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The crn-1 mutant is modeled by setting k6 = 0.
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The biggest challenge with the H300N mutant is modeling the second step of the reaction, as the conventional general base of the enzyme has been removed and the hydrolytic water is lacking.
The GPA2 Q 300 L (Gpa2 constitutively active) mutant was modeled by setting the concentration of GPa to 1 and the parameter V maxGPdeact to 0. The pde2Δ mutant model was simulated as described earlier.
Active EGFR-TKD was modelled on the basis of PDB entries 1M17 (which also provided the initial erlotinib conformation) [ 10] and 2ITX [ 11], and the L834R mutant was modelled on the basis of PDB entry 2ITV [ 11].
DsbG K113N, Q214R, V199A, and KQ mutants were modeled from DsbG crystal structure (PDB 1V57) (11) using Modeler 9.13 (32), as described in the Modeler tutorial (basic modeling).
The reaction kinetics of all the mutants were modeled, and the pH and thermal stabilities of all the mutants were analyzed.
The wild type and mutants were modeled separately.
Mutants were modeled by replacing the side-chain of the mutated residue using the PDBviewer program [28].
The Myo1-E1 and Myo1-S1 mutants were modeled after the severe Myo2-E1 and mild Myo2-S1 mutants of S. pombe myosin-II Myo2 (Balasubramanian et al., 1998; Wong et al., 2000).
The mutant strain is modelled by removing the influence R3 in the dephosphorylation of KdpEp.
The spatial structures of both wild-type and mutant proteins were modeled by the online SWISS-MODEL tool (http://swissmodel.expasy.org/), base on temple: 2lduA (99.9 A).
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