Dr. Richard H. Ebright

Research Summary

Protein Biochemistry

Introduction
Transcription initiation is the first step in gene expression and is the step at which most regulation of gene expression occurs. Our laboratory seeks to understand the structure, function, and regulation of transcription initiation complexes, and to develop gene-specific inhibitors of transcription initiation as potential gene-specific therapeutic agents.

Structure of Transcription Initiation Complexes
Transcription initiation in bacteria requires RNA polymerase and the initiation factor sigma. The bacterial transcription initiation complex contains 4 distinct polypeptides (3 in RNA polymerase, 1 in sigma) and has a molecular mass of 0.5 MDa.
     Transcription initiation at a eukaryotic protein-encoding gene requires RNA polymerase II and up to six general transcription factors: IIA, IIB, IID, IIE, IIF, and IIH. The fully assembled eukaryotic transcription initiation complex contains at least 35 distinct polypeptides (at least 10 in RNA polymerase II, at least 25 in the general transcription factors) and has a molecular mass in excess of 2 MDa.
     Understanding transcription initiation in bacteria and eukaryotes will require understanding the structures of the polypeptides in the respective transcription initiation complexes and the arrangement of these polypeptides relative to each other and relative to promoter DNA.
     High-resolution structures have been determined for several polypeptides and polypeptide fragments of the bacterial and eukaryotic transcription initiation complexes. However, the intact complexes are too large for high-resolution structure determination by current methods. Therefore, efforts to understand the arrangement of polypeptides within the intact complexes rely heavily on biophysical data defining distances within the complexes and on biochemical and genetic data defining contacts within the complexes.
     We are carrying out systematic analyses of distances, protein-protein contacts, and protein-DNA contacts within the bacterial and eukaryotic transcription initiation complexes. We are using fluorescence resonance energy transfer to define distances between pairs of site-specifically incorporated fluorescent probes, photocrosslinking to define polypeptides near to site-specifically incorporated photocrosslinking probes, and protein footprinting and residue scanning to define residues involved in contacts. In addition, we are using binding-site selection to define new promoter DNA-sequence elements recognized by polypeptides and polypeptide fragments. Finally, we are using molecular modelling to integrate structural, biophysical, biochemical, and genetic data in order to construct models for the structures of complexes.

Function of Transcription Initiation Complexes
The bacterial and eukaryotic transcription initiation complexes are molecular machines that carry out complex, multi-step reactions. The transcription initiation pathway involves: (i) binding of RNA polymerase and initiation factor(s) to promoter DNA to form a "closed complex" with duplex DNA; (ii) isomerization through several intermediates to form an "open complex" with an Å14-nucleotide region of melted, single-stranded DNA surrounding the transcription start; (iii) abortive cycles of synthesis and release of 2- to 8-nucleotide RNA oligomers as an "initial transcribing complex"; and (iv) upon synthesis of a 9-nucleotide RNA oligomer, isomerization to break protein-DNA interactions between RNA polymerase and the promoter and protein-protein interactions between RNA polymerase and initiation factor(s), resulting in an "elongation complex" that processively translocates along DNA and extends the RNA product.
     Each of the steps in this pathway appears to involve large conformational changes in both RNA polymerase and promoter DNA. Understanding transcription initiation will require defining the structure of the complex at each step, defining the conformational transitions, and defining the kinetics of the transitions.
     We are addressing these issues in studies of the smaller, and thus more experimentally tractable, bacterial transcription complex. We are using the fluorescence resonance energy transfer and photocrosslinking methods of the preceding section to define distances and contacts within trapped intermediates (e.g., closed complexes trapped at 40C, intermediate complexes trapped at 160C, open complexes trapped at 370C in the absence of NTPs). In addition, we are using fluorescence resonance energy transfer with stop-flow rapid mixing, and photocrosslinking with quench-flow rapid mixing and laser flash photolysis, to monitor kinetics of transitions. Most recently, we have initiated experiments using far-field and near-field optical microscopy for single-molecule, millisecond- to second-scale analysis of transitions within transcription complexes.

