1
|
Prew MS, Camara CM, Botzanowski T, Moroco JA, Bloch NB, Levy HR, Seo HS, Dhe-Paganon S, Bird GH, Herce HD, Gygi MA, Escudero S, Wales TE, Engen JR, Walensky LD. Structural basis for defective membrane targeting of mutant enzyme in human VLCAD deficiency. Nat Commun 2022; 13:3669. [PMID: 35760926 PMCID: PMC9237092 DOI: 10.1038/s41467-022-31466-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
Very long-chain acyl-CoA dehydrogenase (VLCAD) is an inner mitochondrial membrane enzyme that catalyzes the first and rate-limiting step of long-chain fatty acid oxidation. Point mutations in human VLCAD can produce an inborn error of metabolism called VLCAD deficiency that can lead to severe pathophysiologic consequences, including cardiomyopathy, hypoglycemia, and rhabdomyolysis. Discrete mutations in a structurally-uncharacterized C-terminal domain region of VLCAD cause enzymatic deficiency by an incompletely defined mechanism. Here, we conducted a structure-function study, incorporating X-ray crystallography, hydrogen-deuterium exchange mass spectrometry, computational modeling, and biochemical analyses, to characterize a specific membrane interaction defect of full-length, human VLCAD bearing the clinically-observed mutations, A450P or L462P. By disrupting a predicted α-helical hairpin, these mutations either partially or completely impair direct interaction with the membrane itself. Thus, our data support a structural basis for VLCAD deficiency in patients with discrete mutations in an α-helical membrane-binding motif, resulting in pathologic enzyme mislocalization.
Collapse
Affiliation(s)
- Michelle S. Prew
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Christina M. Camara
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Thomas Botzanowski
- grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA
| | - Jamie A. Moroco
- grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA
| | - Noah B. Bloch
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Hannah R. Levy
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Hyuk-Soo Seo
- grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Sirano Dhe-Paganon
- grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Gregory H. Bird
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Henry D. Herce
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Micah A. Gygi
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Silvia Escudero
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| | - Thomas E. Wales
- grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA
| | - John R. Engen
- grid.261112.70000 0001 2173 3359Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA USA
| | - Loren D. Walensky
- grid.65499.370000 0001 2106 9910Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA USA ,grid.65499.370000 0001 2106 9910Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, Boston, MA USA
| |
Collapse
|
2
|
Gorgulla C, Padmanabha Das KM, Leigh KE, Cespugli M, Fischer PD, Wang ZF, Tesseyre G, Pandita S, Shnapir A, Calderaio A, Gechev M, Rose A, Lewis N, Hutcheson C, Yaffe E, Luxenburg R, Herce HD, Durmaz V, Halazonetis TD, Fackeldey K, Patten J, Chuprina A, Dziuba I, Plekhova A, Moroz Y, Radchenko D, Tarkhanova O, Yavnyuk I, Gruber C, Yust R, Payne D, Näär AM, Namchuk MN, Davey RA, Wagner G, Kinney J, Arthanari H. A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening. iScience 2021; 24:102021. [PMID: 33426509 PMCID: PMC7783459 DOI: 10.1016/j.isci.2020.102021] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [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: 08/03/2020] [Revised: 10/28/2020] [Accepted: 12/29/2020] [Indexed: 02/07/2023] Open
Abstract
The unparalleled global effort to combat the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic over the last year has resulted in promising prophylactic measures. However, a need still exists for cheap, effective therapeutics, and targeting multiple points in the viral life cycle could help tackle the current, as well as future, coronaviruses. Here, we leverage our recently developed, ultra-large-scale in silico screening platform, VirtualFlow, to search for inhibitors that target SARS-CoV-2. In this unprecedented structure-based virtual campaign, we screened roughly 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets. In addition to targeting the active sites of viral enzymes, we also targeted critical auxiliary sites such as functionally important protein-protein interactions.
