Talk:Team:UANL Mty-Mexico/Modeling/3Dmodel/Metal-binding

Metal-binding behaviour

Methodology
We used the FoldX force field (Schymkowitz et al. 2005) to predict the metal-binding sites and energies of the predicted partial tertiary structure of rhM. The ionic strength, and pH were adjusted in order to simulate the experimental conditions, we tested the following algorithm replacing the field [M] (6th line) with the  atoms Ca, Mg, Mn, Na, Zn, Fe, Cu, Co, K, also considering the changes in the ionic strength.

<TITLE>FOLDX_runscript;
<JOBSTART>rhMT1a;
<PDBS>rhMT.pdb;
<BATCH>list1.txt
<COMMANDS>FOLDX_commandfile;
<metalbinding_analysis>rhMT1a,[M];
<MetalBindingEnergy>rhMT1a;
<END>rhMT1a;
<OPTIONS>FOLDX_optionfile;
<Temperature>298;
<R>
<pH>6;
<IonStrength>0.00000125;
<metal>-PREDICT;
<water>-PREDICT;
<num_water_partners>2;
<no_Cterm>false;
<no_Nterm>false;
<OutPDB>true;
<pdb_hydrogens>false;
<pdb_waters>false;
<pdb_hydrogens>false;
<overwriteBatch>false;
<pdb_dummys>false;
<END>rhMT1a;
<JOBEND>rhMT1a;
<ENDFILE>FOLDX_runscript;

Results
The algorithm described below did not predict any metal-binding site. Presumably due to the lack of “precision” of the partial model. We expect to obtain metalbinding sites by obtaining more accurate models of rhMT.