1
|
Ledwitch K, Künze G, Okwei E, Sala D, Meiler J. Non-canonical amino acids for site-directed spin labeling of membrane proteins. Curr Opin Struct Biol 2024; 89:102936. [PMID: 39454307 DOI: 10.1016/j.sbi.2024.102936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 09/03/2024] [Accepted: 09/11/2024] [Indexed: 10/28/2024]
Abstract
Membrane proteins remain challenging targets for conventional structural biology techniques because they need to reside within complex hydrophobic lipid environments to maintain proper structure and function. Magnetic resonance combined with site-directed spin labeling is an alternative method that provides atomic-level structural and dynamical information from effects introduced by an electron- or nuclear-based spin label. With the advent of bioorthogonal click chemistries and genetically engineered non-canonical amino acids (ncAAs), options for linking spin probes to biomolecules have substantially broadened outside the conventional cysteine-based labeling scheme. Here, we highlight current strategies to spin-label membrane proteins through ncAAs for nuclear and electron paramagnetic resonance applications. Such advances are critical for developing bioorthogonal spin labeling schemes to achieve in-cell labeling and in-cell measurements of membrane protein conformational dynamics.
Collapse
Affiliation(s)
- Kaitlyn Ledwitch
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA.
| | - Georg Künze
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Elleansar Okwei
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA
| | - Davide Sala
- Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37240, USA; Department of Chemistry, Vanderbilt University, Nashville, TN 37240, USA; Institute of Drug Discovery, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| |
Collapse
|
2
|
Querci L, Piccioli M, Ciofi-Baffoni S, Banci L. Structural aspects of iron‑sulfur protein biogenesis: An NMR view. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119786. [PMID: 38901495 DOI: 10.1016/j.bbamcr.2024.119786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/15/2024] [Accepted: 06/10/2024] [Indexed: 06/22/2024]
Abstract
Over the last decade, structural aspects involving iron‑sulfur (Fe/S) protein biogenesis have played an increasingly important role in understanding the high mechanistic complexity of mitochondrial and cytosolic machineries maturing Fe/S proteins. In this respect, solution NMR has had a significant impact because of its ability to monitor transient protein-protein interactions, which are abundant in the networks of pathways leading to Fe/S cluster biosynthesis and transfer, as well as thanks to the developments of paramagnetic NMR in both terms of new methodologies and accurate data interpretation. Here, we review the use of solution NMR in characterizing the structural aspects of human Fe/S proteins and their interactions in the framework of Fe/S protein biogenesis. We will first present a summary of the recent advances that have been achieved by paramagnetic NMR and then we will focus our attention on the role of solution NMR in the field of human Fe/S protein biogenesis.
Collapse
Affiliation(s)
- Leonardo Querci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy
| | - Mario Piccioli
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy
| | - Simone Ciofi-Baffoni
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy.
| | - Lucia Banci
- Magnetic Resonance Center CERM, University of Florence, Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy; Department of Chemistry, University of Florence, Via della Lastruccia 3, Sesto Fiorentino, 50019 Florence, Italy; Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Via Luigi Sacconi 6, Sesto Fiorentino, 50019 Florence, Italy.
| |
Collapse
|
3
|
Daddi-Moussa-Ider A, Tjhung E, Pradas M, Richter T, Menzel AM. Rotational dynamics of a disk in a thin film of weakly nematic fluid subject to linear friction. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:58. [PMID: 39322774 PMCID: PMC11424714 DOI: 10.1140/epje/s10189-024-00452-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 09/09/2024] [Indexed: 09/27/2024]
Abstract
Dynamics at low Reynolds numbers experiences recent revival in the fields of biophysics and active matter. While in bulk isotropic fluids it is exhaustively studied, this is less so in anisotropic fluids and in confined situations. Here, we combine the latter two by studying the rotation of a disk-like inclusion in a uniaxially anisotropic, globally oriented, incompressible two-dimensional fluid film. In terms of a perturbative expansion in parameters that quantify anisotropies in viscosity and in additional linear friction with a supporting substrate or other type of confinement, we derive analytical expressions for the resulting hydrodynamic flow and pressure fields as well as for the resistance and mobility coefficients of the rotating disk. It turns out that, in contrast to translational motion, the solutions remain well-behaved also in the absence of the additional linear friction. Comparison with results from finite-element simulations shows very good agreement with those from our analytical calculations. Besides applications to describe technological systems, for instance, in the area of microfluidics and thin cells of aligned nematic liquid crystals, our solutions are important for quantitative theoretical approaches to fluid membranes and thin films in general featuring a preferred direction.
Collapse
Affiliation(s)
| | - Elsen Tjhung
- School of Mathematics and Statistics, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
| | - Marc Pradas
- School of Mathematics and Statistics, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
| | - Thomas Richter
- Institut für Analysis und Numerik, Otto-von-Guericke-Universität Magdeburg, Universitätsplatz 2, Magdeburg, 39106, Germany
| | - Andreas M Menzel
- Institut für Physik, Otto-von-Guericke-Universität Magdeburg, Universitätsplatz 2, Magdeburg, 39106, Germany
| |
Collapse
|
4
|
Topping L, Welegedara AP, Judd M, Abdelkader EH, Cox N, Otting G, Butler SJ. A lanthanide tag for a complementary set of pseudocontact shifts. Chem Commun (Camb) 2024; 60:8458-8461. [PMID: 39040014 DOI: 10.1039/d4cc03007a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Pseudocontact shifts (PCS) generated by paramagnetic lanthanide ions deliver powerful restraints for protein structure analysis by NMR spectroscopy. We present a new lanthanide tag that generates different PCSs than that of a related tag, which differs in structure by a single oxygen atom. It is highly reactive towards cysteine and performs well in turn-on luminescence and in EPR spectroscopy.
Collapse
Affiliation(s)
- Lydia Topping
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK.
| | - Adarshi P Welegedara
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Martyna Judd
- 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
| | - Nicholas Cox
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Stephen J Butler
- Department of Chemistry, Loughborough University, Epinal Way, Loughborough, LE11 3TU, UK.
| |
Collapse
|
5
|
Lu YL, Wu K, Huang YH, Li WC, Cao ZM, Yan XH, Zhang XD, Liu CH, Ruan J, Xu HS, Pan M, Su CY. Stereochemical Control of Redox Co II/Co III-Cages with Switchable Cotton Effects Based on Labile-Static States. J Am Chem Soc 2024; 146:20414-20424. [PMID: 38982611 DOI: 10.1021/jacs.4c06102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
The structural dynamics of artificial assemblies, in aspects such as molecular recognition and structural transformation, provide us with a blueprint to achieve bioinspired applications. Here, we describe the assembly of redox-switchable chiral metal-organic cages Λ8/Δ8-[Pd6(CoIIL3)8]28+ and Λ8/Δ8-[Pd6(CoIIIL3)8]36+. These isomeric cages demonstrate an on-off chirality logic gate controlled by their chemical and stereostructural dynamics tunable through redox transitions between the labile CoII-state and static CoIII-state with a distinct Cotton effect. The transition between different states is enabled by a reversible redox process and chiral recognition originating in the tris-chelate Co-centers. All cages in two states are thoroughly characterized by NMR, ESI-MS, CV, CD, and X-ray crystallographic analysis, which clarify their redox-switching behaviors upon chemical reduction/oxidation. The stereochemical lability of the CoII-center endows the Λ8/Δ8-CoII-cages with efficient chiral-induction by enantiomeric guests, leading to enantiomeric isomerization to switch between Λ8/Δ8-CoII-cages, which can be stabilized by oxidation to their chemically inert forms of Λ8/Δ8-CoIII-cages. Kinetic studies reveal that the isomerization rate of the Δ8-CoIII-cage is at least an order of magnitude slower than that of the Δ8-CoII-cage even at an elevated temperature, while its activation energy is 16 kcal mol-1 higher than that of the CoII-cage.