Regulation of Transcription Initiation Complexes
The activities of the bacterial and eukaryotic transcription initiation complexes are regulated in response to environmental, cell-type, and developmental signals. In most cases, regulation is mediated by factors that bind to specific DNA sites in or near a promoter and inhibit ("repressors") or stimulate ("activators") one or more of the steps on the transcription initiation pathway described in the preceding section.
     With the objective of providing the first complete structural and mechanistic descriptions of activation, we study two of the simplest examples of activation: (i) activation of the lac promoter by catabolite activator protein (CAP), and (ii) activation of the CC(-41.5) promoter by CAP. These model systems each involve only a single activator molecule and a single activator DNA site, and, as such, are more experimentally tractable than typical examples of activation in bacteria and substantially more experimentally tractable than typical examples of activation in eukaryotes (which can involve tens of activator molecules and activator DNA sites).
     In work to date, we have established that activation at lac involves an interaction between CAP and the RNA polymerase a subunit C-terminal domain that facilitates closed-complex formation. Activation at CC(-41.5) involves this same interaction and also an interaction between CAP and the RNA polymerase a subunit N-terminal domain that facilitates isomerization of closed complex to open complex.
     In current work, we are using x-ray crystallography to determine the structures of the interfaces between CAP and its targets on RNA polymerase, and we are using the fluorescence resonance energy transfer and photocrosslinking methods of the preceding section to define when each CAP-RNA polymerase interaction is made as RNA polymerase enters the promoter and when each interaction is broken as RNA polymerase leaves the promoter.

Low-Molecular Weight Inhibitors of Transcription Initiation
Inhibition of the interaction of an activator with DNA or with the general transcription machinery results in selectively reduced expression of the gene(s) regulated by the activator. In principle, development of low-molecular-weight inhibitors of interactions of specific activators with DNA or with the general transcription machinery could provide highly selective regulators of gene expression and thus highly selective therapeutic agents (e.g., antimicrobial agents based on inactivation of a critical microbial activator).
     We are using combinatorial-chemistry and peptidomimetic-chemistry approaches to seek low-molecular-weight inhibitors of activator-DNA and activator-transcription-machinery interactions. In addition, in support of this work, we are developing and testing methods for optically encoded combinatorial chemistry.

Initial transcription by RNA polymerase proceeds through a "DNA scrunching"
mechanism, in which the enzyme remains stationary on promoter DNA and pulls
into itself downstream DNA. Proposed movements of the template and
nontemplate DNA strands are indicated by blue-outlined and red-outlined
arrows. Proposed positions at which the scrunched template and nontemplate
DNA strands emerge from the enzyme are indicated by orange and pink dashed
lines. Positions of fluorescent probes used to analyze scrunching are
indicated in green (donor probe on polymerase), brick red (acceptor probe at
promoter position +20 in absence of scrunching), and bright red (acceptor
probe at promoter position +20 in presence of scrunching). [See Revyakin,
A., Liu, C., Ebright, R.H. & Strick, T. (2006) Abortive initiation and
productive initiation by RNA polymerase involve DNA scrunching. Science 314,
1139-1143; Kapanidis, A., Margeat, E., Ho, S.O., Kortkhonjia, E., Weiss, S.
& Ebright, R.H. (2006) Initial transcription by RNA polymerase proceeds
through a DNA-scrunching mechanism. Science 314, 1144-1147.]

Microcin J25 (MccJ25) inhibits bacterial transcription by binding within, and obstructing, the bacterial RNA polymerase nucleotide-uptake channel, acting essentially as a "cork in a bottle." Sites of single-residue substitutions in RNA polymerase that confer MccJ25-resistance are shown in red ( β' subunit) and pink (β subunit). The RNA polymerase active-center Mg2+ is shown in white. [See Mukhopadhyay, J., Sineva, E., Knight, J., Levy, R., and Ebright, R. (2004) Molecular Cell 14, 739–751.]

