Hello,
I am pretty new to molecular dynamics and have a question regarding the
assignment of atomic partial charges to a deprotonated aspartate residue
in a protein. In general, it makes total sense, that both oxygens (OD1,
OD2) receive the same charge of about -0.8, as the negative charged is
delocalized and evenly distributed between the two residues. But this
assignment together with using an non-polarizable ff like Amber poses
problems with my simulation: My protein has a heteroatom in its
catalytic cleft (Zn2+) whose coordination is very well known from former
research. Among others, it is coordinated by two histidines of the
protein (two of the six coordination sites) and of ONE of the
aspartate's oxygens (OD1 or OD2, ONE of the six coordination sites). The
expectation is, that OD1 or OD2 starts coordinating the Zn2+ which in
turn leads to a shift of the negative charge towards this coordinating
oxygen and the interaction is stable (one oxygen interacting with Zn2+,
the other NOT). But in the simulation the assignment of the same and
permanent charge of about -0.8 to OD1 and OD2 leads to the effect, that
both oxygen atoms coordinate the Zn2+ and take up one interaction site
too much, which destroys the assembly of the catalytic cleft.
Is it feasible to assign different atomic partial charges to the two
oxygen atoms? E.g. ones which would correspond to one of the
contributing resonance structures where the negative charge is shifted
stronger towards one of the oxygens?
All the best,
Margareta
--
Margareta Hellmann
PhD student, AG Moerschbacher
Institute of Plant Biology and Biotechnology (IBBP)
University of Münster
Schlossplatz 8
48143 Münster, Germany
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Received on Mon Oct 05 2020 - 08:00:02 PDT