Collapse
Affiliation(s)
- Yu-Lin Lu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Kai Wu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yin-Hui Huang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei-Chun Li
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhong-Min Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiang-Han Yan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiao-Dong Zhang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Chen-Hui Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jia Ruan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Hai-Sen Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Mei Pan
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Cheng-Yong Su
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, GBRCE for Functional Molecular Engineering, LIFM, IGCME, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| |
Collapse
|
6
|
Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
Collapse
Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
| |
Collapse
|
7
|
Wang S, Zhao Y, Yao S, Wang Z, Zhang Z, Wen K, Ma B, Li L. Chirality of Copper-Amino Acid Nanoparticles Determines Chemodynamic Cancer Therapeutic Outcome. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309328. [PMID: 38308407 DOI: 10.1002/smll.202309328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/02/2024] [Indexed: 02/04/2024]
Abstract
Chirality is a prevalent characteristic in nature, where biological systems exhibit a significant preference for specific enantiomers of biomolecules. However, there is a limited exploration into utilizing nanomaterials' chirality to modulate their interactions with intracellular substances. In this study, self-assembled copper-cysteine chiral nanoparticles and explore the influence of their charity on cancer chemodynamic therapy (CDT) are fabricated. Experimental and molecular dynamics (MD) simulation results demonstrate that the copper-l-cysteine chiral nanoparticles (Cu-l-Cys NPs) exhibit a stronger affinity toward l-glutathione (l-GSH) that is overproduced in cancer cells, compared to the copper-d-cysteine enantiomer (Cu-d-Cys NPs). The interaction between Cu-l-Cys NPs and l-GSH triggers a redox reaction that depletes l-GSH and converts Cu2+ into Cu+. Subsequently, Cu+ catalyzes a Fenton-like reaction, decomposing H2O2 into highly cytotoxic hydroxyl radicals (•OH) for cancer CDT. In vivo, results confirm that Cu-l-Cys NPs with good biocompatibility elicit a pronounced cancer cell death and effectively inhibit tumor growth. This work proposes a new perspective on chirality-enhanced cancer therapy.
Collapse
Affiliation(s)
- Shaobo Wang
- Center on Nanoenergy Research, School of Physical Science and Technology, Guangxi University, Nanning, 530004, P. R. China
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, P. R. China
| | - Yunchao Zhao
- Center on Nanoenergy Research, School of Physical Science and Technology, Guangxi University, Nanning, 530004, P. R. China
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, P. R. China
| | - Shuncheng Yao
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, P. R. China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhuo Wang
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, P. R. China
| | - Zeyu Zhang
- Center on Nanoenergy Research, School of Physical Science and Technology, Guangxi University, Nanning, 530004, P. R. China
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, P. R. China
| | - Kaikai Wen
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, P. R. China
| | - Baojin Ma
- School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration & Shandong Provincial Clinical Research Center for Oral Diseases, Jinan, Shandong, 250012, P. R. China
| | - Linlin Li
- Center on Nanoenergy Research, School of Physical Science and Technology, Guangxi University, Nanning, 530004, P. R. China
- Beijing Institute of Nanoenergy and Nanosystems, Chinese Academy of Sciences, Beijing, 101400, P. R. China
- School of Nanoscience and Engineering, University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| |
Collapse
|
8
|
Svítok A, Blahut J, Urbanovský P, Hermann P. Dynamics of Coordinated Phosphonate Group Directly Observed by 17O-NMR in Lanthanide(iii) Complexes of a Mono(ethyl phosphonate) DOTA Analogue. Chemistry 2024; 30:e202400970. [PMID: 38624256 DOI: 10.1002/chem.202400970] [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: 03/08/2024] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 04/17/2024]
Abstract
Biological phosphates can coordinate metal ions and their complexes are common in living systems. Dynamics of mutual oxygen atom exchange in the tetrahedral group in complexes has not been investigated. Here, we present a direct experimental proof of exchange ("phosphonate rotation") in model Ln(III) complexes of monophosphonate H4dota analogue which alters phosphorus atom chirality of coordinated phosphonate monoester. Combination of macrocycle-based isomerism with P-based chirality leads to several diastereoisomers. (Non)-coordinated oxygen atoms were distinguished through 17O-labelled phosphonate group and their mutual exchange was followed by various NMR techniques and DFT calculations. The process is sterically demanding and occurs through bulky bidentate (κ2-PO2)- coordination and was observed only in twisted-square antiprism (TSA) diastereoisomer of large Ln(III) ions. Its energy demands increase for smaller Ln(III) ions (298ΔG≠(exp./DFT)=51.8/52.1 and 61.0/71.5 kJ mol-1 for La(III) and Eu(III), respectively). These results are helpful in design of such complexes as MRI CA and for protein paramagnetic NMR probes. It demonstrates usefulness of 17O NMR to study solution dynamics in complexes involving phosphorus acid derivatives and it may inspire use of this method to study dynamics of phosphoric acid derivatives (as e. g. phosphorus acid-based inhibitors of metalloenzymes) in different areas of chemistry.
Collapse
Affiliation(s)
- Adam Svítok
- Department Department of Inorganic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 12843, Prague 2, Czech Republic
| | - Jan Blahut
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Flemingovo náměstí 2, 16000, Prague 6, Czech Republic
| | - Peter Urbanovský
- Department Department of Inorganic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 12843, Prague 2, Czech Republic
| | - Petr Hermann
- Department Department of Inorganic Chemistry, Faculty of Science, Charles University, Hlavova 2030, 12843, Prague 2, Czech Republic
| |
Collapse
|
9
|
Hong J, Wang L, Zheng Q, Cai C, Yang X, Liao Z. The Recent Applications of Magnetic Nanoparticles in Biomedical Fields. MATERIALS (BASEL, SWITZERLAND) 2024; 17:2870. [PMID: 38930238 PMCID: PMC11204782 DOI: 10.3390/ma17122870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Magnetic nanoparticles (MNPs) have found extensive application in the biomedical domain due to their enhanced biocompatibility, minimal toxicity, and strong magnetic responsiveness. MNPs exhibit great potential as nanomaterials in various biomedical applications, including disease detection and cancer therapy. Typically, MNPs consist of a magnetic core surrounded by surface modification coatings, such as inorganic materials, organic molecules, and polymers, forming a nucleoshell structure that mitigates nanoparticle agglomeration and enhances targeting capabilities. Consequently, MNPs exhibit magnetic responsiveness in vivo for transportation and therapeutic effects, such as enhancing medical imaging resolution and localized heating at the site of injury. MNPs are utilized for specimen purification through targeted binding and magnetic separation in vitro, thereby optimizing efficiency and expediting the process. This review delves into the distinctive functional characteristics of MNPs as well as the diverse bioactive molecules employed in their surface coatings and their corresponding functionalities. Additionally, the advancement of MNPs in various applications is outlined. Additionally, we discuss the advancements of magnetic nanoparticles in medical imaging, disease treatment, and in vitro assays, and we anticipate the future development prospects and obstacles in this field. The objective is to furnish readers with a thorough comprehension of the recent practical utilization of MNPs in biomedical disciplines.
