1
|
Nimerovsky E, Najbauer EE, Movellan KT, Xue K, Becker S, Andreas LB. Modest Offset Difference Internuclear Selective Transfer via Homonuclear Dipolar Coupling. J Phys Chem Lett 2022; 13:1540-1546. [PMID: 35133845 PMCID: PMC8859849 DOI: 10.1021/acs.jpclett.1c03871] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/02/2022] [Indexed: 05/02/2023]
Abstract
Homonuclear dipolar recoupling is routinely used for magic-angle spinning NMR-based structure determination. In fully protonated samples, only short proton-proton distances are accessible to broadband recoupling approaches because of high proton density. Selective methods allow detection of longer distances by directing polarization to a subset of spins. Here we introduce the selective pulse sequence MODIST, which recouples spins that have a modest chemical shift offset difference, and demonstrate it to selectively record correlations between amide protons. The sequence was selected for good retention of total signal, leading to up to twice the intensity for proton-proton correlations compared with other selective methods. The sequence is effective across a range of spinning conditions and magnetic fields, here tested at 55.555 and 100 kHz magic-angle spinning and at proton Larmor frequencies from 600 to 1200 MHz. For influenza A M2 in lipid bilayers, cross-peaks characteristic of a helical conformation are observed.
Collapse
Affiliation(s)
- Evgeny Nimerovsky
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eszter E. Najbauer
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kumar Tekwani Movellan
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kai Xue
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan Becker
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Loren B. Andreas
- Department of NMR Based Structural
Biology, Max Planck Institute for Biophysical
Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| |
Collapse
|
2
|
Nasreddine R, Nehmé R. Microscale thermophoresis for studying protein-small molecule affinity: Application to hyaluronidase. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106763] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
3
|
Shcherbakov AA, Medeiros-Silva J, Tran N, Gelenter MD, Hong M. From Angstroms to Nanometers: Measuring Interatomic Distances by Solid-State NMR. Chem Rev 2021; 122:9848-9879. [PMID: 34694769 DOI: 10.1021/acs.chemrev.1c00662] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Internuclear distances represent one of the main structural constraints in molecular structure determination using solid-state NMR spectroscopy, complementing chemical shifts and orientational restraints. Although a large number of magic-angle-spinning (MAS) NMR techniques have been available for distance measurements, traditional 13C and 15N NMR experiments are inherently limited to distances of a few angstroms due to the low gyromagnetic ratios of these nuclei. Recent development of fast MAS triple-resonance 19F and 1H NMR probes has stimulated the design of MAS NMR experiments that measure distances in the 1-2 nm range with high sensitivity. This review describes the principles and applications of these multiplexed multidimensional correlation distance NMR experiments, with an emphasis on 19F- and 1H-based distance experiments. Representative applications of these long-distance NMR methods to biological macromolecules as well as small molecules are reviewed.
Collapse
Affiliation(s)
- Alexander A Shcherbakov
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - João Medeiros-Silva
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Nhi Tran
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Martin D Gelenter
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
4
|
Cerofolini L, Ravera E, Fragai M, Luchinat C. NMR of Immobilized Enzymes. Methods Mol Biol 2020; 2100:363-383. [PMID: 31939136 DOI: 10.1007/978-1-0716-0215-7_24] [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] [Indexed: 06/10/2023]
Abstract
Solid-state NMR has become the method of choice for the assessment of protein structure for insoluble objects lacking long-range order. In this context, it is apparent that solid-state NMR is also perfectly poised toward the characterization of immobilized proteins. For these systems, it is possible to understand at the atomic level which perturbations, if any, are occurring as a result of the functionalization. Here we describe how it is possible to accomplish the NMR characterization of enzymes that have been immobilized through different approaches, and we introduce the reader to the choice of the experimental strategy that can be useful in different cases. An outlook on the level of information that can be attained is also given, in view of recent methodological advancements.
Collapse
Affiliation(s)
- Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario, Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario, Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy.
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy.
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario, Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence and Consorzio Interuniversitario, Risonanze Magnetiche di Metallo Proteine (CIRMMP), Sesto Fiorentino, Italy
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| |
Collapse
|
5
|
Bolivar JM, Nidetzky B. On the relationship between structure and catalytic effectiveness in solid surface-immobilized enzymes: Advances in methodology and the quest for a single-molecule perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1868:140333. [PMID: 31778816 DOI: 10.1016/j.bbapap.2019.140333] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 11/05/2019] [Accepted: 11/22/2019] [Indexed: 12/31/2022]
Abstract
The integration of enzymes with solid materials is important in many biotechnological applications, including the use of immobilized enzymes for biocatalytic synthesis. The development of functional enzyme-material composites is restrained by the lack of molecular-level insight into the behavior of enzymes in confined, surface-near environments. Here, we review recent advances in surface-sensitive spectroscopic techniques that push boundaries for the determination of enzyme structure and orientation at the solid-liquid interface. We discuss recent evidence from single-molecule studies showing that analyses sensitive to the temporal and spatial heterogeneities in immobilized enzymes can succeed in disentangling the effects of conformational stability and active-site accessibility on activity. Different immobilization methods involve distinct trade-off between these effects, thus emphasizing the need for a holistic (systems) view of immobilized enzymes for the rational development of practical biocatalysts.
