1
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Nguyen H, Podolnikova NP, Ugarova TP, Wang X. α MI-domain of integrin Mac-1 binds the cytokine pleiotrophin using multiple mechanisms. Structure 2024; 32:1184-1196.e4. [PMID: 38729161 PMCID: PMC11316656 DOI: 10.1016/j.str.2024.04.013] [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: 01/24/2024] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 05/12/2024]
Abstract
The integrin Mac-1 (αMβ2, CD11b/CD18, CR3) is an adhesion receptor expressed on macrophages and neutrophils. Mac-1 is also a promiscuous integrin that binds a diverse set of ligands through its αMI-domain. However, the binding mechanism of most ligands remains unclear. We have characterized the interaction of αMI-domain with the cytokine pleiotrophin (PTN), a protein known to bind αMI-domain and induce Mac-1-mediated cell adhesion and migration. Our data show that PTN's N-terminal domain binds a unique site near the N- and C-termini of the αMI-domain using a metal-independent mechanism. However, a stronger interaction is achieved when an acidic amino acid in a zwitterionic motif in PTN's C-terminal domain chelates the divalent cation in the metal ion-dependent adhesion site of active αMI-domain. These results indicate that αMI-domain can bind ligands using multiple mechanisms and that the active αMI-domain has a preference for motifs containing both positively and negatively charged amino acids.
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Affiliation(s)
- Hoa Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA
| | | | - Tatiana P Ugarova
- School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281, USA.
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2
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Réant BL, Mackintosh FJ, Gransbury GK, Mattei CA, Alnami B, Atkinson BE, Bonham KL, Baldwin J, Wooles AJ, Vitorica-Yrezabal IJ, Lee D, Chilton NF, Liddle ST, Mills DP. Tris-Silanide f-Block Complexes: Insights into Paramagnetic Influence on NMR Chemical Shifts. JACS AU 2024; 4:2695-2711. [PMID: 39055148 PMCID: PMC11267535 DOI: 10.1021/jacsau.4c00466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/27/2024]
Abstract
The paramagnetism of f-block ions has been exploited in chiral shift reagents and magnetic resonance imaging, but these applications tend to focus on 1H NMR shifts as paramagnetic broadening makes less sensitive nuclei more difficult to study. Here we report a solution and solid-state (ss) 29Si NMR study of an isostructural series of locally D 3h -symmetric early f-block metal(III) tris-hypersilanide complexes, [M{Si(SiMe3)3}3(THF)2] (1-M; M = La, Ce, Pr, Nd, U); 1-M were also characterized by single crystal and powder X-ray diffraction, EPR, ATR-IR, and UV-vis-NIR spectroscopies, SQUID magnetometry, and elemental analysis. Only one SiMe3 signal was observed in the 29Si ssNMR spectra of 1-M, while two SiMe3 signals were seen in solution 29Si NMR spectra of 1-La and 1-Ce. This is attributed to dynamic averaging of the SiMe3 groups in 1-M in the solid state due to free rotation of the M-Si bonds and dissociation of THF from 1-M in solution to give the locally C 3v -symmetric complexes [M{Si(SiMe3)3}3(THF) n ] (n = 0 or 1), which show restricted rotation of M-Si bonds on the NMR time scale. Density functional theory and complete active space self-consistent field spin-orbit calculations were performed on 1-M and desolvated solution species to model paramagnetic NMR shifts. We find excellent agreement of experimental 29Si NMR data for diamagnetic 1-La, suggesting n = 1 in solution and reasonable agreement of calculated paramagnetic shifts of SiMe3 groups for 1-M (M = Pr and Nd); the NMR shifts for metal-bound 29Si nuclei could only be reproduced for diamagnetic 1-La, showing the current limitations of pNMR calculations for larger nuclei.
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Affiliation(s)
- Benjamin
L. L. Réant
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Fraser J. Mackintosh
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Gemma K. Gransbury
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Carlo Andrea Mattei
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Barak Alnami
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Benjamin E. Atkinson
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Katherine L. Bonham
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Jack Baldwin
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Ashley J. Wooles
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | | | - Daniel Lee
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Nicholas F. Chilton
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
- Research
School of Chemistry, The Australian National
University, Sullivans
Creek Road, Canberra 2601, Australian Capital Territory, Australia
| | - Stephen T. Liddle
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - David P. Mills
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
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3
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Dos Santos K, Bartocci A, Gillet N, Denis-Quanquin S, Roux A, Lin E, Xu Z, Finizola R, Chedozeau P, Chen X, Caradeuc C, Baudin M, Bertho G, Riobé F, Maury O, Dumont E, Giraud N. One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics. Phys Chem Chem Phys 2024; 26:14573-14581. [PMID: 38722087 DOI: 10.1039/d4cp00463a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
The supramolecular interaction between lanthanide complexes and proteins is at the heart of numerous chemical and biological studies. Some of these complexes have demonstrated remarkable interaction properties with proteins or peptides in solution and in the crystalline state. Here we have used the paramagnetism of lanthanide ions to characterize the affinity of two lanthanide complexes for ubiquitin. As the interaction process is dynamic, the acquired NMR data only reflect the time average of the different steps. We have used molecular dynamics (MD) simulations to get a deeper insight into the detailed interaction scenario at the microsecond scale. This NMR/MD approach enabled us to establish that the tris-dipicolinate complex interacts specifically with arginines and lysines, while the crystallophore explores the protein surface through weak interactions with carboxylates. These observations shed new light on the dynamic interaction properties of these complexes, which will ultimately enable us to propose a crystallization mechanism.
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Affiliation(s)
- Karen Dos Santos
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Alessio Bartocci
- Department of Physics, University of Trento, Via Sommarive 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
- Institut de Chimie de Strasbourg, UMR 7177, CNRS, Université de Strasbourg, Strasbourg Cedex 67083, France
| | - Natacha Gillet
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Sandrine Denis-Quanquin
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Amandine Roux
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
- Polyvalan SAS, Lyon, France
| | - Eugene Lin
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Zeren Xu
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Raphael Finizola
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Pauline Chedozeau
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Xi Chen
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Cédric Caradeuc
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - Mathieu Baudin
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
- Laboratoire des Biomolécules, LBM, Département de chimie, École Normale Supérieure, PSL Université, Sorbonne Université 45 Rue d'Ulm, 75005 Paris, France
| | - Gildas Bertho
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
| | - François Riobé
- Univ. Bordeaux CNRS, Bordeaux INP, ICMCB UMR 5026, F-33600 Pessac, France
| | - Olivier Maury
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Via Sommarive 14, I-38123 Trento, Italy
| | - Elise Dumont
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272, 06108 Nice, France.
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
| | - Nicolas Giraud
- Université Paris Cité, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
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4
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Marinova P, Tamahkyarova K. Synthesis and Biological Activities of Some Metal Complexes of Peptides: A Review. BIOTECH 2024; 13:9. [PMID: 38651489 PMCID: PMC11036290 DOI: 10.3390/biotech13020009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Peptides, both natural and synthetic, are well suited for a wide range of purposes and offer versatile applications in different fields such as biocatalysts, injectable hydrogels, tumor treatment, and drug delivery. The research of the better part of the cited papers was conducted using various database platforms such as MetalPDB. The rising prominence of therapeutic peptides encompasses anticancer, antiviral, antimicrobial, and anti-neurodegenerative properties. The metals Na, K, Mg, Ca, Fe, Mn, Co, Cu, Zn, and Mo are ten of the twenty elements that are considered essential for life. Crucial for understanding the biological role of metals is the exploration of metal-bound proteins and peptides. Aside from essential metals, there are other non-essential metals that also interact biologically, exhibiting either therapeutic or toxic effects. Irregularities in metal binding contribute to diseases like Alzheimer's, neurodegenerative disorders, Wilson's, and Menkes disease. Certain metal complexes have potential applications as radiopharmaceuticals. The examination of these complexes was achieved by preforming UV-Vis, IR, EPR, NMR spectroscopy, and X-ray analysis. This summary, although unable to cover all of the studies in the field, offers a review of the ongoing experimentation and is a basis for new ideas, as well as strategies to explore and gain knowledge from the extensive realm of peptide-chelated metals and biotechnologies.
