1
|
Romanuka J, Folkers GE, Gnida M, Kovačič L, Wienk H, Kaptein R, Boelens R. Genetic switching by the Lac repressor is based on two-state Monod-Wyman-Changeux allostery. Proc Natl Acad Sci U S A 2023; 120:e2311240120. [PMID: 38019859 DOI: 10.1073/pnas.2311240120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 07/07/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In the absence of ligands, the dimer exists in a dynamic equilibrium between DNA-bound and inducer-bound conformations. Binding of either effector shifts this equilibrium toward either bound state. Analysis of the ternary complex between repressor, operator DNA, and inducer shows how adding the inducer results in allosteric changes that disrupt the interdomain contacts between the inducer binding and DNA binding domains and how this in turn leads to destabilization of the hinge helices and release of the Lac repressor from the operator. Based on our data, the allosteric mechanism of the induction process is in full agreement with the well-known Monod-Wyman-Changeux model.
Collapse
Affiliation(s)
- Julija Romanuka
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Gert E Folkers
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Manuel Gnida
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Lidija Kovačič
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Robert Kaptein
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
2
|
Corbeski I, Guo X, Eckhardt BV, Fasci D, Wiegant W, Graewert MA, Vreeken K, Wienk H, Svergun DI, Heck AJR, van Attikum H, Boelens R, Sixma TK, Mattiroli F, van Ingen H. Chaperoning of the histone octamer by the acidic domain of DNA repair factor APLF. Sci Adv 2022; 8:eabo0517. [PMID: 35895815 PMCID: PMC9328677 DOI: 10.1126/sciadv.abo0517] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 06/10/2022] [Indexed: 05/26/2023]
Abstract
Nucleosome assembly requires the coordinated deposition of histone complexes H3-H4 and H2A-H2B to form a histone octamer on DNA. In the current paradigm, specific histone chaperones guide the deposition of first H3-H4 and then H2A-H2B. Here, we show that the acidic domain of DNA repair factor APLF (APLFAD) can assemble the histone octamer in a single step and deposit it on DNA to form nucleosomes. The crystal structure of the APLFAD-histone octamer complex shows that APLFAD tethers the histones in their nucleosomal conformation. Mutations of key aromatic anchor residues in APLFAD affect chaperone activity in vitro and in cells. Together, we propose that chaperoning of the histone octamer is a mechanism for histone chaperone function at sites where chromatin is temporarily disrupted.
Collapse
Affiliation(s)
- Ivan Corbeski
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Xiaohu Guo
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Bruna V. Eckhardt
- Hubrecht Institute—KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Domenico Fasci
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Wouter Wiegant
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Melissa A. Graewert
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Kees Vreeken
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Unit, DESY, Notkestrasse 85, D-22607 Hamburg, Germany
| | - Albert J. R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| | - Titia K. Sixma
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
| | - Francesca Mattiroli
- Hubrecht Institute—KNAW & University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Centre for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands
| |
Collapse
|
3
|
Wienk H, Banci L, Daenke S, Pereiro E, Schwalbe H, Stuart DI, Weiss MS, Perrakis A. iNEXT-Discovery and Instruct-ERIC: Integrating High-End Services for Translational Research in Structural Biology. J Vis Exp 2021. [PMID: 34866631 DOI: 10.3791/63435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Affiliation(s)
- Hans Wienk
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Amsterdam;
| | | | | | | | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt
| | | | | | - Anastassis Perrakis
- Division of Biochemistry and Oncode Institute, The Netherlands Cancer Institute, Amsterdam;
| |
Collapse
|
4
|
Ahmad MUD, Fish A, Molenaar J, Sreeramulu S, Richter C, Altincekic N, Schwalbe H, Wienk H, Perrakis A. Nano-Differential Scanning Fluorimetry for Screening in Fragment-based Lead Discovery. J Vis Exp 2021. [PMID: 34057451 DOI: 10.3791/62469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Thermal shift assays (TSAs) examine how the melting temperature (Tm) of a target protein changes in response to changes in its environment (e.g., buffer composition). The utility of TSA, and specifically of nano-Differential Scanning Fluorimetry (nano-DSF), has been established over the years, both for finding conditions that help stabilize a specific protein and for looking at ligand binding by monitoring changes in the apparent Tm. This paper presents an efficient screening of the Diamond-SGC-iNEXT Poised (DSi-Poised) fragment library (768 compounds) by the use of nano-DSF, monitoring Tm to identify potential fragment binding. The prerequisites regarding protein quality and concentration for performing nano-DSF experiments are briefly outlined followed by a step-by-step protocol that uses a nano-liter robotic dispenser commonly used in structural biology laboratories for preparing the required samples in 96-well plates. The protocol describes how the reagent mixtures are transferred to the capillaries needed for nano-DSF measurements. In addition, this paper provides protocols to measure thermal denaturation (monitoring intrinsic tryptophan fluorescence) and aggregation (monitoring light back-scattering) and the subsequent steps for data transfer and analysis. Finally, screening experiments with three different protein targets are discussed to illustrate the use of this procedure in the context of lead discovery campaigns. The overall principle of the method described can be easily transferred to other fragment libraries or adapted to other instruments.
Collapse
Affiliation(s)
- Misbha Ud Din Ahmad
- Oncode Institute and Division of Biochemistry, the Netherlands Cancer Institute
| | - Alexander Fish
- Oncode Institute and Division of Biochemistry, the Netherlands Cancer Institute
| | - Jeroen Molenaar
- Oncode Institute and Division of Biochemistry, the Netherlands Cancer Institute
| | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University
| | - Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University
| | - Hans Wienk
- Oncode Institute and Division of Biochemistry, the Netherlands Cancer Institute
| | - Anastassis Perrakis
- Oncode Institute and Division of Biochemistry, the Netherlands Cancer Institute;
| |
Collapse
|
5
|
Shahul Hameed D, van Tilburg GBA, Merkx R, Flierman D, Wienk H, El Oualid F, Hofmann K, Boelens R, Ovaa H. Diubiquitin-Based NMR Analysis: Interactions Between Lys6-Linked diUb and UBA Domain of UBXN1. Front Chem 2020; 7:921. [PMID: 32039147 PMCID: PMC6987245 DOI: 10.3389/fchem.2019.00921] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/18/2019] [Indexed: 12/03/2022] Open
Abstract
Ubiquitination is a process in which a protein is modified by the covalent attachment of the C-terminal carboxylic acid of ubiquitin (Ub) to the ε-amine of lysine or N-terminal methionine residue of a substrate protein or another Ub molecule. Each of the seven internal lysine residues and the N-terminal methionine residue of Ub can be linked to the C-terminus of another Ub moiety to form 8 distinct Ub linkages and the resulting differences in linkage types elicit different Ub signaling pathways. Cellular responses are triggered when proteins containing ubiquitin-binding domains (UBDs) recognize and bind to specific polyUb linkage types. To get more insight into the differences between polyUb chains, all of the seven lysine-linked di-ubiquitin molecules (diUbs) were prepared and used as a model to study their structural conformations in solution using NMR spectroscopy. We report the synthesis of diUb molecules, fully 15N-labeled on the distal (N-terminal) Ub moiety and revealed their structural orientation with respect to the proximal Ub. As expected, the diUb molecules exist in different conformations in solution, with multiple conformations known to exist for K6-, K48-, and K63-linked diUb molecules. These multiple conformations allow structural flexibility in binding with UBDs thereby inducing unique responses. One of the well-known but poorly understood UBD-Ub interaction is the recognition of K6 polyubiquitin by the ubiquitin-associated (UBA) domain of UBXN1 in the BRCA-mediated DNA repair pathway. Using our synthetic 15N-labeled diUbs, we establish here how a C-terminally extended UBA domain of UBXN1 confers specificity to K6 diUb while the non-extended version of the domain does not show any linkage preference. We show that the two distinct conformations of K6 diUb that exist in solution converge into a single conformation upon binding to this extended form of the UBA domain of the UBXN1 protein. It is likely that more of such extended UBA domains exist in nature and can contribute to linkage-specificity in Ub signaling. The isotopically labeled diUb compounds described here and the use of NMR to study their interactions with relevant partner molecules will help accelerate our understanding of Ub signaling pathways.
Collapse
Affiliation(s)
- Dharjath Shahul Hameed
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Gabrielle B A van Tilburg
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Remco Merkx
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Dennis Flierman
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Farid El Oualid
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,UbiQ Bio BV, Amsterdam, Netherlands
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Huib Ovaa
- Department of Cell Biology II, The Netherlands Cancer Institute, Amsterdam, Netherlands.,Department of Cell and Chemical Biology, Oncode Institute, Leiden University Medical Centre, Leiden, Netherlands
| |
Collapse
|
6
|
Xu Y, Schwede F, Wienk H, Tengholm A, Rehmann H. A Membrane Permeable Prodrug of S223 for Selective Epac2 Activation in Living Cells. Cells 2019; 8:cells8121589. [PMID: 31817822 PMCID: PMC6952820 DOI: 10.3390/cells8121589] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 12/22/2022] Open
Abstract
Signalling by cyclic adenosine monophosphate (cAMP) occurs via various effector proteins, notably protein kinase A and the guanine nucleotide exchange factors Epac1 and Epac2. These proteins are activated by cAMP binding to conserved cyclic nucleotide binding domains. The specific roles of the effector proteins in various processes in different types of cells are still not well defined, but investigations have been facilitated by the development of cyclic nucleotide analogues with distinct selectivity profiles towards a single effector protein. A remaining challenge in the development of such analogues is the poor membrane permeability of nucleotides, which limits their applicability in intact living cells. Here, we report the synthesis and characterisation of S223-AM, a cAMP analogue designed as an acetoxymethyl ester prodrug to overcome limitations of permeability. Using total internal reflection imaging with various fluorescent reporters, we show that S223-AM selectively activates Epac2, but not Epac1 or protein kinase A, in intact insulin-secreting β-cells, and that this effect was associated with pronounced activation of the small G-protein Rap. A comparison of the effects of different cAMP analogues in pancreatic islet cells deficient in Epac1 and Epac2 demonstrates that cAMP-dependent Rap activity at the β-cell plasma membrane is exclusively dependent on Epac2. With its excellent selectivity and permeability properties, S223-AM should get broad utility in investigations of cAMP effector involvement in many different types of cells.