Collapse
Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kendra E. Leigh
- Max Planck Institute of Biophysics, Frankfurt am Main, Hessen 60438, Germany
| | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Saarland 66123, Germany
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | | | | | - Anthony Calderaio
- VirtualFlow Organization, https://virtual-flow.org/, Boston, MA 02115, USA
| | | | - Alexander Rose
- Mol∗ Consortium, https://molstar.org, San Diego, CA 92109, USA
| | | | | | | | | | - Henry D. Herce
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | - Konstantin Fackeldey
- Zuse Institute Berlin (ZIB), Berlin 14195, Germany
- Institute of Mathematics, Technical University Berlin, Berlin 10587, Germany
| | - J.J. Patten
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | | | | | | | - Yurii Moroz
- Chemspace, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | - Dmytro Radchenko
- Enamine, Kyiv 02094, Ukraine
- Taras Shevchenko National University of Kyiv, Kyiv 01601, Ukraine
| | | | | | - Christian Gruber
- Innophore GmbH, Graz 8010, Austria
- Institute of Molecular Biosciences, University of Graz, Graz 8010, Austria
| | - Ryan Yust
- Google, Mountain View, CA 94043, USA
| | | | - Anders M. Näär
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | - Robert A. Davey
- Department of Microbiology, Boston University Medical School, Boston University, Boston, MA 02118, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
| | | | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, MA 02115, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| |
Collapse
|
3
|
Gorgulla C, Padmanabha Das KM, Leigh KE, Cespugli M, Fischer PD, Wang ZF, Tesseyre G, Pandita S, Shnapir A, Calderaio A, Gechev M, Rose A, Lewis N, Hutcheson C, Yaffe E, Luxenburg R, Herce HD, Durmaz V, Halazonetis TD, Fackeldey K, Patten JJ, Chuprina A, Dziuba I, Plekhova A, Moroz Y, Radchenko D, Tarkhanova O, Yavnyuk I, Gruber C, Yust R, Payne D, Näär AM, Namchuk MN, Davey RA, Wagner G, Kinney J, Arthanari H. A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening. ChemRxiv 2020:12682316. [PMID: 33200116 PMCID: PMC7668741 DOI: 10.26434/chemrxiv.12682316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 07/24/2020] [Indexed: 11/23/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of July 7th, 2020, almost seven months into the outbreak, there are no approved vaccines and few treatments available. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics. Here we leverage the power of our recently developed in silico screening platform, VirtualFlow, to identify inhibitors that target SARS-CoV-2. VirtualFlow is able to efficiently harness the power of computing clusters and cloud-based computing platforms to carry out ultra-large scale virtual screens. In this unprecedented structure-based multi-target virtual screening campaign, we have used VirtualFlow to screen an average of approximately 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets in the cloud. In addition to targeting the active sites of viral enzymes, we also target critical auxiliary sites such as functionally important protein-protein interaction interfaces. This multi-target approach not only increases the likelihood of finding a potent inhibitor, but could also help identify a collection of anti-coronavirus drugs that would retain efficacy in the face of viral mutation. Drugs belonging to different regimen classes could be combined to develop possible combination therapies, and top hits that bind at highly conserved sites would be potential candidates for further development as coronavirus drugs. Here, we present the top 200 in silico hits for each target site. While in-house experimental validation of some of these compounds is currently underway, we want to make this array of potential inhibitor candidates available to researchers worldwide in consideration of the pressing need for fast-tracked drug development.
Collapse
Affiliation(s)
- Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Physics, Faculty of Arts and Sciences, Harvard University, Cambridge, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | - Krishna M. Padmanabha Das
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Patrick D. Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
- Department of Pharmacy, Pharmaceutical and Medicinal Chemistry, Saarland University, Saarbrücken, Germany
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | | | | | | | | | | | | | | | | | | | | | - Henry D. Herce
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| | | | | | - Konstantin Fackeldey
- Zuse Institute Berlin (ZIB), Berlin, Germany
- Institute of Mathematics, Technical University Berlin, Berlin, Germany
| | - Justin J. Patten
- Department of Microbiology, Boston University Medical School, Boston University, Boston, USA
| | | | | | | | - Yurii Moroz
- Chemspace, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Ukraine
| | - Dmytro Radchenko
- Enamine, Kyiv, Ukraine
- Taras Shevchenko National University of Kyiv, Ukraine
| | | | | | - Christian Gruber
- Innophore GmbH, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | | | - Anders M. Näär
- Department of Nutritional Sciences & Toxicology, University of California Berkeley, USA
| | - Mark N. Namchuk
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | - Robert A. Davey
- Department of Microbiology, Boston University Medical School, Boston University, Boston, USA
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
| | | | - Haribabu Arthanari
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Harvard University, Boston, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, USA
| |
Collapse
|
4
|
Hauseman ZJ, Harvey EP, Newman CE, Wales TE, Bucci JC, Mintseris J, Schweppe DK, David L, Fan L, Cohen DT, Herce HD, Mourtada R, Ben-Nun Y, Bloch NB, Hansen SB, Wu H, Gygi SP, Engen JR, Walensky LD. Homogeneous Oligomers of Pro-apoptotic BAX Reveal Structural Determinants of Mitochondrial Membrane Permeabilization. Mol Cell 2020; 79:68-83.e7. [PMID: 32533918 PMCID: PMC7472837 DOI: 10.1016/j.molcel.2020.05.029] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 12/23/2019] [Revised: 03/13/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022]
Abstract
BAX is a pro-apoptotic protein that transforms from a cytosolic monomer into a toxic oligomer that permeabilizes the mitochondrial outer membrane. How BAX monomers assemble into a higher-order conformation, and the structural determinants essential to membrane permeabilization, remain a mechanistic mystery. A key hurdle has been the inability to generate a homogeneous BAX oligomer (BAXO) for analysis. Here, we report the production and characterization of a full-length BAXO that recapitulates physiologic BAX activation. Multidisciplinary studies revealed striking conformational consequences of oligomerization and insight into the macromolecular structure of oligomeric BAX. Importantly, BAXO enabled the assignment of specific roles to particular residues and α helices that mediate individual steps of the BAX activation pathway, including unexpected functionalities of BAX α6 and α9 in driving membrane disruption. Our results provide the first glimpse of a full-length and functional BAXO, revealing structural requirements for the elusive execution phase of mitochondrial apoptosis.
