Presented by the Chemical Biology Discussion Group and the New York Chapter of the American Chemical Society
eBriefing 
Toward an In Silico Cell
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Posted May 31, 2011
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Overview
Accurately modeling the spatial arrangement and activity of all the components within a cell over the time frame of a cell cycle (or longer) requires the integration of vast amounts of data from many different types of investigations. A successful model, however, promises to provide unprecedented insight into the interaction between the thousands of processes ongoing in each cell. Molecular simulations allow for direct "observation" of such processes, without the need for fluorescent tagging and other complicated visualization tools. But such models also tend toward oversimplification, in part because researchers need to select simulation projects that will be possible within current computational limits. With these limits and assets of simulations in mind, researchers convened at the New York Academy of Sciences' Toward an in silico Cell on March 18, 2011, to discuss recent advances on the path to computational modeling of an entire cell, its components, and its biochemistry.
Ultimately, Adrian Elcock from the University of Iowa wants to "move beyond static images of cellular components" to see proteins and RNA molecules being synthesized, folded, degraded, and so forth. To get there, Elcock and his group began by using 3D reconstruction of a polyribosome as a starting point for thinking about how amino acid chains are synthesized. To investigate the crowding pressures on protein synthesis, his group modeled the cytoplasm of E. coli bacteria. By detailing all the necessary components of a successful model of the cytoplasm—knowledge of protein abundances and structures, an understanding of the intermolecular forces at play, a simulation algorithm, and the computer code to implement it all—Elcock explained the assets of his model as well as the directions for its improvement. The group has already been able to use their understanding of cytoplasm crowding, electrostatic and hydrophobic interactions, and non-specific interactions to investigate the thermodynamics of protein folding in vivo. Such an understanding will undoubtedly shape future studies of protein synthesis, especially as the group begins to project these data over longer time scales.
As some of the largest molecules (occupying 6%–15% of cellular volume) in bacterial cells, ribosomes are an important piece of the cellular modeling puzzle. As such, they have been the focus of a good deal of research, some of which was featured at the symposium. Julio Ortiz from the Max Planck Institute of Biochemistry showed how experiments in the lab can be combined with computational analysis to get a better understanding ribosomes and their functioning. In particular he used cryoelectron microscopy to assess the structure of ribosomes in vitro and in situ. After imaging and mapping the ribosomes using a process called "template matching," Ortiz and colleagues were able to employ multivariate statistical analysis to identify and classify subpopulations of ribosomes with different conformational states, for example. They could then relate these subpopulations to cellular microenvironments such as the proximity to the cell membrane or to other ribosomes. This combination of experimental work in imaging the ribosomes and computational work to parse the images and relate the structures to other features of the E. coli cells grounded Ortiz's further investigation of the detailed structure and orientation of polyribosomes.
Zaida Luthey-Schulten, a professor at the University of Illinois, uses similar information about the location of ribosomes in a cell, but she is interested in the areas devoid of ribosomes. In her group's attempts to simulate transcription for the duration of an entire cell cycle, they were able to assume that the DNA could be packed anywhere ribosomes were absent. The group used this assumption to investigate how the rebinding kinetics of the lacY gene's repressor were affected by crowding in the DNA environment. They concluded that changing the cellular packing had a noticeable effect on repressor rebinding kinetics, and that, in fact, the repressor would diffuse away from the DNA 60%–70% of the time. These results can help Luthey-Schulten and others see the implications of fundamental questions such as whether an mRNA that encodes a membrane protein diffuses to the membrane before translation or whether the ribosome carrying the nascent protein must diffuse to the membrane after translation.
Delving into the mechanics of translation from a physical chemistry perspective, Ruben L. Gonzalez, a professor at Columbia University, presented his group's work on single molecule studies of ribosomes. His group focuses on the conformation changes underpinning the elongation cycle in translation and specifically on the formation of the "hybrid conformation" in which the tRNA acts as a supplemental intersubunit bridge connecting the small and large ribosome subunits and stabilizing a rotation of the subunits with respect to one another. The scheme involved fluorescence resonance energy transfer between donor and acceptor fluorophore pairs strategically located on the ribosome. These single molecule studies gave the group access to conformational states, the thermodynamics of these states, and ultimately the diverse mechanisms of control exerted on polypeptide elongation. These features are unavailable to whole-cell studies because individual ribosomes' features are averaged out in those studies. One of the important results of their studies was their evaluation of how the translocation factor deals with the energetic barrier to translocation in order to control the directionality of the tRNA's movement through the ribosomes.
