Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations
Hepatitis C virus helicase is a molecular motor that splits duplex DNA while actively moving over it. An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an importa...
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| Veröffentlicht in: | Proceedings of the National Academy of Sciences - PNAS 2010-12, Vol.107 (49), p.20875-20880 |
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| container_issue | 49 |
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| container_title | Proceedings of the National Academy of Sciences - PNAS |
| container_volume | 107 |
| creator | Flechsig, Holger Mikhailov, Alexander S. Ertl, Gerhard |
| description | Hepatitis C virus helicase is a molecular motor that splits duplex DNA while actively moving over it. An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an important protein machine could be followed in structurally resolved dynamical simulations. Ratcheting inchworm translocation and spring-loaded DNA unwinding, suggested by experimental data, were reproduced. Thus, feasibility of coarse-grained simulations, bridging a gap between full molecular dynamics and reduced phenomenological theories of molecular motors, has been demonstrated. |
| doi_str_mv | 10.1073/pnas.1014631107 |
| format | Article |
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An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an important protein machine could be followed in structurally resolved dynamical simulations. Ratcheting inchworm translocation and spring-loaded DNA unwinding, suggested by experimental data, were reproduced. 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An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an important protein machine could be followed in structurally resolved dynamical simulations. Ratcheting inchworm translocation and spring-loaded DNA unwinding, suggested by experimental data, were reproduced. Thus, feasibility of coarse-grained simulations, bridging a gap between full molecular dynamics and reduced phenomenological theories of molecular motors, has been demonstrated.</description><subject>Adenosine triphosphatase</subject><subject>ATP</subject><subject>Biological Sciences</subject><subject>Computer Simulation</subject><subject>Data processing</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA helicase</subject><subject>DNA Helicases - physiology</subject><subject>Genetic equilibrium</subject><subject>Hepacivirus</subject><subject>Hepacivirus - chemistry</subject><subject>Hepatitis</subject><subject>Hepatitis C</subject><subject>Hepatitis C virus</subject><subject>Hydrolysis</subject><subject>Kinetics</subject><subject>Ligands</subject><subject>Molecular Dynamics Simulation</subject><subject>Molecular Motor Proteins - physiology</subject><subject>Motors</subject><subject>Movement</subject><subject>Particle interactions</subject><subject>Physical Sciences</subject><subject>Polymers</subject><subject>Proteins</subject><subject>Simulation</subject><subject>Trajectories</subject><subject>Translocation</subject><subject>Unwinding</subject><subject>Viral Nonstructural Proteins - physiology</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkkuP0zAUhSMEYsrAmhXIYsOqjB3Hrw0SqnhJI7Hp3nKc2xlXThzspFIlfjw3apkCm_HGlv3dY_vcU1WvGf3AqOI34-AKrlgjOcONJ9WKUcPWsjH0abWitFZr3dTNVfWilD2l1AhNn1dXNaOaSaNW1a9tdj4MdwSGKWQgaYTsppAG4o8-QiFpR_oUwc_RZVxNKZN7GBGZQiEbcgh5LrgTg3cFSBhImfLspzm7GI8kQ0nxAB3pjoPrkYmkhB61livKy-rZzsUCr87zdbX98nm7-ba-_fH1--bT7doLI6e1BCUbp1topXA1tKzhlIFwuhHAJN9543GAqzkIbrqa6U5LTWuuoeVC8evq40l2nNseOo9fxdfZMYfe5aNNLth_T4Zwb-_SwXJ0rDYCBd6fBXL6OUOZbB-KhxjdAGkuVquGaSooe5zEzoiaCfM4yaQynBmN5Lv_yH2a84CGIaTQACMlQjcnyOdUSobdw_cYtUtU7BIVe4kKVrz925UH_k82ECBnYKm8yCnbGFtTrRZj3pyQfcFgXCSEEtgAyn8DDq_Rew</recordid><startdate>20101207</startdate><enddate>20101207</enddate><creator>Flechsig, Holger</creator><creator>Mikhailov, Alexander S.</creator><creator>Ertl, Gerhard</creator><general>National Academy of Sciences</general><general>National Acad Sciences</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>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20101207</creationdate><title>Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations</title><author>Flechsig, Holger ; Mikhailov, Alexander S. ; Ertl, Gerhard</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c596t-6e764a8beb65a2eb14301e5a845e163fc9ccccea23e539d218d8680238eb3573</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Adenosine triphosphatase</topic><topic>ATP</topic><topic>Biological Sciences</topic><topic>Computer Simulation</topic><topic>Data processing</topic><topic>Deoxyribonucleic acid</topic><topic>DNA</topic><topic>DNA helicase</topic><topic>DNA Helicases - physiology</topic><topic>Genetic equilibrium</topic><topic>Hepacivirus</topic><topic>Hepacivirus - chemistry</topic><topic>Hepatitis</topic><topic>Hepatitis C</topic><topic>Hepatitis C virus</topic><topic>Hydrolysis</topic><topic>Kinetics</topic><topic>Ligands</topic><topic>Molecular Dynamics Simulation</topic><topic>Molecular Motor Proteins - physiology</topic><topic>Motors</topic><topic>Movement</topic><topic>Particle interactions</topic><topic>Physical Sciences</topic><topic>Polymers</topic><topic>Proteins</topic><topic>Simulation</topic><topic>Trajectories</topic><topic>Translocation</topic><topic>Unwinding</topic><topic>Viral Nonstructural Proteins - physiology</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Flechsig, Holger</creatorcontrib><creatorcontrib>Mikhailov, Alexander S.</creatorcontrib><creatorcontrib>Ertl, Gerhard</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Immunology Abstracts</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Oncogenes and Growth Factors Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Environmental Sciences and Pollution Management</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Flechsig, Holger</au><au>Mikhailov, Alexander S.</au><au>Ertl, Gerhard</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations</atitle><jtitle>Proceedings of the National Academy of Sciences - PNAS</jtitle><addtitle>Proc Natl Acad Sci U S A</addtitle><date>2010-12-07</date><risdate>2010</risdate><volume>107</volume><issue>49</issue><spage>20875</spage><epage>20880</epage><pages>20875-20880</pages><issn>0027-8424</issn><eissn>1091-6490</eissn><abstract>Hepatitis C virus helicase is a molecular motor that splits duplex DNA while actively moving over it. An approximate coarse-grained dynamical description of this protein, including its interactions with DNA and ATP, is constructed. Using such a mechanical model, entire operation cycles of an important protein machine could be followed in structurally resolved dynamical simulations. Ratcheting inchworm translocation and spring-loaded DNA unwinding, suggested by experimental data, were reproduced. Thus, feasibility of coarse-grained simulations, bridging a gap between full molecular dynamics and reduced phenomenological theories of molecular motors, has been demonstrated.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>21081697</pmid><doi>10.1073/pnas.1014631107</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adenosine triphosphatase ATP Biological Sciences Computer Simulation Data processing Deoxyribonucleic acid DNA DNA helicase DNA Helicases - physiology Genetic equilibrium Hepacivirus Hepacivirus - chemistry Hepatitis Hepatitis C Hepatitis C virus Hydrolysis Kinetics Ligands Molecular Dynamics Simulation Molecular Motor Proteins - physiology Motors Movement Particle interactions Physical Sciences Polymers Proteins Simulation Trajectories Translocation Unwinding Viral Nonstructural Proteins - physiology |
| title | Tracing entire operation cycles of molecular motor hepatitis C virus helicase in structurally resolved dynamical simulations |
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