Model for the structural organization of the bacterial RNA polymerase-promoter open complex, derived from systematic fluorescence resonance energy transfer and distance-constrained docking [Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A., Niu, W., Ebright, Y., Levy, R., and Ebright, R. (2002) Cell 108, 599-614]. σ⁷⁰ regions 2 and 4 are shown as yellow ribbons, with the α-helices that mediate recognition of the promoter -10 element and -35 element highlighted in light yellow; σ⁷⁰ regions 1.1, 3.1, and 3.2 are shown as yellow spheres. RNAP subunits β', β, α^I, α^II, and ω are shown in orange, green, light blue, dark blue, and gray. Openings of channels for the nontemplate DNA strand (NT), the template DNA strand (T), and the RNA product (RNA) are indicated in magenta.

Use of systematic fluorescence resonance energy transfer and distance-constrained docking to define the structural organization of the bacterial RNA polymerase-promoter open complex (two orthogonal views) [Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A., Niu, W., Ebright, Y., Levy, R., and Ebright, R. (2002) Cell 108, 599-614]. Measured distances between probes in σ⁷⁰ (yellow spheres) and probes in RNA polymerase core and DNA (white spheres) define the positions of segments of σ⁷⁰ relative to RNA polymerase core and DNA in the RNA polymerase-promoter open complex in solution. σ⁷⁰ region 2 (σR2), which is responsible for recognition of the promoter -10 element, and for which a crystallographic structure is available, is shown as a yellow ribbon with probe sites as yellow spheres. σ⁷⁰ region 4 (σR4), which is responsible for recognition of the promoter -35 element, and for which a homology-modelled structure is available, also is shown as a yellow ribbon with probe sites as yellow spheres. σ⁷⁰ regions 1.1, 3.1, and 3.2 (σR1.1, σR3.1, and σR3.2), for which no structural information is available, are shown as yellow spheres. Distances to σR2, to σR4, and to σR1.1, σR3.1, and σR3.2, are shown in, respectively, green, blue, and white. Docking of segments of σ⁷⁰ onto RNA polymerase core and DNA was performed using 105 measured distances and an automated distance-constrained-docking algorithm employing only geometric information--i.e., the 105 measured distances, and the relative positions of probe sites. [For clarity, each distance is shown as a single Ca-Ca or Ca -P vector. The actual distance-constrained-docking algorithm used ensembles of probe-probe vectors, reflecting ensembles of probe and linker conformations.]

Fluorescence resonance energy transfer (FRET) establishes that, in the majority of transcription complexes, sigma70 is not released from RNA polymerase (RNAP) upon transition to elongation, but, instead, is retained by RNAP and translocates with RNAP. The four conserved regions of sigma70--regions 1, 2, 3, and 4--occupy the same, or nearly the same, positions relative to RNAP in the RNAP-promoter open complex (RPo) and in an RNAP-DNA elongation complex containing 11 nt of RNA (RDe,11). Sigma70 regions 1, 2, 3, and 4 are in yellow; RNAP beta', beta, alpha^I, and omega subunits are in orange, green, blue, and gray; DNA template and nontemplate strands are in pink and gray. [See Mukhopadhyay, J., Kapanidis, A., Mekler, V., Kortkhonjia, E., Ebright, Y., and Ebright, R. Cell 2001 106:453-463.]

Crystallographic structure of a transcriptional activator (catabolite activator protein, CAP; cyan) in complex with its target in the transcriptional machinery (RNA polymerase alpha-subunit C-terminal domain, alphaCTD; green) and DNA (red). There are no large-scale conformational changes in the activator and target, and the interface between the activator and target is small (residues highlighted in navy and yellow)—consistent with the proposal that transcriptional activation involves a simple "recruitment" mechanism. [See Benoff, B., Yang, H., Lawson, C., Parkinson, G., Liu, J., Blatter, E., Ebright, Y., Berman, H., and Ebright, R. (2002) Science 297, 1562–1566.]

