1
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El Battioui K, Chakraborty S, Wacha A, Molnár D, Quemé-Peña M, Szigyártó IC, Szabó CL, Bodor A, Horváti K, Gyulai G, Bősze S, Mihály J, Jezsó B, Románszki L, Tóth J, Varga Z, Mándity I, Juhász T, Beke-Somfai T. In situ captured antibacterial action of membrane-incising peptide lamellae. Nat Commun 2024; 15:3424. [PMID: 38654023 DOI: 10.1038/s41467-024-47708-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Developing unique mechanisms of action are essential to combat the growing issue of antimicrobial resistance. Supramolecular assemblies combining the improved biostability of non-natural compounds with the complex membrane-attacking mechanisms of natural peptides are promising alternatives to conventional antibiotics. However, for such compounds the direct visual insight on antibacterial action is still lacking. Here we employ a design strategy focusing on an inducible assembly mechanism and utilized electron microscopy (EM) to follow the formation of supramolecular structures of lysine-rich heterochiral β3-peptides, termed lamellin-2K and lamellin-3K, triggered by bacterial cell surface lipopolysaccharides. Combined molecular dynamics simulations, EM and bacterial assays confirmed that the phosphate-induced conformational change on these lamellins led to the formation of striped lamellae capable of incising the cell envelope of Gram-negative bacteria thereby exerting antibacterial activity. Our findings also provide a mechanistic link for membrane-targeting agents depicting the antibiotic mechanism derived from the in-situ formation of active supramolecules.
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Affiliation(s)
- Kamal El Battioui
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Hevesy György Ph.D. School of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Sohini Chakraborty
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - András Wacha
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Dániel Molnár
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Doctoral School of Biology and Institute of Biology, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Mayra Quemé-Peña
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Hevesy György Ph.D. School of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
| | - Imola Cs Szigyártó
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Csenge Lilla Szabó
- Hevesy György Ph.D. School of Chemistry, Eötvös Loránd University, Budapest, H-1117, Hungary
- ELTE Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory, Budapest, H-1117, Hungary
| | - Andrea Bodor
- ELTE Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory, Budapest, H-1117, Hungary
| | - Kata Horváti
- MTA-HUN-REN TTK "Momentum" Peptide-Based Vaccines Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Gergő Gyulai
- MTA-HUN-REN TTK "Momentum" Peptide-Based Vaccines Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- ELTE Eötvös Loránd University, Institute of Chemistry, Laboratory of Interfaces and Nanostructures, Budapest, H-1117, Hungary
| | - Szilvia Bősze
- HUN-REN ELTE Research Group of Peptide Chemistry, Hungarian Research Network, Eötvös Loránd University, Budapest, Hungary
| | - Judith Mihály
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Bálint Jezsó
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Loránd Románszki
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Judit Tóth
- Institute of Molecular Life Sciences, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, H-1111, Hungary
| | - Zoltán Varga
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Department of Physical Chemistry and Materials Science, Budapest University of Technology and Economics, Műegyetem rkp. 3, Budapest, 1111, Hungary
| | - István Mándity
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
- Department of Organic Chemistry, Faculty of Pharmacy, Semmelweis University, Budapest, H-1092, Hungary
| | - Tünde Juhász
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary
| | - Tamás Beke-Somfai
- Institute of Materials and Environmental Chemistry, HUN-REN Research Centre for Natural Sciences, Budapest, H-1117, Hungary.
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2
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Csomos A, Madarász M, Turczel G, Cseri L, Bodor A, Matuscsák A, Katona G, Kovács E, Rózsa B, Mucsi Z. A GFP Inspired 8-Methoxyquinoline-Derived Fluorescent Molecular Sensor for the Detection of Zn 2+ by Two-Photon Microscopy. Chemistry 2024:e202400009. [PMID: 38446718 DOI: 10.1002/chem.202400009] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 03/02/2024] [Accepted: 03/06/2024] [Indexed: 03/08/2024]
Abstract
An effective, GFP-inspired fluorescent Zn2+ sensor is developed for two-photon microscopy and related biological application that features an 8-methoxyquinoline moiety. Excellent photophysical characteristics including a 37-fold fluorescence enhancement with excitation and emission maxima at 440 nm and 505 nm, respectively, as well as a high two-photon cross-section of 73 GM at 880 nm are reported. Based on the experimental data, the relationship between the structure and properties was elucidated and explained backed up by DFT calculations, particularly the observed PeT phenomenon for the turn-on process. Biological validation and detailed experimental and theoretical characterization of the free and the zinc-bound compounds are presented.
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Affiliation(s)
- Attila Csomos
- Femtonics Ltd., Tűzoltó utca 59, H-1094, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
| | - Miklós Madarász
- BrainVisionCenter, Liliom utca 43-45, H-1094, Budapest, Hungary
| | - Gábor Turczel
- NMR Research Laboratory, HUN-REN Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117, Budapest, Hungary
| | - Levente Cseri
- BrainVisionCenter, Liliom utca 43-45, H-1094, Budapest, Hungary
- Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Műegyetem rakpart 3, H-1111, Budapest, Hungary
| | - Andrea Bodor
- Analytical and BioNMR Laboratory, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
| | - Anett Matuscsák
- Laboratory of 3D functional network and dendritic imaging, HUN-REN Institute of Experimental Medicine, Szigony utca 43, H-1083, Budapest, Hungary
| | - Gergely Katona
- Two-Photon Measurement Technology Research Group, Pázmány Péter Catholic University Práter, utca 50/a, H-1083, Budapest, Hungary
| | - Ervin Kovács
- Two-Photon Measurement Technology Research Group, Pázmány Péter Catholic University Práter, utca 50/a, H-1083, Budapest, Hungary
- Polymer Chemistry and Physics Research Group, HUN-REN Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117, Budapest, Hungary
| | - Balázs Rózsa
- BrainVisionCenter, Liliom utca 43-45, H-1094, Budapest, Hungary
- Laboratory of 3D functional network and dendritic imaging, HUN-REN Institute of Experimental Medicine, Szigony utca 43, H-1083, Budapest, Hungary
- Two-Photon Measurement Technology Research Group, Pázmány Péter Catholic University Práter, utca 50/a, H-1083, Budapest, Hungary
| | - Zoltán Mucsi
- Femtonics Ltd., Tűzoltó utca 59, H-1094, Budapest, Hungary
- BrainVisionCenter, Liliom utca 43-45, H-1094, Budapest, Hungary
- Faculty of Materials and Chemical Sciences, University of Miskolc, H-3515, Miskolc, Hungary
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3
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Sebák F, Ecsédi P, Nyitray L, Bodor A. Assignment of the disordered, proline-rich N-terminal domain of the tumour suppressor p53 protein using 1H N and 1H α-detected NMR measurements. Biomol NMR Assign 2023; 17:309-314. [PMID: 37861971 PMCID: PMC10630184 DOI: 10.1007/s12104-023-10160-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/07/2023] [Indexed: 10/21/2023]
Abstract
Protein p53 is mostly known for playing a key role in tumour suppression, and mutations in the p53 gene are amongst the most frequent genomic events accompanying oncogenic transformation. Continuous research is conducted to target disordered proteins/protein regions for cancer therapy, for which atomic level information is also necessary. The disordered N-terminal part of p53 contains the transactivation and the proline-rich domains-which besides being abundant in proline residues-contains repetitive Pro-Ala motifs. NMR assignment of such repetitive, proline-rich regions is challenging due to the lack of amide protons in the 1HN-detected approaches, as well as due to the small chemical shift dispersion. In the present study we perform the full assignment of the p531-100 region by applying a combination of 1HN- and 1Hα-detected NMR experiments. We also show the increased information content when using real-time homo- and heteronuclear decoupled acquisition schemes. On the other hand, we highlight the presence of minor proline species, and using Pro-selective experiments we determine the corresponding cis or trans conformation. Secondary chemical shifts for (Cα-Cβ) atoms indicate the disordered nature of this region, with expected helical tendency for the TAD1 region. As the role of the proline-rich domain is yet not well understood our results can contribute to further successful investigations.
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Affiliation(s)
- Fanni Sebák
- Analytical and BioNMR Laboratory, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest, 1117, Hungary
| | - Péter Ecsédi
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest, 1117, Hungary
| | - Andrea Bodor
- Analytical and BioNMR Laboratory, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest, 1117, Hungary.
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4
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Sebák F, Szolomájer J, Papp N, Tóth GK, Bodor A. Proline cis/trans Isomerization in Intrinsically Disordered Proteins and Peptides. FRONT BIOSCI-LANDMRK 2023; 28:127. [PMID: 37395034 DOI: 10.31083/j.fbl2806127] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/15/2023] [Accepted: 05/26/2023] [Indexed: 07/04/2023]
Abstract
BACKGROUND Intrinsically disordered proteins and protein regions (IDPs/IDRs) are important in diverse biological processes. Lacking a stable secondary structure, they display an ensemble of conformations. One factor contributing to this conformational heterogeneity is the proline cis/trans isomerization. The knowledge and value of a given cis/trans proline ratio are paramount, as the different conformational states can be responsible for different biological functions. Nuclear Magnetic Resonance (NMR) spectroscopy is the only method to characterize the two co-existing isomers on an atomic level, and only a few works report on these data. METHODS After collecting the available experimental literature findings, we conducted a statistical analysis regarding the influence of the neighboring amino acid types (i ± 4 regions) on forming a cis-Pro isomer. Based on this, several regularities were formulated. NMR spectroscopy was then used to define the cis-Pro content on model peptides and desired point mutations. RESULTS Analysis of NMR spectra prove the dependence of the cis-Pro content on the type of the neighboring amino acid-with special attention on aromatic and positively charged sidechains. CONCLUSIONS Our results may benefit the design of protein regions with a given cis-Pro content, and contribute to a better understanding of the roles and functions of IDPs.