Building on the benefits of computational methods demonstrated by his colleagues, Klaus Schulten from the University of Illinois closed the symposium with an optimistic view of the power of modern computing. Considering the modern computer by analogy to a microscope, Schulten reviewed the components of the physics, chemistry, mathematics, and computer science tools that helped him uncover the H1N1 virus's mechanism for developing resistance to the Tamiflu anti-viral. As Schulten explained it, when H1N1 was spreading rapidly, researchers needed answers more quickly than biochemical experiments would have produced them, but GPUs (graphics processing units) allowed fast processing of molecular simulation algorithms to visualize the protein changes accompanying resistance. GPUs, by contrast to CPUs (central processing units), run many processes in parallel and have important functions hardwired into the chips, which speeds up processing time considerably. Schulten reviewed some experiments his group has performed to combine results from cryo-electron microscopy and crytallography in detailed, accurate simulations, and he concluded his talk by urging his colleagues to take advantage of the computing power that is available for single-molecule or whole-cell studies.
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Organizers
Tom S. Leyh, PhD
Albert Einstein College of Medicine
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Thomas S. Leyh, currently a member of the Department of Microbiology and Immunology at the Albert Einstein College of Medicine, received his PhD from the Biophysics Graduate Group the University of Pennsylvania, where his research focused on nuclear and electron–paramagnetic resonance studies of metal–ligand complexes at enzyme active sites. His training expanded to general studies of enzyme mechanism and catalysis in his postdoctoral work at The Institute for Cancer Research, PA. Broadly considered, Leyh's laboratory is engaged in a multidisciplinary pursuit of an understanding of the molecular basis of life at many levels. His group discovered the link between sulfur biology and GTPase function, substrate channeling in the sulfate activation pathway, the cysteine metabolome—a group of cysteine biosynthetic enzymes that coalesce to form an 'energy pump', and natural inhibitors of bacterial isoprenoid biosynthesis. The Leyh group is currently working on numerous problems including ancient and novel mechanisms of communication between the RNA and protein "worlds," the molecular basis of selectivity in sulfotransferases, and antibiotic development. Leyh reviews for various journals and has served as a scientific advisor at the NIH and the NSF.
Jennifer Henry, PhD
The New York Academy of Sciences
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Jennifer Henry received her PhD in plant molecular biology from the University of Melbourne, Australia, with Paul Taylor at the University of Melbourne and Phil Larkin at CSIRO Plant Industry in Canberra, specializing in the genetic engineering of transgenic crops. She was then appointed as Associate Editor, then Editor, of Functional Plant Biology at CSIRO Publishing. She moved to New York for her appointment as a Publishing Manager in the Academic Journals division at Nature Publishing Group, where she was responsible for the publication of biomedical journals in nephrology, clinical pharmacology, hypertension, dermatology, and oncology. Jennifer joined the Academy in 2009 as Director of Life Sciences and organizes 35–40 seminars each year. She is responsible for developing scientific content in coordination with the various life sciences Discussion Group steering committees, under the auspices of the Academy's Frontiers of Science program. She also generates alliances with outside organizations interested in the programmatic content.
Speakers
Adrian H. Elcock, PhD
University of Iowa
e-mail | website | publications
Adrian Elcock received his D.Phil. in physical chemistry from Oxford University, UK in 1994, having previously obtained a first-class honors degree in chemistry from the University of East Anglia, UK (1989). In 1995 he was awarded a Wellcome Trust International Prize Traveling Fellowship which took him to the research group of Professor J. Andrew McCammon at the University of California, San Diego. He remained in La Jolla until October 2000, when he joined the faculty of the Biochemistry department at the University of Iowa; he was awarded tenure and promoted to associate professor in summer 2006. Elcock's work centers on developing and applying molecular simulation techniques to model a variety of biochemical systems. Active research projects range from simulations of small-molecule associations in water to simulations of large-scale molecular models of the bacterial cytoplasm.
