2.2 Comparative Homology Modeling and Role of Template
Very often the target protein crystallization is not possible, and no other way but
homology or comparative modeling of structure becomes imperative. Many standard tools and directions are reviewed, and appropriate protocols are included [53,
54]. Many such tools to evaluate the modeled structures are also discussed in the
literature [55, 56]. Here we shall cite a specific example showing importance of
choice of template using homology modeling applied for Mtb isocitrate dehydrogenase (ICD).
Mycobacterium tuberculosis is known to use the glyoxylate shunt during the
persistent stage [57]. Experiments have been performed to understand the glyoxylate shunt by considering the close analogy with Escherichia coli system [58].
For E. coli, glyoxylate shunt pathway is well studied and is initiated by phosphorylation of specific serine-105 residue of isocitrate dehydrogenase (ICD) [59].
Mycobacterium tuberculosis being a prokaryotic organism, same type of functionality was also expected for the glyoxylate bypass pathway [58, 60].
Phylogenetic analysis of the ICD sequences shows that Mtb has NADPdependent ICD which belongs to subfamily II of ICD. Subfamily II has predominantly eukaryotic members, while E. coli ICD is classified in subfamily I [61].
Across the family, ICDs are found to be functional either monomers or dimers.
E. coli, Mtb, and human all have functional homodimeric forms. Dimeric ICDs
contain active sites which are contributed by the residues of both domains. Though
Mtb ICD is regulated by phosphorylation process, it is more equivalent to
eukaryotic ICDs. Eukaryotic ICDs are not found to be regulated by the phosphorylation, and also mammalian system does not possess glyoxylate shunt [62]. So
overall evidence suggest that Mtb ICD has close similarity with eukaryotic system;
however, the presence of glyoxylate shunt pathway makes this system closer to
prokaryotic intracellular pathogenic survivor.
Understanding of shunt pathway shown that regulation of the Mtb’s ICD
depends upon the phosphorylation/de-phosphorylation state which is expected to be
regulated by some of available 11 serine/threonine phosphatase/kinases [63]. In
2009, Vinekar et al. had performed molecular dynamics simulation-based analysis
to understand the effect of selective phosphorylation of serine residues [62].
However, crystal structure of Mtb ICD was not available at that time (Table 2), so
homology modeling had been done using different crystal structures as templates to
select appropriate functional model.
The ultimate goal of the homology-based structure modeling is to model the
structure from its sequence with an accuracy that is comparable to the best results
achieved experimentally. As the crystal structure of Mtb ICD was unavailable,
homology-based structure modeling was the preferred way to understand the structural features of the ICD. For ICD modeling, target sequence (UniProt ID: P9WKL1)
was found to align with many sequences of already crystallized structures from both
prokaryote and eukaryote. Based on the homology rules of %-identity, functionality,
quality of the structure, and association with same taxonomy, three ICDs [64] were
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
119
Very often the target protein crystallization is not possible, and no other way but
homology or comparative modeling of structure becomes imperative. Many standard tools and directions are reviewed, and appropriate protocols are included [53,
54]. Many such tools to evaluate the modeled structures are also discussed in the
literature [55, 56]. Here we shall cite a specific example showing importance of
choice of template using homology modeling applied for Mtb isocitrate dehydrogenase (ICD).
Mycobacterium tuberculosis is known to use the glyoxylate shunt during the
persistent stage [57]. Experiments have been performed to understand the glyoxylate shunt by considering the close analogy with Escherichia coli system [58].
For E. coli, glyoxylate shunt pathway is well studied and is initiated by phosphorylation of specific serine-105 residue of isocitrate dehydrogenase (ICD) [59].
Mycobacterium tuberculosis being a prokaryotic organism, same type of functionality was also expected for the glyoxylate bypass pathway [58, 60].
Phylogenetic analysis of the ICD sequences shows that Mtb has NADPdependent ICD which belongs to subfamily II of ICD. Subfamily II has predominantly eukaryotic members, while E. coli ICD is classified in subfamily I [61].
Across the family, ICDs are found to be functional either monomers or dimers.
E. coli, Mtb, and human all have functional homodimeric forms. Dimeric ICDs
contain active sites which are contributed by the residues of both domains. Though
Mtb ICD is regulated by phosphorylation process, it is more equivalent to
eukaryotic ICDs. Eukaryotic ICDs are not found to be regulated by the phosphorylation, and also mammalian system does not possess glyoxylate shunt [62]. So
overall evidence suggest that Mtb ICD has close similarity with eukaryotic system;
however, the presence of glyoxylate shunt pathway makes this system closer to
prokaryotic intracellular pathogenic survivor.
Understanding of shunt pathway shown that regulation of the Mtb’s ICD
depends upon the phosphorylation/de-phosphorylation state which is expected to be
regulated by some of available 11 serine/threonine phosphatase/kinases [63]. In
2009, Vinekar et al. had performed molecular dynamics simulation-based analysis
to understand the effect of selective phosphorylation of serine residues [62].
However, crystal structure of Mtb ICD was not available at that time (Table 2), so
homology modeling had been done using different crystal structures as templates to
select appropriate functional model.
The ultimate goal of the homology-based structure modeling is to model the
structure from its sequence with an accuracy that is comparable to the best results
achieved experimentally. As the crystal structure of Mtb ICD was unavailable,
homology-based structure modeling was the preferred way to understand the structural features of the ICD. For ICD modeling, target sequence (UniProt ID: P9WKL1)
was found to align with many sequences of already crystallized structures from both
prokaryote and eukaryote. Based on the homology rules of %-identity, functionality,
quality of the structure, and association with same taxonomy, three ICDs [64] were
In Silico Structure-Based Prediction of Receptor–Ligand Binding …
119