Collapse
Affiliation(s)
- Zachary J Hauseman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Edward P Harvey
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Catherine E Newman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Joel C Bucci
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Julian Mintseris
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Devin K Schweppe
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Lixin Fan
- Small Angle X-ray Scattering Core, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Daniel T Cohen
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Henry D Herce
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Rida Mourtada
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Yael Ben-Nun
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Noah B Bloch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA
| | - Scott B Hansen
- The Scripps Research Institute-Florida, Jupiter, FL 33458, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Loren D Walensky
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Linde Program in Cancer Chemical Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA.
| |
Collapse
|
5
|
Ludwig AK, Zhang P, Hastert FD, Meyer S, Rausch C, Herce HD, Müller U, Lehmkuhl A, Hellmann I, Trummer C, Storm C, Leonhardt H, Cardoso MC. Binding of MBD proteins to DNA blocks Tet1 function thereby modulating transcriptional noise. Nucleic Acids Res 2017; 45:2438-2457. [PMID: 27923996 PMCID: PMC5389475 DOI: 10.1093/nar/gkw1197] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 11/20/2016] [Indexed: 12/18/2022] Open
Abstract
Aberrant DNA methylation is a hallmark of various human disorders, indicating that the spatial and temporal regulation of methylation readers and modifiers is imperative for development and differentiation. In particular, the cross-regulation between 5-methylcytosine binders (MBD) and modifiers (Tet) has not been investigated. Here, we show that binding of Mecp2 and Mbd2 to DNA protects 5-methylcytosine from Tet1-mediated oxidation. The mechanism is not based on competition for 5-methylcytosine binding but on Mecp2 and Mbd2 directly restricting Tet1 access to DNA. We demonstrate that the efficiency of this process depends on the number of bound MBDs per DNA molecule. Accordingly, we find 5-hydroxymethylcytosine enriched at heterochromatin of Mecp2-deficient neurons of a mouse model for Rett syndrome and Tet1-induced reexpression of silenced major satellite repeats. These data unveil fundamental regulatory mechanisms of Tet enzymes and their potential pathophysiological role in Rett syndrome. Importantly, it suggests that Mecp2 and Mbd2 have an essential physiological role as guardians of the epigenome.
Collapse
Affiliation(s)
- Anne K Ludwig
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Peng Zhang
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Florian D Hastert
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Stephanie Meyer
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Henry D Herce
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Udo Müller
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Anne Lehmkuhl
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Ines Hellmann
- Anthropology and Human Genomics, Department Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Carina Trummer
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - Christian Storm
- Chemical Plant Ecology, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Heinrich Leonhardt
- Human Biology and BioImaging, Department of Biology II, LMU Munich, 82152 Martinsried, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
6
|
Herce HD, Schumacher D, Schneider AFL, Ludwig AK, Mann FA, Fillies M, Kasper MA, Reinke S, Krause E, Leonhardt H, Cardoso MC, Hackenberger CPR. Cell-permeable nanobodies for targeted immunolabelling and antigen manipulation in living cells. Nat Chem 2017; 9:762-771. [DOI: 10.1038/nchem.2811] [Citation(s) in RCA: 168] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 05/24/2017] [Indexed: 12/19/2022]
|
7
|
Neale C, Herce HD, Pomès R, García AE. Can Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor? Biophys J 2016; 109:1652-62. [PMID: 26488656 DOI: 10.1016/j.bpj.2015.08.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/21/2015] [Accepted: 08/24/2015] [Indexed: 11/16/2022] Open
Abstract
G-protein-coupled receptors are eukaryotic membrane proteins with broad biological and pharmacological relevance. Like all membrane-embedded proteins, their location and orientation are influenced by lipids, which can also impact protein function via specific interactions. Extensive simulations totaling 0.25 ms reveal a process in which phospholipids from the membrane's cytosolic leaflet enter the empty G-protein binding site of an activated β2 adrenergic receptor and form salt-bridge interactions that inhibit ionic lock formation and prolong active-state residency. Simulations of the receptor embedded in an anionic membrane show increased lipid binding, providing a molecular mechanism for the experimental observation that anionic lipids can enhance receptor activity. Conservation of the arginine component of the ionic lock among Rhodopsin-like G-protein-coupled receptors suggests that intracellular lipid ingression between receptor helices H6 and H7 may be a general mechanism for active-state stabilization.
