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Zwirner S, Abu Rmilah AA, Klotz S, Pfaffenroth B, Kloevekorn P, Moschopoulou AA, Schuette S, Haag M, Selig R, Li K, Zhou W, Nelson E, Poso A, Chen H, Amiot B, Jia Y, Minshew A, Michalak G, Cui W, Rist E, Longerich T, Jung B, Felgendreff P, Trompak O, Premsrirut PK, Gries K, Muerdter TE, Heinkele G, Wuestefeld T, Shapiro D, Weissbach M, Koenigsrainer A, Sipos B, Ab E, Zacarias MO, Theisgen S, Gruenheit N, Biskup S, Schwab M, Albrecht W, Laufer S, Nyberg S, Zender L. First-in-class MKK4 inhibitors enhance liver regeneration and prevent liver failure. Cell 2024; 187:1666-1684.e26. [PMID: 38490194 PMCID: PMC11011246 DOI: 10.1016/j.cell.2024.02.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/20/2023] [Accepted: 02/20/2024] [Indexed: 03/17/2024]
Abstract
Diminished hepatocyte regeneration is a key feature of acute and chronic liver diseases and after extended liver resections, resulting in the inability to maintain or restore a sufficient functional liver mass. Therapies to restore hepatocyte regeneration are lacking, making liver transplantation the only curative option for end-stage liver disease. Here, we report on the structure-based development and characterization (nuclear magnetic resonance [NMR] spectroscopy) of first-in-class small molecule inhibitors of the dual-specificity kinase MKK4 (MKK4i). MKK4i increased liver regeneration upon hepatectomy in murine and porcine models, allowed for survival of pigs in a lethal 85% hepatectomy model, and showed antisteatotic and antifibrotic effects in liver disease mouse models. A first-in-human phase I trial (European Union Drug Regulating Authorities Clinical Trials [EudraCT] 2021-000193-28) with the clinical candidate HRX215 was conducted and revealed excellent safety and pharmacokinetics. Clinical trials to probe HRX215 for prevention/treatment of liver failure after extensive oncological liver resections or after transplantation of small grafts are warranted.
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Affiliation(s)
- Stefan Zwirner
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; HepaRegeniX GmbH, Tübingen 72072, Germany
| | - Anan A Abu Rmilah
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Sabrina Klotz
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Bent Pfaffenroth
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Philip Kloevekorn
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Athina A Moschopoulou
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Svenja Schuette
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Mathias Haag
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Roland Selig
- HepaRegeniX GmbH, Tübingen 72072, Germany; Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany
| | - Kewei Li
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Wei Zhou
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Erek Nelson
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Antti Poso
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; School of Pharmacy, University of Eastern Finland, Kuopio 70211, Finland; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany
| | - Harvey Chen
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Bruce Amiot
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Yao Jia
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Anna Minshew
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Gregory Michalak
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Wei Cui
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Elke Rist
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg, Heidelberg 69120, Germany
| | | | - Philipp Felgendreff
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA
| | - Omelyan Trompak
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | | | - Katharina Gries
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Thomas E Muerdter
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Georg Heinkele
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany
| | - Torsten Wuestefeld
- Laboratory for In Vivo Genetics & Gene Therapy, Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore 138672, Singapore; School of Biological Sciences, Nanyang Technological University of Singapore, Singapore 637551, Singapore
| | | | | | - Alfred Koenigsrainer
- iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Department of General-, Visceral, and Transplant Surgery, University Hospital Tübingen, Tübingen 72076, Germany
| | - Bence Sipos
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany
| | - Eiso Ab
- ZoBio B.V., Leiden 2333 CH, the Netherlands
| | | | | | | | | | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart 70376, Germany; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; Department of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tübingen, Tübingen 72076, Germany
| | | | - Stefan Laufer
- Department of Pharmaceutical Chemistry, University of Tübingen, Tübingen 72076, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), Tübingen 72076, Germany.
| | - Scott Nyberg
- William J. von Liebig Center for Transplantation and Clinical Regeneration, Mayo Clinic, Rochester, MN 55905, USA.
| | - Lars Zender
- Department of Medical Oncology and Pneumology (Internal Medicine VIII), University Hospital Tübingen, Tübingen 72076, Germany; iFIT Cluster of Excellence (EXC 2180) "Image-guided and Functionally Instructed Tumor Therapies", University of Tübingen, Tübingen 72076, Germany; German Cancer Research Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany; Tübingen Center for Academic Drug Discovery & Development (TüCAD(2)), Tübingen 72076, Germany.
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Keiffer S, Carneiro MG, Hollander J, Kobayashi M, Pogoryelev D, Ab E, Theisgen S, Müller G, Siegal G. NMR in target driven drug discovery: why not? J Biomol NMR 2020; 74:521-529. [PMID: 32901320 PMCID: PMC7683447 DOI: 10.1007/s10858-020-00343-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/17/2020] [Indexed: 05/09/2023]
Abstract
No matter the source of compounds, drug discovery campaigns focused directly on the target are entirely dependent on a consistent stream of reliable data that reports on how a putative ligand interacts with the protein of interest. The data will derive from many sources including enzyme assays and many types of biophysical binding assays such as TR-FRET, SPR, thermophoresis and many others. Each method has its strengths and weaknesses, but none is as information rich and broadly applicable as NMR. Here we provide a number of examples of the utility of NMR for enabling and providing ongoing support for the early pre-clinical phase of small molecule drug discovery efforts. The examples have been selected for their usefulness in a commercial setting, with full understanding of the need for speed, cost-effectiveness and ease of implementation.