Collapse
Affiliation(s)
- Yunjian Xu
- Department of Medical Cell Biology, Uppsala University, Biomedical Centre, Box 571, SE-75123 Uppsala, Sweden; (Y.X.); (A.T.)
| | - Frank Schwede
- BIOLOG Life Science Institute, Flughafendamm 9a, 28199 Bremen, Germany;
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands;
| | - Anders Tengholm
- Department of Medical Cell Biology, Uppsala University, Biomedical Centre, Box 571, SE-75123 Uppsala, Sweden; (Y.X.); (A.T.)
| | - Holger Rehmann
- Department of Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, 3584 CX Utrecht, The Netherlands
- Correspondence:
| |
Collapse
|
7
|
Bale NJ, Sorokin DY, Hopmans EC, Koenen M, Rijpstra WIC, Villanueva L, Wienk H, Sinninghe Damsté JS. New Insights Into the Polar Lipid Composition of Extremely Halo(alkali)philic Euryarchaea From Hypersaline Lakes. Front Microbiol 2019; 10:377. [PMID: 30930858 PMCID: PMC6423904 DOI: 10.3389/fmicb.2019.00377] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [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: 11/22/2018] [Accepted: 02/13/2019] [Indexed: 12/14/2022] Open
Abstract
We analyzed the polar membrane lipids of 13 strains of halo(alkali)philic euryarchaea from hypersaline lakes. Nine belong to the class Halobacteria, representing two functional groups: aerobic polysaccharide utilizers and sulfur-respiring anaerobes. The other four strains represent halo(alkali)philic methanogens from the class Methanomicrobia and a recently discovered class Methanonatronarchaeia. A wide range of polar lipids were detected across the 13 strains including dialkyl glycerol diethers (archaeols), membrane-spanning glycerol tetraethers and diether-based cardiolipins. The archaeols contained a range of core lipid structures, including combinations of C20 and C25 isoprenoidal alkyl chains, unsaturations, and hydroxy moieties. Several diether lipids were novel, including: (a) a phosphatidylglycerolhexose (PG-Gly) headgroup, (b) a N,N,N-trimethyl aminopentanetetrol (APT)-like lipid with a methoxy group in place of a hydroxy group on the pentanetetrol, (c) a series of polar lipids with a headgroup with elemental composition of either C12H25NO13S or C12H25NO16S2, and (d) novel cardiolipins containing a putative phosphatidylglycerolphosphate glycerophosphate (PGPGP) polar moiety. We found that the lipid distribution of the 13 strains could be generally separated into two groups, the methanogens (group) and the Halobacteria (class) based on the presence of specific core lipids. Within the methanogens, adaption to a high or more moderate salt concentration resulted in different ratios of glycerol dialkyl glycerol tetraethers (GDGTs) to archaeol. The methanogen Methanosalsum natronophilum AME2T had the most complex diether lipid composition of any of the 13 strains, including hydroxy archaeol and macrocyclic archaeol which we surmise is an order-specific membrane adaption. The zwitterionic headgroups APT and APT-Me were detected only in the Methanomicrobiales member Methanocalculus alkaliphilus AMF2T which also contained the highest level of unsaturated lipids. Only alkaliphilic members of the Natrialbales order contained PGPGP cardiolipins and the PG-Gly headgroup. The four analyzed neutrophilic members of the Halobacteria were characterized by the presence of sulfur-containing headgroups and glycolipids. The presence of cardiolipins with one or more i-C25 alkyl chains, generally termed extended archaeol (EXT-AR), in one of the Methanonatronarchaeia strains was unexpected as only one other order of methanogenic archaea has been reported to produce EXT-AR. We examined this further by looking into the genomic potential of various archaea to produce EXT-AR.
Collapse
Affiliation(s)
- Nicole J. Bale
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Dimitry Y. Sorokin
- Research Centre of Biotechnology, Winogradsky Institute of Microbiology, Russian Academy of Sciences, Moscow, Russia
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Delft, Netherlands
| | - Ellen C. Hopmans
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Michel Koenen
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Laura Villanueva
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Institute for Sea Research, Utrecht University, Texel, Netherlands
- Department of Earth Sciences, Faculty of Geosciences, Utrecht University, Utrecht, Netherlands
| |
Collapse
|
8
|
Emendato A, Guerrini R, Marzola E, Wienk H, Boelens R, Leone S, Picone D. Disordered Peptides Looking for Their Native Environment: Structural Basis of CB1 Endocannabinoid Receptor Binding to Pepcans. Front Mol Biosci 2018; 5:100. [PMID: 30505835 PMCID: PMC6250848 DOI: 10.3389/fmolb.2018.00100] [Citation(s) in RCA: 9] [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: 09/20/2018] [Accepted: 10/26/2018] [Indexed: 01/15/2023] Open
Abstract
Endocannabinoid peptides, or “pepcans,” are endogenous ligands of the CB1 cannabinoid receptor. Depending on their length, they display diverse activity: For instance, the nona-peptide Pepcan-9, also known as hemopressin, is a powerful inhibitor of CB1, whereas the longer variant Pepcan-12, which extends by only three amino acid residues at the N-terminus, acts on both CB1 and CB2 as an allosteric modulator, although with diverse effects. Despite active research on their pharmacological applications, very little is known about structure-activity relationships of pepcans. Different structures have been proposed for the nona-peptide, which has also been reported to form fibrillar aggregates. This might have affected the outcome and reproducibility of bioactivity studies. In an attempt of elucidating the determinants of both biological activity and aggregation propensity of Pepcan-9 and Pepcan-12, we have performed their structure characterization in solvent systems characterized by different polarity and pH. We have found that, while disordered in aqueous environment, both peptides display helical structure in less polar environment, mimicking the proteic receptor milieu. In the case of Pepcan-9, this structure is fully consistent with the observed modulation of the CB1. For Pepcan-12, whose allosteric binding site is still unknown, the presented structure is compatible with the binding at one of the previously proposed allosteric sites on CB1. These findings open the way to structure-driven design of selective peptide modulators of CB1.
Collapse
Affiliation(s)
- Alessandro Emendato
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Erika Marzola
- Department of Chemical and Pharmaceutical Sciences, University of Ferrara, Ferrara, Italy
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| |
Collapse
|
9
|
Corbeski I, Dolinar K, Wienk H, Boelens R, van Ingen H. DNA repair factor APLF acts as a H2A-H2B histone chaperone through binding its DNA interaction surface. Nucleic Acids Res 2018; 46:7138-7152. [PMID: 29905837 PMCID: PMC6101569 DOI: 10.1093/nar/gky507] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 11/20/2017] [Revised: 05/02/2018] [Accepted: 05/22/2018] [Indexed: 01/23/2023] Open
Abstract
Genome replication, transcription and repair require the assembly/disassembly of the nucleosome. Histone chaperones are regulators of this process by preventing formation of non-nucleosomal histone-DNA complexes. Aprataxin and polynucleotide kinase like factor (APLF) is a non-homologous end-joining (NHEJ) DNA repair factor that possesses histone chaperone activity in its acidic domain (APLFAD). Here, we studied the molecular basis of this activity using biochemical and structural methods. We find that APLFAD is intrinsically disordered and binds histone complexes (H3-H4)2 and H2A-H2B specifically and with high affinity. APLFAD prevents unspecific complex formation between H2A-H2B and DNA in a chaperone assay, establishing for the first time its specific histone chaperone function for H2A-H2B. On the basis of a series of nuclear magnetic resonance studies, supported by mutational analysis, we show that the APLFAD histone binding domain uses two aromatic side chains to anchor to the α1-α2 patches on both H2A and H2B, thereby covering most of their DNA-interaction surface. An additional binding site on both APLFAD and H2A-H2B may be involved in the handoff between APLF and DNA or other chaperones. Together, our data support the view that APLF provides not only a scaffold but also generic histone chaperone activity for the NHEJ-complex.