Collapse
Affiliation(s)
- Chris Neale
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
| | - Henry D Herce
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
| | - Régis Pomès
- Molecular Structure and Function, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Angel E García
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, Troy, New York; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York.
| |
Collapse
|
8
|
Abstract
The nucleolus is the hallmark of nuclear compartmentalization and has been shown to exert multiple roles in cellular metabolism besides its main function as the place of rRNA synthesis and assembly of ribosomes. Nucleolar proteins dynamically localize and accumulate in this nuclear compartment relative to the surrounding nucleoplasm. In this study, we have assessed the molecular requirements that are necessary and sufficient for the localization and accumulation of peptides and proteins inside the nucleoli of living cells. The data showed that positively charged peptide entities composed of arginines alone and with an isoelectric point at and above 12.6 are necessary and sufficient for mediating significant nucleolar accumulation. A threshold of 6 arginines is necessary for peptides to accumulate in nucleoli, but already 4 arginines are sufficient when fused within 15 amino acid residues of a nuclear localization signal of a protein. Using a pH sensitive dye, we found that the nucleolar compartment is particularly acidic when compared to the surrounding nucleoplasm and, hence, provides the ideal electrochemical environment to bind poly-arginine containing proteins. In fact, we found that oligo-arginine peptides and GFP fusions bind RNA in vitro. Consistent with RNA being the main binding partner for arginines in the nucleolus, we found that the same principles apply to cells from insects to man, indicating that this mechanism is highly conserved throughout evolution.
Collapse
Affiliation(s)
- Robert M Martin
- a Instituto de Medicina Molecular ; Faculdade de Medicina ; Universidade de Lisboa ; Lisboa , Portugal
| | | | | | | | | | | |
Collapse
|
9
|
Abstract
The nucleolus is the hallmark of nuclear compartmentalization and has been shown to exert multiple roles in cellular metabolism besides its main function as the place of ribosomal RNA synthesis and assembly of ribosomes. The nucleolus plays also a major role in nuclear organization as the largest compartment within the nucleus. The prominent structure of the nucleolus can be detected using contrast light microscopy providing an approximate localization of the nucleolus, but this approach does not allow to determine accurately the three-dimensional structure of the nucleolus in cells and tissues. Immunofluorescence staining with antibodies specific to nucleolar proteins albeit very useful is time consuming, normally antibodies recognize their epitopes only within a small range of species and is applicable only in fixed cells. Here, we present a simple method to selectively and accurately label this ubiquitous subnuclear compartment in living cells of a large range of species using a fluorescently labeled cell-penetrating peptide.
Collapse
Affiliation(s)
- Robert M Martin
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028, Lisbon, Portugal
| | - Henry D Herce
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - Anne K Ludwig
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany
| | - M Cristina Cardoso
- Department of Biology, Technische Universität Darmstadt, Schnittspahnstr. 10, 64287, Darmstadt, Germany.
| |
Collapse
|
10
|
Hreha TN, Mezic KG, Herce HD, Duffy EB, Bourges A, Pryshchep S, Juarez O, Barquera B. Complete topology of the RNF complex from Vibrio cholerae. Biochemistry 2015; 54:2443-55. [PMID: 25831459 DOI: 10.1021/acs.biochem.5b00020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
RNF is a redox-driven ion (Na(+) and in one case possibly H(+)) transporter present in many prokaryotes. It has been proposed that RNF performs a variety of reactions in different organisms, delivering low-potential reducing equivalents for specific cellular processes. RNF shares strong homology with the Na(+)-pumping respiratory enzyme Na(+)-NQR, although there are significant differences in subunit and redox cofactor composition. Here we report a topological analysis of the six subunits of RNF from Vibrio cholerae. Although individual subunits from other organisms have previously been studied, this is the first complete, experimentally derived, analysis of RNF from any one source. This has allowed us to identify and confirm key properties of RNF. The putative NADH binding site in RnfC is located on the cytoplasmic side of the membrane. FeS centers in RnfB and RnfC are also located on the cytoplasmic side. However, covalently attached FMNs in RnfD and RnfG are both located in the periplasm. RNF also contains a number of acidic residues that correspond to functionally important groups in Na(+)-NQR. The acidic residues involved in Na(+) uptake and many of those implicated in Na(+) translocation are topologically conserved. The topology of RNF closely matches the topology represented in the newly published structure of Na(+)-NQR, consistent with the close relation between the two enzymes. The topology of RNF is discussed in the context of the current structural model of Na(+)-NQR, and the proposed functionality of the RNF complex itself.
Collapse
|
11
|
Neale C, Herce HD, Pomès R, García AE. Specific Protein-Lipid Interactions Stabilize an Active State of the Beta 2 Adrenergic Receptor. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.1990] [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: 11/27/2022] Open
|
12
|
Nischan N, Herce HD, Natale F, Bohlke N, Budisa N, Cardoso MC, Hackenberger CPR. Kovalente Verknüpfung cyclischer TAT-Peptide mit GFP resultiert in der direkten Aufnahme in lebende Zellen mit sofortiger biologischer Verfügbarkeit. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410006] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
|
13
|
Nischan N, Herce HD, Natale F, Bohlke N, Budisa N, Cardoso MC, Hackenberger CPR. Covalent attachment of cyclic TAT peptides to GFP results in protein delivery into live cells with immediate bioavailability. Angew Chem Int Ed Engl 2014; 54:1950-3. [PMID: 25521313 DOI: 10.1002/anie.201410006] [Citation(s) in RCA: 200] [Impact Index Per Article: 20.0] [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: 10/12/2014] [Indexed: 11/08/2022]
Abstract
The delivery of free molecules into the cytoplasm and nucleus by using arginine-rich cell-penetrating peptides (CPPs) has been limited to small cargoes, while large cargoes such as proteins are taken up and trapped in endocytic vesicles. Based on recent work, in which we showed that the transduction efficiency of arginine-rich CPPs can be greatly enhanced by cyclization, the aim was to use cyclic CPPs to transport full-length proteins, in this study green fluorescent protein (GFP), into the cytosol of living cells. Cyclic and linear CPP-GFP conjugates were obtained by using azido-functionalized CPPs and an alkyne-functionalized GFP. Our findings reveal that the cyclic-CPP-GFP conjugates are internalized into live cells with immediate bioavailability in the cytosol and the nucleus, whereas linear CPP analogues do not confer GFP transduction. This technology expands the application of cyclic CPPs to the efficient transport of functional full-length proteins into live cells.
Collapse
Affiliation(s)
- Nicole Nischan
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Strasse 10, 13125 Berlin (Germany); Freie Universität Berlin, Institut für Chemie und Biochemie, Takustrasse 3, 14195 Berlin (Germany)
| | | | | | | | | | | | | |
Collapse
|
14
|
Abstract
![]()
Guanidinium-rich
molecules, such as cell-penetrating peptides,
efficiently enter living cells in a non-endocytic energy-independent
manner and transport a wide range of cargos, including drugs and biomarkers.
The mechanism by which these highly cationic molecules efficiently
cross the hydrophobic barrier imposed by the plasma membrane remains
a fundamental open question. Here, a combination of computational
results and in vitro and live-cell experimental evidence reveals an
efficient energy-independent translocation mechanism for arginine-rich
molecules. This mechanism unveils the essential role of guanidinium
groups and two universal cell components: fatty acids and the cell
membrane pH gradient. Deprotonated fatty acids in contact with the
cell exterior interact with guanidinium groups, leading to a transient
membrane channel that facilitates the transport of arginine-rich peptides
toward the cell interior. On the cytosolic side, the fatty acids become
protonated, releasing the peptides and resealing the channel. This
fundamental mechanism appears to be universal across cells from different
species and kingdoms.