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Affiliation(s)
| | | | | | | | | | - Eiso Ab
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands
| | | | - Gerhard Müller
- Gotham GmbH, Am Klopferspitz 19a, 82152, Martinsried, Germany
| | - Gregg Siegal
- ZoBio, JH Oortweg 19, 2333CH, Leiden, Netherlands.
- Amsterdam Institute of Molecular and Life Sciences, Free University Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands.
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Makraki E, Carneiro MG, Heyam A, Ab E, Siegal G, Hubbard RE. Correction to: 1H, 13C, 15N backbone and IVL methyl group resonance assignment of the fungal β-glucosidase from Trichoderma reesei. Biomol NMR Assign 2020; 14:269. [PMID: 32654087 PMCID: PMC7462830 DOI: 10.1007/s12104-020-09967-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In the original publication of the article, the name of one of the authors is incorrect. The author's name is Eiso AB, but was modified to A. B. Eiso. The correct name is given in this Correction.
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Affiliation(s)
- Eleni Makraki
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
| | | | - Alex Heyam
- YSBL, Department of Chemistry, University of York, Heslington, York, UK
| | - Eiso Ab
- ZoBio BV, J.H. Oortweg 19, 2333 CH, Leiden, The Netherlands
| | - Gregg Siegal
- ZoBio BV, J.H. Oortweg 19, 2333 CH, Leiden, The Netherlands
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roderick E Hubbard
- YSBL, Department of Chemistry, University of York, Heslington, York, UK.
- Vernalis Research, Granta Park, Abington, Cambridge, UK.
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Kappo MA, Ab E, Hassem F, Atkinson RA, Faro A, Muleya V, Mulaudzi T, Poole JO, McKenzie JM, Chibi M, Moolman-Smook JC, Rees DJG, Pugh DJR. Solution structure of RING finger-like domain of retinoblastoma-binding protein-6 (RBBP6) suggests it functions as a U-box. J Biol Chem 2011; 287:7146-58. [PMID: 22130672 DOI: 10.1074/jbc.m110.217059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Retinoblastoma-binding protein-6 (RBBP6) plays a facilitating role, through its RING finger-like domain, in the ubiquitination of p53 by Hdm2 that is suggestive of E4-like activity. Although the presence of eight conserved cysteine residues makes it highly probable that the RING finger-like domain coordinates two zinc ions, analysis of the primary sequence suggests an alternative classification as a member of the U-box family, the members of which do not bind zinc ions. We show here that despite binding two zinc ions, the domain adopts a homodimeric structure highly similar to those of a number of U-boxes. Zinc ions could be replaced by cadmium ions without significantly disrupting the structure or the stability of the domain, although the rate of substitution was an order of magnitude slower than any previous measurement, suggesting that the structure is particularly stable, a conclusion supported by the high thermal stability of the domain. A hallmark of U-box-containing proteins is their association with chaperones, with which they cooperate in eliminating irretrievably unfolded proteins by tagging them for degradation by the proteasome. Using a yeast two-hybrid screen, we show that RBBP6 interacts with chaperones Hsp70 and Hsp40 through its N-terminal ubiquitin-like domain. Taken together with the structural similarities to U-box-containing proteins, our data suggest that RBBP6 plays a role in chaperone-mediated ubiquitination and possibly in protein quality control.
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Affiliation(s)
- Mautin A Kappo
- Biotechnology Department, University of the Western Cape, Bellville 7535, South Africa
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5
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Van Melckebeke H, Wasmer C, Lange A, Ab E, Loquet A, Böckmann A, Meier BH. Atomic-resolution three-dimensional structure of HET-s(218-289) amyloid fibrils by solid-state NMR spectroscopy. J Am Chem Soc 2011; 132:13765-75. [PMID: 20828131 DOI: 10.1021/ja104213j] [Citation(s) in RCA: 228] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We present a strategy to solve the high-resolution structure of amyloid fibrils by solid-state NMR and use it to determine the atomic-resolution structure of the prion domain of the fungal prion HET-s in its amyloid form. On the basis of 134 unambiguous distance restraints, we recently showed that HET-s(218-289) in its fibrillar state forms a left-handed β-solenoid, and an atomic-resolution NMR structure of the triangular core was determined from unambiguous restraints only. In this paper, we go considerably further and present a comprehensive protocol using six differently labeled samples, a collection of optimized solid-state NMR experiments, and adapted structure calculation protocols. The high-resolution structure obtained includes the less ordered but biologically important C-terminal part and improves the overall accuracy by including a large number of ambiguous distance restraints.
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Affiliation(s)
- Hélène Van Melckebeke
- Physical Chemistry, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zurich, Switzerland
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6
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Früh V, Zhou Y, Chen D, Loch C, Ab E, Grinkova YN, Verheij H, Sligar SG, Bushweller JH, Siegal G. Application of fragment-based drug discovery to membrane proteins: identification of ligands of the integral membrane enzyme DsbB. ACTA ACUST UNITED AC 2011; 17:881-91. [PMID: 20797617 DOI: 10.1016/j.chembiol.2010.06.011] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 05/29/2010] [Accepted: 06/02/2010] [Indexed: 11/29/2022]
Abstract
Membrane proteins are important pharmaceutical targets, but they pose significant challenges for fragment-based drug discovery approaches. Here, we present the first successful use of biophysical methods to screen for fragment ligands to an integral membrane protein. The Escherichia coli inner membrane protein DsbB was solubilized in detergent micelles and lipid bilayer nanodiscs. The solubilized protein was immobilized with retention of functionality and used to screen 1071 drug fragments for binding using target immobilized NMR Screening. Biochemical and biophysical validation of the eight most potent hits revealed an IC(50) range of 7-200 microM. The ability to insert a broad array of membrane proteins into nanodiscs, combined with the efficiency of TINS, demonstrates the feasibility of finding fragments targeting membrane proteins.
