1
|
Nanna V, Marasco M, Kirkpatrick JP, Carlomagno T. Methods for Structure Determination of SH2 Domain-Phosphopeptide Complexes by NMR. Methods Mol Biol 2023; 2705:3-23. [PMID: 37668966 DOI: 10.1007/978-1-0716-3393-9_1] [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: 09/06/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique to solve the structure of biomolecular complexes at atomic resolution in solution. Small proteins such as Src-homology 2 (SH2) domains have fast tumbling rates and long-lived NMR signals, making them particularly suited to be studied by standard NMR methods. SH2 domains are modular proteins whose function is the recognition of sequences containing phosphotyrosines. In this chapter, we describe the application of NMR to assess the interaction between SH2 domains and phosphopeptides and determine the structure of the resulting complexes.
Collapse
Affiliation(s)
- Vittoria Nanna
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Michelangelo Marasco
- Molecular Pharmacology Program, Sloan Kettering Institute for Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Teresa Carlomagno
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK.
| |
Collapse
|
2
|
Opdensteinen P, Sperl LE, Mohamadi M, Kündgen‐Redding N, Hagn F, Buyel JF. The transient expression of recombinant proteins in plant cell packs facilitates stable isotope labelling for NMR spectroscopy. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1928-1939. [PMID: 35702941 PMCID: PMC9491462 DOI: 10.1111/pbi.13873] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 04/05/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy can be used to determine the structure, dynamics and interactions of proteins. However, protein NMR requires stable isotope labelling for signal detection. The cells used for the production of recombinant proteins must therefore be grown in medium containing isotopically labelled substrates. Stable isotope labelling is well established in Escherichia coli, but bacteria are only suitable for the production of simple proteins without post-translational modifications. More complex proteins require eukaryotic production hosts, but their growth can be impaired by labelled media, thus reducing product yields and increasing costs. To address this limitation, we used media supplemented with isotope-labelled substrates to cultivate the tobacco-derived cell line BY-2, which was then cast into plant cell packs (PCPs) for the transient expression of a labelled version of the model protein GB1. Mass spectrometry confirmed the feasibility of isotope labelling with 15 N and 2 H using this approach. The resulting NMR spectrum featured a signal dispersion comparable to recombinant GB1 produced in E. coli. PCPs therefore offer a rapid and cost-efficient alternative for the production of isotope-labelled proteins for NMR analysis, especially suitable for complex proteins that cannot be produced in microbial systems.
Collapse
Affiliation(s)
- Patrick Opdensteinen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
- Institute for Molecular BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Laura E. Sperl
- Bavarian NMR Center (BNMRZ) at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Mariam Mohamadi
- Bavarian NMR Center (BNMRZ) at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | | | - Franz Hagn
- Bavarian NMR Center (BNMRZ) at the Department of ChemistryTechnical University of MunichGarchingGermany
- Institute of Structural BiologyHelmholtz Zentrum MünchenNeuherbergGermany
| | - Johannes Felix Buyel
- Fraunhofer Institute for Molecular Biology and Applied Ecology IMEAachenGermany
- Institute for Molecular BiotechnologyRWTH Aachen UniversityAachenGermany
| |
Collapse
|
3
|
Yanaka S, Yagi H, Yogo R, Onitsuka M, Kato K. Glutamine-free mammalian expression of recombinant glycoproteins with uniform isotope labeling: an application for NMR analysis of pharmaceutically relevant Fc glycoforms of human immunoglobulin G1. JOURNAL OF BIOMOLECULAR NMR 2022; 76:17-22. [PMID: 34978013 DOI: 10.1007/s10858-021-00387-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
Mammalian cells are widely used for producing recombinant glycoproteins of pharmaceutical interest. However, a major drawback of using mammalian cells is the high production costs associated with uniformly isotope-labeled glycoproteins due to the large quantity of labeled L-glutamine required for their growth. To address this problem, we developed a cost-saving method for uniform isotope labeling by cultivating the mammalian cells under glutamine-free conditions, which was achieved by co-expression of glutamine synthase. We demonstrate the utility of this approach using fucosylated and non-fucosylated Fc glycoforms of human immunoglobulin G1.