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Affiliation(s)
- Fanni Sebák
- Analytical and BioNMR Laboratory, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
| | - János Szolomájer
- Department of Medical Chemistry, University of Szeged, 6720 Szeged, Hungary
| | - Nándor Papp
- Analytical and BioNMR Laboratory, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Gábor K Tóth
- Department of Medical Chemistry, University of Szeged, 6720 Szeged, Hungary
| | - Andrea Bodor
- Analytical and BioNMR Laboratory, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
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5
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Kovács D, Bodor A. The influence of random-coil chemical shifts on the assessment of structural propensities in folded proteins and IDPs. RSC Adv 2023; 13:10182-10203. [PMID: 37006359 PMCID: PMC10065145 DOI: 10.1039/d3ra00977g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
In studying secondary structural propensities of proteins by nuclear magnetic resonance (NMR) spectroscopy, secondary chemical shifts (SCSs) serve as the primary atomic scale observables. For SCS calculation, the selection of an appropriate random coil chemical shift (RCCS) dataset is a crucial step, especially when investigating intrinsically disordered proteins (IDPs). The scientific literature is abundant in such datasets, however, the effect of choosing one over all the others in a concrete application has not yet been studied thoroughly and systematically. Hereby, we review the available RCCS prediction methods and to compare them, we conduct statistical inference by means of the nonparametric sum of ranking differences and comparison of ranks to random numbers (SRD-CRRN) method. We try to find the RCCS predictors best representing the general consensus regarding secondary structural propensities. The existence and the magnitude of resulting differences on secondary structure determination under varying sample conditions (temperature, pH) are demonstrated and discussed for globular proteins and especially IDPs.
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Affiliation(s)
- Dániel Kovács
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
- Eötvös Loránd University, Hevesy György PhD School of Chemistry Pázmány Péter sétány 1/A Budapest 1117 Hungary
| | - Andrea Bodor
- ELTE, Eötvös Loránd University, Institute of Chemistry, Analytical and BioNMR Laboratory Pázmány Péter sétány 1/A Budapest 1117 Hungary
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6
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Gamlin CR, Schneider-Mizell CM, Mallory M, Elabbady L, Gouwens N, Williams G, Mukora A, Dalley R, Bodor A, Brittain D, Buchanan J, Bumbarger D, Kapner D, Kinn S, Mahalingam G, Seshamani S, Takeno M, Torres R, Yin W, Nicovich PR, Bae JA, Castro MA, Dorkenwald S, Halageri A, Jia Z, Jordan C, Kemnitz N, Lee K, Li K, Lu R, Macrina T, Mitchell E, Mondal SS, Mu S, Nehoran B, Popovych S, Silversmith W, Turner NL, Wong W, Wu J, Yu S, Berg J, Jarsky T, Lee B, Seung HS, Zeng H, Reid RC, Collman F, da Costa NM, Sorensen SA. Integrating EM and Patch-seq data: Synaptic connectivity and target specificity of predicted Sst transcriptomic types. bioRxiv 2023:2023.03.22.533857. [PMID: 36993629 PMCID: PMC10055412 DOI: 10.1101/2023.03.22.533857] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Neural circuit function is shaped both by the cell types that comprise the circuit and the connections between those cell types 1 . Neural cell types have previously been defined by morphology 2, 3 , electrophysiology 4, 5 , transcriptomic expression 6-8 , connectivity 9-13 , or even a combination of such modalities 14-16 . More recently, the Patch-seq technique has enabled the characterization of morphology (M), electrophysiology (E), and transcriptomic (T) properties from individual cells 17-20 . Using this technique, these properties were integrated to define 28, inhibitory multimodal, MET-types in mouse primary visual cortex 21 . It is unknown how these MET-types connect within the broader cortical circuitry however. Here we show that we can predict the MET-type identity of inhibitory cells within a large-scale electron microscopy (EM) dataset and these MET-types have distinct ultrastructural features and synapse connectivity patterns. We found that EM Martinotti cells, a well defined morphological cell type 22, 23 known to be Somatostatin positive (Sst+) 24, 25 , were successfully predicted to belong to Sst+ MET-types. Each identified MET-type had distinct axon myelination patterns and synapsed onto specific excitatory targets. Our results demonstrate that morphological features can be used to link cell type identities across imaging modalities, which enables further comparison of connectivity in relation to transcriptomic or electrophysiological properties. Furthermore, our results show that MET-types have distinct connectivity patterns, supporting the use of MET-types and connectivity to meaningfully define cell types.
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7
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Haller JD, Bodor A, Luy B. Pure shift amide detection in conventional and TROSY-type experiments of 13C, 15N-labeled proteins. J Biomol NMR 2022; 76:213-221. [PMID: 36399207 PMCID: PMC9712348 DOI: 10.1007/s10858-022-00406-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Large coupling networks in uniformly 13C,15N-labeled biomolecules induce broad multiplets that even in flexible proteins are frequently not recognized as such. The reason is that given multiplets typically consist of a large number of individual resonances that result in a single broad line, in which individual components are no longer resolved. We here introduce a real-time pure shift acquisition scheme for the detection of amide protons which is based on 13C-BIRDr,X. As a result the full homo- and heteronuclear coupling network can be suppressed at low power leading to real singlets at substantially improved resolution and uncompromised sensitivity. The method is tested on a small globular and an intrinsically disordered protein (IDP) where the average spectral resolution is increased by a factor of ~ 2 and higher. Equally important, the approach works without saturation of water magnetization for solvent suppression and exchanging amide protons are not affected by saturation transfer.
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Affiliation(s)
- Jens D. Haller
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Hermann-Von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andrea Bodor
- Institute of Chemistry, Analytical and BioNMR Laboratory, ELTE –Eötvös Loránd University, Pázmány Péter Sétány 1/A, 1117 Budapest, Hungary
| | - Burkhard Luy
- Institute of Organic Chemistry and Institute for Biological Interfaces 4 – Magnetic Resonance, Karlsruhe Institute of Technology (KIT), Hermann-Von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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8
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Szabó CL, Sebák F, Bodor A. Monitoring Protein Global and Local Parameters in Unfolding and Binding Studies: The Extended Applicability of the Diffusion Coefficient─Molecular Size Empirical Relations. Anal Chem 2022; 94:7885-7891. [PMID: 35617314 DOI: 10.1021/acs.analchem.2c00481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Protein unfolding and denaturation are main issues in biochemical and pharmaceutical research. Using a global parameter, the translational diffusion coefficient D, folded, unfolded, and intrinsically disordered proteins of a given molar mass M can be distinguished based on their distinct hydrodynamic properties. For broader applications, we provide generalized, PFG-NMR-based empirical D-M relations validated at different temperatures and ready to use with the corresponding corrections in different media. We demonstrate that these relations enable a more accurate molecular mass determination and show fewer potential errors than those of the common methods based on small-molecular diffusion standards. We monitor unfolding of three model proteins using 8 M urea and dimethyl sulfoxide (DMSO)-water mixtures as denaturing agents, highlighting the effect of disulfide bonds. Denaturation in 8 M urea is pH-dependent; in addition, for proteins with highly stable disulfide bonds, a reducing agent (TCEP) is required to achieve complete unfolding. Regarding the effect of local parameters, we show that at low DMSO concentrations─common conditions in pharmaceutical binding studies─the PFG-NMR-derived global parameters are not significantly affected. Still, the atomic environments can change, and the bound solvent molecule can inhibit the binding of a partner molecule. Using proteins with natural isotopic abundance, this effect can be proven by fast 1H-15N 2D correlation spectra. Our results enable fast and easy estimation of protein molecular mass and the degree of folding in various media; moreover, the effect of the cosolvent on the atomic-level structure can be traced without the need of isotope labeling.
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Affiliation(s)
- Csenge Lilla Szabó
- Institute of Chemistry, Analytical and BioNMR Laboratory, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary.,Hevesy György PhD School of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Fanni Sebák
- Institute of Chemistry, Analytical and BioNMR Laboratory, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Andrea Bodor
- Institute of Chemistry, Analytical and BioNMR Laboratory, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
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9
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Sebák F, Ecsédi P, Bermel W, Luy B, Nyitray L, Bodor A. Selective
1
H
α
NMR Methods Reveal Functionally Relevant Proline
cis/trans
Isomers in Intrinsically Disordered Proteins: Characterization of Minor Forms, Effects of Phosphorylation, and Occurrence in Proteome. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202108361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Fanni Sebák
- Eötvös Loránd University Institute of Chemistry Pázmány Péter s. 1/a 1117 Budapest Hungary
- Semmelweis University Doctoral School of Pharmaceutical Sciences Üllői út 26 1085 Budapest Hungary
| | - Péter Ecsédi
- Eötvös Loránd University Department of Biochemistry Pázmány Péter s. 1/c 1117 Budapest Hungary
| | - Wolfgang Bermel
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Germany
| | - Burkhard Luy
- KIT-Institut für Organische Chemie IBG4—Magnetische Resonanz Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - László Nyitray
- Eötvös Loránd University Department of Biochemistry Pázmány Péter s. 1/c 1117 Budapest Hungary
| | - Andrea Bodor
- Eötvös Loránd University Institute of Chemistry Pázmány Péter s. 1/a 1117 Budapest Hungary
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10
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Sebák F, Horváth LB, Kovács D, Szolomájer J, Tóth GK, Babiczky Á, Bősze S, Bodor A. Novel Lysine-Rich Delivery Peptides of Plant Origin ERD and Human S100: The Effect of Carboxyfluorescein Conjugation, Influence of Aromatic and Proline Residues, Cellular Internalization, and Penetration Ability. ACS Omega 2021; 6:34470-34484. [PMID: 34963932 PMCID: PMC8697381 DOI: 10.1021/acsomega.1c04637] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/25/2021] [Indexed: 06/14/2023]
Abstract
The need for novel drug delivery peptides is an important issue of the modern pharmaceutical research. Here, we test K-rich peptides from plant dehydrin ERD14 (ERD-A, ERD-B, and ERD-C) and the C-terminal CPP-resembling region of S100A4 (S100) using the 5(6)-carboxyfluorescein (Cf) tag at the N-terminus. Via a combined pH-dependent NMR and fluorescence study, we analyze the effect of the Cf conjugation/modification on the structural behavior, separately investigating the (5)-Cf and (6)-Cf forms. Flow cytometry results show that all peptides internalize; however, there is a slight difference between the cellular internalization of (5)- and (6)-Cf-peptides. We indicate the possible importance of residues with an aromatic sidechain and proline. We prove that ERD-A localizes mostly in the cytosol, ERD-B and S100 have partial colocalization with lysosomal staining, and ERD-C mainly localizes within vesicle-like compartments, while the uptake mechanism mainly occurs through energy-dependent paths.
