Residue Specific and Chirality Dependent Interactions between Carbon Nanotubes and Flagellin
Flagellum is a lash-like cellular appendage found in many single-celled living organisms. The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner doma...
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| Veröffentlicht in: | IEEE/ACM transactions on computational biology and bioinformatics 2016-05, Vol.13 (3), p.541-548 |
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| creator | Macwan, Isaac G. Zihe Zhao Sobh, Omar T. Mukerji, Ishita Dharmadhikari, Bhushan Patra, Prabir K. |
| description | Flagellum is a lash-like cellular appendage found in many single-celled living organisms. The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner domains predominantly consist of α-helices, the outer domains are primarily beta sheets with D3. In flagellum, the outermost sub-domain is the only one that is exposed to the native environment. This study focuses on the interactions of the residues of D3 of an R-type flagellin with 5nm long chiral (5,15) and arm-chair (12,12) single-walled carbon nanotubes (SWNT) using molecular dynamics simulation. It presents the interactive forces between the SWNT and the residues of D3 from the perspectives of size and chirality of the SWNT. It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions, and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs. |
| doi_str_mv | 10.1109/TCBB.2015.2459696 |
| format | Article |
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The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner domains predominantly consist of α-helices, the outer domains are primarily beta sheets with D3. In flagellum, the outermost sub-domain is the only one that is exposed to the native environment. This study focuses on the interactions of the residues of D3 of an R-type flagellin with 5nm long chiral (5,15) and arm-chair (12,12) single-walled carbon nanotubes (SWNT) using molecular dynamics simulation. It presents the interactive forces between the SWNT and the residues of D3 from the perspectives of size and chirality of the SWNT. It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions, and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs.</description><identifier>ISSN: 1545-5963</identifier><identifier>EISSN: 1557-9964</identifier><identifier>DOI: 10.1109/TCBB.2015.2459696</identifier><identifier>PMID: 27295637</identifier><identifier>CODEN: ITCBCY</identifier><language>eng</language><publisher>United States: IEEE</publisher><subject>Bacterial Flagellum ; Bioinformatics ; Carbon nanotubes ; Cellular ; Chirality ; Computational biology ; Computer simulation ; Flagellin - chemistry ; Flagellin - metabolism ; Flagellin Domain ; Glycine ; Hydrogen ; Hydrogen Bonding ; Hydrophobicity ; Microorganisms ; Molecular Dynamics ; Molecular Dynamics Simulation ; Nanotube Sorting ; Nanotubes ; Nanotubes, Carbon - chemistry ; Protein engineering ; Proteins ; Residues ; Single wall carbon nanotubes ; Stereoisomerism</subject><ispartof>IEEE/ACM transactions on computational biology and bioinformatics, 2016-05, Vol.13 (3), p.541-548</ispartof><rights>Copyright The Institute of Electrical and Electronics Engineers, Inc. (IEEE) 2016</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c458t-798b401e60e5b8b2d4c91c3f84096ff3a70b17f3f5d142b2879c88173b453fe3</citedby><cites>FETCH-LOGICAL-c458t-798b401e60e5b8b2d4c91c3f84096ff3a70b17f3f5d142b2879c88173b453fe3</cites><orcidid>0000-0002-2917-793X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://ieeexplore.ieee.org/document/7174990$$EHTML$$P50$$Gieee$$H</linktohtml><link.rule.ids>315,781,785,797,27926,27927,54760</link.rule.ids><linktorsrc>$$Uhttps://ieeexplore.ieee.org/document/7174990$$EView_record_in_IEEE$$FView_record_in_$$GIEEE</linktorsrc><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/27295637$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Macwan, Isaac G.</creatorcontrib><creatorcontrib>Zihe Zhao</creatorcontrib><creatorcontrib>Sobh, Omar T.</creatorcontrib><creatorcontrib>Mukerji, Ishita</creatorcontrib><creatorcontrib>Dharmadhikari, Bhushan</creatorcontrib><creatorcontrib>Patra, Prabir K.</creatorcontrib><title>Residue Specific and Chirality Dependent Interactions between Carbon Nanotubes and Flagellin</title><title>IEEE/ACM transactions on computational biology and bioinformatics</title><addtitle>TCBB</addtitle><addtitle>IEEE/ACM Trans Comput Biol Bioinform</addtitle><description>Flagellum is a lash-like cellular appendage found in many single-celled living organisms. The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner domains predominantly consist of α-helices, the outer domains are primarily beta sheets with D3. In flagellum, the outermost sub-domain is the only one that is exposed to the native environment. This study focuses on the interactions of the residues of D3 of an R-type flagellin with 5nm long chiral (5,15) and arm-chair (12,12) single-walled carbon nanotubes (SWNT) using molecular dynamics simulation. It presents the interactive forces between the SWNT and the residues of D3 from the perspectives of size and chirality of the SWNT. It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions, and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs.</description><subject>Bacterial Flagellum</subject><subject>Bioinformatics</subject><subject>Carbon nanotubes</subject><subject>Cellular</subject><subject>Chirality</subject><subject>Computational biology</subject><subject>Computer simulation</subject><subject>Flagellin - chemistry</subject><subject>Flagellin - metabolism</subject><subject>Flagellin Domain</subject><subject>Glycine</subject><subject>Hydrogen</subject><subject>Hydrogen Bonding</subject><subject>Hydrophobicity</subject><subject>Microorganisms</subject><subject>Molecular Dynamics</subject><subject>Molecular Dynamics Simulation</subject><subject>Nanotube Sorting</subject><subject>Nanotubes</subject><subject>Nanotubes, Carbon - chemistry</subject><subject>Protein engineering</subject><subject>Proteins</subject><subject>Residues</subject><subject>Single wall carbon nanotubes</subject><subject>Stereoisomerism</subject><issn>1545-5963</issn><issn>1557-9964</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2016</creationdate><recordtype>article</recordtype><sourceid>RIE</sourceid><sourceid>EIF</sourceid><recordid>eNqNkU2L1TAUhoMozof-ABGkMJvZ9JrPJmfpVEcHBgW9S6Ek6Ylm6E2vSYvMv7f1XmfhRlcncJ735YSHkBeMbhij8HrbXl1tOGVqw6WCBppH5JQppWuARj5e31LVy0KckLNS7ijlEqh8Sk645qAaoU_J189YYj9j9WWPPoboK5v6qv0esx3idF-9xT2mHtNU3aQJs_VTHFOpHE4_EVPV2uzGVH20aZxmh-V3-nqw33AYYnpGngQ7FHx-nOdke_1u236obz-9v2nf3NZeKjPVGoyTlGFDUTnjeC89MC-CkRSaEITV1DEdRFA9k9xxo8Ebw7RwUomA4pxcHmr3efwxY5m6XSx-ucAmHOfSMcOVBKOE_A-UmkZwWIr_iWrQXCkl6YJe_IXejXNOy5dXSoE0oM1CsQPl81hKxtDtc9zZfN8x2q0-u9Vnt_rsjj6XzKtj8-x22D8k_ghcgJcHICLiw1ozLQGo-AVZmqIo</recordid><startdate>201605</startdate><enddate>201605</enddate><creator>Macwan, Isaac G.</creator><creator>Zihe Zhao</creator><creator>Sobh, Omar T.</creator><creator>Mukerji, Ishita</creator><creator>Dharmadhikari, Bhushan</creator><creator>Patra, Prabir K.</creator><general>IEEE</general><general>The Institute of Electrical and Electronics Engineers, Inc. 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chemistry</topic><topic>Flagellin - metabolism</topic><topic>Flagellin Domain</topic><topic>Glycine</topic><topic>Hydrogen</topic><topic>Hydrogen Bonding</topic><topic>Hydrophobicity</topic><topic>Microorganisms</topic><topic>Molecular Dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>Nanotube Sorting</topic><topic>Nanotubes</topic><topic>Nanotubes, Carbon - chemistry</topic><topic>Protein engineering</topic><topic>Proteins</topic><topic>Residues</topic><topic>Single wall carbon nanotubes</topic><topic>Stereoisomerism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Macwan, Isaac G.</creatorcontrib><creatorcontrib>Zihe Zhao</creatorcontrib><creatorcontrib>Sobh, Omar T.</creatorcontrib><creatorcontrib>Mukerji, Ishita</creatorcontrib><creatorcontrib>Dharmadhikari, Bhushan</creatorcontrib><creatorcontrib>Patra, Prabir K.</creatorcontrib><collection>IEEE All-Society Periodicals Package (ASPP) 2005-present</collection><collection>IEEE All-Society Periodicals Package (ASPP) 1998-Present</collection><collection>IEEE Electronic Library (IEL)</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Aluminium Industry Abstracts</collection><collection>Biotechnology Research Abstracts</collection><collection>Ceramic Abstracts</collection><collection>Computer and Information Systems Abstracts</collection><collection>Corrosion Abstracts</collection><collection>Electronics & Communications Abstracts</collection><collection>Engineered Materials Abstracts</collection><collection>Materials Business File</collection><collection>Mechanical & Transportation Engineering Abstracts</collection><collection>Solid State and Superconductivity Abstracts</collection><collection>METADEX</collection><collection>Technology Research Database</collection><collection>ANTE: Abstracts in New Technology & Engineering</collection><collection>Engineering Research Database</collection><collection>Aerospace Database</collection><collection>Materials Research Database</collection><collection>ProQuest Computer Science Collection</collection><collection>Civil Engineering Abstracts</collection><collection>Advanced Technologies Database with Aerospace</collection><collection>Computer and Information Systems Abstracts Academic</collection><collection>Computer and Information Systems Abstracts Professional</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>MEDLINE - 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It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions, and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs.</abstract><cop>United States</cop><pub>IEEE</pub><pmid>27295637</pmid><doi>10.1109/TCBB.2015.2459696</doi><tpages>8</tpages><orcidid>https://orcid.org/0000-0002-2917-793X</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Bacterial Flagellum Bioinformatics Carbon nanotubes Cellular Chirality Computational biology Computer simulation Flagellin - chemistry Flagellin - metabolism Flagellin Domain Glycine Hydrogen Hydrogen Bonding Hydrophobicity Microorganisms Molecular Dynamics Molecular Dynamics Simulation Nanotube Sorting Nanotubes Nanotubes, Carbon - chemistry Protein engineering Proteins Residues Single wall carbon nanotubes Stereoisomerism |
| title | Residue Specific and Chirality Dependent Interactions between Carbon Nanotubes and Flagellin |
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