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Like a fence that encloses a backyard, all of the body's cells are surrounded by membranes. Each membrane has its own complement of membrane proteins, which perform critical functions like letting things in and out of the cell, and keeping the inside of the cell informed of what's happening on the outside. Mark Dumont, Ph.D., professor of Biochemistry and Biophysics and Pediatrics, says that more than half of the drugs on the market today target membrane proteins.

Despite their importance, the structures and mechanisms that determine how these proteins work are not very well understood. In a recent study in Science, Dumont and collaborators at the University of Virginia and the Hauptman-Woodward Institute in Buffalo describe the structure of a particular membrane protein called Ste24p that is involved in cutting up other proteins in yeast. If there's a defect in this protein, yeast can't mate.

The obvious next question is, how is yeast's inability to reproduce relevant to people? It turns out, the human equivalent of the protein Ste24p, when mutated, causes progeria -- a premature aging disorder in which children develop hair loss, joint ailments, and heart disease, which they typically die of in their mid-teens. Dumont says that better understanding how this protein works -- in yeast and in people -- will help scientists to design a drug or other treatment for this devastating disorder and learn more about the human aging process.

Nadia Fedoriw, a technician in Dumont's lab, grows yeast used for protein production

Dumont is a senior investigator of the Membrane Protein Structural Biology Consortium, one of nine NIH-funded centers across the country that are trying to solve the structures of membrane proteins. He worked with Kathleen Clark and Nadia Fedoriw from Pediatrics and Sara Connelly from Biochemistry and Biophysics on the study.

The Provost's Multidisciplinary Award provides pilot funding for especially exciting scholarly research with a high probability of future support from external sources of funding. The Award is designed to foster collaboration between departments and across schools at the University of Rochester. Five diverse research projects at the University were selected as recipients of the sixth annual Provost's Multidisciplinary Awards. The initiative provides $250,000 each year to support faculty research that crosses disciplines.

Crystal structure of the preQ1-II riboswitch.

Department of Biochemistry and Biophysics Associate Professor Joseph Wedekind and members of his research group (Joseph Liberman, Mohammad Salim and Jolanta Krucinska) published a paper in the June 2013 issue of Nature Chemical Biology. The work describes the structure of an RNA molecule called the preQ1 class II riboswitch (featured on the journal's cover) that functions as a gene regulatory element for bacteria within the Firmicutes phylum, including human pathogens such as Streptococcus pneumoniae. The RNA structure is bound to the small molecule preQ1, which is the last soluble metabolite in the biosynthetic pathway that produces queuosine, a hypermodified base at the wobble position of certain tRNAs that promotes accurate genetic decoding. Because preQ1 is unique to the bacterial metabolome, the class II preQ1 riboswitch has potential as an antibacterial drug target.

The research was performed primarily at the University of Rochester and made extensive use of the Structural Biology and Biophysics Facility. The work also required the Stanford Synchrotron Radiation Lightsource (Menlo Park, CA), as well as Cornell High Energy Synchrotron Source (Ithaca, NY) where crystals were subjected to X-ray diffraction analyses. The work in Wedekind' lab was funded by the National Institutes of Health/ National Institute for General Medical Sciences (NIH/NIGMS).

The preQ1-II riboswitch structure reveals the chemical details of preQ1 binding in a pocket formed at the junction of three RNA helices. Complementary work from Wedekind's lab showed that preQ1 promotes a more compact shape that leads to blocking of a signal that is necessary for protein synthesis, which leads to lower levels of preQ1 in the cell. Of special note was the lab's observation that the mechanism of action used by the preQ1-II RNA riboswitch is entirely different than that used by the class I preQ1 riboswitch, whose structure and mode of preQ1 binding were reported previously by Wedekind's lab. Overall the results expand the known repertoire of metabolite-binding modes used by regulatory RNAs.

The Department of Biochemistry & Biophysics held its annual Awards Ceremony on Friday, May 17, 2013. Congratulations to our 2013 Graduates:

Our department was particularly honored this year to receive the University of Rochester's prestigious Wallace O. Fenn Award named after the first Chairman of the Department of Physiology. This award is given annually to a graduating student from any program within the Medical Center judged to have completed especially meritorious Ph.D. thesis research. This year, the award was given to two recipients for their thesis originality, creative thinking and excellence in research and both recipients were students from the Department of Biochemistry & Biophysics! Congratulations to Paul Black and Chenguang Gong! For a complete list of all awards, please see the Awards Ceremony Program. Photos of the event can be viewed on the B&B event photos page.