Collapse
Affiliation(s)
- Ivan Corbeski
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Klemen Dolinar
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Group for Nano- and Biotechnological applications, Department of Fundamentals of Electrical Engineering, Mathematics and Physics, University of Ljubljana, Tržaška cesta 25, 1000 Ljubljana, Slovenia
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hugo van Ingen
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Macromolecular Biochemistry, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| |
Collapse
|
10
|
Oliveira LC, Souza DP, Oka GU, Lima FDS, Oliveira RJ, Favaro DC, Wienk H, Boelens R, Farah CS, Salinas RK. VirB7 and VirB9 Interactions Are Required for the Assembly and Antibacterial Activity of a Type IV Secretion System. Structure 2016; 24:1707-1718. [PMID: 27594685 DOI: 10.1016/j.str.2016.07.015] [Citation(s) in RCA: 8] [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] [Received: 04/17/2016] [Revised: 07/19/2016] [Accepted: 07/22/2016] [Indexed: 11/16/2022]
Abstract
The type IV secretion system (T4SS) from the phytopathogen Xanthomonas citri (Xac) is a bactericidal nanomachine. The T4SS core complex is a ring composed of multiple copies of VirB7-VirB9-VirB10 subunits. Xac-VirB7 contains a disordered N-terminal tail (VirB7NT) that recognizes VirB9, and a C-terminal domain (VirB7CT) involved in VirB7 self-association. Here, we show that VirB7NT forms a short β strand upon binding to VirB9 and stabilizes it. A tight interaction between them is essential for T4SS assembly and antibacterial activity. Abolishing VirB7 self-association or deletion of the VirB7 C-terminal domain impairs this antibacterial activity without disturbing T4SS assembly. These findings reveal protein interactions within the core complex that are critical for the stability and activity of a T4SS.
Collapse
Affiliation(s)
- Luciana Coutinho Oliveira
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Diorge Paulo Souza
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil.
| | - Gabriel Umaji Oka
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Filipe da Silva Lima
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Ronaldo Junio Oliveira
- Departamento de Física, Instituto de Ciências Exatas e Naturais, Universidade Federal do Triângulo Mineiro, Uberaba, Minas Gerais 38064-200, Brazil
| | - Denize Cristina Favaro
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584-CH, the Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht 3584-CH, the Netherlands
| | - Chuck Shaker Farah
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil.
| | - Roberto Kopke Salinas
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, São Paulo 05508-000, Brazil.
| |
Collapse
|
11
|
Dongre R, Folkers GE, Gualerzi CO, Boelens R, Wienk H. A model for the interaction of the G3-subdomain of Geobacillus stearothermophilus IF2 with the 30S ribosomal subunit. Protein Sci 2016; 25:1722-33. [PMID: 27364543 DOI: 10.1002/pro.2977] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 04/08/2016] [Revised: 06/28/2016] [Accepted: 06/29/2016] [Indexed: 11/10/2022]
Abstract
Bacterial translation initiation factor IF2 complexed with GTP binds to the 30S ribosomal subunit, promotes ribosomal binding of fMet-tRNA, and favors the joining of the small and large ribosomal subunits yielding a 70S initiation complex ready to enter the translation elongation phase. Within the IF2 molecule subdomain G3, which is believed to play an important role in the IF2-30S interaction, is positioned between the GTP-binding G2 and the fMet-tRNA binding C-terminal subdomains. In this study the solution structure of subdomain G3 of Geobacillus stearothermophilus IF2 has been elucidated. G3 forms a core structure consisting of two β-sheets with each four anti-parallel strands, followed by a C-terminal α-helix. In line with its role as linker between G3 and subdomain C1, this helix has no well-defined orientation but is endowed with a dynamic nature. The structure of the G3 core is that of a typical OB-fold module, similar to that of the corresponding subdomain of Thermus thermophilus IF2, and to that of other known RNA-binding modules such as IF2-C2, IF1 and subdomains II of elongation factors EF-Tu and EF-G. Structural comparisons have resulted in a model that describes the interaction between IF2-G3 and the 30S ribosomal subunit.
Collapse
Affiliation(s)
- Ramachandra Dongre
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Gert E Folkers
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Claudio O Gualerzi
- Laboratory of Genetics, Department of Biosciences and Biotechnology, University of Camerino, Italy
| | - Rolf Boelens
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| | - Hans Wienk
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands
| |
Collapse
|
12
|
Tuppo L, Spadaccini R, Alessandri C, Wienk H, Boelens R, Giangrieco I, Tamburrini M, Mari A, Picone D, Ciardiello MA. Structure, stability, and IgE binding of the peach allergen Peamaclein (Pru p 7). Biopolymers 2016; 102:416-25. [PMID: 25130872 DOI: 10.1002/bip.22530] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 03/13/2014] [Revised: 06/06/2014] [Accepted: 07/22/2014] [Indexed: 12/20/2022]
Abstract
Knowledge of the structural properties of allergenic proteins is a necessary prerequisite to better understand the molecular bases of their action, and also to design targeted structural/functional modifications. Peamaclein is a recently identified 7 kDa peach allergen that has been associated with severe allergic reactions in sensitive subjects. This protein represents the first component of a new allergen family, which has no 3D structure available yet. Here, we report the first experimental data on the 3D-structure of Peamaclein. Almost 75% of the backbone resonances, including two helical stretches in the N-terminal region, and four out of six cysteine pairs have been assigned by 2D-NMR using a natural protein sample. Simulated gastrointestinal digestion experiments have highlighted that Peamaclein is even more resistant to digestion than the peach major allergen Pru p 3. Only the heat-denatured protein becomes sensitive to intestinal proteases. Similar to Pru p 3, Peamaclein keeps its native 3D-structure up to 90°C, but it becomes unfolded at temperatures of 100-120°C. Heat denaturation affects the immunological properties of both peach allergens, which lose at least partially their IgE-binding epitopes. In conclusion, the data collected in this study provide a first set of information on the molecular properties of Peamaclein. Future studies could lead to the possible use of the denatured form of this protein as a vaccine, and of the inclusion of cooked peach in the diet of subjects allergic to Peamaclein.
Collapse
Affiliation(s)
- Lisa Tuppo
- Institute of Biosciences and BioResources, CNR, Via Pietro Castellino 111, Naples, I-80131, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Zhang R, Loers G, Schachner M, Boelens R, Wienk H, Siebert S, Eckert T, Kraan S, Rojas-Macias MA, Lütteke T, Galuska SP, Scheidig A, Petridis AK, Liang S, Billeter M, Schauer R, Steinmeyer J, Schröder JM, Siebert HC. Molecular Basis of the Receptor Interactions of Polysialic Acid (polySia), polySia Mimetics, and Sulfated Polysaccharides. ChemMedChem 2016; 11:990-1002. [PMID: 27136597 DOI: 10.1002/cmdc.201500609] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 03/01/2016] [Indexed: 02/05/2023]
Abstract
Polysialic acid (polySia) and polySia glycomimetic molecules support nerve cell regeneration, differentiation, and neuronal plasticity. With a combination of biophysical and biochemical methods, as well as data mining and molecular modeling techniques, it is possible to correlate specific ligand-receptor interactions with biochemical processes and in vivo studies that focus on the potential therapeutic impact of polySia, polySia glycomimetics, and sulfated polysaccharides in neuronal diseases. With this strategy, the receptor interactions of polySia and polySia mimetics can be understood on a submolecular level. As the HNK-1 glycan also enhances neuronal functions, we tested whether similar sulfated oligo- and polysaccharides from seaweed could be suitable, in addition to polySia, for finding potential new routes into patient care focusing on an improved cure for various neuronal diseases. The knowledge obtained here on the structural interplay between polySia or sulfated polysaccharides and their receptors can be exploited to develop new drugs and application routes for the treatment of neurological diseases and dysfunctions.
Collapse
Affiliation(s)
- Ruiyan Zhang
- RI-B-NT: Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148, Kiel, Germany
- Zoological Institute, Department of Structural Biology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Gabriele Loers
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, University of Hamburg, Falkenried 94, 20251, Hamburg, Germany
| | - Melitta Schachner
- Center for Molecular Neurobiology Hamburg, University Medical Center Hamburg-Eppendorf, University of Hamburg, Falkenried 94, 20251, Hamburg, Germany
- Center for Neuroscience, Shantou University Medical College, 22 Xin Ling Road, Shantou, Guangdong, 515041, China
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Simone Siebert
- RI-B-NT: Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148, Kiel, Germany
| | - Thomas Eckert
- Institute of Veterinary Physiology and Biochemistry, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
- Clinic for Obstetrics, Gynecology and Andrology of Large and Small Animals, Justus-Liebig-Universität Gießen, Frankfurter Str. 106, 35392, Gießen, Germany
| | - Stefan Kraan
- Ocean Harvest Technology Ltd., N17 Business Park, Milltown, County Galway, Ireland
| | - Miguel A Rojas-Macias
- Institute of Veterinary Physiology and Biochemistry, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Thomas Lütteke
- Institute of Veterinary Physiology and Biochemistry, Fachbereich Veterinärmedizin, Justus-Liebig-Universität Gießen, Frankfurter Str. 100, 35392, Gießen, Germany
| | - Sebastian P Galuska
- Institute of Biochemistry, Faculty of Medicine, Justus-Liebig-Universität Gießen, Friedrichstr. 24, 35392, Gießen, Germany
| | - Axel Scheidig
- Zoological Institute, Department of Structural Biology, Kiel University, Am Botanischen Garten 1-9, 24118, Kiel, Germany
| | - Athanasios K Petridis
- Neurosurgery Clinic, University Düsseldorf, Moorenstraße 5, 40255, Düsseldorf, Germany
| | - Songping Liang
- College of Life Sciences, Hunan Normal University, 410081, Changsha, China
| | - Martin Billeter
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 100, 40530, Gothenburg, Sweden
| | - Roland Schauer
- Institute of Biochemistry, Kiel University, Olshausenstr. 40, 24098, Kiel, Germany
| | - Jürgen Steinmeyer
- Orthopaedic Research Laboratories, Department of Orthopaedic Surgery, University Hospital Giessen and Marburg GmbH, Paul-Meimberg-Str. 3, 35392, Gießen, Germany
| | - Jens-Michael Schröder
- Department of Dermatology, University Hospital Schleswig-Holstein, Campus Kiel, 24105, Kiel, Germany
| | - Hans-Christian Siebert
- RI-B-NT: Research Institute of Bioinformatics and Nanotechnology, Franziusallee 177, 24148, Kiel, Germany.
