Mechanisms of Interaction of Escherichia coli Biopolymers with 4-Hexylresorcinol
In this study, molecular modeling is used to study the interaction of the autoregulatory factor of bacteria, a chemical analog of the inducers of anabiosis of 4-hexylresorcinol (4HR), with the outer and inner membranes, the porin protein, peptidoglycan, DNA, and the DNA stabilizing protein Dps of th...
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| Veröffentlicht in: | Russian journal of physical chemistry. B 2023-06, Vol.17 (3), p.608-619 |
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| container_title | Russian journal of physical chemistry. B |
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| creator | Tereshkin, E. V. Tereshkina, K. B. Loiko, N. G. Generalova, A. A. Kovalenko, V. V. Krupyanskii, Yu. F. |
| description | In this study, molecular modeling is used to study the interaction of the autoregulatory factor of bacteria, a chemical analog of the inducers of anabiosis of 4-hexylresorcinol (4HR), with the outer and inner membranes, the porin protein, peptidoglycan, DNA, and the DNA stabilizing protein Dps of the
Escherichia coli
(
E. coli
) bacterium. The concentration dependence and molecular mechanisms of the interaction of 4HR with cell polymers are studied by molecular dynamics in the full-atomic approximation. The spatial and energy characteristics of 4HR complexes with various cellular components are obtained. Using principal component analysis, the characteristics of DNA and the DNA-binding Dps protein are determined under conditions of various 4HR complexes. The obtained results, which are consistent with the experimental data, allow a deeper understanding of the processes that occur during the protection of the bacterial cell at the level of the envelope and the preservation of DNA by nucleoid proteins. |
| doi_str_mv | 10.1134/S1990793123030132 |
| format | Article |
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Escherichia coli
(
E. coli
) bacterium. The concentration dependence and molecular mechanisms of the interaction of 4HR with cell polymers are studied by molecular dynamics in the full-atomic approximation. The spatial and energy characteristics of 4HR complexes with various cellular components are obtained. Using principal component analysis, the characteristics of DNA and the DNA-binding Dps protein are determined under conditions of various 4HR complexes. The obtained results, which are consistent with the experimental data, allow a deeper understanding of the processes that occur during the protection of the bacterial cell at the level of the envelope and the preservation of DNA by nucleoid proteins.</description><identifier>ISSN: 1990-7931</identifier><identifier>EISSN: 1990-7923</identifier><identifier>DOI: 10.1134/S1990793123030132</identifier><language>eng</language><publisher>Moscow: Pleiades Publishing</publisher><subject>Biopolymers ; Chemistry ; Chemistry and Materials Science ; Coliforms ; E coli ; Molecular dynamics ; ON THE 100th ANNIVERSARY OF THE BIRTH OF ACADEMICIAN V.I. GOLDANSKY ; Physical Chemistry ; Principal components analysis ; Proteins</subject><ispartof>Russian journal of physical chemistry. B, 2023-06, Vol.17 (3), p.608-619</ispartof><rights>Pleiades Publishing, Ltd. 2023. ISSN 1990-7931, Russian Journal of Physical Chemistry B, 2023, Vol. 17, No. 3, pp. 608–619. © Pleiades Publishing, Ltd., 2023. Russian Text © The Author(s), 2023, published in Khimicheskaya Fizika, 2023, Vol. 42, No. 5, pp. 30–42.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c316t-a9ff973a5bd334d52cbb208a098dfcf808126463a61200277cd726ddfa27795b3</citedby><cites>FETCH-LOGICAL-c316t-a9ff973a5bd334d52cbb208a098dfcf808126463a61200277cd726ddfa27795b3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1134/S1990793123030132$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1134/S1990793123030132$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids></links><search><creatorcontrib>Tereshkin, E. V.</creatorcontrib><creatorcontrib>Tereshkina, K. B.</creatorcontrib><creatorcontrib>Loiko, N. G.</creatorcontrib><creatorcontrib>Generalova, A. A.</creatorcontrib><creatorcontrib>Kovalenko, V. V.</creatorcontrib><creatorcontrib>Krupyanskii, Yu. F.</creatorcontrib><title>Mechanisms of Interaction of Escherichia coli Biopolymers with 4-Hexylresorcinol</title><title>Russian journal of physical chemistry. B</title><addtitle>Russ. J. Phys. Chem. B</addtitle><description>In this study, molecular modeling is used to study the interaction of the autoregulatory factor of bacteria, a chemical analog of the inducers of anabiosis of 4-hexylresorcinol (4HR), with the outer and inner membranes, the porin protein, peptidoglycan, DNA, and the DNA stabilizing protein Dps of the
Escherichia coli
(
E. coli