Collapse
Affiliation(s)
- Saeko Yanaka
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Rina Yogo
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, 444-8787, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, 770-8513, Japan
| | - Koichi Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, Okazaki, 444-8787, Japan.
- Graduate School of Pharmaceutical Sciences, Nagoya City University, Nagoya, 467-8603, Japan.
| |
Collapse
|
4
|
Abstract
In the last two decades, solid-state nuclear magnetic resonance (ssNMR) spectroscopy has transformed from a spectroscopic technique investigating small molecules and industrial polymers to a potent tool decrypting structure and underlying dynamics of complex biological systems, such as membrane proteins, fibrils, and assemblies, in near-physiological environments and temperatures. This transformation can be ascribed to improvements in hardware design, sample preparation, pulsed methods, isotope labeling strategies, resolution, and sensitivity. The fundamental engagement between nuclear spins and radio-frequency pulses in the presence of a strong static magnetic field is identical between solution and ssNMR, but the experimental procedures vastly differ because of the absence of molecular tumbling in solids. This review discusses routinely employed state-of-the-art static and MAS pulsed NMR methods relevant for biological samples with rotational correlation times exceeding 100's of nanoseconds. Recent developments in signal filtering approaches, proton methodologies, and multiple acquisition techniques to boost sensitivity and speed up data acquisition at fast MAS are also discussed. Several examples of protein structures (globular, membrane, fibrils, and assemblies) solved with ssNMR spectroscopy have been considered. We also discuss integrated approaches to structurally characterize challenging biological systems and some newly emanating subdisciplines in ssNMR spectroscopy.
Collapse
Affiliation(s)
- Sahil Ahlawat
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Kaustubh R Mote
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| | - Nils-Alexander Lakomek
- University of Düsseldorf, Institute for Physical Biology, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Vipin Agarwal
- Tata Institute of Fundamental Research Hyderabad, Survey No. 36/P Gopanpally, Serilingampally, Ranga Reddy District, Hyderabad 500046, Telangana, India
| |
Collapse
|
5
|
Almeida TB, Panova S, Walser R. NMR Reporter Assays for the Quantification of Weak-Affinity Receptor-Ligand Interactions. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:1020-1028. [PMID: 33899548 DOI: 10.1177/24725552211009782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Biophysical methods are widely employed in academia and the pharmaceutical industry to detect and quantify weak molecular interactions. Such methods find broad application in fragment-based drug discovery (FBDD). In an FBDD campaign, a suitable affinity determination method is key to advancing a project beyond the initial screening phase. Protein-observed (PO) nuclear magnetic resonance (NMR) finds widespread use due to its ability to sensitively detect very weak interactions at residue-level resolution. When there are issues precluding the use of PO-NMR, ligand-observed (LO) NMR reporter assays can be a useful alternative. Such assays can measure affinities in a similar range to PO-NMR while offering some distinct advantages, especially with regard to protein consumption and compound throughput. In this paper, we take a closer look at setting up such assays for routine use, with the aim of getting high-quality, accurate data and good throughput. We assess some of the key characteristics of these assays in the mathematical framework established for fluorescence polarization assays with which the readers may be more familiar. We also provide guidance on setting up such assays and compare their performance with other affinity determination methods that are commonly used in drug discovery.