Representative Publications (1996-)

Cellai, S., Vannini, N., Naryshkin, N., Kortkhonjia, E., Ebright, R., and Rivetti, C. (2007) Upstream promoter sequences and αCTD mediate stable DNA wrapping within the RNA polymerase open promoter complex. EMBO Reports 8, 271-278. [free full text, click here]

Kapanidis, A., Margeat, E., Ho, S.O., Kortkhonjia, E., Weiss, S. & Ebright, R.H. (2006) Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314, 1139-1143. [free full text, click here]

Revyakin, A., Liu, C., Ebright, R.H. & Strick, T. (2006) Abortive initiation and promoter escape involve DNA scrunching: direct observation by single-molecule DNA nanomanipulation. Science 314, 1144-1147. [free full text, click here]

Popovych, N., Sun, S., Ebright, R., and Kalodimos, C. (2006) Dynamically driven protein allostery. Nature Structl. Mol. Biol. 13, 831-838.

Tadigotla, V., O'Maoileidigh, D., Sengupta, A., Epshtein, V., Ebright, R., Nudler, E., and Andrei E. Ruckenstein (2006) Thermodynamic and kinetic modeling of transcriptional pausing. Proc. Natl. Acad. Sci. USA 103, 4439-4444.

Napoli, A., Lawson, C., Ebright, R., and Berman, H. (2006) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: recognition of pyrimidine-purine and purine-purine steps. J. Mol Biol. 357, 173-183.

Margeat, E., Kapanidis, A., Tinnefield, P., Wang, Y., Mukhopadhyay, J., Ebright, R., and Weiss, S. (2006) Direct observation of abortive initiation and promoter escape within immobilized single transcription complexes. Biophys. J. 20, 347-356.
Kapanidis, A., Margeat, E., Laurence, T., Doose, S., Ho, S.O., Mukhopadhyay, J., Kortkhonjia, E., Mekler, V., Ebright, R., and Weiss, S. (2005) Retention of transcription initiation factor s70 in transcription elongation: single-molecule analysis. Mol. Cell 20, 347-356.

Vrentas, C., Gaal, T., Ross, W., Ebright, R., and Gourse, R. (2005) Response of RNA polymerase to ppGpp: requirement for the w subunit and relief of this requirement by DksA. Genes Dev. 19:, 2378-2387.

Tuske, S., Sarafianos, S., Wang, X., Hudson, B., Sineva, E., Mukhopadhyay, J., Birktoft, J, Leroy, O., Ismail, S., Clark, A., Dharia, C., Napoli, A., Laptenko, O., Lee, J., Borukhov, S., Ebright, R., and Arnold, E., (2005) Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. Cell 122, 541-552

Nickels, B. Garrity, S., Mekler, V., Minakhin, L., Severinov, K., Ebright, R.H., and Hochschild, A. (2005) Altering the interaction between sigma70 and the beta-flap of Escherichia coli RNA polymerase provides evidence for a barrier to the extension of the nascent RNA during early elongation. Proc. Natl. Acad. Sci USA 102, 4488-4493.

Revyakin, A., Ebright, R.H., and Strick, T. (2005) Single-molecule DNA nanomanipulation: improved resolution through use of shorter DNA fragments. Nature Meths. 2, 127-138.

Lee, N.K., Kapanidis, A., Wang, Y., Michalet, X., Mukhopadhyay, J., Ebright, R.H., and Weiss, S. (2005) Accurate FRET measurements within diffusing single biomolecules using alternating-laser excitation. Biophys. J. 88, 2939-2953.

Knight, J., Mekler, V., Mukhopadhyay, J., Ebright, R., and Levy, R. (2004) Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: d eveloping benchmarks of model quality and reliability. Biophys. J. 88, 925-938.