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Affiliation(s)
- Fanni Sebák
- Institute
of Chemistry, ELTE−Eötvös
Loránd University, Pázmány Péter sétány 1/a, H-1117 Budapest, Hungary
- Doctoral
School of Pharmaceutical Sciences, Semmelweis
University, Üllői
út 26, H-1085 Budapest, Hungary
| | - Lilla Borbála Horváth
- ELKH-ELTE
Research Group of Peptide Chemistry, Eötvös Loránd
Research Network, Eötvös Loránd
University, Pázmány Péter sétány 1/a, H-1117 Budapest, Hungary
- National
Public Health Center, Albert Flórián út 2-6, Budapest H-1097, Hungary
- Hevesy
György PhD School of Chemistry, ELTE
Eötvös Loránd University, Pázmány Péter sétány
1/a, H-1117 Budapest, Hungary
| | - Dániel Kovács
- Institute
of Chemistry, ELTE−Eötvös
Loránd University, Pázmány Péter sétány 1/a, H-1117 Budapest, Hungary
- Hevesy
György PhD School of Chemistry, ELTE
Eötvös Loránd University, Pázmány Péter sétány
1/a, H-1117 Budapest, Hungary
| | - János Szolomájer
- Department
of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Gábor K. Tóth
- Department
of Medical Chemistry, University of Szeged, Dóm tér 8, H-6720 Szeged, Hungary
| | - Ákos Babiczky
- Institute
of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
- Doctoral
School of Psychology/Cognitive Science, Budapest University of Technology and Economics, Műegyetem rakpart 3, H-1111 Budapest, Hungary
| | - Szilvia Bősze
- ELKH-ELTE
Research Group of Peptide Chemistry, Eötvös Loránd
Research Network, Eötvös Loránd
University, Pázmány Péter sétány 1/a, H-1117 Budapest, Hungary
- National
Public Health Center, Albert Flórián út 2-6, Budapest H-1097, Hungary
| | - Andrea Bodor
- Institute
of Chemistry, ELTE−Eötvös
Loránd University, Pázmány Péter sétány 1/a, H-1117 Budapest, Hungary
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11
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Sebák F, Ecsédi P, Bermel W, Luy B, Nyitray L, Bodor A. Selective 1 H α NMR Methods Reveal Functionally Relevant Proline cis/trans Isomers in Intrinsically Disordered Proteins: Characterization of Minor Forms, Effects of Phosphorylation, and Occurrence in Proteome. Angew Chem Int Ed Engl 2021; 61:e202108361. [PMID: 34585830 PMCID: PMC9299183 DOI: 10.1002/anie.202108361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 06/23/2021] [Revised: 09/21/2021] [Indexed: 11/30/2022]
Abstract
It is important to identify proline cis/trans isomers that appear in several regulatory mechanisms of proteins, and to characterize minor species that are present due to the conformational heterogeneity in intrinsically disordered proteins (IDPs). To obtain residue level information on these mobile systems we introduce two 1Hα‐detected, proline selective, real‐time homodecoupled NMR experiments and analyze the proline abundant transactivation domain of p53. The measurements are sensitive enough to identify minor conformers present in 4–15 % amounts; moreover, we show the consequences of CK2 phosphorylation on the cis/trans‐proline equilibrium. Using our results and available literature data we perform a statistical analysis on how the amino acid type effects the cis/trans‐proline distribution. The methods are applicable under physiological conditions, they can contribute to find key proline isomers in proteins, and statistical analysis results may help in amino acid sequence optimization for biotechnological purposes.
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Affiliation(s)
- Fanni Sebák
- Eötvös Loránd University, Institute of Chemistry, Pázmány Péter s. 1/a, 1117, Budapest, Hungary.,Semmelweis University, Doctoral School of Pharmaceutical Sciences, Üllői út 26, 1085, Budapest, Hungary
| | - Péter Ecsédi
- Eötvös Loránd University, Department of Biochemistry, Pázmány Péter s. 1/c, 1117, Budapest, Hungary
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287, Rheinstetten, Germany
| | - Burkhard Luy
- KIT-Institut für Organische Chemie, IBG4-Magnetische Resonanz, Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - László Nyitray
- Eötvös Loránd University, Department of Biochemistry, Pázmány Péter s. 1/c, 1117, Budapest, Hungary
| | - Andrea Bodor
- Eötvös Loránd University, Institute of Chemistry, Pázmány Péter s. 1/a, 1117, Budapest, Hungary
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12
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Dudás EF, Pálfy G, Menyhárd DK, Sebák F, Ecsédi P, Nyitray L, Bodor A. Front Cover: Tumor‐Suppressor p53TAD
1–60
Forms a Fuzzy Complex with Metastasis‐Associated S100A4: Structural Insights and Dynamics by an NMR/MD Approach (ChemBioChem 21/2020). Chembiochem 2020. [DOI: 10.1002/cbic.202000696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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)
- Erika F. Dudás
- Laboratory of Structural Chemistry and Biology Eötvös Loránd University Pázmány Péter sétány 1/a Budapest 1117 Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and Biology Eötvös Loránd University Pázmány Péter sétány 1/a Budapest 1117 Hungary
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and Biology Eötvös Loránd University Pázmány Péter sétány 1/a Budapest 1117 Hungary
- MTA-ELTE Protein Modelling Research Group Pázmány Péter sétány. 1/a Budapest 1117 Hungary
| | - Fanni Sebák
- Laboratory of Structural Chemistry and Biology Eötvös Loránd University Pázmány Péter sétány 1/a Budapest 1117 Hungary
- Doctoral School of Pharmaceutical Sciences Semmelweis University Üllői út 26 Budapest 1085 Hungary
| | - Péter Ecsédi
- Department of Biochemistry Eötvös Loránd University Pázmány Péter sétány 1/c Budapest 1117 Hungary
| | - László Nyitray
- Department of Biochemistry Eötvös Loránd University Pázmány Péter sétány 1/c Budapest 1117 Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology Eötvös Loránd University Pázmány Péter sétány 1/a Budapest 1117 Hungary
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13
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Dudás EF, Pálfy G, Menyhárd DK, Sebák F, Ecsédi P, Nyitray L, Bodor A. Tumor-Suppressor p53TAD 1-60 Forms a Fuzzy Complex with Metastasis-Associated S100A4: Structural Insights and Dynamics by an NMR/MD Approach. Chembiochem 2020; 21:3087-3095. [PMID: 32511842 PMCID: PMC7689910 DOI: 10.1002/cbic.202000348] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Indexed: 01/05/2023]
Abstract
Conformationally flexible protein complexes represent a major challenge for structural and dynamical studies. We present herein a method based on a hybrid NMR/MD approach to characterize the complex formed between the disordered p53TAD1-60 and the metastasis-associated S100A4. Disorder-to-order transitions of both TAD1 and TAD2 subdomains upon interaction is detected. Still, p53TAD1-60 remains highly flexible in the bound form, with residues L26, M40, and W53 being anchored to identical hydrophobic pockets of the S100A4 monomer chains. In the resulting "fuzzy" complex, the clamp-like binding of p53TAD1-60 relies on specific hydrophobic anchors and on the existence of extended flexible segments. Our results demonstrate that structural and dynamical NMR parameters (cumulative Δδ, SSP, temperature coefficients, relaxation time, hetNOE) combined with MD simulations can be used to build a structural model even if, due to high flexibility, the classical solution structure calculation is not possible.
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Affiliation(s)
- Erika F. Dudás
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
| | - Gyula Pálfy
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
| | - Dóra K. Menyhárd
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
- MTA-ELTE Protein Modelling Research GroupPázmány Péter sétány. 1/aBudapest1117Hungary
| | - Fanni Sebák
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
- Doctoral School of Pharmaceutical SciencesSemmelweis UniversityÜllői út 26Budapest1085Hungary
| | - Péter Ecsédi
- Department of BiochemistryEötvös Loránd UniversityPázmány Péter sétány 1/cBudapest1117Hungary
| | - László Nyitray
- Department of BiochemistryEötvös Loránd UniversityPázmány Péter sétány 1/cBudapest1117Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and BiologyEötvös Loránd UniversityPázmány Péter sétány 1/aBudapest1117Hungary
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14
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Bodor A, Haller JD, Bouguechtouli C, Theillet FX, Nyitray L, Luy B. Power of Pure Shift HαCα Correlations: A Way to Characterize Biomolecules under Physiological Conditions. Anal Chem 2020; 92:12423-12428. [PMID: 32786451 DOI: 10.1021/acs.analchem.0c02182] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intrinsically disordered proteins (IDPs) constitute an important class of biomolecules with high flexibility. Atomic-resolution studies for these molecules are essentially limited to NMR spectroscopy, which should be performed under physiological pH and temperature to populate relevant conformational ensembles. In this context, however, fundamental problems arise with established triple resonance NMR experiments: high solvent accessibility of IDPs promotes water exchange, which disfavors classical amide 1H-detection, while 13C-detection suffers from significantly reduced sensitivity. A favorable alternative, the conventional detection of nonexchangeable 1Hα, so far resulted in broad signals with insufficient resolution and sensitivity. To overcome this, we introduce here a selective Hα,Cα-correlating pure shift detection scheme, the selective Hα,Cα-HSQC (SHACA-HSQC), using extensive hetero- and homonuclear decoupling applicable to aqueous samples (≥90% H2O) and tested on small molecules and proteins. SHACA-HSQC spectra acquired on IDPs provide uncompromised resolution and sensitivity (up to fivefold increased S/N compared to the standard 1H,13C-HSQC), as shown for resonance distinction and unambiguous assignment on the disordered transactivation domain of the tumor suppressor p53, α-synuclein, and folded ubiquitin. The detection scheme can be implemented in any 1Hα-detected triple resonance experiment and may also form the basis for the detection of isotope-labeled markers in biological studies or compound libraries.
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Affiliation(s)
- Andrea Bodor
- Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Jens D Haller
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4-Magnetische Resonanz, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, Karlsruhe 76133, Germany
| | - Chafiaa Bouguechtouli
- Institute of Integrative Biology of the Cell, UMR9198, CNRS/CEA/ University of Paris Saclay, Gif-Sur-Yvette 911991, France
| | - Francois-Xavier Theillet
- Institute of Integrative Biology of the Cell, UMR9198, CNRS/CEA/ University of Paris Saclay, Gif-Sur-Yvette 911991, France
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/c, Budapest 1117, Hungary
| | - Burkhard Luy
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4-Magnetische Resonanz, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, Karlsruhe 76133, Germany
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15
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F Dudás E, Wacha A, Bóta A, Bodor A. Peptide-bicelle interaction: Following variations in size and morphology by a combined NMR-SAXS approach. Biochim Biophys Acta Biomembr 2020; 1862:183095. [PMID: 31672542 DOI: 10.1016/j.bbamem.2019.183095] [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] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/25/2019] [Accepted: 10/16/2019] [Indexed: 10/25/2022]
Abstract
Changes in membrane properties occurring upon protein interaction are key questions in understanding membrane protein function. To report on the occurring size and shape variation we present here a combined NMR-SAXS method performed under physiological conditions using the same samples, enabling determination of a global parameter, the hydration radius (rH) and estimating the bicelle shape. We use zwitterionic (DMPC/DHPC) and negatively charged (DMPC/DHPC/DMPG) bicelles and investigate the interaction with model transmembrane and surface active peptides (KALP23 and melittin). 1H NMR measurements based mostly on the translational diffusion coefficient D determination are used to characterize cmc values of DHPC micelles under the investigated conditions, to describe DHPC distribution with exact determination of the q (long chain/short chain) lipid ratio, to estimate aggregation numbers and effective rH values. The scattering curve is used to fit a lenticular core-shell model enabling us to describe the bicelle shape in terms of ellipsoidal axis length parameters. For all studied systems formation of oblate ellipsoids is found. Even though the rG/rH ratio would be an elegant way to characterize shape variations, we show that changes occurring upon peptide-bicelle interaction in the "effective" size and in the measure on the anisometry - morphology - of the objects can be described by using rH and the simplistic ellipsoidal core-shell model. While the influence of the transmembrane KALP peptide is significant, effects upon addition of surface active melittin peptide seem negligible. This synergy of techniques under controlled conditions can provide information about bicellar shape modulation occurring during peptide-bicelle interactions.
