1
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Becker D, Bharatam PV, Gohlke H. Molecular Mechanisms Underlying Single Nucleotide Polymorphism-Induced Reactivity Decrease in CYP2D6. J Chem Inf Model 2024; 64:6026-6040. [PMID: 38994927 DOI: 10.1021/acs.jcim.4c00276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Cytochrome P450 2D6 (CYP2D6) is one of the most important enzymes involved in drug metabolism. Genetic polymorphism can influence drug metabolism by CYP2D6 such that a therapy is seriously affected by under- or overdosing of drugs. However, a general explanation at the atomistic level for poor activity is missing so far. Here we show for the 20 most common single nucleotide polymorphisms (SNPs) of CYP2D6 that poor metabolism is driven by four mechanisms. We found in extensive all-atom molecular dynamics simulations that the rigidity of the I-helix (central helix), distance between central phenylalanines (stabilizing bound substrate), availability of basic residues on the surface of CYP2D6 (binding of cytochrome P450 reductase), and position of arginine 132 (electron transfer to heme) are essential for an extensive function of the enzyme. These results were applied to SNPs with unknown effects, and potential SNPs that may lead to poor drug metabolism were identified. The revealed molecular mechanisms might be important for other drug-metabolizing cytochrome P450 enzymes.
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Affiliation(s)
- Daniel Becker
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, S. A. S. Nagar, Mohali, Punjab 160 062, India
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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2
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He Y, Wang S, Zeng S, Zhu J, Xu D, Han W, Wang J. NRIMD, a Web Server for Analyzing Protein Allosteric Interactions Based on Molecular Dynamics Simulation. J Chem Inf Model 2024. [PMID: 38991149 DOI: 10.1021/acs.jcim.4c00783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Long-range allosteric communication between distant sites and active sites in proteins is central to biological regulation but still poorly characterized, limiting the development of protein engineering and drug design. Addressing this gap, NRIMD is an open-access web server for analyzing long-range interactions in proteins from molecular dynamics (MD) simulations, such as the effect of mutations at distal sites or allosteric ligand binding at allosteric sites on the active center. Based on our recent works on neural relational inference using graph neural networks, this cloud-based web server accepts MD simulation data on any length of residues in the alpha-carbon skeleton format from mainstream MD software. The input trajectory data are validated at the frontend deployed on the cloud and then processed on the backend deployed on a high-performance computer system with a collection of complementary tools. The web server provides a one-stop-shop MD analysis platform to predict long-range interactions and their paths between distant sites and active sites. It provides a user-friendly interface for detailed analysis and visualization. To the best of our knowledge, NRIMD is the first-of-its-kind online service to provide comprehensive long-range interaction analysis on MD simulations, which significantly lowers the barrier of predictions on protein long-range interactions using deep learning. The NRIMD web server is publicly available at https://nrimd.luddy.indianapolis.iu.edu/.
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Affiliation(s)
- Yi He
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Shuang Wang
- Department of Computer Science, Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, Bloomington, Indiana 47405, United States
| | - Shuai Zeng
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Juexin Wang
- Department of BioHealth Informatics, Luddy School of Informatics, Computing, and Engineering, Indiana University Indianapolis, Indianapolis, Indiana 46202, United States
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3
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He Y, Liu K, Cao F, Song R, Liu J, Zhang Y, Li W, Han W. Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase. Sci Rep 2024; 14:174. [PMID: 38168773 PMCID: PMC10761953 DOI: 10.1038/s41598-023-50686-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/22/2023] [Indexed: 01/05/2024] Open
Abstract
Xanthine oxidase (XO) is a crucial enzyme in the development of hyperuricemia and gout. This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used molecular docking to obtain three systems and then conducted 200 ns molecular dynamics simulations for the Apo, LWM, and ALPM systems. The results reveal a stronger binding affinity of the LWM peptide to XO, potentially due to increased hydrogen bond formation. Notable changes were observed in the XO tunnel upon inhibitor binding, particularly with LWM, which showed a thinner, longer, and more twisted configuration compared to ALPM. The study highlights the importance of residue F914 in the allosteric pathway. Methodologically, we utilized the perturbed response scan (PRS) based on Python, enhancing tools for MD analysis. These findings deepen our understanding of food-derived anti-XO inhibitors and could inform the development of food-based therapeutics for reducing uric acid levels with minimal side effects.
