{"543481":{"#nid":"543481","#data":{"type":"news","title":"DNA\u0027s worm-like moves","body":[{"value":"\u003Ch2\u003EThe genetic material could scrunch its way into a virus.\u003C\/h2\u003E\u003Cp dir=\u0022ltr\u0022\u003EDNA may scrunch like a worm to get inside viral shells, a team including Georgia Tech researchers reports in \u003Ca href=\u0022http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jpcb.6b02149\u0022\u003Ethe Journal of Physical Chemistry B.\u003C\/a\u003E This deeper understanding could \u0026nbsp;lead to new ways to fight pathogens and design powerful DNA transporters.\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EA critical step in viral replication is the packaging of genetic material. To successfully invade host cells, viral particles must hijack the host\u2019s machinery to make copies of viral genetic material and build protein shells called capsids to house viral DNA or RNA. Scientists have been studying how the genetic material is driven into capsids so they might one day block this step.\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EViral capsids are assembled from a number of identical protein subunits, like a soccer ball sewn together from panels. At the lone opening sits a protein complex, called the protein tunnel, through which DNA enters and exits the capsid, analogous to the air valve that allows a soccer ball to be inflated. \u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EThe proteins driving this process are among the strongest biological motors known. Most scientists have assumed that these proteins act like levers, grabbing the DNA and applying force along the axis of the DNA to push it into the capsid. In this simple mechanical picture, DNA plays a passive role.\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EHowever, all molecules are dynamic, says \u003Ca href=\u0022https:\/\/www.physics.gatech.edu\/user\/harold-kim\u0022\u003EHarold D. Kim\u003C\/a\u003E, an associate professor at Georgia Tech\u2019s School of Physics and a coauthor of the study. \u201cThey do not stay in one shape, but constantly change their conformation because of thermal fluctuations,\u201d he explains. DNA is not an exception. It is therefore plausible that DNA itself contributes to genome packaging. \u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EA couple of years ago, \u003Ca href=\u0022http:\/\/www.harveylabpenn.net\/\u0022\u003EStephen C. Harvey,\u003C\/a\u003E then a professor in the School of Biology at Georgia Tech and now at the University of Pennsylvania, proposed a role for DNA. The role is based on DNA\u2019s ability to interconvert between two alternative structures \u2013 called A and B forms \u2013 depending on the number of surrounding water molecules. Called the \u201cscrunchworm\u201d hypothesis, it proposes that DNA changes its form when the protein tunnel changes its shape.\u0026nbsp;\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EAccording to Kim, proteins composing the tunnel are enzymes that burn ATP to do mechanical work, which alternately widens and shrinks the tunnel itself. The hypothesis suggests that DNA assumes the short A form when the tunnel is narrow and converts to the B form when the tunnel is wide, rather than being pushed directly by the protein tunnel. Thus, the DNA itself produces the actual movement along the tunnel, while proteins only grab and release the DNA at two locations in a coordinated manner to guide it in the right direction. \u0026nbsp;\u0026nbsp;\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003ETo test this hypothesis, Harvey, Kim, and \u003Ca href=\u0022https:\/\/www.physics.gatech.edu\/user\/james-jc-gumbart\u0022\u003EJames C. Gumbart\u003C\/a\u003E, an assistant professor in Georgia Tech\u2019s School of Physics embarked on a collaboration. The Kim group had been studying the bending dynamics of DNA that influence genome packaging, and the Gumbart group had expertise in molecular dynamics simulations. James T. Waters, a Ph.D. student in Kim\u2019s group, carried out the molecular dynamics simulations. He and Columbia University research scientist Xiang-Jun Lu performed data analysis. In \u003Ca href=\u0022http:\/\/pubs.acs.org\/doi\/abs\/10.1021\/acs.jpcb.6b02155\u0022\u003Ea previous work\u003C\/a\u003E, the researchers reported a simple way to visualize the A-B transitions of DNA. The same method was used to characterize the DNA structures inside the protein tunnel.\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EThe researchers simulated interactions between a protein and DNA sequences from a virus. The computer models suggest that the DNA scrunches spontaneously without any lever-like protein motions. If further testing bears out this proposed mechanism, it would demonstrate for the first time that changes in DNA\u2019s shape can produce strong forces. \u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003E\u201cThese studies also reinforce our rapidly expanding view that DNA is more than just genetic information: It is an active participant in genome packaging and maintenance,\u201d Kim notes.\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EAlthough these studies were carried out on a non-pathogenic virus, the resulting insights are most likely broadly applicable, because the same packaging mechanism is used by herpes viruses that cause diseases such as chickenpox, shingles, infectious mononucleosis, and oral and genital lesions.\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EThe authors acknowledge funding from the National Institute of Health and the National Science Foundation. \u0026nbsp;\u0026nbsp;\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003E\u003Cbr \/\u003E\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EFor more information, contact:\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EHarold D. Kim\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003ESchool of Physics\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EGeorgia Institute of Technology\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EAtlanta, GA 30332\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EPhone: 404-894-0080\u003C\/p\u003E\u003Cbr \/\u003E","summary":null,"format":"limited_html"}],"field_subtitle":"","field_summary":"","field_summary_sentence":[{"value":"The genetic material could scrunch its way into a virus"}],"uid":"28004","created_gmt":"2016-06-09 13:04:15","changed_gmt":"2016-10-08 03:21:53","author":"Dione Morton","boilerplate_text":"","field_publication":"","field_article_url":"","dateline":{"date":"2016-06-09T00:00:00-04:00","iso_date":"2016-06-09T00:00:00-04:00","tz":"America\/New_York"},"extras":[],"hg_media":{"543471":{"id":"543471","type":"image","title":"Harold Kim and James Waters","body":null,"created":"1465826400","gmt_created":"2016-06-13 14:00:00","changed":"1475895333","gmt_changed":"2016-10-08 02:55:33","alt":"Harold Kim and James Waters","file":{"fid":"217184","name":"harold_and_james_0.png","image_path":"\/sites\/default\/files\/images\/harold_and_james_0.png","image_full_path":"http:\/\/hg.gatech.edu\/\/sites\/default\/files\/images\/harold_and_james_0.png","mime":"image\/png","size":794930,"path_740":"http:\/\/hg.gatech.edu\/sites\/default\/files\/styles\/740xx_scale\/public\/images\/harold_and_james_0.png?itok=uwUIUkA4"}}},"media_ids":["543471"],"groups":[],"categories":[{"id":"150","name":"Physics and Physical Sciences"}],"keywords":[{"id":"166937","name":"School of Physics"}],"core_research_areas":[],"news_room_topics":[],"event_categories":[],"invited_audience":[],"affiliations":[],"classification":[],"areas_of_expertise":[],"news_and_recent_appearances":[],"phone":[],"contact":[{"value":"\u003Cp dir=\u0022ltr\u0022\u003EFor more information, contact:\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EHarold D. Kim\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003ESchool of Physics\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EGeorgia Institute of Technology\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EAtlanta, GA 30332\u003C\/p\u003E\u003Cp dir=\u0022ltr\u0022\u003EPhone: 404-894-0080\u003C\/p\u003E","format":"limited_html"}],"email":["dione.morton@physics.gatech.edu"],"slides":[],"orientation":[],"userdata":""}}}