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Affiliation(s)
- E F Dudás
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - A Wacha
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bóta
- Institute for Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary
| | - A Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary.
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16
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Haller JD, Bodor A, Luy B. Real-time pure shift measurements for uniformly isotope-labeled molecules using X-selective BIRD homonuclear decoupling. J Magn Reson 2019; 302:64-71. [PMID: 30965191 DOI: 10.1016/j.jmr.2019.03.011] [Citation(s) in RCA: 5] [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] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
We introduce a novel selective inversion element for chunked homonuclear decoupling that combines isotope selection via BIRD-filtering with band-selective inversion on the X-heteronucleus and allows efficient real-time decoupling of homonuclear and heteronuclear couplings. It is especially suitable for uniformly isotope-labeled compounds. We discuss in detail the inversion element based on band-selective refocusing on the X-nuclei (BASEREX), highlighting in particular the role of appropriate band-selective shaped refocusing pulses and the application of broadband X-pulses for an effective BIRDd element during homodecoupling. The approach is experimentally verified and studied in detail using uniformly 13C-labeled glucose and a uniformly 15N,13C-labeled amino acid mixture.
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Affiliation(s)
- Jens D Haller
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76133 Karlsruhe, Germany
| | - Andrea Bodor
- Eötvös Loránd University, Institute of Chemistry, Laboratory of Structural Chemistry and Biology, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Burkhard Luy
- Institut für Organische Chemie and Institut für Biologische Grenzflächen 4 - Magnetische Resonanz, Karlsruher Institut für Technologie (KIT), Fritz-Haber-Weg 6, 76133 Karlsruhe, Germany.
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17
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Affiliation(s)
- Erika F. Dudás
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/a, Budapest 1117, Hungary
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18
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Boros E, Sebák F, Héja D, Szakács D, Zboray K, Schlosser G, Micsonai A, Kardos J, Bodor A, Pál G. Directed Evolution of Canonical Loops and Their Swapping between Unrelated Serine Proteinase Inhibitors Disprove the Interscaffolding Additivity Model. J Mol Biol 2019; 431:557-575. [PMID: 30543823 DOI: 10.1016/j.jmb.2018.12.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 07/08/2018] [Revised: 11/26/2018] [Accepted: 12/06/2018] [Indexed: 11/26/2022]
Abstract
Reversible serine proteinase inhibitors comprise 18 unrelated families. Each family has a distinct representative structure but contains a surface loop that adopts the same, canonical conformation in the enzyme-inhibitor complex. The Laskowski mechanism universally applies for the action of all canonical inhibitors independent of their scaffold, but it has two nontrivial extrapolations. Intrascaffolding additivity states that all enzyme-contacting loop residues act independently of each other, while interscaffolding additivity claims that these residues act independently of the scaffold. These theories have great importance for engineering proteinase inhibitors but have not been comprehensively challenged. Therefore, we tested the interscaffolding additivity theory by hard-randomizing all enzyme-contacting canonical loop positions of a Kazal- and a Pacifastin-scaffold inhibitor, displaying the variants on M13 phage, and selecting the libraries on trypsin and chymotrypsin. Directed evolution delivered different patterns on both scaffolds against both enzymes, which contradicts interscaffolding additivity. To quantitatively assess the extent of non-additivity, we measured the affinities of the optimal binding loop variants and their binding loop-swapped versions. While optimal variants have picomolar affinities, swapping the evolved loops results in up to 200,000-fold affinity loss. To decipher the underlying causes, we characterized the stability, overall structure and dynamics of the inhibitors with differential scanning calorimetry, circular dichroism and NMR spectroscopy and molecular dynamic simulations. These studies revealed that the foreign loop destabilizes the lower-stability Pacifastin scaffold, while the higher-stability Kazal scaffold distorts the foreign loop. Our findings disprove interscaffolding additivity and show that loop and scaffold form one integrated unit that needs to be coevolved to provide high-affinity inhibition.
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Affiliation(s)
- Eszter Boros
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Fanni Sebák
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary; Doctoral School of Pharmaceutical Sciences, Semmelweis University, Üllői út 26, H-1085 Budapest, Hungary
| | - Dávid Héja
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Dávid Szakács
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Katalin Zboray
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Gitta Schlosser
- Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - András Micsonai
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - József Kardos
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117 Budapest, Hungary
| | - Gábor Pál
- Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, H-1117 Budapest, Hungary.
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19
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Bounedjoum N, Bodor A, Laczi K, Kis ÁE, Rákhely G, Perei K. Assessment of potentially functional hydrocarbon-degrader bacterial communities in response to Micrococcus luteus EOM using culture-dependent and culture-independent methods. N Biotechnol 2018. [DOI: 10.1016/j.nbt.2018.05.1091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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20
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Ecsédi P, Billington N, Pálfy G, Gógl G, Kiss B, Bulyáki É, Bodor A, Sellers JR, Nyitray L. Multiple S100 protein isoforms and C-terminal phosphorylation contribute to the paralog-selective regulation of nonmuscle myosin 2 filaments. J Biol Chem 2018; 293:14850-14867. [PMID: 30087119 PMCID: PMC6153290 DOI: 10.1074/jbc.ra118.004277] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/06/2018] [Indexed: 12/27/2022] Open
Abstract
Nonmuscle myosin 2 (NM2) has three paralogs in mammals, NM2A, NM2B, and NM2C, which have both unique and overlapping functions in cell migration, formation of cell-cell adhesions, and cell polarity. Their assembly into homo- and heterotypic bipolar filaments in living cells is primarily regulated by phosphorylation of the N-terminally bound regulatory light chain. Here, we present evidence that the equilibrium between these filaments and single NM2A and NM2B molecules can be controlled via S100 calcium-binding protein interactions and phosphorylation at the C-terminal end of the heavy chains. Furthermore, we show that in addition to S100A4, other members of the S100 family can also mediate disassembly of homotypic NM2A filaments. Importantly, these proteins can selectively remove NM2A molecules from heterotypic filaments. We also found that tail phosphorylation (at Ser-1956 and Ser-1975) of NM2B by casein kinase 2, as well as phosphomimetic substitutions at sites targeted by protein kinase C (PKC) and transient receptor potential cation channel subfamily M member 7 (TRPM7), down-regulates filament assembly in an additive fashion. Tail phosphorylation of NM2A had a comparatively minor effect on filament stability. S100 binding and tail phosphorylation therefore preferentially disassemble NM2A and NM2B, respectively. These two distinct mechanisms are likely to contribute to the temporal and spatial sorting of the two NM2 paralogs within heterotypic filaments. The existence of multiple NM2A-depolymerizing S100 paralogs offers the potential for diverse regulatory inputs modulating NM2A filament disassembly in cells and provides functional redundancy under both physiological and pathological conditions.
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Affiliation(s)
| | - Neil Billington
- the Laboratory of Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
| | - Gyula Pálfy
- the Laboratory of Structural Chemistry and Biology, Institute of Chemistry, and
| | | | | | - Éva Bulyáki
- From the Department of Biochemistry
- the ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, ELTE Eötvös Loránd University, Pázmány Péter Sétány 1/C, 1117 Budapest, Hungary and
| | - Andrea Bodor
- the Laboratory of Structural Chemistry and Biology, Institute of Chemistry, and
| | - James R Sellers
- the Laboratory of Physiology, NHLBI, National Institutes of Health, Bethesda, Maryland 20892
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21
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Gógl G, Biri-Kovács B, Póti ÁL, Vadászi H, Szeder B, Bodor A, Schlosser G, Ács A, Turiák L, Buday L, Alexa A, Nyitray L, Reményi A. Dynamic control of RSK complexes by phosphoswitch-based regulation. FEBS J 2017; 285:46-71. [PMID: 29083550 DOI: 10.1111/febs.14311] [Citation(s) in RCA: 20] [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: 09/06/2017] [Revised: 10/18/2017] [Accepted: 10/25/2017] [Indexed: 12/19/2022]
Abstract
Assembly and disassembly of protein-protein complexes needs to be dynamically controlled and phosphoswitches based on linear motifs are crucial in this process. Extracellular signal-regulated kinase 2 (ERK2) recognizes a linear-binding motif at the C-terminal tail (CTT) of ribosomal S6 kinase 1 (RSK1), leading to phosphorylation and subsequent activation of RSK1. The CTT also contains a classical PDZ domain-binding motif which binds RSK substrates (e.g. MAGI-1). We show that autophosphorylation of the disordered CTT promotes the formation of an intramolecular charge clamp, which efficiently masks critical residues and indirectly hinders ERK binding. Thus, RSK1 CTT operates as an autoregulated phosphoswitch: its phosphorylation at specific sites affects its protein-binding capacity and its conformational dynamics. These biochemical feedbacks, which form the structural basis for the rapid dissociation of ERK2-RSK1 and RSK1-PDZ substrate complexes under sustained epidermal growth factor (EGF) stimulation, were structurally characterized and validated in living cells. Overall, conformational changes induced by phosphorylation in disordered regions of protein kinases, coupled to allosteric events occurring in the kinase domain cores, may provide mechanisms that contribute to the emergence of complex signaling activities. In addition, we show that phosphoswitches based on linear motifs can be functionally classified as ON and OFF protein-protein interaction switches or dimmers, depending on the specific positioning of phosphorylation target sites in relation to functional linear-binding motifs. Moreover, interaction of phosphorylated residues with positively charged residues in disordered regions is likely to be a common mechanism of phosphoregulation. DATABASE Structural data are available in the PDB database under the accession numbers 5N7D, 5N7F and 5N7G. NMR spectral assignation data are available in the BMRB database under the accession numbers 27213 and 27214.