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Affiliation(s)
- Yi He
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Kaifeng Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Fuyan Cao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Renxiu Song
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China
| | - Jianxuan Liu
- Jilin Academy of Chinese Medicine Sciences, Chuangju Road 155, Changchun, 130012, China
| | - Yinghua Zhang
- Jilin Academy of Chinese Medicine Sciences, Chuangju Road 155, Changchun, 130012, China.
| | - Wannan Li
- Edmond H. Fischer Signal Transduction Laboratory, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China.
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Qianjin Road 2699, Changchun, 130012, China.
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4
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Lin C, Kuffour EO, Fuchs NV, Gertzen CGW, Kaiser J, Hirschenberger M, Tang X, Xu HC, Michel O, Tao R, Haase A, Martin U, Kurz T, Drexler I, Görg B, Lang PA, Luedde T, Sparrer KMJ, Gohlke H, König R, Münk C. Regulation of STING activity in DNA sensing by ISG15 modification. Cell Rep 2023; 42:113277. [PMID: 37864791 DOI: 10.1016/j.celrep.2023.113277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/06/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023] Open
Abstract
Sensing of human immunodeficiency virus type 1 (HIV-1) DNA is mediated by the cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) signaling axis. Signal transduction and regulation of this cascade is achieved by post-translational modifications. Here we show that cGAS-STING-dependent HIV-1 sensing requires interferon-stimulated gene 15 (ISG15). ISG15 deficiency inhibits STING-dependent sensing of HIV-1 and STING agonist-induced antiviral response. Upon external stimuli, STING undergoes ISGylation at residues K224, K236, K289, K347, K338, and K370. Inhibition of STING ISGylation at K289 suppresses STING-mediated type Ⅰ interferon induction by inhibiting its oligomerization. Of note, removal of STING ISGylation alleviates gain-of-function phenotype in STING-associated vasculopathy with onset in infancy (SAVI). Molecular modeling suggests that ISGylation of K289 is an important regulator of oligomerization. Taken together, our data demonstrate that ISGylation at K289 is crucial for STING activation and represents an important regulatory step in DNA sensing of viruses and autoimmune responses.
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Affiliation(s)
- Chaohui Lin
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Edmund Osei Kuffour
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Nina V Fuchs
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Center for Structural Studies (CSS), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Xiao Tang
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Haifeng C Xu
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Oliver Michel
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ronny Tao
- Institute for Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexandra Haase
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, 30625 Hannover, Germany; REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery (HTTG), Hannover Medical School, 30625 Hannover, Germany; REBIRTH-Research Center for Translational and Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Hannover Medical School, 30625 Hannover, Germany
| | - Thomas Kurz
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ingo Drexler
- Institute for Virology, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Boris Görg
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Philipp A Lang
- Department of Molecular Medicine II, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Tom Luedde
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | | | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Renate König
- Host-Pathogen Interactions, Paul-Ehrlich-Institut, Langen, Germany
| | - Carsten Münk
- Clinic of Gastroenterology, Hepatology and Infectious Diseases, Medical Faculty, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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5
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La Sala G, Pfleger C, Käck H, Wissler L, Nevin P, Böhm K, Janet JP, Schimpl M, Stubbs CJ, De Vivo M, Tyrchan C, Hogner A, Gohlke H, Frolov AI. Combining structural and coevolution information to unveil allosteric sites. Chem Sci 2023; 14:7057-7067. [PMID: 37389247 PMCID: PMC10306073 DOI: 10.1039/d2sc06272k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 06/02/2023] [Indexed: 07/01/2023] Open
Abstract
Understanding allosteric regulation in biomolecules is of great interest to pharmaceutical research and computational methods emerged during the last decades to characterize allosteric coupling. However, the prediction of allosteric sites in a protein structure remains a challenging task. Here, we integrate local binding site information, coevolutionary information, and information on dynamic allostery into a structure-based three-parameter model to identify potentially hidden allosteric sites in ensembles of protein structures with orthosteric ligands. When tested on five allosteric proteins (LFA-1, p38-α, GR, MAT2A, and BCKDK), the model successfully ranked all known allosteric pockets in the top three positions. Finally, we identified a novel druggable site in MAT2A confirmed by X-ray crystallography and SPR and a hitherto unknown druggable allosteric site in BCKDK validated by biochemical and X-ray crystallography analyses. Our model can be applied in drug discovery to identify allosteric pockets.