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Affiliation(s)
- Petja Marinova
- Department of General and Inorganic Chemistry with Methodology of Chemistry Education, Faculty of Chemistry, University of Plovdiv, “Tzar Assen” Str. 24, 4000 Plovdiv, Bulgaria;
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5
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Grifagni D, Silva JM, Querci L, Lepoivre M, Vallières C, Louro RO, Banci L, Piccioli M, Golinelli-Cohen MP, Cantini F. Biochemical and cellular characterization of the CISD3 protein: Molecular bases of cluster release and destabilizing effects of nitric oxide. J Biol Chem 2024; 300:105745. [PMID: 38354784 PMCID: PMC10937110 DOI: 10.1016/j.jbc.2024.105745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024] Open
Abstract
The NEET proteins, an important family of iron-sulfur (Fe-S) proteins, have generated a strong interest due to their involvement in diverse diseases such as cancer, diabetes, and neurodegenerative disorders. Among the human NEET proteins, CISD3 has been the least studied, and its functional role is still largely unknown. We have investigated the biochemical features of CISD3 at the atomic and in cellulo levels upon challenge with different stress conditions i.e., iron deficiency, exposure to hydrogen peroxide, and nitric oxide. The redox and cellular stability properties of the protein agree on a predominance of reduced form of CISD3 in the cells. Upon the addition of iron chelators, CISD3 loses its Fe-S clusters and becomes unstructured, and its cellular level drastically decreases. Chemical shift perturbation measurements suggest that, upon cluster oxidation, the protein undergoes a conformational change at the C-terminal CDGSH domain, which determines the instability of the oxidized state. This redox-associated conformational change may be the source of cooperative electron transfer via the two [Fe2S2] clusters in CISD3, which displays a single sharp voltammetric signal at -31 mV versus SHE. Oxidized CISD3 is particularly sensitive to the presence of hydrogen peroxide in vitro, whereas only the reduced form is able to bind nitric oxide. Paramagnetic NMR provides clear evidence that, upon NO binding, the cluster is disassembled but iron ions are still bound to the protein. Accordingly, in cellulo CISD3 is unaffected by oxidative stress induced by hydrogen peroxide but it becomes highly unstable in response to nitric oxide treatment.
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Affiliation(s)
- Deborah Grifagni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - José Malanho Silva
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Querci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Michel Lepoivre
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cindy Vallières
- CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Lucia Banci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
| | | | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
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6
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Nguyen H, Podolnikova NP, Ugarova TP, Wang X. α MI-domain of Integrin Mac-1 Binds the Cytokine Pleiotrophin Using Multiple Mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.01.578455. [PMID: 38352421 PMCID: PMC10862807 DOI: 10.1101/2024.02.01.578455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
The integrin Mac-1 (αMβ2, CD11b/CD18, CR3) is an important adhesion receptor expressed on macrophages and neutrophils. Mac-1 is also the most promiscuous member of the integrin family that binds a diverse set of ligands through its αMI-domain. However, the binding mechanism of most ligands is not clear. We have determined the interaction of αMI-domain with the cytokine pleiotrophin (PTN), a cationic protein known to bind αMI-domain and induce Mac-1-mediated cell adhesion and migration. Our data show that PTN's N-terminal domain binds a unique site near the N- and C-termini of the αMI-domain using a metal-independent mechanism. However, stronger interaction is achieved when an acidic amino acid in a zwitterionic motif in PTN's C-terminal domain chelates the divalent cation in the metal ion-dependent adhesion site of the active αMI-domain. These results indicate that αMI-domain can bind ligands using multiple mechanisms, and suggest that active αMI-domain prefers acidic amino acids in zwitterionic motifs.
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Affiliation(s)
- Hoa Nguyen
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | | | | | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
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7
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Novakovic M, Kim J, Su XC, Kupče E, Frydman L. Relaxation-Assisted Magnetization Transfer Phenomena for a Sensitivity-Enhanced 2D NMR. Anal Chem 2023; 95:18091-18098. [PMID: 38008904 PMCID: PMC10719887 DOI: 10.1021/acs.analchem.3c03149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/08/2023] [Accepted: 11/08/2023] [Indexed: 11/28/2023]
Abstract
2D NOESY and TOCSY play central roles in contemporary NMR. We have recently discussed how solvent-driven exchanges can significantly enhance the sensitivity of such methods when attempting correlations between labile and nonlabile protons. This study explores two scenarios where similar sensitivity enhancements can be achieved in the absence of solvent exchange: the first one involves biomolecular paramagnetic systems, while the other involves small organic molecules in natural abundance. It is shown that, in both cases, the effects introduced by either differential paramagnetic shift and relaxation or by polarization sharing among networks of protons can provide a similar sensitivity boost, as previously discussed for solvent exchange. The origin and potential of the resulting enhancements are analyzed, and experiments that demonstrate them in protein and natural products are exemplified. Limitations and future improvements of these approaches are also briefly discussed.
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Affiliation(s)
- Mihajlo Novakovic
- Departments
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Jihyun Kim
- Departments
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
- Department
of Chemistry Education, Kyungpook National
University, Daegu 41566, Republic of Korea
| | - Xun-Cheng Su
- State
Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - E̅riks Kupče
- Bruker
Ltd., Banner Lane, Coventry CV4 9GH, United Kingdom
| | - Lucio Frydman
- Departments
of Chemical and Biological Physics, Weizmann
Institute of Science, Rehovot 7610001, Israel
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8
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Cucuzza S, Sitnik M, Jurt S, Michel E, Dai W, Müntener T, Ernst P, Häussinger D, Plückthun A, Zerbe O. Unexpected dynamics in femtomolar complexes of binding proteins with peptides. Nat Commun 2023; 14:7823. [PMID: 38016954 PMCID: PMC10684580 DOI: 10.1038/s41467-023-43596-2] [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: 02/18/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023] Open
Abstract
Ultra-tight binding is usually observed for proteins associating with rigidified molecules. Previously, we demonstrated that femtomolar binders derived from the Armadillo repeat proteins (ArmRPs) can be designed to interact very tightly with fully flexible peptides. Here we show for ArmRPs with four and seven sequence-identical internal repeats that the peptide-ArmRP complexes display conformational dynamics. These dynamics stem from transient breakages of individual protein-residue contacts that are unrelated to overall unbinding. The labile contacts involve electrostatic interactions. We speculate that these dynamics allow attaining very high binding affinities, since they reduce entropic losses. Importantly, only NMR techniques can pick up these local events by directly detecting conformational exchange processes without complications from changes in solvent entropy. Furthermore, we demonstrate that the interaction surface of the repeat protein regularizes upon peptide binding to become more compatible with the peptide geometry. These results provide novel design principles for ultra-tight binders.
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Affiliation(s)
- Stefano Cucuzza
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Malgorzata Sitnik
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Erich Michel
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
- Department of Biochemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Wenzhao Dai
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Thomas Müntener
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056, Basel, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland.
| | - Oliver Zerbe
- Department of Chemistry, University of Zürich, Winterthurerstrasse, 190, 8057, Zürich, Switzerland.
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9
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Wieske LHE, Peintner S, Erdélyi M. Ensemble determination by NMR data deconvolution. Nat Rev Chem 2023:10.1038/s41570-023-00494-x. [PMID: 37169885 DOI: 10.1038/s41570-023-00494-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/03/2023] [Indexed: 05/13/2023]
Abstract
Nuclear magnetic resonance (NMR) is the spectroscopic technique of choice for determining molecular conformations in solution at atomic resolution. As solution NMR spectra are rich in structural and dynamic information, the way in which the data should be acquired and handled to deliver accurate ensembles is not trivial. This Review provides a guide to the NMR experiment selection and parametrization process, the generation of viable theoretical conformer pools and the deconvolution of time-averaged NMR data into a conformer ensemble that accurately represents a flexible molecule in solution. In addition to reviewing the key elements of solution ensemble determination of flexible mid-sized molecules, the feasibility and pitfalls of data deconvolution are discussed with a comparison of the performance of representative algorithms.
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Affiliation(s)
| | - Stefan Peintner
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden.
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10
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Koehler Leman J, Künze G. Recent Advances in NMR Protein Structure Prediction with ROSETTA. Int J Mol Sci 2023; 24:ijms24097835. [PMID: 37175539 PMCID: PMC10178863 DOI: 10.3390/ijms24097835] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/15/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful method for studying the structure and dynamics of proteins in their native state. For high-resolution NMR structure determination, the collection of a rich restraint dataset is necessary. This can be difficult to achieve for proteins with high molecular weight or a complex architecture. Computational modeling techniques can complement sparse NMR datasets (<1 restraint per residue) with additional structural information to elucidate protein structures in these difficult cases. The Rosetta software for protein structure modeling and design is used by structural biologists for structure determination tasks in which limited experimental data is available. This review gives an overview of the computational protocols available in the Rosetta framework for modeling protein structures from NMR data. We explain the computational algorithms used for the integration of different NMR data types in Rosetta. We also highlight new developments, including modeling tools for data from paramagnetic NMR and hydrogen-deuterium exchange, as well as chemical shifts in CS-Rosetta. Furthermore, strategies are discussed to complement and improve structure predictions made by the current state-of-the-art AlphaFold2 program using NMR-guided Rosetta modeling.