Collapse
Affiliation(s)
| | | | - Reto Walser
- Molecular Sciences, Astex Pharmaceuticals, Cambridge, UK
| |
Collapse
|
6
|
Yagi H, Yanaka S, Yogo R, Ikeda A, Onitsuka M, Yamazaki T, Kato T, Park EY, Yokoyama J, Kato K. Silkworm Pupae Function as Efficient Producers of Recombinant Glycoproteins with Stable-Isotope Labeling. Biomolecules 2020; 10:biom10111482. [PMID: 33114581 PMCID: PMC7692867 DOI: 10.3390/biom10111482] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 11/16/2022] Open
Abstract
Baculovirus-infected silkworms are promising bioreactors for producing recombinant glycoproteins, including antibodies. Previously, we developed a method for isotope labeling of glycoproteins for nuclear magnetic resonance (NMR) studies using silkworm larvae reared on an artificial diet containing 15N-labeled yeast crude protein extract. Here, we further develop this method by introducing a technique for the expression of isotope-labeled glycoproteins by silkworm pupae, which has several potential advantages relative to larvae-based techniques in terms of production yield, ease of handling, and storage. Here, we fed fifth instar larvae an artificial diet with an optimized composition containing [methyl-13C]methionine, leading to pupation. Nine-day-old pupae were then injected with recombinant Bombyx mori nucleopolyhedrovirus (BmNPV) bacmid for expression of recombinant human immunoglobulin G (IgG). From the whole-body homogenates of pupae, 0.35 mg/pupa of IgG was harvested, which is a yield that is five times higher than can be obtained from larvae. Recombinant IgG, thus prepared, exhibited mainly three kinds of pauci-mannose-type oligosaccharides and had a 13C-enrichment ratio of approximately 80%. This enabled selective observation of NMR signals originating from the methionyl methyl group of IgG, confirming its conformational integrity. These data demonstrate the utility of silkworm pupae as factories for producing recombinant glycoproteins with amino-acid-selective isotope labeling.
Collapse
Affiliation(s)
- Hirokazu Yagi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; (H.Y.); (S.Y.); (R.Y.)
| | - Saeko Yanaka
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; (H.Y.); (S.Y.); (R.Y.)
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
| | - Rina Yogo
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; (H.Y.); (S.Y.); (R.Y.)
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
| | - Akari Ikeda
- Taiyo Nippon Sanso Corporation, SI Innovation Center, 2008-2 Wada, Tama, Tokyo 206-0001, Japan; (A.I.); (J.Y.)
| | - Masayoshi Onitsuka
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Minamijosanjima-cho 2-1, Tokushima 770-8513, Japan;
| | - Toshio Yamazaki
- SPring-8 Center RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan;
| | - Tatsuya Kato
- Laboratory of Biotechnology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan; (T.K.); (E.Y.P.)
| | - Enoch Y. Park
- Laboratory of Biotechnology, Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya Suruga-ku, Shizuoka 422-8529, Japan; (T.K.); (E.Y.P.)
| | - Jun Yokoyama
- Taiyo Nippon Sanso Corporation, SI Innovation Center, 2008-2 Wada, Tama, Tokyo 206-0001, Japan; (A.I.); (J.Y.)
| | - Koichi Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan; (H.Y.); (S.Y.); (R.Y.)
