Proteins hydrogen-bonding

Podtelezhnikov, A.A., Wild, D.L. Exhaustive Metropolis Monte Carlo sampling and analysis of polyalanine conformations adopted under the influence of hydrogen bonds. Protein. Struct. Funct. Genet. 2005, 61, 94—104. 

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. 

N181D Hydrogen bonding, protein-solvent interactions... 

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,... 

Shifting from one interdisciplinary nomenclature to another we can view the bidentate molecule as an amino acid, the amide becomes a peptide and the polyamide a polypeptide or a protein. Hence, we have abjured organic chemistry in favour of biochemistry. Proteins are built up from approximately 20-25 different a-amino acids, the individual order of which decide the chemical and physical properties of a particular protein. Due to a combination of certain attributes of e peptide linkage, and the presence of functionalities enabling the formation of hydrogen bonds, protein strands fall into one of three geometrically different categories random coil, a-helix and pleated sheet. 

Fleming, R.J., and Rose, G.D. (2005) Do all backbone polar groups in proteins form hydrogen bonds Protein Sci. 14, 1911-7. 

O-H stretching vibration (v) of water molecules in protein-wata-hydrogen bonding O-H (v) (as intense and very broad band assigned to protein-water hydrogen bonding Protein... 

Tjandra N and Bax A 1997 Solution NMR measurement of amide proton chemical shift anisotropy in N-15-enriched proteins. Correlation with hydrogen bond length J. Am. Chem. Soc. 119 8076-82... 

Baker E N and Flubbard R E 1984 Hydrogen bonding in globular proteins Prog. Biophys. Molec. Biol. 44 97-179... 

The pathway model makes a number of key predictions, including (a) a substantial role for hydrogen bond mediation of tunnelling, (b) a difference in mediation characteristics as a function of secondary and tertiary stmcture, (c) an intrinsically nonexponential decay of rate witlr distance, and (d) patlrway specific Trot and cold spots for electron transfer. These predictions have been tested extensively. The most systematic and critical tests are provided witlr mtlrenium-modified proteins, where a syntlretic ET active group cair be attached to the protein aird tire rate of ET via a specific medium stmcture cair be probed (figure C3.2.5). 

In addition to testing predictions of tire patlrway model in proteins, experiments have also examined tire prediction tlrat tire decay across a hydrogen bond (from heteroatom to heteroatom) should be about as costly as tire decay across two covalent bonds. Indeed, by syntlresizing a family of hydrogen bonded aird covalently bonded systems witlr equal bond counts (according to this recipe), it was demonstrated tlrat coupling across hydrogen bonded... 

Figure C3.2.18.(a) Model a-helix, (b) hydrogen bonding contacts in tire helix, and (c) schematic representation of tire effective Hamiltonian interactions between atoms in tire protein backbone. From [23].

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. 

By using an effective, distance-dependent dielectric constant, the ability of bulk water to reduce electrostatic interactions can be mimicked without the presence of explicit solvent molecules. One disadvantage of aU vacuum simulations, corrected for shielding effects or not, is the fact that they cannot account for the ability of water molecules to form hydrogen bonds with charged and polar surface residues of a protein. As a result, adjacent polar side chains interact with each other and not with the solvent, thus introducing additional errors. 

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