Collapse
Affiliation(s)
| | | | | | | | | | - Zhenlin Liao
- College of Food Science, South China Agricultural University, Guangzhou 510642, China; (J.H.); (L.W.); (Q.Z.); (C.C.); (X.Y.)
| |
Collapse
|
10
|
Aspholm EE, Lidman J, Burmann BM. Structural basis of substrate recognition and allosteric activation of the proapoptotic mitochondrial HtrA2 protease. Nat Commun 2024; 15:4592. [PMID: 38816423 DOI: 10.1038/s41467-024-48997-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/14/2024] [Indexed: 06/01/2024] Open
Abstract
The mitochondrial serine protease HtrA2 is a human homolog of the Escherichia coli Deg-proteins exhibiting chaperone and proteolytic roles. HtrA2 is involved in both apoptotic regulation via its ability to degrade inhibitor-of-apoptosis proteins (IAPs), as well as in cellular maintenance as part of the cellular protein quality control machinery, by preventing the possible toxic accumulation of aggregated proteins. In this study, we use advanced solution NMR spectroscopy methods combined with biophysical characterization and biochemical assays to elucidate the crucial role of the substrate recognizing PDZ domain. This domain regulates the protease activity of HtrA2 by triggering an intricate allosteric network involving the regulatory loops of the protease domain. We further show that divalent metal ions can both positively and negatively modulate the activity of HtrA2, leading to a refined model of HtrA2 regulation within the apoptotic pathway.
Collapse
Affiliation(s)
- Emelie E Aspholm
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden
| | - Jens Lidman
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden
| | - Björn M Burmann
- Department of Chemistry and Molecular Biology, University of Gothenburg, Göteborg, Sweden.
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden.
| |
Collapse
|
11
|
Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [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
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
Collapse
Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| |
Collapse
|
12
|
Hazra N, Gayen K, Ghosh P, Hansda B, Banerjee A. Stabilization of a Photoradiated Naphthalene Diimide-Based Organic Radical Anion Inside a Peptide-Based Gel Matrix with an Improvement of Optoelectronic Properties. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:9462-9470. [PMID: 38652709 DOI: 10.1021/acs.langmuir.3c03947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
An amino acid-conjugated naphthalene diimide (NDI)-based highly red fluorescent radical anion has been found in a water medium under the photoradiated condition. This molecule has failed to form the radical anion in the monomeric state; however, the J aggregation in the aqueous medium has ensured the formation of radical anion in the ambient condition after the irradiation of both sunlight and UV light exposure. Electron paramagnetic resonance (EPR) studies clearly suggest the formation of radical anions. Herein, the stability of the radical anion in the aqueous medium is only a few minutes as a small amount of shaking is enough to quench the radical anion in the solution state. Furthermore, the incorporation of this molecule into a peptide-based hydrogel matrix and the consequent photoirradiation have not only helped to develop radical anion in the gel matrix but also increased the enormous stability of the radical anion inside the hydrogel matrix even for 30 days. It is envisaged that the formation of the radical anion within the gel matrix prevents the free movement of the NDI molecules and restricts the diffusion of molecular oxygen in the system, which leads to the stability of the radical anions in the gel. Moreover, the stability of the radical anion within the gel has helped to enhance the conductivity of the hybrid gel to a great extent. Interestingly, the radical anion-containing hybrid hydrogel has shown a potential photoswitching property.
Collapse
Affiliation(s)
- Niladri Hazra
- School of Biological Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Kousik Gayen
- School of Biological Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Purnadas Ghosh
- School of Biological Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Biswanath Hansda
- School of Biological Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| | - Arindam Banerjee
- School of Biological Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700 032, India
| |
Collapse
|
13
|
Chai Z, Li C. In-Cell 19F NMR of Proteins: Recent Progress and Future Opportunities. Chemistry 2024; 30:e202303988. [PMID: 38269421 DOI: 10.1002/chem.202303988] [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: 11/29/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
In vitro, 19F NMR methodology is preferably selected as a complementary and straightforward method for unveiling the conformations, dynamics, and interactions of biological molecules. Its effectiveness in vivo has seen continuous improvement, addressing challenges faced by conventional heteronuclear NMR experiments on structured proteins, such as severe line broadening, low signal-to-noise ratio, and background signals. Herein, we summarize the distinctive advantages of 19F NMR, along with recent progress in sample preparation and applications within the realm of in-cell NMR. Additionally, we offer insights into the future directions and prospects of this methodology based on our understanding.
Collapse
Affiliation(s)
- Zhaofei Chai
- 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 National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, 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 National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, 430071, Wuhan, China
| |
Collapse
|
14
|
Shi M, Xiong W, Feng J, Wu L, Yang J, Lu Y, Lu X, Fan Q, Nie H, Dai Y, Yan C, Tian Y, Shen Z. Kilogram scale facile synthesis and systematic characterization of a Gd-macrochelate as T 1-weighted magnetic resonance imaging contrast agent. J Nanobiotechnology 2024; 22:162. [PMID: 38594700 PMCID: PMC11005285 DOI: 10.1186/s12951-024-02394-8] [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: 11/04/2023] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
To overcome the problems of commercial magnetic resonance imaging (MRI) contrast agents (CAs) (i.e., small molecule Gd chelates), we have proposed a new concept of Gd macrochelates based on the coordination of Gd3+ and macromolecules, e.g., poly(acrylic acid) (PAA). To further decrease the r2/r1 ratio of the reported Gd macrochelates that is an important factor for T1 imaging, in this study, a superior macromolecule hydrolyzed polymaleic anhydride (HPMA) was found to coordinate Gd3+. The synthesis conditions were optimized and the generated Gd-HPMA macrochelate was systematically characterized. The obtained Gd-HPMA29 synthesized in a 100 L of reactor has a r1 value of 16.35 mM-1 s-1 and r2/r1 ratio of 2.05 at 7.0 T, a high Gd yield of 92.7% and a high product weight (1074 g), which demonstrates the feasibility of kilogram scale facile synthesis. After optimization of excipients and sterilization at a high temperature, the obtained Gd-HPMA30 formulation has a pH value of 7.97, osmolality of 691 mOsmol/kg water, density of 1.145 g/mL, and viscosity of 2.2 cP at 20 ℃ or 1.8 cP at 37 ℃, which meet all specifications and physicochemical criteria for clinical injections indicating the immense potential for clinical applications.
