By a News Reporter-Staff News Editor at Physics Week -- Current study results on Molecular Mechanics have been published. According to news reporting originating from Hamilton, Canada, by VerticalNews correspondents, research stated, "We present a quantum mechanics/molecular mechanics (QM/MM) method to evaluate the partial charges of amino acid residues for use in MM potentials based on their protein environment. For each residue of interest, the nearby residues are included in the QM system while the rest of the protein is treated at the MM level of theory."
Our news editors obtained a quote from the research from McMaster University, "After a short structural optimization, the partial charges of the central residue are fit to the electrostatic potential using the restrained electrostatic potential (RESP) method. The resulting charges and electrostatic potential account for the individual environment of the residue, although they lack the transferable nature of library partial charges. To evaluate the quality of the QM/MM RESP charges, thermodynamic integration is used to measure the pK(a) shift of the aspartic acid residues in three different proteins, turkey egg lysozyme, beta-cryptogein, and Thioredoxin."
According to the news editors, the research concluded: "Compared to the AMBER ff99SB library values, the QM/MM RESP charges show better agreement between the calculated and experimental pK(a) values for almost all of the residues considered."
For more information on this research see: Quantum Mechanics/Molecular Mechanics Restrained Electrostatic Potential Fitting. Journal of Physical Chemistry B, 2013;117(48):14960-14966. Journal of Physical Chemistry B can be contacted at: Amer Chemical Soc, 1155 16TH St, NW, Washington, DC 20036, USA. (American Chemical Society - www.acs.org; Journal of Physical Chemistry B - www.pubs.acs.org/journal/jpcbfk)
The news editors report that additional information may be obtained by contacting S.K. Burger, McMaster University, Dept. of Chem & Chem Biol, Hamilton, ON L8S 4L8, Canada. Additional authors for this research include J. Schofield and P.W. Ayers.
Keywords for this news article include: Canada, Ontario, Hamilton, Nanotechnology, Quantum Physics, Quantum Mechanics, Molecular Mechanics, Emerging Technologies, North and Central America
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