Mukhopadhyay, J., Sineva, E., Knight, J., Levy, R., and Ebright, R. (2004) Antibacterial peptide microcin J25 (MccJ25) inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Mol. Cell. 14, 739-751.

Nickels, B., Mukhopadhyay, J., Garrity, S., Ebright, R., and Hochschild, A. (2004) The sigma(70) subunit of RNA polymerase mediates a promoter-proximal pause at the lac promoter.Nature Structl. Mol. Biol. 11, 544-550.

Revyakin, A., Ebright, R., and Strick, T. (2004) Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation. Proc. Natl. Acad. Sci. USA 101, 4776-4780.

Lawson, C., Swigon, D., Murakami, K., Darst, S., Berman, H., and Ebright, R., (2004) Catabolite activator protein (CAP): DNA binding and transcription activation. Curr. Opin. Structl. Biol. 14, 10-20.

Renfrow, M., Naryshkin, N., Lewis, M., Chen, H.-T., Ebright, R., and Scott, R. (2004) Transcription factor B contacts promoter DNA near the transcription start site of the archaeal transcription initiation complex. J. Biol. Chem. 279, 2825-2831.

Bayro, M., Mukhopadhyay, J., Swapna, G.V.T., Huang, J., Ma, L.-C., Sineva, E., Dawson, P., Montelione, G., and Ebright, R. (2003) Structure of antibacterial peptide microcin J25: a 21-residue lariat protoknot. J. Amer. Chem. Soc. 125, 12382-12383.

Chen, H., Tang, H., and Ebright, R.H. (2003) Functional interaction between RNA polymerase α subunit C-terminal domain and σ70 in UP-element- and activator-dependent transcription. Mol. Cell 11, 1621-1633.

Lloyd, G., Niu, W., Trebbutt, J., Ebright, R., and Busby, S. (2002) Requirement for two copies of RNA polymerase alpha subunit C-terminal domain for synergistic transcription activation at complex bacterial promoters. Genes & Development 16, 2557-2565

Benoff, B., Yang, H., Lawson, C., Parkinson, G., Liu, J., Blatter, E., Ebright, Y., Berman, H., and Ebright, R. (2002) Structural basis of transcription activation: the CAP-alphaCTD-DNA complex. Science 297, 1562-1566 [free full text, click here]

Mekler, V., Kortkhonjia, E., Mukhopadhyay, J., Knight, J., Revyakin, A., Kapanidis, A., Niu, W., Ebright, Y., Levy, R., and Ebright, R.(2002) Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell 108, 599-614.

Kapanidis, A., Ebright, Y., and Ebright, R. (2001) Site-specific incorporation of fluorescent probes into protein: hexahistidine-tag-mediated fluorescent labeling using (Ni++:nitrilotriacetic acid)n-fluorochrome conjugates. J. Amer. Chem. Soc. 123, 12123-12125.

Kapanidis, A., Ebright, Y., Ludescher, R., Chan, S., and Ebright, R. (2001) Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution. J. Mol. Biol. 312, 453-468.

Chen, S., Vojtechovsky, J., Parkinson, G., Ebright, R., and Berman, H. (2001) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: I. DNA binding specificity based on energetics of DNA kinking. J. Mol. Biol. 314, 63-74.

Chen, S., Gunasekera, A., Zhang, X., Kunkel, T., Ebright, R., and Berman, H. (2001) Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: II. Alteration of DNA binding specificity through alteration of DNA kinking. J. Mol. Biol. 314, 75-82.

Mukhopadhyay, J., Kapanidis, A., Mekler, V., Kortkhonjia, E., Ebright, Y., and Ebright, R. (2001) Translocation of sigma70 with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell 106, 453-463.

