March 26, 2010
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the Vol. 64B - No. 10 ulletin March 26, 2010 Grooving Down the Helix ‘Communicating Science’ Researchers show that proteins slide along DNA to carry out vital biological processes Alan Alda To Talk at Workshop, 4/9 A team of scientists from BNL, A Message From Lab Harvard University, and the In- dian Institute of Science (IIS) has Director Sam Aronson made a major step in understand- Alan Alda, the highly acclaimed ing how molecules locate the ge- actor and host of PBS’ “Scien- netic information in DNA that is tific American Frontiers,” and necessary to carry out important Stoutenburgh Roger Howie Schneider, Dean of the biological processes. The research, Stony Brook University School published in the December 1, of Journalism and one of the 2009 edition of Nature Structural founders of its Center for Com- D30680809 & Molecular Biology, confirms that municating Science, are both many proteins responsible for in- deeply committed to helping teracting at specific sites on DNA D0021008 scientists — and all who care find their targets by sliding along about science — talk about one of the grooves of the DNA their research and what is hap- Alan Alda and Sam Aronson Joseph Rubino double helix in a spiraling fash- Walter Mangel pening in the field with greater ion. The research was funded by clarity and understanding. that Alan and Howie are con- the DNA. They could not see the tative Israel secured $214,000 in the National Institute of Allergy Last fall, Alan and Howie tinuing this effort and coming exact path the molecules were start-up funds for the program and Infectious Diseases, part of piloted an innovative pro- back to the Lab on Friday, April sliding on, but they could mea- because he believes that as the National Institutes of Health, gram at Stony Brook and at 9 for a full-day program. The sure the speed of the molecules. public citizens, it is our obliga- the National Science Foundation, Brookhaven to help advance improvisational workshop is Depending on how a protein tion to be able to communicate and the Department of Science these goals. one of four sessions that will moves along a DNA axis — either much more effectively what we and Technology of India. Designed by Alan, the pro- help us hone our communica- in a linear or helical pattern — it do and what it means to our “Essentially, proteins that gram uses improvisational tion skills; a complete agenda will encounter different degrees society. search for specific information theater techniques to help sci- can be found at http://www.bnl. of resistance, as shown in the I’d like to encourage as spin down the double helix of entists describe their work in a gov/csw/. earlier paper. If protein motion many of you as possible to the DNA, like traveling along the variety of situations. I watched Last week I met with Con- is linear, its speed will decrease participate in the workshop threads of a screw, until they lo- as 12 of our scientific staff prac- gressman Steve Israel in D.C. proportionately as its radius sessions, as well as to join Alan cate their target,” said co-author ticed these techniques, engaged He, too, commented on the increases. If a protein exhibits Alda and a panel of experts Walter Mangel of BNL’s Biology with each other — and had fun importance of better commu- helical motion, it will experience — including BNL’s Joanna Department. in the process. The results were nication by scientists and his additional friction and its speed Fowler — for the morning talks This research provides experi- very impressive — so much so, belief in this program. Represen- will decrease much faster as its about science communication. mental proof of a recent theory radius increases. All are welcome, with supervisory approval, to attend Lab Director Sam Aronson’s welcoming remarks, Alan put forth by the team. It could Using a human DNA repair Alda’s talk, and the expert panel discussion on science communication, starting at 9 a.m. on April 9 in lead to new ways to alter the be- protein as a test for the protein Berkner Hall. Registration is required to attend the workshops in the afternoon. Please go to http://www.bnl. havior of DNA-binding proteins, rotation model, Paul Blainey, gov/csw/ to learn more about the workshops and to register. which are responsible for repli- now at Stanford University, cating and repairing DNA, and found the latter case to be true. for turning genes on and off. IBM Nano Study Paves Way for Remote Access at NSLS When he increased the size of For decades, scientists have the protein, the rate of motion Synchrotron-based x-ray diffrac- known that proteins searching decreased much more rapidly tion techniques have become for genetic sequences are able to than it would have for a simple