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Affiliation(s)
- Giuseppina La Sala
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
| | - Helena Käck
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Lisa Wissler
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Philip Nevin
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Kerstin Böhm
- Discovery Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Jon Paul Janet
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Marianne Schimpl
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Christopher J Stubbs
- Mechanistic and Structural Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca Cambridge UK
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Design, Istituto Italiano di Tecnologia Via Morego 30 16163 Genoa Italy
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Anders Hogner
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf 40225 Düsseldorf Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Institute of Bio- and Geosciences (IBG-4: Bioinformatics) Forschungszentrum Jülich GmbH 52425 Jülich Germany
| | - Andrey I Frolov
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca Gothenburg Sweden
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6
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Kaiser J, Gertzen CG, Bernauer T, Höfner G, Niessen KV, Seeger T, Paintner FF, Wanner KT, Worek F, Thiermann H, Gohlke H. A novel binding site in the nicotinic acetylcholine receptor for MB327 can explain its allosteric modulation relevant for organophosphorus-poisoning treatment. Toxicol Lett 2022; 373:160-171. [DOI: 10.1016/j.toxlet.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022]
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7
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Yüksel S, Bonus M, Schwabe T, Pfleger C, Zimmer T, Enke U, Saß I, Gohlke H, Benndorf K, Kusch J. Uncoupling of Voltage- and Ligand-Induced Activation in HCN2 Channels by Glycine Inserts. Front Physiol 2022; 13:895324. [PMID: 36091400 PMCID: PMC9452628 DOI: 10.3389/fphys.2022.895324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 06/20/2022] [Indexed: 11/24/2022] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels are tetramers that generate electrical rhythmicity in special brain neurons and cardiomyocytes. The channels are activated by membrane hyperpolarization. The binding of cAMP to the four available cyclic nucleotide-binding domains (CNBD) enhances channel activation. We analyzed in the present study the mechanism of how the effect of cAMP binding is transmitted to the pore domain. Our strategy was to uncouple the C-linker (CL) from the channel core by inserting one to five glycine residues between the S6 gate and the A′-helix (constructs 1G to 5G). We quantified in full-length HCN2 channels the resulting functional effects of the inserted glycines by current activation as well as the structural dynamics and statics using molecular dynamics simulations and Constraint Network Analysis. We show functionally that already in 1G the cAMP effect on activation is lost and that with the exception of 3G and 5G the concentration-activation relationships are shifted to depolarized voltages with respect to HCN2. The strongest effect was found for 4G. Accordingly, the activation kinetics were accelerated by all constructs, again with the strongest effect in 4G. The simulations reveal that the average residue mobility of the CL and CNBD domains is increased in all constructs and that the junction between the S6 and A′-helix is turned into a flexible hinge, resulting in a destabilized gate in all constructs. Moreover, for 3G and 4G, there is a stronger downward displacement of the CL-CNBD than in HCN2 and the other constructs, resulting in an increased kink angle between S6 and A′-helix, which in turn loosens contacts between the S4-helix and the CL. This is suggested to promote a downward movement of the S4-helix, similar to the effect of hyperpolarization. In addition, exclusively in 4G, the selectivity filter in the upper pore region and parts of the S4-helix are destabilized. The results provide new insights into the intricate activation of HCN2 channels.
