Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study
Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecul...
Gespeichert in:
| Veröffentlicht in: | International journal of molecular sciences 2023-10, Vol.24 (20), p.15423 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | |
|---|---|
| container_issue | 20 |
| container_start_page | 15423 |
| container_title | International journal of molecular sciences |
| container_volume | 24 |
| creator | Yamane, Tsutomu Nakayama, Takahiro Ekimoto, Toru Inoue, Masao Ikezaki, Keigo Sekiguchi, Hiroshi Kuramochi, Masahiro Terao, Yasuo Judai, Ken Saito, Minoru Ikeguchi, Mitsunori Sasaki, Yuji C |
| description | Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different. |
| doi_str_mv | 10.3390/ijms242015423 |
| format | Article |
| fullrecord | <record><control><sourceid>gale_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10607685</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A771910753</galeid><sourcerecordid>A771910753</sourcerecordid><originalsourceid>FETCH-LOGICAL-c416t-c07bb196fc38e0a7eb17794bc92fa821af9d276202c029dbd94dc224db83f78f3</originalsourceid><addsrcrecordid>eNptkstv1DAQxiMEoqVw5G6JC5cUP5I45oKqLY9KRRy6SNwsx4-tFz8W20HKnT8cR62gi5APHs_8vs8ae5rmJYLnhDD4xu59xh2GqO8wedScog7jFsKBPn4QnzTPct5DiAnu2dPmhNCR9Qii0-bXJvqDSDbHAKIB5VaDz9FpOTuRalSss2VZK9t5mp0N4NJ6nawEVzmamHx--4C_XILwVmZwY31NFBtDBiKoKjImCVm0At_aJBawrafvNuzATZnV8rx5YoTL-sX9ftZ8_fB-u_nUXn_5eLW5uG5lh4bSSkinCbHBSDJqKKieEKWsmyTDRowYCcMUpgOGWELM1KRYpyTGnZpGYuhoyFnz7s73ME9eK6lDScLxQ7JepIVHYflxJdhbvos_OYIDpMPYV4fX9w4p_ph1LtzbLLVzIug4Z47HkfQUEUQq-uofdB_nFGp_K1X_oSdD95faCae5DSbWi-Vqyi8oRQxB2q9e5_-h6lK6vncM2tiaPxK0dwKZYs5Jmz9NIsjXueFHc0N-A42ktX4</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2882595364</pqid></control><display><type>article</type><title>Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study</title><source>MDPI - Multidisciplinary Digital Publishing Institute</source><source>PubMed Central</source><source>EZB Electronic Journals Library</source><creator>Yamane, Tsutomu ; Nakayama, Takahiro ; Ekimoto, Toru ; Inoue, Masao ; Ikezaki, Keigo ; Sekiguchi, Hiroshi ; Kuramochi, Masahiro ; Terao, Yasuo ; Judai, Ken ; Saito, Minoru ; Ikeguchi, Mitsunori ; Sasaki, Yuji C</creator><creatorcontrib>Yamane, Tsutomu ; Nakayama, Takahiro ; Ekimoto, Toru ; Inoue, Masao ; Ikezaki, Keigo ; Sekiguchi, Hiroshi ; Kuramochi, Masahiro ; Terao, Yasuo ; Judai, Ken ; Saito, Minoru ; Ikeguchi, Mitsunori ; Sasaki, Yuji C</creatorcontrib><description>Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.</description><identifier>ISSN: 1422-0067</identifier><identifier>ISSN: 1661-6596</identifier><identifier>EISSN: 1422-0067</identifier><identifier>DOI: 10.3390/ijms242015423</identifier><identifier>PMID: 37895101</identifier><language>eng</language><publisher>Basel: MDPI AG</publisher><subject>Amino acids ; Comparative analysis ; Interfaces ; Molecular dynamics ; Motility ; Neurons ; Proteins ; Simulation ; Simulation methods ; Tubulins</subject><ispartof>International journal of molecular sciences, 2023-10, Vol.24 (20), p.15423</ispartof><rights>COPYRIGHT 2023 MDPI AG</rights><rights>2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2023 by the authors. 2023</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c416t-c07bb196fc38e0a7eb17794bc92fa821af9d276202c029dbd94dc224db83f78f3</cites><orcidid>0000-0003-1643-3997 ; 0000-0003-3403-237X ; 0000-0002-0249-7773 ; 0000-0003-3064-3536 ; 0000-0002-7419-3146 ; 0000-0001-7590-3624</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10607685/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10607685/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,53766,53768</link.rule.ids></links><search><creatorcontrib>Yamane, Tsutomu</creatorcontrib><creatorcontrib>Nakayama, Takahiro</creatorcontrib><creatorcontrib>Ekimoto, Toru</creatorcontrib><creatorcontrib>Inoue, Masao</creatorcontrib><creatorcontrib>Ikezaki, Keigo</creatorcontrib><creatorcontrib>Sekiguchi, Hiroshi</creatorcontrib><creatorcontrib>Kuramochi, Masahiro</creatorcontrib><creatorcontrib>Terao, Yasuo</creatorcontrib><creatorcontrib>Judai, Ken</creatorcontrib><creatorcontrib>Saito, Minoru</creatorcontrib><creatorcontrib>Ikeguchi, Mitsunori</creatorcontrib><creatorcontrib>Sasaki, Yuji C</creatorcontrib><title>Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study</title><title>International journal of molecular sciences</title><description>Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.