| |
Collapse
|
14
|
Nieto L, Tharun IM, Balk M, Wienk H, Boelens R, Ottmann C, Milroy LG, Brunsveld L. Estrogen Receptor Folding Modulates cSrc Kinase SH2 Interaction via a Helical Binding Mode. ACS Chem Biol 2015; 10:2624-32. [PMID: 26352092 DOI: 10.1021/acschembio.5b00568] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The estrogen receptors (ERs) feature, next to their transcriptional role, important nongenomic signaling actions, with emerging clinical relevance. The Src Homology 2 (SH2) domain mediated interaction between cSrc kinase and ER plays a key role in this; however the molecular determinants of this interaction have not been elucidated. Here, we used phosphorylated ER peptide and semisynthetic protein constructs in a combined biochemical and structural study to, for the first time, provide a quantitative and structural characterization of the cSrc SH2-ER interaction. Fluorescence polarization experiments delineated the SH2 binding motif in the ER sequence. Chemical shift perturbation analysis by nuclear magnetic resonance (NMR) together with molecular dynamics (MD) simulations allowed us to put forward a 3D model of the ER-SH2 interaction. The structural basis of this protein-protein interaction has been compared with that of the high affinity SH2 binding sequence GpYEEI. The ER features a different binding mode from that of the "two-pronged plug two-hole socket" model in the so-called specificity determining region. This alternative binding mode is modulated via the folding of ER helix 12, a structural element directly C-terminal of the key phosphorylated tyrosine. The present findings provide novel molecular entries for understanding nongenomic ER signaling and targeting the corresponding disease states.
Collapse
Affiliation(s)
- Lidia Nieto
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Inga M. Tharun
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Mark Balk
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Hans Wienk
- Bijvoet
Center for Biomolecular Research, NMR Spectroscopy Utrecht University, 3584CH Utrecht, The Netherlands
| | - Rolf Boelens
- Bijvoet
Center for Biomolecular Research, NMR Spectroscopy Utrecht University, 3584CH Utrecht, The Netherlands
| | - Christian Ottmann
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Lech-Gustav Milroy
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - Luc Brunsveld
- Laboratory
of Chemical Biology, Department of Biomedical Engineering and Institute
of Complex Molecular Systems, Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| |
Collapse
|
15
|
Furse S, Wienk H, Boelens R, de Kroon AIPM, Killian JA. E. coli MG1655 modulates its phospholipid composition through the cell cycle. FEBS Lett 2015; 589:2726-30. [PMID: 26272829 DOI: 10.1016/j.febslet.2015.07.043] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [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: 05/22/2015] [Revised: 07/07/2015] [Accepted: 07/28/2015] [Indexed: 10/23/2022]
Abstract
This paper describes a study of the phospholipid profile of Escherichia coli MG1655 cultures at the B and D periods of the cell cycle. The results indicate that the phosphatidyl glycerol fraction grows relatively rapidly and that the size of the cardiolipin (CL) fraction does not grow at all during cell elongation. This is consistent with observations that CL is located preferentially at the poles of E. coli. It also suggests that lipid production is controlled as a function of the cell cycle.
Collapse
Affiliation(s)
- Samuel Furse
- Membrane Biochemistry and Biophysics, Department of Chemistry, Universiteit Utrecht, Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Hans Wienk
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Universiteit Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Universiteit Utrecht, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Anton I P M de Kroon
- Membrane Biochemistry and Biophysics, Department of Chemistry, Universiteit Utrecht, Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - J Antoinette Killian
- Membrane Biochemistry and Biophysics, Department of Chemistry, Universiteit Utrecht, Kruytgebouw, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
16
|
Moore EK, Hopmans EC, Rijpstra WIC, Sánchez-Andrea I, Villanueva L, Wienk H, Schoutsen F, Stams AJM, Sinninghe Damsté JS. Lysine and novel hydroxylysine lipids in soil bacteria: amino acid membrane lipid response to temperature and pH in Pseudopedobacter saltans. Front Microbiol 2015; 6:637. [PMID: 26175720 PMCID: PMC4484230 DOI: 10.3389/fmicb.2015.00637] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 06/12/2015] [Indexed: 01/08/2023] Open
Abstract
Microbial decomposition of organic matter is an essential process in the global carbon cycle. The soil bacteria Pseudopedobacter saltans and Flavobacterium johnsoniae are both able to degrade complex organic molecules, but it is not fully known how their membrane structures are adapted to their environmental niche. The membrane lipids of these species were extracted and analyzed using high performance liquid chromatography-electrospray ionization/ion trap/mass spectrometry (HPLC-ESI/IT/MS) and high resolution accurate mass/mass spectrometry (HRAM/MS). Abundant unknown intact polar lipids (IPLs) from P. saltans were isolated and further characterized using amino acid analysis and two dimensional nuclear magnetic resonance (NMR) spectroscopy. Ornithine IPLs (OLs) with variable (hydroxy) fatty acid composition were observed in both bacterial species. Lysine-containing IPLs (LLs) were also detected in both species and were characterized here for the first time using HPLC-MS. Novel LLs containing hydroxy fatty acids and novel hydroxylysine lipids with variable (hydroxy) fatty acid composition were identified in P. saltans. The confirmation of OL and LL formation in F. johnsoniae and P. saltans and the presence of OlsF putative homologs in P. saltans suggest the OlsF gene coding protein is possibly involved in OL and LL biosynthesis in both species, however, potential pathways of OL and LL hydroxylation in P. saltans are still undetermined. Triplicate cultures of P. saltans were grown at three temperature/pH combinations: 30°C/pH 7, 15°C/pH 7, and 15°C/pH 9. The fractional abundance of total amino acid containing IPLs containing hydroxylated fatty acids was significantly higher at higher temperature, and the fractional abundance of lysine-containing IPLs was significantly higher at lower temperature and higher pH. These results suggest that these amino acid-containing IPLs, including the novel hydroxylysine lipids, could be involved in temperature and pH stress response of soil bacteria.
Collapse
Affiliation(s)
- Eli K. Moore
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea ResearchTexel, Netherlands
| | - Ellen C. Hopmans
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea ResearchTexel, Netherlands
| | - W. Irene C. Rijpstra
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea ResearchTexel, Netherlands
| | | | - Laura Villanueva
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea ResearchTexel, Netherlands
| | - Hans Wienk
- NMR Spectroscopy Research Group, Bijvoet Center for Biomolecular Research, Utrecht UniversityUtrecht, Netherlands
| | | | - Alfons J. M. Stams
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands
| | - Jaap S. Sinninghe Damsté
- Department of Marine Organic Biogeochemistry, Royal Netherlands Institute for Sea ResearchTexel, Netherlands
- Faculty of Geosciences, Utrecht UniversityUtrecht, Netherlands
| |
Collapse
|
17
|
Faridounnia M, Wienk H, Kovačič L, Folkers GE, Jaspers NGJ, Kaptein R, Hoeijmakers JHJ, Boelens R. The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex. J Biol Chem 2015; 290:20541-55. [PMID: 26085086 DOI: 10.1074/jbc.m114.635169] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [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: 01/22/2015] [Indexed: 12/15/2022] Open
Abstract
The ERCC1-XPF heterodimer, a structure-specific DNA endonuclease, is best known for its function in the nucleotide excision repair (NER) pathway. The ERCC1 point mutation F231L, located at the hydrophobic interaction interface of ERCC1 (excision repair cross-complementation group 1) and XPF (xeroderma pigmentosum complementation group F), leads to severe NER pathway deficiencies. Here, we analyze biophysical properties and report the NMR structure of the complex of the C-terminal tandem helix-hairpin-helix domains of ERCC1-XPF that contains this mutation. The structures of wild type and the F231L mutant are very similar. The F231L mutation results in only a small disturbance of the ERCC1-XPF interface, where, in contrast to Phe(231), Leu(231) lacks interactions stabilizing the ERCC1-XPF complex. One of the two anchor points is severely distorted, and this results in a more dynamic complex, causing reduced stability and an increased dissociation rate of the mutant complex as compared with wild type. These data provide a biophysical explanation for the severe NER deficiencies caused by this mutation.
Collapse
Affiliation(s)
- Maryam Faridounnia
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hans Wienk
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Lidija Kovačič
- the Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia, and
| | - Gert E Folkers
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nicolaas G J Jaspers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Robert Kaptein
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jan H J Hoeijmakers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands,
| |
Collapse
|
18
|
Schwede F, Bertinetti D, Langerijs CN, Hadders MA, Wienk H, Ellenbroek JH, de Koning EJP, Bos JL, Herberg FW, Genieser HG, Janssen RAJ, Rehmann H. Structure-guided design of selective Epac1 and Epac2 agonists. PLoS Biol 2015; 13:e1002038. [PMID: 25603503 PMCID: PMC4300089 DOI: 10.1371/journal.pbio.1002038] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2014] [Accepted: 12/03/2014] [Indexed: 12/25/2022] Open
Abstract
The second messenger cAMP is known to augment glucose-induced insulin secretion. However, its downstream targets in pancreatic β-cells have not been unequivocally determined. Therefore, we designed cAMP analogues by a structure-guided approach that act as Epac2-selective agonists both in vitro and in vivo. These analogues activate Epac2 about two orders of magnitude more potently than cAMP. The high potency arises from increased affinity as well as increased maximal activation. Crystallographic studies demonstrate that this is due to unique interactions. At least one of the Epac2-specific agonists, Sp-8-BnT-cAMPS (S-220), enhances glucose-induced insulin secretion in human pancreatic cells. Selective targeting of Epac2 is thus proven possible and may be an option in diabetes treatment. cAMP is a small molecule produced by cells that activates proteins involved in a wide range of biological processes, including olfaction, pacemaker activity, regulation of gene expression, insulin secretion, and many others. In the case of insulin secretion, cAMP seems to impinge on different stages of the signalling cascade to regulate secretory activity in pancreatic β-cells. Here we have developed a chemically modified version of cAMP that specifically only activates Epac2, one of the cAMP-responsive proteins in this cascade. Furthermore, our cAMP analogue activates Epac2 more potently than cAMP itself does. We have determined several crystal structures of Epac2 in complex with cAMP analogues to help us explain the molecular basis of the observed selectivity and the strong activation potential. In addition, we were able to show that the analogue is able to potentiate glucose-induced secretion of insulin from human pancreatic islets. The principal challenge during this study was identifying and understanding small differences in the cAMP-binding domains of cAMP-regulated proteins and matching these differences with suitable modifications of the cAMP molecule. A newly developed analogue of cAMP that selectively activates Epac2 can potentiate glucose-induced insulin secretion from human pancreatic β-cells.
Collapse
Affiliation(s)
| | | | | | - Michael A. Hadders
- Department of Chemistry, Laboratory of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Hans Wienk
- Department of Chemistry, NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | | | - Eelco J. P. de Koning
- Department of Nephrology, Leiden University Medical Center, Leiden, The Netherlands
- Hubrecht Institute/KNAW and University Medical Center Utrecht, Utrecht, The Netherlands
| | - Johannes L. Bos
- Molecular Cancer Research and Cancer Genomics Netherlands, Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
| | | | | | | | - Holger Rehmann
- Molecular Cancer Research and Cancer Genomics Netherlands, Center for Molecular Medicine, UMC Utrecht, Utrecht, The Netherlands
- * E-mail:
| |
Collapse
|
19
|
Jamalian A, Sneekes EJ, Wienk H, Dekker LJM, Ruttink PJA, Ursem M, Luider TM, Burgers PC. Identifying Ca2+-binding sites in proteins by liquid chromatography-mass spectrometry using Ca2+-directed dissociations. Mol Cell Proteomics 2014; 13:3177-83. [PMID: 25023127 PMCID: PMC4223500 DOI: 10.1074/mcp.m114.038182] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 07/07/2014] [Indexed: 11/06/2022] Open
Abstract
Here we describe a new method to identify calcium-binding sites in proteins using high-resolution liquid chromatography-mass spectrometry in concert with calcium-directed collision-induced dissociations. Our method does not require any modifications to the liquid chromatography-mass spectrometry apparatus, uses standard digestion protocols, and can be applied to existing high-resolution MS data files. In contrast to NMR, our method is applicable to very small amounts of complex protein mixtures (femtomole level). Calcium-bound peptides can be identified using three criteria: (1) the calculated exact mass of the calcium containing peptide; (2) specific dissociations of the calcium-containing peptide from threonine and serine residues; and (3) the very similar retention times of the calcium-containing peptide and the free peptide.
Collapse
Affiliation(s)
- Azadeh Jamalian
- From the ‡Department of Neurology, Laboratory of Neuro-Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands; §Thermo Fisher Scientific/Dionex, Abberdaan 114, 1046 AA, Amsterdam, The Netherlands
| | - Evert-Jan Sneekes
- From the ‡Department of Neurology, Laboratory of Neuro-Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands; §Thermo Fisher Scientific/Dionex, Abberdaan 114, 1046 AA, Amsterdam, The Netherlands
| | - Hans Wienk
- ¶NMR Spectroscopy, Bijvoet Center for Biomolecular Research, P.O. Box 80.075, 3508 TB, Utrecht University, Utrecht, The Netherlands
| | - Lennard J M Dekker
- From the ‡Department of Neurology, Laboratory of Neuro-Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Paul J A Ruttink
- ‖Theoretical Chemistry Group, University of Utrecht, 3508 TC, Utrecht, The Netherlands
| | - Mario Ursem
- §Thermo Fisher Scientific/Dionex, Abberdaan 114, 1046 AA, Amsterdam, The Netherlands
| | - Theo M Luider
- From the ‡Department of Neurology, Laboratory of Neuro-Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Peter C Burgers
- From the ‡Department of Neurology, Laboratory of Neuro-Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA, Rotterdam, The Netherlands;
| |
Collapse
|
20
|
Ferguson FM, Dias DM, Rodrigues JPGLM, Wienk H, Boelens R, Bonvin AMJJ, Abell C, Ciulli A. Binding hotspots of BAZ2B bromodomain: Histone interaction revealed by solution NMR driven docking. Biochemistry 2014; 53:6706-16. [PMID: 25266743 DOI: 10.1021/bi500909d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Bromodomains are epigenetic reader domains, which have come under increasing scrutiny both from academic and pharmaceutical research groups. Effective targeting of the BAZ2B bromodomain by small molecule inhibitors has been recently reported, but no structural information is yet available on the interaction with its natural binding partner, acetylated histone H3K14ac. We have assigned the BAZ2B bromodomain and studied its interaction with H3K14ac acetylated peptides by NMR spectroscopy using both chemical shift perturbation (CSP) data and clean chemical exchange (CLEANEX-PM) NMR experiments. The latter was used to characterize water molecules known to play an important role in mediating interactions. Besides the anticipated Kac binding site, we consistently found the bromodomain BC loop as hotspots for the interaction. This information was used to create a data-driven model for the complex using HADDOCK. Our findings provide both structure and dynamics characterization that will be useful in the quest for potent and selective inhibitors to probe the function of the BAZ2B bromodomain.
Collapse
Affiliation(s)
- Fleur M Ferguson
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge, CB2 1EW, U.K
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Scheepstra M, Nieto L, Hirsch AKH, Fuchs S, Leysen S, Lam CV, in het Panhuis L, van Boeckel CAA, Wienk H, Boelens R, Ottmann C, Milroy L, Brunsveld L. A Natural‐Product Switch for a Dynamic Protein Interface. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403773] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Marcel Scheepstra
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Lidia Nieto
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Anna K. H. Hirsch
- Stratingh Institue for Chemistry, University of Groningen, Nijenborgh 7, 9747AG Groningen (The Netherlands)
| | - Sascha Fuchs
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Seppe Leysen
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Chan Vinh Lam
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Leslie in het Panhuis
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Constant A. A. van Boeckel
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584CH Utrecht (The Netherlands)
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584CH Utrecht (The Netherlands)
| | - Christian Ottmann
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Lech‐Gustav Milroy
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | - Luc Brunsveld
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| |
Collapse
|
22
|
Scheepstra M, Nieto L, Hirsch AKH, Fuchs S, Leysen S, Lam CV, in het Panhuis L, van Boeckel CAA, Wienk H, Boelens R, Ottmann C, Milroy LG, Brunsveld L. A natural-product switch for a dynamic protein interface. Angew Chem Int Ed Engl 2014; 53:6443-8. [PMID: 24821627 DOI: 10.1002/anie.201403773] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Indexed: 01/11/2023]
Abstract
Small ligands are a powerful way to control the function of protein complexes via dynamic binding interfaces. The classic example is found in gene transcription where small ligands regulate nuclear receptor binding to coactivator proteins via the dynamic activation function 2 (AF2) interface. Current ligands target the ligand-binding pocket side of the AF2. Few ligands are known, which selectively target the coactivator side of the AF2, or which can be selectively switched from one side of the interface to the other. We use NMR spectroscopy and modeling to identify a natural product, which targets the retinoid X receptor (RXR) at both sides of the AF2. We then use chemical synthesis, cellular screening and X-ray co-crystallography to split this dual activity, leading to a potent and molecularly efficient RXR agonist, and a first-of-kind inhibitor selective for the RXR/coactivator interaction. Our findings justify future exploration of natural products at dynamic protein interfaces.