largely automated, yet researchers locate them at rates much faster linear motion. must still travel from all over the than expected. They found that Relying on the same tech- world to BNL’s National Synchro- nique, the group went on to tron Light Source (NSLS) simply analyze the diffusion rates of to load their samples and pro- Visualization eight different proteins of various gram a few computer parameters of a protein sizes. These molecules had highly before the system takes over. molecule diverse functions — such as DNA “We would like to figure out sliding along ways to offer more flexibility for DNA. The replication, cleavage, and repair researchers using the NSLS,” said D3020210 protein (the — and DNA-binding mecha- sphere) nisms. They were also taken from Kathy Nasta, the NSLS user ad- travels along a range of organisms, including ministration office manager. “We the DNA helix mammals, bacteria, and human are trying to learn how to use the as if it were viruses. system we have in place to build spinning The researchers observed the a remote access program.” Joseph Rubino along same pattern: The speed of each IBM researcher Jean Jordan- IBM’s Jean Jordan-Sweet loads a silicon wafer sample into the diffractom- the threads eter at NSLS X20A for colleagues performing a remote access experiment. protein decreased dramatically as Sweet had plenty of reasons to of a screw. its radius increased, as predicted volunteer one of IBM’s beam- leagues, Bin Yang, a technical chips, but the commute to use by the theory for helical sliding. lines, X20A, for pioneering re- staff member at IBM’s alliance this resource can be difficult. “The data present strong evi- mote access protocols. partner, GlobalFoundries, and My drive is only two hours from dence that proteins seek out tar- “IBM has multiple worksites his collaborator at IBM, Chris- Westchester County, New York, rather than moving around the geted DNA sequences by spinning statewide and numerous U.S. tian Lavoie, eagerly volunteered but other researchers come from entire three-dimensional space down the helix rather than lin- and international partner al- their beam time for a remote all over the world.” inside a cell, they moved in one early sliding along its axis,” said liances,” said Jordan-Sweet. access attempt. For Jordan-Sweet, getting the dimension, along DNA molecules. Biman Bigachi, an IIS co-author. “Remote access can help our “Our studies are pushing the necessary software for remote ac- The Harvard group showed, in This work validates the new researchers who can’t get here physical limits of nanomaterials cess was as simple as download- 2006, that the proteins slide back equation for describing and pre- or who are really busy and have since technological devices are ing and configuring free online and forth in direct contact with dicting the motion of protein other work they need to do dur- becoming so small,” said Yang. programs called PuTTY and NX the DNA as part of the search for molecules along strands of DNA ing the hours that data are auto- “We need synchrotron sources to Client. She received software specific sequences. with a higher degree of accuracy matically collected.” study thin silicide films in order guidance from NSLS Controls Until now, however, the exact than ever before. It enhances the IBM’s researchers use the x-ray to understand processes better Computing Leader Zhijian Yin. nature of the path these mol- possibility of future research in beamline to investigate how dif- and to make better computer After BNL’s Information ecules take along the DNA has understanding and manipulat- ferent nanomaterials “behave” Technology Division provided not been known. One challenge ing the DNA-binding and sliding after exposure to thermal treat- the team with a gateway server is that the very fine and quick behavior of proteins. ments that mimic the microelec- for secure access to the BNL net- motions occur at extremely small Said Mangel, “By being able to tronics manufacturing process. work and Jordan-Sweet relayed a space and time scales and the predict the DNA-sliding rate of a The technique allows researchers quick software tutorial to Yang precise motions of a DNA-binding protein, one could alter the size to determine the best combina- and Lavoie, they were ready for molecule are difficult to observe of a protein and thereby alter its tion of materials and processes to testing. directly. So the researchers used sliding rate. For example, certain use when advancing, and shrink- For the first test experiment, indirect methods to determine viral proteins need to slide along ing, new technologies. they chose a relatively simple the protein’s path. DNA in order to cause infec- Two of Jordan-Sweet’s col- study that involved collecting With a special fluorescence tion.