Catalysis-Enhancement via Rotary Fluctuation of F1-ATPase
Protein conformational fluctuations modulate the catalytic powers of enzymes. The frequency of conformational fluctuations may modulate the catalytic rate at individual reaction steps. In this study, we modulated the rotary fluctuation frequency of F1-ATPase (F1) by attaching probes with different v...
Gespeichert in:
| Veröffentlicht in: | Biophysical journal 2013-11, Vol.105 (10), p.2385-2391 |
|---|---|
| Hauptverfasser: | , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 2391 |
|---|---|
| container_issue | 10 |
| container_start_page | 2385 |
| container_title | Biophysical journal |
| container_volume | 105 |
| creator | Watanabe, Rikiya Hayashi, Kumiko Ueno, Hiroshi Noji, Hiroyuki |
| description | Protein conformational fluctuations modulate the catalytic powers of enzymes. The frequency of conformational fluctuations may modulate the catalytic rate at individual reaction steps. In this study, we modulated the rotary fluctuation frequency of F1-ATPase (F1) by attaching probes with different viscous drag coefficients at the rotary shaft of F1. Individual rotation pauses of F1 between rotary steps correspond to the waiting state of a certain elementary reaction step of ATP hydrolysis. This allows us to investigate the impact of the frequency modulation of the rotary fluctuation on the rate of the individual reaction steps by measuring the duration of rotation pauses. Although phosphate release was significantly decelerated, the ATP-binding and hydrolysis steps were less sensitive or insensitive to the viscous drag coefficient of the probe. Brownian dynamics simulation based on a model similar to the Sumi-Marcus theory reproduced the experimental results, providing a theoretical framework for the role of rotational fluctuation in F1 rate enhancement. |
| doi_str_mv | 10.1016/j.bpj.2013.09.050 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3838750</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S0006349513011272</els_id><sourcerecordid>1461871960</sourcerecordid><originalsourceid>FETCH-LOGICAL-c4560-7f192d9590c91ff11688dc076d336dd8e66b5522ea58fd111c6716ac2f0231be3</originalsourceid><addsrcrecordid>eNp9kcFuEzEURS0EoiHwAWxglmxmeM8ee2whIVVRQ5EqgaBdW47taR1NxsGeidS_xyFtBRu88cLnHV_dR8hbhAYBxcdts9lvGwrIGlANcHhGFshbWgNI8ZwsAEDUrFX8jLzKeQuAlAO-JGe0pUIihwVRKzOZ4T6HXF-Md2a0fufHqToEU_2Ik0n31XqY7TSbKcSxin21xvr8-rvJ_jV50Zsh-zcP95LcrC-uV5f11bcvX1fnV7VtuYC661FRp7gCq7DvEYWUzkInHGPCOemF2HBOqTdc9g4RrehQGEt7oAw3ni3J55N3P2923tkSL5lB71PYlXg6mqD_fRnDnb6NB80kkx2HIvjwIEjx1-zzpHchWz8MZvRxzhpbgbJDJY4onlCbYs7J90_fIOhj5XqrS-X6WLkGpeGP_t3f-Z4mHjsuwPsT0JuozW0KWd_8LAZe9oHseJbk04nwpcdD8ElnG3zZhQvJ20m7GP4T4DcOdpmr</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1461871960</pqid></control><display><type>article</type><title>Catalysis-Enhancement via Rotary Fluctuation of F1-ATPase</title><source>MEDLINE</source><source>Cell Press Free Archives</source><source>Elsevier ScienceDirect Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>PubMed Central</source><creator>Watanabe, Rikiya ; Hayashi, Kumiko ; Ueno, Hiroshi ; Noji, Hiroyuki</creator><creatorcontrib>Watanabe, Rikiya ; Hayashi, Kumiko ; Ueno, Hiroshi ; Noji, Hiroyuki</creatorcontrib><description>Protein conformational fluctuations modulate the catalytic powers of enzymes. The frequency of conformational fluctuations may modulate the catalytic rate at individual reaction steps. In this study, we modulated the rotary fluctuation frequency of F1-ATPase (F1) by attaching probes with different viscous drag coefficients at the rotary shaft of F1. Individual rotation pauses of F1 between rotary steps correspond to the waiting state of a certain elementary reaction step of ATP hydrolysis. This allows us to investigate the impact of the frequency modulation of the rotary fluctuation on the rate of the individual reaction steps by measuring the duration of rotation pauses. Although phosphate release was significantly decelerated, the ATP-binding and hydrolysis steps were less sensitive or insensitive to the viscous drag coefficient of the probe. Brownian dynamics simulation based on a model similar to the Sumi-Marcus theory reproduced the experimental results, providing a theoretical framework for the role of rotational fluctuation in F1 rate enhancement.