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Affiliation(s)
- Julia Koehler Leman
- Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY 10010, USA
| | - Georg Künze
- Institute for Drug Discovery, Medical Faculty, University of Leipzig, Brüderstr. 34, D-04103 Leipzig, Germany
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstr. 16-18, D-04107 Leipzig, Germany
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11
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Parigi G, Ravera E, Piccioli M, Luchinat C. Paramagnetic NMR restraints for the characterization of protein structural rearrangements. Curr Opin Struct Biol 2023; 80:102595. [PMID: 37075534 DOI: 10.1016/j.sbi.2023.102595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/21/2023]
Abstract
Mobility is a common feature of biomacromolecules, often fundamental for their function. Thus, in many cases, biomacromolecules cannot be described by a single conformation, but rather by a conformational ensemble. NMR paramagnetic data demonstrated quite informative to monitor this conformational variability, especially when used in conjunction with data from different sources. Due to their long-range nature, paramagnetic data can, for instance, i) clearly demonstrate the occurrence of conformational rearrangements, ii) reveal the presence of minor conformational states, sampled only for a short time, iii) indicate the most representative conformations within the conformational ensemble sampled by the molecule, iv) provide an upper limit to the weight of each conformation.
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Affiliation(s)
- Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino, 50019, Italy
| | - Mario Piccioli
- Magnetic Resonance Center (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via Sacconi 6, Sesto Fiorentino, 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Via Sacconi 6, Sesto Fiorentino, 50019, Italy.
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12
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Silva JM, Cerofolini L, Carvalho AL, Ravera E, Fragai M, Parigi G, Macedo AL, Geraldes CFGC, Luchinat C. Elucidating the concentration-dependent effects of thiocyanate binding to carbonic anhydrase. J Inorg Biochem 2023; 244:112222. [PMID: 37068394 DOI: 10.1016/j.jinorgbio.2023.112222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/28/2023] [Accepted: 04/09/2023] [Indexed: 04/19/2023]
Abstract
Many proteins naturally carry metal centers, with a large share of them being in the active sites of several enzymes. Paramagnetic effects are a powerful source of structural information and, therefore, if the native metal is paramagnetic, or it can be functionally substituted with a paramagnetic one, paramagnetic effects can be used to study the metal sites, as well as the overall structure of the protein. One notable example is cobalt(II) substitution for zinc(II) in carbonic anhydrase. In this manuscript we investigate the effects of sodium thiocyanate on the chemical environment of the metal ion of the human carbonic anhydrase II. The electron paramagnetic resonance (EPR) titration of the cobalt(II) protein with thiocyanate shows that the EPR spectrum changes from A-type to C-type on passing from 1:1 to 1:1000-fold ligand excess. This indicates the occurrence of a change in the electronic structure, which may reflect a sizable change in the metal coordination environment in turn caused by a modification of the frozen solvent glass. However, paramagnetic nuclear magnetic resonance (NMR) data indicate that the metal coordination cage remains unperturbed even in 1:1000-fold ligand excess. This result proves that the C-type EPR spectrum observed at large ligand concentration should be ascribed to the low temperature at which EPR measurements are performed, which impacts on the structure of the protein when it is destabilized by a high concentration of a chaotropic agent.
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Affiliation(s)
- José Malanho Silva
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Ana Luísa Carvalho
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy
| | - Anjos L Macedo
- UCIBIO, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Carlos F G C Geraldes
- Department of Life Sciences, Faculty of Science and Technology, 3000-393 Coimbra, Portugal; Coimbra Chemistry Center- Institute of Molecular Sciences (CCC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Sesto Fiorentino 50019, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), Sesto Fiorentino, 50019, Italy; Giotto Biotech, S.R.L, Sesto Fiorentino, Florence 50019, Italy.
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13
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Studying Peptide-Metal Ion Complex Structures by Solution-State NMR. Int J Mol Sci 2022; 23:ijms232415957. [PMID: 36555599 PMCID: PMC9782655 DOI: 10.3390/ijms232415957] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Metal chelation can provide structural stability and form reactive centers in metalloproteins. Approximately one third of known protein structures are metalloproteins, and metal binding, or the lack thereof, is often implicated in disease, making it necessary to be able to study these systems in detail. Peptide-metal complexes are both present in nature and can provide a means to focus on the binding region of a protein and control experimental variables to a high degree. Structural studies of peptide complexes with metal ions by nuclear magnetic resonance (NMR) were surveyed for all the essential metal complexes and many non-essential metal complexes. The various methods used to study each metal ion are presented together with examples of recent research. Many of these metal systems have been individually reviewed and this current overview of NMR studies of metallopeptide complexes aims to provide a basis for inspiration from structural studies and methodology applied in the field.
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14
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Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
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Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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15
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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16
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Poulin-Ponnelle C, Duvail M, Dumas T, Berthon C. Contribution of Molecular Dynamics in pNMR for the Structural Determination of An V and An VI Complexes in Solution. Inorg Chem 2022; 61:15895-15909. [PMID: 36166623 DOI: 10.1021/acs.inorgchem.2c02040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, we propose to use classical molecular dynamics (MD) coupled with 1H NMR spectroscopy to study the conformations of different actinyl AnVI (An = U, Np, and Pu) and AnV (An = Np) complexes with tetra-ethyl dyglicolamide (TEDGA) ligands in order to have a better representation of such complexes in solution. Molecular dynamics simulations showed its effectiveness in interpreting the experiments by the calculation of geometric factors needed for the determination of magnetic properties of these complexes. We demonstrated that different conformations of the AnV and AnVI complexes with TEDGA exist in solution with different coordination modes, which is experimentally confirmed by 1H NMR and EXAFS spectroscopies. Furthermore, MD simulations provide additional insights into the structures of complexes in solution since conformations with fast exchanges, which are not accessible from NMR experiments, have been observed by MD simulations.
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Affiliation(s)
| | - Magali Duvail
- ICSM, Univ. Montpellier, CEA, CNRS, ENSCM, Bagnols sur Cèze 30207, France
| | - Thomas Dumas
- LILA, Univ. Montpellier, CEA, Bagnols sur Cèze 30207, France
| | - Claude Berthon
- LILA, Univ. Montpellier, CEA, Bagnols sur Cèze 30207, France
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17
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Mekkattu Tharayil S, Mahawaththa MC, Feintuch A, Maleckis A, Ullrich S, Morewood R, Maxwell MJ, Huber T, Nitsche C, Goldfarb D, Otting G. Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:169-182. [PMID: 37904871 PMCID: PMC10539774 DOI: 10.5194/mr-3-169-2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 11/01/2023]
Abstract
The paramagnetism of a lanthanoid tag site-specifically installed on a protein provides a rich source of structural information accessible by nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy. Here we report a lanthanoid tag for selective reaction with cysteine or selenocysteine with formation of a (seleno)thioether bond and a short tether between the lanthanoid ion and the protein backbone. The tag is assembled on the protein in three steps, comprising (i) reaction with 4-fluoro-2,6-dicyanopyridine (FDCP); (ii) reaction of the cyano groups with α -cysteine, penicillamine or β -cysteine to complete the lanthanoid chelating moiety; and (iii) titration with a lanthanoid ion. FDCP reacts much faster with selenocysteine than cysteine, opening a route for selective tagging in the presence of solvent-exposed cysteine residues. Loaded with Tb 3 + and Tm 3 + ions, pseudocontact shifts were observed in protein NMR spectra, confirming that the tag delivers good immobilisation of the lanthanoid ion relative to the protein, which was also manifested in residual dipolar couplings. Completion of the tag with different 1,2-aminothiol compounds resulted in different magnetic susceptibility tensors. In addition, the tag proved suitable for measuring distance distributions in double electron-electron resonance experiments after titration with Gd 3 + ions.
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Affiliation(s)
| | - Mithun C. Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Akiva Feintuch
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, 1006 Riga, Latvia
| | - Sven Ullrich
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Richard Morewood
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michael J. Maxwell
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Daniella Goldfarb
- Department of Chemical Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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18
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Trindade IB, Coelho A, Cantini F, Piccioli M, Louro RO. NMR of paramagnetic metalloproteins in solution: Ubi venire, quo vadis? J Inorg Biochem 2022; 234:111871. [DOI: 10.1016/j.jinorgbio.2022.111871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 05/16/2022] [Accepted: 05/19/2022] [Indexed: 10/18/2022]
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19
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Ravera E, Gigli L, Fiorucci L, Luchinat C, Parigi G. The evolution of paramagnetic NMR as a tool in structural biology. Phys Chem Chem Phys 2022; 24:17397-17416. [PMID: 35849063 DOI: 10.1039/d2cp01838a] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Paramagnetic NMR data contain extremely accurate long-range information on metalloprotein structures and, when used in the frame of integrative structural biology approaches, they allow for the retrieval of structural details to a resolution that is not achievable using other techniques. Paramagnetic data thus represent an extremely powerful tool to refine protein models in solution, especially when coupled to X-ray or cryoelectron microscopy data, to monitor the formation of complexes and determine the relative arrangements of their components, and to highlight the presence of conformational heterogeneity. More recently, theoretical and computational advancements in quantum chemical calculations of paramagnetic NMR observables are progressively opening new routes in structural biology, because they allow for the determination of the structure within the coordination sphere of the metal center, thus acting as a loupe on sites that are difficult to observe but very important for protein function.