Collapse
Affiliation(s)
- Meng Shi
- School of Biomedical Engineering, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China
| | - Wei Xiong
- Medical Imaging Center, Nanfang Hospital, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China.
| | - Jie Feng
- Medical Imaging Center, Nanfang Hospital, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China
| | - Lihe Wu
- School of Biomedical Engineering, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China
| | - Jing Yang
- School of Biomedical Engineering, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China
| | - Yudie Lu
- School of Biomedical Engineering, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China
| | - Xuanyi Lu
- School of Biomedical Engineering, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China
| | - Qingdeng Fan
- School of Biomedical Engineering, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China
| | - Hemin Nie
- Department of Biomedical Sciences, College of Biology, Hunan University, 52 Tianmu Road, Yuelu, Changsha, 410082, Hunan, China
| | - Yunlu Dai
- Faculty of Health Sciences and MoE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, 999078, China
| | - Chenggong Yan
- Medical Imaging Center, Nanfang Hospital, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China.
| | - Ye Tian
- School of Biomedical Engineering, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China.
| | - Zheyu Shen
- School of Biomedical Engineering, Southern Medical University, 1023 Shatai South Road, Baiyun, Guangzhou, 510515, Guangdong, China.
| |
Collapse
|
15
|
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.
Collapse
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.
| |
Collapse
|
16
|
Bartholow T, Burroughs PW, Elledge SK, Byrnes JR, Kirkemo LL, Garda V, Leung KK, Wells JA. Photoproximity Labeling from Single Catalyst Sites Allows Calibration and Increased Resolution for Carbene Labeling of Protein Partners In Vitro and on Cells. ACS CENTRAL SCIENCE 2024; 10:199-208. [PMID: 38292613 PMCID: PMC10823516 DOI: 10.1021/acscentsci.3c01473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 02/01/2024]
Abstract
The cell surface proteome (surfaceome) plays a pivotal role in virtually all extracellular biology, and yet we are only beginning to understand the protein complexes formed in this crowded environment. Recently, a high-resolution approach (μMap) was described that utilizes multiple iridium-photocatalysts attached to a secondary antibody, directed to a primary antibody of a protein of interest, to identify proximal neighbors by light-activated conversion of a biotin-diazirine to a highly reactive carbene followed by LC/MS (Geri, J. B.; Oakley, J. V.; Reyes-Robles, T.; Wang, T.; McCarver, S. J.; White, C. H.; Rodriguez-Rivera, F. P.; Parker, D. L.; Hett, E. C.; Fadeyi, O. O.; Oslund, R. C.; MacMillan, D. W. C. Science2020, 367, 1091-1097). Here we calibrated the spatial resolution for carbene labeling using site-specific conjugation of a single photocatalyst to a primary antibody drug, trastuzumab (Traz), in complex with its structurally well-characterized oncogene target, HER2. We observed relatively uniform carbene labeling across all amino acids, and a maximum distance of ∼110 Å from the fixed photocatalyst. When targeting HER2 overexpression cells, we identified 20 highly enriched HER2 neighbors, compared to a nonspecific membrane tethered catalyst. These studies identify new HER2 interactors and calibrate the radius of carbene photoprobe labeling for the surfaceome.
Collapse
Affiliation(s)
- Thomas
G. Bartholow
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Paul W.W. Burroughs
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Susanna K. Elledge
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James R. Byrnes
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Lisa L. Kirkemo
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Virginia Garda
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - Kevin K. Leung
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
| | - James A. Wells
- Department
of Pharmaceutical Chemistry, University
of California San Francisco, San Francisco, California 94158, United States
- Department
of Cellular & Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| |
Collapse
|
17
|
Kormschikov ID, Polovkova MA, Kirakosyan GA, Martynov AG, Gorbunova YG, Tsivadze AY. Magnetic Anisotropy of Homo- and Heteronuclear Terbium(III) and Dysprosium(III) Trisphthalocyaninates Derived from Paramagnetic 1H-NMR Investigation. Molecules 2024; 29:510. [PMID: 38276588 PMCID: PMC11154240 DOI: 10.3390/molecules29020510] [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: 12/23/2023] [Revised: 01/13/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
1H-NMR spectroscopy of lanthanide complexes is a powerful tool for deriving spectral-structural correlations, which provide a clear link between the symmetry of the coordination environment of paramagnetic metal centers and their magnetic properties. In this work, we have first synthesized a series of homo- (M = M* = Dy) and heteronuclear (M ≠ M* = Dy/Y and Dy/Tb) triple-decker complexes [(BuO)8Pc]M[(BuO)8Pc]M*[(15C5)4Pc], where BuO- and 15C5- are, respectively, butoxy and 15-crown-5 substituents on phthalocyanine (Pc) ligands. We provide an algorithmic approach to assigning the 1H-NMR spectra of these complexes and extracting the axial component of the magnetic susceptibility tensor, χax. We show how this term is related to the nature of the lanthanide ion and the shape of its coordination polyhedron, providing an experimental basis for further theoretical interpretation of the revealed correlations.
Collapse
Affiliation(s)
- Ilya D. Kormschikov
- Faculty of Chemistry, Lomonosov Moscow State University, GSP-1, Leninskie Gory, 119991 Moscow, Russia;
| | - Marina A. Polovkova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia; (M.A.P.); (G.A.K.); (Y.G.G.); (A.Y.T.)
| | - Gayane A. Kirakosyan
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia; (M.A.P.); (G.A.K.); (Y.G.G.); (A.Y.T.)
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninsky pr., 31, 119991 Moscow, Russia
| | - Alexander G. Martynov
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia; (M.A.P.); (G.A.K.); (Y.G.G.); (A.Y.T.)
| | - Yulia G. Gorbunova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia; (M.A.P.); (G.A.K.); (Y.G.G.); (A.Y.T.)
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninsky pr., 31, 119991 Moscow, Russia
| | - Aslan Yu. Tsivadze
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninsky pr., 31, Building 4, 119071 Moscow, Russia; (M.A.P.); (G.A.K.); (Y.G.G.); (A.Y.T.)
- Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Leninsky pr., 31, 119991 Moscow, Russia
| |
Collapse
|
18
|
Querci L, Grifagni D, Trindade IB, Silva JM, Louro RO, Cantini F, Piccioli M. Paramagnetic NMR to study iron sulfur proteins: 13C detected experiments illuminate the vicinity of the metal center. JOURNAL OF BIOMOLECULAR NMR 2023; 77:247-259. [PMID: 37853207 PMCID: PMC10687126 DOI: 10.1007/s10858-023-00425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 09/25/2023] [Indexed: 10/20/2023]
Abstract
The robustness of NMR coherence transfer in proximity of a paramagnetic center depends on the relaxation properties of the nuclei involved. In the case of Iron-Sulfur Proteins, different pulse schemes or different parameter sets often provide complementary results. Tailored versions of HCACO and CACO experiments significantly increase the number of observed Cα/C' connectivities in highly paramagnetic systems, by recovering many resonances that were lost due to paramagnetic relaxation. Optimized 13C direct detected experiments can significantly extend the available assignments, improving the overall knowledge of these systems. The different relaxation properties of Cα and C' nuclei are exploited in CACO vs COCA experiments and the complementarity of the two experiments is used to obtain structural information. The two [Fe2S2]+ clusters containing NEET protein CISD3 and the one [Fe4S4]2+ cluster containing HiPIP protein PioC have been taken as model systems. We show that tailored experiments contribute to decrease the blind sphere around the cluster, to extend resonance assignment of cluster bound cysteine residues and to retrieve details on the topology of the iron-bound ligand residues.
