3.4 Analyses of Mutations
RIN methods may be used for analysis and prediction of effects of amino acid
mutation on protein properties, which may be useful for protein design, investigations of disease-associated single nucleotide polymorphisms, or mechanism of
the drug resistance [27, 90–92].
Recently, we used RIN for investigation of the influence of several mutations on
structure and flexibility of b-lactamase [93]. b-lactamases are class of enzymes
responsible for bacteria resistant to b-lactam antibiotics. Besides, the key mutations,
responsible for the extended spectrum b-lactamases or inhibitor resistance phenotype, secondary mutations, located far from active site and with a weak impact on
the protein structure and enzyme activity, have been often appeared [94]. Analysis
of MD trajectories showed that the secondary mutations, and the key mutations can
exhibit opposite effect on the flexibility of the X-loop of b-lactamase that participate
in antibiotic hydrolysis and transport in the active site [93]. Detailed analysis of
RIN maps of proteins of consistent mutations from wild-type TEM-1 to TEM-72
(carrying two key mutations G238S and E240K and two secondary ones M182T
and Q39K) showed that key mutations (responding for extended spectrum
b-lactamases) lead to weakening interactions of the X-loop with protein globule.
The appearance of secondary mutation M182T resulted in dramatic changing of
conformation of R65, and this residue began to interact with the X-loop and fixed it
near protein globule (manuscript submitted) (Fig. 3).
4 Conclusion
Herein, we have reviewed the development and current stage of RINs and their
application for drug discovery.
RINs provide complex analysis of the proteins and their complexes. Residues are
in tight contact with each other in protein globules, and RINs allowed to estimate
their interdependence and to predict different properties and functionality of the
individual residues and the whole proteins. In addition to topology, RINs allow to
use chemicophysical properties of residues and energy of their interaction in RIN
construction and analysis of proteins.
Besides, using RINs for investigation protein structure and functions, they may
be applied in drug design in several ways.
Prediction of functionally important residues and sites can be helpful for
understanding functions and regulation of uncharacterized proteins, finding active
sites, allosteric and cryptic ligand binding sites. It may decrease the amount of
“undruggable” protein, increasing field for drug design. On the other hand, many
drug candidates fail in the late and costly stages of clinical trials [95]. Side effects
are one of the main reasons for drug failure [96]. The detection of similarity in
64
D. Shcherbinin and A. Veselovsky
RIN methods may be used for analysis and prediction of effects of amino acid
mutation on protein properties, which may be useful for protein design, investigations of disease-associated single nucleotide polymorphisms, or mechanism of
the drug resistance [27, 90–92].
Recently, we used RIN for investigation of the influence of several mutations on
structure and flexibility of b-lactamase [93]. b-lactamases are class of enzymes
responsible for bacteria resistant to b-lactam antibiotics. Besides, the key mutations,
responsible for the extended spectrum b-lactamases or inhibitor resistance phenotype, secondary mutations, located far from active site and with a weak impact on
the protein structure and enzyme activity, have been often appeared [94]. Analysis
of MD trajectories showed that the secondary mutations, and the key mutations can
exhibit opposite effect on the flexibility of the X-loop of b-lactamase that participate
in antibiotic hydrolysis and transport in the active site [93]. Detailed analysis of
RIN maps of proteins of consistent mutations from wild-type TEM-1 to TEM-72
(carrying two key mutations G238S and E240K and two secondary ones M182T
and Q39K) showed that key mutations (responding for extended spectrum
b-lactamases) lead to weakening interactions of the X-loop with protein globule.
The appearance of secondary mutation M182T resulted in dramatic changing of
conformation of R65, and this residue began to interact with the X-loop and fixed it
near protein globule (manuscript submitted) (Fig. 3).
4 Conclusion
Herein, we have reviewed the development and current stage of RINs and their
application for drug discovery.
RINs provide complex analysis of the proteins and their complexes. Residues are
in tight contact with each other in protein globules, and RINs allowed to estimate
their interdependence and to predict different properties and functionality of the
individual residues and the whole proteins. In addition to topology, RINs allow to
use chemicophysical properties of residues and energy of their interaction in RIN
construction and analysis of proteins.
Besides, using RINs for investigation protein structure and functions, they may
be applied in drug design in several ways.
Prediction of functionally important residues and sites can be helpful for
understanding functions and regulation of uncharacterized proteins, finding active
sites, allosteric and cryptic ligand binding sites. It may decrease the amount of
“undruggable” protein, increasing field for drug design. On the other hand, many
drug candidates fail in the late and costly stages of clinical trials [95]. Side effects
are one of the main reasons for drug failure [96]. The detection of similarity in
64
D. Shcherbinin and A. Veselovsky