Showing papers on "Salt bridge (protein and supramolecular) published in 2004"

The mighty arginine, the stable quaternary amines, the powerful aromatics, and the aggressive phosphate: their role in the noncovalent minuet.

Abstract: In the age of proteomics, the role of certain amino acid residues and some post-translational modifications in noncovalent complex formation are gaining in importance, as the understanding of interactions between biological molecules, is at the heart of the structure function relationship puzzle. In this work, mass spectrometry is used to highlight ammonium− or guanidinium−aromatic interactions through Cation-π bonds and ammonium− or guanidinium−phosphate interactions through salt bridge formation. Such interactions are crucial factors in certain ligand−receptor interactions and receptor−receptor interactions. In addition, the ability of phosphorylated residues and phosphorylated lipids to form noncovalent complexes with guanidinium and quaternary ammonium (mostly through Coulombic interactions) is demonstrated, and could explain the stability of certain membrane embedded protein, or a possible role for phosphorylation in protein−protein interactions. Dougherty's work demonstrates cation−π interactions in...

Gas-Phase Zwitterions in the Absence of a Net Charge

Abstract: The ground state for neutral, isolated molecules in the gas phase can be zwitterionic under appropriate conditions. Quantum chemical calculations show that increasing the basicity of the basic component of a zwitterion leads to enhanced stability for the charge-separated state, which can lead to a ground-state zwitterion. Density functional theory calculations show that methylation of the side chain of arginine is sufficient to induce a ground-state zwitterion. The results for the stepwise methylation of arginine are given, and clearly illustrate enhanced zwitterion stabilization with increasing basicity. In protonated systems, guanidinylation of the N-terminus of arginine yields a salt bridge or charge-stabilized zwitterion structure. The enhanced basicity of guanidino versus amino groups is responsible for the charge separation in this case, which is not observed to be the ground state for protonated arginine itself. These results indicate that charge separation can be favorable in the gas phase and are discussed in light of future experimental efforts.

Simulation of Molecular Dynamics of the Tetrapeptide Ala-Gly-Asp-Pro

Abstract: A quantum-chemical calculation procedure intended for studying geometries and electronic structures of various peptides was tested using the tetrapeptide Ala-Gly-Asp-Pro as example The trajectory of the molecular dynamics of the Ala-Gly-Asp-Pro molecule in the surrounding of water molecules was followed for a period of 1500 ps The conformation of the peptide molecule does not change within this period The water surrounding of the Ala-Gly-Asp-Pro molecule prevents formation of an intramolecular salt bridge between the nitrogen atom of the terminal amino group and oxygen atoms of the side carboxy group of Asp It is suggested that the mechanism of the physiological action of Ala-Gly-Asp-Pro may involve hydrogen bonding with one or several functional groups of this molecule

Peptides enhancing CEH activity, pharmaceutical compositions comprising these peptides and their use in the treatment of atherosclerosis

Abstract: There is disclosed an isolated peptide or a mimetic thereof which enhances cholesterol ester hydrolase activity, said isolated peptide comprising a formula: X1X2X3X4X5X6X7X8X9X10X11X12X13X14X15X16X17X18 (SEQ ID NO: 29) or a portion thereof wherein X1 and X9, X12 or X18 are amino acids capable of forming a salt bridge; X6 is glutamic acid or lysine or an amino acid which is a conservative substitution thereof; and X2, X3, X4, X5, X7, X8, X10, X11, X13, X14, X15, X16, and X17 are independently any amino acid, and wherein the isolated peptide or mimetic thereof has less than 80 amino acid residues with the proviso that said isolated peptide does not consist of: