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Dubey A, Takeuchi K, Reibarkh M, Arthanari H. The role of NMR in leveraging dynamics and entropy in drug design. JOURNAL OF BIOMOLECULAR NMR 2020; 74:479-498. [PMID: 32720098 PMCID: PMC7686249 DOI: 10.1007/s10858-020-00335-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 07/11/2020] [Indexed: 05/03/2023]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has contributed to structure-based drug development (SBDD) in a unique way compared to the other biophysical methods. The potency of a ligand binding to a protein is dictated by the binding free energy, which is an intricate interplay between entropy and enthalpy. In addition to providing the atomic resolution structural information, NMR can help to identify protein-ligand interactions that potentially contribute to the enthalpic component of the free energy. NMR can also illuminate dynamic aspects of the interaction, which correspond to the entropic term of the free energy. The ability of NMR to access both terms in the free energy equation stems from the suite of experiments developed to shed light on various aspects that contribute to both entropy and enthalpy, deepening our understanding of the biological function of macromolecules and assisting to target them in physiological conditions. Here we provide a brief account of the contribution of NMR to SBDD, highlighting hallmark examples and discussing the challenges that demand further method development. In the era of integrated biology, the unique ability of NMR to directly ascertain structural and dynamical aspects of macromolecule and monitor changes in these properties upon engaging a ligand can be combined with computational and other structural and biophysical methods to provide a more complete picture of the energetics of drug engagement with the target. Such efforts can be used to engineer better drugs.
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Affiliation(s)
- Abhinav Dubey
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute & Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, 135-0064, Japan.
| | - Mikhail Reibarkh
- Analytical Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Haribabu Arthanari
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.
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Li Q, Kang C. A Practical Perspective on the Roles of Solution NMR Spectroscopy in Drug Discovery. Molecules 2020; 25:molecules25132974. [PMID: 32605297 PMCID: PMC7411973 DOI: 10.3390/molecules25132974] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 06/21/2020] [Accepted: 06/26/2020] [Indexed: 11/26/2022] Open
Abstract
Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool to study structures and dynamics of biomolecules under physiological conditions. As there are numerous NMR-derived methods applicable to probe protein–ligand interactions, NMR has been widely utilized in drug discovery, especially in such steps as hit identification and lead optimization. NMR is frequently used to locate ligand-binding sites on a target protein and to determine ligand binding modes. NMR spectroscopy is also a unique tool in fragment-based drug design (FBDD), as it is able to investigate target-ligand interactions with diverse binding affinities. NMR spectroscopy is able to identify fragments that bind weakly to a target, making it valuable for identifying hits targeting undruggable sites. In this review, we summarize the roles of solution NMR spectroscopy in drug discovery. We describe some methods that are used in identifying fragments, understanding the mechanism of action for a ligand, and monitoring the conformational changes of a target induced by ligand binding. A number of studies have proven that 19F-NMR is very powerful in screening fragments and detecting protein conformational changes. In-cell NMR will also play important roles in drug discovery by elucidating protein-ligand interactions in living cells.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, China
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
| | - CongBao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), 10 Biopolis Road, Chromos, #05-01, Singapore 138670, Singapore
- Correspondence: (Q.L.); (C.K.); Tel.: +86-020-84168436 (Q.L.); +65-64070602 (C.K.)
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Theonellamide A, a marine-sponge-derived bicyclic peptide, binds to cholesterol in aqueous DMSO: Solution NMR-based analysis of peptide-sterol interactions using hydroxylated sterol. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:228-235. [DOI: 10.1016/j.bbamem.2018.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 07/06/2018] [Accepted: 07/23/2018] [Indexed: 11/21/2022]
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Boulton S, Selvaratnam R, Blondeau JP, Lezoualc'h F, Melacini G. Mechanism of Selective Enzyme Inhibition through Uncompetitive Regulation of an Allosteric Agonist. J Am Chem Soc 2018; 140:9624-9637. [PMID: 30016089 DOI: 10.1021/jacs.8b05044] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Classical uncompetitive inhibitors are potent pharmacological modulators of enzyme function. Since they selectively target enzyme-substrate complexes (E:S), their inhibitory potency is amplified by increasing substrate concentrations. Recently, an unconventional uncompetitive inhibitor, called CE3F4R, was discovered for the exchange protein activated by cAMP isoform 1 (EPAC1). Unlike conventional uncompetitive inhibitors, CE3F4R is uncompetitive with respect to an allosteric effector, cAMP, as opposed to the substrate (i.e., CE3F4R targets the E:cAMP rather than the E:S complex). However, the mechanism of CE3F4R as an uncompetitive inhibitor is currently unknown. Here, we elucidate the mechanism of CE3F4R's action using NMR spectroscopy. Due to limited solubility and line broadening, which pose major challenges for traditional structural determination approaches, we resorted to a combination of protein- and ligand-based NMR experiments to comparatively analyze EPAC mutations, inhibitor analogs, and cyclic nucleotide derivatives that trap EPAC at different stages of activation. We discovered that CE3F4R binds within the EPAC cAMP-binding domain (CBD) at a subdomain interface distinct from the cAMP binding site, acting as a wedge that stabilizes a cAMP-bound mixed-intermediate. The mixed-intermediate includes attributes of both the apo/inactive and cAMP-bound/active states. In particular, the intermediate targeted by CE3F4R traps a CBD's hinge helix in its inactive conformation, locking EPAC into a closed domain topology that restricts substrate access to the catalytic domain. The proposed mechanism of action also explains the isoform selectivity of CE3F4R in terms of a single EPAC1 versus EPAC2 amino acid difference that destabilizes the active conformation of the hinge helix.
