Use of multiple molecular dynamics trajectories to study biomolecules in solution: the YTGP peptide

Article Abstract:

A study was conducted to analyze the YTGP tetrapeptide in aqueous solution using multiple molecular dynamics trajectories. Random coil values were utilized to determine the chemical shifts for the protons in an unstructured peptide. Trajectories were generated by propagation for 300 ps at 300 K an 1 atm. Experimental results indicated that the structural shift spectra for different conformation states correlated with the experimental spectrum.

Research, Peptides, Biomolecules

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Temperature dependence of looping rates in a short peptide

Article Abstract:

The temperature-dependent looping rates of the Dbo-AlaGlyGln-Trp-N[H.sub.2] peptide (where Dbo = 2,3-diazabicyclo-[2.2.2]oct-2-ene-labeled asparagine) is investigated by using a mix of time-resolved spectroscopy and molecular dynamics (MD) simulations techniques. It is observed that the diffusion-limited rate and associated activation energy of any initial protein folding step depends on the amino acid sequence.

Polypeptides, Amino acid sequence, Amino acid sequencing, Mechanical properties, Structure

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Measuring coexisting densities from a two-phase molecular dynamics simulation by Voronoi tessellations

Article Abstract:

A new algorithm is described for determining bulk liquid and vapor densities from a two-phase Molecular Dynamics simulation. The new method has utilized Voronoi tessellations to determine the molecular volume of every point at every instance in a molecular dynamics simulation.

Usage, Vapors, Properties, Vapours, Tessellations (Mathematics)

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