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Affiliation(s)
- Sezin Yüksel
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Michele Bonus
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Tina Schwabe
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Christopher Pfleger
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Thomas Zimmer
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Uta Enke
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Inga Saß
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
| | - Holger Gohlke
- Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich, Germany
- *Correspondence: Holger Gohlke, ; Klaus Benndorf, ; Jana Kusch,
| | - Klaus Benndorf
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
- *Correspondence: Holger Gohlke, ; Klaus Benndorf, ; Jana Kusch,
| | - Jana Kusch
- Universitätsklinikum Jena, Institut für Physiologie II, Jena, Germany
- *Correspondence: Holger Gohlke, ; Klaus Benndorf, ; Jana Kusch,
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8
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Zhu J, Wang J, Han W, Xu D. Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations. Nat Commun 2022; 13:1661. [PMID: 35351887 PMCID: PMC8964751 DOI: 10.1038/s41467-022-29331-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 03/10/2022] [Indexed: 12/03/2022] Open
Abstract
Protein allostery is a biological process facilitated by spatially long-range intra-protein communication, whereby ligand binding or amino acid change at a distant site affects the active site remotely. Molecular dynamics (MD) simulation provides a powerful computational approach to probe the allosteric effect. However, current MD simulations cannot reach the time scales of whole allosteric processes. The advent of deep learning made it possible to evaluate both spatially short and long-range communications for understanding allostery. For this purpose, we applied a neural relational inference model based on a graph neural network, which adopts an encoder-decoder architecture to simultaneously infer latent interactions for probing protein allosteric processes as dynamic networks of interacting residues. From the MD trajectories, this model successfully learned the long-range interactions and pathways that can mediate the allosteric communications between distant sites in the Pin1, SOD1, and MEK1 systems. Furthermore, the model can discover allostery-related interactions earlier in the MD simulation trajectories and predict relative free energy changes upon mutations more accurately than other methods.
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Affiliation(s)
- Jingxuan Zhu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States
| | - Juexin Wang
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States
| | - Weiwei Han
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China.
| | - Dong Xu
- Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, Missouri, United States.
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9
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Hüdig M, Tronconi MA, Zubimendi JP, Sage TL, Poschmann G, Bickel D, Gohlke H, Maurino VG. Respiratory and C4-photosynthetic NAD-malic enzyme coexist in bundle sheath cell mitochondria and evolved via association of differentially adapted subunits. THE PLANT CELL 2022; 34:597-615. [PMID: 34734993 PMCID: PMC8773993 DOI: 10.1093/plcell/koab265] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/26/2021] [Indexed: 05/29/2023]
Abstract
In plant mitochondria, nicotinamide adenine dinucleotide-malic enzyme (NAD-ME) has a housekeeping function in malate respiration. In different plant lineages, NAD-ME was independently co-opted in C4 photosynthesis. In the C4 Cleome species, Gynandropsis gynandra and Cleome angustifolia, all NAD-ME genes (NAD-MEα, NAD-MEβ1, and NAD-MEβ2) were affected by C4 evolution and are expressed at higher levels than their orthologs in the C3 species Tarenaya hassleriana. In T. hassleriana, the NAD-ME housekeeping function is performed by two heteromers, NAD-MEα/β1 and NAD-MEα/β2, with similar biochemical properties. In both C4 species, this role is restricted to NAD-MEα/β2. In the C4 species, NAD-MEα/β1 is exclusively present in the leaves, where it accounts for most of the enzymatic activity. Gynandropsis gynandra NAD-MEα/β1 (GgNAD-MEα/β1) exhibits high catalytic efficiency and is differentially activated by the C4 intermediate aspartate, confirming its role as the C4-decarboxylase. During C4 evolution, NAD-MEβ1 lost its catalytic activity; its contribution to the enzymatic activity results from a stabilizing effect on the associated α-subunit and the acquisition of regulatory properties. We conclude that in bundle sheath cell mitochondria of C4 species, the functions of NAD-ME as C4 photosynthetic decarboxylase and as a housekeeping enzyme coexist and are performed by isoforms that combine the same α-subunit with differentially adapted β-subunits.