Collapse
Affiliation(s)
- Marcel Scheepstra
- Laboratory of Chemical Biology and Institute of Complex Molecular Systems (ICMS), Department of Biomedical Engineering, Technische Universiteit Eindhoven, Den Dolech 2, 5612 AZ Eindhoven (The Netherlands) http://www.tue.nl/cb
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Weiss J, Wienk H, Boelens R, Laschewsky A. Block Copolymer Micelles with an Intermediate Star-/Flower-Like Structure Studied by1H NMR Relaxometry. MACROMOL CHEM PHYS 2014. [DOI: 10.1002/macp.201300753] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jan Weiss
- Institute Charles Sadron; UPR22-CNRS; 23 Rue de Loess 67034 Strasbourg Cedex 2 France
| | - Hans Wienk
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584CH Utrecht The Netherlands
| | - Rolf Boelens
- NMR Spectroscopy; Bijvoet Center for Biomolecular Research; Utrecht University; Padualaan 8 3584CH Utrecht The Netherlands
| | - André Laschewsky
- Department of Chemistry; University of Potsdam; Karl-Liebknecht-Strasse 24-25 14476 Potsdam-Golm Germany
- Fraunhofer Institute for Applied Polymer Research; Geiselbergstrasse 69 14476 Potsdam-Golm Germany
| |
Collapse
|
24
|
Popovic M, Wienk H, Coglievina M, Boelens R, Pongor S, Pintar A. The basic helix-loop-helix region of the transcriptional repressor hairy and enhancer of split 1 is preorganized to bind DNA. Proteins 2014; 82:537-45. [DOI: 10.1002/prot.24507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/19/2013] [Accepted: 01/06/2014] [Indexed: 12/26/2022]
Affiliation(s)
- Matija Popovic
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| | - Hans Wienk
- Bijvoet Center for Biomolecular Research, Utrecht University; 3584 CH Utrecht the Netherlands
| | - Maristella Coglievina
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University; 3584 CH Utrecht the Netherlands
| | - Sándor Pongor
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| | - Alessandro Pintar
- Protein Structure and Bioinformatics Group; International Centre for Genetic Engineering and Biotechnology (ICGEB); AREA Science Park I-34149 Trieste Italy
| |
Collapse
|
25
|
Augustyniak W, Wienk H, Boelens R, Reetz MT. ¹H, ¹³C and ¹⁵N resonance assignments of wild-type Bacillus subtilis Lipase A and its mutant evolved towards thermostability. Biomol NMR Assign 2013; 7:249-252. [PMID: 22996591 DOI: 10.1007/s12104-012-9420-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 09/05/2012] [Indexed: 06/01/2023]
Abstract
Previously, we evolved Lipase A from Bacillus subtilis towards increased thermostability. The resulting mutant retains significant catalytic activity upon heating above 60 °C (and up to 100 °C) and cooling down, whereas wild-type lipase precipitates irreversibly and does not show significant activity in these conditions. Kinetic thermostability of proteins has not been characterized well on the molecular structure level so far, therefore our aim is to study it using NMR spectroscopy. Here, nearly complete (1)H, (13)C and (15)N resonance assignments are reported for wild-type and mutant Lipase A. Chemical shifts were used to predict secondary structure elements of both Lipase A variants.
Collapse
Affiliation(s)
- Wojciech Augustyniak
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
| | | | | | | |
Collapse
|
26
|
Wienk H, Slootweg JC, Speerstra S, Kaptein R, Boelens R, Folkers GE. The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition. Nucleic Acids Res 2013; 41:6739-49. [PMID: 23661679 PMCID: PMC3711432 DOI: 10.1093/nar/gkt354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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] [Indexed: 01/24/2023] Open
Abstract
To maintain the integrity of the genome, multiple DNA repair systems exist to repair damaged DNA. Recognition of altered DNA, including bulky adducts, pyrimidine dimers and interstrand crosslinks (ICL), partially depends on proteins containing helix-hairpin-helix (HhH) domains. To understand how ICL is specifically recognized by the Fanconi anemia proteins FANCM and FAAP24, we determined the structure of the HhH domain of FAAP24. Although it resembles other HhH domains, the FAAP24 domain contains a canonical hairpin motif followed by distorted motif. The HhH domain can bind various DNA substrates; using nuclear magnetic resonance titration experiments, we demonstrate that the canonical HhH motif is required for double-stranded DNA (dsDNA) binding, whereas the unstructured N-terminus can interact with single-stranded DNA. Both DNA binding surfaces are used for binding to ICL-like single/double-strand junction-containing DNA substrates. A structural model for FAAP24 bound to dsDNA has been made based on homology with the translesion polymerase iota. Site-directed mutagenesis, sequence conservation and charge distribution support the dsDNA-binding model. Analogous to other HhH domain-containing proteins, we suggest that multiple FAAP24 regions together contribute to binding to single/double-strand junction, which could contribute to specificity in ICL DNA recognition.
Collapse
Affiliation(s)
- Hans Wienk
- Bijvoet Center For Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | | | | | | | | |
Collapse
|
27
|
Stötzel S, Schurink M, Wienk H, Siebler U, Burg-Roderfeld M, Eckert T, Kulik B, Wechselberger R, Sewing J, Steinmeyer J, Oesser S, Boelens R, Siebert HC. Cover Picture: Molecular Organization of Various Collagen Fragments as Revealed by Atomic Force Microscopy and Diffusion-Ordered NMR Spectroscopy (ChemPhysChem 13/2012). Chemphyschem 2012. [DOI: 10.1002/cphc.201290060] [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: 11/10/2022]
|
28
|
Stötzel S, Schurink M, Wienk H, Siebler U, Burg-Roderfeld M, Eckert T, Kulik B, Wechselberger R, Sewing J, Steinmeyer J, Oesser S, Boelens R, Siebert HC. Molecular Organization of Various Collagen Fragments as Revealed by Atomic Force Microscopy and Diffusion-Ordered NMR Spectroscopy. Chemphyschem 2012; 13:3117-25. [DOI: 10.1002/cphc.201200284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Indexed: 12/22/2022]
|
29
|
Augustyniak W, Brzezinska AA, Pijning T, Wienk H, Boelens R, Dijkstra BW, Reetz MT. Biophysical characterization of mutants of Bacillus subtilis lipase evolved for thermostability: factors contributing to increased activity retention. Protein Sci 2012; 21:487-97. [PMID: 22267088 DOI: 10.1002/pro.2031] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 12/14/2011] [Accepted: 01/08/2012] [Indexed: 11/10/2022]
Abstract
Previously, Lipase A from Bacillus subtilis was subjected to in vitro directed evolution using iterative saturation mutagenesis, with randomization sites chosen on the basis of the highest B-factors available from the crystal structure of the wild-type (WT) enzyme. This provided mutants that, unlike WT enzyme, retained a large part of their activity after heating above 65 °C and cooling down. Here, we subjected the three best mutants along with the WT enzyme to biophysical and biochemical characterization. Combining thermal inactivation profiles, circular dichroism, X-ray structure analyses and NMR experiments revealed that mutations of surface amino acid residues counteract the tendency of Lipase A to undergo precipitation under thermal stress. Reduced precipitation of the unfolding intermediates rather than increased conformational stability of the evolved mutants seems to be responsible for the activity retention.
Collapse
Affiliation(s)
- Wojciech Augustyniak
- Max-Planck-Institut fur Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mulheim an der Ruhr, Germany
| | | | | | | | | | | | | |
Collapse
|
30
|
Wienk H, Tishchenko E, Belardinelli R, Tomaselli S, Dongre R, Spurio R, Folkers GE, Gualerzi CO, Boelens R. Structural dynamics of bacterial translation initiation factor IF2. J Biol Chem 2012; 287:10922-32. [PMID: 22308033 DOI: 10.1074/jbc.m111.333393] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial translation initiation factor IF2 promotes ribosomal subunit association, recruitment, and binding of fMet-tRNA to the ribosomal P-site and initiation dipeptide formation. Here, we present the solution structures of GDP-bound and apo-IF2-G2 of Bacillus stearothermophilus and provide evidence that this isolated domain binds the 50 S ribosomal subunit and hydrolyzes GTP. Differences between the free and GDP-bound structures of IF2-G2 suggest that domain reorganization within the G2-G3-C1 regions underlies the different structural requirements of IF2 during the initiation process. However, these structural signals are unlikely forwarded from IF2-G2 to the C-terminal fMet-tRNA binding domain (IF2-C2) because the connected IF2-C1 and IF2-C2 modules show completely independent mobility, indicating that the bacterial interdomain connector lacks the rigidity that was found in the archaeal IF2 homolog aIF5B.
Collapse
Affiliation(s)
- Hans Wienk
- Bijvoet Center for Biomolecular Research, NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | | | | | | | | | | | | | | |
Collapse
|
31
|
de Graaf AJ, Boere KWM, Kemmink J, Fokkink RG, van Nostrum CF, Rijkers DTS, van der Gucht J, Wienk H, Baldus M, Mastrobattista E, Vermonden T, Hennink WE. Looped structure of flowerlike micelles revealed by 1H NMR relaxometry and light scattering. Langmuir 2011; 27:9843-9848. [PMID: 21755924 DOI: 10.1021/la2019605] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We present experimental proof that so-called "flowerlike micelles" exist and that they have some distinctly different properties compared to their "starlike" counterparts. Amphiphilic AB diblock and BAB triblock copolymers consisting of poly(ethylene glycol) (PEG) as hydrophilic A block and thermosensitive poly(N-isopropylacrylamide) (pNIPAm) B block(s) were synthesized via atom transfer radical polymerization (ATRP). In aqueous solutions, both block copolymer types form micelles above the cloud point of pNIPAm. Static and dynamic light scattering measurements in combination with NMR relaxation experiments proved the existence of flowerlike micelles based on pNIPAm(16kDa)-PEG(4kDa)-pNIPAm(16kDa) which had a smaller radius and lower mass and aggregation number than starlike micelles based on mPEG(2kDa)-pNIPAm(16kDa). Furthermore, the PEG surface density was much lower for the flowerlike micelles, which we attribute to the looped configuration of the hydrophilic PEG block. (1)H NMR relaxation measurements showed biphasic T(2) relaxation for PEG, indicating rigid PEG segments close to the micelle core and more flexible distal segments. Even the flexible distal segments were shown to have a lower mobility in the flowerlike micelles compared to the starlike micelles, indicating strain due to loop formation. Taken together, it is demonstrated that self-assemblies of BAB triblock copolymers have their hydrophilic block in a looped conformation and thus indeed adopt a flowerlike conformation.