Minakhin, L., Bhagat, S. Brunning, A., Campbell, E., Darst, S., Ebright, R. and Severinov, K. (2001) Bacterial RNA polymerase subunit omega and eukaryotic RNA polymerase subunit RPB6 are sequence, structural, and functional homologs and promote RNA polymerase assembly Proc. Natl. Acad. Sci. USA 98, 892-897.

Naryshkin, N., Revyakin, A., Kim, Y., Mekler, V., and Ebright, R. (2000) Structural organization of the RNA polymerase- promoter open complex. Cell 101: 601-611.

Kim, T.-K., Ebright, R., and Reinberg, D. (2000) Mechanism of ATP-dependent promoter melting by transcription factor IIH. Science 288:1418-1421.

Ebright, R. (2000) RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J. Mol. Biol. 304, 687-698.

Meibom, K., Kallipolitis, B., Ebright, R., and Valentin-Hansen, P. (2000) Identification of the subunit of CRP that functionally interacts with CytR in CRP-CytR-mediated transcriptional repression. J. Biol. Chem. 275, 12123-12128.

Boyer, L., Shao, X., Ebright, R., and Peterson, C. (2000) Roles of the histone H2A/H2B dimers and (H3/H4)2 tetramer in nucleosome remodeling by SWI/SNF complex. J. Biol. Chem. 275, 11545-11552.

Tan, Q., Linask, K.L., Ebright, R. and Woychik, N. (2000) Activation mutants in yeast RNA polymerase subunit RPB3 provide evidence for a structurally conserved surface required for activation in eukaryotes and bacteria. Genes & Development 14, 339-348.

Busby, S. and Ebright, R. (1999) Transcription activation by catabolite activator protein (CAP). J. Mol. Biol. 293, 199-213.

Estrem, S., Ross, W., Gaal., Chen, Z.W.S., Niu, W., Ebright, R., and Gourse, R. (1999) Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxyl-terminal domain of RNA polymerase alpha subunit. Genes & Development 13, 2134-2147.

Harrison-McMonagle, P., Denissova, N., Martinez-Hackert, E., Ebright, R., and Stock, A. (1999) Orientation of OmpR monomers within an OmpR-DNA complex determined by DNA affinity cleaving. J. Mol. Biol. 285, 555-566.

Lagrange, T., Kapanidis, A.N., Tang, H., Reinberg, D., Ebright, R.H. (1998). New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev. 12(1): 34-44.

Sullivan, S., Horn, P., Olson, V., Koop, A., Niu, W., Ebright, R., and Triezenberg, S. (1998) Mutational analysis of the transcriptional activation region of the VP16 protein of herpes simplex virus. Nucl. Acids Res. 26, 4487-4496.

Savery, N., Lloyd, G., Kainz, M., Gaal, T., Ross, W., Ebright, R., Gourse, R. and Busby, S. (1998) Transcription activation at Class II CRP-dependent promoters: identification of determinants in the C-terminal domain of the RNA polymerase alpha subunit EMBO J. 17, 3439-3447.

Kim, T.K., Lagrange, T., Wang, Y.H., Griffith, J.D., Reinberg, D., Ebright, R.H. (1997). Trajectory of DNA in the RNA polymerase II transcription preinitiation complex. Proc Natl Acad Sci U S A. 94(23): 12268-12273. Review.

Miller, A., Wood, D., Ebright, R., and Rothman-Denes, L. (1997). RNA polymerase beta': a target for DNA-binding-independent activation. Science 275: 1655-1657.

Busby, S. and Ebright, R. (1997) Transcription activation at Class II CAP-dependent promoters. Mol. Microbiol. 23, 853-859.

Niu, W., Kim, Y., Tau, G., Heyduk, and Ebright, R. (1996). Transcription activation at Class II CAP-dependent promoters: two interactions between CAP and RNA polymerase. Cell 87: 1123-1134.