Collapse
Affiliation(s)
- Leonardo Querci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Deborah Grifagni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Inês B Trindade
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal
- Division of Biology and Biological Engineering, California Institute of Technology, CA 91125, Pasadena, USA
| | - José Malanho Silva
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Ricardo O Louro
- Instituto de Tecnologia Química e Biológica António Xavier (ITQB-NOVA), Universidade Nova de Lisboa, Av. da República (EAN), 2780-157, Oeiras, Portugal
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019, Sesto Fiorentino, Italy.
| |
Collapse
|
19
|
Maier KB, Rust LN, Kupara CI, Woods M. Diastereoselective Synthesis of α-Aryl-Substituted LnDOTA Chelates from Achiral Starting Materials by Deracemization Under Mild Conditions. Chemistry 2023; 29:e202301887. [PMID: 37519104 DOI: 10.1002/chem.202301887] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/26/2023] [Accepted: 07/26/2023] [Indexed: 08/01/2023]
Abstract
Substituted derivatives of the DOTA framework are of general interest to alter chelate properties and facilitate the conjugation of chelates to other molecular structures. However, the scope of substituents that can be introduced into the α-position has traditionally been limited by the availability of a suitable enantiopure starting materials to facilitate a stereoselective synthesis. Tetra-substituted DOTA derivatives with phenyl and benzoate substituents in the α-position have been prepared. Initial syntheses used enantiopure starting materials but did not afford enantiopure products. This indicates that the integrity of the stereocenters was not preserved during synthesis, despite the homo-chiral diastereoisomer being the major reaction product. The homochiral diastereoisomer could be produced as the major or sole reaction product when starting from racemic or even achiral materials. Deracemization was found to occur during chelation through the formation of an enolate stabilized by the aryl substituent. This general ability of aryl groups to enable deracemization greatly increases the range of substituents that can be introduced into DOTA-type ligands with diastereochemical selectivity.
Collapse
Affiliation(s)
- Karley B Maier
- Department of Chemistry, Portland State University 1719, SW 10th Ave, Portland, OR 97201, USA
| | - Lauren N Rust
- Department of Chemistry, Portland State University 1719, SW 10th Ave, Portland, OR 97201, USA
| | - Charlene I Kupara
- Department of Chemistry, Portland State University 1719, SW 10th Ave, Portland, OR 97201, USA
| | - Mark Woods
- Department of Chemistry, Portland State University 1719, SW 10th Ave, Portland, OR 97201, USA
- Advanced Imaging Research Center, Oregon Health and Science University, 1381 SW Sam Jackson Park Road, Portland, OR 97239, USA
| |
Collapse
|
20
|
Bartholow TG, Burroughs P, Elledge SK, Byrnes JR, Kirkemo LL, Garda V, Leung KK, Wells JA. Site-specific proximity labeling at single residue resolution for identification of protein partners in vitro and on cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550738. [PMID: 37546992 PMCID: PMC10402114 DOI: 10.1101/2023.07.27.550738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The cell surface proteome, or surfaceome, is encoded by more than 4000 genes, but we are only beginning to understand the complexes they form. Rapid proximity labeling around specific membrane targets allows for capturing weak and transient interactions expected in the crowded and dynamic environment of the surfaceome. Recently, a high-resolution approach called μMap has been described (Geri, J. B., Oakley, J. V., Reyes-Robles, T., Wang, T., McCarver, S. J., White, C. H., Rodriguez-Rivera, F. P., Parker, D. L., Hett, E. C., Fadeyi, O. O., Oslund, R. C., and MacMillan, D. W. C. (2020) Science 367 , 1091-1097) in which an iridium (Ir)-based photocatalyst is attached to a specific antibody to target labeling of neighbors utilizing light-activated generation of carbenes from diazirine compounds via Dexter Energy Transfer (DET). Here we studied and optimized the spatial resolution for the method using an oncoprotein complex between the antibody drug, trastuzumab (Traz), and its target HER2. A set of eight single site-specific Ir-catalytic centers were engineered into Traz to study intra- and inter-molecular labeling in vitro and on cells by mass spectrometry. From this structurally well-characterized complex we observed a maximum distance of ∼110 Å for labeling. Labeling occurred almost uniformly over the full range of amino acids, unlike the residue specific labeling of other techniques. To examine on cell labeling that is specific to HER2 as opposed to simply being on the membrane, we compared the labeling patterns for the eight Traz-catalyst species to random labeling of membrane proteins using a metabolically integrated fatty acid catalyst. Our results identified 20 high confidence HER2 neighbors, many novel, that were more than 6-fold enriched compared to the non-specific membrane tethered catalyst. These studies define distance labeling parameters from single-site catalysts placed directly on the membrane target of interest, and more accurately compare to non-specific labeling to identify membrane complexes with higher confidence.
Collapse
|
21
|
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: 11] [Impact Index Per Article: 11.0] [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.
Collapse
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
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
Canales A, Sastre J, Orduña JM, Spruit CM, Pérez-Castells J, Domínguez G, Bouwman KM, van der Woude R, Cañada FJ, Nycholat CM, Paulson JC, Boons GJ, Jiménez-Barbero J, de Vries RP. Revealing the Specificity of Human H1 Influenza A Viruses to Complex N-Glycans. JACS AU 2023; 3:868-878. [PMID: 37006776 PMCID: PMC10052259 DOI: 10.1021/jacsau.2c00664] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 05/18/2023]
Abstract
Influenza virus infection remains a threat to human health since viral hemagglutinins are constantly drifting, escaping infection and vaccine-induced antibody responses. Viral hemagglutinins from different viruses display variability in glycan recognition. In this context, recent H3N2 viruses have specificity for α2,6 sialylated branched N-glycans with at least three N-acetyllactosamine units (tri-LacNAc). In this work, we combined glycan arrays and tissue binding analyses with nuclear magnetic resonance experiments to characterize the glycan specificity of a family of H1 variants, including the one responsible for the 2009 pandemic outbreak. We also analyzed one engineered H6N1 mutant to understand if the preference for tri-LacNAc motifs could be a general trend in human-type receptor-adapted viruses. In addition, we developed a new NMR approach to perform competition experiments between glycans with similar compositions and different lengths. Our results point out that pandemic H1 viruses differ from previous seasonal H1 viruses by a strict preference for a minimum of di-LacNAc structural motifs.