- Exploratory Research Center on Life and Living Systems (ExCELLS) and Institute for Molecular Science (IMS), National Institutes of Natural Sciences, 5-1 Higashiyama, Myodaiji-cho, Okazaki 444-8787, Japan
- Correspondence: ; Tel.: +81-564-59-5225
| |
Collapse
|
7
|
Rößler P, Mathieu D, Gossert AD. NMR‐Studien an biologischen Makromolekülen (>100 kDa) ohne Notwendigkeit der Deuterierung: Das XL‐ALSOFAST Experiment mit verzögerter Entkopplung. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Philip Rößler
- Institut für Molekularbiologie und Biophysik Department Biologie und Biomolekulare NMR Spektroskopie Plattform Department Biologie ETH Zürich Otto-Stern-Weg 5 8093 Zürich Schweiz
| | - Daniel Mathieu
- Bruker BioSpin GmbH Silberstreifen 4 76287 Rheinstetten Deutschland
| | - Alvar D. Gossert
- Institut für Molekularbiologie und Biophysik Department Biologie und Biomolekulare NMR Spektroskopie Plattform Department Biologie ETH Zürich Otto-Stern-Weg 5 8093 Zürich Schweiz
| |
Collapse
|
8
|
Rößler P, Mathieu D, Gossert AD. Enabling NMR Studies of High Molecular Weight Systems Without the Need for Deuteration: The XL-ALSOFAST Experiment with Delayed Decoupling. Angew Chem Int Ed Engl 2020; 59:19329-19337. [PMID: 32743971 PMCID: PMC7589290 DOI: 10.1002/anie.202007715] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Indexed: 11/30/2022]
Abstract
Current biological research increasingly focusses on large human proteins and their complexes. Such proteins are difficult to study by NMR spectroscopy because they often can only be produced in higher eukaryotic expression systems, where deuteration is hardly feasible. Here, we present the XL-ALSOFAST-[13 C,1 H]-HMQC experiment with much improved sensitivity for fully protonated high molecular weight proteins. For the tested systems ranging from 100 to 240 kDa in size, 3-fold higher sensitivity was obtained on average for fast relaxing signals compared to current state-of-the-art experiments. In the XL-ALSOFAST approach, non-observed magnetisation is optimally exploited and transverse relaxation is minimized by the newly introduced concept of delayed decoupling. The combination of high sensitivity and superior artefact suppression makes it ideal for studying inherently unstable membrane proteins or for analysing therapeutic antibodies at natural 13 C abundance. The XL-ALSOFAST and delayed decoupling will therefore expand the range of biomolecular systems accessible to NMR spectroscopy.
Collapse
Affiliation(s)
- Philip Rößler
- Institute of Molecular Biology and BiophysicsDepartment of Biology and Biomolecular NMR Spectroscopy PlatformDepartment of BiologyETH ZürichOtto-Stern-Weg 58093ZürichSwitzerland
| | - Daniel Mathieu
- Bruker BioSpin GmbHSilberstreifen 476287RheinstettenGermany
| | - Alvar D. Gossert
- Institute of Molecular Biology and BiophysicsDepartment of Biology and Biomolecular NMR Spectroscopy PlatformDepartment of BiologyETH ZürichOtto-Stern-Weg 58093ZürichSwitzerland
| |
Collapse
|
9
|
Delhommel F, Gabel F, Sattler M. Current approaches for integrating solution NMR spectroscopy and small-angle scattering to study the structure and dynamics of biomolecular complexes. J Mol Biol 2020; 432:2890-2912. [DOI: 10.1016/j.jmb.2020.03.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 02/27/2020] [Accepted: 03/10/2020] [Indexed: 01/24/2023]
|
10
|
Zhang M. Recent developments of methyl-labeling strategies in Pichia pastoris for NMR spectroscopy. Protein Expr Purif 2020; 166:105521. [DOI: 10.1016/j.pep.2019.105521] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/16/2019] [Accepted: 10/18/2019] [Indexed: 11/26/2022]
|
11
|
Integrative Structural Biology of Protein-RNA Complexes. Structure 2020; 28:6-28. [DOI: 10.1016/j.str.2019.11.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 11/17/2019] [Accepted: 11/27/2019] [Indexed: 12/16/2022]
|
12
|
Becker W, Wimberger F, Zangger K. Vibrio natriegens: An Alternative Expression System for the High-Yield Production of Isotopically Labeled Proteins. Biochemistry 2019; 58:2799-2803. [DOI: 10.1021/acs.biochem.9b00403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Walter Becker
- Institute of Chemistry, University of Graz, Graz 8010, Austria
| | | | - Klaus Zangger
- Institute of Chemistry, University of Graz, Graz 8010, Austria
| |
Collapse
|
13
|
Iorgu AI, Cliff MJ, Waltho JP, Scrutton NS, Hay S. Isotopically labeled flavoenzymes and their uses in probing reaction mechanisms. Methods Enzymol 2019; 620:145-166. [PMID: 31072485 DOI: 10.1016/bs.mie.2019.03.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The incorporation of stable isotopes into proteins is beneficial or essential for a range of experiments, including NMR, neutron scattering and reflectometry, proteomic mass spectrometry, vibrational spectroscopy and "heavy" enzyme kinetic isotope effect (KIE) measurements. Here, we present detailed protocols for the stable isotopic labeling of pentaerythritol tetranitrate reductase (PETNR) via recombinant expression in E. coli. PETNR is an ene-reductase belonging to the Old Yellow Enzyme (OYE) family of flavoenzymes, and is regarded as a model system for studying hydride transfer reactions. Included is a discussion of how efficient back-exchange of amide protons in the protein core can be achieved and how the intrinsic flavin mononucleotide (FMN) cofactor can be exchanged, allowing the production of isotopologues with differentially labeled protein and cofactor. In addition to a thorough description of labeling strategies, we briefly exemplify how data analysis and interpretation of "heavy" enzyme KIEs can be performed.