Collapse
Affiliation(s)
- Albert J de Graaf
- Utrecht Institute for Pharmaceutical Sciences, Pharmaceutics, Utrecht University, P.O. Box 80.082, 3508TB Utrecht, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Lange A, Hoeller D, Wienk H, Marcillat O, Lancelin JM, Walker O. NMR reveals a different mode of binding of the Stam2 VHS domain to ubiquitin and diubiquitin. Biochemistry 2010; 50:48-62. [PMID: 21121635 DOI: 10.1021/bi101594a] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The VHS domain of the Stam2 protein is a ubiquitin binding domain involved in the recognition of ubiquitinated proteins committed to lysosomal degradation. Among all VHS domains, the VHS domain of Stam proteins is the strongest binder to monoubiqiuitin and exhibits preferences for K63-linked chains. In the present paper, we report the solution NMR structure of the Stam2-VHS domain in complex with monoubiquitin by means of chemical shift perturbations, spin relaxation, and paramagnetic relaxation enhancements. We also characterize the interaction of Stam2-VHS with K48- and K63-linked diubiquitin chains and report the first evidence that VHS binds differently to these two chains. Our data reveal that VHS enters the hydrophobic pocket of K48-linked diubiquitin and binds the two ubiquitin subunits with different affinities. In contrast, VHS interacts with K63-linked diubiquitin in a mode similar to its interaction with monoubiquitin. We also suggest possible structural models for both K48- and K63-linked diubiquitin in interaction with VHS. Our results, which demonstrate a different mode of binding of VHS for K48- and K63-linked diubiquitin, may explain the preference of VHS for K63- over K48-linked diubiquitin chains and monoubiquitin.
Collapse
Affiliation(s)
- Anja Lange
- Université de Lyon, UMR-CNRS 5180 Sciences Analytiques, 69622 Villeurbanne, France
| | | | | | | | | | | |
Collapse
|
33
|
Wienk H, Lammers I, Hotze A, Wu J, Wechselberger RW, Owens R, Stammers DK, Stuart D, Kaptein R, Folkers GE. The Tandem Zinc-Finger Region of Human ZHX Adopts a Novel C2H2 Zinc Finger Structure with a C-Terminal Extension. Biochemistry 2009; 48:4431-9. [DOI: 10.1021/bi9001997] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
34
|
Romanuka J, Folkers GE, Biris N, Tishchenko E, Wienk H, Bonvin AMJJ, Kaptein R, Boelens R. Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes. J Mol Biol 2009; 390:478-89. [PMID: 19450607 DOI: 10.1016/j.jmb.2009.05.022] [Citation(s) in RCA: 34] [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] [Received: 02/23/2009] [Revised: 05/08/2009] [Accepted: 05/13/2009] [Indexed: 10/20/2022]
Abstract
The structures of a dimeric mutant of the Lac repressor DNA-binding domain complexed with the auxiliary operators O2 and O3 have been determined using NMR spectroscopy and compared to the structures of the previously determined Lac-O1 and Lac-nonoperator complexes. Structural analysis of the Lac-O1 and Lac-O2 complexes shows highly similar structures with very similar numbers of specific and nonspecific contacts, in agreement with similar affinities for these two operators. The left monomer of the Lac repressor in the Lac-O3 complex retains most of these specific contacts. However, in the right half-site of the O3 operator, there is a significant loss of protein-DNA contacts, explaining the low affinity of the Lac repressor for the O3 operator. The binding mode in the right half-site resembles that of the nonspecific complex. In contrast to the Lac-nonoperator DNA complex where no hinge helices are formed, the stability of the hinge helices in the weak Lac-O3 complex is the same as in the Lac-O1 and Lac-O2 complexes, as judged from the results of hydrogen/deuterium experiments.
Collapse
Affiliation(s)
- Julija Romanuka
- Bijvoet Center for Biomolecular Research, Utrecht University, the Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
35
|
Huang A, de Jong RN, Wienk H, Winkler GS, Timmers HTM, Boelens R. E2-c-Cbl recognition is necessary but not sufficient for ubiquitination activity. J Mol Biol 2008; 385:507-19. [PMID: 18996392 DOI: 10.1016/j.jmb.2008.10.044] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Revised: 10/06/2008] [Accepted: 10/13/2008] [Indexed: 01/21/2023]
Abstract
The E2 ubiquitin-conjugating enzymes UbcH7 and UbcH5B both show specific binding to the RING (really interesting new gene) domain of the E3 ubiquitin-protein ligase c-Cbl, but UbcH7 hardly supports ubiquitination of c-Cbl and substrate in a reconstituted system. Here, we found that neither structural changes nor subtle differences in the E2-E3 interaction surface are possible explanations for the functional specificity of UbcH5B and UbcH7 in their interaction with c-Cbl. The quick transfer of ubiquitin from the UbcH5B-Ub thioester to c-Cbl or other ubiquitin acceptors suggests that UbcH5B might functionally be a relatively pliable E2 enzyme. In contrast, the UbcH7-Ub thioester is too stable to transfer ubiquitin under our assay conditions, indicating that UbcH7 might be a more specific E2 enzyme. Our results imply that the interaction specificity between c-Cbl and E2 is required but not sufficient for transfer of ubiquitin to potential targets.
Collapse
Affiliation(s)
- Anding Huang
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | | | | | | | | | | |
Collapse
|
36
|
van Ingen H, van Schaik FMA, Wienk H, Ballering J, Rehmann H, Dechesne AC, Kruijzer JAW, Liskamp RMJ, Timmers HTM, Boelens R. Structural insight into the recognition of the H3K4me3 mark by the TFIID subunit TAF3. Structure 2008; 16:1245-56. [PMID: 18682226 DOI: 10.1016/j.str.2008.04.015] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2008] [Revised: 04/26/2008] [Accepted: 04/28/2008] [Indexed: 01/02/2023]
Abstract
Trimethylation of lysine residue K4 of histone H3 (H3K4me3) strongly correlates with active promoters for RNA polymerase II-transcribed genes. Several reader proteins, including the basal transcription factor TFIID, for this nucleosomal mark have been identified. Its TAF3 subunit specifically binds the H3K4me3 mark via its conserved plant homeodomain (PHD) finger. Here, we report the solution structure of the TAF3-PHD finger and its complex with an H3K4me3 peptide. Using a combination of NMR, mutagenesis, and affinity measurements, we reveal the structural basis of binding affinity, methylation-state specificity, and crosstalk with asymmetric dimethylation of R2. A unique local structure rearrangement in the K4me3-binding pocket of TAF3 due to a conserved sequence insertion underscores the requirement for cation-pi interactions by two aromatic residues. Interference by asymmetric dimethylation of arginine 2 suggests that a H3R2/K4 "methyl-methyl" switch in the histone code dynamically regulates TFIID-promoter association.
Collapse
Affiliation(s)
- Hugo van Ingen
- Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Stordeur C, Dallüge R, Birkenmeier O, Wienk H, Rudolph R, Lange C, Lücke C. The NMR solution structure of the artificial protein M7 matches the computationally designed model. Proteins 2008; 72:1104-7. [DOI: 10.1002/prot.22107] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
38
|
Abstract
Epac1 is a cAMP-responsive exchange factor for the small G-protein Rap. It consists of a regulatory region containing a cyclic nucleotide binding (CNB) domain and a catalytic region that activates Rap. In the absence of cAMP, access of Rap to the catalytic site is blocked by the regulatory region. We analyzed the conformational states of the CNB domain in the absence and in the presence of cAMP and cAMP analogues by NMR spectroscopy, resulting in the first direct insights into the activation mechanism of Epac. We prove that the CNB domain exists in equilibrium between the inactive and the active conformation, which is shifted by binding of cAMP. cAMP binding results in conformational changes in both the ligand binding pocket and the outer helical segments. We used two different cAMP antagonists that block these successive changes to elucidate the steps of this process. Highlighting the role of dynamics, the superactivator 8-pCPT-2'-O-Me-cAMP induces similar conformational changes as cAMP but causes different internal mobility. The results reveal the critical elements of the CNB domain of Epac required for activation and highlight the role of dynamics in this process.
Collapse
Affiliation(s)
- Shannon M Harper
- Department of Physiological Chemistry and Centre for Biomedical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | | | | | | |
Collapse
|
39
|
Wienk H, Tomaselli S, Bernard C, Spurio R, Picone D, Gualerzi CO, Boelens R. Solution structure of the C1-subdomain of Bacillus stearothermophilus translation initiation factor IF2. Protein Sci 2005; 14:2461-8. [PMID: 16081655 PMCID: PMC2253463 DOI: 10.1110/ps.051531305] [Citation(s) in RCA: 17] [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: 10/25/2022]
Abstract
IF2 is one of three bacterial translation initiation factors that are conserved through all kingdoms of life. It binds the 30S and 50S ribosomal subunits, as well as fMet-tRNAf(Met). After these interactions, fMet-tRNAf(Met) is oriented to the ribosomal P-site where the first amino acid of the nascent polypeptide, formylmethionine, is presented. The C-terminal domain of Bacillus stearothermophilus IF2, which is responsible for recognition and binding of fMet-tRNAf(Met), contains two structured modules. Previously, the solution structure of the most C-terminal module, IF2-C2, has been elucidated by NMR spectroscopy and direct interactions between this subdomain and fMet-tRNAf(Met) were reported. In the present NMR study we have obtained the spectral assignment of the other module of the C-terminal domain (IF2-C1) and determined its solution structure and backbone dynamics. The IF2-C1 core forms a flattened fold consisting of a central four-stranded parallel beta-sheet flanked by three alpha-helices. Although its overall organization resembles that of subdomain III of the archaeal IF2-homolog eIF5B whose crystal structure had previously been reported, some differences of potential functional significance are evident.