Collapse
Affiliation(s)
- Angeles Canales
- Department
of Organic Chemistry, Faculty of Chemistry, Universidad Complutense de Madrid, Avd. Complutense s/n, Madrid 28040, Spain
| | - Javier Sastre
- Centro
de Investigaciones Biológicas Margarita Salas, CSIC, C/Ramiro de Maetzu 9, Madrid 28040, Spain
| | - Jose M. Orduña
- Department
of Chemistry and Biochemistry Facultad de Farmacia, Universidad San
Pablo-CEU, CEU Universities Urbanización
Montepríncipe, Boadilla del Monte, Madrid 28660, Spain
| | - Cindy M. Spruit
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
| | - Javier Pérez-Castells
- Department
of Chemistry and Biochemistry Facultad de Farmacia, Universidad San
Pablo-CEU, CEU Universities Urbanización
Montepríncipe, Boadilla del Monte, Madrid 28660, Spain
| | - Gema Domínguez
- Department
of Chemistry and Biochemistry Facultad de Farmacia, Universidad San
Pablo-CEU, CEU Universities Urbanización
Montepríncipe, Boadilla del Monte, Madrid 28660, Spain
| | - Kim M. Bouwman
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
| | - Roosmarijn van der Woude
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
| | - Francisco Javier Cañada
- Centro
de Investigaciones Biológicas Margarita Salas, CSIC, C/Ramiro de Maetzu 9, Madrid 28040, Spain
- Centro
de Investigación Biomédica en Red-Enfermedades Respiratorias
(CIBERES), Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón
11, Madrid 28029, Spain
| | - Corwin M. Nycholat
- Department
of Molecular Medicine, The Scripps Research
Institute, La Jolla, California 92037, United States
| | - James C. Paulson
- Department
of Molecular Medicine, The Scripps Research
Institute, La Jolla, California 92037, United States
| | - Geert-Jan Boons
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
- Complex
Carbohydrate Research Center, University
of Georgia, 315 Riverbend
Road, Athens, Georgia 30602, United States
| | - Jesús Jiménez-Barbero
- Centro
de Investigación Biomédica en Red-Enfermedades Respiratorias
(CIBERES), Instituto de Salud Carlos III, C/ Monforte de Lemos 3-5, Pabellón
11, Madrid 28029, Spain
- CIC
bioGUNE, Bizkaia Science and Technology
Park, Bilbao 48160, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48009, Spain
- Department
of Organic Chemistry, II Faculty of Science
and Technology University of the Basque Country, EHU-UPV, Leioa 48940, Spain
| | - Robert P. de Vries
- Department
of Chemical Biology & Drug Discovery, Utrecht Institute for Pharmaceutical
Sciences, Utrecht University, Utrecht 3584 CG, The Netherlands
| |
Collapse
|
24
|
Belov AS, Belova SA, Efimov NN, Zlobina VV, Novikov VV, Nelyubina YV, Zubavichus YV, Voloshin YZ, Pavlov AA. Synthesis, X-ray structure and magnetic properties of the apically functionalized monocapped cobalt(II) tris-pyridineoximates possessing SMM behaviour. Dalton Trans 2023; 52:2928-2932. [PMID: 36811361 DOI: 10.1039/d2dt04073e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
The title cobalt(II) pseudoclathrochelate complexes possess an intermediate trigonal prismatic-trigonal antiprismatic geometry. As follows from PPMS data, they exhibit an SMM behaviour with Orbach relaxation barriers of approximately 90 K. Paramagnetic NMR experiments confirmed a persistence of these magnetic characteristics in solution. Therefore, a straightforward apical functionalization of this 3D molecular platform for its targeted delivery to a given biosystem can be performed without substantial changes.
Collapse
Affiliation(s)
- Alexander S Belov
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr., 119991 Moscow, Russia. .,Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia
| | - Svetlana A Belova
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr., 119991 Moscow, Russia. .,Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia
| | - Nikolay N Efimov
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr., 119991 Moscow, Russia.
| | - Veronika V Zlobina
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia
| | - Valentin V Novikov
- Moscow Institute of Physics and Technology, National Research University, Institutsliy per. 9, Dolgoprudny, 141700 Moscow Region, Russia.,BMSTU Center of National Technological Initiative "Digital Material Science: New Material and Substances", Bauman Moscow State Technical University, 2nd Baumanskaya st. 5, 105005, Moscow, Russia
| | - Yulya V Nelyubina
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia.,BMSTU Center of National Technological Initiative "Digital Material Science: New Material and Substances", Bauman Moscow State Technical University, 2nd Baumanskaya st. 5, 105005, Moscow, Russia
| | - Yan V Zubavichus
- Synchrotron Radiation Facility SKIF, G.K. Boreskov Institute of Catalysis of the Siberian Branch of the Russian Academy of Sciences, 1 Nikolskii pr., 630559 Koltsovo, Russia
| | - Yan Z Voloshin
- Kurnakov Institute of General and Inorganic Chemistry of the Russian Academy of Sciences, 31 Leninsky pr., 119991 Moscow, Russia. .,Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia
| | - Alexander A Pavlov
- Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28-1 Vavilova st., 119334 Moscow, Russia.,BMSTU Center of National Technological Initiative "Digital Material Science: New Material and Substances", Bauman Moscow State Technical University, 2nd Baumanskaya st. 5, 105005, Moscow, Russia.,National Research University Higher School of Economics, 101000 Moscow, Russia
| |
Collapse
|
25
|
Huang K, Fang X. A review on recent advances in methods for site-directed spin labeling of long RNAs. Int J Biol Macromol 2023; 239:124244. [PMID: 37001783 DOI: 10.1016/j.ijbiomac.2023.124244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
RNAs are important biomolecules that play essential roles in various cellular processes and are crucially linked with many human diseases. The key to elucidate the mechanisms underlying their biological functions and develop RNA-based therapeutics is to investigate RNA structure and dynamics and their connections to function in detail using a variety of approaches. Magnetic resonance techniques including paramagnetic nuclear magnetic resonance (NMR) and electron magnetic resonance (EPR) spectroscopies have proved to be powerful tools to gain insights into such properties. The prerequisites for paramagnetic NMR and EPR studies on RNAs are to achieve site-specific spin labeling of the intrinsically diamagnetic RNAs, which however is not trivial, especially for long ones. In this review, we present some covalent labeling strategies that allow site-specific introduction of electron spins to long RNAs. Generally, these strategies include assembly of long RNAs via enzymatic ligation of short oligonucleotides, co- and post-transcriptional site-specific labeling empowered with the unnatural base pair system, and direct enzymatic functionalization of natural RNAs. We introduce a few case studies to discuss the advantages and limitations of each strategy, and to provide a vision for the future development.
Collapse
|
26
|
Zhu W, Yang DT, Gronenborn AM. Ligand-Capped Cobalt(II) Multiplies the Value of the Double-Histidine Motif for PCS NMR Studies. J Am Chem Soc 2023; 145:4564-4569. [PMID: 36786809 PMCID: PMC10032564 DOI: 10.1021/jacs.2c12021] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 02/15/2023]
Abstract
In structural studies by NMR, pseudocontact shifts (PCSs) provide both angular and distance information. For proteins, incorporation of a di-histidine (diHis) motif, coordinated to Co2+, has emerged as an important tool to measure PCS. Here, we show that using different Co(II)-chelating ligands, such as nitrilotriacetic acid (NTA) and iminodiacetic acid (IDA), resolves the isosurface ambiguity of Co2+-diHis and yields orthogonal PCS data sets with different Δχ-tensors for the same diHis-bearing protein. Importantly, such capping ligands effectively eliminate undesired intermolecular interactions, which can be detrimental to PCS studies. Devising and employing ligand-capping strategies afford versatile and powerful means to obtain multiple orthogonal PCS data sets, significantly extending the use of the diHis motif for structural studies by NMR.