Dr. David Mathews will head one of the primary units within the recently announced $7.5M Center for Aids Research at the University. The NIH-funded center is one of only 18 in the country and brings together University scientists from numerous disciplines. Dr. Mathews, Associate Director of the Center for RNA Biology and Associate Professor within the Department of Biochemistry and Biophysics, will head the working group focused on the biology of the AIDS virus genome, which is comprised of RNA.

University of Rochester President Joel Seligman, with 2013 Diversity Award winners Suzanne Piotrowski (THSP), Kevin Graham (THSP), Alyssa Cannarozzo (THSP), Lynne Maquat of the Medical Center, Kim Muratore (THSP), and Vice Provost for Faculty Development & Diversity Vivian Lewis.

Lynne Maquat, Ph.D., J. Lowell Orbison Endowed Chair & Professor, Biochemistry & Biophysics; Director, University of Rochester Center for RNA Biology: From Genome to Therapeutics; Chair, University of Rochester Graduate Women in Science, has been selected to receive one of two 2013 Presidential Diversity Awards for exemplary contributions to the University's diversity and inclusion efforts. Dr. Maquat is being honored for combining her groundbreaking research agenda with a lifelong commitment to helping women succeed in science. Her remarkable accomplishments include the networking and mentoring programs she initiated as president of the RNA Society; her creation in 2003 of the University of Rochester Graduate Women in Science (GWIS) program; and her award and renewal of an NIH training grant that supports graduate students, including underrepresented minorities, in the cellular, biochemical and molecular sciences.

The Presidential Diversity Awards were created in 2009 by President Joel Seligman to recognize faculty, staff, students, units, departments or teams that demonstrate a commitment to diversity and inclusion through recruitment and retention efforts, teaching, research, multi-cultural programming, cultural competency, community outreach activities, or other initiatives.

Sayeeda Zain, Ph.D.

Longtime Biochemistry & Biophysics member, Sayeeda Zain, Ph.D. passed away last week after a long and courageous battle with cancer. Services were held last Sunday for Sayeeda.

Sayeeda did her Ph.D. work with Sherman Weissman in the Dept of Human Genetics, Molecular Biophysics and Biochemistry at Yale University where she carried out some of the very earliest nucleic acid sequencing experiments, determining the sequence of parts of the SV40 virus. She then went to Richard Roberts' group at The Cold Spring Harbor Laboratories, where she applied her knowledge of sequencing to both adenovirus transcripts and genomic DNA -- and co-discovered, with Louise Chow, the phenomenon of mRNA splicing. Roberts later received the Nobel Prize for this work, with Philip Sharp (Nobel Prize in Physiology or Medicine, 1993.

In 1978 Sayeeda took a faculty position in the Microbiology Department at the University of Rochester and later was hired into to the Biochemistry Department by Fred Sherman. Sayeeda's research program focused on eukaryotic gene expression with specific emphasis on proteins involved in Alzheimer's disease and molecular mechanisms of metastasis. She remained an active member of the department, teaching in Molecules-to-Cells, until last year.

Alan E. Senior, Emeritus Professor in the department of Biochemistry & Biophysics, recently published a Reflections article in The Journal of Biological Chemistry. The article details his life and work defining the F1F0-ATPase (also known as ATP synthase), which is a fundamental component of oxidative phosphorylation, and P-glycoprotein, an important enzyme that confers multidrug resistance to anti-cancer drugs and other therapeutics.

The BSCB program will hold it's annual retreat at the Memorial Art Gallery on Monday, October 8. Our Ph.D. candidates will be presenting short talks throughout the day and posters during an afternoon session. A major highlight of the retreat is a Career Discussion Panel comprising five diverse scientists:

• Prof. Hong Li (Florida State U.)
• Prof. Doros Petasis (Alleghany College)
• Prof. Barry Goldstein (U. Rochester/professional photographer)
• Dr. Matthew Benning (Bruker-AXS, Inc.)
• Dr. Chris Strohsahl (CellTraffix, Inc.)

Lunch and refreshments will be served, courtesy of the BSCB Program's Neuman Educational Endowment, as well as corporate sponsorship from Genscript, Inc., Bruker-AXS, Inc., and GE Healthcare, Inc.

Drs. Clara Kielkopf and Joseph Wedekind are the faculty organizers and student organizers are Anant Agrawal and Karl Smith. Program and additional information will be available in September.

Congratulations to Professor Mahin Maines, Ph.D., who received recognition for her lifetime contribution to the Heme Oxygenase Community. Dr. Maines was presented with a certificate acknowledging her contribution, by her peers at the 7^th International Congress on Heme Oxygenases and Related Enzymes, 28^th May - 1^st June, held at the University of Edinburgh

William A. Bernhard, Ph.D., a faculty member of the University of Rochester Medical Center for more than 40 years and an internationally known expert on the effects of ionizing radiation on the chemical structure of DNA, died May 9 at his home in Mendon, N.Y., after a brief illness.

