A-helix 3-sheet

Approximately 500 of the 820 amino acid residues of the myosin head are highly conserved between various species. One conserved region, located approximately at residues 170 to 214, constitutes part of the ATP-binding site. Whereas many ATP-binding proteins and enzymes employ a /3-sheet-a-helix-/3-sheet motif, this region of myosin forms a related a-f3-a structure, beginning with an Arg at (approximately) residue 192. The /3-sheet in this region of all myosins includes the amino acid sequence... 

In Section 7.7.3.3, methods for quantitating a-helix and other secondary structural types in peptides were described. These are generally applicable to a series of peptides in which a regular conformation [a-helix, (3-sheet, poly(Pro)II] is in equilibrium with an ensemble of unordered conformations, as evidenced by an isodichroic point observed over a range of temperature, pH, or solvent composition. 

The polypeptide backbone does not assume a random three-dimensional structure, but instead generally forms regular arrangements of amino acids that are located near to each other in the linear sequence. These arrangements are termed the secondary structure of the polypeptide. The a-helix, 3-sheet, and 3-bend are examples of secondary structures frequently encountered in proteins. [Note The collagen helix, another example of secondary structure, is discussed on p. 43.]... 

Comparison of a p-sheet and an a-helix Unlike the a-helix, 3-sheets are composed of two or more peptide chains (3-strands), or segments of polypeptide chains, which are almost fully extended. Note also that in 3-sheets the hydrogen bonds are per pendicular to the polypeptide backbone (see Figure 2.1k). 

Both amide I and amide III bands are seen in Raman spectra of proteins.30 Lippert et al. devised the following method for estimating the fractions of a-helix, (3 sheet, and random coil conformations in proteins.31 The amide I Raman bands are recorded at 1632 and 1660 cm 1 in DzO (amide I ). The amide III band, which is weak in DzO, is measured at 1240 cm-1 in H20. The intensities of the three bands relative to the intensity of an internal standard (the 1448 cm 1 CH2... 

The coiled-coil motif is an ideal model system for the following reasons there is only one type of secondary structure present (the a-helix) the a-helical structure can be easily monitored by circular dichroism spectroscopy the two-stranded coiled coil contains two subunits stabilized by both intrachain and interchain interactions and, lastly, its small size reduces the potential complexity in the analysis and interpretation of results encountered in the analysis of globular proteins, which have multiple elements of secondary structure (a-helix, (3-sheet, (3-turns, loops, and regions of undefined structure). 

Figure 2.15. Conformational plot showing location of a helix, (3 sheet, and collagen triple helix. The plot shows the locahzation of the predominant chain structures found in proteins, including the a helix (a), (3 sheet ((3), and collagen triple helix (C).The it stands for a helix that does not occur in nature.

Amino acid a helix 3 sheet Reverse turn... 

Abbreviations Ala, L-alanine Leu, L-leucine Glu(OBzl), 7-benzyl L-glutamate NHBu, n-butyl amide OBzl, benzyl ester PG, polyglycine NCA, A-carboxy-a-amino acid anhydride a-helix, right-handed a-helix , 3-sheet, anti-parallel /3-sheet. 

Ramachandran s stereochemical plot diagram) of dipeptides has been widely used to predict the secondary structures of proteins [306-309]. It is well known that the calculations on the polypeptides are limited by the number of atoms and hence high level ab initio and DFT calculations have been possible recently only. Several theoretical calculations with different levels of accuracy have been made on the polypeptides to study the < )- 1> plot distribution, H-bonding interactions, and stability [1-4, 308-322]. In the stability of polypeptides and proteins, H-bond plays an important role in the formation of the secondary structures such as the a-helix, (3-sheet, etc., and higher-order structures [1-4]. Quantum chemical calculations on some of the secondary structures in peptides and proteins ((3-sheets, (3-turns, and y-turns) at the HF and MP2 levels have been performed with special emphasis to the H-bonded structures... 

Table 2. Isotropic 15N chemical shifts of some homopolypeptides with various conformations (a-helix, /3-sheet, aL-helix, wL-helix, PGI, PGII, PPI and PPII forms) in the solid state (ppm from 15NH4N03, 0.5ppm).

Abbreviations a-helix, right-handed a-helix aL-helix, left-handed a-helix /3-sheet, antiparallel /3-sheet. 

Synthetic polypeptides consist of a repeating sequence of certain amino acids and their primary structures are not as complicated as those in proteins. The polypeptides are very important polymers in both polymer and protein science. The characteristic properties related to the structure lead to possible expansion for research in the field of polymer science, to provide very different moplecules from conventional synthetic polymers. For example, the concept of the liquid crystal is expanded by revealing the variety of structures and properties of liquid crystals. Furthermore, the polypeptides are sometimes used as biomimic materials. On the other hand, synthetic polypeptides are sometimes used as model biomolecules for proteins because they take the a-helix, /3-sheet, o)-helix structure, and so on, under appropriate conditions. From such situations, it can be said that synthetic polypeptides are interdisplinary macromolecules and are very important for research work in both polymer and protein science. 

Fig. 22.3. 300 MHz H CRAMPS NMR spectra of (Ala) in the solid state. (A) H-(Ala)8-NHBu(j8-sheet form) and (B) (Ala) (a-helix + /3-sheet form) and (Ala) (a-helix).

In a dilute protein solution, the nano length scale or the molecular structure of protein molecules determines the thermodynamic equilibrium between protein-protein and protein-water interactions. The consequent surface and hydrodynamic properties of proteins are resulted from the proportion of hydrophobic, hydrophilic, and charged amino acid residues. For example, caseins could adopt a random coil structure due to their flexible structure as a result of phosphorylated serine residues caseins indeed lack the ordered structures of a-helix, 3-sheet, and 3-turn found in globular proteins. This gives rise to better multifunctionality of caseins over globular proteins. 

Early work by Davidson and Fasman showed that one could prepare poly(L-lysine) in the a helix, /3 sheet, and random coil by varying the pH, temperature, and salt conditions. Subsequently the different conformations were shown to have remarkable differences in their Raman spectra. The amide I band shows a large change in frequency with change in conformation. The amide I is a vibration of the peptide group that may be considered to consist of two resonance forms ... 

Block copolymers containing a biologically active, polypeptide block were originally studied as models for biological membranes. The variety of conformations of polypeptides (a-helix, )3-sheet, and random coil) were expected to produee new copolymers of technical interest [10]. 

Owing to the well-defined stereochemistry, the diversities in choosing hydropbobic/hydrophilic amino acids, and specific secondary structures, polypeptides have been intensively investigated as a biomaterial.Contrary to the random hydrophobically driven self-assembly of the most synthetic polymer, the secondary structures of the polypeptides such as a-helix, /3-sheet, and random coil significantly affect the gelation behavior. 

There are various levels of structural organization of proteins primary, secondary, tertiary and quaternary. The primary structure has been defined as the sequential order of amino acid residues linked by covalent peptide bonds. The secondary structure refers to the molecular geometry located in the polypeptide chains within ordered structures, such as a-helix, (3-sheet and random coil (unordered). The tertiary structure contains the information on how the elements of the secondary structure are folded. Finally, the quaternary structure of a protein with more than one polypeptide chain shows how the different principal chains are associated and oriented with one another. The structure of proteins is stabilized by different types of interactions covalent and hydrogen bonds, hydrophobic interactions, electrostatic and van der Waals forces [3,4]. 

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