Assessing the Quality of the Homology-Modeled 3d Structures From Electrostatic Standpoint: Test on Bacterial Nucleoside Monophosphate Kinase Families

Abstract

In this study, we address the issue of performing meaningful pK(a) calculations using homology modeled three-dimensional (3D) structures and analyze the possibility of using the calculated pK(a) values to detect structural defects in the models. For this purpose, the 3D structure of each member of five large protein families of a bacterial nucleoside monophosphate kinases (NMPK) have been modeled by means of homology-based approach. Further, we performed pK(a) calculations for the each model and for the template X-ray structures. Each bacterial NMPK family used in the study comprised on average 100 members providing a pool of sequences and 3D models large enough for reliable statistical analysis. It was shown that pK(a) values of titratable groups, which are highly conserved within a family, tend to be conserved among the models too. We demonstrated that homology modeled structures with sequence identity larger than 35% and gap percentile smaller than 10% can be used for meaningful pK(a) calculations. In addition, it was found that some highly conserved titratable groups either exhibit large pK(a) fluctuations among the models or have pK(a) values shifted by several pH units with respect to the pK(a) calculated for the X-ray structure. We demonstrated that such case usually indicates structural errors associated with the model. Thus, we argue that pK(a) calculations can be used for assessing the quality of the 3D models by monitoring fluctuations of the pK(a) values for highly conserved titratable residues within large sets of homologous proteins.

On the role of electrostatics in protein–protein interactions

“…In both cases, however, the 3D structure of the protein-protein complex must be known by either experimental means (x-ray or NMR experiments) or must be predicted in silico [61,62]; however, the last case was not extensively explored in the past due to the significant structural imperfections generated in the models predicted by ab initio docking methods [63,64]. As an alternative, accurate models of the 3D structures of proteinprotein complexes can be delivered by homology methods using highly homologous templates [65][66][67][68][69]. In the boundbound approach, sometimes termed 'rigid body approach', the structures of unbound monomers are taken from the proteinprotein complex and no conformational changes upon the binding are assumed (solid lines in figure 1).…”

Modeling Effects of Human Single Nucleotide Polymorphisms on Protein-Protein Interactions

“…The pKa values of the ionizable groups were calculated using the Multi Conformation Continuum Electrostatics (MCCE) method as previously described (53)(54)(55). Recently, we demonstrated that MCCE can be utilized to calculate pKas using 3D structures that were built by homology (56). Calculations were performed for all 264 protein complexes corresponding to the first allele, and another set of pKa calculations were done for the protein complexes with corresponding nsSNP mutation.…”

Advances in Human Biology: Combining Genetics and Molecular Biophysics to Pave the Way for Personalized Diagnostics and Medicine

“…As summarized by Moult, there is a significant improvement in methods utilizing template-based approaches which can be seen comparing the results of tenth Critical Assessment of Structure Prediction (CASP) experiments [88]. The resulting 3D models of individual macromolecules, especially if based on highly homologous template(s), are of a higher quality that allows for meaningful structural analysis [89,90] and even for carrying out various energy calculations [91,92].…”