Collapse
Affiliation(s)
- Henry D Herce
- Department of Physics, Applied Physics and Astronomy and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | | | | |
Collapse
|
15
|
Abstract
Proliferating Cell Nuclear Antigen (PCNA) is a key protein in DNA replication and repair. The dynamics of replication and repair in live cells is usually studied introducing translational fusions of PCNA. To obviate the need for transfection and bypass the problem of difficult to transfect and/or short lived cells, we have now developed a cell permeable replication and/or repair marker. The design of this marker has three essential molecular components: (1) an optimized artificial PCNA binding peptide; (2) a cell-penetrating peptide, derived from the HIV-1 Trans Activator of Transcription (TAT); (3) an in vivo cleavable linker, linking the two peptides. The resulting construct was taken up by human, hamster and mouse cells within minutes of addition to the media. Inside the cells, the cargo separated from the vector peptide and bound PCNA effectively. Both replication and repair sites could be directly labeled in live cells making it the first in vivo cell permeable peptide marker for these two fundamental cellular processes. Concurrently, we also introduced a quick peptide based PCNA staining method as an alternative to PCNA antibodies for immunofluorescence applications. In summary, we present here a versatile tool to instantaneously label repair and replication processes in fixed and live cells.
Collapse
Affiliation(s)
- Henry D Herce
- a Department of Biology , Technische Universität Darmstadt ; Darmstadt , Germany
| | | | | | | | | |
Collapse
|
16
|
Kind B, Muster B, Staroske W, Herce HD, Sachse R, Rapp A, Schmidt F, Koss S, Cardoso MC, Lee-Kirsch MA. Altered spatio-temporal dynamics of RNase H2 complex assembly at replication and repair sites in Aicardi-Goutières syndrome. Hum Mol Genet 2014; 23:5950-60. [PMID: 24986920 DOI: 10.1093/hmg/ddu319] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Ribonuclease H2 plays an essential role for genome stability as it removes ribonucleotides misincorporated into genomic DNA by replicative polymerases and resolves RNA/DNA hybrids. Biallelic mutations in the genes encoding the three RNase H2 subunits cause Aicardi-Goutières syndrome (AGS), an early-onset inflammatory encephalopathy that phenotypically overlaps with the autoimmune disorder systemic lupus erythematosus. Here we studied the intracellular dynamics of RNase H2 in living cells during DNA replication and in response to DNA damage using confocal time-lapse imaging and fluorescence cross-correlation spectroscopy. We demonstrate that the RNase H2 complex is assembled in the cytosol and imported into the nucleus in an RNase H2B-dependent manner. RNase H2 is not only recruited to DNA replication foci, but also to sites of PCNA-dependent DNA repair. By fluorescence recovery after photobleaching, we demonstrate a high mobility and fast exchange of RNase H2 at sites of DNA repair and replication. We provide evidence that recruitment of RNase H2 is not only PCNA-dependent, mediated by an interaction of the B subunit with PCNA, but also PCNA-independent mediated via the catalytic domain of the A subunit. We found that AGS-associated mutations alter complex formation, recruitment efficiency and exchange kinetics at sites of DNA replication and repair suggesting that impaired ribonucleotide removal contributes to AGS pathogenesis.
Collapse
Affiliation(s)
- Barbara Kind
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus and
| | - Britta Muster
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Wolfgang Staroske
- Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Henry D Herce
- Department of Physics, Applied Physics and Astronomy, Rensselaer Polytechnic Institute, New York 12180-3590, USA and
| | - René Sachse
- Institute of Earth and Environmental Science, Potsdam University, 14476 Potsdam, Germany
| | - Alexander Rapp
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Franziska Schmidt
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus and
| | - Sarah Koss
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus and
| | - M Cristina Cardoso
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany,
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus and
| |
Collapse
|
17
|
Herce HD, Casas-Delucchi CS, Cardoso MC. New image colocalization coefficient for fluorescence microscopy to quantify (bio-)molecular interactions. J Microsc 2013; 249:184-94. [PMID: 23301670 PMCID: PMC3599484 DOI: 10.1111/jmi.12008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 12/03/2012] [Indexed: 11/26/2022]
Abstract
The spatial relationship, or degree of colocalization, between two or more types of molecules in live cells is commonly detected using fluorescence microscopy. This spatial distribution can be used to estimate the interaction between fluorescently labelled molecules. These interactions are usually quantified by analysing the correlation and/or the overlap between images, using the Pearson's and Manders' coefficients, respectively. However, the correlation and overlap coefficients are parameters not designed to quantify molecular interactions. Here we propose a new colocalization coefficient specifically designed to quantify the interactions between molecules. In well-defined thermodynamic ensembles, this coefficient can in principle be used to calculate relevant statistical thermodynamic quantities such as binding free energies.
