Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation
Oligopeptidase B (OPB) is the least studied group from the prolyl oligopeptidase family. OPBs are found in bacteria and parasitic protozoa and represent pathogenesis factors of the corresponding infections. OPBs consist of two domains connected by a hinge region and have the characteristics of confo...
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MDPI AG
2022-05-01
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| author | Vladimir V. Britikov Vladimir I. Timofeev Dmitry E. Petrenko Elena V. Britikova Alena Y. Nikolaeva Anna V. Vlaskina Konstantin M. Boyko Anna G. Mikhailova Tatiana V. Rakitina |
| author_facet | Vladimir V. Britikov Vladimir I. Timofeev Dmitry E. Petrenko Elena V. Britikova Alena Y. Nikolaeva Anna V. Vlaskina Konstantin M. Boyko Anna G. Mikhailova Tatiana V. Rakitina |
| author_sort | Vladimir V. Britikov |
| collection | DOAJ |
| description | Oligopeptidase B (OPB) is the least studied group from the prolyl oligopeptidase family. OPBs are found in bacteria and parasitic protozoa and represent pathogenesis factors of the corresponding infections. OPBs consist of two domains connected by a hinge region and have the characteristics of conformational dynamics, which include two types of movements: the bridging/separation of α/β-hydrolase catalytic and β-propeller-regulatory domains and the movement of a loop carrying catalytic histidine, which regulates an assembly/disassembly of the catalytic triad. In this work, an elucidation of the interdomain dynamics of OPB from <i>Serratia proteamaculans</i> (SpOPB) with and without modification of the hinge region was performed using a combination of X-ray diffraction analysis and small-angle X-ray scattering, which was complemented with an essential dynamics sampling (EDS) simulation. The first crystal structure of catalytically deficient SpOPB (SpOPBS532A) with an intact hinge sequence is reported. Similarly to SpOPB with modified hinges, SpOPBS532A was crystallized in the presence of spermine and adopted an intermediate conformation in the crystal lattice. Despite the similarity of the crystal structures, a difference in the catalytic triad residue arrangement was detected, which explained the inhibitory effect of the hinge modification. The SpOPBS532A structure reconstituted to the wild-type form was used as a starting point to the classical MD followed by EDS simulation, which allowed us to simulate the domain separation and the transition of the enzyme from the intermediate to open conformation. The obtained open state model was in good agreement with the experimental SAXS data. |
| first_indexed | 2024-03-10T03:05:03Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-10T03:05:03Z |
| publishDate | 2022-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Crystals |
| spelling | doaj.art-ac4b8e153c764cd4849e6103dc00ad0d2023-11-23T10:35:55ZengMDPI AGCrystals2073-43522022-05-0112571210.3390/cryst12050712Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling SimulationVladimir V. Britikov0Vladimir I. Timofeev1Dmitry E. Petrenko2Elena V. Britikova3Alena Y. Nikolaeva4Anna V. Vlaskina5Konstantin M. Boyko6Anna G. Mikhailova7Tatiana V. Rakitina8Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, BelarusShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, RussiaComplex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, RussiaInstitute of Bioorganic Chemistry, National Academy of Sciences of Belarus, 220141 Minsk, BelarusComplex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, RussiaComplex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, RussiaBach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, RussiaShemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 117997 Moscow, RussiaOligopeptidase B (OPB) is the least studied group from the prolyl oligopeptidase family. OPBs are found in bacteria and parasitic protozoa and represent pathogenesis factors of the corresponding infections. OPBs consist of two domains connected by a hinge region and have the characteristics of conformational dynamics, which include two types of movements: the bridging/separation of α/β-hydrolase catalytic and β-propeller-regulatory domains and the movement of a loop carrying catalytic histidine, which regulates an assembly/disassembly of the catalytic triad. In this work, an elucidation of the interdomain dynamics of OPB from <i>Serratia proteamaculans</i> (SpOPB) with and without modification of the hinge region was performed using a combination of X-ray diffraction analysis and small-angle X-ray scattering, which was complemented with an essential dynamics sampling (EDS) simulation. The first crystal structure of catalytically deficient SpOPB (SpOPBS532A) with an intact hinge sequence is reported. Similarly to SpOPB with modified hinges, SpOPBS532A was crystallized in the presence of spermine and adopted an intermediate conformation in the crystal lattice. Despite the similarity of the crystal structures, a difference in the catalytic triad residue arrangement was detected, which explained the inhibitory effect of the hinge modification. The SpOPBS532A structure reconstituted to the wild-type form was used as a starting point to the classical MD followed by EDS simulation, which allowed us to simulate the domain separation and the transition of the enzyme from the intermediate to open conformation. The obtained open state model was in good agreement with the experimental SAXS data.https://www.mdpi.com/2073-4352/12/5/712crystal structureprolyl oligopeptidaseoligopeptidase Bintermediate statehinge regionX-ray diffraction analysis |
| spellingShingle | Vladimir V. Britikov Vladimir I. Timofeev Dmitry E. Petrenko Elena V. Britikova Alena Y. Nikolaeva Anna V. Vlaskina Konstantin M. Boyko Anna G. Mikhailova Tatiana V. Rakitina Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation Crystals crystal structure prolyl oligopeptidase oligopeptidase B intermediate state hinge region X-ray diffraction analysis |
| title | Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation |
| title_full | Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation |
| title_fullStr | Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation |
| title_full_unstemmed | Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation |
| title_short | Elucidation of the Conformational Transition of Oligopeptidase B by an Integrative Approach Based on the Combination of X-ray, SAXS, and Essential Dynamics Sampling Simulation |
| title_sort | elucidation of the conformational transition of oligopeptidase b by an integrative approach based on the combination of x ray saxs and essential dynamics sampling simulation |
| topic | crystal structure prolyl oligopeptidase oligopeptidase B intermediate state hinge region X-ray diffraction analysis |
| url | https://www.mdpi.com/2073-4352/12/5/712 |
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