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Sui S, Mulichak A, Kulathila R, McGee J, Filiatreault D, Saha S, Cohen A, Song J, Hung H, Selway J, Kirby C, Shrestha OK, Weihofen W, Fodor M, Xu M, Chopra R, Perry SL. A capillary-based microfluidic device enables primary high-throughput room-temperature crystallographic screening. J Appl Crystallogr 2021; 54:1034-1046. [PMID: 34429718 PMCID: PMC8366422 DOI: 10.1107/s1600576721004155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 04/18/2021] [Indexed: 11/10/2022] Open
Abstract
A novel capillary-based microfluidic strategy to accelerate the process of small-molecule-compound screening by room-temperature X-ray crystallography using protein crystals is reported. The ultra-thin microfluidic devices are composed of a UV-curable polymer, patterned by cleanroom photolithography, and have nine capillary channels per chip. The chip was designed for ease of sample manipulation, sample stability and minimal X-ray background. 3D-printed frames and cassettes conforming to SBS standards are used to house the capillary chips, providing additional mechanical stability and compatibility with automated liquid- and sample-handling robotics. These devices enable an innovative in situ crystal-soaking screening workflow, akin to high-throughput compound screening, such that quantitative electron density maps sufficient to determine weak binding events are efficiently obtained. This work paves the way for adopting a room-temperature microfluidics-based sample delivery method at synchrotron sources to facilitate high-throughput protein-crystallography-based screening of compounds at high concentration with the aim of discovering novel binding events in an automated manner.
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Affiliation(s)
- Shuo Sui
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Anne Mulichak
- IMCA-CAT, Argonne National Laboratory, Lemont, IL, USA
| | | | - Joshua McGee
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | | | - Sarthak Saha
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
| | - Aina Cohen
- Macromolecular Crystallography Group, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | - Jinhu Song
- Macromolecular Crystallography Group, Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, USA
| | | | - Jonathan Selway
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Christina Kirby
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Om K. Shrestha
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Michelle Fodor
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Mei Xu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Rajiv Chopra
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Sarah L. Perry
- Department of Chemical Engineering, University of Massachusetts Amherst, Amherst, MA, USA
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2
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Palacios DS, Meredith E, Kawanami T, Adams C, Chen X, Darsigny V, Geno E, Palermo M, Baird D, Boynton G, Busby SA, George EL, Guy C, Hewett J, Tierney L, Thigale S, Weihofen W, Wang L, White N, Yin M, Argikar UA. Structure based design of nicotinamide phosphoribosyltransferase (NAMPT) inhibitors from a phenotypic screen. Bioorg Med Chem Lett 2018; 28:365-370. [DOI: 10.1016/j.bmcl.2017.12.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 10/18/2022]
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3
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Ross P, Weihofen W, Siu F, Xie A, Katakia H, Wright SK, Hunt I, Brown RK, Freire E. Isothermal chemical denaturation to determine binding affinity of small molecules to G-protein coupled receptors. Anal Biochem 2014; 473:41-5. [PMID: 25481736 DOI: 10.1016/j.ab.2014.11.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/21/2014] [Accepted: 11/24/2014] [Indexed: 12/12/2022]
Abstract
The determination of accurate binding affinities is critical in drug discovery and development. Several techniques are available for characterizing the binding of small molecules to soluble proteins. The situation is different for integral membrane proteins. Isothermal chemical denaturation has been shown to be a valuable biophysical method to determine, in a direct and label-free fashion, the binding of ligands to soluble proteins. In this study, the application of isothermal chemical denaturation was applied to an integral membrane protein, the A2a G-protein coupled receptor. Binding affinities for a set of 19 small molecule agonists/antagonists of the A2a receptor were determined and found to be in agreement with data from surface plasmon resonance and radioligand binding assays previously reported in the literature. Therefore, isothermal chemical denaturation expands the available toolkit of biophysical techniques to characterize and study ligand binding to integral membrane proteins, specifically G-protein coupled receptors in vitro.