Collapse
Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom.
| |
Collapse
|
14
|
Proudfoot A, Frank AO, Frommlet A, Lingel A. Selective Methyl Labeling of Proteins: Enabling Structural and Mechanistic Studies As Well As Drug Discovery Applications by Solution-State NMR. Methods Enzymol 2018; 614:1-36. [PMID: 30611421 DOI: 10.1016/bs.mie.2018.08.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Escherichia coli expression protocols for selective labeling of methyl groups in proteins have been essential in expanding the size range of targets that can be studied by biomolecular NMR. Based on the initial work achieving selective labeling of isoleucine, leucine, and valine residues, additional methods were developed over the past years which enabled the individual and/or simultaneous combinatorial labeling of all methyl containing amino acids. Together with the introduction of new methyl-optimized NMR experiments, this now allows the detailed characterization of protein-ligand interactions as well as mechanistic and dynamic processes of protein-protein complexes up to 1MDa in size. In this chapter, we provide a general introduction to selective labeling of proteins using E. coli-based expression systems, describe the considerations taken into account prior to the selective labeling of a protein, and include the protocols used to produce such proteins. An overview of applications using selectively labeled proteins with an emphasis on examples relevant to the drug discovery process is then presented.
Collapse
Affiliation(s)
- Andrew Proudfoot
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Andreas O Frank
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Alexandra Frommlet
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States
| | - Andreas Lingel
- Structural and Biophysical Chemistry, Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Emeryville, CA, United States; Global Discovery Chemistry, Novartis Institutes for BioMedical Research, Novartis Campus, Basel, Switzerland.
| |
Collapse
|
15
|
Gossert AD, Jahnke W. NMR in drug discovery: A practical guide to identification and validation of ligands interacting with biological macromolecules. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2016; 97:82-125. [PMID: 27888841 DOI: 10.1016/j.pnmrs.2016.09.001] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 09/07/2016] [Accepted: 09/07/2016] [Indexed: 05/12/2023]
Abstract
Protein-ligand interactions are at the heart of drug discovery research. NMR spectroscopy is an excellent technology to identify and validate protein-ligand interactions. A plethora of NMR methods are available which are powerful, robust and information-rich, but also have pitfalls and limitations. In this review, we will focus on how to choose between different experiments, and assess their strengths and liabilities. We introduce the concept of the validation cross, which helps to categorize experiments according to their information content and to simplify the choice of the right experiment in order to address a specific question. Additionally, we will provide the framework for drawing correct conclusions from experimental results in order to accurately evaluate such interactions. Out of scope for this review are methods for subsequent characterization of the interaction such as quantitative KD determination, binding mode analysis, or structure determination.
Collapse
Affiliation(s)
- Alvar D Gossert
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland.
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, 4002 Basel, Switzerland
| |
Collapse
|