The maximum entropy production requirement for proton transfers enhances catalytic efficiency for β-lactamases
Movement of charges during enzyme catalytic cycle may be due to conformational changes, or to fast electron or proton transfer, or to both events. In each case, entropy production can be calculated using Terrel L. Hill's method, if relevant microscopic rate constants are known. When ranked by t...
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Veröffentlicht in: | Biophysical chemistry 2019-01, Vol.244, p.11-21 |
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creator | Juretić, Davor Bonačić Lošić, Željana Kuić, Domagoj Simunić, Juraj Dobovišek, Andrej |
description | Movement of charges during enzyme catalytic cycle may be due to conformational changes, or to fast electron or proton transfer, or to both events. In each case, entropy production can be calculated using Terrel L. Hill's method, if relevant microscopic rate constants are known. When ranked by their evolutionary distance from putative common ancestor, three β-lactamases considered in this study show correspondingly increased catalytic constant, catalytic efficiency, and overall entropy production. The acylation and deacylation steps with concomitant proton shuttles are the most important contributors to overall entropy production. The maximal entropy production requirement for the ES↔EP or EP↔E + P step leads to optimal rate constants, performance parameters, and entropy production values, which are close to those extracted from experiments and also rank in accordance with evolutionary distances. Concurrent maximization of entropy productions for both proton transfer steps revealed that evolvability potential of different β-lactamases is similarly high. These results may have implications in particular for latent potential of β-lactamases to evolve further and in general for selection of optimized enzymes through natural or directed evolution.
[Display omitted]
•Catalytic efficiency and entropy production increases for more evolved lactamases.•Proton transfer steps contribute most to overall entropy production.•Maximal entropy production requirement can augment performance parameters.•Natural upper limits are similar for dissipation-driven efficiency of β-lactamases. |
doi_str_mv | 10.1016/j.bpc.2018.10.004 |
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[Display omitted]
•Catalytic efficiency and entropy production increases for more evolved lactamases.•Proton transfer steps contribute most to overall entropy production.•Maximal entropy production requirement can augment performance parameters.•Natural upper limits are similar for dissipation-driven efficiency of β-lactamases.</description><identifier>ISSN: 0301-4622</identifier><identifier>EISSN: 1873-4200</identifier><identifier>DOI: 10.1016/j.bpc.2018.10.004</identifier><identifier>PMID: 30448627</identifier><language>eng</language><publisher>Netherlands: Elsevier B.V</publisher><subject>beta-Lactamases - genetics ; Catalysis ; Catalytic efficiency ; Directed Molecular Evolution ; Entropy ; Entropy production ; Enzyme evolution ; Evolution, Molecular ; Kinetics ; Optimal rate constants ; Proton transfer steps ; Protons ; β-lactamases</subject><ispartof>Biophysical chemistry, 2019-01, Vol.244, p.11-21</ispartof><rights>2018 Elsevier B.V.</rights><rights>Copyright © 2018 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c353t-32c6a544c230503675612729792fe3d6e2a26790145102cc4aecb70b50e495843</citedby><cites>FETCH-LOGICAL-c353t-32c6a544c230503675612729792fe3d6e2a26790145102cc4aecb70b50e495843</cites><orcidid>0000-0002-3058-7311</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0301462218302904$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,776,780,3537,27901,27902,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30448627$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Juretić, Davor</creatorcontrib><creatorcontrib>Bonačić Lošić, Željana</creatorcontrib><creatorcontrib>Kuić, Domagoj</creatorcontrib><creatorcontrib>Simunić, Juraj</creatorcontrib><creatorcontrib>Dobovišek, Andrej</creatorcontrib><title>The maximum entropy production requirement for proton transfers enhances catalytic efficiency for β-lactamases</title><title>Biophysical chemistry</title><addtitle>Biophys Chem</addtitle><description>Movement of charges during enzyme catalytic cycle may be due to conformational changes, or to fast electron or proton transfer, or to both events. In each case, entropy production can be calculated using Terrel L. Hill's method, if relevant microscopic rate constants are known. When ranked by their evolutionary distance from putative common ancestor, three β-lactamases considered in this study show correspondingly increased catalytic constant, catalytic efficiency, and overall entropy production. The acylation and deacylation steps with concomitant proton shuttles are the most important contributors to overall entropy production. The maximal entropy production requirement for the ES↔EP or EP↔E + P step leads to optimal rate constants, performance parameters, and entropy production values, which are close to those extracted from experiments and also rank in accordance with evolutionary distances. Concurrent maximization of entropy productions for both proton transfer steps revealed that evolvability potential of different β-lactamases is similarly high. These results may have implications in particular for latent potential of β-lactamases to evolve further and in general for selection of optimized enzymes through natural or directed evolution.