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Affiliation(s)
- Virginie Früh
- Leiden Institute of Chemistry, Leiden University, Leiden 2300RA, The Netherlands
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7
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Kobayashi M, Retra K, Figaroa F, Hollander JG, Ab E, Heetebrij RJ, Irth H, Siegal G. Target Immobilization as a Strategy for NMR-Based Fragment Screening. ACTA ACUST UNITED AC 2010; 15:978-89. [DOI: 10.1177/1087057110375614] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Fragment-based drug discovery (FBDD) has become a widely accepted tool that is complementary to high-throughput screening (HTS) in developing small-molecule inhibitors of pharmaceutical targets. Because a fragment campaign can only be as successful as the hit matter found, it is critical that the first stage of the process be optimized. Here the authors compare the 3 most commonly used methods for hit discovery in FBDD: high concentration screening (HCS), solution ligand-observed nuclear magnetic resonance (NMR), and surface plasmon resonance (SPR). They selected the commonly used saturation transfer difference (STD) NMR spectroscopy and the proprietary target immobilized NMR screening (TINS) as representative of the array of possible NMR methods. Using a target typical of FBDD campaigns, the authors find that HCS and TINS are the most sensitive to weak interactions. They also find a good correlation between TINS and STD for tighter binding ligands, but the ability of STD to detect ligands with affinity weaker than 1 mM KD is limited. Similarly, they find that SPR detection is most suited to ligands that bind with KD better than 1 mM. However, the good correlation between SPR and potency in a bioassay makes this a good method for hit validation and characterization studies.
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Affiliation(s)
| | - Kim Retra
- Biomolecular Analysis and Spectroscopy, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije University Amsterdam, Amsterdam, The Netherlands
| | | | | | - Eiso Ab
- ZoBio B.V, Einsteinweg 55, 2333CC, Leiden, The Netherlands
| | | | - Hubertus Irth
- Biomolecular Analysis and Spectroscopy, Department of Chemistry and Pharmaceutical Sciences, Faculty of Sciences, Vrije University Amsterdam, Amsterdam, The Netherlands
| | - Gregg Siegal
- ZoBio B.V, Einsteinweg 55, 2333CC, Leiden, The Netherlands
- Leiden Institute of Chemistry, Leiden University, Leiden, The Netherlands
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8
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Kobayashi M, Ab E, Bonvin AMJJ, Siegal G. Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA complex. J Biol Chem 2010; 285:10087-10097. [PMID: 20081198 DOI: 10.1074/jbc.m109.054106] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BRCA1 C-terminal domain (BRCT)-containing proteins are found widely throughout the animal and bacteria kingdoms where they are exclusively involved in cell cycle regulation and DNA metabolism. Whereas most BRCT domains are involved in protein-protein interactions, a small subset has bona fide DNA binding activity. Here, we present the solution structure of the BRCT region of the large subunit of replication factor C bound to DNA and a model of the structure-specific complex with 5'-phosphorylated double-stranded DNA. The replication factor C BRCT domain possesses a large basic patch on one face, which includes residues that are structurally conserved and ligate the phosphate in phosphopeptide binding BRCT domains. An extra alpha-helix at the N terminus, which is required for DNA binding, inserts into the major groove and makes extensive contacts to the DNA backbone. The model of the protein-DNA complex suggests 5'-phosphate recognition by the BRCT domains of bacterial NAD(+)-dependent ligases and a nonclamp loading role for the replication factor C complex in DNA transactions.
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Affiliation(s)
| | - Eiso Ab
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht 3584, Netherlands
| | - Alexander M J J Bonvin
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, University of Utrecht, Utrecht 3584, Netherlands
| | - Gregg Siegal
- Leiden Institute of Chemistry, Leiden University, Leiden 2300RA.
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9
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de Jong RN, Truffault V, Diercks T, Ab E, Daniels MA, Kaptein R, Folkers GE. Structure and DNA binding of the human Rtf1 Plus3 domain. Structure 2008; 16:149-59. [PMID: 18184592 DOI: 10.1016/j.str.2007.10.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2007] [Revised: 09/17/2007] [Accepted: 10/16/2007] [Indexed: 11/30/2022]
Abstract
The yeast Paf1 complex consists of Paf1, Rtf1, Cdc73, Ctr9, and Leo1 and regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. We provide structural insight into the Paf1 complex with the NMR structure of the conserved and functionally important Plus3 domain of human Rtf1. A predominantly beta-stranded subdomain displays structural similarity to Dicer/Argonaute PAZ domains and to Tudor domains. We further demonstrate that the highly basic Rtf1 Plus3 domain can interact in vitro with single-stranded DNA via residues on the rim of the beta sheet, reminiscent of siRNA binding by PAZ domains, but did not detect binding to double-stranded DNA or RNA. We discuss the potential role of Rtf1 Plus3 ssDNA binding during transcription elongation.
