Scientific Report 2006

Molecular Biology

Chairman’s Overview

Research in the Department of Molecular Biology encompasses a broad range of disciplines, extending from structural and computational biology at one extreme to molecular genetics at the other. During the past year, our scientists have continued to make rapid progress toward understanding the fundamental molecular events underlying the processes of life. Major advances have been made in elucidating the structural biology of signal transduction and viral assembly, in understanding mechanisms of viral infectivity, in determining the structures of membrane proteins and multidrug transporters, in understanding the molecular basis of nucleic acid recognition and DNA repair, and in determining the mechanisms of protein folding and ribosome assembly. Progress has been made in elucidating the molecular events involved in regulation of the cell cycle, in tumor development, in induction of sleep, in the molecular origins of neuronal development and of CNS disorders, in the regulation of transcription, and in the decoding of genetic information in translation. Finally, new advances have been made in the design of novel low molecular weight compounds that can specifically regulate genes, and in the area of biomolecular engineering, building novel functions into viruses, antibodies, and zinc finger proteins, RNA, and DNA. Progress in these and other areas is described in detail on the following pages, and only a few highlights are mentioned below. The Department of Molecular Biology is also home to two major National Institutes of Health initiatives, the Joint Center for Structural Genomics and the Consortium for Functional Glycomics.

One of the outstanding achievements of the past year was the determination of the structure of the intact and infectious P22 virion by electron cryomicroscopy. Research led by Jack Johnson has provided a remarkably detailed view of the virion structure at an unprecedented 17-Å resolution. The structure revealed the DNA tightly spooled around the portal in the interior of the capsid and suggested that the virus uses a pressure-sensing mechanism to control DNA packaging. The structure also provides insights into the mechanisms of virion assembly and injection of DNA into target cells.

Structural biology continues to be a major focus in the department, and many new x-ray and nuclear magnetic resonance structures of major biomedical significance were completed during the past year. Geoffrey Chang and colleagues reported new structural studies of the Escherichia coli multidrug transporter EmrD, obtaining new insights into the mechanisms by which a diverse range of drugs are transported through the cell membrane. Such understanding is of major importance, given the rapidly growing problem of drug resistance in bacteria. John Tainer and his coworkers used a combination of electron cryomicroscopy and x-ray crystallography to determine the structure of the Type IV pilus filament of Neisseria gonorrhoeae. These studies provide new insights into assembly and disassembly mechanisms and are of importance because of the role played by Type IV pili in allowing antibiotic resistant strains to escape the immune system and cause persistent infections. Dr. Tainer and colleagues have also determined new structures of DNA repair enzymes; these include the xeroderma pigmentosum group B helicase, an enzyme that plays an essential role in nucleotide-excision repair by removing DNA lesions caused through exposure to ultraviolet light, and the exonuclease domain of WRN, a protein that protects against premature aging and cancer. Defects in the gene for WRN result in Werner’s syndrome, an inherited disease that causes premature aging.

Research in the laboratories of Jane Dyson and Peter Wright has provided new insights into the role of protein conformational fluctuations in enzyme catalysis. Protein dynamics have long been thought to play an important role in catalysis. This new work shows how the dynamic energy landscape of the enzyme dihydrofolate reductase channels the protein through the reaction cycle. Conformational transitions between the various conformational substates of the enzyme occur at a rate that is directly relevant to catalysis.

Several research groups are working in areas directly related to drug discovery and protein therapeutics. Joel Gottesfeld and his colleagues have developed small-molecule histone deacetylase inhibitors that reactivate frataxin, the gene responsible for the neurodegenerative disease Friedreich’s ataxia, a disease that is associated with the expansion of triplet repeats in DNA. These compounds hold great promise as potential therapeutics for Freidreich’s ataxia. Subhash Sinha, Carlos Barbas, and Richard Lerner have developed a unique self-assembly strategy to direct antibodies against specific cellular targets. Their novel approach has led to new compounds targeted against metastatic breast cancer.

Many of the research groups in this department are applying the tools of molecular and structural biology to understand the molecular basis of human disease. In research led by James Paulson and Ian Wilson, glycan microarray technology is being used to identify mutations that could allow avian influenza viruses to adapt to the human population. The glycan array is a powerful surveillance tool for mapping the pathways by which new human pathogenic viruses can emerge. This research has revealed a potential mutational pathway that could switch the specificity of the highly pathogenic H5N1 avian influenza virus and allow it to adapt to humans. Strikingly, the 3-dimensional structure of the H5N1 hemagglutinin, the protein responsible for binding the virus to host cell receptors, bears a closer resemblance to the hemagglutinin from the virus that caused the 1918 influenza pandemic than to that associated with more recent influenza outbreaks.

Finally, research during the past year has greatly advanced our understanding of the complex mechanisms of cell-cycle regulation. Curt Wittenberg and his colleagues have identified a yeast protein that plays a central role in repressing transcription during the cell cycle. The protein functions in a parallel manner to the important metazoan transcriptional regulator E2F. Work in Steven Reed’s laboratory has provided new insights into the mechanisms of multiubiquitinylation and degradation of cyclin E, a process that is essential for the normal regulation of the cell cycle. Misregulation of either of these processes, transcriptional repression or cyclin turnover, is associated with cancer.

Molecular biology remains a field of enormous opportunity and excitement. The scientists in this department are taking full advantage of powerful new technologies to advance our understanding of fundamental biological processes at the molecular level. Their discoveries will ultimately be translated into new advances in biotechnology and in medicine.