Emeritus Professor of Chemistry and Biochemistry
B.A., Massachusetts Institute of Technology;
M.S., Massachusetts Institute of Technology;
Ph.D., Massachusetts Institute of Technology
Member of: Institute of Molecular Biology
Office: Klamath Hall Room 215A
Lab: Klamath Hall Room 205
Telephone: 541-346-4212 or 5147
My associates and I are using physical biochemical approaches to study what might be called the molecular basis of gene expression. Most of our experimental work is concerned with the function and regulation of the complexes that control DNA transcription and replication, with studies focused primarily on transcription with the E. coli DNA-dependent RNA polymerase and its regulatory factors and on replication with the seven-protein bacteriophage T4-coded DNA replication system. Comparative studies are also underway using selected components of some equivalent eukaryotic systems.
In transcription our group is studying the transcription cycle, both at the overall operon level and at the level of the various steps of the single-nucleotide addition-excision cycle. At the operon level we are studying regulatory interactions that control activation and repression at initiation, the kinetics of elongation, and the molecular bases of the elongation-termination decision at both intrinsic and rho-dependent transcription terminators, together with the mechanisms of action antitermination factors. We have recently completed a study of E. coli transcription termination factor rho, in terms of its function as a specific RNA-DNA helicase and as a transcript terminator. Our antitermination studies have focussed on the mechanisms of action of the N protein of phage lambda in N-dependent antitermination systems. At the single-nucleotide addition-excision cycle level we are using various kinetic techniques to understand the molecular origins of transcriptional processivity and fidelity.
In replication our work began with studies of the cooperative binding of the T4 gene 32 (single-stranded DNA binding) protein to the single-stranded DNA (and RNA). This then led us to examine the interactions of the other components of the system, including those of the DNA polymerase with the primer-template and the polymerase accessory proteins. These studies have shown that the basically nonprocessive T4 DNA polymerase can be rendered fully processive by means of "sliding-clamp" processivity factor, and that the role of the other accessory proteins is to carry out the specific and ATP-dependent loading of the processivity factor onto the polymerase at the primer-template junction in the replication fork. The resulting complex can carry out leading strand DNA replication with essentially in vivo rate, fidelity, and processivity. The helicase of the T4 DNA replication system functions as a hexamer and, in combination with a single T4 primase subunit, forms a stable primosome subassembly. We have recently also shown a direct coupling between the polymerase and the helicase. This complex alone, if properly loaded onto a model replication fork, can carry out processive synthesis on a double-stranded DNA construct at the physiological rate. The mode of assembly of these components into a fully functional and coupled DNA replication system is currently being studied.
In all these studies we emphasize the elucidation of the detailed mechanisms and general principles of protein-nucleic acid and protein-protein interactions that underlie the function of these biologically central complexes.
* Professor von Hippel is retired from teaching, but continues to run fully active and funded research program(s).
Applications from potential postdoctoral fellows and undergraduate research participants are welcome.
Datta, K., Johnson, N.P. and P.H. von Hippel. DNA conformational changes at the primer-template junction regulate the fidelity of replication by DNA polymerase. Proc. Natl. Acad. Scis. USA 107, 17980-17985 (2010).
Datta, K., Johnson, N.P., LiCata V.J. and P.H. von Hippel. Local conformations and competitive binding affinities of single- and double-stranded primer-template DNA at the polymerization and editing active sites of DNA polymerases. J. Biol. Chem. 284, 17180-17193 (2009).
Jose, D., Datta, K., Johnson, N.P. and P.H. von Hippel. Spectroscopic studies of position-specific DNA "breathing" fluctuations at replication forks and primer-template junctions. Proc. Natl. Acad. Scis., USA. 106, 4231-4236 (2009).
Pietroni, P. and P.H. von Hippel. Multiple ATP binding is required to stabilize the 'activated' (clamp-open) clamp loader of the T4 DNA replication complex. J. Biol. Chem. 283, 28338-28353 (2008).
Kausiki Datta and Peter H. von Hippel. Direct spectroscopic study of reconstituted transcription complexes reveals that intrinsic termination is driven primarily by thermodynamic destabilization of the nucleic acid framework. J. Biol. Chem. 283:3537-49 (2008)
von Hippel, P.H. From 'simple' protein-DNA interactions to the macromolecular machines of gene expression. Ann. Rev. Biophys. & Biomol. Struct. 36, June 2007
von Hippel, P.H. Transcriptional pausing caught in the act (Commentary). Cell 125, 1027-1029 (2006).