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Affiliation(s)
- Rob N de Jong
- Bijvoet Centre for Biomolecular Research, Utrecht University, Faculty of Chemistry, Department NMR Spectroscopy, Padualaan 8, Utrecht, The Netherlands
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10
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Ortega Roldan JL, Romero Romero ML, Ora A, Ab E, Lopez Mayorga O, Azuaga AI, van Nuland NAJ. The high resolution NMR structure of the third SH3 domain of CD2AP. J Biomol NMR 2007; 39:331-336. [PMID: 17922258 DOI: 10.1007/s10858-007-9201-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 09/14/2007] [Indexed: 05/25/2023]
Abstract
CD2 associated protein (CD2AP) is an adaptor protein that plays an important role in cell to cell union needed for the kidney function. CD2AP interacts, as an adaptor protein, with different natural targets, such as CD2, nefrin, c-Cbl and podocin. These proteins are believed to interact to one of the three SH3 domains that are positioned in the N-terminal region of CD2AP. To understand the network of interactions between the natural targets and the three SH3 domains (SH3-A, B and C), we have started to determine the structures of the individual SH3 domains. Here we present the high-resolution structure of the SH3-C domain derived from NMR data. Full backbone and side-chain assignments were obtained from triple-resonance spectra. The structure was determined from distance restraints derived from high-resolution 600 and 800 MHz NOESY spectra, together with phi and psi torsion angle restraints based on the analysis of 1HN, 15N, 1Halpha, 13Calpha, 13CO and 13Cbeta chemical shifts. Structures were calculated using CYANA and refined in water using RECOORD. The three-dimensional structure of CD2AP SH3-C contains all the features that are typically found in other SH3 domains, including the general binding site for the recognition of polyproline sequences.
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Affiliation(s)
- Jose L Ortega Roldan
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Campus Fuentenueva s/n, Granada 18071, Spain
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11
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Siegal G, Ab E, Schultz J. Integration of fragment screening and library design. Drug Discov Today 2007; 12:1032-9. [PMID: 18061882 DOI: 10.1016/j.drudis.2007.08.005] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2007] [Revised: 08/02/2007] [Accepted: 08/03/2007] [Indexed: 10/22/2022]
Abstract
With more than 10 years of practical experience and theoretical analysis, fragment-based drug discovery (FBDD) has entered the mainstream of the pharmaceutical and biotech industries. An array of biophysical techniques has been used to detect the weak interaction between a fragment and the target. Each technique presents its own requirements regarding the fragment collection and the target; therefore, in order to optimize the potential of FBDD, the nature of the target should be a driving factor for simultaneous development of both the library and the screening technology. A roadmap is now available to guide fragment-to-lead evolution when structural information is available. The next challenge is to apply FBDD to targets for which high-resolution structural information is not available.
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Affiliation(s)
- Gregg Siegal
- Leiden Institute of Chemistry, Leiden University, The Netherlands.
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12
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Grenha R, Rzechorzek NJ, Brannigan JA, de Jong RN, Ab E, Diercks T, Truffault V, Ladds JC, Fogg MJ, Bongiorni C, Perego M, Kaptein R, Wilson KS, Folkers GE, Wilkinson AJ. Structural Characterization of Spo0E-like Protein-aspartic Acid Phosphatases That Regulate Sporulation in Bacilli. J Biol Chem 2006; 281:37993-8003. [PMID: 17001075 DOI: 10.1074/jbc.m607617200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Spore formation is an extreme response of many bacterial species to starvation. In the case of pathogenic species of Bacillus and Clostridium, it is also a component of disease transmission. Entry into the pathway of sporulation in Bacillus subtilis and its relatives is controlled by an expanded two-component system in which starvation signals lead to the activation of sensor kinases and phosphorylation of the master sporulation response regulator Spo0A. Accumulation of threshold concentrations of Spo0A approximately P heralds the commitment to sporulation. Countering the activities of the sensor kinases are phosphatases such as Spo0E, which dephosphorylate Spo0A approximately P and inhibit sporulation. Spo0E-like protein-aspartic acid-phosphate phosphatases, consisting of 50-90 residues, are conserved in sporeforming bacteria and unrelated in sequence to proteins of known structure. Here we determined the structures of the Spo0A approximately P phosphatases BA1655 and BA5174 from Bacillus anthracis using nuclear magnetic resonance spectroscopy. Each is composed of two anti-parallel alpha-helices flanked by flexible regions at the termini. The signature SQELD motif (SRDLD in BA1655) is situated in the middle of helix alpha2 with its polar residues projecting outward. BA5174 is a monomer, whereas BA1655 is a dimer. The four-helix bundle structure in the dimer is reminiscent of the phosphotransferase Spo0B and the chemotaxis phosphatase CheZ, although in contrast to these systems, the subunits in BA1655 are in head-to-tail rather than head-to-head apposition. The implications of the structures for interactions between the phosphatases and their substrate Spo0A approximately P are discussed.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Bacillus anthracis/enzymology
- Bacillus anthracis/genetics
- Bacillus anthracis/physiology
- Bacterial Proteins/chemistry
- Bacterial Proteins/genetics
- Bacterial Proteins/physiology
- Base Sequence
- DNA, Bacterial/genetics
- Dimerization
- Genes, Bacterial
- Models, Molecular
- Molecular Sequence Data
