Winter 2001
Volume 3, Number 2
  


Protein and RNA folding
Sharing perspectives through outreach

By Celena E. Kusch


In June 2000, the Human Genome Project announced the completion of a working draft of the human genome sequence. At that time, project scientists collaborating in a number of university labs had identified 90 percent of the 3.3 billion chemical bases that make up human DNA. In the next three years, they hope to refine and expand their results to produce a complete reference sequence for use in medicine and basic research.

For these researchers, however, knowing the sequence map of DNA is only the beginning. The sequence is just that, a multibillion member series of the letters A, T, C and G, signaling the chemical make-up of individual genes. The order is useful in identifying the chemical composition of the RNA and proteins that do all the work in the cell. What remains is to understand how these RNA and protein sequences fold into three-dimensional shapes in order to function properly.

The 19th Summer Symposium in Molecular Biology at The Penn Stater Conference Center Hotel called together researchers in the RNA and protein folding communities to promote the exchange of ideas and fresh insights into the folding of these macromolecules. The 2000 conference, “The Protein and RNA Folding Problems: Sharing Perspectives,” was the latest in this internationally recognized series hosted at Penn State since 1982. More than 150 participants, including faculty, industry scientists, graduate students, postdoctoral scholars and undergraduates from as far away as the University of Granada and Nagoya University, attended the event.

According to symposium co-chair Dr. John Desjarlais, assistant professor of chemistry at Penn State, “From a scientific standpoint, this is the first meeting on record that intimately brings together RNA and protein folding communities.”

Symposium co-chair Dr. Philip Bevilacqua, assistant professor of chemistry at Penn State, added that with today’s rapid advances in science and technology such cross-field collaborations are “timely throughout science.” “When researchers from different fields can share their perspectives and findings, new ideas come out of it,” he said. “RNA folding is an emerging field, becoming particularly prominent in the last five years. It has borrowed extensively from the protein folding field, and much more work needs to be done to determine how the two fields are similar and different.”

In order to achieve that comparative perspective, conference organizers chose a plenary speaker from outside both fields. Desjarlais explained that the goal was to broaden the dialogue between RNA and protein scientists by bringing in speakers from one area who “dip into the other field.”

In his address, Dr. Peter Moore, professor of chemistry at Yale University, admitted that he was not part of the folding community, joking, “When unfolded molecules show up in my lab, we throw them away.” Nonetheless, Moore’s presentation of the best-ever images of the large ribosomal subunit, the structure in cells responsible for producing proteins, had important implications for both groups.

The ribosome itself is composed of both proteins and ribosomal RNA folded into what Moore characterized as a smooth, monolithic structure like a Portuguese man-of-war (the RNA) with its tentacles (proteins) wrapped up tightly within itself. Moore cautioned all those who study the 31 proteins that are part of the ribosome section to take into account their complex relationships with the RNA to which they bind. “When you are folding the jellyfish,” Moore said, “it is impossible to understand the structure of the protein out of context with RNA around it.”

The term “folding,” suggestive of the simplicity of piles of laundered towels or the angled geometry of origami, does not fully describe the complexity of these actions. In fact, protein and RNA folding more closely resembles the repeated coiling and twisting of a phone cord until it begins to conform to a highly irregular, relatively inflexible shape. Once coiled, the original line of the cord is still recognizable within the coiled block, but only certain curves twist to the surface while other segments are completely inaccessible.

The symposium’s protein and RNA folding scientists examine this molecular phone cord, coiled not by the force of two giant hands at either end, but by complex chemical attractions and repulsions between their surrounding structures and environment and the various parts of the cord itself. The scientists’ task is eventually to be able to predict the shape of the various three-dimensional structures and the way proteins and RNA assume those shapes.

Using images displayed at atomic resolution, Moore revealed an extremely restrictive and “nonstick” hole running through the roughly mitten-shaped ribosomal subunit. Identifying it as the “exit tunnel” for all of the proteins formed within the ribosome, Moore confirmed past theoretical predictions about the location of protein-formation within the ribosome. He also explained that due to the tunnel’s narrow diameter, all proteins are constructed and emerge in alpha helix form. “All folding happens at the end of the exit tunnel,” Moore said, adding a number of propositions for what may activate folding once outside the tunnel.

Highlighting the significance of Moore’s presentation, Dr. Song Tan, assistant professor of biochemistry at Penn State, said, “It is rare to find scientific discoveries that change the way we think. Moore shows us the machinery responsible for the fundamental translation of proteins. It is the largest structure ever determined with the techniques used.” Tan’s lab studies the structural biology of gene regulatory complexes through crystallographic experiments similar to those employed by Moore.

Reflecting the conference theme of shared perspectives, Moore’s experimental focus was balanced by the theoretical approach of keynote speaker Dr. George Rose, professor of biophysics in the Department of Biophysics and Biophysical Chemistry at Johns Hopkins University School of Medicine. Formerly a professor in Penn State’s College of Medicine at The Milton S. Hershey Medical Center, Rose approached the folding problem by using computer simulations and complex calculations to test long-held assumptions about the way proteins move from an unfolded state to their functional three-dimensional structures.