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Affiliation(s)
- Gergő Gógl
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary.,Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Beáta Biri-Kovács
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Ádám L Póti
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Henrietta Vadászi
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Bálint Szeder
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Gitta Schlosser
- MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, ELTE Eötvös Loránd University, Budapest, Hungary
| | - András Ács
- MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anita Alexa
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, ELTE Eötvös Loránd University, Budapest, Hungary
| | - Attila Reményi
- Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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Biri-Kovács B, Kiss B, Vadászi H, Gógl G, Pálfy G, Török G, Homolya L, Bodor A, Nyitray L. Ezrin interacts with S100A4 via both its N- and C-terminal domains. PLoS One 2017; 12:e0177489. [PMID: 28493957 PMCID: PMC5426754 DOI: 10.1371/journal.pone.0177489] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Accepted: 04/27/2017] [Indexed: 11/19/2022] Open
Abstract
Ezrin belongs to the ERM (ezrin, radixin, moesin) protein family that has a role in cell morphology changes, adhesion and migration as an organizer of the cortical cytoskeleton by linking actin filaments to the apical membrane of epithelial cells. It is highly expressed in a variety of human cancers and promotes metastasis. Members of the Ca2+-binding EF-hand containing S100 proteins have similar pathological properties; they are overexpressed in cancer cells and involved in metastatic processes. In this study, using tryptophan fluorescence and stopped-flow kinetics, we show that S100A4 binds to the N-terminal ERM domain (N-ERMAD) of ezrin with a micromolar affinity. The binding involves the F2 lobe of the N-ERMAD and follows an induced fit kinetic mechanism. Interestingly, S100A4 binds also to the unstructured C-terminal actin binding domain (C-ERMAD) with similar affinity. Using NMR spectroscopy, we characterized the complex of S100A4 with the C-ERMAD and demonstrate that no ternary complex is simultaneously formed with the two ezrin domains. Furthermore, we show that S100A4 co-localizes with ezrin in HEK-293T cells. However, S100A4 very weakly binds to full-length ezrin in vitro indicating that the interaction of S100A4 with ezrin requires other regulatory events such as protein phosphorylation and/or membrane binding, shifting the conformational equilibrium of ezrin towards the open state. As both proteins play an important role in promoting metastasis, the characterization of their interaction could shed more light on the molecular events contributing to this pathological process.
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Affiliation(s)
- Beáta Biri-Kovács
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Bence Kiss
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Henrietta Vadászi
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Gergő Gógl
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Gyula Pálfy
- Institute of Chemistry, Laboratory of Structural Chemistry and Biology, Eötvös Loránd University, Budapest, Hungary
| | - György Török
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - László Homolya
- Molecular Cell Biology Research Group, Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Andrea Bodor
- Institute of Chemistry, Laboratory of Structural Chemistry and Biology, Eötvös Loránd University, Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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23
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Pipek O, Ribli D, Molnár J, Póti Á, Krzystanek M, Bodor A, Tusnády GE, Szallasi Z, Csabai I, Szüts D. Fast and accurate mutation detection in whole genome sequences of multiple isogenic samples with IsoMut. BMC Bioinformatics 2017; 18:73. [PMID: 28143617 PMCID: PMC5282906 DOI: 10.1186/s12859-017-1492-4] [Citation(s) in RCA: 20] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/20/2017] [Indexed: 01/11/2023] Open
Abstract
Background Detection of somatic mutations is one of the main goals of next generation DNA sequencing. A wide range of experimental systems are available for the study of spontaneous or environmentally induced mutagenic processes. However, most of the routinely used mutation calling algorithms are not optimised for the simultaneous analysis of multiple samples, or for non-human experimental model systems with no reliable databases of common genetic variations. Most standard tools either require numerous in-house post filtering steps with scarce documentation or take an unpractically long time to run. To overcome these problems, we designed the streamlined IsoMut tool which can be readily adapted to experimental scenarios where the goal is the identification of experimentally induced mutations in multiple isogenic samples. Methods Using 30 isogenic samples, reliable cohorts of validated mutations were created for testing purposes. Optimal values of the filtering parameters of IsoMut were determined in a thorough and strict optimization procedure based on these test sets. Results We show that IsoMut, when tuned correctly, decreases the false positive rate compared to conventional tools in a 30 sample experimental setup; and detects not only single nucleotide variations, but short insertions and deletions as well. IsoMut can also be run more than a hundred times faster than the most precise state of art tool, due its straightforward and easily understandable filtering algorithm. Conclusions IsoMut has already been successfully applied in multiple recent studies to find unique, treatment induced mutations in sets of isogenic samples with very low false positive rates. These types of studies provide an important contribution to determining the mutagenic effect of environmental agents or genetic defects, and IsoMut turned out to be an invaluable tool in the analysis of such data. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1492-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- O Pipek
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - D Ribli
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - J Molnár
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Á Póti
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - M Krzystanek
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark
| | - A Bodor
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - G E Tusnády
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary
| | - Z Szallasi
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, DK-2800, Lyngby, Denmark.,Computational Health Informatics Program (CHIP), Boston Children's Hospital, Boston, USA.,Harvard Medical School, Boston, MA, 02215, USA.,MTA-SE-NAP, Brain Metastasis Research Group, 2nd Department of Pathology, Semmelweis University, H-1091, Budapest, Hungary
| | - I Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, H-1117, Budapest, Hungary
| | - D Szüts
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117, Budapest, Hungary.
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24
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Pálfy G, Kiss B, Nyitray L, Bodor A. Cover Picture: Multilevel Changes in Protein Dynamics upon Complex Formation of the Calcium-Loaded S100A4 with a Nonmuscle Myosin IIA Tail Fragment (ChemBioChem 19/2016). Chembiochem 2016. [DOI: 10.1002/cbic.201600499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Gyula Pálfy
- Laboratory of Structural Chemistry and Biology; Institute of Chemistry; Eötvös Loránd University; Pázmány Péter sétány 1 A 1117 Budapest Hungary
| | - Bence Kiss
- Department of Biochemistry; Eötvös Loránd University; Pázmány Péter sétány 1/C 1117 Budapest Hungary
| | - László Nyitray
- Department of Biochemistry; Eötvös Loránd University; Pázmány Péter sétány 1/C 1117 Budapest Hungary
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology; Institute of Chemistry; Eötvös Loránd University; Pázmány Péter sétány 1 A 1117 Budapest Hungary
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25
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Pálfy G, Kiss B, Nyitray L, Bodor A. Multilevel Changes in Protein Dynamics upon Complex Formation of the Calcium-Loaded S100A4 with a Nonmuscle Myosin IIA Tail Fragment. Chembiochem 2016; 17:1829-1838. [PMID: 27418229 DOI: 10.1002/cbic.201600280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 11/11/2022]
Abstract
Dysregulation of Ca2+ -binding S100 proteins plays important role in various diseases. The asymmetric complex of Ca2+ -bound S100A4 with nonmuscle myosin IIA has high stability and highly increased Ca2+ affinity. Here we investigated the possible causes of this allosteric effect by NMR spectroscopy. Chemical shift-based secondary-structure analysis did not show substantial changes for the complex. Backbone dynamics revealed slow-timescale local motions in the H1 helices of homodimeric S100A4; these were less pronounced in the complex form and might be accompanied by an increase in dimer stability. Different mobilities in the Ca2+ -coordinating EF-hand sites indicate that they communicate by an allosteric mechanism operating through changes in protein dynamics; this must be responsible for the elevated Ca2+ affinity. These multilevel changes in protein dynamics as conformational adaptation allow S100A4 fine-tuning of its protein-protein interactions inside the cell during Ca2+ signaling.
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Affiliation(s)
- Gyula Pálfy
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1 A, 1117, Budapest, Hungary
| | - Bence Kiss
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117, Budapest, Hungary.
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1 A, 1117, Budapest, Hungary.
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26
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Bartok A, Fehér K, Bodor A, Rákosi K, Tóth GK, Kövér KE, Panyi G, Varga Z. An engineered scorpion toxin analogue with improved Kv1.3 selectivity displays reduced conformational flexibility. Sci Rep 2015; 5:18397. [PMID: 26689143 PMCID: PMC4686915 DOI: 10.1038/srep18397] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/04/2015] [Indexed: 12/11/2022] Open
Abstract
The voltage-gated Kv1.3 K+ channel plays a key role in the activation of T lymphocytes. Kv1.3 blockers selectively suppress immune responses mediated by effector memory T cells, which indicates the great potential of selective Kv1.3 inhibitors in the therapy of certain autoimmune diseases. Anuroctoxin (AnTx), a 35-amino-acid scorpion toxin is a high affinity blocker of Kv1.3, but also blocks Kv1.2 with similar potency. We designed and produced three AnTx variants: ([F32T]-AnTx, [N17A]-AnTx, [N17A/F32T]-AnTx) using solid-phase synthesis with the goal of improving the selectivity of the toxin for Kv1.3 over Kv1.2 while keeping the high affinity for Kv1.3. We used the patch-clamp technique to determine the blocking potency of the synthetic toxins on hKv1.3, mKv1.1, hKv1.2 and hKCa3.1 channels. Of the three variants [N17A/F32T]-AnTx maintained the high affinity of the natural peptide for Kv1.3 but became more than 16000-fold selective over Kv1.2. NMR data and molecular dynamics simulations suggest that the more rigid structure with restricted conformational space of the double substituted toxin compared to the flexible wild-type one is an important determinant of toxin selectivity. Our results provide the foundation for the possibility of the production and future therapeutic application of additional, even more selective toxins targeting various ion channels.