- Nuclear Magnetic Resonance, Biomolecular
- Phosphoric Monoester Hydrolases/chemistry
- Phosphoric Monoester Hydrolases/genetics
- Phosphoric Monoester Hydrolases/physiology
- Protein Structure, Quaternary
- Protein Structure, Secondary
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Sequence Homology, Amino Acid
- Spores, Bacterial/enzymology
- Spores, Bacterial/genetics
- Spores, Bacterial/physiology
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Affiliation(s)
- Rosa Grenha
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
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13
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Tomaselli S, Crescenzi O, Sanfelice D, Ab E, Wechselberger R, Angeli S, Scaloni A, Boelens R, Tancredi T, Pelosi P, Picone D. Solution structure of a chemosensory protein from the desert locust Schistocerca gregaria. Biochemistry 2006; 45:10606-13. [PMID: 16939212 DOI: 10.1021/bi060998w] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [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: 11/28/2022]
Abstract
Chemical stimuli, generally constituted by small volatile organic molecules, are extremely important for the survival of different insect species. In the course of evolution, insects have developed very sophisticated biochemical systems for the binding and the delivery of specific semiochemicals to their cognate membrane-bound receptors. Chemosensory proteins (CSPs) are a class of small soluble proteins present at high concentration in insect chemosensory organs; they are supposed to be involved in carrying the chemical messages from the environment to the chemosensory receptors. In this paper, we report on the solution structure of CSPsg4, a chemosensory protein from the desert locust Schistocerca gregaria, which is expressed in the antennae and other chemosensory organs. The 3D NMR structure revealed an overall fold consisting of six alpha-helices, spanning residues 13-18, 20-31, 40-54, 62-78, 80-90, and 97-103, connected by loops which in some cases show dihedral angles typical of beta-turns. As in the only other chemosensory protein whose structure has been solved so far, namely, CSP from the moth Mamestra brassicae, four helices are arranged to form a V-shaped motif; another helix runs across the two V's, and the last one is packed against the external face. Analysis of the tertiary structure evidenced multiple hydrophobic cavities which could be involved in ligand binding. In fact, incubation of the protein with a natural ligand, namely, oleamide, produced substantial changes to the NMR spectra, suggesting extensive conformational transitions upon ligand binding.
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Affiliation(s)
- Simona Tomaselli
- Department of Chemistry, University of Naples Federico II, 80126 Napoli, Italy
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14
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Ab E, Atkinson AR, Banci L, Bertini I, Ciofi-Baffoni S, Brunner K, Diercks T, Dötsch V, Engelke F, Folkers GE, Griesinger C, Gronwald W, Günther U, Habeck M, de Jong RN, Kalbitzer HR, Kieffer B, Leeflang BR, Loss S, Luchinat C, Marquardsen T, Moskau D, Neidig KP, Nilges M, Piccioli M, Pierattelli R, Rieping W, Schippmann T, Schwalbe H, Travé G, Trenner J, Wöhnert J, Zweckstetter M, Kaptein R. NMR in the SPINE Structural Proteomics project. Acta Crystallogr D Biol Crystallogr 2006; 62:1150-61. [PMID: 17001092 DOI: 10.1107/s0907444906032070] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 08/14/2006] [Indexed: 11/10/2022]
Abstract
This paper describes the developments, role and contributions of the NMR spectroscopy groups in the Structural Proteomics In Europe (SPINE) consortium. Focusing on the development of high-throughput (HTP) pipelines for NMR structure determinations of proteins, all aspects from sample preparation, data acquisition, data processing, data analysis to structure determination have been improved with respect to sensitivity, automation, speed, robustness and validation. Specific highlights are protonless (13)C-direct detection methods and inferential structure determinations (ISD). In addition to technological improvements, these methods have been applied to deliver over 60 NMR structures of proteins, among which are five that failed to crystallize. The inclusion of NMR spectroscopy in structural proteomics pipelines improves the success rate for protein structure determinations.
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Affiliation(s)
- E Ab
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, CH Utrecht, The Netherlands
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15
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Tripsianes K, Folkers G, Ab E, Das D, Odijk H, Jaspers NGJ, Hoeijmakers JHJ, Kaptein R, Boelens R. The structure of the human ERCC1/XPF interaction domains reveals a complementary role for the two proteins in nucleotide excision repair. Structure 2006; 13:1849-58. [PMID: 16338413 DOI: 10.1016/j.str.2005.08.014] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 08/26/2005] [Accepted: 08/28/2005] [Indexed: 11/21/2022]
Abstract
The human ERCC1/XPF complex is a structure-specific endonuclease with defined polarity that participates in multiple DNA repair pathways. We report the heterodimeric structure of the C-terminal domains of both proteins responsible for ERCC1/XPF complex formation. Both domains exhibit the double helix-hairpin-helix motif (HhH)2, and they are related by a pseudo-2-fold symmetry axis. In the XPF domain, the hairpin of the second motif is replaced by a short turn. The ERCC1 domain folds properly only in the presence of the XPF domain, which implies a role for XPF as a scaffold for the folding of ERCC1. The intersubunit interactions are largely hydrophobic in nature. NMR titration data show that only the ERCC1 domain of the ERCC1/XPF complex is involved in DNA binding. On the basis of these findings, we propose a model for the targeting of XPF nuclease via ERCC1-mediated interactions in the context of nucleotide excision repair.