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Affiliation(s)
- Meike Hüdig
- Molekulare Pflanzenphysiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Kirschallee, Bonn 53115, Germany
| | - Marcos A Tronconi
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Juan P Zubimendi
- Centro de Estudios Fotosintéticos y Bioquímicos, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario 2000, Argentina
| | - Tammy L Sage
- Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Gereon Poschmann
- Molecular Proteomics Laboratory, Biomedical Research Centre (BMFZ) & Institute of Molecular Medicine, Proteome Research, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - David Bickel
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätsstraße 1, Düsseldorf 40225, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Veronica G Maurino
- Molekulare Pflanzenphysiologie, Rheinische Friedrich-Wilhelms-Universität Bonn, Kirschallee, Bonn 53115, Germany
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10
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Miyashita N, Yonezawa Y. Mutual information analysis of the dynamic correlation between side chains in proteins. J Chem Phys 2021; 155:044107. [PMID: 34340388 DOI: 10.1063/5.0055662] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Protein dynamics play an essential role in function regulation. In recent years, many experimental and theoretical studies have shown that changes in protein fluctuations in the backbone and side chains fulfill a pivotal role associated with amino acid mutations, chemical modifications, and ligand binding. The dynamic correlations between protein side chains have not been sufficiently studied, and no reliable analysis method has been available so far. Therefore, we developed a method to evaluate the dynamic correlation between protein side chains using mutual information and molecular dynamics simulations. To eliminate the structural superposition errors dealing with conventional analysis methods, and to accurately extract the intrinsic fluctuation properties of the side chains, we employed distance principal component analysis (distPCA). The motion of the side chain was then projected onto the eigenvector space obtained by distPCA, and the mutual information between the projected motions was calculated. The proposed method was then applied to a small protein "eglin c" and the mutants. The results show that even a single mutation significantly changed the dynamic correlations and also suggest that the dynamic change is deeply related to the stability. Those results indicate that our developed method could be useful for analyzing the molecular mechanism of allosteric communication in proteins.
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Affiliation(s)
- Naoyuki Miyashita
- Department of Computational Systems Biology, Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
| | - Yasushige Yonezawa
- High Pressure Protein Research Center, Institute of Advanced Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama 649-6493, Japan
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11
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Becker D, Bharatam PV, Gohlke H. F/G Region Rigidity is Inversely Correlated to Substrate Promiscuity of Human CYP Isoforms Involved in Metabolism. J Chem Inf Model 2021; 61:4023-4030. [PMID: 34370479 DOI: 10.1021/acs.jcim.1c00558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Of 57 human cytochrome P450 (CYP) enzymes, 12 metabolize 90% of xenobiotics. To our knowledge, no study has addressed the relation between enzyme dynamics and substrate promiscuity for more than three CYPs. Here, we show by constraint dilution simulations with the Constraint Network Analysis for the 12 isoforms that structural rigidity of the F/G region is significantly inversely correlated to the enzymes' substrate promiscuity. This highlights the functional importance of structural dynamics of the substrate tunnel.
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Affiliation(s)
- Daniel Becker
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany
| | - Prasad V Bharatam
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER), Sector 67, Sahibzada Ajit Singh Nagar, Mohali 160062, Punjab, India
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße 1, 40225 Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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12
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El Harrar T, Frieg B, Davari MD, Jaeger KE, Schwaneberg U, Gohlke H. Aqueous ionic liquids redistribute local enzyme stability via long-range perturbation pathways. Comput Struct Biotechnol J 2021; 19:4248-4264. [PMID: 34429845 PMCID: PMC8355836 DOI: 10.1016/j.csbj.2021.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/05/2021] [Accepted: 07/06/2021] [Indexed: 01/25/2023] Open
Abstract
Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for biocatalysis due to their unique properties. On the other hand, the incubation of enzymes in IL or aIL often reduces enzyme activity. Recent studies proposed various aIL-induced effects to explain the reduction, classified as direct effects, e.g., local dehydration or competitive inhibition, and indirect effects, e.g., structural perturbations or disturbed catalytic site integrity. However, the molecular origin of indirect effects has largely remained elusive. Here we show by multi-μs long molecular dynamics simulations, free energy computations, and rigidity analyses that aIL favorably interact with specific residues of Bacillus subtilis Lipase A (BsLipA) and modify the local structural stability of this model enzyme by inducing long-range perturbations of noncovalent interactions. The perturbations percolate over neighboring residues and eventually affect the catalytic site and the buried protein core. Validation against a complete experimental site saturation mutagenesis library of BsLipA (3620 variants) reveals that the residues of the perturbation pathways are distinguished sequence positions where substitutions highly likely yield significantly improved residual activity. Our results demonstrate that identifying these perturbation pathways and specific IL ion-residue interactions there effectively predicts focused variant libraries with improved aIL tolerance.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Benedikt Frieg
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mehdi D. Davari
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, 52428 Jülich, Germany
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ulrich Schwaneberg
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany
- DWI – Leibniz Institute for Interactive Materials e.V., 52074 Aachen, Germany
| | - Holger Gohlke
- John-von-Neumann-Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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13
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Huang Q, Song P, Chen Y, Liu Z, Lai L. Allosteric Type and Pathways Are Governed by the Forces of Protein-Ligand Binding. J Phys Chem Lett 2021; 12:5404-5412. [PMID: 34080881 DOI: 10.1021/acs.jpclett.1c01253] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Allostery is central to many cellular processes, by up- or down-regulating target function. However, what determines the allosteric type remains elusive and currently it is impossible to predict whether the allosteric compounds would activate or inhibit target function before experimental studies. We demonstrated that the allosteric type and allosteric pathways are governed by the forces imposed by ligand binding to target protein using the anisotropic network model and developed an allosteric type prediction method (AlloType). AlloType correctly predicted 13 of the 16 allosteric systems in the data set with experimentally determined protein and complex structures as well as verified allosteric types, which was also used to identify allosteric pathways. When applied to glutathione peroxidase 4, a protein with no complex structure information, AlloType could still be able to predict the allosteric type of the recently reported allosteric activators, demonstrating its potential application in designing specific allosteric drugs and uncovering allosteric mechanisms.
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Affiliation(s)
- Qiaojing Huang
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Pengbo Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yixin Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Zhirong Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Luhua Lai
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
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14
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Pfleger C, Kusch J, Kondapuram M, Schwabe T, Sattler C, Benndorf K, Gohlke H. Allosteric signaling in C-linker and cyclic nucleotide-binding domain of HCN2 channels. Biophys J 2021; 120:950-963. [PMID: 33515603 DOI: 10.1016/j.bpj.2021.01.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/04/2021] [Accepted: 01/19/2021] [Indexed: 12/22/2022] Open
Abstract
Opening of hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels is controlled by membrane hyperpolarization and binding of cyclic nucleotides to the tetrameric cyclic nucleotide-binding domain (CNBD), attached to the C-linker (CL) disk. Confocal patch-clamp fluorometry revealed pronounced cooperativity of ligand binding among protomers. However, by which pathways allosteric signal transmission occurs remained elusive. Here, we investigate how changes in the structural dynamics of the CL-CNBD of mouse HCN2 upon cAMP binding relate to inter- and intrasubunit signal transmission. Applying a rigidity-theory-based approach, we identify two intersubunit and one intrasubunit pathways that differ in allosteric coupling strength between cAMP-binding sites or toward the CL. These predictions agree with results from electrophysiological and patch-clamp fluorometry experiments. Our results map out distinct routes within the CL-CNBD that modulate different cAMP-binding responses in HCN2 channels. They signify that functionally relevant submodules may exist within and across structurally discernable subunits in HCN channels.
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Affiliation(s)
- Christopher Pfleger
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Jana Kusch
- Institute of Physiology II, Jena University Hospital, Jena, Germany
| | | | - Tina Schwabe
- Institute of Physiology II, Jena University Hospital, Jena, Germany
| | | | - Klaus Benndorf
- Institute of Physiology II, Jena University Hospital, Jena, Germany
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany; John von Neumann Institute for Computing, Jülich Supercomputing Centre, and Institute of Biological Information Processing (IBI-7, Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany.