Collapse
Affiliation(s)
- HD Herce
- Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
- Instituto de Física de Líquidos y Sistemas Biológicos (CONICET)La Plata
| | - CS Casas-Delucchi
- Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
| | - MC Cardoso
- Department of Biology, Technische Universität DarmstadtDarmstadt, Germany
| |
Collapse
|
18
|
Becker A, Allmann L, Hofstätter M, Casà V, Weber P, Lehmkuhl A, Herce HD, Cardoso MC. Direct homo- and hetero-interactions of MeCP2 and MBD2. PLoS One 2013; 8:e53730. [PMID: 23335972 PMCID: PMC3546041 DOI: 10.1371/journal.pone.0053730] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 12/04/2012] [Indexed: 01/11/2023] Open
Abstract
Epigenetic marks like methylation of cytosines at CpG dinucleotides are essential for mammalian development and play a major role in the regulation of gene expression and chromatin architecture. The methyl-cytosine binding domain (MBD) protein family recognizes and translates this methylation mark. We have recently shown that the level of MeCP2 and MBD2, two members of the MBD family, increased during differentiation and their ectopic expression induced heterochromatin clustering in vivo. As oligomerization of these MBD proteins could constitute a factor contributing to the chromatin clustering effect, we addressed potential associations among the MBD family performing a series of different interaction assays in vitro as well as in vivo. Using recombinant purified MBDs we found that MeCP2 and MBD2 showed the stronger self and cross association as compared to the other family members. Besides demonstrating that these homo- and hetero-interactions occur in the absence of DNA, we could confirm them in mammalian cells using co-immunoprecipitation analysis. Employing a modified form of the fluorescent two-hybrid protein-protein interaction assay, we could clearly visualize these associations in single cells in vivo. Deletion analysis indicated that the region of MeCP2 comprising amino acids 163–309 as well the first 152 amino acids of MBD2 are the domains responsible for MeCP2 and MBD2 associations. Our results strengthen the possibility that MeCP2 and MBD2 direct interactions could crosslink chromatin fibers and therefore give novel insight into the molecular mechanism of MBD mediated global heterochromatin architecture.
Collapse
Affiliation(s)
- Annette Becker
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Lena Allmann
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - Valentina Casà
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Patrick Weber
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Anne Lehmkuhl
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - Henry D. Herce
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
| | - M. Cristina Cardoso
- Department of Biology, Technische Universität Darmstadt, Darmstadt, Germany
- * E-mail:
| |
Collapse
|
19
|
Herce HD, Deng W, Helma J, Leonhardt H, Cardoso MC. Visualization and targeted disruption of protein interactions in living cells. Nat Commun 2013; 4:2660. [PMID: 24154492 PMCID: PMC3826628 DOI: 10.1038/ncomms3660] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/23/2013] [Indexed: 11/10/2022] Open
Abstract
Protein-protein interactions are the basis of all processes in living cells, but most studies of these interactions rely on biochemical in vitro assays. Here we present a simple and versatile fluorescent-three-hybrid (F3H) strategy to visualize and target protein-protein interactions. A high-affinity nanobody anchors a GFP-fusion protein of interest at a defined cellular structure and the enrichment of red-labelled interacting proteins is measured at these sites. With this approach, we visualize the p53-HDM2 interaction in living cells and directly monitor the disruption of this interaction by Nutlin 3, a drug developed to boost p53 activity in cancer therapy. We further use this approach to develop a cell-permeable vector that releases a highly specific peptide disrupting the p53 and HDM2 interaction. The availability of multiple anchor sites and the simple optical readout of this nanobody-based capture assay enable systematic and versatile analyses of protein-protein interactions in practically any cell type and species.
Collapse
Affiliation(s)
- Henry D. Herce
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
- These authors contributed equally to this work
| | - Wen Deng
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
- These authors contributed equally to this work
| | - Jonas Helma
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig Maximilians University Munich, 82152 Planegg-Martinsried, Germany
| | - M. Cristina Cardoso
- Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
20
|
Hörner S, Fabritz S, Herce HD, Avrutina O, Dietz C, Stark RW, Cardoso MC, Kolmar H. Cube-octameric silsesquioxane-mediated cargo peptide delivery into living cancer cells. Org Biomol Chem 2013; 11:2258-65. [DOI: 10.1039/c2ob26808f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
21
|
Casas-Delucchi CS, van Bemmel JG, Haase S, Herce HD, Nowak D, Meilinger D, Stear JH, Leonhardt H, Cardoso MC. Histone hypoacetylation is required to maintain late replication timing of constitutive heterochromatin. Nucleic Acids Res 2011; 40:159-69. [PMID: 21908399 PMCID: PMC3245938 DOI: 10.1093/nar/gkr723] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The replication of the genome is a spatio-temporally highly organized process. Yet, its flexibility throughout development suggests that this process is not genetically regulated. However, the mechanisms and chromatin modifications controlling replication timing are still unclear. We made use of the prominent structure and defined heterochromatic landscape of pericentric regions as an example of late replicating constitutive heterochromatin. We manipulated the major chromatin markers of these regions, namely histone acetylation, DNA and histone methylation, as well as chromatin condensation and determined the effects of these altered chromatin states on replication timing. Here, we show that manipulation of DNA and histone methylation as well as acetylation levels caused large-scale heterochromatin decondensation. Histone demethylation and the concomitant decondensation, however, did not affect replication timing. In contrast, immuno-FISH and time-lapse analyses showed that lowering DNA methylation, as well as increasing histone acetylation, advanced the onset of heterochromatin replication. While dnmt1−/− cells showed increased histone acetylation at chromocenters, histone hyperacetylation did not induce DNA demethylation. Hence, we propose that histone hypoacetylation is required to maintain normal heterochromatin duplication dynamics. We speculate that a high histone acetylation level might increase the firing efficiency of origins and, concomitantly, advances the replication timing of distinct genomic regions.
