Structure of Polypeptides

Polypeptides (or more simply peptides) are amino acid polymers comprising up to approximately 50 units. 

Larger polymers are known as proteins. Aside from the amide linkages, the polymer chain is very flexible, giving rise to the possibility of an enormous number of different conformers. It is nothing short of remarkable, therefore, that proteins rapidly fold into a single conformation. Very strong forces must be at work. 

Two of the most common motifs in the hundreds of known protein structures are the so-called a helix and the P sheet. 

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Schlaad H, Smarsly B, Losik M (2004) The role of chain-length distribution in the formation of solid-state structures of polypeptide-based rod-coil block copolymers. Macromolecules 37 2210-2214... 

Knowledge of DNA sequences permits deduction of the primary structures of polypeptides. DNA sequencing requires only minute amounts of DNA and can readily yield the sequence of hundreds of nucleotides. To clone and sequence the DNA that encodes a partic-... 

The primary structure of a polypeptide is its sequence of amino acids. It is customary to write primary structures of polypeptides using the three-letter abbreviation for each amino acid. By convention, the structure is written so that the amino acid on the left bears the terminal amino group of the polypeptide and the amino acid on the right bears the terminal carboxyl group. Figure 13-35 shows the two dipeptides that can be made from glycine and serine. Although they contain the same amino acids, they are different molecules whose chemical and physical properties differ. Example shows how to draw the primary stmcture of a peptide. 

The computational verification and prediction of the conformations (tertiary structures) of polypeptides presents a considerable challenge for theoretical chemists. Attempts towards this goal have so far made use of force field calculations to a large extent. Levitt... 

Solid state 2H NMR parameters are almost exclusively governed by the quadrupole interaction with the electric field gradient (EFG) tensor at the deuteron site.1 8 The EFG is entirely intramolecular in nature. Thus molecular order and mobility are monitored through the orientation of individual C-2H bond directions. Therefore, 2H NMR is a powerful technique for studying local molecular motions. It enables us to discriminate different types of motions and their correlation times over a wide frequency range. Dynamics of numerous polymers has been examined by solid state 2H NMR.1 3,7,9 Dynamic information on polypeptides by NMR is however limited,10 26 although the main-chain secondary structures of polypeptides in the solid have been extensively evaluated by 13C and 15N CP/MAS NMR.27,28... 

Figure 2.1 Chemical structure of polypeptides. The R, and R2 J group possibilities are shown in Fig. 2.2, and n is the number of...

Fig. 26a,b. High resolution height SFM-micrographs of a 14-ABG-PS on mica [86] b Twisted ribbon structure of polypeptide /i-sheets [ 167]. The plectoneme conformation is caused by the backward folding of the torsionally stressed molecules [86]. Insert in (a) depicts a plectoneme supercoil... 

A. Nayeem, J. Vila, and H. A. Scheraga. A comparative study of the simulated-annealing and monte carlo-with-minimization approaches to the minimum-energy structures of polypeptides [met]-enkephalin. J. Comp. Chem., 12(5) 594-605, 1991. 

Such a conclusive consideration is certainly speculative. Nevertheless, it may be acceptable because of the detailed analysis of the experimental data. When each of the PLA, PDA, PG, PLIL and PLV samples was treated under the same conditions as in the individual cases of their blends as described above, the structure of polypeptides after its treatment did not change from the original structure as seen from the 13C CP/MAS NMR experiments. On the other hand, the structure of blended polypeptides after the treatment changes significantly. Therefore, it can be said that such a change comes from intermolecular interactions. 

So far, we have investigated higher-order structure of polypeptides by solid-state high-resolution NMR not only using experimental but also theoretical methods[2-4]. The chem cal shifts can be characterized by variations in the electronic states of the local conformation as defined by the dihedral angles(4>,W). Ando et al. have calculated contour map for the Cp carbons of an alanine dipeptide by using the FPT INDO method within the semi-empirical MO framework. The calculated map reasonably predicts the experimental version. This shows that the chemical shift behavior of the L-alanine residue Cp-carbonyl carbons in the... 

Most receptors are proteins, presumably because the structures of polypeptides provide both the necessary diversity and the necessary specificity of shape and electrical charge. The section How Are New Receptors Discovered describes some of the methods by which receptors are discovered and defined. 

Scheme 2 Chemical structure of polypeptides containing p-phenylazo-L-phenylalanine and y-benzyl-L-glutamate residues (II).

Boulmedais F, Schwinte P, Gergely C et al (2002) Secondary structure of polypeptide multilayer films an example of locally ordered polyelectrolyte multilayers. Langmuir 18 ... 

The enormous structural diversity of proteins begins with different amino acid sequences (primary structure) of polypeptide chains that fold into complex 3D structures. The final folded arrangement of the polypeptide chain is referred to as its conformation (secondary and tertiary structures). It appears that the information for folding to the native conformation is present in the amino acid sequences (Anfinsen, 1973) however, a special class of proteins known as chaperons is required to facilitate in vivo folding of a protein to form its native conformation (Martin and Hartl, 1997). 

Perhaps even more esoteric than antisense nucleic acids are RNA molecules that are able to specifically cleave other RNA molecules. Until several years ago, it was generally thought that all cellular processes were dictated by DNA through the structure of polypeptides, which performed all the functions. During studies conducted on RNA, it was discovered that some RNA strands had catalytic properties. These nonprotein biocatalysts are referred to as ribozymes and combine the properties of antisense RNA with the ability to cleave target RNA. 

Biochemists say that the two amino acids are connected by a peptide bond, but, of course, the peptide bond is just an amide bond. A slightly more complex example, the phagocytosis-stimulating tetrapeptide known as tuftsin, derived from four amino acids, can be employed to illustrate some of the conventions that are used in writing the structures of polypeptides and proteins ... 

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