Datta, K., Johnson, N.P. and P.H. von Hippel. Mapping the conformation of the nucleic acid framework of the T7 RNA polymerase elongation complex in solution using low energy CD and fluorescence spectroscopy. J. Mol. Biol. 360, 800-813 (2006).
Greive, S.J., Lins, A.F. and P.H. von Hippel. Assembly of an RNA-protein complex: binding of NusB and NusE (S10) proteins to boxA RNA nucleates the formation of the antitermination complex involved in controlling rRNA transcription in E. coli. J. Biol. Chem. 280, 32171-32183 (2005).
Johnson, N.P., Baase, W.A. and P.H. von Hippel. Low energy CD of RNA hairpin unveils a loop conformation required for lN-antitermination activity. J. Biol. Chem. 280 32177-32183 (2005). [Fig. corrections: JBC, 280, 41123-41124, (2005).]
Johnson, N.P., Baase, W.A. and P.H. von Hippel. Investigating local conformations of double-stranded DNA by low energy circular dichroism of pyrrolo-cytosine. Proc. Natl. Acad. Scis., USA 102, 7169-7173 (2005).
Conant, C.R., Van Gilst, M.R., Weitzel, S.E., Rees, W.A. and P.H. von Hippel. A quantitative decription of the binding states and in vitro function of antitermination protein N of bacteriophage l. J. Mol. Biol. 348, 1039-1059 (2005).
Delagoutte, E. and P.H. von Hippel. Mechanistic studies of the T4 DNA (gp41) replication helicase: Functional interactions of the C-terminal tails of the helicase subunits with the T4 (gp59) helicase loader protein. J. Mol. Biol. 347. 257-275 (2005).
Greive S.J. and P.H. von Hippel. (2005) Thinking quantitatively about transcriptional regulation. Nat Rev Mol Cell Biol 6:221-32.
von Hippel P.H. (2004) Biochemistry. Completing the view of transcriptional regulation. Science 305:350-2. No abstract available.
von Hippel P.H. (2004) Helicases become mechanistically simpler and functionally more complex. Nat Struct Mol Biol 11:494-6. No abstract available.
Johnson N.P., W.A. Baase, and P.H. Von Hippel (2004) Low-energy circular dichroism of 2-aminopurine dinucleotide as a probe of local conformation of DNA and RNA. PNAS 101:3426-31.
von Hippel, P.H. and E. Delagoutte (2003) Macromolecular complexes that unwind nucleic acids. BioEssays 25:1168-77.
Delagoutte E. and P.H. von Hippel (2003) Function and assembly of the bacteriophage T4 DNA replication complex: interactions of the T4 polymerase with various model DNA constructs. J Biol Chem 278:25435-47.
Delagoutte, E. and P.H. von Hippel (2003) Helicase mechanisms and the coupling of helicases within macromolecular machines. II. Integration of helicases into cellular processes. Q Rev Biophys 36:1-69.
Delagoutte, E. and P.H. von Hippel (2002) Helicase mechanisms and the coupling of helicases within macromolecular machines. I. Structure and function of isolated helicases. Q Rev Biophys 35:431-78.
Pasman, Z. and P.H. von Hippel (2002) Active Escherichia coli transcription elongation complexes are functionally homogeneous. J Mol Biol 322:505-19.
von Hippel, P.H. and Z. Pasman (2002) Reaction pathways in transcript elongation. Biophys Chem 101-02:401-23.
Pietroni, P., M.C. Young, G.J. Latham, and P.H. von Hippel (2001) Dissections of the ATP-driven reaction cycle of the bacteriophage T4 DNA replication processivity clamp loading system. J Mol Biol 309:869-91.
von Hippel, P.H. and E. Delagoutte (2001) A general model for nucleic acid helicases and their "coupling" within macromolecular machines. Cell 104:177-90.
Delagoutte, E. and P.H. von Hippel (2001) Molecular mechanisms of the functional coupling of the helicase (gp41) and DNA polymerase (gp43) of bacteriophage T4 within the DNA replication fork. Biochemistry 40:4459-77.