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Affiliation(s)
- Adam Bartok
- Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, Debrecen, H-4012, Hungary
| | - Krisztina Fehér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary.,Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium
| | - Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - Kinga Rákosi
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, Szeged, H-6720, Hungary
| | - Gábor K Tóth
- Department of Medical Chemistry, University of Szeged, Dóm tér 8, Szeged, H-6720, Hungary
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, H-4032, Hungary
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, Debrecen, H-4012, Hungary.,MTA-DE Cell Biology and Signaling Research Group, University of Debrecen, Debrecen, Egyetem tér 1, H-4032, Hungary
| | - Zoltan Varga
- MTA-DE-NAP B Ion Channel Structure-Function Research Group, RCMM, University of Debrecen, Debrecen, Egyetem tér 1, H-4032, Hungary.,Department of Biophysics and Cell Biology, University of Debrecen, Egyetem tér 1, Debrecen, H-4012, Hungary
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27
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Gógl G, Alexa A, Kiss B, Katona G, Kovács M, Bodor A, Reményi A, Nyitray L. Structural Basis of Ribosomal S6 Kinase 1 (RSK1) Inhibition by S100B Protein: MODULATION OF THE EXTRACELLULAR SIGNAL-REGULATED KINASE (ERK) SIGNALING CASCADE IN A CALCIUM-DEPENDENT WAY. J Biol Chem 2015; 291:11-27. [PMID: 26527685 DOI: 10.1074/jbc.m115.684928] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [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: 08/18/2015] [Indexed: 12/31/2022] Open
Abstract
Mitogen-activated protein kinases (MAPK) promote MAPK-activated protein kinase activation. In the MAPK pathway responsible for cell growth, ERK2 initiates the first phosphorylation event on RSK1, which is inhibited by Ca(2+)-binding S100 proteins in malignant melanomas. Here, we present a detailed in vitro biochemical and structural characterization of the S100B-RSK1 interaction. The Ca(2+)-dependent binding of S100B to the calcium/calmodulin-dependent protein kinase (CaMK)-type domain of RSK1 is reminiscent of the better known binding of calmodulin to CaMKII. Although S100B-RSK1 and the calmodulin-CAMKII system are clearly distinct functionally, they demonstrate how unrelated intracellular Ca(2+)-binding proteins could influence the activity of the CaMK domain-containing protein kinases. Our crystallographic, small angle x-ray scattering, and NMR analysis revealed that S100B forms a "fuzzy" complex with RSK1 peptide ligands. Based on fast-kinetics experiments, we conclude that the binding involves both conformation selection and induced fit steps. Knowledge of the structural basis of this interaction could facilitate therapeutic targeting of melanomas.
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Affiliation(s)
| | - Anita Alexa
- the "Momentum" Protein Interaction Group, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary, and
| | | | - Gergely Katona
- the Department of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Mihály Kovács
- ELTE-MTA "Momentum" Motor Enzymology Research Group, Department of Biochemistry, and
| | - Andrea Bodor
- Institute of Chemistry Eötvös Loránd University, 1117 Budapest, Hungary
| | - Attila Reményi
- the "Momentum" Protein Interaction Group, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary, and
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28
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Katona G, Duelli A, Kiss B, Lundholm I, Bodor A, Petoukhov M, Svergun D, Nyitray L. Conformational regulation of the C‐terminal random coil in S100A4 by Ca2+ ions. FASEB J 2015. [DOI: 10.1096/fasebj.29.1_supplement.563.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gergely Katona
- Department of Chemistry and Molecular BiologyUniversity of GothenburgSweden
| | - Annette Duelli
- Department of Chemistry and Molecular BiologyUniversity of GothenburgSweden
| | - Bence Kiss
- Department of BiochemistryEötvös Lorand UniversityHungary
| | - Ida Lundholm
- Department of Chemistry and Molecular BiologyUniversity of GothenburgSweden
| | - Andrea Bodor
- Institute of ChemistryLaboratory of Structural Chemistry and Biology Eötvös Lorand UniversityUnited States
| | - Maxim Petoukhov
- Hamburg Outstation European Molecular Biology Laboratory (EMBL)Germany
| | - Dmitri Svergun
- Hamburg Outstation European Molecular Biology Laboratory (EMBL)Germany
| | - Laszlo Nyitray
- Department of BiochemistryEötvös Lorand UniversityHungary
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29
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Bodor A, Kövér KE, Mäler L. Membrane interactions in small fast-tumbling bicelles as studied by 31P NMR. Biochim Biophys Acta 2014; 1848:760-6. [PMID: 25497765 DOI: 10.1016/j.bbamem.2014.12.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 11/11/2014] [Accepted: 12/01/2014] [Indexed: 01/02/2023]
Abstract
Small fast-tumbling bicelles are ideal for studies of membrane interactions at molecular level; they allow analysis of lipid properties using solution-state NMR. In the present study we used 31P NMR relaxation to obtain detailed information on lipid head-group dynamics. We explored the effect of two topologically different membrane-interacting peptides on bicelles containing either dimyristoylphosphocholine (DMPC), or a mixture of DMPC and dimyristoylphosphoglycerol (DMPG), and dihexanoylphosphocholine (DHPC). KALP21 is a model transmembrane peptide, designed to span a DMPC bilayer and dynorphin B is a membrane surface active neuropeptide. KALP21 causes significant increase in bicelle size, as evidenced by both dynamic light scattering and 31P T2 relaxation measurements. The effect of dynorphin B on bicelle size is more modest, although significant effects on T2 relaxation are observed at higher temperatures. A comparison of 31P T1 values for the lipids with and without the peptides showed that dynorphin B has a greater effect on lipid head-group dynamics than KALP21, especially at elevated temperatures. From the field-dependence of T1 relaxation data, a correlation time describing the overall lipid motion was derived. Results indicate that the positively charged dynorphin B decreases the mobility of the lipid molecules--in particular for the negatively charged DMPG--while KALP21 has a more modest influence. Our results demonstrate that while a transmembrane peptide has severe effects on overall bilayer properties, the surface bound peptide has a more dramatic effect in reducing lipid head-group mobility. These observations may be of general importance for understanding peptide-membrane interactions.
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Affiliation(s)
- Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, H-1117 Budapest, Hungary.
| | - Katalin E Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, H-4032 Debrecen, Hungary
| | - Lena Mäler
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm Sweden.
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30
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Bodor A, Radnai L, Hetényi C, Rapali P, Láng A, Kövér KE, Perczel A, Wahlgren WY, Katona G, Nyitray L. DYNLL2 dynein light chain binds to an extended linear motif of myosin 5a tail that has structural plasticity. Biochemistry 2014; 53:7107-22. [PMID: 25312846 DOI: 10.1021/bi500574z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
LC8 dynein light chains (DYNLL) are conserved homodimeric eukaryotic hub proteins that participate in diverse cellular processes. Among the binding partners of DYNLL2, myosin 5a (myo5a) is a motor protein involved in cargo transport. Here we provide a profound characterization of the DYNLL2 binding motif of myo5a in free and DYNLL2-bound form by using nuclear magnetic resonance spectroscopy, X-ray crystallography, and molecular dynamics simulations. In the free form, the DYNLL2 binding region, located in an intrinsically disordered domain of the myo5a tail, has a nascent helical character. The motif becomes structured and folds into a β-strand upon binding to DYNLL2. Despite differences of the myo5a sequence from the consensus binding motif, one peptide is accommodated in each of the parallel DYNLL2 binding grooves, as for all other known partners. Interestingly, while the core motif shows a similar interaction pattern in the binding groove as seen in other complexes, the flanking residues make several additional contacts, thereby lengthening the binding motif. The N-terminal extension folds back and partially blocks the free edge of the β-sheet formed by the binding motif itself. The C-terminal extension contacts the dimer interface and interacts with symmetry-related residues of the second myo5a peptide. The involvement of flanking residues of the core binding site of myo5a could modify the quaternary structure of the full-length myo5a and affect its biological functions. Our results deepen the knowledge of the diverse partner recognition of DYNLL proteins and provide an example of a Janus-faced linear motif.
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Affiliation(s)
- Andrea Bodor
- Laboratory of Structural Chemistry and Biology, Institute of Chemistry, and ‡Department of Biochemistry, Eötvös Loránd University , Budapest, 1117 Hungary
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31
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Duelli A, Kiss B, Lundholm I, Bodor A, Petoukhov MV, Svergun DI, Nyitray L, Katona G. The C-terminal random coil region tunes the Ca²⁺-binding affinity of S100A4 through conformational activation. PLoS One 2014; 9:e97654. [PMID: 24830809 PMCID: PMC4022583 DOI: 10.1371/journal.pone.0097654] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [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: 02/18/2014] [Accepted: 04/22/2014] [Indexed: 11/19/2022] Open
Abstract
S100A4 interacts with many binding partners upon Ca2+ activation and is strongly associated with increased metastasis formation. In order to understand the role of the C-terminal random coil for the protein function we examined how small angle X-ray scattering of the wild-type S100A4 and its C-terminal deletion mutant (residues 1–88, Δ13) changes upon Ca2+ binding. We found that the scattering intensity of wild-type S100A4 changes substantially in the 0.15–0.25 Å−1 q-range whereas a similar change is not visible in the C-terminus deleted mutant. Ensemble optimization SAXS modeling indicates that the entire C-terminus is extended when Ca2+ is bound. Pulsed field gradient NMR measurements provide further support as the hydrodynamic radius in the wild-type protein increases upon Ca2+ binding while the radius of Δ13 mutant does not change. Molecular dynamics simulations provide a rational explanation of the structural transition: the positively charged C-terminal residues associate with the negatively charged residues of the Ca2+-free EF-hands and these interactions loosen up considerably upon Ca2+-binding. As a consequence the Δ13 mutant has increased Ca2+ affinity and is constantly loaded at Ca2+ concentration ranges typically present in cells. The activation of the entire C-terminal random coil may play a role in mediating interaction with selected partner proteins of S100A4.
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Affiliation(s)
- Annette Duelli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Bence Kiss
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
| | - Ida Lundholm
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Andrea Bodor
- Institute of Chemistry, Laboratory of Structural Chemistry and Biology, Eötvös Loránd University, Budapest, Hungary
| | - Maxim V. Petoukhov
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Hamburg, Germany
| | - Dmitri I. Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Hamburg, Germany
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
- * E-mail: (LN); (GK)
| | - Gergely Katona
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
- * E-mail: (LN); (GK)
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Barabás O, Németh V, Bodor A, Perczel A, Rosta E, Kele Z, Zagyva I, Szabadka Z, Grolmusz VI, Wilmanns M, Vértessy BG. Catalytic mechanism of α-phosphate attack in dUTPase is revealed by X-ray crystallographic snapshots of distinct intermediates, 31P-NMR spectroscopy and reaction path modelling. Nucleic Acids Res 2013; 41:10542-55. [PMID: 23982515 PMCID: PMC3905902 DOI: 10.1093/nar/gkt756] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Enzymatic synthesis and hydrolysis of nucleoside phosphate compounds play a key role in various biological pathways, like signal transduction, DNA synthesis and metabolism. Although these processes have been studied extensively, numerous key issues regarding the chemical pathway and atomic movements remain open for many enzymatic reactions. Here, using the Mason–Pfizer monkey retrovirus dUTPase, we study the dUTPase-catalyzed hydrolysis of dUTP, an incorrect DNA building block, to elaborate the mechanistic details at high resolution. Combining mass spectrometry analysis of the dUTPase-catalyzed reaction carried out in and quantum mechanics/molecular mechanics (QM/MM) simulation, we show that the nucleophilic attack occurs at the α-phosphate site. Phosphorus-31 NMR spectroscopy (31P-NMR) analysis confirms the site of attack and shows the capability of dUTPase to cleave the dUTP analogue α,β-imido-dUTP, containing the imido linkage usually regarded to be non-hydrolyzable. We present numerous X-ray crystal structures of distinct dUTPase and nucleoside phosphate complexes, which report on the progress of the chemical reaction along the reaction coordinate. The presently used combination of diverse structural methods reveals details of the nucleophilic attack and identifies a novel enzyme–product complex structure.
