alanyl-alanyl-alanine and alanylalanine

X-ray free-electrons lasers have revolutionized the method of imaging biological macromolecules such as proteins, viruses and cells by opening the door to structural determination of both single particles and crystals at room temperature. By utilizing high intensity X-ray pulses on femtosecond timescales, the effects of radiation damage can be reduced. Achieving high resolution structures will likely require knowledge of how radiation damage affects the structure on an atomic scale, since the experimentally obtained electron densities will be reconstructed in the presence of radiation damage. Detailed understanding of the expected damage scenarios provides further information, in addition to guiding possible corrections that may need to be made to obtain a damage free reconstruction. In this work, we have quantified the effects of ionizing photon-matter interactions using first principles molecular dynamics. We utilize density functional theory to calculate bond breaking and charge dynamics in three ultracharged molecules and two different structural conformations that are important to the structural integrity of biological macromolecules, comparing to our previous studies on amino acids. The effects of the ultracharged states and subsequent bond breaking in real space are studied in reciprocal space using coherent diffractive imaging of an ensemble of aligned biomolecules in the gas phase.

Topics: Cysteine; Density Functional Theory; Dipeptides; Models, Chemical; Molecular Dynamics Simulation; Oligopeptides; Protein Conformation; Static Electricity; Time Factors

We propose a general framework for the efficient sampling of conformational equilibria in complex systems and the generation of associated free energy hypersurfaces in terms of a set of collective variables. The method is a strategic synthesis of the adiabatic free energy dynamics approach, previously introduced by us and others, and existing schemes using Gaussian-based adaptive bias potentials to disfavor previously visited regions. In addition, we suggest sampling the thermodynamic force instead of the probability density to reconstruct the free energy hypersurface. All these elements are combined into a robust extended phase-space formalism that can be easily incorporated into existing molecular dynamics packages. The unified scheme is shown to outperform both metadynamics and adiabatic free energy dynamics in generating two-dimensional free energy surfaces for several example cases including the alanine dipeptide in the gas and aqueous phases and the met-enkephalin oligopeptide. In addition, the method can efficiently generate higher dimensional free energy landscapes, which we demonstrate by calculating a four-dimensional surface in the Ramachandran angles of the gas-phase alanine tripeptide.

Topics: Dipeptides; Enkephalins; Gases; Hot Temperature; Models, Molecular; Oligopeptides; Protein Conformation; Thermodynamics; Water

A molecular mechanics (MM) force field-based empirical electrostatic potential map (MM map) for amide-I vibrations is developed with the aim of seeking a quick and reasonable approach to computing local mode parameters and their distributions in solution phase. Using N-methylacetamide (NMA) as a model compound, the instantaneous amide-I normal-mode parameters (transition frequency and dipole) obtained at the level of MM force fields are converted to solution phase values by a four-site potential scheme, but without the need for quantum mechanical frequency computations of solute-solvent clusters as are required in constructing ab initio-based electrostatic potential or field maps. The linear IR line shape of the amide-I mode in NMA obtained from the frequency-time correlation function on the basis of the MM map are found to be comparable to those from the ab initio-based maps. Our results show that the amide-I local mode parameters are largely determined by the solvated peptide structure rather than by explicit solvent molecules, suggesting an inherent local structure sensitivity of the amide-I mode in solvated peptides. Applications to alanine di- and tripeptides are satisfactorily demonstrated, showing its usefulness as an alternative approach in providing vibrational parameters for the simulation of linear IR and 2D IR spectra of the amide-I modes in polypeptides.

Topics: Acetamides; Amides; Dimethyl Sulfoxide; Dipeptides; Molecular Dynamics Simulation; Oligopeptides; Protein Conformation; Solutions; Solvents; Spectroscopy, Fourier Transform Infrared

The H(+)/peptide cotransporters PEPT1 and PEPT2 have gained considerable interest in pharmaceutical sciences as routes for drug delivery. It is, therefore, of interest to develop uncommon artificial substrates for the two carriers. This study was initiated to investigate the binding affinity of 2-aminothiazole-4-acetic acid (ATAA) conjugates with amino acids to PEPT1 and PEPT2. The 2-aminothiazole-4-acetic acid derivatives have been synthesised and tested for their affinity to PEPT1 and PEPT2. The K(i) values were compared with in silico predicted values from CoMSIA models. C-terminal ATAA-Xaa conjugates proved to be low to medium inhibitors of the [(14)C]Gly-Sar uptake at both carrier systems whereas N-terminal Xaa-ATAA conjugates exhibited medium to high affinity. A promising candidate for further functionalisation is Val-ATAA which shows extraordinary high affinity to PEPT1.