</description><identifier>ISSN: 0006-3495</identifier><identifier>EISSN: 1542-0086</identifier><identifier>DOI: 10.1016/j.bpj.2013.09.050</identifier><identifier>PMID: 24268150</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>adenosine triphosphate ; Adenosine Triphosphate - metabolism ; Biocatalysis ; Biomechanical Phenomena ; drag coefficient ; enzymes ; Friction ; Hydrolysis ; Kinetics ; Models, Biological ; Molecular Machines, Motors and Nanoscale Biophysics ; Molecular Probes - metabolism ; Phosphates - metabolism ; protein conformation ; Proton-Translocating ATPases - metabolism ; Rotation ; Viscosity</subject><ispartof>Biophysical journal, 2013-11, Vol.105 (10), p.2385-2391</ispartof><rights>2013 Biophysical Society</rights><rights>Copyright © 2013 Biophysical Society. Published by Elsevier Inc. All rights reserved.</rights><rights>2013 by the Biophysical Society. 2013 Biophysical Society</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c4560-7f192d9590c91ff11688dc076d336dd8e66b5522ea58fd111c6716ac2f0231be3</citedby><cites>FETCH-LOGICAL-c4560-7f192d9590c91ff11688dc076d336dd8e66b5522ea58fd111c6716ac2f0231be3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838750/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.sciencedirect.com/science/article/pii/S0006349513011272$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,3537,27901,27902,53766,53768,65306</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24268150$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Watanabe, Rikiya</creatorcontrib><creatorcontrib>Hayashi, Kumiko</creatorcontrib><creatorcontrib>Ueno, Hiroshi</creatorcontrib><creatorcontrib>Noji, Hiroyuki</creatorcontrib><title>Catalysis-Enhancement via Rotary Fluctuation of F1-ATPase</title><title>Biophysical journal</title><addtitle>Biophys J</addtitle><description>Protein conformational fluctuations modulate the catalytic powers of enzymes. The frequency of conformational fluctuations may modulate the catalytic rate at individual reaction steps. In this study, we modulated the rotary fluctuation frequency of F1-ATPase (F1) by attaching probes with different viscous drag coefficients at the rotary shaft of F1. Individual rotation pauses of F1 between rotary steps correspond to the waiting state of a certain elementary reaction step of ATP hydrolysis. This allows us to investigate the impact of the frequency modulation of the rotary fluctuation on the rate of the individual reaction steps by measuring the duration of rotation pauses. Although phosphate release was significantly decelerated, the ATP-binding and hydrolysis steps were less sensitive or insensitive to the viscous drag coefficient of the probe. Brownian dynamics simulation based on a model similar to the Sumi-Marcus theory reproduced the experimental results, providing a theoretical framework for the role of rotational fluctuation in F1 rate enhancement.</description><subject>adenosine triphosphate</subject><subject>Adenosine Triphosphate - metabolism</subject><subject>Biocatalysis</subject><subject>Biomechanical Phenomena</subject><subject>drag coefficient</subject><subject>enzymes</subject><subject>Friction</subject><subject>Hydrolysis</subject><subject>Kinetics</subject><subject>Models, Biological</subject><subject>Molecular Machines, Motors and Nanoscale Biophysics</subject><subject>Molecular Probes - metabolism</subject><subject>Phosphates - metabolism</subject><subject>protein conformation</subject><subject>Proton-Translocating ATPases - metabolism</subject><subject>Rotation</subject><subject>Viscosity</subject><issn>0006-3495</issn><issn>1542-0086</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kcFuEzEURS0EoiHwAWxglmxmeM8ee2whIVVRQ5EqgaBdW47taR1NxsGeidS_xyFtBRu88cLnHV_dR8hbhAYBxcdts9lvGwrIGlANcHhGFshbWgNI8ZwsAEDUrFX8jLzKeQuAlAO-JGe0pUIihwVRKzOZ4T6HXF-Md2a0fufHqToEU_2Ik0n31XqY7TSbKcSxin21xvr8-rvJ_jV50Zsh-zcP95LcrC-uV5f11bcvX1fnV7VtuYC661FRp7gCq7DvEYWUzkInHGPCOemF2HBOqTdc9g4RrehQGEt7oAw3ni3J55N3P2923tkSL5lB71PYlXg6mqD_fRnDnb6NB80kkx2HIvjwIEjx1-zzpHchWz8MZvRxzhpbgbJDJY4onlCbYs7J90_fIOhj5XqrS-X6WLkGpeGP_t3f-Z4mHjsuwPsT0JuozW0KWd_8LAZe9oHseJbk04nwpcdD8ElnG3zZhQvJ20m7GP4T4DcOdpmr</recordid><startdate>20131119</startdate><enddate>20131119</enddate><creator>Watanabe, Rikiya</creator><creator>Hayashi, Kumiko</creator><creator>Ueno, Hiroshi</creator><creator>Noji, Hiroyuki</creator><general>Elsevier Inc</general><general>The Biophysical Society</general><scope>6I.