) bacterium. The concentration dependence and molecular mechanisms of the interaction of 4HR with cell polymers are studied by molecular dynamics in the full-atomic approximation. The spatial and energy characteristics of 4HR complexes with various cellular components are obtained. Using principal component analysis, the characteristics of DNA and the DNA-binding Dps protein are determined under conditions of various 4HR complexes. The obtained results, which are consistent with the experimental data, allow a deeper understanding of the processes that occur during the protection of the bacterial cell at the level of the envelope and the preservation of DNA by nucleoid proteins.</description><subject>Biopolymers</subject><subject>Chemistry</subject><subject>Chemistry and Materials Science</subject><subject>Coliforms</subject><subject>E coli</subject><subject>Molecular dynamics</subject><subject>ON THE 100th ANNIVERSARY OF THE BIRTH OF ACADEMICIAN V.I. GOLDANSKY</subject><subject>Physical Chemistry</subject><subject>Principal components analysis</subject><subject>Proteins</subject><issn>1990-7931</issn><issn>1990-7923</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><recordid>eNp1kFFLwzAUhYMoOKc_wLeCz9Wb3DZpHnXMbTBRUJ9LmiY2o2tm0qH793ZM9EF8uudevnMuHEIuKVxTitnNM5UShETKEBAosiMy2p9SIRke_2ikp-QsxhUAZ0LCiDw9GN2ozsV1TLxNFl1vgtK9891-nUbdmOB041SifeuSO-c3vt2tTYjJh-ubJEvn5nPXBhN90K7z7Tk5saqN5uJ7jsnr_fRlMk-Xj7PF5HaZaqS8T5W0VgpUeVUjZnXOdFUxKBTIorbaFlBQxjOOilMGwITQtWC8rq0atMwrHJOrQ-4m-PetiX258tvQDS9LVmRY5BnndKDogdLBxxiMLTfBrVXYlRTKfXHln-IGDzt44sB2byb8Jv9v-gLX0m8a</recordid><startdate>20230601</startdate><enddate>20230601</enddate><creator>Tereshkin, E. V.</creator><creator>Tereshkina, K. B.</creator><creator>Loiko, N. G.</creator><creator>Generalova, A. A.</creator><creator>Kovalenko, V. V.</creator><creator>Krupyanskii, Yu. F.</creator><general>Pleiades Publishing</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope></search><sort><creationdate>20230601</creationdate><title>Mechanisms of Interaction of Escherichia coli Biopolymers with 4-Hexylresorcinol</title><author>Tereshkin, E. V. ; Tereshkina, K. B. ; Loiko, N. G. ; Generalova, A. A. ; Kovalenko, V. V. ; Krupyanskii, Yu. F.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c316t-a9ff973a5bd334d52cbb208a098dfcf808126463a61200277cd726ddfa27795b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Biopolymers</topic><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Coliforms</topic><topic>E coli</topic><topic>Molecular dynamics</topic><topic>ON THE 100th ANNIVERSARY OF THE BIRTH OF ACADEMICIAN V.I. GOLDANSKY</topic><topic>Physical Chemistry</topic><topic>Principal components analysis</topic><topic>Proteins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tereshkin, E. V.</creatorcontrib><creatorcontrib>Tereshkina, K. B.</creatorcontrib><creatorcontrib>Loiko, N. G.</creatorcontrib><creatorcontrib>Generalova, A. A.</creatorcontrib><creatorcontrib>Kovalenko, V. V.</creatorcontrib><creatorcontrib>Krupyanskii, Yu. F.</creatorcontrib><collection>CrossRef</collection><jtitle>Russian journal of physical chemistry. B</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tereshkin, E. V.</au><au>Tereshkina, K. B.</au><au>Loiko, N. G.</au><au>Generalova, A. A.</au><au>Kovalenko, V. V.</au><au>Krupyanskii, Yu. F.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Mechanisms of Interaction of Escherichia coli Biopolymers with 4-Hexylresorcinol</atitle><jtitle>Russian journal of physical chemistry. B</jtitle><stitle>Russ. J. Phys. Chem. B</stitle><date>2023-06-01</date><risdate>2023</risdate><volume>17</volume><issue>3</issue><spage>608</spage><epage>619</epage><pages>608-619</pages><issn>1990-7931</issn><eissn>1990-7923</eissn><abstract>In this study, molecular modeling is used to study the interaction of the autoregulatory factor of bacteria, a chemical analog of the inducers of anabiosis of 4-hexylresorcinol (4HR), with the outer and inner membranes, the porin protein, peptidoglycan, DNA, and the DNA stabilizing protein Dps of the
Escherichia coli
(
E. coli
) bacterium. The concentration dependence and molecular mechanisms of the interaction of 4HR with cell polymers are studied by molecular dynamics in the full-atomic approximation. The spatial and energy characteristics of 4HR complexes with various cellular components are obtained. Using principal component analysis, the characteristics of DNA and the DNA-binding Dps protein are determined under conditions of various 4HR complexes. The obtained results, which are consistent with the experimental data, allow a deeper understanding of the processes that occur during the protection of the bacterial cell at the level of the envelope and the preservation of DNA by nucleoid proteins.</abstract><cop>Moscow</cop><pub>Pleiades Publishing</pub><doi>10.1134/S1990793123030132</doi><tpages>12</tpages></addata></record> |
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| issn | 1990-7931 1990-7923 |
| language | eng |
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| source | SpringerNature Journals |
| subjects | Biopolymers Chemistry Chemistry and Materials Science Coliforms E coli Molecular dynamics ON THE 100th ANNIVERSARY OF THE BIRTH OF ACADEMICIAN V.I. GOLDANSKY Physical Chemistry Principal components analysis Proteins |
| title | Mechanisms of Interaction of Escherichia coli Biopolymers with 4-Hexylresorcinol |
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