Bill was a biophysicist of the highest order, working at the forefront of understanding how radiation damages our genetic material. His unique command of both the biological and physical aspects of radiation damage earned him the respect and recognition of colleagues worldwide, said Jeffrey J. Hayes, Ph.D., chair of the Department of Biochemistry and Biophysics. The longevity of his research program, funded by the National Cancer Institute for 37 consecutive years, and the successful careers of his many trainees are testaments to the consistent high quality of his work, the high regard his peers, and his commitment to training future scientists. Bill also was a wonderful person and colleague.

Today, the department of Biomedical Genetics 24^th Annual Genetics Day was highlighted by the 10^th Annual Fred Sherman Lecture. Dr. Fred Sherman, Professor Emeritus of Biochemistry & Biophysics has been honored for his contributions to Genetics and Yeast Genetics for the past nine years with a lecture named after him. The NIH has funded Fred for a remarkable 45 years, during which time he has published over 280 papers, with more on the way.

In 1970, Fred initiated the famous yeast course at Cold Spring Harbor, which has trained scores of today’s leading investigators. He served as an instructor in this course for 17 years. Fred’s many landmark contributions to several fields of molecular biology were recognized by his election to the National Academy of Sciences in 1985.

Genetics Day is an annual event, including a poster session and plenary lectures, that brings together the University genetics community defined in its broadest sense. This year, Dr. Gary Ruvkun, Professor of Genetics at Harvard Medical School, gave the Sherman Lecture entitled, The tiny RNA pathways of C. elegans.

Paul L. LaCelle, M.D., a University of Rochester Medical Center faculty member for more than 40 years, a former department chair and former senior dean, died March 9. He was 82.

Dr. LaCelle, a 1959 graduate of the University's School of Medicine and Dentistry, joined the faculty in 1964 as an instructor of what was then the Department of Radiation Biology and Biophysics. He was named a professor in 1974 and chaired what is now the Department of Biochemistry and Biophysics from 1977 to 1996.

The Biophysics, Structural and Computational Biology Retreat took place on Monday, October 10, 2011 at the Memorial Art Gallery in Rochester, NY. There was a great turnout for the event with presentations by postdoctoral fellow's and students from the Dumont, Mathews, Miller, Miao, Kielkopf and Wedekind labs.

In addition to those talks, Dr. Tom Gunter who recently retired from the Biophysics program gave a retrospective talk of the history of the Biophysics program. There was also a Career Panel Discussion featuring Dr. Lea Michel (alumnus, Dr. Kara Bren's lab) from the Rochester Institute of Technology, Dr. Thomas Gaborski who is the President and CEO of SiMPore Inc. as well as Dr. Jack Daiss, Consultant and Chief Scientific Officer at Codevax. The retreat also featured over 20 poster presentations.

At this year's opening convocation on October 5, two graduate students from the department of Biochemistry & Biophysics received Graduate Fellowship's. Dejun Lin, a Ph.D. student in the Biophysics, Structural and Computational Biology graduate program, was awarded the Leon L. Miller Graduate Fellowship. This fellowship, established by the Miller family, honors Dr. Leon Miller, Professor Emeritus of Biochemistry & Biophysics, for his contributions to science and the School of Medicine and Dentistry. It is awarded annually to a student with interest in developing a biophysics-related research career.

Sarah Amie, a Ph.D. student in the Biochemistry and Molecular Biology graduate program, was awarded the Elmer H. Stotz Graduate Fellowship. This fellowship, established by the Stotz family to honor Dr. Elmer Stotz, Professor Emeritus and former Chair of the Department of Biochemistry, is awarded to a Ph.D. student in biochemistry.

Robert Bambara and Biochemistry & Biophysics Graduates.

The department of Biochemistry & Biophysics held its annual awards ceremony to celebrate those students that received their doctoral degree this year. Awards were also given out to various students and faculty members for their respective research and teaching contributions. The following awards were given:

Walter Bloor Award for Excellent Ph.D. Thesis

Keith Connolly and Christopher Hine

George Metzger Award for Excellence in Biophysics Ph.D. Thesis

Jessica Snyder

Marvel-Dare Nutting Award Recognizing an Outstanding Biochemistry Ph.D.

Tamara Caterino

William Neuman Award in Biophysics

Paul Black

William Neuman Travel Awards

Paul Black, He Fang, Nicholas Leioatts, and Wenhua Wang

Excellent Student Seminar Presentations

Wen Shen, Karyn Schmidt, Krystle McLaughlin, and Nicholas Leioatts

Faculty Teaching Awards

David Mathews, Ph.D. and Lynne Maquat, Ph.D.

Staff Recognition Award

Melissa Vera