[Display omitted]
•Catalytic efficiency and entropy production increases for more evolved lactamases.•Proton transfer steps contribute most to overall entropy production.•Maximal entropy production requirement can augment performance parameters.•Natural upper limits are similar for dissipation-driven efficiency of β-lactamases.</description><subject>beta-Lactamases - genetics</subject><subject>Catalysis</subject><subject>Catalytic efficiency</subject><subject>Directed Molecular Evolution</subject><subject>Entropy</subject><subject>Entropy production</subject><subject>Enzyme evolution</subject><subject>Evolution, Molecular</subject><subject>Kinetics</subject><subject>Optimal rate constants</subject><subject>Proton transfer steps</subject><subject>Protons</subject><subject>β-lactamases</subject><issn>0301-4622</issn><issn>1873-4200</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2019</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kE1uGzEMhYUiQe2mPUA3xSyzGZf6nTG6CowkDWCgm2QtyBwOImN-bElT1NfKQXqmyLHTZbkRSL73QH2MfeWw4MDN9-1is8OFAF7nfgGgPrA5rytZKgFwweYggZfKCDFjn2LcQq4a4CObSVCqNqKas_HxmYre_fH91Bc0pDDuDsUujM2EyY9DEWg_-UB9XhXtGI6rlMcpuCG2FGL2PLsBKRbokusOyWNBbevR04CHN8vfl7JzmFzvIsXP7LJ1XaQv5_eKPd3dPq5-lutf9w-rm3WJUstUSoHGaaVQSNAgTaUNF5VYVkvRkmwMCSdMtQSuNAeBqBzhpoKNBlJLXSt5xa5Pufng_UQx2d5HpK5zA41TtIJLbaRWFc9SfpJiGGMM1Npd8L0LB8vBHjnbrc2c7ZHzcZQ5Z8-3c_y06an553gHmwU_TgLKn_ztKdj4hoSaTBOTbUb_n_hXM4yPRQ</recordid><startdate>201901</startdate><enddate>201901</enddate><creator>Juretić, Davor</creator><creator>Bonačić Lošić, Željana</creator><creator>Kuić, Domagoj</creator><creator>Simunić, Juraj</creator><creator>Dobovišek, Andrej</creator><general>Elsevier B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-3058-7311</orcidid></search><sort><creationdate>201901</creationdate><title>The maximum entropy production requirement for proton transfers enhances catalytic efficiency for β-lactamases</title><author>Juretić, Davor ; Bonačić Lošić, Željana ; Kuić, Domagoj ; Simunić, Juraj ; Dobovišek, Andrej</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c353t-32c6a544c230503675612729792fe3d6e2a26790145102cc4aecb70b50e495843</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>beta-Lactamases - genetics</topic><topic>Catalysis</topic><topic>Catalytic efficiency</topic><topic>Directed Molecular Evolution</topic><topic>Entropy</topic><topic>Entropy production</topic><topic>Enzyme evolution</topic><topic>Evolution, Molecular</topic><topic>Kinetics</topic><topic>Optimal rate constants</topic><topic>Proton transfer steps</topic><topic>Protons</topic><topic>β-lactamases</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Juretić, Davor</creatorcontrib><creatorcontrib>Bonačić Lošić, Željana</creatorcontrib><creatorcontrib>Kuić, Domagoj</creatorcontrib><creatorcontrib>Simunić, Juraj</creatorcontrib><creatorcontrib>Dobovišek, Andrej</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Biophysical chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Juretić, Davor</au><au>Bonačić Lošić, Željana</au><au>Kuić, Domagoj</au><au>Simunić, Juraj</au><au>Dobovišek, Andrej</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The maximum entropy production requirement for proton transfers enhances catalytic efficiency for β-lactamases</atitle><jtitle>Biophysical chemistry</jtitle><addtitle>Biophys Chem</addtitle><date>2019-01</date><risdate>2019</risdate><volume>244</volume><spage>11</spage><epage>21</epage><pages>11-21</pages><issn>0301-4622</issn><eissn>1873-4200</eissn><abstract>Movement of charges during enzyme catalytic cycle may be due to conformational changes, or to fast electron or proton transfer, or to both events. In each case, entropy production can be calculated using Terrel L. Hill's method, if relevant microscopic rate constants are known. When ranked by their evolutionary distance from putative common ancestor, three β-lactamases considered in this study show correspondingly increased catalytic constant, catalytic efficiency, and overall entropy production. The acylation and deacylation steps with concomitant proton shuttles are the most important contributors to overall entropy production. The maximal entropy production requirement for the ES↔EP or EP↔E + P step leads to optimal rate constants, performance parameters, and entropy production values, which are close to those extracted from experiments and also rank in accordance with evolutionary distances. Concurrent maximization of entropy productions for both proton transfer steps revealed that evolvability potential of different β-lactamases is similarly high. These results may have implications in particular for latent potential of β-lactamases to evolve further and in general for selection of optimized enzymes through natural or directed evolution.
[Display omitted]
•Catalytic efficiency and entropy production increases for more evolved lactamases.•Proton transfer steps contribute most to overall entropy production.•Maximal entropy production requirement can augment performance parameters.•Natural upper limits are similar for dissipation-driven efficiency of β-lactamases.</abstract><cop>Netherlands</cop><pub>Elsevier B.V</pub><pmid>30448627</pmid><doi>10.1016/j.bpc.2018.10.004</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-3058-7311</orcidid></addata></record> |
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subjects | beta-Lactamases - genetics Catalysis Catalytic efficiency Directed Molecular Evolution Entropy Entropy production Enzyme evolution Evolution, Molecular Kinetics Optimal rate constants Proton transfer steps Protons β-lactamases |
title | The maximum entropy production requirement for proton transfers enhances catalytic efficiency for β-lactamases |
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