1
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Kang K, Wang L, Song C. ProtRAP: Predicting Lipid Accessibility Together with Solvent Accessibility of Proteins in One Run. J Chem Inf Model 2023; 63:1058-1065. [PMID: 36693122 DOI: 10.1021/acs.jcim.2c01235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Solvent accessibility has been extensively used to characterize and predict the chemical properties of the surface residues of soluble proteins. However, there is not yet a widely accepted quantity of the same dimension for the study of lipid-accessible residues of membrane proteins. In this study, we propose that lipid accessibility, defined in a similar way to solvent accessibility, can be used to characterize the lipid-accessible residues of membrane proteins. Moreover, we developed a deep learning-based method, ProtRAP (Protein Relative Accessibility Predictor), to predict the relative lipid accessibility and relative solvent accessibility of residues from a given protein sequence, which can infer which residues are likely accessible to lipids, accessible to solvent, or buried in the protein interior in one run.
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Affiliation(s)
- Kai Kang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Lei Wang
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
| | - Chen Song
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China.,Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100871, China
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2
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Raingeval C, Cala O, Brion B, Le Borgne M, Hubbard RE, Krimm I. 1D NMR WaterLOGSY as an efficient method for fragment-based lead discovery. J Enzyme Inhib Med Chem 2019; 34:1218-1225. [PMID: 31286785 PMCID: PMC6691826 DOI: 10.1080/14756366.2019.1636235] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
WaterLOGSY is a sensitive ligand-observed NMR experiment for detection of interaction between a ligand and a protein and is now well-established as a screening technique for fragment-based lead discovery. Here we develop and assess a protocol to derive ligand epitope mapping from WaterLOGSY data and demonstrate its general applicability in studies of fragment-sized ligands binding to six different proteins (glycogen phosphorylase, protein peroxiredoxin 5, Bcl-xL, Mcl-1, HSP90, and human serum albumin). We compare the WaterLOGSY results to those obtained from the more widely used saturation transfer difference experiments and to the 3D structures of the complexes when available. In addition, we evaluate the impact of ligand labile protons on the WaterLOGSY data. Our results demonstrate that the WaterLOGSY experiment can be used as an additional confirmation of the binding mode of a ligand to a protein.
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Affiliation(s)
- Claire Raingeval
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| | - Olivier Cala
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| | - Béatrice Brion
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
| | - Marc Le Borgne
- b Université de Lyon, Université Claude Bernard Lyon 1, Faculté de Pharmacie - ISPB, EA 4446 Bioactive Molecules and Medicinal Chemistry, SFR Santé Lyon-Est CNRS UMS3453 - INSERM US7 , Lyon , France
| | - Roderick Eliot Hubbard
- c YSBL, University of York , Heslington , York , UK.,d Vernalis (R&D) Ltd, Granta Park, Abington , Cambridge , UK
| | - Isabelle Krimm
- a Université de Lyon, CNRS, Université Claude Bernard Lyon 1, ENS Lyon, CRMN FRE 2034 , Villeurbanne , France
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3
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Kessler D, Gmachl M, Mantoulidis A, Martin LJ, Zoephel A, Mayer M, Gollner A, Covini D, Fischer S, Gerstberger T, Gmaschitz T, Goodwin C, Greb P, Häring D, Hela W, Hoffmann J, Karolyi-Oezguer J, Knesl P, Kornigg S, Koegl M, Kousek R, Lamarre L, Moser F, Munico-Martinez S, Peinsipp C, Phan J, Rinnenthal J, Sai J, Salamon C, Scherbantin Y, Schipany K, Schnitzer R, Schrenk A, Sharps B, Siszler G, Sun Q, Waterson A, Wolkerstorfer B, Zeeb M, Pearson M, Fesik SW, McConnell DB. Drugging an undruggable pocket on KRAS. Proc Natl Acad Sci U S A 2019; 116:15823-15829. [PMID: 31332011 PMCID: PMC6689897 DOI: 10.1073/pnas.1904529116] [Citation(s) in RCA: 248] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The 3 human RAS genes, KRAS, NRAS, and HRAS, encode 4 different RAS proteins which belong to the protein family of small GTPases that function as binary molecular switches involved in cell signaling. Activating mutations in RAS are among the most common oncogenic drivers in human cancers, with KRAS being the most frequently mutated oncogene. Although KRAS is an excellent drug discovery target for many cancers, and despite decades of research, no therapeutic agent directly targeting RAS has been clinically approved. Using structure-based drug design, we have discovered BI-2852 (1), a KRAS inhibitor that binds with nanomolar affinity to a pocket, thus far perceived to be "undruggable," between switch I and II on RAS; 1 is mechanistically distinct from covalent KRASG12C inhibitors because it binds to a different pocket present in both the active and inactive forms of KRAS. In doing so, it blocks all GEF, GAP, and effector interactions with KRAS, leading to inhibition of downstream signaling and an antiproliferative effect in the low micromolar range in KRAS mutant cells. These findings clearly demonstrate that this so-called switch I/II pocket is indeed druggable and provide the scientific community with a chemical probe that simultaneously targets the active and inactive forms of KRAS.
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Affiliation(s)
- Dirk Kessler
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Michael Gmachl
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Mantoulidis
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Laetitia J Martin
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Zoephel
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Moriz Mayer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Gollner
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - David Covini
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Silke Fischer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Thomas Gerstberger
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Teresa Gmaschitz
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Craig Goodwin
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Peter Greb
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Daniela Häring
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Wolfgang Hela
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Johann Hoffmann
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Jale Karolyi-Oezguer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Petr Knesl
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Stefan Kornigg
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Manfred Koegl
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Roland Kousek
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Lyne Lamarre
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Franziska Moser
- Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, D-88397 Biberach an der Riss, Germany
| | - Silvia Munico-Martinez
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Christoph Peinsipp
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Jason Phan
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Jörg Rinnenthal
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Jiqing Sai
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Christian Salamon
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Yvonne Scherbantin
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Katharina Schipany
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Renate Schnitzer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Andreas Schrenk
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Bernadette Sharps
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Gabriella Siszler
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Qi Sun
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
| | - Alex Waterson
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37235
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Bernhard Wolkerstorfer
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Markus Zeeb
- Discovery Research, Boehringer Ingelheim Pharma GmbH & Co KG, D-88397 Biberach an der Riss, Germany
| | - Mark Pearson
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Stephen W Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37235
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37235
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235
| | - Darryl B McConnell
- Discovery Research, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, 1120 Vienna, Austria;
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4
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Abstract
WaterLOGSY is a ligand-observed NMR method that is widely used for the studies of protein-small molecule interactions. The basis of waterLOGSY relies on the transfer of magnetization between water molecules, proteins, and small molecules via the nuclear Overhauser effect and chemical exchange. WaterLOGSY is used extensively for the screening of protein ligands, as it is a robust, relatively high-throughput, and reliable method to identify small molecules that bind proteins with a binding affinity (KD) in the μM to mM region. WaterLOGSY also enables the determination of KD via ligand titration, although careful optimization of the experimental setup is required to avoid overestimation of binding constants. Finally, waterLOGSY allows the water-accessible ligand protons of protein-bound ligands to be identified, thus providing structural information of the ligand binding orientation. In this chapter, we introduce and describe the waterLOGSY method, and provide a practical guide for ligand screening and KD determination. The use of waterLOGSY to study water accessibility is also discussed.
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Affiliation(s)
- Renjie Huang
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand
| | - Ivanhoe K H Leung
- School of Chemical Sciences, The University of Auckland, Auckland, New Zealand.
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5
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Geist L, Mayer M, Cockcroft XL, Wolkerstorfer B, Kessler D, Engelhardt H, McConnell DB, Konrat R. Direct NMR Probing of Hydration Shells of Protein Ligand Interfaces and Its Application to Drug Design. J Med Chem 2017; 60:8708-8715. [DOI: 10.1021/acs.jmedchem.7b00845] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Leonhard Geist
- Christian Doppler Laboratory for High-Content Structural
Biology and Biotechnology, Department of Structural and Computational
Biology, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
| | - Moriz Mayer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Xiao-Ling Cockcroft
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Bernhard Wolkerstorfer
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Dirk Kessler
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Harald Engelhardt
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Darryl B. McConnell
- Boehringer Ingelheim RCV GmbH & Co. KG, Dr.-Boehringer-Gasse 5-11, A-1121 Vienna, Austria
| | - Robert Konrat
- Christian Doppler Laboratory for High-Content Structural
Biology and Biotechnology, Department of Structural and Computational
Biology, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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6
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Fechner P, Bleher O, Ewald M, Freudenberger K, Furin D, Hilbig U, Kolarov F, Krieg K, Leidner L, Markovic G, Proll G, Pröll F, Rau S, Riedt J, Schwarz B, Weber P, Widmaier J. Size does matter! Label-free detection of small molecule-protein interaction. Anal Bioanal Chem 2014; 406:4033-51. [PMID: 24817356 DOI: 10.1007/s00216-014-7834-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 04/07/2014] [Accepted: 04/11/2014] [Indexed: 11/28/2022]
Abstract
This review is focused on methods for detecting small molecules and, in particular, the characterisation of their interaction with natural proteins (e.g. receptors, ion channels). Because there are intrinsic advantages to using label-free methods over labelled methods (e.g. fluorescence, radioactivity), this review only covers label-free techniques. We briefly discuss available techniques and their advantages and disadvantages, especially as related to investigating the interaction between small molecules and proteins. The reviewed techniques include well-known and widely used standard analytical methods (e.g. HPLC-MS, NMR, calorimetry, and X-ray diffraction), newer and more specialised analytical methods (e.g. biosensors), biological systems (e.g. cell lines and animal models), and in-silico approaches.