</description><subject>Amino acids</subject><subject>Comparative analysis</subject><subject>Interfaces</subject><subject>Molecular dynamics</subject><subject>Motility</subject><subject>Neurons</subject><subject>Proteins</subject><subject>Simulation</subject><subject>Simulation methods</subject><subject>Tubulins</subject><issn>1422-0067</issn><issn>1661-6596</issn><issn>1422-0067</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>8G5</sourceid><sourceid>BENPR</sourceid><sourceid>GUQSH</sourceid><sourceid>M2O</sourceid><recordid>eNptkstv1DAQxiMEoqVw5G6JC5cUP5I45oKqLY9KRRy6SNwsx4-tFz8W20HKnT8cR62gi5APHs_8vs8ae5rmJYLnhDD4xu59xh2GqO8wedScog7jFsKBPn4QnzTPct5DiAnu2dPmhNCR9Qii0-bXJvqDSDbHAKIB5VaDz9FpOTuRalSss2VZK9t5mp0N4NJ6nawEVzmamHx--4C_XILwVmZwY31NFBtDBiKoKjImCVm0At_aJBawrafvNuzATZnV8rx5YoTL-sX9ftZ8_fB-u_nUXn_5eLW5uG5lh4bSSkinCbHBSDJqKKieEKWsmyTDRowYCcMUpgOGWELM1KRYpyTGnZpGYuhoyFnz7s73ME9eK6lDScLxQ7JepIVHYflxJdhbvos_OYIDpMPYV4fX9w4p_ph1LtzbLLVzIug4Z47HkfQUEUQq-uofdB_nFGp_K1X_oSdD95faCae5DSbWi-Vqyi8oRQxB2q9e5_-h6lK6vncM2tiaPxK0dwKZYs5Jmz9NIsjXueFHc0N-A42ktX4</recordid><startdate>20231001</startdate><enddate>20231001</enddate><creator>Yamane, Tsutomu</creator><creator>Nakayama, Takahiro</creator><creator>Ekimoto, Toru</creator><creator>Inoue, Masao</creator><creator>Ikezaki, Keigo</creator><creator>Sekiguchi, Hiroshi</creator><creator>Kuramochi, Masahiro</creator><creator>Terao, Yasuo</creator><creator>Judai, Ken</creator><creator>Saito, Minoru</creator><creator>Ikeguchi, Mitsunori</creator><creator>Sasaki, Yuji C</creator><general>MDPI AG</general><general>MDPI</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>8G5</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>GUQSH</scope><scope>K9.</scope><scope>M0S</scope><scope>M1P</scope><scope>M2O</scope><scope>MBDVC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope><orcidid>https://orcid.org/0000-0003-1643-3997</orcidid><orcidid>https://orcid.org/0000-0003-3403-237X</orcidid><orcidid>https://orcid.org/0000-0002-0249-7773</orcidid><orcidid>https://orcid.org/0000-0003-3064-3536</orcidid><orcidid>https://orcid.org/0000-0002-7419-3146</orcidid><orcidid>https://orcid.org/0000-0001-7590-3624</orcidid></search><sort><creationdate>20231001</creationdate><title>Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study</title><author>Yamane, Tsutomu ; Nakayama, Takahiro ; Ekimoto, Toru ; Inoue, Masao ; Ikezaki, Keigo ; Sekiguchi, Hiroshi ; Kuramochi, Masahiro ; Terao, Yasuo ; Judai, Ken ; Saito, Minoru ; Ikeguchi, Mitsunori ; Sasaki, Yuji C</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c416t-c07bb196fc38e0a7eb17794bc92fa821af9d276202c029dbd94dc224db83f78f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Amino acids</topic><topic>Comparative analysis</topic><topic>Interfaces</topic><topic>Molecular dynamics</topic><topic>Motility</topic><topic>Neurons</topic><topic>Proteins</topic><topic>Simulation</topic><topic>Simulation methods</topic><topic>Tubulins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yamane, Tsutomu</creatorcontrib><creatorcontrib>Nakayama, Takahiro</creatorcontrib><creatorcontrib>Ekimoto, Toru</creatorcontrib><creatorcontrib>Inoue, Masao</creatorcontrib><creatorcontrib>Ikezaki, Keigo</creatorcontrib><creatorcontrib>Sekiguchi, Hiroshi</creatorcontrib><creatorcontrib>Kuramochi, Masahiro</creatorcontrib><creatorcontrib>Terao, Yasuo</creatorcontrib><creatorcontrib>Judai, Ken</creatorcontrib><creatorcontrib>Saito, Minoru</creatorcontrib><creatorcontrib>Ikeguchi, Mitsunori</creatorcontrib><creatorcontrib>Sasaki, Yuji C</creatorcontrib><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medicine (ProQuest)</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Research