NDLI: A Molecular Dynamics Method for Calculating Molecular Volume Changes Appropriate for Biomolecular Simulation

Content Provider	PubMed Central
Author	Devane, Russell Ridley, Christina Larsen, Randy W. Space, Brian Moore, Preston B. Chan, Sunney I.
Copyright Year	2003
Abstract	Photothermal methods permit measurement of molecular volume changes of solvated molecules over nanosecond timescales. Such experiments are an important tool in investigating complex biophysical phenomena including identifying transient species in solution. Developing a microscopic understanding of the origin of volume changes in the condensed phase is needed to complement the experimental measurements. A molecular dynamics (MD) method exploiting available simulation methodology is demonstrated here that both mimics experimental measurements and provides microscopic resolution to the thermodynamic measurements. To calculate thermodynamic volume changes over time, isothermal-isobaric (NPT) MD is performed on a solution for a chosen length of time and the volume of the system is thus established. A further simulation is then performed by “plucking” out a solute molecule of interest to determine the volume of the system in its absence. The difference between these volumes is the thermodynamic volume of the solute molecule. NPT MD allows the volume of the system to fluctuate over time and this results in a statistical uncertainty in volumes that are calculated. It is found in the systems investigated here that simulations lasting a few nanoseconds can discern volume changes of ∼1.0 ml/mole. This precision is comparable to that achieved empirically, making the experimental and theoretical techniques synergistic. The technique is demonstrated here on model systems including neat water, both charged and neutral aqueous methane, and an aqueous β-sheet peptide.
Related Links	http://dx.doi.org/10.1016/s0006-3495(03)74703-1
Ending Page	2807
Page Count	7
Starting Page	2801
File Format	PDF
ISSN	00063495
e-ISSN	15420086
Journal	Biophysical Journal
Issue Number	5
Volume Number	85
Language	English
Publisher	Biophysical Society
Publisher Date	2003-11-01
Access Restriction	Open
Rights Holder	Biophysical Society
Subject Keyword	Biophysics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Biophysics

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