert between) extended polypeptide chains. If the sum of the van der Waals volumes of a protein s constituent amino acids is divided by the volume occupied by the protein, packing densities of 0.72 to 0.77 are typically obtained. This means that, even with close packing, approximately 25% of the total volume of a protein is not occupied by protein atoms. Nearly all of this space is in the form of very small cavities. Cavities the size of water molecules or larger do occasionally occur, but they make up only a small fraction of the total protein volume. It is likely that such cavities provide flexibility for proteins and facilitate conformation changes and a wide range of protein dynamics (discussed later). 

Figure 3-4. Dimensions of a fully extended polypeptide chain. The four atoms of the peptide bond (colored blue) are coplanar. The unshaded atoms are the a-carbon atom, the a-hydrogen atom, and the a-R group of the particular amino acid. Free rotation can occur about the bonds that connect the a-carbon with the a-nitrogen and with the a-carbonyl carbon (blue arrows). The extended polypeptide chain is thus a semirigid structure with two-thirds of the atoms of the backbone held in a fixed planar relationship one to another. The distance between adjacent a-carbon atoms is 0.36 nm (3.6 A). The interatomic distances and bond angles, which are not equivalent, are also shown. (Redrawn and reproduced, with permission, from Pauling L, Corey LP, Branson PIR The structure of proteins Two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 1951 37 205.)...

The three-dimensional shape of a polypeptide chain or a portion of a chain is known as the secondary structure. In its simplest form the fully extended polypeptide chain would show a structure similar to that indicated in Figure 11.2(a). However, it often assumes a helical structure similar to that shown in Figure 11.2(b) which is stabilized by intra-chain hydrogen... 

P-Sbeet structures are made from bigbly extended polypeptide chains that link together by hydrogen bonds between the neighboring strands and can be oriented in parallel or antiparallel arrays (Figure 2-2). 

There are two stable arrangements of nearly completely extended polypeptide chains forming hydrogen bonds with neighboring chains.114 They are the parallel-chain pleated sheet (Fig. 12-19) and the anti-parallel-chain pleated sheet (Fig. 12-20). The identity distance in the direction of the chains is found to be different for the two structures when the requirement that the N—H---0 bonds be linear is imposed ... 

The P structure is one of the most important secondary structures in proteins. It occurs in about 80% of the soluble globular proteins whose structures have been determined. In many cases almost the entire protein is made up of P structure. Single strands of extended polypeptide chain are sometimes present within globular proteins but more often a chain folds back on itself to form a hairpin loop. A second fold may be added to form an antiparallel "P meander"102 and additional folds to form P sheets. Beta structures are found in silk fibers (Box 2-B) as well as in soluble proteins. 

The Structure of the a-Keratins Was Determined with the Help of Molecular Models The fi-Keratins Form Sheetlike Structures with Extended Polypeptide Chains Collagen Forms a Unique Triple-Stranded Structure Globular Protein Structures Are Extremely Varied and Require a More Sophisticated Form of Analysis Folding of Globular Proteins Reveals a Hierarchy of Structural Organization... 

The fi-Keratins Form Sheetlike Structures with Extended Polypeptide Chains... 

Antiparallel /3-pleated sheet (/3 sheet). A hydrogen-bonded secondary structure formed between two or more extended polypeptide chains. 

Fig. 4-7 /3-Sheet structures (a) polypeptide segment in an extended conformation (b) sheet formed by the assembly of extended polypeptide chains side b side (ci detail showing H bonding between adjacent polypeptide chains in t I lei sheet. 15...

Figure 25-1 Diagrammatic representation of a fully extended polypeptide chain with the bond lengths and the bond angles derived from crystal structures and other experimental evidence. (From Corey, R. B., and Pauling, L Proc, R. Soc Lond. Ser. B 141 10. 1953.)...

In polypeptides, successive R groups occur on alternate sides of the peptide bonds. Note that this illustration is a diagrammatic view of an extended polypeptide chain, not a representation of native structure. 

In they sheet several, extended, polypeptide chains run approximately parallel or antiparallel to each other allowing hydrogen bonds to form between the NH and CO in adjacent chains. Both antiparallel and parallel fi sheet types can occur in a globular protein (figures 3.5 and 3.6). The formation of many hydrogen bonds in the sheet therefore produces a stable structure. 

Fig. 4. Schematic drawings of the NAD binding region in dehydrogenases (a) viewed from top, perpendicular to the six-stranded parallel sheet and (b) viewed from end, looking along the extended polypeptide chains in the sheet, with their amino terminal end closest to the observer. The various secondary structural elements have been labeled according to the usually accepted nomenclature.

The nomenclature used to describe the structure of s-MDH, as shown in Fig. 1, applies as well to dogfish LDH 45,60) and is the same as that used in the homology chapter (Chapter 2, this volume). Extended polypeptide chain is given the prefix p and helical regions are... 

Model A shows the reference structure for extended polypeptide chain with ( ) = 180° and / = 180°, so the answer is c. Models C and E have one torsion angle identical to model A and the other angle changed to 0°. In model C (j) is changed to 0° (answer d), and in model E / is changed to 0° (answer b). Comparing model B with a reference for which... 

In 2002, Perutz et al. (2002a) proposed an alternative structure for amyloid protofibrils, a water-filled nanotube formed by a polyglutamine protein. This model is a parallel P-helix consisting of an extended polypeptide chain wrapping around a cylindrical terr late, where adjacent strands of the hehx are connected through H-bonds (Fig. 4) and is based on two key features of the polyglutamine diflraction data the absence of a 10-A reflection and the presence of a weak, low-angle reflection of 31 A. 

The excited state of a single extended polypeptide chain is made up of a band of states with an energy spread which depends on the magnitude of the coupling constants. The transition moment to any one of these states is the sum of all the individual transition moments in the molecule, each multiplied by a phase factor (Schellman and Schellman, 1964). In the important special situation of the polypeptide chain with a twofold screw axis (sheet structures), a group of two peptide groups in sequence can be considered as a unit cell. In this situation (Davydov, 1962) the allowed motions can be described in terms of transition moments that are either in phase with one another or 180° out of phase n radians). The former case produces a parallel absorption band, the latter a perpendicular band thus, the component of the transition moments in the direction of the molecular axis contributes only to the parallel band and the component perpendicular to this axis contributes to the perpendicular band. 

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