Lagrange, T., Kim, T.-K., Orphanides, G. Ebright, Y., Ebright, R., and Reinberg, D. (1996). High-resolution mapping of nucleoprotein complexes by site-specific protein-DNA photocrosslinking: organization of the human TBP-TFIIA-TFIIB-DNA quaternary complex. Proc. Natl. Acad. Sci. USA 93:10620-10625.

Heyduk, T., Heyduk, E., Severinov, K., Tang, H. and Ebright, R. (1996). Determinants of RNA polymerase alpha subunit for interaction with beta and beta' subunits: hydroxyl-radical protein footprinting. Proc. Natl. Acad Sci. USA 93: 10162-10166.

Parkinson, G., Gunasekera, A., Vojtechovsky, J., Zhang, X., Kunkel, T., Berman, H. and Ebright, R. (1996). Aromatic hydrogen bond in sequence-specific protein-DNA interaction. Nature Structl. Biol. 3: 837-841.

Pellegrini, M. and Ebright, R. (1996). Artificial DNA binding peptides: branched-chain basic regions. J. Amer. Chem. Soc. 118: 5831-5835.

Tang, H., Sun, X., Reinberg, D. and Ebright, R. (1996). Protein-protein interactions in eukaryotic transcription initiation: structure of the pre-initiation complex. Proc. Natl. Acad. Sci. USA 93: 1119-1124.

Parkinson, G., Wilson, C., Gunasekera, A., Ebright, Y., Ebright, R. and Berman, H. (1996) Structure of the CAP-DNA complex at 2.5 E resolution: a complete picture of the protein-DNA interface. J. Mol. Biol. 260, 395-408.

Sheehan, B., Klarsfeld, A., Ebright, R. and Cossart, P. (1996) A single substitution in the putative helix-turn-helix motif of the pleiotropic activator PrfA attenuates Listeria monocytogenes virulence. Mol. Microbiol. 20, 785-797.

Ebright, Y., Chen, Y., Kim, Y. and Ebright, R. (1996) S-[2-(4-azidosalicylamido)ethanethio]-2-thiopyridine: radioiodinatable, cleavable photoactivatible crosslinking agent. Bioconj. Chem. 7, 380-384.

Dumoulin, P., Ebright, R., Knegtel, R., Kaptein, R., Granger-Schnarr, M. and Schnarr, M. (1996) Structure of the LexA-DNA complex probed by affinity cleavage and affinity photocrosslinking. Biochem. 35, 4279-4286.

Gaal, T., Ross, W., Blatter, E., Tang, H., Jia, X., Krishnan, V., Assa-Munt, N., Ebright, R., and Gourse, R. (1996) DNA binding determinants of the alpha subunit of RNA polymerase: a novel DNA binding domain architecture. Genes & Development 10, 16-26.

Lab Members

Dr. Yon Ebright, Research Associate
Dr. Jayanta Mukhopadhyay, Research Associate
Dr. Vladimir Mekler, Research Associate
Dr. Sergei Druzhinin, Research Associate
Dr. Aashish Srivastava, Research Associate
Dr. Tatyana Naryshkina, Research Associate
Dr. Rui Rong Neidfeldt, Research Associate
Dr. Candida Perera, Laboratory Manager
Dr. Yi Jiang, Postdoctoral Fellow
Dr. Sukhendru Mandal, Postdoctoral Fellow
Dr. Sujoy Chatterjee, Postdoctoral Fellow
Dongye Wang, Graduate Assistant
Charles O'Brien, Graduate Assistant
Qumiao Xu, Graduate Assistant
Soma Mandal, Graduate Assistant
Nimish Gupta, Graduate Assistant
David Degen, Graduate Assistant
Anirban Chakraborty, Graduate Assistant
Fang Da, Graduate Assistant
Sarah Brown, Undergraduate Assistant
Mihir Sarwade, Undergraduate Assistant
Hoa Pham, High School Research Intern
Kyle Skalenko, Undergraduate Assistant
Qiaorong Jiang, Research Technician