Modification of peptide sequence offers versatile control over their self-organization capability within adlayers adsorbed on surfaces. However, to gain full the self-organization, clear links between and lateral ordering in these must be established. Using molecular dynamics simulations WA or AW dipeptides, spontaneous emergence ordered nano-patterns containing neutral, zwitterion, neutral-zwi...

A fundamental question in protein science is what is the intrinsic propensity for an amino acid to be in an α-helix, β-sheet, or other backbone dihedral angle ( ϕ-ψ) conformation. This question has been hotly debated for many years because including all protein crystal structures from the protein database, increases the probabilities for α-helical structures, while experiments on small peptides...

We present an analysis of the thermodynamics, conformational dynamics, and kinetics of the solvated alanine dipeptide molecule. Solvation was treated in the framework of the OPLS/analytic generalized born with nonpolar interactions effective potential model. The effective free energy map was generated in a series of multiwindow umbrella sampling all-atom simulations using the weighted histogram...

Objective: To prepare a new series of [Cu(L-dipeptide)(5-NO2-phen)] complexes and study the influence of the nitro group on the structure, DNA interaction and cytotoxic activity, aimed at finding new copper compounds with antitumor activity. Methodology and results: A series of mononuclear mixed ligand copper(II) complexes of the type [Cu(L-dipeptide)(5-NO2-phen)]∙nH2O (where L-dipeptide: Ala-P...

To investigate dipeptide assimilation by the liver, a series of interrelated experiments were performed in rats. Partial hepatectomy prolonged the plasma halflife (min) of Gly-Ala (3.42 f 0.22 uersus 4.90 f 0.35, p < 0.05) but had no significant effect on plasma halflife of Gly-Leu, Gly-Pro, or Gly-Sar. We then investigated the rate of disappearance (pmol*(g liver. h)”) of the above four dipept...

Vancomycin is a glycopeptide antibiotic used for the treatment of serious infections by Gram-positive pathogens. Vancomycin inhibits cell wall biosynthesis by targeting the d-Ala-d-Ala terminus of peptidoglycan (PG). The highly cross-linked heptapeptide aglycon structure of vancomycin is the d-Ala-d-Ala binding site. The first residue of vancomycin is N-methyl-leucine, which is crucial for the ...

Nuclear receptors are key transcription factors that regulate crucial gene networks responsible for cell growth, differentiation, and homeostasis. Nuclear receptors form a superfamily of phylogenetically related proteins and control functions associated with major diseases (e.g. diabetes, osteoporosis, and cancer). In this study, a novel method has been developed for classifying the subfamilies...

The premise that a dietary dipeptide approach will improve the understanding of amino acid utilization in the fastest-growing vertebrate, the teleost fish, was tested by examining the muscle free amino acid (FAA) pool and enzyme activities, in concert with growth response, when dietary amino acids were provided in free, dipeptide or protein molecular forms. We present the first evidence in fish...

YjdL from E. coli is an unusual proton-coupled oligopeptide transporter (POT). Unlike prototypical POTs, dipeptides are preferred over tripeptides, in particular dipeptides with a positively charged C-terminal residue. To further understand this difference in peptide specificity, the sequences of YjdL and YdgR, a prototypical E. coli POT, were compared in light of the crystal structure of a POT...