Peptides hydration

The success of our calculations and the availability of more extensive computational resources has led to extending this research to larger molecules. Figure 7 shows optimized supermolecule structures for ala-ala peptide hydrated with water (R.W. Williams, A.H. Lowrey, unpublished results). A scaled force-field has been used to calculate the frequencies for this molecule as a function of discrete values for the torsional angle /. The amide I frequencies do not change in this harmonic... 

Fig. 22.1. H 0 hydrogen-bond length distributions in carbohydrate, purine, pyrimidine, nucleoside, nucleotide and peptide hydrates. Note that OH - Ow

Table 22.3. Some water hydrogen bond configurations observed only in the amino acid and peptide hydrates. (Numbers in parentheses are the number of examples observed)...

Mild K, Westh P, KogaY (2008) Interactions of Na-salts and 1-propanol in l-propanol-Na-salt-H20 systems toward an understanding of the Hofmeister series (IV). J Phys Chem B 112 4680-4686 Modig K, Liepinsh E, Otting G, HaUe B (2004) Dynamics of protein and peptide hydration. J Am Chem Soc 126 102-114... 

PEPTIDE HYDRATES. INFLUENCE OF THE HYDRATION STATE ON THE PROPERTIES OF ALPHA-AMINOBENZYL-PENICILLIN. 

Fig. 1 Selected IR/UV spectra of isolated peptides, hydrates and clusters in various spectral ranges. Far-IR (a) conformer X of the Ac-Phe-NH2 monohydrate [51] amide I and II. (b) Ac-Ala-Phe-NH-Me dipeptide (adapted from [52] with permission of AIP), amide A NH stretch region, (c) Ac-Phe-NH2 H2O (X) (adapted from [53] with the permission of ACS), (d) Gramicidin S (adapted from [54] with the permission of Wiley), (e) H-Trp-OH (methanol) clusters. Adapted from [55] with the permission of ACS...

Bella, J., Brodsky, B., Berman, H.M. Hydration structure of a collagen peptide. Structure 3 893-906, 1995. 

Calcium-binding proteins, 6, 564, 572, 596 intestinal, 6, 576 structure, 6, 573 Calcium carbonate calcium deposition as, 6, 597 Calcium complexes acetylacetone, 2, 372 amides, 2,164 amino acids, 3, 33 arsine oxides, 3, 9 biology, 6, 549 bipyridyl, 3, 13 crown ethers, 3, 39 dimethylphthalate, 3, 16 enzyme stabilization, 6, 549 hydrates, 3, 7 ionophores, 3, 66 malonic acid, 2, 444 peptides, 3, 33 phosphines, 3, 9 phthalocyanines, 2,863 porphyrins, 2, 820 proteins, 2, 770 pyridine oxide, 3,9 Schiff bases, 3, 29 urea, 3, 9... 

The cytoplasmic domains reconstructed from negatively stained [90] and from frozen-hydrated samples [91,177] have similar shapes. Both include the protruding lobe and the bridge region that links the Ca " -ATPase molecules into dimers. The intramembranous peptide domains of the two ATPase molecules which make up a dimer spread apart as they pass through the bilayer toward the luminal side of the membrane, establishing contacts with the Ca -ATPase molecules in the neighboring dimer chains. The lateral association of dimer chains into extended crystal lattice is... 

Another PDF inhibitor series derived from comparisons with known metalloprotease inhibitor classes has been reported by Merck [68]. Their study investigated a small set of peptide aldehyde inhibitors, postulating that the aldehyde might bind to the metal centre in the form of a hydrate,... 

McCracken, P. G. Bolton, J. L. Thatcher, G. R. J. Covalent modification of proteins and peptides by the quinone methide from 2-ZerZ-butyl-4,6-dimethylphenol selectivity and reactivity with respect to competitive hydration, j. Org. Chem. 1997, 62, 1820-1825. 

K. Mizutani, T. Electronic and structural requirements for metabolic activation of butylated hydroxytoluene analogs to their quinone methides, intermediates responsible for lung toxicity in mice. Biol. Pharm. Bull. 1997, 20, 571-573. (c) McCracken, P. G. Bolton, J. L. Thatcher, G. R. J. Covalent modification of proteins and peptides by the quinone methide from 2-rm-butyl-4,6-dimethylphenol selectivity and reactivity with respect to competitive hydration. J. Org. Chem. 1997, 62, 1820-1825. (d) Reed, M. Thompson, D. C. Immunochemical visualization and identification of rat liver proteins adducted by 2,6-di- m-butyl-4-methylphenol (BHT). Chem. Res. Toxicol. 1997, 10, 1109-1117. (e) Lewis, M. A. Yoerg, D. G. Bolton, J. L. Thompson, J. Alkylation of 2 -deoxynucleosides and DNA by quinone methides derived from 2,6-di- m-butyl-4-methylphenol. Chem. Res. Toxicol. 1996, 9, 1368-1374. 

Solid state 13C CPMAS NMR spectra of Wheat High Molecular Weight (W.HMW) subunits show well resolved resonances identical with spectra of dry protein and peptide samples [24], Most of the amino acids side-chain resonances are found in the 0-35 ppm region followed by the alpha resonances of the most abundant amino acids glycine, glutamine and proline at chemical shifts of 42, 52 and 60 ppm, respectively, and the carbonyl carbons show a broad peak in 172-177 ppm region. The CPMAS spectra of hydrated whole HMW provides important information on the structural characteristics. 

Kostic et al. recently reported the use of various palladium(II) aqua complexes as catalysts for the hydration of nitriles.456 crossrefil. 34 Reactivity of coordination These complexes, some of which are shown in Figure 36, also catalyze hydrolytic cleavage of peptides, decomposition of urea to carbon dioxide and ammonia, and alcoholysis of urea to ammonia and various carbamate esters.420-424, 427,429,456,457 Qggj-jy palladium(II) aqua complexes are versatile catalysts for hydrolytic reactions. Their catalytic properties arise from the presence of labile water or other solvent ligands which can be displaced by a substrate. In many cases the coordinated substrate becomes activated toward nucleophilic additions of water/hydroxide or alcohols. New palladium(II) complexes cis-[Pd(dtod)Cl2] and c - Pd(dtod)(sol)2]2+ contain the bidentate ligand 3,6-dithiaoctane-l,8-diol (dtod) and unidentate ligands, chloride anions, or the solvent (sol) molecules. The latter complex is an efficient catalyst for the hydration and methanolysis of nitriles, reactions shown in Equation (3) 435... 

Considering only the lipid phase as the transport pathway for the peptide, as the solute enters and diffuses across the membrane it will encounter a number of different microenvironments. The first is the aqueous membrane interface (Fig. 23). In this region, the hydrated polar headgroups of the membrane phospholipids separate the aqueous phase from the apolar membrane interior. It has been shown that this region is capable of satisfying up to 70% of the hydrophobic effect... 

Three theory papers are also included. Determinants of the Polyproline II Helix from Modeling Studies by Creamer and Campbell reexamines and extends an earlier hypothesis about Pn and its determinants. Hydration Theory for Molecular Biophysics by Paulaitis and Pratt discusses the crucial role of water in both folded and unfolded proteins. Unfolded State of Peptides by Daura et al. focuses on the unfolded state of peptides studied primarily by molecular dynamics. 

Thomas, S. T., Loladze, V. V., and Makhatadze, G. I. (2001). Hydration of the peptide backbone largely defines the thermodynamic propensity scale of residues at the i position of the c-capping box of a helices. Proc. Natl. Acad. Sci. USA 98, 10670-10675. 

McAllister, M. A., Perczel, P. Csaszar, W. Viviani, J.-L. Rivail, and I. G. Csizmadia. 1993b. Peptide Models 4. Topological Features of Molecular Mechanics and Ab Initio 2D-Ramachandran Maps. Conformational Data for For-Gly-NH2, For-L-Ala-NH2, Ac-l-Ala-NHMe and For-L-Val-NH2. J. Mol. Struct. (Theochem) 288, 161-179. Mehrotra, P. K., M. Mezei, and D. L. Beveridge. 1984. Monte Carlo Determination of the Internal Energies of Hydration for the Ala Dipeptide in the C7, C5, aR, and Pn Conformations. Int. J. Quantum Chem. Quantum Biol. Symp. 11, 301-308. 

Several works have been reported for macroscopically orientated biological membranes.106-109 The biomembrane alignment can be carried out mechanically or magnetically. The first one relies on the deposition of lipid bilayers on the surface of a rigid support (glass plates) such that the bilayer normal is perpendicular to the surface of the support itself. Small peptides and the lipid bilayers can be dissolved in organic solvents which are successively removed under vacuum.105 The re-hydration of the system in a chamber of an optimized temperature, humidity and time gives rise to the desired orientation. 

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