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Affiliation(s)
- Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Lucia Gigli
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Letizia Fiorucci
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
| | - Giacomo Parigi
- Magnetic Resonance Center (CERM), University of Florence, via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.,Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino, 50019, Italy.,Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Luigi Sacconi 6, Sesto Fiorentino, 50019, Italy.
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20
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Hunashal Y, Percipalle M, Molnár T, Kardos J, Percipalle P, Esposito G. Approaching Protein Aggregation and Structural Dynamics by Equilibrium and Nonequilibrium Paramagnetic Perturbation. Anal Chem 2022; 94:10949-10958. [PMID: 35877130 DOI: 10.1021/acs.analchem.2c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
PENELOP (Paramagnetic Equilibrium vs Nonequilibrium magnetization Enhancement or LOss Perturbation) is the presented nuclear magnetic resonance (NMR) approach to identify at once the location of proteins' exposed surface, hindered accessibility, and exchange processes occurring on a μs-ms time scale. In addition to mapping the protein surface accessibility, the application of this method under specific conditions makes it possible to distinguish conformational mobility and chemical exchange processes, thereby providing an alternative to characterization by more demanding techniques (transverse relaxation dispersion, saturation transfer, and high-pressure NMR). Moreover, its high sensitivity enables studying samples at low, physiologically more relevant concentrations. Association, dynamics, and oligomerization are addressed by PENELOP for a component of SARS-CoV-2 replication transcription complex and an amyloidogenic protein.
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Affiliation(s)
- Yamanappa Hunashal
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,Dipartimento di Area Medica, Universita' di Udine, P.le Kolbe 4, 33100 Udine, Italy
| | - Mathias Percipalle
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,Department of Chemistry and Magnetic Resonance Center, University of Florence, 50019 Florence, Italy
| | - Tamás Molnár
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Jòzsef Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University, Budapest 1117, Hungary
| | - Piergiorgio Percipalle
- Biology Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,Department of Molecular Bioscience, The Wenner Gren Institute Stockholm University, Stockholm SE-106 91, Sweden
| | - Gennaro Esposito
- Chemistry Program, Science Division, New York University Abu Dhabi, Abu Dhabi 129188, United Arab Emirates.,INBB, Viale Medaglie d'Oro 305, Roma 00136, Italy
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21
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Parigi G, Ravera E, Luchinat C. Paramagnetic effects in NMR for protein structures and ensembles: Studies of metalloproteins. Curr Opin Struct Biol 2022; 74:102386. [DOI: 10.1016/j.sbi.2022.102386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/28/2022]
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22
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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23
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Orton HW, Abdelkader EH, Topping L, Butler SJ, Otting G. Localising nuclear spins by pseudocontact shifts from a single tagging site. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2022; 3:65-76. [PMID: 37905181 PMCID: PMC10539793 DOI: 10.5194/mr-3-65-2022] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/18/2022] [Indexed: 11/01/2023]
Abstract
Ligating a protein at a specific site with a tag molecule containing a paramagnetic metal ion provides a versatile way of generating pseudocontact shifts (PCSs) in nuclear magnetic resonance (NMR) spectra. PCSs can be observed for nuclear spins far from the tagging site, and PCSs generated from multiple tagging sites have been shown to enable highly accurate structure determinations at specific sites of interest, even when using flexible tags, provided the fitted effective magnetic susceptibility anisotropy (Δ χ ) tensors accurately back-calculate the experimental PCSs measured in the immediate vicinity of the site of interest. The present work investigates the situation where only the local structure of a protein region or bound ligand is to be determined rather than the structure of the entire molecular system. In this case, the need for gathering structural information from tags deployed at multiple sites may be queried. Our study presents a computational simulation of the structural information available from samples produced with single tags attached at up to six different sites, up to six different tags attached to a single site, and in-between scenarios. The results indicate that the number of tags is more important than the number of tagging sites. This has important practical implications, as it is much easier to identify a single site that is suitable for tagging than multiple ones. In an initial experimental demonstration with the ubiquitin mutant S57C, PCSs generated with four different tags at a single site are shown to accurately pinpoint the location of amide protons in different segments of the protein.
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Affiliation(s)
- Henry W Orton
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Lydia Topping
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Stephen J Butler
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, United Kingdom
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
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Abstract
In-cell structural biology aims at extracting structural information about proteins or nucleic acids in their native, cellular environment. This emerging field holds great promise and is already providing new facts and outlooks of interest at both fundamental and applied levels. NMR spectroscopy has important contributions on this stage: It brings information on a broad variety of nuclei at the atomic scale, which ensures its great versatility and uniqueness. Here, we detail the methods, the fundamental knowledge, and the applications in biomedical engineering related to in-cell structural biology by NMR. We finally propose a brief overview of the main other techniques in the field (EPR, smFRET, cryo-ET, etc.) to draw some advisable developments for in-cell NMR. In the era of large-scale screenings and deep learning, both accurate and qualitative experimental evidence are as essential as ever to understand the interior life of cells. In-cell structural biology by NMR spectroscopy can generate such a knowledge, and it does so at the atomic scale. This review is meant to deliver comprehensive but accessible information, with advanced technical details and reflections on the methods, the nature of the results, and the future of the field.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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25
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Stiller JB, Otten R, Häussinger D, Rieder PS, Theobald DL, Kern D. Structure determination of high-energy states in a dynamic protein ensemble. Nature 2022; 603:528-535. [PMID: 35236984 PMCID: PMC9126080 DOI: 10.1038/s41586-022-04468-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 01/25/2022] [Indexed: 01/24/2023]
Abstract
Macromolecular function frequently requires that proteins change conformation into high-energy states1-4. However, methods for solving the structures of these functionally essential, lowly populated states are lacking. Here we develop a method for high-resolution structure determination of minorly populated states by coupling NMR spectroscopy-derived pseudocontact shifts5 (PCSs) with Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion6 (PCS-CPMG). Our approach additionally defines the corresponding kinetics and thermodynamics of high-energy excursions, thereby characterizing the entire free-energy landscape. Using a large set of simulated data for adenylate kinase (Adk), calmodulin and Src kinase, we find that high-energy PCSs accurately determine high-energy structures (with a root mean squared deviation of less than 3.5 angström). Applying our methodology to Adk during catalysis, we find that the high-energy excursion involves surprisingly small openings of the AMP and ATP lids. This previously unresolved high-energy structure solves a longstanding controversy about conformational interconversions that are rate-limiting for catalysis. Primed for either substrate binding or product release, the high-energy structure of Adk suggests a two-step mechanism combining conformational selection to this state, followed by an induced-fit step into a fully closed state for catalysis of the phosphoryl-transfer reaction. Unlike other methods for resolving high-energy states, such as cryo-electron microscopy and X-ray crystallography, our solution PCS-CPMG approach excels in cases involving domain rearrangements of smaller systems (less than 60 kDa) and populations as low as 0.5%, and enables the simultaneous determination of protein structure, kinetics and thermodynamics while proteins perform their function.
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Affiliation(s)
- John B Stiller
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | - Renee Otten
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA
| | | | - Pascal S Rieder
- Department of Chemistry, University of Basel, Basel, Switzerland
| | | | - Dorothee Kern
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, MA, USA.
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26
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Hou XN, Tochio H. Characterizing conformational ensembles of multi-domain proteins using anisotropic paramagnetic NMR restraints. Biophys Rev 2022; 14:55-66. [PMID: 35340613 PMCID: PMC8921464 DOI: 10.1007/s12551-021-00916-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/16/2021] [Indexed: 01/13/2023] Open
Abstract
It has been over two decades since paramagnetic NMR started to form part of the essential techniques for structural analysis of proteins under physiological conditions. Paramagnetic NMR has significantly expanded our understanding of the inherent flexibility of proteins, in particular, those that are formed by combinations of two or more domains. Here, we present a brief overview of techniques to characterize conformational ensembles of such multi-domain proteins using paramagnetic NMR restraints produced through anisotropic metals, with a focus on the basics of anisotropic paramagnetic effects, the general procedures of conformational ensemble reconstruction, and some representative reweighting approaches.