Collapse
Affiliation(s)
- Wenkai Zhu
- Department
of Structural Biology, University of Pittsburgh,
School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
| | - Darian T. Yang
- Department
of Structural Biology, University of Pittsburgh,
School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
- Department
of Chemistry, University of Pittsburgh,
Dietrich School of Arts and Sciences, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Angela M. Gronenborn
- Department
of Structural Biology, University of Pittsburgh,
School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15261, United States
- Department
of Chemistry, University of Pittsburgh,
Dietrich School of Arts and Sciences, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
27
|
Grifagni D, Silva JM, Cantini F, Piccioli M, Banci L. Relaxation-based NMR assignment: Spotlights on ligand binding sites in human CISD3. J Inorg Biochem 2023; 239:112089. [PMID: 36502664 DOI: 10.1016/j.jinorgbio.2022.112089] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/26/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
CISD3 is a mitochondrial protein belonging to the NEET proteins family, bearing two [Fe2S2] clusters coordinated by CDGSH domains. At variance with the other proteins of the NEET family, very little is known about its structure-function relationships. NMR is the only technique to obtain information at the atomic level in solution on the residues involved in intermolecular interactions; however, in paramagnetic proteins this is limited by the broadening of signals of residues around the paramagnetic center. Tailored experiments can revive signals of the cluster surrounding; however, signals identification without specific residue assignment remains useless. Here, we show how paramagnetic relaxation can drive the signal assignment of residues in the proximity of the paramagnetic center(s). This allowed us to identify the potential key players of the biological function of the CISD3 protein.
Collapse
Affiliation(s)
- Deborah Grifagni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - José M Silva
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Lucia Banci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| |
Collapse
|
28
|
Rogals M, Eletsky A, Huang C, Morris LC, Moremen KW, Prestegard JH. Glycan Conformation in the Heavily Glycosylated Protein, CEACAM1. ACS Chem Biol 2022; 17:3527-3534. [PMID: 36417668 PMCID: PMC9764281 DOI: 10.1021/acschembio.2c00714] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Glycans attached to glycoproteins can contribute to stability, mediate interactions with other proteins, and initiate signal transduction. Glycan conformation, which is critical to these processes, is highly variable and often depicted as sampling a multitude of conformers. These conformers can be generated by molecular dynamics simulations, and more inclusively by accelerated molecular dynamics, as well as other extended sampling methods. However, experimental assessments of the contribution that various conformers make to a native ensemble are rare. Here, we use long-range pseudo-contact shifts (PCSs) of NMR resonances from an isotopically labeled glycoprotein to identify preferred conformations of its glycans. The N-terminal domain from human Carcinoembryonic Antigen Cell Adhesion Molecule 1, hCEACAM1-Ig1, was used as the model glycoprotein in this study. It has been engineered to include a lanthanide-ion-binding loop that generates PCSs, as well as a homogeneous set of three 13C-labeled N-glycans. Analysis of the PCSs indicates that preferred glycan conformers have extensive contacts with the protein surface. Factors leading to this preference appear to include interactions between N-acetyl methyls of GlcNAc residues and hydrophobic surface pockets on the protein surface.
Collapse
|
29
|
Gama Lima Costa R, Fushman D. Reweighting methods for elucidation of conformation ensembles of proteins. Curr Opin Struct Biol 2022; 77:102470. [PMID: 36183447 PMCID: PMC9771963 DOI: 10.1016/j.sbi.2022.102470] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/24/2022] [Accepted: 08/28/2022] [Indexed: 12/24/2022]
Abstract
Proteins are inherently dynamic macromolecules that exist in equilibrium among multiple conformational states, and motions of protein backbone and side chains are fundamental to biological function. The ability to characterize the conformational landscape is particularly important for intrinsically disordered proteins, multidomain proteins, and weakly bound complexes, where single-structure representations are inadequate. As the focus of structural biology shifts from relatively rigid macromolecules toward larger and more complex systems and molecular assemblies, there is a need for structural approaches that can paint a more realistic picture of such conformationally heterogeneous systems. Here, we review reweighting methods for elucidation of structural ensembles based on experimental data, with the focus on applications to multidomain proteins.
Collapse
Affiliation(s)
- Raquel Gama Lima Costa
- Chemical Physics Program, Institute for Physical Sciences and Technology, University of Maryland, College Park, 20742, MD, USA.
| | - David Fushman
- Chemical Physics Program, Institute for Physical Sciences and Technology, University of Maryland, College Park, 20742, MD, USA; Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, 20742, MD, USA.
| |
Collapse
|
30
|
Andrałojć W, Wieruszewska J, Pasternak K, Gdaniec Z. Solution Structure of a Lanthanide-binding DNA Aptamer Determined Using High Quality pseudocontact shift restraints. Chemistry 2022; 28:e202202114. [PMID: 36043489 PMCID: PMC9828363 DOI: 10.1002/chem.202202114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 01/12/2023]
Abstract
In this contribution we report the high-resolution NMR structure of a recently identified lanthanide-binding aptamer (LnA). We demonstrate that the rigid lanthanide binding by LnA allows for the measurement of anisotropic paramagnetic NMR restraints which to date remain largely inaccessible for nucleic acids. One type of such restraints - pseudocontact shifts (PCS) induced by four different paramagnetic lanthanides - was extensively used throughout the current structure determination study and the measured PCS turned out to be exceptionally well reproduced by the final aptamer structure. This finding opens the perspective for a broader application of paramagnetic effects in NMR studies of nucleic acids through the transplantation of the binding site found in LnA into other DNA/RNA systems.
Collapse
Affiliation(s)
- Witold Andrałojć
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| | - Julia Wieruszewska
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| | - Karol Pasternak
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| | - Zofia Gdaniec
- Institute of Bioorganic ChemistryPolish Academy of SciencesNoskowskiego 12/1461-704 PoznanPoland
| |
Collapse
|
31
|
Wu FJ, Rieder PS, Abiko LA, Rößler P, Gossert AD, Häussinger D, Grzesiek S. Nanobody GPS by PCS: An Efficient New NMR Analysis Method for G Protein Coupled Receptors and Other Large Proteins. J Am Chem Soc 2022; 144:21728-21740. [DOI: 10.1021/jacs.2c09692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Feng-Jie Wu
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland
| | - Pascal S. Rieder
- Department of Chemistry, University of Basel, CH-4056 Basel, Switzerland
| | | | - Philip Rößler
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Daniel Häussinger
- Department of Chemistry, University of Basel, CH-4056 Basel, Switzerland
| | | |
Collapse
|
32
|
Zalewski M, Janasik D, Wierzbicka A, Krawczyk T. Design Principles of Responsive Relaxometric 19F Contrast Agents: Evaluation from the Point of View of Relaxation Theory and Experimental Data. Inorg Chem 2022; 61:19524-19542. [DOI: 10.1021/acs.inorgchem.2c03451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Mariusz Zalewski
- Department of Chemical Organic Technology and Petrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 4, 44-100Gliwice, Poland
| | - Dawid Janasik
- Department of Chemical Organic Technology and Petrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 4, 44-100Gliwice, Poland
| | - Adrianna Wierzbicka
- Department of Chemical Organic Technology and Petrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 4, 44-100Gliwice, Poland
| | - Tomasz Krawczyk
- Department of Chemical Organic Technology and Petrochemistry, Faculty of Chemistry, Silesian University of Technology, Krzywoustego 4, 44-100Gliwice, Poland
| |
Collapse
|
33
|
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.