Past theories held that the unfolded state was largely random, wandering through an infinite range of positions until it arrived at its stationary state. Such theories, according to Rose, have made the unfolded state “a mystery” to researchers unable to calculate the infinite and unpredictable possibilities for movement into the folded structure.

Rose, however, examined texts and equations from as far back as 1935 and, applying today’s computing power, recalculated more than 2 million simulations to test the past assumptions. What he found was that the number of possible transitional positions is much smaller than previously predicted and that the unfolded proteins have a much greater degree of three-dimensional structure than researchers had believed. His conclusion was somewhat novel: protein and RNA folding scientists can drastically simplify their models for understanding the folding process.

Along with Rose and Moore, nearly 20 speakers presented their research, including four Penn State faculty members from the Hershey Medical Center and University Park.

Among them, Dr. Ira Ropson, assistant professor of biological chemistry in the College of Medicine, offered his research into proteins with nearly identical folded structures. He found that even proteins with the most similar structures follow very different paths to fold into them. As the proteins in that family mutated over generations to fulfill different functions, he explained, there was no selective pressure to maintain the same folding pathway. “The protein is only concerned with the fact that it gets into its end state, not how it gets there,” Ropson added, suggesting that similarities in chemical sequence alone cannot predict similar folding behaviors.

In addition to the formal lectures, 50 poster presentations and many industrial exhibits provided opportunities for participants to exchange information while viewing the latest applicable biotechnology-oriented products and services. Lecture and poster abstracts were published in the annual conference proceedings.

Dr. James L. McDonel, director of the Summer Symposium in Molecular Biology and instructor in the Department of Biochemistry and Molecular Biology at Penn State, commented that the University provided an excellent setting for these exchanges. “One of our great strengths at Penn State is in the area of protein folding. With all of the meetings in this series, there is always a link between University strengths and the topic of the symposium.”

The annual Summer Symposium in Molecular Biology is administered by the Department of Biochemistry and Molecular Biology at Penn State, with the conference being coordinated through Penn State Continuing Education’s Conferences and Institutes. Over nearly two decades, the symposium has used outreach to disseminate new research in a broad range of topics, including DNA-protein interactions, AIDS, neurobiology, nuclear structure, microbial differentiation, plant/bacteria symbiosis, regulation of gene expression and chromatin structure and DNA function. According to McDonel, next year’s topic will be in the area of virology.

Beyond its potential to open new research perspectives, the conference also offers important learning opportunities for students in the field.

“The relatively small size of the conference is especially good for the students who attend from Penn State and throughout the Mid-Atlantic area. During the symposium, they have an opportunity to interact with speakers and leading researchers in the field,” Bevilacqua said.

“The registration fees are nominal,” McDonel added, “and they are intended to be that way in order to make the symposium easily accessible to graduate and undergraduate students and postdoctoral scholars.”

In order to keep participant fees low, the symposium devotes extra energy to securing funding from other sources.

Support for this year’s program was provided by Penn State colleges and campuses and by industry sponsors. University sponsors included the Eberly College of Science, the College of Agricultural Sciences, The Milton S. Hershey Medical Center College of Medicine, the College of Health and Human Development, the Life Sciences Consortium and the departments of Biochemistry and Molecular Biology, Biology, Chemistry, Chemical Engineering, Veterinary Sciences, Biochemistry and Molecular Biology at Hershey, Graduate Studies at Hershey and Cellular and Molecular Physiology at Hershey. Industry sponsorship was provided by Bristol-Myers Squibb, Johnson & Johnson, March of Dimes, New England Biolabs and Schering-Plough.



An outreach program of the Eberly College of Science, Department of Biochemistry and Molecular Biology


Penn Staters, from left, Dr. Robert Schlegel, professor and head of the Department of Biochemistry and Molecular Biology; Dr. Philip Bevilacqua, assistant professor of chemistry; Dr. Beatrice Sirakaya, instructor for the Hands-on Biotechnology and Bioprocessing Training Program; and Dr. James L. McDonel, director of the Summer Symposium in Molecular Biology, meet during the 19th Summer Symposium in Molecular Biology.

 Speakers and conveners gather before one of the posters at the Protein and RNA Folding Problems Symposium in the Hetzel Union Building/Robeson Cultural Center. From left are Dr. John Desjarlais, assistant professor of chemistry at Penn State and symposium co-chair; Dr. George Rose, professor of biophysics at the Johns Hopkins University School of Medicine; Dr. Peter Moore, professor of chemistry at Yale University; and Dr. Philip Bevilacqua, assistant professor of chemistry at Penn State and symposium co-chair.
Dr. James R. Williamson (photo at left), professor of molecular biology at the Scripps Research Institute, and Dr. Sarah A. Woodson, professor of biophysics and biology at Johns Hopkins University, share their research into RNA folding and assembly at Penn State’s Summer Symposium in Molecular Biology. In her address, Woodson explored the many opportunities for RNA misfolding and collapse due to interactions with ions in the surrounding environment. Citing Williamson’s lecture on the role of protein binding in RNA folding, Woodson noted that “in trying to understand how a molecule gets into biological conformation,” RNA interactions with proteins are as important as the physical landscape of the RNA chain.
  

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