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Affiliation(s)
- Xue-Ni Hou
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Hidehito Tochio
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502 Japan
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27
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Mahawaththa MC, Orton HW, Adekoya I, Huber T, Otting G, Nitsche C. Organoarsenic probes to study proteins by NMR spectroscopy. Chem Commun (Camb) 2022; 58:701-704. [PMID: 34927186 DOI: 10.1039/d1cc06497e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Arsenical probes enable structural studies of proteins. We report the first organoarsenic probes for nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy to study proteins in solutions. These probes can be attached to irregular loop regions. A lanthanide-binding tag induces sizable pseudocontact shifts in protein NMR spectra of a magnitude never observed for small paramagnetic probes before.
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Affiliation(s)
- Mithun C Mahawaththa
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Henry W Orton
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Ibidolapo Adekoya
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Thomas Huber
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Christoph Nitsche
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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28
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Müntener T, Joss D, Häussinger D, Hiller S. Pseudocontact Shifts in Biomolecular NMR Spectroscopy. Chem Rev 2022; 122:9422-9467. [PMID: 35005884 DOI: 10.1021/acs.chemrev.1c00796] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Paramagnetic centers in biomolecules, such as specific metal ions that are bound to a protein, affect the nuclei in their surrounding in various ways. One of these effects is the pseudocontact shift (PCS), which leads to strong chemical shift perturbations of nuclear spins, with a remarkably long range of 50 Å and beyond. The PCS in solution NMR is an effect originating from the anisotropic part of the dipole-dipole interaction between the magnetic momentum of unpaired electrons and nuclear spins. The PCS contains spatial information that can be exploited in multiple ways to characterize structure, function, and dynamics of biomacromolecules. It can be used to refine structures, magnify effects of dynamics, help resonance assignments, allows for an intermolecular positioning system, and gives structural information in sensitivity-limited situations where all other methods fail. Here, we review applications of the PCS in biomolecular solution NMR spectroscopy, starting from early works on natural metalloproteins, following the development of non-natural tags to chelate and attach lanthanoid ions to any biomolecular target to advanced applications on large biomolecular complexes and inside living cells. We thus hope to not only highlight past applications but also shed light on the tremendous potential the PCS has in structural biology.
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Affiliation(s)
- Thomas Müntener
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
| | - Daniel Joss
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sebastian Hiller
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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29
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Pavlov AA, Novikov VV, Nikovskiy IA, Melnikova EK, Nelyubina YV, Aleshin DY. Analysis of reduced paramagnetic shifts as an effective tool in NMR spectroscopy. Phys Chem Chem Phys 2022; 24:1167-1173. [PMID: 34931208 DOI: 10.1039/d1cp04648a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A recently introduced concept of reduced paramagnetic shifts (RPS) in NMR spectroscopy is applied here to a series of paramagnetic complexes with different metal ions, such as iron(II), iron(III) and cobalt(II), in different coordination environments of N-donor ligands, including a unique trigonal-prismatic geometry that is behind some record single-molecule magnet behaviours. A simple, almost visual analysis of the chemical shifts as a function of temperature, which is at the core of this approach, allows for a correct signal assignment and evaluation of the anisotropy of the magnetic susceptibility, the key indicator of a good single molecule magnet, that often cannot be done using traditional techniques rooted in quantum chemistry and NMR spectroscopy. The proposed approach thus emerged as a powerful alternative in deciphering the NMR spectra of paramagnetic compounds for applications in data processing and storage, magnetic resonance imaging and structural biology.
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Affiliation(s)
- Alexander A Pavlov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia. .,Moscow Institute of Physics and Technology, Institutskiy per., 9, Dolgoprudny, Moscow Region, 141701, Russia
| | - Valentin V Novikov
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia. .,National Research University Higher School of Economics, Miasnitskaya Str. 20, Moscow 101000, Russia
| | - Igor A Nikovskiy
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia.
| | - Elizaveta K Melnikova
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia. .,Lomonosov Moscow State University, Leninskie Gory, Moscow, 119991, Russia
| | - Yulia V Nelyubina
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia. .,Moscow Institute of Physics and Technology, Institutskiy per., 9, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitry Y Aleshin
- A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilova str. 28, 119991, Moscow, Russia.
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30
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Ma B, Chen JL, Cui CY, Yang F, Gong YJ, Su XC. Rigid, Highly Reactive and Stable DOTA-like Tags Containing a Thiol-Specific Phenylsulfonyl Pyridine Moiety for Protein Modification and NMR Analysis*. Chemistry 2021; 27:16145-16152. [PMID: 34595784 DOI: 10.1002/chem.202102495] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Indexed: 11/06/2022]
Abstract
Site specific installation of a paramagnetic ion with magnetic anisotropy in a biomolecule generates valuable structural restraints, such as pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs). These paramagnetic effects can be used to characterize the structures, interactions and dynamics of biological macromolecules and their complexes. Two single-armed DOTA-like tags, BrPSPy-DO3M(S)A-Ln and BrPSPy-6M-DO3M(S)A-Ln, each containing a thiol-specific reacting group, that is, a phenylsulfonyl pyridine moiety, are demonstrated as rigid, reactive and stable paramagnetic tags for protein modification by formation of a reducing resistant thioether bond between the protein and the tag. The two tags present high reactivity with the solvent exposed thiol group in aqueous solution at room temperature. The introduction of Br at the meta-position in pyridine enhances the reactivity of 4-phenylsulfonyl pyridine towards the solvent exposed thiol group in a protein, whereas the ortho-methyl group in pyridine increases the rigidity of the tag in the protein conjugates. The high performance of these two tags has been demonstrated in different cysteine mutants of ubiquitin and GB1. The high reactivity and rigidity of these two tags can be added in the toolbox of paramagnetic tags suitable for the high-resolution NMR measurements of biological macromolecules and their complexes.
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Affiliation(s)
- Bo Ma
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Chao-Yu Cui
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Feng Yang
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Yan-Jun Gong
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, P.R. China
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31
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Novikov VV, Nelyubina YV. Modern physical methods for the molecular design of single-molecule magnets. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr5002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Abstract
Many paramagnetic metal complexes have emerged as unique magnetic materials (single-molecule magnets), which behave as conventional magnets at the single-molecule level, thereby making it possible to use them in modern devices for data storage and processing. The rational design of these complexes, however, requires a deep understanding of the physical laws behind a single-molecule magnet behaviour, the mechanisms of magnetic relaxation that determines the magnetic properties and the relationship of these properties with the structure of single-molecule magnets. This review focuses on the physical methods providing such understanding, including different versions and various combinations of magnetometry, electron paramagnetic and nuclear magnetic resonance spectroscopy, optical spectroscopy and X-ray diffraction. Many of these methods are traditionally used to determine the composition and structure of new chemical compounds. However, they are rarely applied to study molecular magnetism.
The bibliography includes 224 references.
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32
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Vogel R, Müntener T, Häussinger D. Intrinsic anisotropy parameters of a series of lanthanoid complexes deliver new insights into the structure-magnetism relationship. Chem 2021. [DOI: 10.1016/j.chempr.2021.08.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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33
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Ott JC, Suturina EA, Kuprov I, Nehrkorn J, Schnegg A, Enders M, Gade LH. Observability of Paramagnetic NMR Signals at over 10 000 ppm Chemical Shifts. Angew Chem Int Ed Engl 2021; 60:22856-22864. [PMID: 34351041 PMCID: PMC8518043 DOI: 10.1002/anie.202107944] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Indexed: 12/27/2022]
Abstract
We report an experimental observation of 31 P NMR resonances shifted by over 10 000 ppm (meaning percent range, and a new record for solutions), and similar 1 H chemical shifts, in an intermediate-spin square planar ferrous complex [tBu (PNP)Fe-H], where PNP is a carbazole-based pincer ligand. Using a combination of electronic structure theory, nuclear magnetic resonance, magnetometry, and terahertz electron paramagnetic resonance, the influence of magnetic anisotropy and zero-field splitting on the paramagnetic shift and relaxation enhancement is investigated. Detailed spin dynamics simulations indicate that, even with relatively slow electron spin relaxation (T1 ≈10-11 s), it remains possible to observe NMR signals of directly metal-bonded atoms because pronounced rhombicity in the electron zero-field splitting reduces nuclear paramagnetic relaxation enhancement.
