Amino acids hydrogen bond between

Proteins are biopolymers formed by one or more continuous chains of covalently linked amino acids. Hydrogen bonds between non-adjacent amino acids stabilize the so-called elements of secondary structure, a-helices and / —sheets. A number of secondary structure elements then assemble to form a compact unit with a specific fold, a so-called domain. Experience has shown that a number of folds seem to be preferred, maybe because they are especially suited to perform biological protein function. A complete protein may consist of one or more domains. 

The adsorption of proteins at interfaces is a key step in the stabilization of numerous food and non-food foams and emulsions. Our goal is to improve our understanding of the relationships between the sequence of proteins and their surface properties. A theoretical approach has been developed to model the structure and properties of protein adsorption layers using the analogy between proteins and multiblock copolymers. This model seems to be particularly well suited to /5-casein. However, the exponent relating surface pressure to surface concentration is indicative of a polymer structure intermediate between that of a two-dimensional excluded volume chain and a partially collapsed chain. For the protein structure, this would correspond to attractive interactions between some amino acids (hydrogen bonds, for instance). To test this possibility, guanidine hydrochloride was added to the buffer. A transition in the structure and properties of the layer is noticed for a 1.5 molar concentration of the denaturant. Beyond the transition, the properties of the layer are those of a two-dimensional excluded volume chain, a situation expected when there are no attractive interac-... 

An alternative efficient formation of hydrogen bonds occurs between a sheet of parallel or antiparallel runs of amino acids these are known as a p-sheets. The runs of amino acids face in alternate directions so that alternate amino acids hydrogen bond to neighbouring runs on each side. The spectroscopic characterization of p-sheets has proved more difficult than that of a-helices due to the practical reason that they are less soluble in solvents with a good UV transmission, and due to the intrinsic reason that they are generally structurally less well-defined they may be parallel or antiparallel and of varying lengths and widths. Furthermore, an extended p-sheet is usually found to show a marked twist, rather than to be planar. Such tertiary structure influences the overall CD spectrum. 

V Hel IX (Section 27 19) One type of protein secondary struc ture It IS a right handed helix characterized by hydrogen bonds between NH and C=0 groups It contains approxi mately 3 6 amino acids per turn... 

Fig. 3. (a) Chemical stmcture of a synthetic cycHc peptide composed of an alternating sequence of D- and L-amino acids. The side chains of the amino acids have been chosen such that the peripheral functional groups of the dat rings are hydrophobic and allow insertion into Hpid bilayers, (b) Proposed stmcture of a self-assembled transmembrane pore comprised of hydrogen bonded cycHc peptides. The channel is stabilized by hydrogen bonds between the peptide backbones of the individual molecules. These synthetic pores have been demonstrated to form ion channels in Hpid bilayers (71). 

Fig. 2. Protein secondary stmcture (a) the right-handed a-helix, stabilized by intrasegmental hydrogen-bonding between the backbone CO of residue i and the NH of residue t + 4 along the polypeptide chain. Each turn of the helix requires 3.6 residues. Translation along the hehcal axis is 0.15 nm per residue, or 0.54 nm per turn and (b) the -pleated sheet where the polypeptide is in an extended conformation and backbone hydrogen-bonding occurs between residues on adjacent strands. Here, the backbone CO and NH atoms are in the plane of the page and the amino acid side chains extend from C ...

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

Also important for stabilizing a protein s tertiary stmcture are the formation of disulfide bridges between cysteine residues, the formation of hydrogen bonds between nearby amino acid residues, and the presence of ionic attractions, called salt bridges, between positively and negatively charged sites on various amino acid side chains within the protein. 

Collagen forms a triple helix, where three chains of connected amino acids form weak hydrogen bonds between the double-bonded oxygen atoms and the hydrogen atoms attached to the adjacent chain s nitrogens. The three chains then twist together like three cords in a rope. 

The secondary structure of a protein is the shape adopted by the polypeptide chain—in particular, how it coils or forms sheets. The order of the amino acids in the chain controls the secondary structure, because their intermolecular forces hold the chains together. The most common secondary structure in animal proteins is the a helix, a helical conformation of a polypeptide chain held in place by hydrogen bonds between residues (Fig. 19.19). One alternative secondary structure is the P sheet, which is characteristic of the protein that we know as silk. In silk, protein... 

Figure 5-7. A p-turn that links two segments of antiparallel p sheet. The dotted line indicates the hydrogen bond between the first and fourth amino acids of the four-residue segment Ala-Gly-Asp-Ser.

Figure 35-11. Typical aminoacyl tRNA in which the amino acid (aa) is attached to the 3 CCA terminal. The anticodon, "PPC, and dihydrouracil (D) arms are indicated, as are the positions of the intramolecular hydrogen bonding between these base pairs. (From Watson JD Molecular Biology of the Gene, 3rd ed. Copyright ...

Fig. 21.1 The interactions between the bound coenzyme molecule and the amino acids at positions 47 and 369 in the / , / 2, and / 3 polymorphic variants as observed in their respective structures determined by X-ray crystallography. The dashed lines indicate possible hydrogen-bonds between the amino acids and the phosphate oxygens of the bound coenzyme molecule, NAD(H). Arg47 is substituted by a His residue in the f 2 isozyme and Arg369 is substituted by a Cys residue in the / 3 isozyme. In each case, the substitution results in a net loss of hydrogen-bonding interactions and weaker affinity for the coenzyme.

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