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Affiliation(s)
| | | | - Jean-Paul Blondeau
- Université Paris-Sud , Faculté de Pharmacie , 92296 Cedex Châtenay-Malabry , France
| | - Frank Lezoualc'h
- Inserm, UMR-1048, Institut des Maladies Métaboliques et Cardiovasculaires, Université de Toulouse III Paul Sabatier , 31432 Cedex 04 Toulouse , France
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Combined use of optical spectroscopy and computational methods to study the binding and the photoinduced conformational modification of proteins when NMR and X-ray structural determinations are not an option. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016. [PMID: 24018324 DOI: 10.1016/b978-0-12-416596-0.00004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register]
Abstract
The functions of proteins depend on their interactions with various ligands and these interactions are controlled by the structure of the polypeptides. If one can manipulate the structure of proteins, their functions can in principle be modulated. The issue of protein structure-function relationship is not only a central problem in biophysics, but is becoming clear that the ability to "artificially" modify the structure of proteins could be relevant in fields beyond the biomedical area to provide, for instance, light responses in proteins which would not possess such properties in their native state. This chapter presents an overview of the combination of optical electronic and vibrational spectroscopy with various computational methods to investigate the binding between photoactive ligands and proteins.
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Chung J, Ulyanov NB, Guilbert C, Mujeeb A, James TL. Binding characteristics of small molecules that mimic nucleocapsid protein-induced maturation of stem-loop 1 of HIV-1 RNA. Biochemistry 2010; 49:6341-51. [PMID: 20565056 PMCID: PMC2921804 DOI: 10.1021/bi100660r] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
As a retrovirus, the human immunodeficiency virus (HIV-1) packages two copies of the RNA genome as a dimer in the infectious virion. Dimerization is initiated at the dimer initiation site (DIS) which encompasses stem-loop 1 (SL1) in the 5'-UTR of the genome. Study of genomic dimerization has been facilitated by the discovery that short RNA fragments containing SL1 can dimerize spontaneously without any protein factors. On the basis of the palindromic nature of SL1, a kissing loop model has been proposed. First, a metastable kissing dimer is formed via standard Watson-Crick base pairs and then converted into a more stable extended dimer by the viral nucleocapsid protein (NCp7). This dimer maturation in vitro is believed to mimic initial steps in the RNA maturation in vivo, which is correlated with viral infectivity. We previously discovered a small molecule activator, Lys-Ala-7-amido-4-methylcoumarin (KA-AMC), which facilitates dimer maturation in vitro, and determined aspects of its structure-activity relationship. In this report, we present measurements of the binding affinity of the activators and characterization of their interactions with the SL1 RNA. Guanidinium groups and increasing positive charge on the side chain enhance affinity and activity, but features in the aromatic ring at least partially decouple affinity from activity. Although KA-AMC can bind to multiple structural motifs, the NMR study showed KA-AMC preferentially binds to unique structural motifs, such as the palindromic loop and the G-rich internal loop in the SL1 RNA. NCp7 binds to SL1 only 1 order of magnitude more tightly than the best small molecule ligand tested. This study provides guidelines for the design of superior small molecules that bind to the SL1 RNA that have the potential of being developed as an antiviral by interfering with SL1-NCp7 interaction at the packaging and/or maturation stages.
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Affiliation(s)
| | - Nikolai B. Ulyanov
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16 Street, San Francisco, California 94158-2517
| | - Christophe Guilbert
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16 Street, San Francisco, California 94158-2517
| | | | - Thomas L. James
- Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16 Street, San Francisco, California 94158-2517
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Hiller S, Wagner G. The role of solution NMR in the structure determinations of VDAC-1 and other membrane proteins. Curr Opin Struct Biol 2009; 19:396-401. [PMID: 19665886 DOI: 10.1016/j.sbi.2009.07.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2009] [Revised: 07/16/2009] [Accepted: 07/24/2009] [Indexed: 11/30/2022]
Abstract
The voltage-dependent anion channel (VDAC) is an essential protein in the eukaryotic outer mitochondrial membrane, providing the pore for substrate diffusion. Three high-resolution structures of the isoform 1 of VDAC in detergent micelles and bicelles have recently been published, using solution NMR and X-ray crystallography. They resolve longstanding discussions about the membrane topology of VDAC and provide the first eukaryotic beta-barrel membrane protein structure. The structure contains a surprising feature that had not been observed in an integral membrane protein before: A parallel beta-strand pairing and thus an odd number of strands. The studies also give a structural and functional basis for the voltage gating mechanism of VDAC and its modulation by NADH; however, they do not fully explain these functions yet. With the de novo structure of VDAC-1, as well as those of half a dozen other proteins, the number of integral membrane protein structures solved by solution NMR has doubled in the past two years. Numerous further structural and functional studies on many different membrane proteins show that solution NMR has become an important tool for membrane protein molecular biology.