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Affiliation(s)
- Jonas C. Ott
- Anorganisch-Chemisches InstitutUniversität HeidelbergIm Neuenheimer Feld 27669120HeidelbergGermany
| | | | - Ilya Kuprov
- School of ChemistryUniversity of SouthamptonSouthamptonSO17 1BJUK
| | - Joscha Nehrkorn
- EPR Research GroupMPI for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim RuhrGermany
| | - Alexander Schnegg
- EPR Research GroupMPI for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim RuhrGermany
| | - Markus Enders
- Anorganisch-Chemisches InstitutUniversität HeidelbergIm Neuenheimer Feld 27669120HeidelbergGermany
| | - Lutz H. Gade
- Anorganisch-Chemisches InstitutUniversität HeidelbergIm Neuenheimer Feld 27669120HeidelbergGermany
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34
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Ott JC, Suturina EA, Kuprov I, Nehrkorn J, Schnegg A, Enders M, Gade LH. Observability of Paramagnetic NMR Signals at over 10 000 ppm Chemical Shifts. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202107944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jonas C. Ott
- Anorganisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 276 69120 Heidelberg Germany
| | | | - Ilya Kuprov
- School of Chemistry University of Southampton Southampton SO17 1BJ UK
| | - Joscha Nehrkorn
- EPR Research Group MPI for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim Ruhr Germany
| | - Alexander Schnegg
- EPR Research Group MPI for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim Ruhr Germany
| | - Markus Enders
- Anorganisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 276 69120 Heidelberg Germany
| | - Lutz H. Gade
- Anorganisch-Chemisches Institut Universität Heidelberg Im Neuenheimer Feld 276 69120 Heidelberg Germany
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35
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Herath ID, Breen C, Hewitt SH, Berki TR, Kassir AF, Dodson C, Judd M, Jabar S, Cox N, Otting G, Butler SJ. A Chiral Lanthanide Tag for Stable and Rigid Attachment to Single Cysteine Residues in Proteins for NMR, EPR and Time-Resolved Luminescence Studies. Chemistry 2021; 27:13009-13023. [PMID: 34152643 PMCID: PMC8518945 DOI: 10.1002/chem.202101143] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 12/12/2022]
Abstract
A lanthanide-binding tag site-specifically attached to a protein presents a tool to probe the protein by multiple spectroscopic techniques, including nuclear magnetic resonance, electron paramagnetic resonance and time-resolved luminescence spectroscopy. Here a new stable chiral LnIII tag, referred to as C12, is presented for spontaneous and quantitative reaction with a cysteine residue to generate a stable thioether bond. The synthetic protocol of the tag is relatively straightforward, and the tag is stable for storage and shipping. It displays greatly enhanced reactivity towards selenocysteine, opening a route towards selective tagging of selenocysteine in proteins containing cysteine residues. Loaded with TbIII or TmIII ions, the C12 tag readily generates pseudocontact shifts (PCS) in protein NMR spectra. It produces a relatively rigid tether between lanthanide and protein, which is beneficial for interpretation of the PCSs by single magnetic susceptibility anisotropy tensors, and it is suitable for measuring distance distributions in double electron-electron resonance experiments. Upon reaction with cysteine or other thiol compounds, the TbIII complex exhibits a 100-fold enhancement in luminescence quantum yield, affording a highly sensitive turn-on luminescence probe for time-resolved FRET assays and enzyme reaction monitoring.
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Affiliation(s)
- Iresha D. Herath
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Colum Breen
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Sarah H. Hewitt
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Thomas R. Berki
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Ahmad F. Kassir
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
| | - Charlotte Dodson
- Department of Pharmacy & PharmacologyUniversity of Bath Claverton DownBathBA2 7AYUK
| | - Martyna Judd
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Shereen Jabar
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Nicholas Cox
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Gottfried Otting
- Research School of ChemistryThe Australian National UniversityCanberraACT 2605Australia
| | - Stephen J. Butler
- Department of ChemistryLoughborough UniversityEpinal WayLoughboroughLE11 3TUUK
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36
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Cucuzza S, Güntert P, Plückthun A, Zerbe O. An automated iterative approach for protein structure refinement using pseudocontact shifts. JOURNAL OF BIOMOLECULAR NMR 2021; 75:319-334. [PMID: 34338940 PMCID: PMC8473369 DOI: 10.1007/s10858-021-00376-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/19/2021] [Indexed: 05/02/2023]
Abstract
NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing.
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Affiliation(s)
- Stefano Cucuzza
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Peter Güntert
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438, Frankfurt am Main, Germany
- Laboratory of Physical Chemistry, ETH Zürich, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
- Department of Chemistry, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji, 192-0397, Tokyo, Japan
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
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37
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Denis-Quanquin S, Bartocci A, Szczepaniak F, Riobé F, Maury O, Dumont E, Giraud N. Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration. Phys Chem Chem Phys 2021; 23:11224-11232. [PMID: 34010374 DOI: 10.1039/d0cp06570f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the realm of biomolecules, peptides can present a large diversity of structures. Our study sheds new light on the structural interplay between a tris-dipicolinate lanthanide probe and a decapeptide SASYKTLPRG. Although a rather trivial, electrostatically driven interaction was expected, the combination of paramagnetic NMR and molecular dynamics simulations reveals a highly dynamic association process and allows for providing extensive insights into the interaction sites and their occupancy. This study highlights the importance of a large conformational sampling to reconcile characteristic time in NMR with molecular dynamics simulations, where sampling in the microsecond range is needed. This study opens the door for a detailed mechanistic elucidation of the early steps of lanthanide complex-peptide or lanthanide complex-protein interaction or self-assembly processes.
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Affiliation(s)
- Sandrine Denis-Quanquin
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Alessio Bartocci
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Florence Szczepaniak
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Francois Riobé
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Olivier Maury
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France.
| | - Elise Dumont
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France. and Institut Universitaire de France, 5 rue Descartes, 75005, Paris, France
| | - Nicolas Giraud
- Université de Paris, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR CNRS 8601, Paris, France.
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38
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Saio T, Hiramatsu S, Asada M, Nakagawa H, Shimizu K, Kumeta H, Nakamura T, Ishimori K. Conformational ensemble of a multidomain protein explored by Gd 3+ electron paramagnetic resonance. Biophys J 2021; 120:2943-2951. [PMID: 34242587 DOI: 10.1016/j.bpj.2021.06.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/07/2021] [Accepted: 06/28/2021] [Indexed: 10/20/2022] Open
Abstract
Despite their importance in function, the conformational state of proteins and its changes are often poorly understood, mainly because of the lack of an efficient tool. MurD, a 47-kDa protein enzyme responsible for peptidoglycan biosynthesis, is one of those proteins whose conformational states and changes during their catalytic cycle are not well understood. Although it has been considered that MurD takes a single conformational state in solution as shown by a crystal structure, the solution nuclear magnetic resonance (NMR) study suggested the existence of multiple conformational state of apo MurD in solution. However, the conformational distribution has not been evaluated. In this work, we investigate the conformational states of MurD by the use of electron paramagnetic resonance (EPR), especially intergadolinium distance measurement using double electron-electron resonance (DEER) measurement. The gadolinium ions are fixed on specific positions on MurD via a rigid double-arm paramagnetic lanthanide tag that has been originally developed for paramagnetic NMR. The combined use of NMR and EPR enables accurate interpretation of the DEER distance information to the structural information of MurD. The DEER distance measurement for apo MurD shows a broad distance distribution, whereas the presence of the inhibitor narrows the distance distribution. The results suggest that MurD exists in a wide variety of conformational states in the absence of ligands, whereas binding of the inhibitor eliminates variation in conformational states. The multiple conformational states of MurD were previously implied by NMR experiments, but our DEER data provided structural characterization of the conformational variety of MurD.
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Affiliation(s)
- Tomohide Saio
- Division of Molecular Life Science, Institute of Advanced Medical Sciences, Tokushima University, Tokushima, Japan.
| | - Soya Hiramatsu
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan
| | - Mizue Asada
- Instrument Center, Institute for Molecular Science, Okazaki, Japan
| | - Hiroshi Nakagawa
- Materials Sciences Research CenterTokai, Ibaraki, Japan; J-PARC Center, Japan Atomic Energy Agency, Tokai, Ibaraki, Japan
| | - Kazumi Shimizu
- Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
| | | | | | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo, Japan; Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan.
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39
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Abstract
Nuclear Magnetic Resonance is particularly sensitive to the electronic structure of matter and is thus a powerful tool to characterize in-depth the magnetic properties of a system. NMR is indeed increasingly recognized as an ideal tool to add precious structural information for the development of Single Ion Magnets, small complexes that are recently gaining much popularity due to their quantum computing and spintronics applications. In this review, we recall the theoretical principles of paramagnetic NMR, with particular attention to lanthanoids, and we give an overview of the recent advances in this field.
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40
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Rogals MJ, Yang JY, Williams RV, Moremen KW, Amster IJ, Prestegard JH. Sparse isotope labeling for nuclear magnetic resonance (NMR) of glycoproteins using 13C-glucose. Glycobiology 2021; 31:425-435. [PMID: 32902634 PMCID: PMC8091466 DOI: 10.1093/glycob/cwaa071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/22/2020] [Accepted: 07/24/2020] [Indexed: 01/02/2023] Open
Abstract
Preparation of samples for nuclear magnetic resonance (NMR) characterization of larger proteins requires enrichment with less abundant, NMR-active, isotopes such as 13C and 15N. This is routine for proteins that can be expressed in bacterial culture where low-cost isotopically enriched metabolic substrates can be used. However, it can be expensive for glycosylated proteins expressed in mammalian culture where more costly isotopically enriched amino acids are usually used. We describe a simple, relatively inexpensive procedure in which standard commercial media is supplemented with 13C-enriched glucose to achieve labeling of all glycans plus all alanines of the N-terminal domain of the highly glycosylated protein, CEACAM1. We demonstrate an ability to detect partially occupied N-glycan sites, sites less susceptible to processing by an endoglycosidase, and some unexpected truncation of the amino acid sequence. The labeling of both the protein (through alanines) and the glycans in a single culture requiring no additional technical expertise past standard mammalian expression requirements is anticipated to have several applications, including structural and functional screening of the many glycosylated proteins important to human health.
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Affiliation(s)
- Monique J Rogals
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
| | - Robert V Williams
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Biochemistry and Molecular Biology
| | | | - James H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602, USA
- Department of Chemistry
- Department of Biochemistry and Molecular Biology
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41
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Chen JL, Chen BG, Li B, Yang F, Su XC. Assessing multiple conformations of lanthanide binding tags for proteins using a sensitive 19F-reporter. Chem Commun (Camb) 2021; 57:4291-4294. [PMID: 33913982 DOI: 10.1039/d1cc00791b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Quantifying the isomeric species of metal complexes in solution is difficult. 19F NMR herein was used to determine the abundance of isomeric species and dynamic properties of lanthanide binding tags. The results suggest that 19F is an efficient reporter in assessing and screening paramagnetic tags suitable for protein NMR analysis.
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Affiliation(s)
- Jia-Liang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Ben-Guang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Bin Li
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Feng Yang
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
| | - Xun-Cheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
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42
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Camponeschi F, Gallo A, Piccioli M, Banci L. The long-standing relationship between paramagnetic NMR and iron-sulfur proteins: the mitoNEET example. An old method for new stories or the other way around? MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:203-221. [PMID: 37904758 PMCID: PMC10539769 DOI: 10.5194/mr-2-203-2021] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/18/2021] [Indexed: 11/01/2023]
Abstract
Paramagnetic NMR spectroscopy and iron-sulfur (Fe-S) proteins have maintained a synergic relationship for decades. Indeed, the hyperfine shifts with their temperature dependencies and the relaxation rates of nuclei of cluster-bound residues have been extensively used as a fingerprint of the type and of the oxidation state of the Fe-S cluster within the protein frame. The identification of NMR signals from residues surrounding the metal cofactor is crucial for understanding the structure-function relationship in Fe-S proteins, but it is generally impaired in standard NMR experiments by paramagnetic relaxation enhancement due to the presence of the paramagnetic cluster(s). On the other hand, the availability of systems of different sizes and stabilities has, over the years, stimulated NMR spectroscopists to exploit iron-sulfur proteins as paradigmatic cases to develop experiments, models, and protocols. Here, the cluster-binding properties of human mitoNEET have been investigated by 1D and 2D 1 H diamagnetic and paramagnetic NMR, in its oxidized and reduced states. The NMR spectra of both oxidation states of mitoNEET appeared to be significantly different from those reported for previously investigated [ Fe 2 S 2 ] 2 + / + proteins. The protocol we have developed in this work conjugates spectroscopic information arising from "classical" paramagnetic NMR with an extended mapping of the signals of residues around the cluster which can be taken, even before the sequence-specific assignment is accomplished, as a fingerprint of the protein region constituting the functional site of the protein. We show how the combined use of 1D NOE experiments, 13 C direct-detected experiments, and double- and triple-resonance experiments tailored using R1 - and/or R2 -based filters significantly reduces the "blind" sphere of the protein around the paramagnetic cluster. This approach provided a detailed description of the unique electronic properties of mitoNEET, which are responsible for its biological function. Indeed, the NMR properties suggested that the specific electronic structure of the cluster possibly drives the functional properties of different [ Fe 2 S 2 ] proteins.
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Affiliation(s)
- Francesca Camponeschi
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine,
Sesto Fiorentino, 50019, Italy
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, 26504,
Greece
| | - Mario Piccioli
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine,
Sesto Fiorentino, 50019, Italy
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, 50019, Italy
| | - Lucia Banci
- Consorzio Interuniversitario Risonanze Magnetiche MetalloProteine,
Sesto Fiorentino, 50019, Italy
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Sesto Fiorentino, 50019, Italy
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43
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Gauto D, Dakhlaoui O, Marin-Montesinos I, Hediger S, De Paëpe G. Targeted DNP for biomolecular solid-state NMR. Chem Sci 2021; 12:6223-6237. [PMID: 34084422 PMCID: PMC8115112 DOI: 10.1039/d0sc06959k] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 03/18/2021] [Indexed: 12/23/2022] Open
Abstract
High-field dynamic nuclear polarization is revolutionizing the scope of solid-state NMR with new applications in surface chemistry, materials science and structural biology. In this perspective article, we focus on a specific DNP approach, called targeted DNP, in which the paramagnets introduced to polarize are not uniformly distributed in the sample but site-specifically located on the biomolecular system. After reviewing the various targeting strategies reported to date, including a bio-orthogonal chemistry-based approach, we discuss the potential of targeted DNP to improve the overall NMR sensitivity while avoiding the use of glass-forming DNP matrix. This is especially relevant to the study of diluted biomolecular systems such as, for instance, membrane proteins within their lipidic environment. We also discuss routes towards extracting structural information from paramagnetic relaxation enhancement (PRE) induced by targeted DNP at cryogenic temperature, and the possibility to recover site-specific information in the vicinity of the paramagnetic moieties using high-resolution selective DNP spectra. Finally, we review the potential of targeted DNP for in-cell NMR studies and how it can be used to extract a given protein NMR signal from a complex cellular background.
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Affiliation(s)
- Diego Gauto
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Ons Dakhlaoui
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- Univ. Grenoble Alpes, CNRS, CERMAV Grenoble France
| | - Ildefonso Marin-Montesinos
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
- University of Aveiro, CICECO Chem. Dept. Aveiro Portugal
| | - Sabine Hediger
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
| | - Gaël De Paëpe
- Univ. Grenoble Alpes, CEA, CNRS, IRIG-MEM Grenoble France
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44
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Welegedara AP, Maleckis A, Bandara R, Mahawaththa MC, Dilhani Herath I, Jiun Tan Y, Giannoulis A, Goldfarb D, Otting G, Huber T. Cell-Free Synthesis of Selenoproteins in High Yield and Purity for Selective Protein Tagging. Chembiochem 2021; 22:1480-1486. [PMID: 33319405 DOI: 10.1002/cbic.202000785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/10/2020] [Indexed: 01/10/2023]
Abstract
The selenol group of selenocysteine is much more nucleophilic than the thiol group of cysteine. Selenocysteine residues in proteins thus offer reactive points for rapid post-translational modification. Herein, we show that selenoproteins can be expressed in high yield and purity by cell-free protein synthesis by global substitution of cysteine by selenocysteine. Complete alkylation of solvent-exposed selenocysteine residues was achieved in 10 minutes with 4-chloromethylene dipicolinic acid (4Cl-MDPA) under conditions that left cysteine residues unchanged even after overnight incubation. GdIII -GdIII distances measured by double electron-electron resonance (DEER) experiments of maltose binding protein (MBP) containing two selenocysteine residues tagged with 4Cl-MDPA-GdIII were indistinguishable from GdIII -GdIII distances measured of MBP containing cysteine reacted with 4Br-MDPA tags.
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Affiliation(s)
- Adarshi P Welegedara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia.,Department of Chemistry, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Ansis Maleckis
- Latvian Institute of Organic Synthesis, 1006, Riga, Latvia
| | - Ruchira Bandara
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Mithun C Mahawaththa
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Iresha Dilhani Herath
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Yi Jiun Tan
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Angeliki Giannoulis
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Daniella Goldfarb
- Department of Chemical and Biological Physics Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gottfried Otting
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
| | - Thomas Huber
- Australian National University, Research School of Chemistry, Canberra, ACT 2601, Australia
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45
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Kim H, Bang KM, Ha H, Cho NH, Namgung SD, Im SW, Cho KH, Kim RM, Choi WI, Lim YC, Shin JY, Song HK, Kim NK, Nam KT. Tyrosyltyrosylcysteine-Directed Synthesis of Chiral Cobalt Oxide Nanoparticles and Peptide Conformation Analysis. ACS NANO 2021; 15:979-988. [PMID: 33332089 DOI: 10.1021/acsnano.0c07655] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chiral inorganic nanomaterials have revealed opportunities in various fields owing to their strong light-matter interactions. In particular, chiral metal oxide nanomaterials that can control light and biochemical reactions have been highlighted due to their catalytic activity and biocompatibility. In this study, we present the synthesis of chiral cobalt oxide nanoparticles with a g-factor of 0.01 in the UV-visible region using l- and d-Tyr-Tyr-Cys ligands. The conformation of the Tyr-Tyr-Cys peptide on the nanoparticle surfaces was identified by 2D NMR spectroscopy analysis. In addition, the sequence effect of Tyr-Tyr-Cys developing chiral nanoparticles was analyzed. The revealed peptide structure, along with the experimental results, demonstrate the important role of the thiol group and carboxyl group of the Tyr-Tyr-Cys ligand in chirality evolution. Importantly, due to the magnetic properties of chiral cobalt oxide nanoparticles and their strong absorption in the UV region, the circular dichroism (CD) responses can be dramatically modulated under an external magnetic field.