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Affiliation(s)
- Peter Fechner
- Biametrics GmbH, Auf der Morgenstelle 18, 72076, Tübingen, Germany,
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7
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NMR-based analysis of protein-ligand interactions. Anal Bioanal Chem 2013; 406:943-56. [PMID: 23591643 DOI: 10.1007/s00216-013-6931-0] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/12/2013] [Accepted: 03/19/2013] [Indexed: 10/27/2022]
Abstract
Physiological processes are mainly controlled by intermolecular recognition mechanisms involving protein-protein and protein-ligand (low molecular weight molecules) interactions. One of the most important tools for probing these interactions is high-field solution nuclear magnetic resonance (NMR) through protein-observed and ligand-observed experiments, where the protein receptor or the organic compounds are selectively detected. NMR binding experiments rely on comparison of NMR parameters of the free and bound states of the molecules. Ligand-observed methods are not limited by the protein molecular size and therefore have great applicability for analysing protein-ligand interactions. The use of these NMR techniques has considerably expanded in recent years, both in chemical biology and in drug discovery. We review here three major ligand-observed NMR methods that depend on the nuclear Overhauser effect-transferred nuclear Overhauser effect spectroscopy, saturation transfer difference spectroscopy and water-ligand interactions observed via gradient spectroscopy experiments-with the aim of reporting recent developments and applications for the characterization of protein-ligand complexes, including affinity measurements and structural determination.
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8
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Henen M, Coudevylle N, Geist L, Konrat R. Toward rational fragment-based lead design without 3D structures. J Med Chem 2012; 55:7909-19. [PMID: 22889313 PMCID: PMC3557921 DOI: 10.1021/jm301016m] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Indexed: 01/21/2023]
Abstract
Fragment-based lead discovery (FBLD) has become a prime component of the armamentarium of modern drug design programs. FBLD identifies low molecular weight ligands that weakly bind to important biological targets. Three-dimensional structural information about the binding mode is provided by X-ray crystallography or NMR spectroscopy and is subsequently used to improve the lead compounds. Despite tremendous success rates, FBLD relies on the availability of high-resolution structural information, still a bottleneck in drug discovery programs. To overcome these limitations, we recently demonstrated that the meta-structure approach provides an alternative route to rational lead identification in cases where no 3D structure information about the biological target is available. Combined with information-rich NMR data, this strategy provides valuable information for lead development programs. We demonstrate with several examples the feasibility of the combined NMR and meta-structure approach to devise a rational strategy for fragment evolution without resorting to highly resolved protein complex structures.
