|别名||DL-丙氨酰-DL-丙氨酸 ;DL-Alanyl-DL-alanine DL-丙氨酰-DL-氨基丙酸;DL-Alanyl-DL-alanine|
Replica-exchange is a powerful simulation method for sampling the basins of a rugged energy landscape. The replica-exchange method's sampling is efficient because it allows replicas to perform ro...Read More
The calculation of free-energy barriers by umbrella sampling and many other methods is hampered by the necessity for an a priori choice of the reaction coordinate along which to sample. We avoid this ...Read More
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 var...Read More
Insufficient oral bioavailability is considered as a key limitation for the widespread development of peptides as therapeutics. While the oral bioavailability of small organic compounds is often estim...Read More
Atomic multipoles: electrostatic potential fit, local reference axis systems, and conformational dependence.
Currently, all standard force fields for biomolecular simulations use point charges to model intermolecular electrostatic interactions. This is a fast and simple approach but has deficiencies when the...Read More
Biochemical characterisation of the chlamydial MurF ligase, and possible sequence of the chlamydial peptidoglycan pentapeptide stem.
Chlamydiaceae are obligate intracellular bacteria that do not synthesise detectable peptidoglycan although they possess an almost complete arsenal of genes encoding peptidoglycan biosynthetic activiti...Read More
A general, transferable coarse-grain (CG) framework based on the Gay-Berne potential and electrostatic point multipole expansion is presented for polypeptide simulations. The solvent effect is describ...Read More
We have applied the recently developed multiple state transition interface sampling approach to alanine dipeptide in explicit water. We extract the rate constant matrix for configurational changes bet...Read More
Conformational fluctuations of a protein molecule are important to its function, and it is known that environmental molecules, such as water molecules, ions, and ligand molecules, significantly affect...Read More
A redesigned vancomycin engineered for dual D-Ala-D-ala And D-Ala-D-Lac binding exhibits potent antimicrobial activity against vancomycin-resistant bacteria.
The emergence of bacteria resistant to vancomycin, often the antibiotic of last resort, poses a major health problem. Vancomycin-resistant bacteria sense a glycopeptide antibiotic challenge and remode...Read More
Nonlinear dimensionality reduction techniques can be applied to molecular simulation trajectories to systematically extract a small number of variables with which to parametrize the important dynamica...Read More
This work derives a quantitative description of the conformational distribution in self-guided Langevin dynamics (SGLD) simulations. SGLD simulations employ guiding forces calculated from local averag...Read More
The processes of negative ions formation of dipeptides glycyl-glycine, glycyl-alanine and alanyl-alanine in the conditions of resonant electron capture have been studied with a help of negative ions m...Read More
We extend the weighted ensemble (WE) path sampling method to perform rigorous statistical sampling for systems at steady state. A straightforward steady-state implementation of WE is directly practica...Read More
Synthesis of a d-Ala-d-Ala peptide isostere via olefin cross-metathesis and evaluation of vancomycin binding
The alkene peptide isostere for the d-Ala-d-Ala dipeptide was synthesized via a convergent approach utilizing olefin cross-metathesis. The new isostere was then evaluated for binding to the last resor...Read More
Infrared spectroscopy of the alanine dipeptide analog in liquid water with DFT-MD. Direct evidence for P(II)/beta conformations.
Following our previous work [J. Phys. Chem. B. Lett., 2009, 113, 10059], DFT-based molecular dynamics (DFTMD) simulations of 2-Ala peptide (i.e. Ac-Ala-NHMe dialanine peptide analog with methyl group ...Read More
Fluoroolefins as peptide mimetics. 2. A computational study of the conformational ramifications of peptide bond replacement.
The design of peptide mimetic compounds is greatly facilitated by the identification of functionalities that can act as peptide replacements. The fluoroalkene moiety has recently been employed for tha...Read More
Kinetic mechanism and inhibition of Mycobacterium?tuberculosis d-alanine:d-alanine ligase by the antibiotic d-cycloserine.
d-cycloserine (DCS) is an antibiotic that is currently used in second-line treatment of tuberculosis. DCS is a structural analogue of d-alanine, and targets two enzymes involved in the cytosolic stage...Read More
We implemented a GPU-powered parallel k-centers algorithm to perform clustering on the conformations of molecular dynamics (MD) simulations. The algorithm is up to two orders of magnitude faster than ...Read More
Umbrella integration is a method to analyze umbrella sampling simulations. It calculates free-energy changes from distributions obtained from molecular dynamics. While it can be formulated on the full...Read More
Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble.
The self-guided Langevin dynamics (SGLD) is a method to accelerate conformational searching. This method is unique in the way that it selectively enhances and suppresses molecular motions based on the...Read More
Reactivity of alanylalanine diastereoisomers in neutral and acid aqueous solutions: a versatile stereoselectivity.
A good comprehension of the reactivity of peptides in aqueous solution is fundamental in prebiotic chemistry, namely for understanding their stability and behavior in primitive oceans. Relying on the ...Read More
Probing peptide-inorganic surface interaction at the single molecule level using force spectroscopy.
We investigate the interaction between D-Ala-D-Ala peptide and a stainless steel (SS) surface by AFM force spectroscopy with view to understand the role and nature of interfacial processes at the sing...Read More
Bond dissociation of the dipeptide dialanine and its derivative alanine anhydride induced by low energy electrons.
Dissociative electron attachment to dialanine and alanine anhydride has been studied in the gas phase utilizing a double focusing two sector field mass spectrometer. We show that low-energy electrons ...Read More
Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.
We present a new type of the Hamiltonian replica-exchange method, where the van der Waals radius parameter and not the temperature is exchanged. By decreasing the van der Waals radii, which control sp...Read More
A review is presented to highlight several approaches for coupling capillary electrophoresis (CE) and electrospray ionization-mass spectrometry (ESI-MS) for analysis of chiral compounds. A short discu...Read More
Enantiomeric separation of chiral dipeptides by CE-ESI-MS employing a partial filling technique with chiral crown ether
Enantiomer of chiral dipeptides were separated by CE-ESI-MS in a bare fused-silica capillary using (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid (18C6H4) as the chiral selector. As 18C6H4 is a kind ...Read More
Synthesis and binding studies of two new macrocyclic receptors for the stereoselective recognition of dipeptides.
We present here the design, synthesis, and analysis of a series of receptors for peptide ligands inspired by the hydrogen-bonding pattern of protein β-sheets. The receptors themselves can be regarded...Read More