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Affiliation(s)
- Hyeohn Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyeong-Mi Bang
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Heonjin Ha
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Nam Heon Cho
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Seok Daniel Namgung
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Won Im
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Kang Hee Cho
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Ryeong Myeong Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Il Choi
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yae-Chan Lim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji-Yeon Shin
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
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46
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Hu Y, Cheng K, He L, Zhang X, Jiang B, Jiang L, Li C, Wang G, Yang Y, Liu M. NMR-Based Methods for Protein Analysis. Anal Chem 2021; 93:1866-1879. [PMID: 33439619 DOI: 10.1021/acs.analchem.0c03830] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a well-established method for analyzing protein structure, interaction, and dynamics at atomic resolution and in various sample states including solution state, solid state, and membranous environment. Thanks to rapid NMR methodology development, the past decade has witnessed a growing number of protein NMR studies in complex systems ranging from membrane mimetics to living cells, which pushes the research frontier further toward physiological environments and offers unique insights in elucidating protein functional mechanisms. In particular, in-cell NMR has become a method of choice for bridging the huge gap between structural biology and cell biology. Herein, we review the recent developments and applications of NMR methods for protein analysis in close-to-physiological environments, with special emphasis on in-cell protein structural determination and the analysis of protein dynamics, both difficult to be accessed by traditional methods.
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Affiliation(s)
- Yunfei Hu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Kai Cheng
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China
| | - Lichun He
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Xu Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Bin Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Ling Jiang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Guan Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Yunhuang Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan 430071, China.,University of Chinese Academy of Sciences, Beijing 10049, China
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47
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Mekkattu Tharayil S, Mahawaththa M, Loh CT, Adekoya I, Otting G. Phosphoserine for the generation of lanthanide-binding sites on proteins for paramagnetic nuclear magnetic resonance spectroscopy. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:1-13. [PMID: 37904776 PMCID: PMC10539748 DOI: 10.5194/mr-2-1-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/12/2020] [Indexed: 11/01/2023]
Abstract
Pseudocontact shifts (PCSs) generated by paramagnetic lanthanide ions provide valuable long-range structural information in nuclear magnetic resonance (NMR) spectroscopic analyses of biological macromolecules such as proteins, but labelling proteins site-specifically with a single lanthanide ion remains an ongoing challenge, especially for proteins that are not suitable for ligation with cysteine-reactive lanthanide complexes. We show that a specific lanthanide-binding site can be installed on proteins by incorporation of phosphoserine in conjunction with other negatively charged residues, such as aspartate, glutamate or a second phosphoserine residue. The close proximity of the binding sites to the protein backbone leads to good immobilization of the lanthanide ion, as evidenced by the excellent quality of fits between experimental PCSs and PCSs calculated with a single magnetic susceptibility anisotropy (Δ χ ) tensor. An improved two-plasmid system was designed to enhance the yields of proteins with genetically encoded phosphoserine, and good lanthanide ion affinities were obtained when the side chains of the phosphoserine and aspartate residues are not engaged in salt bridges, although the presence of too many negatively charged residues in close proximity can also lead to unfolding of the protein. In view of the quality of the Δ χ tensors that can be obtained from lanthanide-binding sites generated by site-specific incorporation of phosphoserine, this method presents an attractive tool for generating PCSs in stable proteins, particularly as it is independent of cysteine residues.
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Affiliation(s)
- Sreelakshmi Mekkattu Tharayil
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Mithun Chamikara Mahawaththa
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Choy-Theng Loh
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
- present address: Hangzhou Wayland Bioscience Co. Ltd, Hangzhou
310030, PR China
| | - Ibidolapo Adekoya
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide and Protein
Science, Research School of Chemistry, Australian National University,
Canberra ACT 2601, Australia
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48
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Wang Y, An L, Yang Y, Yao L. Generating Five Independent Molecular Alignments for Simultaneous Protein Structure and Dynamics Determination Using Nuclear Magnetic Resonance Spectroscopy. Anal Chem 2020; 92:15263-15269. [PMID: 33166130 DOI: 10.1021/acs.analchem.0c02882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Residual dipolar couplings (RDCs) are commonly used in NMR for protein structure and dynamics studies, but it is challenging to generate five independent RDC data sets (required for simultaneous structure and dynamics determination) for most protein molecules in the magnetic field. In this work, a reporter protein with a lanthanide tag is introduced to create five independent alignments. This reporter protein is then attached to target proteins where five independent sets of RDCs are also obtained for the target proteins. The fitting of RDCs provides important information about the structure and dynamics of the target proteins. The method is simple and effective and, in principle, can be used to generate complete sets of RDCs for different protein molecules.
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Affiliation(s)
| | - Liaoyuan An
- University of Chinese Academy of Sciences, Beijing 100049, China
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49
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Ben Bdira F, Waudby CA, Volkov AN, Schröder SP, AB E, Codée JDC, Overkleeft HS, Aerts JMFG, Ingen H, Ubbink M. Dynamics of Ligand Binding to a Rigid Glycosidase**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Christopher A. Waudby
- Institute of Structural and Molecular Biology University College London and Birkbeck College London WC1E 6BT UK
| | - Alexander N. Volkov
- VIB-VUB Center for Structural Biology Pleinlaan 2 1050 Brussels Belgium
- Jean Jeener NMR Centre VUB Pleinlaan 2 1050 Brussels Belgium
| | - Sybrin P. Schröder
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Eiso AB
- ZoBio BV BioPartner 2 building J.H. Oortweg 19 2333 CH Leiden The Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic Synthesis Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Hugo Ingen
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
- Present address: NMR Spectroscopy Research Group Bijvoet Center for Biomolecular Research Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular Biochemistry Leiden Institute of Chemistry Einsteinweg 55 2333 CC Leiden The Netherlands
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Ben Bdira F, Waudby CA, Volkov AN, Schröder SP, AB E, Codée JDC, Overkleeft HS, Aerts JMFG, van Ingen H, Ubbink M. Dynamics of Ligand Binding to a Rigid Glycosidase*. Angew Chem Int Ed Engl 2020; 59:20508-20514. [PMID: 32533782 PMCID: PMC7693232 DOI: 10.1002/anie.202003236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/29/2020] [Indexed: 11/09/2022]
Abstract
The single-domain GH11 glycosidase from Bacillus circulans (BCX) is involved in the degradation of hemicellulose, which is one of the most abundant renewable biomaterials in nature. We demonstrate that BCX in solution undergoes minimal structural changes during turnover. NMR spectroscopy results show that the rigid protein matrix provides a frame for fast substrate binding in multiple conformations, accompanied by slow conversion, which is attributed to an enzyme-induced substrate distortion. A model is proposed in which the rigid enzyme takes advantage of substrate flexibility to induce a conformation that facilitates the acyl formation step of the hydrolysis reaction.
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Affiliation(s)
- Fredj Ben Bdira
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Christopher A. Waudby
- Institute of Structural and Molecular BiologyUniversity College London and Birkbeck CollegeLondonWC1E 6BTUK
| | - Alexander N. Volkov
- VIB-VUB Center for Structural BiologyPleinlaan 21050BrusselsBelgium
- Jean Jeener NMR CentreVUBPleinlaan 21050BrusselsBelgium
| | - Sybrin P. Schröder
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Eiso AB
- ZoBio BVBioPartner 2 buildingJ.H. Oortweg 192333 CHLeidenThe Netherlands
| | - Jeroen D. C. Codée
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hermen S. Overkleeft
- Department of Bio-organic SynthesisLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Johannes M. F. G. Aerts
- Department of Medical BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
| | - Hugo van Ingen
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
- Present address: NMR Spectroscopy Research GroupBijvoet Center for Biomolecular ResearchUtrecht UniversityPadualaan 83584 CHUtrechtThe Netherlands
| | - Marcellus Ubbink
- Department of Macromolecular BiochemistryLeiden Institute of ChemistryEinsteinweg 552333 CCLeidenThe Netherlands
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