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Affiliation(s)
| | - Wilhelm Weihofen
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Fai Siu
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Amy Xie
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Hetal Katakia
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - S Kirk Wright
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Ian Hunt
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | | | - Ernesto Freire
- AVIA Biosystems, Norton, MA 02766, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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4
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Sotomayor MM, Weihofen W, Gaudet R, Corey D. Structural Determinants of Cadherin-23 Function in Hearing and Deafness. Biophys J 2010. [DOI: 10.1016/j.bpj.2009.12.2770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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5
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Dutz H, Helbing K, Krimmer J, Speckner T, Zeitler G, Ahrens J, Altieri S, Annand JRM, Anton G, Arends HJ, Beck R, Bock A, Bradtke C, Braghieri A, v Drachenfels W, Frommberger F, Godo M, Goertz S, Grabmayr P, Hasegawa S, Hansen K, Harmsen J, Heid E, Hillert W, Holvoet H, Horikawa N, Iwata T, Van Hoorebeke L, d'Hose N, Jennewein P, Kiel B, Klein F, Kondratiev R, Lang M, Lannoy B, Leukel R, Lisin V, Menze D, Meyer W, Michel T, Naumann J, Panzeri A, Pedroni P, Pinelli T, Preobrajenski I, Radtke E, Reicherz G, Rohlof C, Rostomyan T, Sauer M, Schoch B, Schumacher M, Tamas G, Thomas A, van de Vyver R, Weihofen W, Zapadtka F. Measurement of helicity-dependent photoabsorption cross sections on the neutron from 815 to 1825 MeV. Phys Rev Lett 2005; 94:162001. [PMID: 15904214 DOI: 10.1103/physrevlett.94.162001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Indexed: 05/02/2023]
Abstract
Helicity-dependent total photoabsorption cross sections on the deuteron have been measured for the first time at ELSA (Bonn) in the photon energy range from 815 to 1825 MeV. Circularly polarized tagged photons impinging on a longitudinally polarized LiD target have been used together with a highly efficient 4pi detector system. The data around 1 GeV are not compatible with predictions from existing multipole analyses. From the measured energy range an experimental contribution to the GDH integral on the neutron of [33.9 +/- 5.5(stat) +/- 4.5(syst)] microb is extracted.
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Affiliation(s)
- H Dutz
- Physikalisches Institut, Universität Bonn, D-53115 Bonn, Germany
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6
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Dutz H, Helbing K, Krimmer J, Speckner T, Zeitler G, Ahrens J, Altieri S, Annand JRM, Anton G, Arends HJ, Beck R, Bock A, Bradtke C, Braghieri A, v Drachenfels W, Frommberger F, Godo M, Goertz S, Grabmayr P, Hasegawa S, Hansen K, Harmsen J, Heid E, Hillert W, Holvoet H, Horikawa N, Iwata T, Hoorebeke LV, D'Hose N, Jennewein P, Kiel B, Klein F, Kondratiev R, Lang M, Lannoy B, Leukel R, Lisin V, Menze D, Meyer W, Michel T, Naumann J, Panzeri A, Pedroni P, Pinelli T, Preobrajenski I, Radtke E, Reicherz G, Rohlof C, Rostomyan T, Sauer M, Schoch B, Schumacher M, Tamas G, Thomas A, van de Vyver R, Weihofen W, Zapadtka F. Experimental check of the Gerasimov-Drell-Hearn sum rule for 1H. Phys Rev Lett 2004; 93:032003. [PMID: 15323817 DOI: 10.1103/physrevlett.93.032003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2004] [Indexed: 05/24/2023]
Abstract
For the first time we checked the fundamental Gerasimov-Drell-Hearn (GDH) sum rule for the proton experimentally in the photon energy range from 0.2-2.9 GeV with the tagged photon facilities at MAMI (Mainz) and ELSA (Bonn). New data of the doubly polarized total cross section difference are presented in the energy range from 1.6 to 2.9 GeV. The contribution to the GDH integral from 0.2-2.9 GeV yields [254+/-5(stat)+/-12(syst)] microb with negative contributions in the Regge regime at photon energies above 2.1 GeV. This trend supports the validity of the GDH sum rule.