Collapse
Affiliation(s)
- Hans Wienk
- Bijvoet Center for Biomolecular Research, Department of NMR Spectroscopy, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
40
|
Lin YJ, Dancea F, Löhr F, Klimmek O, Pfeiffer-Marek S, Nilges M, Wienk H, Kröger A, Rüterjans H. Solution structure of the 30 kDa polysulfide-sulfur transferase homodimer from Wolinella succinogenes. Biochemistry 2004; 43:1418-24. [PMID: 14769017 DOI: 10.1021/bi0356597] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [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: 11/29/2022]
Abstract
The periplasmic polysulfide-sulfur transferase (Sud) protein encoded by Wolinella succinogenes is involved in oxidative phosphorylation with polysulfide-sulfur as a terminal electron acceptor. The polysulfide-sulfur is covalently bound to the catalytic Cys residue of the Sud protein and transferred to the active site of the membranous polysulfide reductase. The solution structure of the homodimeric Sud protein has been determined using heteronuclear multidimensional NMR techniques. The structure is based on NOE-derived distance restraints, backbone hydrogen bonds, and torsion angle restraints as well as residual dipolar coupling restraints for a refinement of the relative orientation of the monomer units. The monomer structure consists of a five-stranded parallel beta-sheet enclosing a hydrophobic core, a two-stranded antiparallel beta-sheet, and six alpha-helices. The dimer fold is stabilized by hydrophobic residues and ion pairs found in the contact area between the two monomers. Similar to rhodanese enzymes, Sud catalyzes the transfer of the polysulfide-sulfur to the artificial acceptor cyanide. Despite their similar functions and active sites, the amino acid sequences and structures of these proteins are quite different.
Collapse
Affiliation(s)
- Yi-Jan Lin
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, J. W. Goethe-University, Marie-Curie-Strasse 9, D-60439 Frankfurt am Main, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Betz M, Löhr F, Wienk H, Rüterjans H. Long-Range Nature of the Interactions between Titratable Groups in Bacillus agaradhaerens Family 11 Xylanase: pH Titration of B. agaradhaerens Xylanase. Biochemistry 2004; 43:5820-31. [PMID: 15134456 DOI: 10.1021/bi049948m] [Citation(s) in RCA: 16] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Xylanase from Bacillus agaradhaerens belongs to a large group of glycosyl hydrolases which catalyze the degradation of xylan. The protonation behavior of titratable groups of the uniformly (15)N- and (13)C-labeled xylanase was investigated by multinuclear NMR spectroscopy. A total of 224 chemical shift titration curves corresponding to (1)H, (13)C, and (15)N resonances revealed pK(a) values for all aspartic and glutamic acid residues, as well as for the C-terminal carboxylate and histidine residues. Most of the titratable groups exhibit a complex titration behavior, which is most likely due to the mutual interactions with other neighboring groups or due to an unusual local microenvironment. Subsite -1 containing the catalytic dyad shows a long-range interaction over 9 A with Asp21 via two hydrogen bonds with Asn45 as the mediator. This result illuminates the pivotal role of the conserved position 45 among family 11 endoxylanases, determining an alkaline pH optimum by asparagine residues or an acidic pH optimum by an aspartate. The asymmetric interactions of neighboring tryptophan side chains with respect to the catalytic dyad can be comprehended as a result of hydrogen bonding and aromatic stacking. Most of the chemical shift-pH profiles of the backbone amides exhibit biphasic behavior with two distinct inflection points, which correspond to the pK(a) values of the nearby acidic side chains. However, the alternation of both positive and negative slopes of individual amide titration curves is interpreted as a consequence of a simultaneous reorganization of side chain conformational space at pH approximately 6 and/or an overall change in the hydrogen network in the substrate binding cleft.
Collapse
Affiliation(s)
- Marco Betz
- Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Biocentre N230, Marie Curie-Strasse 9, D-60439 Frankfurt am Main, Germany
| | | | | | | |
Collapse
|
42
|
Rogov VV, Lücke C, Muresanu L, Wienk H, Kleinhaus I, Werner K, Löhr F, Pristovsek P, Rüterjans H. Solution structure and stability of the full-length excisionase from bacteriophage HK022. ACTA ACUST UNITED AC 2004; 270:4846-58. [PMID: 14653811 DOI: 10.1111/j.1432-1033.2003.03884.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Heteronuclear high-resolution NMR spectroscopy was employed to determine the solution structure of the excisionase protein (Xis) from the lambda-like bacteriophage HK022 and to study its sequence-specific DNA interaction. As wild-type Xis was previously characterized as a generally unstable protein, a biologically active HK022 Xis mutant with a single amino acid substitution Cys28-->Ser was used in this work. This substitution has been shown to diminish the irreversibility of Xis denaturation and subsequent degradation, but does not affect the structural or thermodynamic properties of the protein, as evidenced by NMR and differential scanning calorimetry. The solution structure of HK022 Xis forms a compact, highly ordered protein core with two well-defined alpha-helices (residues 5-11 and 18-27) and five beta-strands (residues 2-4, 30-31, 35-36, 41-44 and 48-49). These data correlate well with 1H2O-2H2O exchange experiments and imply a different organization of the HK022 Xis secondary structure elements in comparison with the previously determined structure of the bacteriophage lambda excisionase. Superposition of both Xis structures indicates a better correspondence of the full-length HK022 Xis to the typical 'winged-helix' DNA-binding motif, as found, for example, in the DNA-binding domain of the Mu-phage repressor. Residues 51-72, which were not resolved in the lambda Xis, do not show any regular structure in HK022 Xis and thus appear to be completely disordered in solution. The resonance assignments have shown, however, that an unusual connectivity exists between residues Asn66 and Gly67 owing to asparagine-isoaspartyl isomerization. Such an isomerization has been previously observed and characterized only in eukaryotic proteins.
Collapse
Affiliation(s)
- Vladimir V Rogov
- Institute of Biophysical Chemistry, J.W. Goethe-University of Frankfurt, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Wienk H, Maneg O, Lücke C, Pristovsek P, Löhr F, Ludwig B, Rüterjans H. Interaction of cytochrome c with cytochrome c oxidase: an NMR study on two soluble fragments derived from Paracoccus denitrificans. Biochemistry 2003; 42:6005-12. [PMID: 12755602 DOI: 10.1021/bi027198f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The functional interactions between the various components of the respiratory chain are relatively short-lived, thus allowing high turnover numbers but at the same time complicating the structural analysis of the complexes. Chemical shift mapping by NMR spectroscopy is a useful tool to investigate such transient contacts, since it can monitor changes in the electron-shielding properties of a protein as the result of temporary contacts with a reaction partner. In this study, we investigated the molecular interaction between two components of the electron-transfer chain from Paracoccus denitrificans: the engineered, water-soluble fragment of cytochrome c(552) and the Cu(A) domain from the cytochrome c oxidase. Comparison of [(15)N,(1)H]-TROSY spectra of the [(15)N]-labeled cytochrome c(552) fragment in the absence and in the presence of the Cu(A) fragment showed chemical shift changes for the backbone amide groups of several, mostly uncharged residues located around the exposed heme edge in cytochrome c(552). The detected contact areas on the cytochrome c(552) surface were comparable under both fully reduced and fully oxidized conditions, suggesting that the respective chemical shift changes represent biologically relevant protein-protein interactions.
Collapse
Affiliation(s)
- Hans Wienk
- Institute of Biophysical Chemistry, J.W. Goethe-University, Marie-Curie-Strasse 9, D-60439 Frankfurt am Main, Germany
| | | | | | | | | | | | | |
Collapse
|
44
|
Betz M, Löhr F, Wienk H, Rüterjans H. 1H, 13C and 15N chemical shift assignment of Bacillus agaradhaerens family 11 xylanase. J Biomol NMR 2002; 23:333-334. [PMID: 12398358 DOI: 10.1023/a:1020248110530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
|
45
|
Pilon M, Wienk H, Sips W, de Swaaf M, Talboom I, van 't Hof R, de Korte-Kool G, Demel R, Weisbeek P, de Kruijff B. Functional domains of the ferredoxin transit sequence involved in chloroplast import. J Biol Chem 1995; 270:3882-93. [PMID: 7876133 DOI: 10.1074/jbc.270.8.3882] [Citation(s) in RCA: 83] [Impact Index Per Article: 2.9] [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: 01/27/2023] Open
Abstract
In order to analyze the information content of a chloroplast transit sequence, we have constructed and analyzed by in vitro assays seven substitution and 20 deletion mutants of the ferredoxin transit sequence. The N-terminal part and the C-terminal part are important for targeting, and in addition the C-terminal region is required for processing. A third region is important for translocation but not for the initial interaction with the envelope. A fourth region is less essential for in vitro import. Purified precursors were tested for their ability to compete for the in vitro import of radiolabeled wild-type precursor, which confirmed the important role in chloroplast recognition of both the N- and the C-terminal domain of the transit sequence. Monolayer experiments showed that the N terminus was mainly involved in the insertion into mono-galactolipid-containing lipid surfaces whereas the C terminus mediates the recognition of negatively charged lipids. A sequence comparison to other transit sequences suggests that the domain structure of the ferredoxin transit sequence can be extended to these sequences and thus reveals a general structural design of transit sequences.
Collapse
Affiliation(s)
- M Pilon
- Institute of Biomembranes, Utrecht University, The Netherlands
| | | | | | | | | | | | | | | | | | | |
Collapse
|