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Sebők-Nagy K, Kóta Z, Kincses A, Fazekas ÁF, Dér A, László Z, Páli T. Spin-Label Electron Paramagnetic Resonance Spectroscopy Reveals Effects of Wastewater Filter Membrane Coated with Titanium Dioxide Nanoparticles on Bovine Serum Albumin. Molecules 2023; 28:6750. [PMID: 37836593 PMCID: PMC10574081 DOI: 10.3390/molecules28196750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
The accumulation of proteins in filter membranes limits the efficiency of filtering technologies for cleaning wastewater. Efforts are ongoing to coat commercial filters with different materials (such as titanium dioxide, TiO2) to reduce the fouling of the membrane. Beyond monitoring the desired effect of the retention of biomolecules, it is necessary to understand what the biophysical changes are in water-soluble proteins caused by their interaction with the new coated filter membranes, an aspect that has received little attention so far. Using spin-label electron paramagnetic resonance (EPR), aided with native fluorescence spectroscopy and dynamic light scattering (DLS), here, we report the changes in the structure and dynamics of bovine serum albumin (BSA) exposed to TiO2 (P25) nanoparticles or passing through commercial polyvinylidene fluoride (PVDF) membranes coated with the same nanoparticles. We have found that the filtering process and prolonged exposure to TiO2 nanoparticles had significant effects on different regions of BSA, and denaturation of the protein was not observed, neither with the TiO2 nanoparticles nor when passing through the TiO2-coated filter membranes.
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Affiliation(s)
- Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
| | - Zoltán Kóta
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
| | - András Kincses
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
| | - Ákos Ferenc Fazekas
- Department of Biosystems Engineering, Faculty of Engineering, University of Szeged, 6725 Szeged, Hungary; (Á.F.F.); (Z.L.)
| | - András Dér
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
| | - Zsuzsanna László
- Department of Biosystems Engineering, Faculty of Engineering, University of Szeged, 6725 Szeged, Hungary; (Á.F.F.); (Z.L.)
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre Szeged, 6726 Szeged, Hungary; (K.S.-N.); (Z.K.); (A.K.); (A.D.)
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2
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Galazzo L, Bordignon E. Electron paramagnetic resonance spectroscopy in structural-dynamic studies of large protein complexes. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2023; 134-135:1-19. [PMID: 37321755 DOI: 10.1016/j.pnmrs.2022.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Macromolecular protein assemblies are of fundamental importance for many processes inside the cell, as they perform complex functions and constitute central hubs where reactions occur. Generally, these assemblies undergo large conformational changes and cycle through different states that ultimately are connected to specific functions further regulated by additional small ligands or proteins. Unveiling the 3D structural details of these assemblies at atomic resolution, identifying the flexible parts of the complexes, and monitoring with high temporal resolution the dynamic interplay between different protein regions under physiological conditions is key to fully understanding their properties and to fostering biomedical applications. In the last decade, we have seen remarkable advances in cryo-electron microscopy (EM) techniques, which deeply transformed our vision of structural biology, especially in the field of macromolecular assemblies. With cryo-EM, detailed 3D models of large macromolecular complexes in different conformational states became readily available at atomic resolution. Concomitantly, nuclear magnetic resonance (NMR) and electron paramagnetic resonance spectroscopy (EPR) have benefited from methodological innovations which also improved the quality of the information that can be achieved. Such enhanced sensitivity widened their applicability to macromolecular complexes in environments close to physiological conditions and opened a path towards in-cell applications. In this review we will focus on the advantages and challenges of EPR techniques with an integrative approach towards a complete understanding of macromolecular structures and functions.
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Affiliation(s)
- Laura Galazzo
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
| | - Enrica Bordignon
- Department of Physical Chemistry, University of Geneva, Quai Ernest Ansermet 30, CH-1211 Genève 4, Switzerland.
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3
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Fábregas-Ibáñez L, Mertens V, Ritsch I, von Hagens T, Stoll S, Jeschke G. Dipolar pathways in multi-spin and multi-dimensional dipolar EPR spectroscopy. Phys Chem Chem Phys 2022; 24:22645-22660. [PMID: 36106486 PMCID: PMC9516884 DOI: 10.1039/d2cp03048a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/07/2022] [Indexed: 11/24/2022]
Abstract
Dipolar electron paramagnetic resonance (EPR) experiments, such as double electron-electron resonance (DEER), measure distributions of nanometer-scale distances between unpaired electrons, which provide valuable information for structural characterization of proteins and other macromolecular systems. We present an extension to our previously published general model based on dipolar pathways valid for multi-dimensional dipolar EPR experiments with more than two spin-1/2 labels. We examine the 4-pulse DEER and TRIER experiments in terms of dipolar pathways and show experimental results confirming the theoretical predictions. This extension to the dipolar pathways model allows the analysis of previously challenging datasets and the extraction of multivariate distance distributions.
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Affiliation(s)
- Luis Fábregas-Ibáñez
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
| | - Valerie Mertens
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
| | - Irina Ritsch
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
| | - Tona von Hagens
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, WA 98195, Washington, USA
| | - Gunnar Jeschke
- ETH Zurich, Laboratory of Physical Chemistry, Vladimir-Prelog-Weg 2, Zurich, Switzerland
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4
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Himani, Pratap Singh Raman A, Babu Singh M, Jain P, Chaudhary P, Bahadur I, Lal K, Kumar V, Singh P. An Update on Synthesis, Properties, Applications and Toxicity of the ILs. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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5
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Schiemann O, Heubach CA, Abdullin D, Ackermann K, Azarkh M, Bagryanskaya EG, Drescher M, Endeward B, Freed JH, Galazzo L, Goldfarb D, Hett T, Esteban Hofer L, Fábregas Ibáñez L, Hustedt EJ, Kucher S, Kuprov I, Lovett JE, Meyer A, Ruthstein S, Saxena S, Stoll S, Timmel CR, Di Valentin M, Mchaourab HS, Prisner TF, Bode BE, Bordignon E, Bennati M, Jeschke G. Benchmark Test and Guidelines for DEER/PELDOR Experiments on Nitroxide-Labeled Biomolecules. J Am Chem Soc 2021; 143:17875-17890. [PMID: 34664948 PMCID: PMC11253894 DOI: 10.1021/jacs.1c07371] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Distance distribution information obtained by pulsed dipolar EPR spectroscopy provides an important contribution to many studies in structural biology. Increasingly, such information is used in integrative structural modeling, where it delivers unique restraints on the width of conformational ensembles. In order to ensure reliability of the structural models and of biological conclusions, we herein define quality standards for sample preparation and characterization, for measurements of distributed dipole-dipole couplings between paramagnetic labels, for conversion of the primary time-domain data into distance distributions, for interpreting these distributions, and for reporting results. These guidelines are substantiated by a multi-laboratory benchmark study and by analysis of data sets with known distance distribution ground truth. The study and the guidelines focus on proteins labeled with nitroxides and on double electron-electron resonance (DEER aka PELDOR) measurements and provide suggestions on how to proceed analogously in other cases.
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Affiliation(s)
- Olav Schiemann
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Caspar A Heubach
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Katrin Ackermann
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, U.K
| | - Mykhailo Azarkh
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Elena G Bagryanskaya
- N.N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Lavrentieva aven 9, 630090 Novosibirsk, Russia
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Burkhard Endeward
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany
| | - Jack H Freed
- Department of Chemistry and Chemical Biology, and ACERT, National Biomedical Center for Advanced Electron Spin Resonance Technology, Cornell University, Ithaca, New York 14853-1301, United States
| | - Laura Galazzo
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tobias Hett
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstraße 12, 53115 Bonn, Germany
| | - Laura Esteban Hofer
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Luis Fábregas Ibáñez
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Eric J Hustedt
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Svetlana Kucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Highfield Campus, Southampton SO17 1BJ, U.K
| | - Janet Eleanor Lovett
- SUPA School of Physics and Astronomy and BSRC, University of St Andrews, North Haugh, St Andrews KY16 9SS, U.K
| | - Andreas Meyer
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sharon Ruthstein
- Department of Chemistry, Bar Ilan University, Ramat Gan 5290002, Israel
| | - Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Stefan Stoll
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Christiane R Timmel
- Department of Chemistry, Centre for Advanced Electron Spin Resonance, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K
| | - Marilena Di Valentin
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Hassane S Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry and Center of Biomolecular Magnetic Resonance, Goethe University, 60438 Frankfurt am Main, Germany
| | - Bela Ernest Bode
- EaStCHEM School of Chemistry, Biomedical Sciences Research Complex, and Centre of Magnetic Resonance, University of St Andrews North Haugh, St Andrews KY16 9ST, U.K
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Marina Bennati
- Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Gunnar Jeschke
- Department of Chemistry and Applied Biosciences, ETH Hönggerberg, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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6
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Teucher M, Qi M, Cati N, Hintz H, Godt A, Bordignon E. Strategies to identify and suppress crosstalk signals in double electron-electron resonance (DEER) experiments with gadolinium III and nitroxide spin-labeled compounds. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2020; 1:285-299. [PMID: 37904822 PMCID: PMC10500692 DOI: 10.5194/mr-1-285-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/31/2020] [Indexed: 11/01/2023]
Abstract
Double electron-electron resonance (DEER) spectroscopy applied to orthogonally spin-labeled biomolecular complexes simplifies the assignment of intra- and intermolecular distances, thereby increasing the information content per sample. In fact, various spin labels can be addressed independently in DEER experiments due to spectroscopically nonoverlapping central transitions, distinct relaxation times, and/or transition moments; hence, they are referred to as spectroscopically orthogonal. Molecular complexes which are, for example, orthogonally spin-labeled with nitroxide (NO) and gadolinium (Gd) labels give access to three distinct DEER channels that are optimized to selectively probe NO-NO, NO-Gd, and Gd-Gd distances. Nevertheless, it has been previously recognized that crosstalk signals between individual DEER channels can occur, for example, when a Gd-Gd distance appears in a DEER channel optimized to detect NO-Gd distances. This is caused by residual spectral overlap between NO and Gd spins which, therefore, cannot be considered as perfectly orthogonal. Here, we present a systematic study on how to identify and suppress crosstalk signals that can appear in DEER experiments using mixtures of NO-NO, NO-Gd, and Gd-Gd molecular rulers characterized by distinct, nonoverlapping distance distributions. This study will help to correctly assign the distance peaks in homo- and heterocomplexes of biomolecules carrying not perfectly orthogonal spin labels.
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Affiliation(s)
- Markus Teucher
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Mian Qi
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Ninive Cati
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Henrik Hintz
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2), Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Enrica Bordignon
- Faculty of Chemistry and Biochemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
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7
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Kaczmarski JA, Mahawaththa MC, Feintuch A, Clifton BE, Adams LA, Goldfarb D, Otting G, Jackson CJ. Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme. Nat Commun 2020; 11:5945. [PMID: 33230119 PMCID: PMC7683729 DOI: 10.1038/s41467-020-19695-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 10/21/2020] [Indexed: 02/07/2023] Open
Abstract
Several enzymes are known to have evolved from non-catalytic proteins such as solute-binding proteins (SBPs). Although attention has been focused on how a binding site can evolve to become catalytic, an equally important question is: how do the structural dynamics of a binding protein change as it becomes an efficient enzyme? Here we performed a variety of experiments, including propargyl-DO3A-Gd(III) tagging and double electron-electron resonance (DEER) to study the rigid body protein dynamics of reconstructed evolutionary intermediates to determine how the conformational sampling of a protein changes along an evolutionary trajectory linking an arginine SBP to a cyclohexadienyl dehydratase (CDT). We observed that primitive dehydratases predominantly populate catalytically unproductive conformations that are vestiges of their ancestral SBP function. Non-productive conformational states, including a wide-open state, are frozen out of the conformational landscape via remote mutations, eventually leading to extant CDT that exclusively samples catalytically relevant compact states. These results show that remote mutations can reshape the global conformational landscape of an enzyme as a mechanism for increasing catalytic activity.
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Affiliation(s)
- Joe A Kaczmarski
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Mithun C Mahawaththa
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia
| | - Akiva Feintuch
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ben E Clifton
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia.,Protein Engineering and Evolution Unit, Okinawa Institute of Science and Technology, 1919-1 Tancha, Onna-son, Okinawa, 904-0412, Japan
| | - Luke A Adams
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Gottfried Otting
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, 2601, ACT, Australia.
| | - Colin J Jackson
- Research School of Chemistry, The Australian National University, Canberra, ACT, 2601, Australia. .,Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, 2601, ACT, Australia. .,Australian Research Council Centre of Excellence in Synthetic Biology, Research School of Chemistry, Australian National University, Canberra, 2601, ACT, Australia.
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8
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Arabi SH, Aghelnejad B, Volmer J, Hinderberger D. Hydrogels from serum albumin in a molten globule-like state. Protein Sci 2020; 29:2459-2467. [PMID: 33058378 PMCID: PMC7679958 DOI: 10.1002/pro.3976] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/06/2020] [Accepted: 10/06/2020] [Indexed: 01/01/2023]
Abstract
We demonstrate that a molten globule‐like (MG) state of a protein, usually described as a compact yet non‐folded conformation that is only present in a narrow and delicate parameter range, is preserved in the high concentration environment of the protein hydrogel. We reveal mainly by means of electron paramagnetic resonance (EPR) spectroscopy that bovine serum albumin (BSA) retains the known basic MG state after a hydrogel has been formed from 20 wt% precursor solutions. At pH values of ~11.4, BSA hydrogels made from MG‐BSA remain stable for weeks, while gels formed at slightly different (~0.2) pH units above and below the MG‐state value dissolve into viscous solutions. On the contrary, when hydrophobic screening agents are added such as amphiphilic, EPR‐active stearic acid derivatives (16‐DOXYL‐stearic acid, 16‐DSA), the MG‐state based hydrogel is the least long‐lived, as the hydrophobic interaction of delicately exposed hydrophobic patches of BSA molecules is screened by the amphiphilic molecules. These bio‐ and polymer‐physically unexpected findings may lead to new bio‐compatible MG‐based hydrogels that display novel properties in comparison to conventional gels.
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Affiliation(s)
- Seyed Hamidreza Arabi
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Behdad Aghelnejad
- Département de chimie, École normale supérieure, PSL University, Sorbonne Université, Paris, France
| | - Jonas Volmer
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Dariush Hinderberger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
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9
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Haeri HH, Tomaszewski J, Phytides B, Schimm H, Möslein G, Niedergethmann M, Hinderberger D, Gelos M. Identification of Patients with Pancreatic Cancer by Electron Paramagnetic Resonance Spectroscopy of Fatty Acid Binding to Human Serum Albumin. ACS Pharmacol Transl Sci 2020; 3:1188-1198. [PMID: 33344896 DOI: 10.1021/acsptsci.0c00116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 12/11/2022]
Abstract
An effective biological marker for pancreatic adenocarcinoma (PAC) is not available so far. Here, we investigate how electron paramagnetic resonance (EPR) spectroscopy of spin-labeled fatty acid (FA) molecules binding to human serum albumin (HSA) in human serum is a suitable method for the identification of patients with PAC through detection of PAC-induced changes of FA binding to albumin. The functionality of HSA to bind FA is investigated in serum samples of 35 patients with PAC, 26 patients with benign pancreatic tumors (BPD), and 24 healthy individuals by continuous wave (CW) EPR spectroscopy by simply dissolving 16-DOXYL stearic acid as spin-labeled FA. It is found that FA binding to HSA in PAC is significantly modified when compared with healthy and BPD individuals. The PAC group could best be discriminated from the healthy group based on EPR characteristics at the loading ratio of 1:4 (HSA:FA), while patients with PAC and BPD are distinguishable at a loading ratio of 1:6. Using nanoscale distance measurements through double electron-electron resonance (DEER), it is found that the distribution of FAs in the HSA of one PAC patient is similar to that of FAs in healthy individuals. Combining all EPR spectroscopic data, this leads to a tentative molecular interpretation of only small changes in hydration at the protein's surface as origin of the detectable characteristics for PAC patients. Thus, EPR of FA/HSA binding is a simple and promising tool for clinical detection of patients with PAC and needs to be tested with larger ensembles of different patient groups.
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Affiliation(s)
- Haleh H Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jörg Tomaszewski
- Department of General and Visceral Surgery, Alfried Krupp Krankenhaus Essen, Essen, Nordrhein-Westfalen 45276, Germany
| | - Bettina Phytides
- Department of General and Visceral Surgery, Alfried Krupp Krankenhaus Essen, Essen, Nordrhein-Westfalen 45276, Germany
| | - Heike Schimm
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Gabriela Möslein
- Faculty of Health Sciences, University of Witten/Herdecke, Witten, Nordrhein-Westfalen 58448, Germany
| | - Marco Niedergethmann
- Department of General and Visceral Surgery, Alfried Krupp Krankenhaus Essen, Essen, Nordrhein-Westfalen 45276, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Marcos Gelos
- Faculty of Health Sciences, University of Witten/Herdecke, Witten, Nordrhein-Westfalen 58448, Germany
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10
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Probing the Y 2 Receptor on Transmembrane, Intra- and Extra-Cellular Sites for EPR Measurements. Molecules 2020; 25:molecules25184143. [PMID: 32927734 PMCID: PMC7571237 DOI: 10.3390/molecules25184143] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/04/2020] [Accepted: 09/09/2020] [Indexed: 02/07/2023] Open
Abstract
The function of G protein-coupled receptors is intrinsically linked to their conformational dynamics. In conjugation with site-directed spin labeling, electron paramagnetic resonance (EPR) spectroscopy provides powerful tools to study the highly dynamic conformational states of these proteins. Here, we explored positions for nitroxide spin labeling coupled to single cysteines, introduced at transmembrane, intra- and extra-cellular sites of the human neuropeptide Y2 receptor. Receptor mutants were functionally analyzed in cell culture system, expressed in Escherichia coli fermentation with yields of up to 10 mg of purified protein per liter expression medium and functionally reconstituted into a lipid bicelle environment. Successful spin labeling was confirmed by a fluorescence assay and continuous wave EPR measurements. EPR spectra revealed mobile and immobile populations, indicating multiple dynamic conformational states of the receptor. We found that the singly mutated positions by MTSL ((1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl) methyl methanesulfonothioate) have a water exposed immobilized conformation as their main conformation, while in case of the IDSL (bis(1-oxyl-2,2,5,5-tetramethyl-3-imidazolin-4-yl) disulfide) labeled positions, the main conformation are mainly of hydrophobic nature. Further, double cysteine mutants were generated and examined for potential applications of distance measurements by double electron–electron resonance (DEER) pulsed EPR technique on the receptor.
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11
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Hunold J, Eisermann J, Brehm M, Hinderberger D. Characterization of Aqueous Lower-Polarity Solvation Shells Around Amphiphilic 2,2,6,6-Tetramethylpiperidine-1-oxyl Radicals in Water. J Phys Chem B 2020; 124:8601-8609. [DOI: 10.1021/acs.jpcb.0c04863] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Johannes Hunold
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Jana Eisermann
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Martin Brehm
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Dariush Hinderberger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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12
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Goryunov A, Rozhkov S, Rozhkova N. Fatty acid transfer between serum albumins and shungite carbon nanoparticles and its effect on protein aggregation and association. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 49:85-94. [PMID: 31865396 DOI: 10.1007/s00249-019-01414-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/10/2019] [Accepted: 12/08/2019] [Indexed: 10/25/2022]
Abstract
The bioactivity of the natural ultrafine carbon form shungite nanocarbon (ShC) is of particular interest both for biomedical applications of such nanomaterials and their negative impact on the aquatic environmental. Here we studied the interaction of serum albumin (SA) with ShC nanoparticles in aqueous dispersion with respect to its structural-dynamic, thermodynamic, and hydrodynamic effects. Electron spin resonance (EPR) with a 5-DOXYL-stearic acid spin probe (5DSA) demonstrates that ShC can affect fatty acid (FA) binding by SA, protein conformation in the stearic FA spin probe binding region, and protein aggregation due to the partial transfer of FA to the ShC nanoparticles. The ratio of SA fractions changes in the presence of ShC in favor of the fraction that is less saturated with FA as shown by differential scanning calorimetry (DSC). The stability of interaction with ShC is significantly higher for aggregates of SA molecules that carry physiological amounts of FA, compared to aggregates of the FA-free protein, as studied by dynamic light scattering (DLS) analysis. Generally, the mixed dispersion of SA and ShC nanoparticles is more homogeneous than the SA solution alone. This is manifested both in the size of the molecular associates and in the microenvironment of the protein-bound FA. The formation of the SA-ShC interface is likely to result in a greater uniformity of the FA binding sites and a decrease in protein fractions and "hot patches" on the protein surface responsible for the supramolecular heterogeneity of the protein in solution.
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Affiliation(s)
- Andrey Goryunov
- Institute of Biology, Karelian Research Center RAS, Pushkinskaya 11, 185910, Petrozavodsk, Russia
| | - Sergei Rozhkov
- Institute of Biology, Karelian Research Center RAS, Pushkinskaya 11, 185910, Petrozavodsk, Russia.
| | - Natalia Rozhkova
- Institute of Geology, Karelian Research Center RAS, Pushkinskaya 11, 185910, Petrozavodsk, Russia
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Reichenwallner J, Hauenschild T, Schmelzer CEH, Hülsmann M, Godt A, Hinderberger D. Fatty Acid Triangulation in Albumins Using a Landmark Spin Label. Isr J Chem 2019. [DOI: 10.1002/ijch.201900073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jörg Reichenwallner
- Institute of ChemistryMartin Luther University Halle-Wittenberg Von-Danckelmann-Platz 4 D-06120 Halle (Saale) Germany
| | - Till Hauenschild
- Institute of ChemistryMartin Luther University Halle-Wittenberg Von-Danckelmann-Platz 4 D-06120 Halle (Saale) Germany
| | - Christian E. H. Schmelzer
- Fraunhofer Institute for Microstructure of Materials and Systems IMWS Walter-Hülse-Straße 1 D-06120 Halle (Saale) Germany
- Institute of PharmacyMartin Luther University Halle-Wittenberg Wolfgang-Langenbeck-Straße 4 D-06120 Halle (Saale) Germany
| | - Miriam Hülsmann
- Faculty of Chemistry and Center for Molecular Materials (CM2)Bielefeld University Universitätsstraße 25 D-33615 Bielefeld Germany
| | - Adelheid Godt
- Faculty of Chemistry and Center for Molecular Materials (CM2)Bielefeld University Universitätsstraße 25 D-33615 Bielefeld Germany
| | - Dariush Hinderberger
- Institute of ChemistryMartin Luther University Halle-Wittenberg Von-Danckelmann-Platz 4 D-06120 Halle (Saale) Germany
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14
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Reichenwallner J, Thomas A, Steinbach T, Eisermann J, Schmelzer CEH, Wurm F, Hinderberger D. Ligand-Binding Cooperativity Effects in Polymer–Protein Conjugation. Biomacromolecules 2019; 20:1118-1131. [DOI: 10.1021/acs.biomac.9b00016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Jörg Reichenwallner
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Anja Thomas
- Institute of Organic Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Tobias Steinbach
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute of Organic Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Jana Eisermann
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Christian E. H. Schmelzer
- Fraunhofer Institute for Microstructure of Materials and Systems (IMWS), Walter-Hülse-Strasse 1, 06120 Halle (Saale), Germany
- Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Wolfgang-Langenbeck-Strasse 4, 06120 Halle (Saale), Germany
| | - Frederik Wurm
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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15
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Exploring the pH-Induced Functional Phase Space of Human Serum Albumin by EPR Spectroscopy. MAGNETOCHEMISTRY 2018. [DOI: 10.3390/magnetochemistry4040047] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A systematic study on the self-assembled solution system of human serum albumin (HSA) and paramagnetic doxyl stearic acid (5-DSA and 16-DSA) ligands is reported covering the broad pH range 0.7–12.9, mainly using electron paramagnetic resonance (EPR) methods. It is tested to which extent the pH-induced conformational isomers of HSA reveal themselves in continuous wave (CW) EPR spectra from this spin probing approach in comparison to an established spin-labeling strategy utilizing 3-maleimido proxyl (5-MSL). Most analyses are conducted on empirical levels with robust strategies that allow for the detection of dynamic changes of ligand, as well as protein. Special emphasis has been placed on the EPR spectroscopic detection of a molten globule (MG) state of HSA that is typically found by the fluorescent probe 8-Anilino- naphthalene-1-sulfonic acid (ANS). Moreover, four-pulse double electron-electron resonance (DEER) experiments are conducted and substantiated with dynamic light scattering (DLS) data to determine changes in the solution shape of HSA with pH. All results are ultimately combined in a detailed scheme that describes the pH-induced functional phase space of HSA.
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16
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Arabi SH, Aghelnejad B, Schwieger C, Meister A, Kerth A, Hinderberger D. Serum albumin hydrogels in broad pH and temperature ranges: characterization of their self-assembled structures and nanoscopic and macroscopic properties. Biomater Sci 2018; 6:478-492. [PMID: 29446432 DOI: 10.1039/c7bm00820a] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We report extended pH- and temperature-induced preparation procedures and explore the materials and molecular properties of different types of hydrogels made from human and bovine serum albumin, the major transport protein in the blood of mammals. We describe the diverse range of properties of these hydrogels at three levels: (1) their viscoelastic (macroscopic) behavior, (2) protein secondary structure changes during the gelation process (via ATR-FTIR spectroscopy), and (3) the hydrogel fatty acid (FA) binding capacity and derive from this the generalized tertiary structure through CW EPR spectroscopy. We describe the possibility of preparing hydrogels from serum albumin under mild conditions such as low temperatures (notably below albumin's denaturation temperature) and neutral pH value. As such, the proteins retain most of their native secondary structure. We find that all the combined data indicate a two-stage gelation process that is studied in detail. We summarize these findings and the explored dependences of the gels on pH, temperature, concentration, and incubation time by proposing phase diagrams for both HSA and BSA gel-states. As such, it has become possible to prepare gels that have the desired nanoscopic and macroscopic properties, which can, in future, be tested for, e.g., drug delivery applications.
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Affiliation(s)
- S Hamidreza Arabi
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Saale, Germany.
| | - Behdad Aghelnejad
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Saale, Germany.
| | - Christian Schwieger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Saale, Germany.
| | - Annette Meister
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Saale, Germany.
| | - Andreas Kerth
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Saale, Germany.
| | - Dariush Hinderberger
- Institut für Chemie, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle, Saale, Germany.
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17
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Affiliation(s)
- Katrin Ackermann
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and EaStCHEM School of Chemistry, University of St Andrews, St Andrews, KY16 9ST, Scotland
| | - Bela E. Bode
- Biomedical Sciences Research Complex, Centre of Magnetic Resonance and EaStCHEM School of Chemistry, University of St Andrews, St Andrews, KY16 9ST, Scotland
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18
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Ackermann K, Pliotas C, Valera S, Naismith JH, Bode BE. Sparse Labeling PELDOR Spectroscopy on Multimeric Mechanosensitive Membrane Channels. Biophys J 2017; 113:1968-1978. [PMID: 29117521 PMCID: PMC5685675 DOI: 10.1016/j.bpj.2017.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 08/31/2017] [Accepted: 09/05/2017] [Indexed: 11/17/2022] Open
Abstract
Pulse electron paramagnetic resonance (EPR) is being applied to ever more complex biological systems comprising multiple subunits. Membrane channel proteins are of great interest as pulse EPR reports on functionally significant but distinct conformational states in a native environment without the need for crystallization. Pulse EPR, in the form of pulsed electron-electron double resonance (PELDOR), using site-directed spin labeling, is most commonly employed to accurately determine distances (in the nanometer range) between different regions of the structure. However, PELDOR data analysis is more challenging in systems containing more than two spins (e.g., homomultimers) due to distorting multispin effects. Without suppression of these effects, much of the information contained in PELDOR data cannot be reliably retrieved. Thus, it is of utmost importance for future PELDOR applications in structural biology to develop suitable approaches that can overcome the multispin problem. Here, two different approaches for suppressing multispin effects in PELDOR, sparse labeling of the protein (reducing the labeling efficiency f) and reducing the excitation probability of spins (λ), are compared on two distinct bacterial mechanosensitive channels. For both the pentameric channel of large conductance (MscL) and the heptameric channel of small conductance (MscS) of Escherichia coli, mutants containing a spin label in the cytosolic or the transmembrane region were tested. Data demonstrate that distance distributions can be significantly improved with either approach compared to the standard PELDOR measurement, and confirm that λ < 1/(n−1) is needed to sufficiently suppress multispin effects (with n being the number of spins in the system). A clear advantage of the sparse labeling approach is demonstrated for the cytosolic mutants due to a significantly smaller loss in sensitivity. For the transmembrane mutants, this advantage is less pronounced but still useful for MscS, but performance is inferior for MscL possibly due to structural perturbations by the bulkier diamagnetic spin label analog.
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Affiliation(s)
- Katrin Ackermann
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Christos Pliotas
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Silvia Valera
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - James H Naismith
- Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom
| | - Bela E Bode
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom; Biomedical Sciences Research Complex and EaStCHEM School of Chemistry, University of St Andrews, North Haugh, St Andrews, Fife, United Kingdom.
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19
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Maleimido-proxyl as an EPR spin label for the evaluation of conformational changes of albumin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 46:773-787. [DOI: 10.1007/s00249-017-1257-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 08/04/2017] [Accepted: 09/16/2017] [Indexed: 11/25/2022]
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20
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Halbmair K, Wegner J, Diederichsen U, Bennati M. Pulse EPR Measurements of Intramolecular Distances in a TOPP-Labeled Transmembrane Peptide in Lipids. Biophys J 2016; 111:2345-2348. [PMID: 27836102 PMCID: PMC5153538 DOI: 10.1016/j.bpj.2016.10.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 10/12/2016] [Accepted: 10/19/2016] [Indexed: 11/15/2022] Open
Abstract
We present the performance of nanometer-range pulse electron paramagnetic resonance distance measurements (pulsed electron-electron double resonance/double electron-electron resonance, PELDOR/DEER) on a transmembrane WALP24 peptide labeled with the semirigid unnatural amino acid 4-(3,3,5,5-tetra-methyl-2,6-dioxo-4-oxylpiperazin-1-yl)-l-phenylglycine (TOPP). Distances reported by the TOPP label are compared to the ones reported by the more standard MTSSL spin label, commonly employed in protein studies. Using high-power pulse electron paramagnetic resonance spectroscopy at Q-band frequencies (34 GHz), we show that in contrast to MTSSL, our label reports one-peak, sharp (Δr ≤ 0.4 nm) intramolecular distances. Orientational selectivity is not observed. When spin-labeled WALP24 was inserted in two representative lipid bilayers with different bilayer thickness, i.e., DMPC and POPC, the intramolecular distance reported by TOPP did not change with the bilayer environment. In contrast, the distance measured with MTSSL was strongly affected by the hydrophobic thickness of the lipid. The results demonstrate that the TOPP label is well suited to study the intrinsic structure of peptides immersed in lipids.
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Affiliation(s)
- Karin Halbmair
- Electron Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Janine Wegner
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany
| | - Ulf Diederichsen
- Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany
| | - Marina Bennati
- Electron Spin Resonance Spectroscopy, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Institute for Organic and Biomolecular Chemistry, Georg-August-University, Göttingen, Germany.
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21
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Hauenschild T, Reichenwallner J, Enkelmann V, Hinderberger D. Characterizing Active Pharmaceutical Ingredient Binding to Human Serum Albumin by Spin-Labeling and EPR Spectroscopy. Chemistry 2016; 22:12825-38. [DOI: 10.1002/chem.201601810] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Till Hauenschild
- Martin-Luther-Universität Halle-Wittenberg; Institute of Chemistry; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
| | - Jörg Reichenwallner
- Martin-Luther-Universität Halle-Wittenberg; Institute of Chemistry; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
| | - Volker Enkelmann
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Dariush Hinderberger
- Martin-Luther-Universität Halle-Wittenberg; Institute of Chemistry; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
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22
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Valera S, Ackermann K, Pliotas C, Huang H, Naismith JH, Bode BE. Accurate Extraction of Nanometer Distances in Multimers by Pulse EPR. Chemistry 2016; 22:4700-3. [PMID: 26865468 PMCID: PMC4848767 DOI: 10.1002/chem.201505143] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 12/15/2022]
Abstract
Pulse electron paramagnetic resonance (EPR) is gaining increasing importance in structural biology. The PELDOR (pulsed electron–electron double resonance) method allows extracting distance information on the nanometer scale. Here, we demonstrate the efficient extraction of distances from multimeric systems such as membrane‐embedded ion channels where data analysis is commonly hindered by multi‐spin effects.
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Affiliation(s)
- Silvia Valera
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Katrin Ackermann
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Christos Pliotas
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Hexian Huang
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - James H Naismith
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK
| | - Bela E Bode
- Centre of Magnetic Resonance, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK. .,Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, KY16 9ST, UK.
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23
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Meyer A, Abdullin D, Schnakenburg G, Schiemann O. Single and double nitroxide labeled bis(terpyridine)-copper(ii): influence of orientation selectivity and multispin effects on PELDOR and RIDME. Phys Chem Chem Phys 2016; 18:9262-71. [DOI: 10.1039/c5cp07621h] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The structure of Jahn–Teller distorted copper–nitroxide complexes in neutral and acidic solutions is investigated using EPR distance measurements taking into account the influence of orientation selectivity and multispin effects.
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Affiliation(s)
- Andreas Meyer
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Dinar Abdullin
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
| | - Gregor Schnakenburg
- Institute of Inorganic Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53121 Bonn
- Germany
| | - Olav Schiemann
- Institute of Physical and Theoretical Chemistry
- Rheinische Friedrich-Wilhelms-University Bonn
- 53115 Bonn
- Germany
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24
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Stein RA, Beth AH, Hustedt EJ. A Straightforward Approach to the Analysis of Double Electron-Electron Resonance Data. Methods Enzymol 2015; 563:531-67. [PMID: 26478498 PMCID: PMC5231402 DOI: 10.1016/bs.mie.2015.07.031] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Double electron-electron resonance (DEER) is now widely utilized to measure distance distributions in the 20-70Å range. DEER is frequently applied to biological systems that have multiple conformational states leading to complex distance distributions. These complex distributions raise issues regarding the best approach to analyze DEER data. A widely used method utilizes a priori background correction followed by Tikhonov regularization. Unfortunately, the underlying assumptions of this approach can impact the analysis. In this chapter, a method of analyzing DEER data is presented that is ideally suited to obtain these complex distance distributions. The approach allows the fitting of raw experimental data without a priori background correction as well as the rigorous determination of uncertainties for all fitting parameters. This same methodological approach can be used for the simultaneous or global analysis of multiple DEER data sets using variable ratios of a common set of components, thus allowing direct correlation of distance components with functionally relevant conformational and biochemical states. Examples are given throughout to highlight this robust fitting approach.
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Affiliation(s)
- Richard A Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Albert H Beth
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA
| | - Eric J Hustedt
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, USA.
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25
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Stangenberg R, Wu Y, Hedrich J, Kurzbach D, Wehner D, Weidinger G, Kuan SL, Jansen MI, Jelezko F, Luhmann HJ, Hinderberger D, Weil T, Müllen K. A polyphenylene dendrimer drug transporter with precisely positioned amphiphilic surface patches. Adv Healthc Mater 2015; 4:377-84. [PMID: 25182694 DOI: 10.1002/adhm.201400291] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/19/2014] [Indexed: 01/14/2023]
Abstract
The design and synthesis of a polyphenylene dendrimer (PPD 3) with discrete binding sites for lipophilic guest molecules and characteristic surface patterns is presented. Its semi-rigidity in combination with a precise positioning of hydrophilic and hydrophobic groups at the periphery yields a refined architecture with lipophilic binding pockets that accommodate defined numbers of biologically relevant guest molecules such as fatty acids or the drug doxorubicin. The size, architecture, and surface textures allow to even penetrate brain endothelial cells that are a major component of the extremely tight blood-brain barrier. In addition, low to no toxicity is observed in in vivo studies using zebrafish embryos. The unique PPD scaffold allows the precise placement of functional groups in a given environment and offers a universal platform for designing drug transporters that closely mimic many features of proteins.
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Affiliation(s)
- René Stangenberg
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Yuzhou Wu
- Institute of Organic Chemistry III; Ulm University; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Jana Hedrich
- Institute for Physiology; Johannes Gutenberg University Mainz; Duesbergweg 6 55128 Mainz Germany
| | - Dennis Kurzbach
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
| | - Daniel Wehner
- Institute for Biochemistry and Molecular Biology; Ulm University; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Gilbert Weidinger
- Institute for Biochemistry and Molecular Biology; Ulm University; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Seah Ling Kuan
- Institute of Organic Chemistry III; Ulm University; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Malin Insa Jansen
- Institute for Physiology; Johannes Gutenberg University Mainz; Duesbergweg 6 55128 Mainz Germany
| | - Fedor Jelezko
- Institute for Quantum Optics; Ulm University; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Heiko J. Luhmann
- Institute for Physiology; Johannes Gutenberg University Mainz; Duesbergweg 6 55128 Mainz Germany
| | - Dariush Hinderberger
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
- Institute of Chemistry; Martin-Luther-Universität; Halle-Wittenberg Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
| | - Tanja Weil
- Institute of Organic Chemistry III; Ulm University; Albert-Einstein-Allee 11 89081 Ulm Germany
| | - Klaus Müllen
- Max Planck Institute for Polymer Research; Ackermannweg 10 55128 Mainz Germany
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26
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Feintuch A, Otting G, Goldfarb D. Gd3+ Spin Labeling for Measuring Distances in Biomacromolecules. Methods Enzymol 2015; 563:415-57. [DOI: 10.1016/bs.mie.2015.07.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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27
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Edwards D, Huber T, Hussain S, Stone K, Kinnebrew M, Kaminker I, Matalon E, Sherwin M, Goldfarb D, Han S. Determining the Oligomeric Structure of Proteorhodopsin by Gd3+-Based Pulsed Dipolar Spectroscopy of Multiple Distances. Structure 2014; 22:1677-86. [DOI: 10.1016/j.str.2014.09.008] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 08/15/2014] [Accepted: 09/04/2014] [Indexed: 12/30/2022]
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28
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Pavićević AA, Popović-Bijelić AD, Mojović MD, Šušnjar SV, Bačić GG. Binding of Doxyl Stearic Spin Labels to Human Serum Albumin: An EPR Study. J Phys Chem B 2014; 118:10898-905. [DOI: 10.1021/jp5068928] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Aleksandra A. Pavićević
- Faculty
of Physical Chemistry, University of Belgrade, Studentski trg 12-16, P.O. Box 47, 11158 Belgrade, Serbia
| | - Ana D. Popović-Bijelić
- Faculty
of Physical Chemistry, University of Belgrade, Studentski trg 12-16, P.O. Box 47, 11158 Belgrade, Serbia
| | - Miloš D. Mojović
- Faculty
of Physical Chemistry, University of Belgrade, Studentski trg 12-16, P.O. Box 47, 11158 Belgrade, Serbia
| | | | - Goran G. Bačić
- Faculty
of Physical Chemistry, University of Belgrade, Studentski trg 12-16, P.O. Box 47, 11158 Belgrade, Serbia
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29
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Goldfarb D. Gd3+ spin labeling for distance measurements by pulse EPR spectroscopy. Phys Chem Chem Phys 2014; 16:9685-99. [DOI: 10.1039/c3cp53822b] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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30
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Kattnig DR, Reichenwallner J, Hinderberger D. Modeling Excluded Volume Effects for the Faithful Description of the Background Signal in Double Electron–Electron Resonance. J Phys Chem B 2013; 117:16542-57. [DOI: 10.1021/jp408338q] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Jörg Reichenwallner
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Chemistry, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz
4, 06120 Halle (Saale), Germany
| | - Dariush Hinderberger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Institute
of Chemistry, Martin-Luther-Universität Halle-Wittenberg, Von-Danckelmann-Platz
4, 06120 Halle (Saale), Germany
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31
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Matalon E, Faingold O, Eisenstein M, Shai Y, Goldfarb D. The topology, in model membranes, of the core peptide derived from the T-cell receptor transmembrane domain. Chembiochem 2013; 14:1867-75. [PMID: 23881822 DOI: 10.1002/cbic.201300191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Indexed: 01/16/2023]
Abstract
The T-cell receptor-CD3 complex (TCR-CD3) serves a critical role in protecting organisms from infectious agents. The TCR is a heterodimer composed of α- and β-chains, which are responsible for antigen recognition. Within the transmembrane domain of the α-subunit, a region has been identified to be crucial for the assembly and function of the TCR. This region, termed core peptide (CP), consists of nine amino acids (GLRILLLKV), two of which are charged (lysine and arginine) and are crucial for the interaction with CD3. Earlier studies have shown that a synthetic peptide corresponding to the CP sequence can suppress the immune response in animal models of T-cell-mediated inflammation, by disrupting proper assembly of the TCR. As a step towards the understanding of the source of the CP activity, we focused on CP in egg phosphatidylcholine/cholesterol (9:1, mol/mol) model membranes and determined its secondary structure, oligomerization state, and orientation with respect to the membrane. To achieve this goal, 15-residue segments of TCRα, containing the CP, were synthesized and spin-labeled at different locations with a nitroxide derivative. Electron spin-echo envelope modulation spectroscopy was used to probe the position and orientation of the peptides within the membrane, and double electron-electron resonance measurements were used to probe its conformation and oligomerization state. We found that the peptide is predominantly helical in a membrane environment and tends to form oligomers (mostly dimers) that are parallel to the membrane plane.
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Affiliation(s)
- Erez Matalon
- Department of Chemical Physics, Weizmann Institute of Science, 234 Hertzl St, Rehovot, 7632700 (Israel)
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Kattnig DR, Hinderberger D. Analytical distance distributions in systems of spherical symmetry with applications to double electron-electron resonance. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2013; 230:50-63. [PMID: 23454574 DOI: 10.1016/j.jmr.2013.01.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 05/24/2023]
Abstract
Based on a simple geometrical approach, we derive analytical expression of the probability density functions (pdfs) of distance of probe molecules distributed homogeneously in spherical aggregates with shell structure. These distance distributions can be utilized in the investigation of double electron-electron resonance (DEER) data of disordered nanometer-sized spin clusters. Structural insights and geometrical parameters of the aggregates can be extracted by modeling the DEER time traces based on the analytical pdfs. This approach is efficient and avoids difficulties of the model-free solution of the inverse problem that are related to multi-spin effects, limited excitation bandwidth, bias introduced by the regularization scheme, or ambiguity resulting from broad distance distributions. The derived pdfs can serve as building blocks, from which the distance distributions in arbitrary spherically symmetric objects can be assembled. The scenario of the pumped species being chemically distinct from the observed species is covered as well as that of a single type of probe molecules. We demonstrate the merits of analytical distance distributions by studying the distribution of three different spin probes in SDS micelles. By simultaneously analyzing DEER data corresponding to different spin probe concentrations, the distribution of the spin probes over the micelle can be determined. Employing Bayesian inference it is found that for all probes studied, a spherical shell model is most appropriate among the studied models and by orders of magnitude more likely than a homogeneous distribution in a ball. This statement also applies to probes that are deemed nonpolar. We envisage that the spin probe distributions in disordered soft and hard matter systems can now be quantified using DEER spectroscopy with greater precision and reduced ambiguity.
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Affiliation(s)
- Daniel R Kattnig
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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33
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Reichenwallner J, Hinderberger D. Using bound fatty acids to disclose the functional structure of serum albumin. Biochim Biophys Acta Gen Subj 2013; 1830:5382-93. [PMID: 23643928 DOI: 10.1016/j.bbagen.2013.04.031] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/23/2013] [Accepted: 04/24/2013] [Indexed: 11/16/2022]
Abstract
BACKGROUND Serum albumin is a major transport protein in mammals and is known to have at least seven binding sites for long-chain fatty acids (FAs). SCOPE OF REVIEW We have devised a new electron paramagnetic resonance (EPR) spectroscopic approach to gain information on the functional structure of serum albumin in solution in a "coarse-grained" manner from the ligands' point of view. Our approach is based on using spin labeled (paramagnetic) stearic acids self-assembled with albumin and subsequent nanoscale distance measurements between the FAs using double electron-electron resonance spectroscopy (DEER). Simple continuous wave (CW) EPR spectroscopy, which allows for quantification of bound ligands, complements our studies. MAJOR CONCLUSIONS Based on DEER nanoscale distance measurements, the functional solution structure of human serum albumin (HSA) has remarkably been found to have a much more symmetric distribution of entry points to the FA binding sites than expected from the crystal structure, indicating increased surface flexibility and plasticity for HSA in solution. In contrast, for bovine serum albumin (BSA), the entry point topology is in good agreement with that expected from the crystal structure of HSA. Changes in the solution structures between albumins can hence be revealed and extended to more albumins to detect functional differences at the nanoscale. Going beyond fundamental structural studies, our research platform is also excellently suited for general studies of protein-solvent interactions, temperature effects and ligand binding. GENERAL SIGNIFICANCE We discuss how our research platform helps illuminate protein dynamics and function and can be used to characterize albumin-based hybrid materials. This article is part of a Special Issue entitled Serum Albumin.
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Affiliation(s)
- Jörg Reichenwallner
- Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany; Institute for Pharmacy and Biochemistry, Johannes Gutenberg-Universität Mainz, Johann-Joachim-Becher-Weg 30, D-55128 Mainz, Germany
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34
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Nikolakopoulou Z, Shaikh MH, Dehlawi H, Michael-Titus AT, Parkinson EK. The induction of apoptosis in pre-malignant keratinocytes by omega-3 polyunsaturated fatty acids docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) is inhibited by albumin. Toxicol Lett 2013; 218:150-8. [DOI: 10.1016/j.toxlet.2013.01.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 01/24/2013] [Accepted: 01/25/2013] [Indexed: 11/25/2022]
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35
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Matalon E, Kaminker I, Zimmermann H, Eisenstein M, Shai Y, Goldfarb D. Topology of the trans-membrane peptide WALP23 in model membranes under negative mismatch conditions. J Phys Chem B 2013; 117:2280-93. [PMID: 23311473 DOI: 10.1021/jp310056h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The organization and orientation of membrane-inserted helices is important for better understanding the mode of action of membrane-active peptides and of protein-membrane interactions. Here we report on the application of ESEEM (electron spin-echo envelope modulation) and DEER (double electron-electron resonance) techniques to probe the orientation and oligomeric state of an α-helical trans-membrane model peptide, WALP23, under conditions of negative mismatch between the hydrophobic cores of the model membrane and the peptide. Using ESEEM, we measured weak dipolar interactions between spin-labeled WALP23 and (2)H nuclei of either the solvent (D2O) or of lipids specifically deuterated at the choline group. The ESEEM data obtained from the deuterated lipids were fitted using a model that provided the spin label average distance from a layer of (2)H nuclei in the hydrophilic region of the membrane and the density of the (2)H nuclei in the layer. DEER was used to probe oligomerization through the dipolar interaction between two spin-labels on different peptides. We observed that the center of WALP23 does not coincide with the bilayer midplane and its N-terminus is more buried than the C-terminus. In addition, the ESEEM data fitting yielded a (2)H layer density that was much lower than expected. The DEER experiments revealed the presence of oligomers, the presence of which was attributable to the negative mismatch and the electrostatic dipole of the peptide. A discussion of a possible arrangement of the individual helices in the oligomers that is consistent with the ESEEM and DEER data is presented.
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Affiliation(s)
- Erez Matalon
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot, Israel 76100
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36
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Kuan SL, Stöckle B, Reichenwallner J, Ng DYW, Wu Y, Doroshenko M, Koynov K, Hinderberger D, Müllen K, Weil T. Dendronized albumin core-shell transporters with high drug loading capacity. Biomacromolecules 2013; 14:367-76. [PMID: 23210662 DOI: 10.1021/bm301531c] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We describe the synthesis of a core-shell biohybrid consisting of a human serum albumin (HSA) core that serves as a reservoir for lipophilic molecules and a cationized shell region consisting of ethynyl-G2.0-PAMAM or ethynyl-G3.0-PAMAM dendrons. The binding capacity of lipophilic guests was quantified applying electron paramagnetic resonance (EPR) spectroscopy, and five to six out of seven pockets were still available compared with HSA. The attachment of ethynyl-G2.0-PAMAM dendrons to HSA yielded a nontoxic core-shell macromolecule that was clearly uptaken by A549 human epithelial cells due to the presence of the dendritic PAMAM shell. Significantly higher loading of doxorubicin was observed for dendronized G2-DHSA compared with the native protein due to the availability of binding pockets of the HSA core, and interaction with the dendritic shell. Dendronized G2-DHSA-doxorubicin displayed significant cytotoxicity resulting from high drug loading and high stability under different conditions, thus demonstrating its great potential as a transporter for drug molecules.
