Hydrogen bonding protein secondary structure

Since infrared spectroscopy also provides information about physical structure, infrared imaging can be used to determine spatial distribution of physical properties as well. Some of the properties include intermolecular and intramolecular order, hydrogen bonding, protein secondary structure, complexation and functional group orientation. 

A protein s secondary structure arises from the formation of intra- and inter-molecular hydrogen bonds. All carboxyl group oxygens and amine hydrogens of a polypeptide participate in H-bonding. Protein secondary structure also derives from the fact that although all C-N bonds in peptides have some double bond character and cannot rotate, rotation about the Co-N and Ca-C bonds is possible and is... 

Main-chain to water hydrogen bonding plays a significant role in proteins, as the numbers in Ihble 19.2a indicate, 43% for C=0 and 21% for N-H groups. Because the water molecules are predominantly at the periphery of the protein molecules with a few enclosed in the interior, this means that main-chain to main-chain hydrogen bonding (or secondary structure) predominates in the core of the proteins. Secondary structure is less well defined at the periphery where the peptide C=0 and N-H groups are more free to interact with water molecules. 

Oi Hel ix (Section 27.19) One type of protein secondary structure. It is a right-handed helix characterized by hydrogen bonds between NH and C=0 groups. It contains approximately 3.6 amino acids per turn. 

Kabsch, W., and C. Sander. 1983. Dictionary of Protein Secondary Structure Pattern Recognition of Hydrogen-Bonded and Geometrical Features. Biopol. 22,2577-2637. 

Hydrogen bond formation drives protein secondary structure... 

The term secondary structure is used to describe the molecular shape or conformation of a molecule. The most important factor in determining the secondary structure of a material is its precise structure. For proteins, it is the amino acid sequence. Hydrogen bonding is also an important factor in determining the secondary structures of natural materials and those synthetic materials that can hydrogen-bond. In fact, for proteins, secondary structures are... 

Hydrogen-bonding interactions are considerably weaker than ionic interactions and covalent bonds but have a profound effect on many chemical and physical properties [221] and determine the shapes of large molecules such as proteins and nucleic acids. Protein secondary structure is determined by H bonding between the carbonyl oxygen of one amide unit and the N—H bond of another. The two strands of the double helix of... 

Kabsch, W., and Sander, C. (1983). Dictionary of protein secondary structure Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637. 

Illustration of hydrogen bonds between N and O atoms in peptide linkages, which constitutes protein secondary structures... 

Wang Z-X, Wu C, Lei H, Duan Y (2007) Accurate ab initio study on the hydrogen-bond pairs in protein secondary structures. J Chem Theory Comput 3 1527—1537... 

Sheridan RP, Lee RH, Peters N, Allen LC (1979) Hydrogen-bond cooperativity in protein secondary structure. Biopolymers 18 2451-2458... 

The above description is a considerable simplification of protein secondary structure possibilities. Thus a number of helix types are possible in addition to the a-helix. Further, particular structured 3-turns exist that are stabilized by hydrogen bonding and link other secondary structure elements. Relatively unstructured coils, loops and random coils can also link a-helical and 3-strand elements. 

Protein structure is typically classified as consisting of four levels primary (1°), secondary (11°), tertiary (III°), and quaternary (IV°). Primary structure is the sequence of amino acids in the protein. Secondary structure is the local three-dimensional spatial arrangement of amino acids that are close to one another in the primary sequence. a-Helices and P-sheets compose the majority of secondary structures in all known proteins. Tertiary structure is the spatial arrangement of amino acid residues that are far apart in the linear primary sequence of a single polypeptide chain, and it includes disulfide bonds and noncovalent forces. These noncovalent forces include hydrogen bonding, which is also the primary stabilization force for the formation of a-helices and P-sheets, electrostatic interactions, van der Waals forces, and hydrophobic effects. Quaternary structure is the manner in which subunits of a multi-subunit protein are arranged with respect to one another. 

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