Topics: Amino Acids; Animals; Anti-Bacterial Agents; Biological Transport; Caco-2 Cells; Ceftibuten; Cells, Cultured; Cephalosporins; Dipeptides; Humans; Kidney Tubules, Proximal; Kinetics; Models, Molecular; Molecular Structure; Oligopeptides; Peptide Transporter 1; Protein Binding; Rats; Symporters

Our aim was to compare the repertoires of conformers formed by the model zwitterionic peptides AA and AAA in aqueous solution with the conformational profiles of a range of their peptide isosteres, so as to facilitate selection of isosteres for synthesis and testing as biologically stable surrogates of bioactive di- and tripeptides. Comparisons were based upon the results of conformational analysis using a random search approach implemented within the SYBYL molecular modelling package, using zwitterionic molecules, simulated aqueous solvation using a dielectric constant of 80 and allowing all torsions to vary. For each compound, individual conformers were grouped on the basis of specific combinations of psi, phi and omega torsions and, using their energies, the aggregated percentage for each group was calculated using a Boltzmann distribution and displayed using a 3D pseudo Ramachandran plot relating percentage conformer to psi and phi torsions. Retroamide, N-methylamide and thioamide isosteres showed the best match to natural peptides and to the molecular recognition parameters defined for substrates of peptide transporters. The results should aid rational design of therapeutic agents in various areas, e.g. oral delivery of drugs by peptide transporters and of peptidase inhibitors. This approach may usefully be applied to various biochemical and pharmaceutical topics.

Topics: Dipeptides; Drug Design; Models, Molecular; Molecular Mimicry; Oligopeptides; Peptides; Protein Conformation; Structure-Activity Relationship

A variety of oligopeptides are probably released within the intestinal tissue under inflammatory conditions or during peptide absorption. To examine whether some of these peptides can affect intestinal transport functions, we determined the effects of L-alanine oligopeptide on short-circuit current (I(sc)) and transmucosal conductance (G(t)) in submucosa-mucosa preparations from the mouse cecum and guinea pig distal colon in vitro in Ussing chambers. L-Alanyl-L-alanine (Ala-Ala, 10 mM) added to the serosal side increased I(sc) and G(t), giving a peak followed by a sustained phase (the peak increase in I(sc) was 45 +/-6 microA/cm(2) and the increase in G(t) was 0.55+/-0.11 mS/cm(2)). The tripeptide, L-alanyl-L-alanyl-L-alanine (Ala-Ala-Ala, 10 mM), added to the serosal side also induced increases in I(sc) and G(t) by a similar degree. On the other hand, luminal Ala-Ala, and serosal L-alanine and L-alanine (10 mM) caused significantly smaller increases in I(sc) and G(t) ( approximately 15 microA/cm(2) and approximately 0. 15 mS/cm(2), respectively). The Ala-Ala induced increase in I(sc) was partially inhibited by serosal bumetanide (0.1 mM) and mucosal 5-nitro-2-(3-phenylpropylamino)benzoic acid (0.1 mM), and largely suppressed by removing Cl(-) from the bathing solution. The increase in I(sc) was largely suppressed by serosal low Ca(2+) and tetrodotoxin, but was not affected by indomethacin. In the guinea pig distal colon, serosal Ala-Ala (10 mM) evoked a transient increase in I(sc) by 23+/-7 microA/cm(2) and an increase in G(t) by 1.2+/-0.3 mS/cm(2). These results suggest that Ala-Ala, and probably also Ala-Ala-Ala, added to the serosal side stimulated electrogenic Cl(-) secretion mainly through the activation of submucosal secretomotor neurons in the mammalian large intestine.

Topics: Alanine; Animals; Antioxidants; Biological Transport; Bumetanide; Carrier Proteins; Cecum; Chlorides; Dipeptides; Diuretics; Dose-Response Relationship, Drug; Enteric Nervous System; Guinea Pigs; Intestinal Mucosa; Intestine, Large; Male; Mammals; Mice; Oligopeptides; Sodium-Potassium-Chloride Symporters; Sucrose; Taurine

The di-, tri-, and tetrapeptides of L-alanine have been studied in aqueous solution by 13C n.m.r. spectroscopy at 25 and 50 MHz. By using selectively 13C enriched analogs containing either 90% 13C methyl or carbonyl carbons and measurements as a function of pH, assignment of the chemical shifts of the peptides has been made. T1 and NOE measurements of the peptides in their cationic, anionic, and zwitterionic states have been recorded as a function of concentration. The results show considerable segmental motion along the backbone carbons of the peptides, with only small changes occurring in the dynamic motions of the peptides as their charge states are altered. The lack of concentration dependence of the chemical shift and T1 values, as well as the similarity of T1 values for individual peptides in the three charge states, indicate that the peptides do not self-associate in aqueous solution.

Topics: Alanine; Dipeptides; Hydrogen-Ion Concentration; Magnetic Resonance Spectroscopy; Oligopeptides; Protein Conformation; Structure-Activity Relationship