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Affiliation(s)
- Seah Ling Kuan
- Institute of Organic Chemistry III, University of Ulm, Albert-Einstein-Allee 11, Ulm, Germany
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37
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von Hagens T, Polyhach Y, Sajid M, Godt A, Jeschke G. Suppression of ghost distances in multiple-spin double electron–electron resonance. Phys Chem Chem Phys 2013; 15:5854-66. [DOI: 10.1039/c3cp44462g] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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38
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Kattnig DR, Bund T, Boggs JM, Harauz G, Hinderberger D. Lateral self-assembly of 18.5-kDa myelin basic protein (MBP) charge component-C1 on membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012; 1818:2636-47. [DOI: 10.1016/j.bbamem.2012.06.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Revised: 05/23/2012] [Accepted: 06/14/2012] [Indexed: 11/16/2022]
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39
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Akdogan Y, Reichenwallner J, Hinderberger D. Evidence for water-tuned structural differences in proteins: an approach emphasizing variations in local hydrophilicity. PLoS One 2012; 7:e45681. [PMID: 23049837 PMCID: PMC3458090 DOI: 10.1371/journal.pone.0045681] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Accepted: 08/22/2012] [Indexed: 11/19/2022] Open
Abstract
We present experimental evidence for the significant effect that water can have on the functional structure of proteins in solution. Human (HSA) and Bovine Serum Albumin (BSA) have an amino acid sequence identity of 75.52% and are chosen as model proteins. We employ EPR-based nanoscale distance measurements using double electron-electron resonance (DEER) spectroscopy and both albumins loaded with long chain fatty acids (FAs) in solution to globally (yet indirectly) characterize the tertiary protein structures from the bound ligands’ points of view. The complete primary structures and crystal structures of HSA and as of recently also BSA are available. We complement the picture as we have recently determined the DEER-derived solution structure of HSA and here present the corresponding BSA solution structure. The characteristic asymmetric FA distribution in the crystal structure of HSA can surprisingly be observed by DEER in BSA in solution. This indicates that the BSA conformational ensemble in solution seems to be narrow and close to the crystal structure of HSA. In contrast, for HSA in solution a much more symmetric FA distribution was found. Thus, conformational adaptability and flexibility dominate in the HSA solution structure while BSA seems to lack these properties. We further show that differences in amino acid hydropathies of specific structural regions in both proteins can be used to correlate the observed difference in the global (tertiary) solution structures with the differences on the primary structure level.
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Affiliation(s)
- Yasar Akdogan
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Jörg Reichenwallner
- Max Planck Institute for Polymer Research, Mainz, Germany
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
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40
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Yulikov M, Lueders P, Farooq Warsi M, Chechik V, Jeschke G. Distance measurements in Au nanoparticles functionalized with nitroxide radicals and Gd3+–DTPA chelate complexes. Phys Chem Chem Phys 2012; 14:10732-46. [DOI: 10.1039/c2cp40282c] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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41
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Akdogan Y, Hinderberger D. Solvent-Induced Protein Refolding at Low Temperatures. J Phys Chem B 2011; 115:15422-9. [DOI: 10.1021/jp209646f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yasar Akdogan
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Dariush Hinderberger
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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42
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Spiess HW. Addendum to the paper "Dead-time free measurement of dipole-dipole interactions between electron spins" by M. Pannier, S. Veit, A. Godt, G. Jeschke, and H.W. Spiess [J. Magn. Reson. 142 (2000) 331-340]. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2011; 213:326-328. [PMID: 21890390 DOI: 10.1016/j.jmr.2011.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The development of four-pulse DEER as described, which has been published in the Journal of Magnetic Resonance more than 10 years ago. The corresponding paper is an example where a slight advance, such as adding a refocusing pulse, which in retrospect looks so simple, can have a remarkable impact on an entire field of science. In our case it offered a simple way to exact measurements of distances between defined species in the nanometer range. The current applications are mainly in determining structures of proteins and nucleic acids.
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43
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Flaender M, Sicoli G, Aci-Seche S, Reignier T, Maurel V, Saint-Pierre C, Boulard Y, Gambarelli S, Gasparutto D. A triple spin-labeling strategy coupled with DEER analysis to detect DNA modifications and enzymatic repair. Chembiochem 2011; 12:2560-3. [PMID: 21984076 DOI: 10.1002/cbic.201100550] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Indexed: 12/20/2022]
Abstract
In a spin: Spin-labeled oligonucleotides produced by click chemistry can be studied by EPR, by using a DEER sequence. This was used to test a complex triple-labeling strategy with damaged DNA. Extensive and accurate analysis of DNA structure and enzymatic repair processes were performed after digestion by EndoIV. Modified DNA structures and DNA-protein interactions can now be readily studied.
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Affiliation(s)
- Mélanie Flaender
- Institut Nanoscience et Cryogénie, Laboratoire de Chimie Inorganique et Biologique, UMR-E n°3 CEA-UJF, CEA-Grenoble, 17 Avenue des Martyrs, 38054 Grenoble Cedex 9, France
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44
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Junk MJN, Spiess HW, Hinderberger D. Characterization of the solution structure of human serum albumin loaded with a metal porphyrin and fatty acids. Biophys J 2011; 100:2293-301. [PMID: 21539799 DOI: 10.1016/j.bpj.2011.03.050] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 03/21/2011] [Accepted: 03/25/2011] [Indexed: 10/18/2022] Open
Abstract
The structure of human serum albumin loaded with a metal porphyrin and fatty acids in solution is characterized by orientation-selective double electron-electron resonance (DEER) spectroscopy. Human serum albumin, spin-labeled fatty acids, and Cu(II) protoporphyrin IX-a hemin analog-form a fully self-assembled system that allows obtaining distances and mutual orientations between the paramagnetic guest molecules. We report a simplified analysis for the orientation-selective DEER data which can be applied when the orientation selection of one spin in the spin pair dominates the orientation selection of the other spin. The dipolar spectra reveal a dominant distance of 3.85 nm and a dominant orientation of the spin-spin vectors between Cu(II) protoporphyrin IX and 16-doxyl stearic acid, the electron paramagnetic resonance reporter group of the latter being located near the entry points to the fatty acid binding sites. This observation is in contrast to crystallographic data that suggest an asymmetric distribution of the entry points in the protein and hence the occurrence of various distances. In conjunction with the findings of a recent DEER study, the obtained data are indicative of a symmetric distribution of the binding site entries on the protein's surface. The overall anisotropic shape of the protein is reflected by one spin-spin vector orientation dominating the DEER data.
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