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Affiliation(s)
- Konstantinos Tripsianes
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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16
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de Jong RN, Ab E, Diercks T, Truffault V, Daniëls M, Kaptein R, Folkers GE. Solution Structure of the Human Ubiquitin-specific Protease 15 DUSP Domain. J Biol Chem 2006; 281:5026-31. [PMID: 16298993 DOI: 10.1074/jbc.m510993200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [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: 11/06/2022] Open
Abstract
Ubiquitin-specific proteases (USPs) can remove covalently attached ubiquitin moieties from target proteins and regulate both the stability and ubiquitin-signaling state of their substrates. All USPs contain a conserved catalytic domain surrounded by one or more subdomains, some of which contribute to target recognition. One such specific subdomain, the DUSP domain (domain present in ubiquitin-specific proteases), is present in at least seven different human USPs that regulate the stability of or interact with the hypoxia-inducible transcription factor HIF1-alpha, the Von Hippel-Lindau protein (pVHL), cullin E3 ligases, and BRCA2. We describe the NMR solution structure of the DUSP domain of human USP15, recently implicated in COP9 (constitutive photomorphogenic gene 9)-signalosome regulation. Its tripod-like structure consists of a 3-fold alpha-helical bundle supporting a triple-stranded anti-parallel beta-sheet. The DUSP domain displays a novel fold, an alpha/beta tripod (AB3). DUSP domain surface properties and previously described work suggest a potential role in protein/protein interaction or substrate recognition.
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Affiliation(s)
- Rob N de Jong
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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17
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Tripsianes K, Folkers G, Ab E, Das D, Odijk H, Jaspers NGJ, Hoeijmakers JHJ, Kaptein R, Boelens R. The structure of the human ERCC1/XPF interaction domains reveals a complementary role for the two proteins in nucleotide excision repair. Structure 2005. [PMID: 16338413 DOI: 10.1016/j.str.2005.08.01] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2023]
Abstract
The human ERCC1/XPF complex is a structure-specific endonuclease with defined polarity that participates in multiple DNA repair pathways. We report the heterodimeric structure of the C-terminal domains of both proteins responsible for ERCC1/XPF complex formation. Both domains exhibit the double helix-hairpin-helix motif (HhH)2, and they are related by a pseudo-2-fold symmetry axis. In the XPF domain, the hairpin of the second motif is replaced by a short turn. The ERCC1 domain folds properly only in the presence of the XPF domain, which implies a role for XPF as a scaffold for the folding of ERCC1. The intersubunit interactions are largely hydrophobic in nature. NMR titration data show that only the ERCC1 domain of the ERCC1/XPF complex is involved in DNA binding. On the basis of these findings, we propose a model for the targeting of XPF nuclease via ERCC1-mediated interactions in the context of nucleotide excision repair.
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Affiliation(s)
- Konstantinos Tripsianes
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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18
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Patterson HM, Brannigan JA, Cutting SM, Wilson KS, Wilkinson AJ, Ab E, Diercks T, de Jong RN, Truffault V, Folkers GE, Kaptein R. The Structure of Bypass of Forespore C, an Intercompartmental Signaling Factor during Sporulation in Bacillus. J Biol Chem 2005; 280:36214-20. [PMID: 16049010 DOI: 10.1074/jbc.m506910200] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Sporulation in Bacillus subtilis begins with an asymmetric cell division giving rise to smaller forespore and larger mother cell compartments. Different programs of gene expression are subsequently directed by compartment-specific RNA polymerase sigma-factors. In the final stages, spore coat proteins are synthesized in the mother cell under the control of RNA polymerase containing sigma(K), (Esigma(K)). sigma(K) is synthesized as an inactive zymogen, pro-sigma(K), which is activated by proteolytic cleavage. Processing of pro-sigma(K) is performed by SpoIVFB, a metalloprotease that resides in a complex with SpoIVFA and bypass of forespore (Bof)A in the outer forespore membrane. Ensuring coordination of events taking place in the two compartments, pro-sigma(K) processing in the mother cell is delayed until appropriate signals are received from the forespore. Cell-cell signaling is mediated by SpoIVB and BofC, which are expressed in the forespore and secreted to the intercompartmental space where they regulate pro-sigma(K) processing by mechanisms that are not yet fully understood. Here we present the three-dimensional structure of BofC determined by solution state NMR. BofC is a monomer made up of two domains. The N-terminal domain, containing a four-stranded beta-sheet onto one face of which an alpha-helix is packed, closely resembles the third immunoglobulin-binding domain of protein G from Streptococcus. The C-terminal domain contains a three-stranded beta-sheet and three alpha-helices in a novel domain topology. The sequence connecting the domains contains a conserved DISP motif to which mutations that affect BofC activity map. Possible roles for BofC in the sigma(K) checkpoint are discussed in the light of sequence and structure comparisons.
