Hydrogen bonds, protein structure

FIGURE 3-22 Hydrogen -Bonded Protein Structures, (a) A protein a helix. Peptide carbonyls and N—H hydrogens on adjacent turns of the helix are hydrogen-bonded. (From T. L. Brown and H. E. LeMay, Jr., Chemistry, the Central Science, Prentice Hall, Englewood Clifts,... 

The rational synthesis of peptide-based nanotubes by self-assembling of polypeptides into a supramolecular structure was demonstrated. This self-organization leads to peptide nanotubes, having channels of 0.8 nm in diameter and a few hundred nanometer long (68). The connectivity of the proteins in these nanotubes is provided by weak bonds, like hydrogen bonds. These structures benefit from the relative flexibility of the protein backbone, which does not exist in nanotubes of covalently bonded inorganic compounds. 

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. 

The life that we know also uses proteins for the majority of structural and catalytic functions. Proteins are particularly suited for these functions because of the structural properties of polymers of amino acids. The polyamide backbone of proteins is neutral, unlike that of nucleic acids. Further, the backbone has a repeating dipole able to make hydrogen bonds. These structural features are exploited as proteins fold into globular structures, as they promote the formation of stable secondary structures such as alpha helices and beta sheets. 

In this chapter, we discuss the hydrogen bonding in structures where water is the sole or majority molecular species present. These are structures which are determined wholly or primarily by the hydrogen-bonding characteristics of the water molecules. They demonstrate the consequences of the dual hydrogen-bond donor-acceptor functionality, which, when combined with the cooperative and flip-flop dynamic properties of the hydroxyl groups, are essential for the formation of the hydration shells around the proteins and nucleic acids, and help to maintain their three-dimensional structures. 

The most obvious structural building blocks in proteins are the elements of secondary structure, the a-helix and the P-strand. These elements arise, in part, through the formation of intramolecular hydrogen bonds. Secondary structure prediction usually attempts to assign the conformational state of a residue as helix (H), extended (E), or coil (C), based on the local sequence (i.e., the surrounding residues). However, other ordered structures, such as P-tums and Q-loops, do exist. Secondary... 

Deoxyribonucleic acid (DNA) stores the genetic information present in living cells. It allows the cell to make proteins according to a definite sequence of atoms. The DNA molecule consists of two long chains molecules twisted around each other and held together by hydrogen bonds This structure is called a double helix (Fig. 5.20). For this discovery, F. Crick, M. Wilkins and J. Watson gained the Nobel Prize for Medicine in 1962. 

The requirements for hydrogen bond preservation in the folded structure result in the cooperative formation of hydrogen-bonded secondary structure regions in proteins. The secondary structure specifies regular polypeptide chain folding patterns of helices, sheets, coils and tnms that are combined/folded into tertiary structure. Studies of two-state structural transition suggest that a statistical method can be developed to predict the... 

Silk fibers, which are obtained from the secretion of the silkworm, are double filaments that are enclosed by a coating of a gum (sericin) as they are secreted. The amino acid sequence of the silk protein was shown to be (glycine-serine-glycine-alanine-glycine-alanine). The polypeptide chains are bound into antiparallel pleated )ff-sheet structures by hydrogen bonding. The structures are also held together by van der Waal forces. ... 

---