Other Types of Secondary Structure

Other distinct types of protein secondary structure include the type present in collagen, a fibrous connective tissue protein and the most abundant of all human proteins. Collagen peptide chains are twisted together into a three-stranded helix. The resultant three-stranded rope is then twisted into a superhelix (Chapter 10). 

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Even in the atomic-scale graphical representation of macromolecules it is easy to recognize helical segments. In our display we represent any helical portion of a molecule by a single rod. Properties of the rod would include the number of turns and the number and nature of atoms or residues involved in the local helical structure. Other types of secondary structure lend themselves to representation by generalized cylinders, but have not been incorporated into our code, which is in an early stage of development. 

Some amino acids are accommodated better than others in the different types of secondary structures. An overall summary is presented in Figure 4-10. Some... 

The nucleotide sequences of many tRNAs from a wide variety of organisms have been determined. All contain approximately 80 nucleotides, many of them of unusual structure (see Chap. 7). There is at least one tRNA corresponding to each amino acid, and while the sequences within individual tRNAs vary, they all form a common type of secondary structure (cloverleaf) in which the RNA chain folds back on itself to give a maximum amount of base pairing. One part of this structure is involved in the binding of an amino acid, and another part contains a sequence of three nucleotides complementary to one (or more) of the codons for this amino acid. This sequence of three nucleotides interacts with codons in the mRNA during the translational process. There are other features of the structure that are essential for the action of tRNA. 

Although homonuclear resonance assignment is almost exclusively carried out using the sequential assignment method, one other approach has found use in some applications. The main-chain-directed (MCD) method46 is based on the identification of cyclic patterns of NOEs, which are characteristic of the different types of secondary structure. Because of this, it is less suitable for the assignment of unstructured or irregularly structured sections of a protein. 

The p Sheet Another type of secondary structure, the p sheet, consists of laterally packed p strands. Each p strand is a short (5- to 8-residue), nearly fully extended polypeptide segment. Hydrogen bonding between backbone atoms in adjacent p strands, within either the same polypeptide chain or between different polypeptide chains, forms a p sheet (Figure 3-4a). The planarity of the peptide bond forces a p sheet to be pleated hence this structure is also called a 3 pleated sheet, or simply a pleated sheet. Like a helices, p strands have a directionality defined by the orientation of the peptide bond. Therefore, in a pleated sheet, adjacent p strands can be oriented in the same (parallel) or opposite (antiparallel) directions with respect to each other. In both arrangements, the side chains project from both faces of the sheet (Figure 3-4b). In some proteins, p sheets form the floor of a binding pocket the hydrophobic core of other proteins contains multiple P sheets. 

Frequencies of one band alone (either Amide I or Amide III) do not yield clear-cut distinctive information on conformations. The frequencies due to one type of secondary structure are influenced by the presence of other structures and therefore, the frequencies can be used to yield information about the relative ratios of structures. 

Protein stmcture can be classified in a hierarchical fashion (Figure 1). The first level is the amino acid sequence or primary stmcture, and the next is the secondary stmcture, which is the regular repetition of backbone dihedral angles in a linear stretch of amino acids that gives rise to a common stmctural unit. The two dominant types of secondary structure in proteins are -helices and -sheets. Elements of secondary structure are connected by loops or turns, which allow them to fold back on themselves and to associate to form a globular tertiary stmcture. In some proteins the folded tertiary stmcture of a monomer is the active form, whereas in others monomers associate with other similar or dissimilar subunits to give specific higher-order complexes or quaternary stmcture. ... 

The secondary structure describes the overall conformation or shape of the protein molecule. Typical types of secondary structure are helices (cf Sections 4.2 and 4.6) and pleated sheets (j5 structures). Secondary structure results from main-chain hydrogen-bonded interactions. In pleated sheets, the a-amino acid chains can be arranged parallel or antiparallel to each other, with the antiparallel structure being thermodynamically more stable. a-Amino acids that yield helical homopolymers usually (but not inevitably) form helical sequences in proteins and polypeptides. The random coil that results from the rupture or lack of stabilizing hydrogens is not considered a secondary structure. Segments of a-helix, pleated sheet, and random coil are possible in the same molecule. 

A major portion of the petroleum used today is derived from lipids of plants deposited in past eons. The structures of most compounds isolated from petroleum suggest a derivation from fatty acids. Various chemical changes have occurred, mostly reduction and decarboxylation, so that most petroleum is comprised of a mixture of odd- and even-chain-length hydrocarbons. Some petroleums have a variety of other compounds that appear to be derived from chemical modification of other types of secondary metabolites. 

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