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Affiliation(s)
- H Dutz
- Physikalisches Institut, Universität Bonn, D-53115 Bonn, Germany
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7
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de la Hoz AB, Pratto F, Misselwitz R, Speck C, Weihofen W, Welfle K, Saenger W, Welfle H, Alonso JC. Recognition of DNA by omega protein from the broad-host range Streptococcus pyogenes plasmid pSM19035: analysis of binding to operator DNA with one to four heptad repeats. Nucleic Acids Res 2004; 32:3136-47. [PMID: 15190131 PMCID: PMC434439 DOI: 10.1093/nar/gkh633] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
pSM19035-encoded omega protein forms a dimer (omega2) that binds to a set of 7-bp repeats with sequence 5'-NATCACN-3'. Upon binding to its cognate sites, omega2 regulates transcription of genes required for copy number control and stable inheritance of plasmids, and promotes accurate plasmid segregation. Protein omega2 binds poorly to one heptad but the affinity to DNA increases with two and more unspaced heptads in direct or inverted orientation. DNA titration of increasing numbers of heptads with omega2, monitored by circular dichroism measurements, indicates the binding of one omega2 to one heptad (omega2:heptad stoichiometry of 1:1). Spacing of two directly or inversely oriented heptads by 1 to 7 bp reduces the affinity of the protein for its cognate target site. The binding affinity of omega2 for two directly repeated heptads was severely reduced if one of the base pairs of the core 5'-ATCAC-3' sequence of one of the heptads was individually substituted by any other base pair. Hydroxyl radical footprinting shows a protection pattern at the 5'-ATCAC-3' core. These data suggest that each heptad defines an operator half-site and that tight binding of the symmetric omega2 to the central 5'-TCA-3' core of symmetric or asymmetric targets (differently oriented heptads) is probably achieved by structural changes of DNA and/or protein or both.
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Affiliation(s)
- Ana B de la Hoz
- Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia, CSIC, 28049 Madrid, Spain
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Manjasetty BA, Delbrück H, Pham DT, Mueller U, Fieber-Erdmann M, Scheich C, Sievert V, Büssow K, Niesen FH, Weihofen W, Loll B, Saenger W, Heinemann U, Neisen FH. Crystal structure of Homo sapiens protein hp14.5. Proteins 2004; 54:797-800. [PMID: 14997576 DOI: 10.1002/prot.10619] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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9
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Manjasetty BA, Delbrück H, Pham DT, Mueller U, Fieber-Erdmann M, Scheich C, Sievert V, Büssow K, Niesen FH, Weihofen W, Loll B, Saenger W, Heinemann U. Crystal structure of Homo sapiens protein hp14.5. Proteins 2004. [DOI: 10.1002/prot.20188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Dutz H, Helbing K, Krimmer J, Speckner T, Zeitler G, Ahrens J, Altieri S, Annand JRM, Anton G, Arends HJ, Beck R, Bock A, Bradtke C, Braghieri A, v Drachenfels W, Frommberger F, Godo M, Goertz S, Grabmayr P, Hasegawa S, Hansen K, Harmsen J, Heid E, Hillert W, Holvoet H, Horikawa N, Iwata T, Van Hoorebeke L, d'Hose N, Jennewein P, Kiel B, Klein F, Kondratiev R, Lang M, Lannoy B, Leukel R, Lisin V, Menze D, Meyer W, Michel T, Naumann J, Panzeri A, Pedroni P, Pinelli T, Preobrajenski I, Radtke E, Reicherz G, Rohlof C, Rostomyan T, Sauer M, Schoch B, Schumacher M, Tamas G, Thomas A, van de Vyver R, Weihofen W, Zapadtka F. First Measurement of the Gerasimov-Drell-Hearn Sum Rule for 1H from 0.7 to 1.8 GeV at ELSA. Phys Rev Lett 2003; 91:192001. [PMID: 14611575 DOI: 10.1103/physrevlett.91.192001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2003] [Indexed: 05/24/2023]
Abstract
To verify the fundamental Gerasimov-Drell-Hearn (GDH) sum rule for the first time experimentally, we measured the helicity dependent total photoabsorption cross section with circularly polarized real photons and longitudinally polarized nucleons in the photon energy range 0.68-1.82 GeV with the tagged photon facility at ELSA. The experiment was carried out with a 4pi detection system, a circularly polarized tagged photon beam, and a frozen spin polarized proton target. The contribution to the GDH sum rule in this photon energy range is [49.9+/-2.4(stat)+/-2.2(syst)] microb.