Collapse
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
| |
Collapse
|
34
|
Wei X, Wen X, Liu Y, Chen C, Xie C, Wang D, Qiu M, He N, Zhou P, Chen W, Cheng J, Lin H, Jia J, Fu XZ, Wang S. Oxygen Vacancy-Mediated Selective C-N Coupling toward Electrocatalytic Urea Synthesis. J Am Chem Soc 2022; 144:11530-11535. [PMID: 35748598 DOI: 10.1021/jacs.2c03452] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The electrocatalytic C-N coupling for one-step urea synthesis under ambient conditions serves as the promising alternative to the traditional urea synthetic protocol. However, the hydrogenation of intermediate species hinders the efficient urea synthesis. Herein, the oxygen vacancy-enriched CeO2 was demonstrated as the efficient electrocatalyst with the stabilization of the crucial intermediate of *NO via inserting into vacant sites, which is conducive to the subsequent C-N coupling process rather than protonation, whereas the poor selectivity of C-N coupling with protonation was observed on the vacancy-deficient catalyst. The oxygen vacancy-mediated selective C-N coupling was distinguished and validated by the in situ sum frequency generation spectroscopy. The introduction of oxygen vacancies tailors the common catalyst carrier into an efficient electrocatalyst with a high urea yield rate of 943.6 mg h-1 g-1, superior than that of partial noble-metal-based electrocatalysts. This work provides novel insights into the catalyst design and developments of coupling systems.
Collapse
Affiliation(s)
- Xiaoxiao Wei
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China.,College of Materials Science and Engineering, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518000, P. R. China
| | - Xiaojian Wen
- College of Materials Science and Engineering, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518000, P. R. China
| | - Yingying Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Chen Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Chao Xie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Dongdong Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Mengyi Qiu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Nihan He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Peng Zhou
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China.,College of Materials Science and Engineering, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518000, P. R. China
| | - Wei Chen
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Jun Cheng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, iChEM, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361000, P. R. China
| | - Hongzhen Lin
- i-LAB, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu 215000, P. R. China
| | - Jianfeng Jia
- Key Laboratory of Magnetic Molecules and Magnetic Information Materials (Ministry of Education), School of Chemistry and Material Science, Shanxi Normal University, Taiyuan, Shanxi 030031, P. R. China
| | - Xian-Zhu Fu
- College of Materials Science and Engineering, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong 518000, P. R. China
| | - Shuangyin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Advanced Catalytic Engineering Research Center of the Ministry of Education, Hunan University, Changsha, Hunan 410082, P. R. China
| |
Collapse
|
35
|
Islam MA, Autillo M, Guérin L, Tamain C, Moisy P, Bolvin H, Berthon C. Dipolar and Contact Paramagnetic NMR Chemical Shifts in An IV Complexes with Dipicolinic Acid Derivatives. Inorg Chem 2022; 61:10329-10341. [PMID: 35749686 DOI: 10.1021/acs.inorgchem.2c00845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Actinide +IV complexes (AnIV = ThIV, UIV, NpIV, and PuIV) with two dipicolinic acid derivatives (DPA and Et-DPA) have been studied by 1H and 13C NMR spectroscopies and first-principles calculations. The Fermi contact and dipolar contributions to the actinide-induced shifts (AIS) are evaluated from a temperature dependence analysis, combined with ab initio results. It allows an experimental estimation of the axial anisotropy of the magnetic susceptibility Δχax and of the hyperfine coupling constants of the NMR-active nuclei. Due to the compactness of the coordination sphere, the magnetic anisotropy of the paramagnetic center is small, and this makes the contact contribution to be the dominant one, even on the remote atoms. The sign of the hyperfine coupling constants and related spin densities is alternating on the nuclei of the ligand cycle, denoting a preponderant spin polarization mechanism. This is well reproduced by unrestricted density functional theory (DFT) calculations. Those values are furthermore slightly decreasing in the actinide series, which indicates a small decrease of the covalency from UIV to PuIV.
Collapse
Affiliation(s)
- Md Ashraful Islam
- Laboratoire de Chimie et Physique Quantiques, CNRS, Université Toulouse III, 118 Route de Narbonne, 31062 Toulouse, France
| | | | - Laetitia Guérin
- CEA, DES, ISEC, DMRC, Univ. Montpellier, Marcoule 30207, France
| | | | - Philippe Moisy
- CEA, DES, ISEC, DMRC, Univ. Montpellier, Marcoule 30207, France
| | - Hélène Bolvin
- Laboratoire de Chimie et Physique Quantiques, CNRS, Université Toulouse III, 118 Route de Narbonne, 31062 Toulouse, France
| | - Claude Berthon
- CEA, DES, ISEC, DMRC, Univ. Montpellier, Marcoule 30207, France
| |
Collapse
|
36
|
Santana FS, Perfetti M, Briganti M, Sacco F, Poneti G, Ravera E, Soares JF, Sessoli R. A dysprosium single molecule magnet outperforming current pseudocontact shift agents. Chem Sci 2022; 13:5860-5871. [PMID: 35685802 PMCID: PMC9132026 DOI: 10.1039/d2sc01619b] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 04/26/2022] [Indexed: 12/19/2022] Open
Abstract
A common criterion for designing performant single molecule magnets and pseudocontact shift tags is a large magnetic anisotropy. In this article we present a dysprosium complex chemically designed to exhibit strong easy-axis type magnetic anisotropy that is preserved in dichloromethane solution at room temperature. Our detailed theoretical and experimental studies on the magnetic properties allowed explaining several features typical of highly performant SMMs. Moreover, the NMR characterization shows remarkably large chemical shifts, outperforming the current state-of-the art PCS tags.
Collapse
Affiliation(s)
- Francielli S Santana
- Departamento de Química, Universidade Federal do Paraná, Centro Politécnico 81530-900 Curitiba PR Brazil
| | - Mauro Perfetti
- Department of Chemistry "U. Schiff", University of Florence Via della Lastruccia 3-13, Sesto Fiorentino 50019 Italy
- Research Unit Firenze, INSTM I-50019 Sesto Fiorentino Firenze Italy
| | - Matteo Briganti
- Departamento de Química, Universidade Federal do Paraná, Centro Politécnico 81530-900 Curitiba PR Brazil
- Department of Chemistry "U. Schiff", University of Florence Via della Lastruccia 3-13, Sesto Fiorentino 50019 Italy
| | - Francesca Sacco
- Department of Chemistry "U. Schiff", University of Florence Via della Lastruccia 3-13, Sesto Fiorentino 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence Via Luigi Sacconi 6, Sesto Fiorentino 50019 Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine Via Luigi Sacconi 6, Sesto Fiorentino 50019 Italy
| | - Giordano Poneti
- Instituto de Química, Universidade Federal do Rio de Janeiro, Centro de Tecnologia - Cidade Universitária Avenida Athos da Silveira Ramos, 149 21941-909 Rio de Janeiro Brazil
| | - Enrico Ravera
- Department of Chemistry "U. Schiff", University of Florence Via della Lastruccia 3-13, Sesto Fiorentino 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence Via Luigi Sacconi 6, Sesto Fiorentino 50019 Italy
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine Via Luigi Sacconi 6, Sesto Fiorentino 50019 Italy
| | - Jaísa F Soares
- Departamento de Química, Universidade Federal do Paraná, Centro Politécnico 81530-900 Curitiba PR Brazil
| | - Roberta Sessoli
- Department of Chemistry "U. Schiff", University of Florence Via della Lastruccia 3-13, Sesto Fiorentino 50019 Italy
- Research Unit Firenze, INSTM I-50019 Sesto Fiorentino Firenze Italy
| |
Collapse
|
37
|
Orton H, Abdelkader E, Topping L, Butler S, 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.
Collapse
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
| |
Collapse
|
38
|
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.
Collapse
Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| |
Collapse
|