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Affiliation(s)
- Sebastian Hiller
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Davis MF, Gracz H, Vendeix FAP, de Serrano V, Somasundaram A, Decatur SM, Franzen S. Different Modes of Binding of Mono-, Di-, and Trihalogenated Phenols to the Hemoglobin Dehaloperoxidase from Amphitrite ornata. Biochemistry 2009; 48:2164-72. [DOI: 10.1021/bi801568s] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael F. Davis
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Hanna Gracz
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Franck A. P. Vendeix
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Vesna de Serrano
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Aswin Somasundaram
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Sean M. Decatur
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27606, Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27606, and Chemistry Department, Oberlin College, Oberlin, Ohio 44074
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Riedinger C, Endicott JA, Kemp SJ, Smyth LA, Watson A, Valeur E, Golding BT, Griffin RJ, Hardcastle IR, Noble ME, McDonnell JM. Analysis of Chemical Shift Changes Reveals the Binding Modes of Isoindolinone Inhibitors of the MDM2-p53 Interaction. J Am Chem Soc 2008; 130:16038-44. [DOI: 10.1021/ja8062088] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christiane Riedinger
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Jane A. Endicott
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Stuart J. Kemp
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Lynette A. Smyth
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Anna Watson
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Eric Valeur
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Bernard T. Golding
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Roger J. Griffin
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Ian R. Hardcastle
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - Martin E. Noble
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
| | - James M. McDonnell
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K., and Northern Institute for Cancer Research, Bedson Building, University of Newcastle, NE1 4RW, U.K
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Marcaurelle LA, Johannes CW. Application of natural product-inspired diversity-oriented synthesis to drug discovery. PROGRESS IN DRUG RESEARCH. FORTSCHRITTE DER ARZNEIMITTELFORSCHUNG. PROGRES DES RECHERCHES PHARMACEUTIQUES 2008; 66:187, 189-216. [PMID: 18416306 DOI: 10.1007/978-3-7643-8595-8_3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
Natural products have played a critical role in the identification of numerous medicines. Synthetic organic chemistry and combinatorial chemistry strategies such as diversity-oriented synthesis (DOS) have enabled the synthesis of natural product-like compounds. The combination of these approaches has both improved the desired biological properties of natural products as well as the identification of novel compounds. Diversity concepts and strategies to access novel compounds inspired by natural products will be reviewed.
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Affiliation(s)
- Lisa A Marcaurelle
- Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02412, USA.
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Takeuchi K, Roehrl MHA, Sun ZYJ, Wagner G. Structure of the calcineurin-NFAT complex: defining a T cell activation switch using solution NMR and crystal coordinates. Structure 2007; 15:587-97. [PMID: 17502104 PMCID: PMC1989110 DOI: 10.1016/j.str.2007.03.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 03/10/2007] [Accepted: 03/27/2007] [Indexed: 10/23/2022]
Abstract
Calcineurin (Cn) is a serine/threonine protein phosphatase that plays pivotal roles in many physiological processes, including cell proliferation, development, and apoptosis. Most prominently, Cn targets the nuclear factors of activated T cell (NFATs), transcription factors that activate cytokine genes. Calcium-activated Cn dephosphorylates multiple residues within the regulatory domain of NFAT, triggering joint nuclear translocation. This relies crucially on the interaction between the catalytic domain of Cn (CnCat) and the conserved PxIxIT motif located in a region distinct from the dephosphorylation sites of NFAT. Here, we present the structure of the complex between the 39 kDa CnCat and a 14 residue peptide containing a PVIVIT segment that was derived from affinity-driven peptide selection based on the conserved PxIxIT motif of NFATs. The structure of the complex was determined by using NMR assignments and structural constraints and the coordinates of the CnCat crystal structure. The NMR analysis relied on recently developed labeling and spectroscopic techniques. The VIVIT peptide is accommodated in a hydrophobic cleft formed by beta strands 11 and 14, and the loop between beta strands 11 and 12, forming a short parallel beta sheet with the exposed beta strand 14 in Cn. The side chains of conserved residues in the PxIxIT sequences make extensive interactions with conserved residues in Cn, while those of nonconserved residues are solvent exposed. The architecture of the interface explains the diversity of recognition sequences compatible with NFAT function and uncovers a potential targeting site for immune-suppressive agents. The structure reveals that the orientation of the bound PxIxIT directs the phosphorylation sites in NFAT's regulatory domain toward the Cn catalytic site.
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Affiliation(s)
- Koh Takeuchi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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