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MESH Headings
- Amino Acid Motifs
- Amino Acid Sequence
- Bacillus subtilis/metabolism
- Bacterial Outer Membrane Proteins/metabolism
- Bacterial Proteins/chemistry
- Bacterial Proteins/physiology
- Cell Communication
- Cell Membrane/metabolism
- DNA-Directed RNA Polymerases/chemistry
- Electrophoresis, Polyacrylamide Gel
- Gene Deletion
- Gene Expression Regulation, Bacterial
- Magnetic Resonance Spectroscopy
- Models, Biological
- Models, Molecular
- Molecular Sequence Data
- Mutation
- Phenotype
- Plasmids/metabolism
- Protein Conformation
- Protein Folding
- Protein Structure, Secondary
- Protein Structure, Tertiary
- Recombinant Proteins/chemistry
- Sequence Homology, Amino Acid
- Signal Transduction
- Spectrometry, Mass, Electrospray Ionization
- Spores, Bacterial/metabolism
- Spores, Bacterial/physiology
- Transcription Factors/chemistry
- Transcription Factors/physiology
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Affiliation(s)
- Hayley M Patterson
- Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, United Kingdom
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19
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Ab E, van Diemen-Steenvoorde JAAM, de Jong TPVM. [Urine incontinence in childhood; the importance of a good micturition history]. Ned Tijdschr Geneeskd 2002; 146:193-6. [PMID: 11851076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Four children, three girls aged 9, 5.5 and 6.5 years, and a boy aged 8 years, suffered from urinary incontinence. The underlying conditions, urge syndrome with urge incontinence, ectopic ureter, meatus stenosis, and pelvic floor dysfunction, respectively, were identified and treated, after which the children were no longer incontinent. Diurnal incontinence is present in 2-3% of 7-year-olds. Incontinence is accompanied by recurrent urinary tract infections and vesicoureteric reflux in 40% of cases. A combination of these two disorders can lead to impaired renal function. Especially in girls, involuntary urine loss is usually based on dysfunctional voiding, a non-neurogenic coordination problem between the detrusor muscle of the bladder and the pelvic floor. A careful history is the most important tool in reaching the correct diagnosis.
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Affiliation(s)
- E Ab
- Universitair Medisch Centrum, Wilhelmina Kinderziekenhuis, afd. Kinderurologie, Postbus 85.090, 3508 AB Utrecht
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20
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Ab E, Schuurman-Wolters GK, Nijlant D, Dijkstra K, Saier MH, Robillard GT, Scheek RM. NMR structure of cysteinyl-phosphorylated enzyme IIB of the N,N′-diacetylchitobiose-specific phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli. J Mol Biol 2001; 308:993-1009. [PMID: 11352587 DOI: 10.1006/jmbi.2001.4623] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [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: 11/22/2022]
Abstract
The determination by NMR of the solution structure of the phosphorylated enzyme IIB (P-IIB(Chb)) of the N,N'-diacetylchitobiose-specific phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli is presented. Most of the backbone and side-chain resonances were assigned using a variety of mostly heteronuclear NMR experiments. The remaining resonances were assigned with the help of the structure calculations.NOE-derived distance restraints were used in distance geometry calculations followed by molecular dynamics and simulated annealing protocols. In addition, combinations of ambiguous restraints were used to resolve ambiguities in the NOE assignments. By combining sets of ambiguous and unambiguous restraints into new ambiguous restraints, an error function was constructed that was less sensitive to information loss caused by assignment uncertainties. The final set of structures had a pairwise rmsd of 0.59 A and 1.16 A for the heavy atoms of the backbone and side-chains, respectively. Comparing the P-IIB(Chb) solution structure with the previously determined NMR and X-ray structures of the wild-type and the Cys10Ser mutant shows that significant differences between the structures are limited to the active-site region. The phosphoryl group at the active-site cysteine residue is surrounded by a loop formed by residues 10 through 16. NOE and chemical shift data suggest that the phosphoryl group makes hydrogen bonds with the backbone amide protons of residues 12 and 15. The binding mode of the phosphoryl group is very similar to that of the protein tyrosine phosphatases. The differences observed are in accordance with the presumption that IIB(Chb) has to be more resistant to hydrolysis than the protein tyrosine phosphatases. We propose a proton relay network by which a transfer occurs between the cysteine SH proton and the solvent via the hydroxyl group of Thr16.
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Affiliation(s)
- E Ab
- The Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
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21
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van Houten MA, Ab E, Zwierstra RP, Kimpen JL. [Primary peritonitis due to Streptococcus pneumoniae in childhood]. Ned Tijdschr Geneeskd 1998; 142:793-6. [PMID: 9646612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Three patients, two boys of 5 months and 6 years and one girl aged 4 years, presented with acute abdominal pain, vomiting and fever, suggesting peritonitis. Imaging examinations (abdominal survey roentgenogram and (or) echography), exploratory laparotomy (in two patients) and blood cultures with growth of Streptococcus pneumoniae led to the diagnosis of primary peritonitis. Intravenous antibiotics led to recovery, in one patient complicated by paralytic ileus, which was treated surgically. Primary peritonitis is a rare condition which should be considered in the differential diagnosis of children with an acute abdominal syndrome. Conditions requiring surgery should be excluded by imaging examinations or laparotomy. When the diagnosis is confirmed by paracentesis or laparotomy, antibiotic treatment has to be started.