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Affiliation(s)
- Morkos
A. Henen
- Department of Structural and Computational Biology,
Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
| | - Nicolas Coudevylle
- Department of Structural and Computational Biology,
Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
| | - Leonhard Geist
- Department of Structural and Computational Biology,
Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
| | - Robert Konrat
- Department of Structural and Computational Biology,
Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter Campus 5, A-1030 Vienna, Austria
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9
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Liu X, Piao YS, Arnold JT. Transforming growth factor β1 increase of hydroxysteroid dehydrogenase proteins is partly suppressed by red clover isoflavones in human primary prostate cancer-derived stromal cells. Carcinogenesis 2011; 32:1648-54. [PMID: 21914638 DOI: 10.1093/carcin/bgr206] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Transforming growth factor β1 (TGF-β1) increases dehydro-epiandrosterone (DHEA) metabolism to androgens and prostate-specific antigen (PSA) in a prostate tissue model where stromal (6S) cells and epithelial (LAPC-4) cells are cocultured. Red clover (RC) isoflavones inhibits transforming growth factor (TGF)-β-induced androgenicity. Mechanisms controlling those activities were explored. Three hydroxysteroid dehydrogenases (HSDs), 3β-HSD, HSD-17β1 and HSD-17β5 involved in metabolizing DHEA to testosterone (TESTO) were investigated. Individual depletion of HSDs in 6S cells significantly reduced TGF-β1/DHEA-induced PSA in LAPC-4 cells in cocultures. Monomer amounts of 3β-HSD were similar without or with TGF-β1 in both cell types but aggregates of 3β-HSD in 6S cells were much higher than those in LAPC-4 cells and were upregulated by TGFβ in 6S cells. Basal and TGF-β1-treated levels of HSD-17β1 and HSD-17β5 in LAPC-4 cells were significantly lower than in 6S cells, whereas levels of HSD-17β1 but not HSD-17β5 were TGFβ inducible. 6S cell HSD genes expression induced by TGFβ or androgen signaling was insignificant to contribute TGF-β1/DHEA-upregulated protein levels of HSDs. RC decreased TGF-β1- upregulation of aggregates of 3β-HSD but not HSD-17β1. Depletion of TGFβ receptors (TGFβ Rs) reduced TGF-β1/DHEA-upregulated HSDs and TESTO. Immunoprecipitation studies demonstrated that TGF-β1 disrupted associations of TGFβ Rs/HSDs aggregates, whereas RC suppressed the dissociations of aggregates of 3β-HSD but not HSD-17β1 from the receptors. Given that TGFβ Rs are recycled with or without ligand, TGF-β1-induced disassociation of the HSDs from TGFβ Rs may increase stability and activity of the HSDs. These data suggest a pathway connecting overproduction of TGFβ with increased PSA in prostate cancer.
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Affiliation(s)
- Xunxian Liu
- Endocrine Section, Intramural Research Program, National Center for Complementary and Alternative Medicine, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, MD 20892, USA.
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10
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Szczepina MG, Bleile DW, Müllegger J, Lewis AR, Pinto BM. WaterLOGSY NMR Experiments in Conjunction with Molecular-Dynamics Simulations Identify Immobilized Water Molecules That Bridge Peptide Mimic MDWNMHAA to Anticarbohydrate Antibody SYA/J6. Chemistry 2011; 17:11438-45. [DOI: 10.1002/chem.201101464] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2011] [Indexed: 11/11/2022]
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11
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Auer R, Kloiber K, Vavrinska A, Geist L, Coudevylle N, Konrat R. Pharmacophore mapping via cross-relaxation during adiabatic fast passage. J Am Chem Soc 2010; 132:1480-1. [PMID: 20078057 DOI: 10.1021/ja910098s] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A novel NMR method is demonstrated for the investigation of protein ligand interactions. In this approach an adiabatic fast passage pulse, i.e. a long, weak pulse with a linear frequency sweep, is used to probe (1)H-(1)H NOEs. During the adiabatic fast passage the effective rotating-frame NOE is a weighted average of transverse and longitudinal cross-relaxation contributions that can be tuned by pulse power and frequency sweep rate. It is demonstrated that the occurrence of spin diffusion processes leads to sizable deviations from the theoretical relationship between effective relaxation rate and effective tilt angle in the spin lock frame and can be used to probe protein-ligand binding. This methodology comprises high sensitivity and ease of implementation. The feasibility of this technique is demonstrated with two protein complexes, vanillic acid bound to the quail lipocalin Q83 and NAD(+) and AMP binding to alcohol dehydrogenase (ADH).
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Affiliation(s)
- Renate Auer
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Campus Vienna Biocenter 5, A-1030 Vienna, Austria
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12
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Zhou P, Wagner G. Overcoming the solubility limit with solubility-enhancement tags: successful applications in biomolecular NMR studies. JOURNAL OF BIOMOLECULAR NMR 2010; 46:23-31. [PMID: 19731047 PMCID: PMC2879018 DOI: 10.1007/s10858-009-9371-6] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2009] [Accepted: 08/18/2009] [Indexed: 05/20/2023]
Abstract
Although the rapid progress of NMR technology has significantly expanded the range of NMR-trackable systems, preparation of NMR-suitable samples that are highly soluble and stable remains a bottleneck for studies of many biological systems. The application of solubility-enhancement tags (SETs) has been highly effective in overcoming solubility and sample stability issues and has enabled structural studies of important biological systems previously deemed unapproachable by solution NMR techniques. In this review, we provide a brief survey of the development and successful applications of the SET strategy in biomolecular NMR.We also comment on the criteria for choosing optimal SETs, such as for differently charged target proteins, and recent new developments on NMR-invisible SETs.
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Affiliation(s)
- Pei Zhou
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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