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Affiliation(s)
- Orsolya Barabás
- Laboratory of Genome Metabolism, Institute of Enzymology, Research Center for Natural Sciences, Hungarian Academy of Sciences, Budapest H-1113, Hungary, Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, MD 20892, USA, Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg D-69117, Germany, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Protein Modelling Group MTA-ELTE, Institute of Chemistry, Eötvös Loránd University, Budapest H-1117, Hungary, Department of Chemistry, King's College London, London, SE1 1UL, UK, Department of Medical Chemistry, University of Szeged, Hungary, Department of Computer Science, Eötvös Loránd University, Budapest, Hungary, European Molecular Biology Laboratory, Hamburg Outstation, Hamburg D-22603, Germany and Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
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Kali G, Szesztay M, Bodor A, Iván B. Star and Hyperbranched Polyisobutylenes via Terminally Reactive Polyisobutylene-Polystyrene Block Copolymers. ACTA ACUST UNITED AC 2013. [DOI: 10.1002/masy.201100116] [Citation(s) in RCA: 12] [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] [Indexed: 11/11/2022]
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Kiss K, Holczbauer T, Czugler M, Sohár P, Bodor A, Csámpai A. Synthesis, IR-, NMR-, DFT- and X-ray analysis of novel C2-chiral diferrocenyl–salen complexes. J Organomet Chem 2012. [DOI: 10.1016/j.jorganchem.2012.01.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zotter Á, Oláh J, Hlavanda E, Bodor A, Perczel A, Szigeti K, Fidy J, Ovádi J. Zn²+-induced rearrangement of the disordered TPPP/p25 affects its microtubule assembly and GTPase activity. Biochemistry 2011; 50:9568-78. [PMID: 21995432 DOI: 10.1021/bi201447w] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [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
Tubulin polymerization promoting protein/p25 (TPPP/p25) modulates the dynamics and stability of the microtubule system and plays crucial role in the myelination of oligodendrocytes. Here we showed by CD, fluorescence, and NMR spectroscopies that Zn(2+) is the first ligand that induces considerable rearrangement of the disordered TPPP/p25. Zinc finger motif (His(2)Cys(2)) (His(61)-Cys(83)) was identified within the flexible region of TPPP/p25 straddled by extended unstructured N- and C-terminal regions. The specific binding of the Zn(2+) to TPPP/p25 induced the formation of molten globule but not that of a well-defined tertiary structure. The Zn(2+)-induced partially folded structure accommodating the zinc binding motif is localized at the single Trp(76)-containing region as demonstrated by fluorescence resonance energy transfer and quenching experiments. We showed that the Zn(2+)-induced change in the TPPP/p25 structure modified its interaction with tubulin and GTP coupled with functional consequences: the TPPP/p25-promoted tubulin polymerization was increased while the TPPP/p25-catalyzed GTPase activity was decreased as detected by turbidimetry and by malachite green phosphate release/(31)P NMR assays, respectively. The finding that the Zn(2+) of the bivalent cations can uniquely influence physiological relavant interactions significantly contributes to our understanding of the role of Zn(2+)-related TPPP/p25 processes in the differentiation/myelination of oligodendrocytes possessing a high-affinity Zn(2+) uptake mechanism.
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Affiliation(s)
- Ágnes Zotter
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1113 Budapest, Hungary
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Szolnoki Z, Kondacs A, Mandi Y, Bodor A, Somogyvari F. A homozygous genetic variant of mitochondrial uncoupling protein 4 affects the occurrence of leukoaraiosis. Acta Neurol Scand 2011; 123:352-7. [PMID: 20545631 DOI: 10.1111/j.1600-0404.2010.01391.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
OBJECTIVES We hypothesized that an appropriate balance of the mitochondrial energy production is essential in the maintenance of the glia cells in the brain. The aim of this study was to examine the roles of the rs10807344 and rs2270450 genetic variants of mitochondrial uncoupling protein 4 in the development of vascular demyelinization of the white matter of the brain, referred to as leukoaraiosis (LA). The mUCPs are presumed to be of great importance in the regulation of the mitochondrial membrane potential (MMP) and the cellular energy metabolism. MATERIALS AND METHODS An analysis was performed on the clinical and genetic data on 401 LA patients without infarction and on 451 neuroimaging alteration-free subjects. After univariate statistical approaches, logistic regression models were also used to adjust differences in significant clinical factors between the patients and controls. RESULTS The rs10807344 CC genotype proved to exert a protective effect on the occurrence of LA (neuroimaging alteration-free controls: 57.7%, LA group: 44.9%, P < 0.0002; adjusted OR: 0.41, 95% CI: 0.2-0.68, P < 0.005). CONCLUSION The present findings indirectly raise the possibility that a shift or imbalance in the finely regulated MMP may play a role in the development of LA.
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Affiliation(s)
- Z Szolnoki
- Department of Cerebrovascular Diseases, Pándy Kálmán County Hospital, Gyula, Hungary.
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Zotter A, Bodor A, Oláh J, Hlavanda E, Orosz F, Perczel A, Ovádi J. Disordered TPPP/p25 binds GTP and displays Mg2+-dependent GTPase activity. FEBS Lett 2011; 585:803-8. [PMID: 21316364 DOI: 10.1016/j.febslet.2011.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 02/01/2011] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
Abstract
The disordered Tubulin Polymerization Promoting Protein/p25 (TPPP/p25) modulates the dynamics and stability of the microtubule system and plays a crucial role in differentiation of oligodendrocytes. Here we first demonstrated by multinuclear NMR that the extended disordered segments are localized at the N- and C-terminals straddling a flexible region. We showed by affinity chromatography, fluorescence spectroscopy and circular dichroism that GTP binds to TPPP/p25 likely within the flexible region; neither positions nor intensities of the peaks in the assigned terminals were affected by GTP. In addition, we demonstrated that TPPP/p25 specifically hydrolyses GTP in an Mg(2+)-dependent manner. The GTPase activity is comparable with the intrinsic activities of small G proteins suggesting its potential role in multiple physiological processes.
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Affiliation(s)
- Agnes Zotter
- Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, H-1113 Budapest, Hungary
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Szőllősi E, Bokor M, Bodor A, Perczel A, Klement E, Medzihradszky KF, Tompa K, Tompa P. Intrinsic Structural Disorder of DF31, a Drosophila Protein of Chromatin Decondensation and Remodeling Activities. J Proteome Res 2008; 7:2291-9. [DOI: 10.1021/pr700720c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Edit Szőllősi
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary, Research Institute for Solid State Physics and Optics of Hungarian Academy of Sciences, Budapest, Hungary, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary, Proteomics Research Group, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary, and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco,
| | - Monika Bokor
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary, Research Institute for Solid State Physics and Optics of Hungarian Academy of Sciences, Budapest, Hungary, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary, Proteomics Research Group, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary, and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco,
| | - Andrea Bodor
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary, Research Institute for Solid State Physics and Optics of Hungarian Academy of Sciences, Budapest, Hungary, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary, Proteomics Research Group, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary, and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco,
| | - Andras Perczel
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary, Research Institute for Solid State Physics and Optics of Hungarian Academy of Sciences, Budapest, Hungary, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary, Proteomics Research Group, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary, and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco,
| | - Eva Klement
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary, Research Institute for Solid State Physics and Optics of Hungarian Academy of Sciences, Budapest, Hungary, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary, Proteomics Research Group, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary, and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco,
| | - Katalin F. Medzihradszky
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary, Research Institute for Solid State Physics and Optics of Hungarian Academy of Sciences, Budapest, Hungary, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary, Proteomics Research Group, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary, and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco,
| | - Kalman Tompa
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary, Research Institute for Solid State Physics and Optics of Hungarian Academy of Sciences, Budapest, Hungary, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary, Proteomics Research Group, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary, and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco,
| | - Peter Tompa
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary, Research Institute for Solid State Physics and Optics of Hungarian Academy of Sciences, Budapest, Hungary, Laboratory of Structural Chemistry and Biology, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary, Proteomics Research Group, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary, and Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco,
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Manea M, Kalászi A, Mezo G, Horváti K, Bodor A, Horváth A, Farkas O, Perczel A, Przybylski M, Hudecz F. Antibody recognition and conformational flexibility of a plaque-specific beta-amyloid epitope modulated by non-native peptide flanking regions. J Med Chem 2008; 51:1150-61. [PMID: 18284185 DOI: 10.1021/jm070196e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we report on the synthesis, antibody binding, and QSAR studies of a series of linear and cyclic peptides containing a beta-amyloid plaque-specific epitope (Abeta(4-10); FRHDSGY). In these constructs, two or three alpha- l-Ala, alpha- d-Ala, or beta-Ala residues were introduced at both N- and C-termini of the epitope as non-native flanking sequences. Cyclization of the linear Abeta(4-10) epitope peptide resulted in reduced antibody binding. However, the antibody binding could be fully compensated by insertion of alanine flanks into the corresponding cyclic peptides. These results indicate that the modification of a beta-amyloid plaque-specific epitope by combination of cyclization and flanking sequences could generate highly antigenic peptides compared to the native sequence. A novel 3D QSAR method, which explicitly handles conformational flexibility, was developed for the case of such molecular libraries. This method led to the prediction of the binding conformation for the common FRHDSGY sequence.