Library (Alumni Edition)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>Research Library Prep</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>ProQuest research library</collection><collection>Research Library (Corporate)</collection><collection>Publicly Available Content Database (Proquest) (PQ_SDU_P3)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>International journal of molecular sciences</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yamane, Tsutomu</au><au>Nakayama, Takahiro</au><au>Ekimoto, Toru</au><au>Inoue, Masao</au><au>Ikezaki, Keigo</au><au>Sekiguchi, Hiroshi</au><au>Kuramochi, Masahiro</au><au>Terao, Yasuo</au><au>Judai, Ken</au><au>Saito, Minoru</au><au>Ikeguchi, Mitsunori</au><au>Sasaki, Yuji C</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study</atitle><jtitle>International journal of molecular sciences</jtitle><date>2023-10-01</date><risdate>2023</risdate><volume>24</volume><issue>20</issue><spage>15423</spage><pages>15423-</pages><issn>1422-0067</issn><issn>1661-6596</issn><eissn>1422-0067</eissn><abstract>Tubulin has been recently reported to form a large family consisting of various gene isoforms; however, the differences in the molecular features of tubulin dimers composed of a combination of these isoforms remain unknown. Therefore, we attempted to elucidate the physical differences in the molecular motility of these tubulin dimers using the method of measurable pico-meter-scale molecular motility, diffracted X-ray tracking (DXT) analysis, regarding characteristic tubulin dimers, including neuronal TUBB3 and ubiquitous TUBB5. We first conducted a DXT analysis of neuronal (TUBB3-TUBA1A) and ubiquitous (TUBB5-TUBA1B) tubulin dimers and found that the molecular motility around the vertical axis of the neuronal tubulin dimer was lower than that of the ubiquitous tubulin dimer. The results of molecular dynamics (MD) simulation suggest that the difference in motility between the neuronal and ubiquitous tubulin dimers was probably caused by a change in the major contact of Gln245 in the T7 loop of TUBB from Glu11 in TUBA to Val353 in TUBB. The present study is the first report of a novel phenomenon in which the pico-meter-scale molecular motility between neuronal and ubiquitous tubulin dimers is different.</abstract><cop>Basel</cop><pub>MDPI AG</pub><pmid>37895101</pmid><doi>10.3390/ijms242015423</doi><orcidid>https://orcid.org/0000-0003-1643-3997</orcidid><orcidid>https://orcid.org/0000-0003-3403-237X</orcidid><orcidid>https://orcid.org/0000-0002-0249-7773</orcidid><orcidid>https://orcid.org/0000-0003-3064-3536</orcidid><orcidid>https://orcid.org/0000-0002-7419-3146</orcidid><orcidid>https://orcid.org/0000-0001-7590-3624</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1422-0067 |
| ispartof | International journal of molecular sciences, 2023-10, Vol.24 (20), p.15423 |
| issn | 1422-0067 1661-6596 1422-0067 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_10607685 |
| source | MDPI - Multidisciplinary Digital Publishing Institute; PubMed Central; EZB Electronic Journals Library |
| subjects | Amino acids Comparative analysis Interfaces Molecular dynamics Motility Neurons Proteins Simulation Simulation methods Tubulins |
| title | Comparison of the Molecular Motility of Tubulin Dimeric Isoforms: Molecular Dynamics Simulations and Diffracted X-ray Tracking Study |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-04T15%3A27%3A33IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Comparison%20of%20the%20Molecular%20Motility%20of%20Tubulin%20Dimeric%20Isoforms:%20Molecular%20Dynamics%20Simulations%20and%20Diffracted%20X-ray%20Tracking%20Study&rft.jtitle=International%20journal%20of%20molecular%20sciences&rft.au=Yamane,%20Tsutomu&rft.date=2023-10-01&rft.volume=24&rft.issue=20&rft.spage=15423&rft.pages=15423-&rft.issn=1422-0067&rft.eissn=1422-0067&rft_id=info:doi/10.3390/ijms242015423&rft_dat=%3Cgale_pubme%3EA771910753%3C/gale_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2882595364&rft_id=info:pmid/37895101&rft_galeid=A771910753&rfr_iscdi=true |