Collapse
|
22
|
Herce HD, Garcia AE, Litt J, Kane RS, Martin P, Enrique N, Rebolledo A, Milesi V. Arginine-rich peptides destabilize the plasma membrane, consistent with a pore formation translocation mechanism of cell-penetrating peptides. Biophys J 2009; 97:1917-25. [PMID: 19804722 DOI: 10.1016/j.bpj.2009.05.066] [Citation(s) in RCA: 206] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 05/22/2009] [Accepted: 05/29/2009] [Indexed: 10/20/2022] Open
Abstract
Recent molecular-dynamics simulations have suggested that the arginine-rich HIV Tat peptides translocate by destabilizing and inducing transient pores in phospholipid bilayers. In this pathway for peptide translocation, Arg residues play a fundamental role not only in the binding of the peptide to the surface of the membrane, but also in the destabilization and nucleation of transient pores across the bilayer. Here we present a molecular-dynamics simulation of a peptide composed of nine Args (Arg-9) that shows that this peptide follows the same translocation pathway previously found for the Tat peptide. We test experimentally the hypothesis that transient pores open by measuring ionic currents across phospholipid bilayers and cell membranes through the pores induced by Arg-9 peptides. We find that Arg-9 peptides, in the presence of an electrostatic potential gradient, induce ionic currents across planar phospholipid bilayers, as well as in cultured osteosarcoma cells and human smooth muscle cells. Our results suggest that the mechanism of action of Arg-9 peptides involves the creation of transient pores in lipid bilayers and cell membranes.
Collapse
Affiliation(s)
- H D Herce
- Department of Physics, Rensselaer Polytechnic Institute, Troy, New York, USA
| | | | | | | | | | | | | | | |
Collapse
|
23
|
Abstract
Cell penetrating peptides consist of short sequences of amino acids containing a large net positive charge that are able to penetrate almost any cell, carrying with them relatively large cargoes such as proteins, oligonucleotides, and drugs. During the 10 years since their discovery, the question of how they manage to translocate across the membrane has remained unanswered. The main discussion has been centered on whether they follow an energy-independent or an energy-dependent pathway. Recently, we have discovered the possibility of an energy-independent pathway that challenges fundamental concepts associated with protein-membrane interactions (Herce and Garcia, PNAS, 104: 20805 (2007) [1]). It involves the translocation of charged residues across the hydrophobic core of the membrane and the passive diffusion of these highly charged peptides across the membrane through the formation of aqueous toroidal pores. The aim of this review is to discuss the details of the mechanism and interpret some experimental results consistent with this view.
Collapse
Affiliation(s)
- Henry D Herce
- Department of Physics and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | | |
Collapse
|
24
|
Abstract
Molecular dynamics simulations of lipids bilayers have reported that the average area per lipid increases with the size of the simulated unit cell under constant temperature, pressure, and number of molecules. Here we show that the cause of this finite size effect are artifacts associated with the heat bath coupling. This can be corrected by coupling individually each degree of freedom to the heat bath, instead of coupling globally the system. We present the results of the investigation on three aspects of molecular dynamics simulations and their effect on the computed average area per lipid: (I) the accuracy in the computation of electrostatic interactions, the energy, and the virial, (II) long range Lennard-Jones interactions for systems with symmetry in one plane, and (III) thermodynamic baths. We show that the average area per lipid remains constant for simulations of systems containing 32, 64, and 256 lipids.
Collapse
Affiliation(s)
- Henry D Herce
- Department of Physics, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
| | | |
Collapse
|