Collapse
Affiliation(s)
- Juan M Bolivar
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010 Graz, Austria; Austrian Centre of Industrial Biotechnology, Petersgasse 12, A-8010 Graz, Austria; Chemical and Materials Engineering Department, Complutense University of Madrid, 28040 Madrid, Spain
| | - Bernd Nidetzky
- Institute of Biotechnology and Biochemical Engineering, Graz University of Technology, NAWI Graz, Petersgasse 12, A-8010 Graz, Austria; Austrian Centre of Industrial Biotechnology, Petersgasse 12, A-8010 Graz, Austria.
| |
Collapse
|
6
|
Malär AA, Dong S, Kehr G, Erker G, Meier BH, Wiegand T. Characterization of H 2 -Splitting Products of Frustrated Lewis Pairs: Benefit of Fast Magic-Angle Spinning. Chemphyschem 2019; 20:672-679. [PMID: 30663843 DOI: 10.1002/cphc.201900006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 01/19/2019] [Indexed: 11/09/2022]
Abstract
Proton spectroscopy in solid-state NMR on catalytic materials offers new opportunities in structural characterization, in particular of reaction products of catalytic reactions such as hydrogenation reactions. Unfortunately, the 1 H NMR line widths in magic-angle spinning solid-state spectra are often broadened by an incomplete averaging of 1 H-1 H dipolar couplings. We herein discuss two model compounds, namely the H2 -splitting products of two phosphane-borane Frustrated Lewis Pairs (FLPs), to study potentials and limitations of proton solid-state NMR experiments employing magic-angle spinning frequencies larger than 100 kHz at a static magnetic field strength of 20.0 T. The 1 H lines are homogeneously broadened as illustrated by spin-echo decay experiments. We study two structurally similar materials which however show significant differences in 1 H line widths which we explain by differences in their 1 H-1 H dipolar networks. We discuss the benefit of fast MAS experiments up to 110 kHz to detect the resonances of the H+ /H- pair in the hydrogenation products of FLPs.
Collapse
Affiliation(s)
- Alexander A Malär
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Shunxi Dong
- Organisch-Chemisches Institut, WWU Münster, Corrensstraße 40, 48149, Münster, Germany
| | - Gerald Kehr
- Organisch-Chemisches Institut, WWU Münster, Corrensstraße 40, 48149, Münster, Germany
| | - Gerhard Erker
- Organisch-Chemisches Institut, WWU Münster, Corrensstraße 40, 48149, Münster, Germany
| | - Beat H Meier
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| | - Thomas Wiegand
- Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093, Zurich, Switzerland
| |
Collapse
|
7
|
Yoshimoto M, Walde P. Immobilized carbonic anhydrase: preparation, characteristics and biotechnological applications. World J Microbiol Biotechnol 2018; 34:151. [PMID: 30259182 DOI: 10.1007/s11274-018-2536-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 09/18/2018] [Indexed: 12/15/2022]
Abstract
Carbonic anhydrase (CA) is an essential metalloenzyme in living systems for accelerating the hydration and dehydration of carbon dioxide. CA-catalyzed reactions can be applied in vitro for capturing industrially emitted gaseous carbon dioxide in aqueous solutions. To facilitate this type of practical application, the immobilization of CA on or inside solid or soft support materials is of great importance because the immobilization of enzymes in general offers the opportunity for enzyme recycling or long-term use in bioreactors. Moreover, the thermal/storage stability and reactivity of immobilized CA can be modulated through the physicochemical nature and structural characteristics of the support material used. This review focuses on (i) immobilization methods which have been applied so far, (ii) some of the characteristic features of immobilized forms of CA, and (iii) biotechnological applications of immobilized CA. The applications described not only include the CA-assisted capturing and sequestration of carbon dioxide, but also the CA-supported bioelectrochemical conversion of CO2 into organic molecules, and the detection of clinically important CA inhibitors. Furthermore, immobilized CA can be used in biomimetic materials synthesis involving cascade reactions, e.g. for bone regeneration based on calcium carbonate formation from urea with two consecutive reactions catalyzed by urease and CA.
Collapse
Affiliation(s)
- Makoto Yoshimoto
- Department of Applied Chemistry, Yamaguchi University, Tokiwadai 2-16-1, Ube, 755-8611, Japan.
| | - Peter Walde
- Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 5, 8093, Zurich, Switzerland
| |
Collapse
|
8
|
Müntener T, Kottelat J, Huber A, Häussinger D. New Lanthanide Chelating Tags for PCS NMR Spectroscopy with Reduction Stable, Rigid Linkers for Fast and Irreversible Conjugation to Proteins. Bioconjug Chem 2018; 29:3344-3351. [DOI: 10.1021/acs.bioconjchem.8b00512] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Thomas Müntener
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Jérémy Kottelat
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Annika Huber
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Daniel Häussinger
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| |
Collapse
|