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15
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Pitard I, Monet D, Goossens PL, Blondel A, Malliavin TE. Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin. Front Mol Biosci 2020; 7:586544. [PMID: 33344505 PMCID: PMC7746812 DOI: 10.3389/fmolb.2020.586544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 11/02/2020] [Indexed: 11/25/2022] Open
Abstract
Molecular dynamics (MD) simulations have been recorded on the complex between the edema factor (EF) of Bacilllus anthracis and calmodulin (CaM), starting from a structure with the orthosteric inhibitor adefovir bound in the EF catalytic site. The starting structure has been destabilized by alternately suppressing different co-factors, such as adefovir ligand or ions, revealing several long-distance correlations between the conformation of CaM, the geometry of the CaM/EF interface, the enzymatic site and the overall organization of the complex. An allosteric communication between CaM/EF interface and the EF catalytic site, highlighted by these correlations, was confirmed by several bioinformatics approaches from the literature. A network of hydrogen bonds and stacking interactions extending from the helix V of of CaM, and the residues of the switches A, B and C, and connecting to catalytic site residues, is a plausible candidate for the mediation of allosteric communication. The greatest variability in volume between the different MD conditions was also found for cavities present at the EF/CaM interface and in the EF catalytic site. The similarity between the predictions from literature and the volume variability might introduce the volume variability as new descriptor of allostery.
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Affiliation(s)
- Irène Pitard
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR 3528, Paris, France.,Center de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR 3756, Paris, France.,Ecole Doctorale Université Paris Sorbonne, Paris, France
| | - Damien Monet
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR 3528, Paris, France.,Center de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR 3756, Paris, France.,Ecole Doctorale Université Paris Sorbonne, Paris, France
| | | | - Arnaud Blondel
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR 3528, Paris, France.,Center de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR 3756, Paris, France
| | - Thérèse E Malliavin
- Unité de Bioinformatique Structurale, Institut Pasteur and CNRS UMR 3528, Paris, France.,Center de Bioinformatique, Biostatistique et Biologie Intégrative, Institut Pasteur and CNRS USR 3756, Paris, France
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16
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Dittrich J, Kather M, Holzberger A, Pich A, Gohlke H. Cumulative Submillisecond All-Atom Simulations of the Temperature-Induced Coil-to-Globule Transition of Poly(N-vinylcaprolactam) in Aqueous Solution. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c01896] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Jonas Dittrich
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Michael Kather
- DWI-Leibniz-Institute for Interactive Materials, RWTH Aachen University, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Anna Holzberger
- DWI-Leibniz-Institute for Interactive Materials, RWTH Aachen University, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Andrij Pich
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- DWI-Leibniz-Institute for Interactive Materials, RWTH Aachen University, 52056 Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, 52074 Aachen, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, 52425 Jülich, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
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17
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Structural and dynamic insights revealing how lipase binding domain MD1 of Pseudomonas aeruginosa foldase affects lipase activation. Sci Rep 2020; 10:3578. [PMID: 32107397 PMCID: PMC7046727 DOI: 10.1038/s41598-020-60093-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/10/2020] [Indexed: 01/13/2023] Open
Abstract
Folding and cellular localization of many proteins of Gram-negative bacteria rely on a network of chaperones and secretion systems. Among them is the lipase-specific foldase Lif, a membrane-bound steric chaperone that tightly binds (KD = 29 nM) and mediates folding of the lipase LipA, a virulence factor of the pathogenic bacterium P. aeruginosa. Lif consists of five-domains, including a mini domain MD1 essential for LipA folding. However, the molecular mechanism of Lif-assisted LipA folding remains elusive. Here, we show in in vitro experiments using a soluble form of Lif (sLif) that isolated MD1 inhibits sLif-assisted LipA activation. Furthermore, the ability to activate LipA is lost in the variant sLifY99A, in which the evolutionary conserved amino acid Y99 from helix α1 of MD1 is mutated to alanine. This coincides with an approximately three-fold reduced affinity of the variant to LipA together with increased flexibility of sLifY99A in the complex as determined by polarization-resolved fluorescence spectroscopy. We have solved the NMR solution structures of P. aeruginosa MD1 and variant MD1Y99A revealing a similar fold indicating that a structural modification is likely not the reason for the impaired activity of variant sLifY99A. Molecular dynamics simulations of the sLif:LipA complex in connection with rigidity analyses suggest a long-range network of interactions spanning from Y99 of sLif to the active site of LipA, which might be essential for LipA activation. These findings provide important details about the putative mechanism for LipA activation and point to a general mechanism of protein folding by multi-domain steric chaperones.