</scope><scope>AAFTH</scope><scope>FBQ</scope><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><scope>5PM</scope></search><sort><creationdate>20131119</creationdate><title>Catalysis-Enhancement via Rotary Fluctuation of F1-ATPase</title><author>Watanabe, Rikiya ; Hayashi, Kumiko ; Ueno, Hiroshi ; Noji, Hiroyuki</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4560-7f192d9590c91ff11688dc076d336dd8e66b5522ea58fd111c6716ac2f0231be3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>adenosine triphosphate</topic><topic>Adenosine Triphosphate - metabolism</topic><topic>Biocatalysis</topic><topic>Biomechanical Phenomena</topic><topic>drag coefficient</topic><topic>enzymes</topic><topic>Friction</topic><topic>Hydrolysis</topic><topic>Kinetics</topic><topic>Models, Biological</topic><topic>Molecular Machines, Motors and Nanoscale Biophysics</topic><topic>Molecular Probes - metabolism</topic><topic>Phosphates - metabolism</topic><topic>protein conformation</topic><topic>Proton-Translocating ATPases - metabolism</topic><topic>Rotation</topic><topic>Viscosity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Watanabe, Rikiya</creatorcontrib><creatorcontrib>Hayashi, Kumiko</creatorcontrib><creatorcontrib>Ueno, Hiroshi</creatorcontrib><creatorcontrib>Noji, Hiroyuki</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>AGRIS</collection><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><collection>PubMed Central (Full Participant titles)</collection><jtitle>Biophysical journal</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Watanabe, Rikiya</au><au>Hayashi, Kumiko</au><au>Ueno, Hiroshi</au><au>Noji, Hiroyuki</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Catalysis-Enhancement via Rotary Fluctuation of F1-ATPase</atitle><jtitle>Biophysical journal</jtitle><addtitle>Biophys J</addtitle><date>2013-11-19</date><risdate>2013</risdate><volume>105</volume><issue>10</issue><spage>2385</spage><epage>2391</epage><pages>2385-2391</pages><issn>0006-3495</issn><eissn>1542-0086</eissn><abstract>Protein conformational fluctuations modulate the catalytic powers of enzymes. The frequency of conformational fluctuations may modulate the catalytic rate at individual reaction steps. In this study, we modulated the rotary fluctuation frequency of F1-ATPase (F1) by attaching probes with different viscous drag coefficients at the rotary shaft of F1. Individual rotation pauses of F1 between rotary steps correspond to the waiting state of a certain elementary reaction step of ATP hydrolysis. This allows us to investigate the impact of the frequency modulation of the rotary fluctuation on the rate of the individual reaction steps by measuring the duration of rotation pauses. Although phosphate release was significantly decelerated, the ATP-binding and hydrolysis steps were less sensitive or insensitive to the viscous drag coefficient of the probe. Brownian dynamics simulation based on a model similar to the Sumi-Marcus theory reproduced the experimental results, providing a theoretical framework for the role of rotational fluctuation in F1 rate enhancement.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>24268150</pmid><doi>10.1016/j.bpj.2013.09.050</doi><tpages>7</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0006-3495 |
| ispartof | Biophysical journal, 2013-11, Vol.105 (10), p.2385-2391 |
| issn | 0006-3495 1542-0086 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_3838750 |
| source | MEDLINE; Cell Press Free Archives; Elsevier ScienceDirect Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central |
| subjects | adenosine triphosphate Adenosine Triphosphate - metabolism Biocatalysis Biomechanical Phenomena drag coefficient enzymes Friction Hydrolysis Kinetics Models, Biological Molecular Machines, Motors and Nanoscale Biophysics Molecular Probes - metabolism Phosphates - metabolism protein conformation Proton-Translocating ATPases - metabolism Rotation Viscosity |
| title | Catalysis-Enhancement via Rotary Fluctuation of F1-ATPase |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-11T07%3A19%3A56IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Catalysis-Enhancement%20via%20Rotary%20Fluctuation%20of%20F1-ATPase&rft.jtitle=Biophysical%20journal&rft.au=Watanabe,%20Rikiya&rft.date=2013-11-19&rft.volume=105&rft.issue=10&rft.spage=2385&rft.epage=2391&rft.pages=2385-2391&rft.issn=0006-3495&rft.eissn=1542-0086&rft_id=info:doi/10.1016/j.bpj.2013.09.050&rft_dat=%3Cproquest_pubme%3E1461871960%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1461871960&rft_id=info:pmid/24268150&rft_els_id=S0006349513011272&rfr_iscdi=true |