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Affiliation(s)
- H Dutz
- Physikalisches Institut, Universität Bonn, D-53115 Bonn, Germany
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11
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Ahrens J, Altieri S, Annand JRM, Anton G, Arends HJ, Aulenbacher K, Beck R, Bradtke C, Braghieri A, Degrande N, D'Hose N, Drechsel D, Dutz H, Goertz S, Grabmayr P, Hansen K, Harmsen J, Von Harrach D, Hasegawa S, Hasegawa T, Heid E, Helbing K, Holvoet H, Van Hoorebeke L, Horikawa N, Iwata T, Jahn O, Jennewein P, Kageya T, Kamalov S, Kiel B, Klein F, Kondratiev R, Kossert K, Krimmer J, Lang M, Lannoy B, Leukel R, Lisin V, Matsuda T, McGeorge JC, Meier A, Menze D, Meyer W, Michel T, Naumann J, Panzeri A, Pedroni P, Pinelli T, Preobrajenski I, Radtke E, Reichert E, Reicherz G, Rohlof C, Rosner G, Ryckbosch D, Sauer M, Schoch B, Schumacher M, Seitz B, Speckner T, Takabayashi N, Tamas G, Thomas A, Tiator L, Van Vyver R, Wakai A, Weihofen W, Wissmann F, Zapadtka F, Zeitler G. Helicity amplitudes A1/2 and A3/2 for the D13(1520) resonance obtained from the gamma-->p-->-->ppi(0) Reaction. Phys Rev Lett 2002; 88:232002. [PMID: 12059355 DOI: 10.1103/physrevlett.88.232002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2002] [Indexed: 05/23/2023]
Abstract
The helicity dependence of the gamma-->p-->-->ppi(0) reaction has been measured for the first time in the photon-energy range from 550 to 790 MeV. The experiment, performed at the Mainz microtron MAMI, used a 4pi-detector system, a circularly polarized, tagged photon beam, and a longitudinally polarized frozen-spin target. These data are predominantly sensitive to the D13(1520) resonance and are used to determine its helicity amplitudes.
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Affiliation(s)
- J Ahrens
- Institut für Kernphysik, Universität Mainz, D-55099 Mainz, Germany
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12
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Kossert K, Camen M, Wissmann F, Ahrens J, Annand JRM, Arends HJ, Beck R, Caselotti G, Grabmayr P, Jahn O, Jennewein P, Levchuk MI, L'vov AI, McGeorge JC, Natter A, Olmos de León V, Petrun'kin VA, Rosner G, Schumacher M, Seitz B, Smend F, Thomas A, Weihofen W, Zapadtka F. Neutron polarizabilities investigated by quasifree Compton scattering from the deuteron. Phys Rev Lett 2002; 88:162301. [PMID: 11955229 DOI: 10.1103/physrevlett.88.162301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2001] [Indexed: 05/23/2023]
Abstract
Measuring Compton scattered photons and recoil neutrons in coincidence, quasifree Compton scattering by the neutron has been investigated at MAMI (Mainz) at theta(lab)(gamma) = 136 degrees in an energy range from 200 to 400 MeV. From the data a polarizability difference of alpha(n)-beta(n) = 9.8+/-3.6(stat)+2.1-1.1(syst)+/-2.2(model) in units of 10(-4) fm(3) has been determined. In combination with the polarizability sum alpha(n)+beta(n) = 15.2+/-0.5 deduced from photoabsorption data, the first precise results for the neutron electric and magnetic polarizabilities, alpha(n) = 12.5+/-1.8(stat)+1.1-0.6(syst)+/-1.1(model) and beta(n) = 2.7-/+1.8(stat)+0.6-1.1(syst)-/+1.1(model), are obtained.
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Affiliation(s)
- K Kossert
- Zweites Physikalisches Institut, Universität Göttingen, D-37073 Göttingen, Germany
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