Structural characterization of alpha-helices of implicitly solvated poly-alanine

Article Abstract:

The structural characterization of alpha-helices in poly-alanine-based peptides were investigated through molecular dynamics simulation to understand the basic features of peptide simulations and the formation and stabilization of alpha-helices in short peptides. Results reveal that within the context of classical generalized Born (GB) simulations the alpha-helix was not inherently stable at room-temperature, although it is a common secondary structural motif in equilibrium with turn and extended structures.

Alanine, Chemical properties

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Analysis and parametric optimization of [.sup.1.H] off-resonance relaxation NMR experiments designed to map poplypeptide self-recognition and other noncovalent interactions

Article Abstract:

The measurement of [.sup.1.H] off-resonance nonselective relaxation rates is proposed as an effective method to probe peptide self-recognition, opening new perspectives in the understanding of the prefibrillization oligomerization processes in amylodogenesis. Results reveal that the tilt angle [theta] = 35.5 degree is optimal not only for the suppression of spin-diffusion effects but also for the preservation of good adiabaticity, the J-transfer suppression, and the sensitivity to peptide self-recognition.

Usage, Observations, Amyloidosis, Nuclear magnetic resonance

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Diffusion-limited unbinding of small peptides from PDZ domains

Article Abstract:

The influence of native state topology on the thermodynamics and dissociation kinetics for a PDZ/peptide complex analyzed by using molecular dynamics simulations based on a coarse-grained description of PDZ domains is presented. Results reveal that the bound state is stabilized over a physiologically relevant temperature interval.

Chemical thermodynamics

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