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Affiliation(s)
- Marilena Manea
- Laboratory of Analytical Chemistry and Biopolymer Structure Analysis, University of Konstanz, 78457 Konstanz, Germany
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Gyimesi M, Kintses B, Bodor A, Perczel A, Fischer S, Bagshaw CR, Málnási-Csizmadia A. The mechanism of the reverse recovery step, phosphate release, and actin activation of Dictyostelium myosin II. J Biol Chem 2008; 283:8153-63. [PMID: 18211892 DOI: 10.1074/jbc.m708863200] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The rate-limiting step of the myosin basal ATPase (i.e. in absence of actin) is assumed to be a post-hydrolysis swinging of the lever arm (reverse recovery step), that limits the subsequent rapid product release steps. However, direct experimental evidence for this assignment is lacking. To investigate the binding and the release of ADP and phosphate independently from the lever arm motion, two single tryptophan-containing motor domains of Dictyostelium myosin II were used. The single tryptophans of the W129+ and W501+ constructs are located at the entrance of the nucleotide binding pocket and near the lever arm, respectively. Kinetic experiments show that the rate-limiting step in the basal ATPase cycle is indeed the reverse recovery step, which is a slow equilibrium step (k(forward) = 0.05 s(-1), k(reverse) = 0.15 s(-1)) that precedes the phosphate release step. Actin directly activates the reverse recovery step, which becomes practically irreversible in the actin-bound form, triggering the power stroke. Even at low actin concentrations the power stroke occurs in the actin-attached states despite the low actin affinity of myosin in the pre-power stroke conformation.
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Affiliation(s)
- Máté Gyimesi
- Department of Biochemistry, Institute of Biology, Eötvös University, Pázmány Péter Sétány 1/A, Budapest, Hungary
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Fábos V, Lantos D, Bodor A, Bálint AM, Mika LT, Sielcken OE, Cuiper A, Horváth IT. Epsilon-caprolactamium hydrogen sulfate: an ionic liquid used for decades in the large-scale production of epsilon-caprolactam. ChemSusChem 2008; 1:189-192. [PMID: 18605204 DOI: 10.1002/cssc.200700135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Viktória Fábos
- Institute of Chemistry, Eörtvös University, Budapest, Hungary
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Kali G, Szesztay M, Bodor A, Iván B. A New Synthetic Method for the Preparation of Star-Shaped Polyisobutylene with Hyperbranched Polystyrene Core. MACROMOL CHEM PHYS 2007. [DOI: 10.1002/macp.200700135] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Mezo G, Czajlik A, Manea M, Jakab A, Farkas V, Majer Z, Vass E, Bodor A, Kapuvári B, Boldizsár M, Vincze B, Csuka O, Kovács M, Przybylski M, Perczel A, Hudecz F. Structure, enzymatic stability and antitumor activity of sea lamprey GnRH-III and its dimer derivatives. Peptides 2007; 28:806-20. [PMID: 17254668 DOI: 10.1016/j.peptides.2006.12.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 12/19/2006] [Accepted: 12/20/2006] [Indexed: 11/24/2022]
Abstract
Direct antitumor activity of sea lamprey (Petromyzon marinus) gonadotropin-releasing hormone III (Glp-His-Trp-Ser-His-Asp-Trp-Lys-Pro-Gly-NH(2); lGnRH-III) was described on several tumor cells. To improve the selectivity of antitumor effects without increasing the hormone releasing activity and to enhance the enzymatic stability, lGnRH-III dimers were prepared via disulfide bond formation. Our results demonstrate that the lGnRH-III dimer derivatives exhibited higher antiproliferative effect and enzymatic stability in comparison with the native lGnRH-III, while lower LH-releasing potency was determined. In order to find a correlation between the biological and structural features of these compounds, the conformation of lGnRH-III and its dimer derivatives was determined by ECD, VCD, FT-IR and (1)H NMR.
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Affiliation(s)
- Gábor Mezo
- Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University, POB 32, 1518 Budapest 112, Hungary.
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Mehdi H, Bodor A, Lantos D, Horváth IT, De Vos DE, Binnemans K. Imidazolium Ionic Liquids as Solvents for Cerium(IV)-Mediated Oxidation Reactions. J Org Chem 2006; 72:517-24. [PMID: 17221969 DOI: 10.1021/jo061909o] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Use of imidazolium ionic liquids as solvents for organic transformations with tetravalent cerium salts as oxidizing agents was evaluated. Good solubility was found for ammonium hexanitratocerate(IV) (ceric ammonium nitrate, CAN) and cerium(IV) triflate in 1-alkyl-3-methylimidazolium triflate ionic liquids. Oxidation of benzyl alcohol to benzaldehyde in 1-ethyl-3-methylimidazolium triflate was studied by in-situ FTIR spectroscopy and 13C NMR spectroscopy on carbon-13-labeled benzyl alcohol. Careful control of the reaction conditions is necessary because ammonium hexanitratocerate(IV) dissolved in an ionic liquid can transform benzyl alcohol not only into benzaldehyde but also into benzyl nitrate or benzoic acid. The selectivity of the reaction of cerium(IV) triflate with benzyl alcohol in dry ionic liquids depends on the degree of hydration of cerium(IV) triflate: anhydrous cerium(IV) triflate transforms benzyl alcohol into dibenzyl ether, whereas hydrated cerium(IV) triflate affords benzaldehyde as the main reaction product. Reactions of ammonium hexanitratocerate(IV) with organic substrates other than benzyl alcohol have been explored. 1,4-Hydroquinone is quantitatively transformed into 1,4-quinone. Anisole and naphthalene are nitrated. For the cerium-mediated oxidation reactions in ionic liquids, high reaction temperatures are an advantage because under these conditions smaller amounts of byproducts are formed.
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Affiliation(s)
- Hasan Mehdi
- Department of Chemical Technology and Environmental Chemistry, Eötvös University, PAzmAny Péter SétAny 1/A, 1117 Budapest, Hungary
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Szabó D, Mohl J, Bálint AM, Bodor A, Rábai J. Novel generation ponytails in fluorous chemistry: Syntheses of primary, secondary, and tertiary (nonafluoro-tert-butyloxy)ethyl amines. J Fluor Chem 2006. [DOI: 10.1016/j.jfluchem.2006.06.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Hódi Z, Németh AL, Radnai L, Hetényi C, Schlett K, Bodor A, Perczel A, Nyitray L. Alternatively Spliced Exon B of Myosin Va Is Essential for Binding the Tail-Associated Light Chain Shared by Dynein. Biochemistry 2006; 45:12582-95. [PMID: 17029413 DOI: 10.1021/bi060991e] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A 10 kDa dynein light chain (DLC), previously identified as a tail light chain of myosin Va, may function as a cargo-binding and/or regulatory subunit of both myosin and dynein. Here, we identify and characterize the binding site of DLC on myosin Va. Fragments of the human myosin Va tail and the DLC2 isoform were expressed, and their complex formation was analyzed by pull-down assays, gel filtration, and spectroscopic methods. DLC2 was found to bind as a homodimer to a approximately 15 residue segment (Ile1280-Ile1294) localized between the medial and distal coiled-coil domains of the tail. The binding region contains the three residues coded by the alternatively spliced exon B (Asp1284-Lys1286). Removal of exon B eliminates DLC2 binding. Co-localization experiments in a transfected mammalian cell line confirm our finding that exon B is essential for DLC2 binding. Using circular dichroism, we demonstrate that binding of DLC2 to a approximately 85 residue disordered domain (Pro1235-Arg1320) induces some helical structure and stabilizes both flanking coiled-coil domains (melting temperature increases by approximately 7 degrees C). This result shows that DLC2 promotes the assembly of the coiled-coil domains of myosin Va. Nuclear magnetic resonance spectroscopy and docking simulations show that a 15 residue peptide (Ile1280-Ile1294) binds to the surface grooves on DLC2 similarly to other known binding partners of DLCs. When our data are taken together, they suggest that exon B and its associated DLC2 have a significant effect on the structure of parts of the coiled-coil tail domains and such a way could influence the regulation and cargo-binding function of myosin Va.
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Affiliation(s)
- Zsuzsa Hódi
- Department of Biochemistry, Eötvös Loránd University, Budapest, Hungary
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Orosz A, Szabo A, Szeman G, Janaky T, Somlai C, Penke B, Bodor A, Perczel A. Novel nontoxic heat shock protein 90 inhibitors having selective antiproliferative effect. Int J Biochem Cell Biol 2006; 38:1352-62. [PMID: 16540363 DOI: 10.1016/j.biocel.2006.01.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [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: 10/14/2005] [Revised: 01/20/2006] [Accepted: 01/27/2006] [Indexed: 11/23/2022]
Abstract
Almost all heat shock protein 90 inhibitors reported so far, which are natural product derivatives, have problems mainly with toxic side effects, and with bioavailability and solubility. In our earlier studies, we compared the steric conformational structures of substance P[6-11] with our substance P antagonists in silico, and used the diverse biological effects of these compounds as tools in our modeling and design studies for discovering antiproliferative drugs. Here, we present a new synthesized short peptide-derivative compound family that inhibits only the function of the tumor cell's heat shock protein 90 and selectively kills in vitro more cancer cells than normal cells. During the lead generation, we observed that the difference between the most effective inhibitors was only one residue or group that caused diverse effects in vitro on the studied cell lines. According to our in vivo experiments on nude mice bearing lung cancer xenografts, the inhibitors restrained tumor growth, but not caused overt toxicity. We undertook NMR spectroscopy studies to analyze the 3D molecular structural differences of our inhibitors that control their binding to the target molecule. In conclusion, we demonstrated the efficacy of new selective and small molecule anticancerogen heat shock protein 90 inhibitors with peptide nature, without in vivo toxicity on nude mouse xenograft model. Our results also shed light on the mechanism of anticancerogen action of some substance P antagonists and their derivatives.
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Affiliation(s)
- Antal Orosz
- Tumor Cell Biology Laboratory, Foundation for Cancer Prevention and Effective Treatment, Eötvös Loránd University, Pázmány sétány 1/C, H-1117 Budapest, Hungary.
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Pusztai Z, Vlád G, Bodor A, Horváth IT, Laas HJ, Halpaap R, Richter FU. In Situ NMR Spectroscopic Observation of a Catalytic Intermediate in Phosphine-Catalyzed Cyclo-Oligomerization of Isocyanates. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200502415] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Pusztai Z, Vlád G, Bodor A, Horváth IT, Laas HJ, Halpaap R, Richter FU. In Situ NMR Spectroscopic Observation of a Catalytic Intermediate in Phosphine-Catalyzed Cyclo-Oligomerization of Isocyanates. Angew Chem Int Ed Engl 2006; 45:107-10. [PMID: 16304659 DOI: 10.1002/anie.200502415] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Zoltán Pusztai
- Eötvös University, Department of Chemical Technology and Environmental Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
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