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Affiliation(s)
- M A van Houten
- Beatrix Kinderkliniek, afd. Infectieziekten, Academisch Ziekenhuis, Groningen
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22
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Dijkstra K, Kroon GJA, Ab E, Scheek RM, Kemmink J. Correlation of the 15N(i + 1), 13Calpha(i), and 1Halpha(i) Backbone Resonances in 13C/15N-Labeled Proteins by the (CO)N(CO)CAH Experiment. J Magn Reson 1997; 125:149-152. [PMID: 9245371 DOI: 10.1006/jmre.1996.1096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- K Dijkstra
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
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23
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Ab E, Schuurman-Wolters G, Reizer J, Saier MH, Dijkstra K, Scheek RM, Robillard GT. The NMR side-chain assignments and solution structure of enzyme IIBcellobiose of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli. Protein Sci 1997; 6:304-14. [PMID: 9041631 PMCID: PMC2143641 DOI: 10.1002/pro.5560060205] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [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: 02/03/2023]
Abstract
The assignment of the side-chain NMR resonances and the determination of the three-dimensional solution structure of the C10S mutant of enzyme IIBcellobiose (IIBcel) of the phosphoenolpyruvate-dependent phosphotransferase system of Escherichia coli are presented. The side-chain resonances were assigned nearly completely using a variety of mostly heteronuclear NMR experiments, including HCCH-TOCSY, HCCH-COSY, and COCCH-TOCSY experiments as well as CBCACOHA, CBCA(CO)NH, and HBHA(CBCA)(CO)NH experiments. In order to obtain the three-dimensional structure, NOE data were collected from 15N-NOESY-HSQC, 13C-HSQC-NOESY, and 2D NOE experiments. The distance restraints derived from these NOE data were used in distance geometry calculations followed by molecular dynamics and simulated annealing protocols. In an iterative procedure, additional NOE assignments were derived from the calculated structures and new structures were calculated. The final set of structures, calculated with approximately 2000 unambiguous and ambiguous distance restraints, has an rms deviation of 1.1 A on C alpha atoms. IIBcel consists of a four stranded parallel beta-sheet, in the order 2134. The sheet is flanked with two and three alpha-helices on either side. Residue 10, a cysteine in the wild-type enzyme, which is phosphorylated during the catalytic cycle, is located at the end of the first beta-strand. A loop that is proposed to be involved in the binding of the phosphoryl-group follows the cysteine. The loop appears to be disordered in the unphosphorylated state.
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Affiliation(s)
- E Ab
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands
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24
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Ab E, Schuurman-Wolters GK, Saier MH, Reizer J, Jacuinod M, Roepstorff P, Dijkstra K, Scheek RM, Robillard GT. Enzyme IIBcellobiose of the phosphoenol-pyruvate-dependent phosphotransferase system of Escherichia coli: backbone assignment and secondary structure determined by three-dimensional NMR spectroscopy. Protein Sci 1994; 3:282-90. [PMID: 8003964 PMCID: PMC2142798 DOI: 10.1002/pro.5560030212] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [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: 01/28/2023]
Abstract
The assignment of backbone resonances and the secondary structure determination of the Cys 10 Ser mutant of enzyme IIBcellobiose of the Escherichia coli cellobiose-specific phosphoenol-pyruvate-dependent phosphotransferase system are presented. The backbone resonances were assigned using 4 triple resonance experiments, the HNCA and HN(CO)CA experiments, correlating backbone 1H, 15N, and 13C alpha resonances, and the HN(CA)CO and HNCO experiments, correlating backbone 1H,15N and 13CO resonances. Heteronuclear 1H-NOE 1H-15N single quantum coherence (15N-NOESY-HSQC) spectroscopy and heteronuclear 1H total correlation 1H-15N single quantum coherence (15N-TOCSY-HSQC) spectroscopy were used to resolve ambiguities arising from overlapping 13C alpha and 13CO frequencies and to check the assignments from the triple resonance experiments. This procedure, together with a 3-dimensional 1H alpha-13C alpha-13CO experiment (COCAH), yielded the assignment for all observed backbone resonances. The secondary structure was determined using information both from the deviation of observed 1H alpha and 13C alpha chemical shifts from their random coil values and 1H-NOE information from the 15N-NOESY-HSQC. These data show that enzyme IIBcellobiose consists of a 4-stranded parallel beta-sheet and 5 alpha-helices. In the wild-type enzyme IIBcellobiose, the catalytic residue appears to be located at the end of a beta-strand.
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Affiliation(s)
- E Ab
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, The Netherlands
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25
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Thunnissen MM, Ab E, Kalk KH, Drenth J, Dijkstra BW, Kuipers OP, Dijkman R, de Haas GH, Verheij HM. X-ray structure of phospholipase A2 complexed with a substrate-derived inhibitor. Nature 1990; 347:689-91. [PMID: 2215698 DOI: 10.1038/347689a0] [Citation(s) in RCA: 198] [Impact Index Per Article: 5.8] [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: 12/30/2022]
Abstract
Phospholipases A2 play a part in a number of physiologically important cellular processes such as inflammation, blood platelet aggregation and acute hypersensitivity. These processes are all initiated by the release of arachidonic acid from cell membranes which is catalysed by intracellular phospholipases A2 and followed by conversion of arachidonic acid to prostaglandins, leukotrienes or thromboxanes. An imbalance in the production of these compounds can lead to chronic inflammatory diseases such as rheumatoid arthritis and asthma. Inhibitors of phospholipase A2 might therefore act to reduce the effects of inflammation, so structural information about the binding of phospholipase A2 to its substrates could be helpful in the design of therapeutic drugs. The three-dimensional structure is not known for any intracellular phospholipase A2, but these enzymes share significant sequence homology with secreted phospholipases, for which some of the structures have been determined. Here we report the structure of a complex between an extracellular phospholipase A2 and a competitively inhibiting substrate analogue, which reveals considerable detail about the interaction and suggests a mechanism for catalysis by this enzyme.
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Affiliation(s)
- M M Thunnissen
- Laboratory of Chemical Physics, University of Groningen, The Netherlands
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