کد مقاله کد نشریه سال انتشار مقاله انگلیسی نسخه تمام متن
503407 863764 2007 4 صفحه PDF دانلود رایگان
عنوان انگلیسی مقاله ISI
Simulating botulinum neurotoxin with constant pH molecular dynamics in Generalized Born implicit solvent
موضوعات مرتبط
مهندسی و علوم پایه شیمی شیمی تئوریک و عملی
پیش نمایش صفحه اول مقاله
Simulating botulinum neurotoxin with constant pH molecular dynamics in Generalized Born implicit solvent
چکیده انگلیسی

A new method was proposed by Mongan et al. for constant pH molecular dynamics simulation and was implemented in AMBER 8 package. Protonation states are modeled with different charge sets, and titrating residues are sampled from a Boltzmann distribution of protonation states. The simulation periodically adopts Monte Carlo sampling based on Generalized Born (GB) derived energies. However, when this approach was applied to a bio-toxin, Botulinum Neurotoxin Type A (BoNT/A) at pH 4.4, 4.7, 5.0, 6.8 and 7.2, the pKapKa predictions yielded by the method were inconsistent with the experimental values. The systems being simulated were divergent. Furthermore, the system behaviors in a very weak acidic solution (pH 6.8) and in a very weak basic solution (pH 7.2) were significantly different from the neutral case (pH 7.0). Hence, we speculate this method may require further study for modeling large biomolecule.

ناشر
Database: Elsevier - ScienceDirect (ساینس دایرکت)
Journal: Computer Physics Communications - Volume 177, Issues 1–2, July 2007, Pages 210–213
نویسندگان
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