Ruben L. Gonzalez, Jr., PhD
Columbia University
e-mail | website | publications
Ruben Gonzalez received a BS in Chemistry and Biochemistry from Florida International University (FIU) in 1995. Gonzalez then moved to the Department of Chemistry at the University of California, Berkeley to do his doctoral research with Prof. Ignacio Tinoco. While in Prof. Tinoco's laboratory, Gonzalez's research interests focused on the structure and thermodynamics of a specific RNA structure, known as an RNA pseudoknot, which is involved in the translational control of gene expression in many viruses. Upon obtaining his PhD in Chemistry in 2000, Gonzalez moved to Stanford University where he did postdoctoral research as an American Cancer Society Postdoctoral Fellow in the laboratories of Prof. Joseph D. Puglisi in the Department of Structural Biology and Prof. Steven Chu in the Department of Physics and Applied Physics. While at Stanford, Gonzalez pioneered the first single-molecule fluorescence investigations of the ribosome. Gonzalez joined the Department of Chemistry at Columbia University as an Assistant Professor in 2006. Research in his laboratory focuses on the biophysical chemistry and biochemistry of Nature's RNA-based molecular machines, with a current emphasis on the mechanism and regulation of protein synthesis by the ribosome.
Zaida Luthey-Schulten, PhD
University of Illinois at Urbana–Champaign
e-mail | website | publications
Zaida (Zan) Luthey-Schulten received her PhD in Applied Mathematics and Chemistry from Harvard University. She went on to do post-doctoral research in biophysics at the Max-Planck Institute and the Department of Physics at the Technical University of Munich, developing together with K. Schulten and A. Szabo a first-passage time description of chemical reactions of polymer chains. Upon joining the faculty at the University of Illinois, Zan has worked on a number of fields ranging from the theory of protein folding, evolutionary and energetic analysis of protein/RNA complexes in translation, and most recently stochastic simulations of reactions in entire bacterial cells. Luthey-Schulten has served on numerous panels for the NSF, NIH, and DOE, and is a Fellow of the American Physical Society. As a co-PI of the NIH Resource for Macromolecular Modeling and Bioinformatics, she makes her programs publicly available through their popular visualization and analysis program, VMD. She is currently a William and Janet Lycan Professor of Chemistry with affiliate positions in the Department of Physics, Beckman Institute, and the Institute for Genomic Biology.
Julio Ortiz, PhD
Max Planck Institute of Biochemistry, Germany
e-mail | website | publications
Julio Ortiz began his career in electron microscopy with a helical reconstruction of myosin thick filaments, under the supervision of Raúl Padrón at the Venezuelan Institute for Scientific Research (IVIC). After receiving a fellowship from the DAAD (Deutscher Akademischer Austausch Dienst), he moved to Germany where he received first hand training in cryoelectron microscopy from Kevin Leonard (Heidelberg). Ortiz's doctoral thesis was focused on actomyosin complexes and supervised by Rasmus Schroeder in the Department of Ken Holmes at the Max Plank Institute for Medical Research.Turning his attention to tomography and associated techniques. Julio Ortiz went to the Max Planck Institute of Biochemistry in Martinsried for his post-doctoral studies in the dept. of Wolfgang Baumeister. Ortiz and his supervised doctoral students, in collaboration with U. Hartl, addressed several problems related with spatial organization of ribosomes. They revealed the native 3D organization of polysomes and solved the structure of hibernating ribosomes in vitro and inside intact bacterial cells.
Klaus Schulten, PhD
University of Illinois at Urbana–Champaign
e-mail | website | publications
Klaus Schulten received his PhD in Chemical Physics from Harvard University. He then moved on to do his post-doctoral research in biophysics at the Max-Planck Institute of Biophysical Chemistry in Göttingen, Germany. From there he moved on to his first faculty position at the Technical University Munich. In 1988 he joined the faculty of the University of Illinois in Urbana–Champaign (UIUC) where he is now serving as Swanlund Professor of Physics. He is also the Director of the National Institute of Health Resource of Macromolecular Modeling and Bioinformatics at the Beckman Institute at UIUC. Schulten develops and distributes innovative software tools that are used by thousands of researchers and students worldwide to explore biomolecular systems—VMD, a molecular dynamics graphics program; NAMD, scalable molecular dynamics for clusters and supercomputers; BioCoRE, a web-based collaborative biological research environment. In his research Schulten combines physics, chemistry, biology, computer science theory, and experiments as well as mathematics and software engineering; the group engages in many computational–experimental collaborations.