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18
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Wifling D, Pfleger C, Kaindl J, Ibrahim P, Kling RC, Buschauer A, Gohlke H, Clark T. Basal Histamine H 4 Receptor Activation: Agonist Mimicry by the Diphenylalanine Motif. Chemistry 2019; 25:14613-14624. [PMID: 31498478 PMCID: PMC7687114 DOI: 10.1002/chem.201902801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/08/2019] [Indexed: 12/20/2022]
Abstract
Histamine H4 receptor (H4 R) orthologues are G-protein-coupled receptors (GPCRs) that exhibit species-dependent basal activity. In contrast to the basally inactive mouse H4 R (mH4 R), human H4 R (hH4 R) shows a high degree of basal activity. We have performed long-timescale molecular dynamics simulations and rigidity analyses on wild-type hH4 R, the experimentally characterized hH4 R variants S179M, F169V, F169V+S179M, F168A, and on mH4 R to investigate the molecular nature of the differential basal activity. H4 R variant-dependent differences between essential motifs of GPCR activation and structural stabilities correlate with experimentally determined basal activities and provide a molecular explanation for the differences in basal activation. Strikingly, during the MD simulations, F16945.55 dips into the orthosteric binding pocket only in the case of hH4 R, thus adopting the role of an agonist and contributing to the stabilization of the active state. The results shed new light on the molecular mechanism of basal H4 R activation that are of importance for other GPCRs.
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Affiliation(s)
- David Wifling
- Department of Pharmaceutical/Medicinal Chemistry IIInstitute of PharmacyUniversity of RegensburgUniversitätsstr. 3193053RegensburgGermany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Jonas Kaindl
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Passainte Ibrahim
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Ralf C. Kling
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Armin Buschauer
- Department of Pharmaceutical/Medicinal Chemistry IIInstitute of PharmacyUniversity of RegensburgUniversitätsstr. 3193053RegensburgGermany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
- John von Neumann Institute for Computing (NIC)Jülich Supercomputing Centre (JSC) &Institute for Complex Systems—Structural Biochemistry (ICS 6)Forschungszentrum Jülich GmbHWilhelm-Johnen-Str.52425JülichGermany
| | - Timothy Clark
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
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19
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Nussinov R, Tsai CJ, Jang H. Does Ras Activate Raf and PI3K Allosterically? Front Oncol 2019; 9:1231. [PMID: 31799192 PMCID: PMC6874141 DOI: 10.3389/fonc.2019.01231] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/28/2019] [Indexed: 12/11/2022] Open
Abstract
The mechanism through which oncogenic Ras activates its effectors is vastly important to resolve. If allostery is at play, then targeting allosteric pathways could help in quelling activation of MAPK (Raf/MEK/ERK) and PI3K (PI3K/Akt/mTOR) cell proliferation pathways. On the face of it, allosteric activation is reasonable: Ras binding perturbs the conformational ensembles of its effectors. Here, however, we suggest that at least for Raf, PI3K, and NORE1A (RASSF5), that is unlikely. Raf's long disordered linker dampens effective allosteric activation. Instead, we suggest that the high-affinity Ras–Raf binding relieves Raf's autoinhibition, shifting Raf's ensemble from the inactive to the nanocluster-mediated dimerized active state, as Ras also does for NORE1A. PI3K is recruited and allosterically activated by RTK (e.g., EGFR) at the membrane. Ras restrains PI3K's distribution and active site orientation. It stabilizes and facilitates PIP2 binding at the active site and increases the PI3K residence time at the membrane. Thus, RTKs allosterically activate PI3Kα; however, merging their action with Ras accomplishes full activation. Here we review their activation mechanisms in this light and draw attention to implications for their pharmacology.
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Affiliation(s)
- Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States.,Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chung-Jung Tsai
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, United States
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20
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Verma N, Dollinger P, Kovacic F, Jaeger KE, Gohlke H. The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A. J Comput Chem 2019; 41:500-512. [PMID: 31618459 DOI: 10.1002/jcc.26085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/22/2019] [Accepted: 09/25/2019] [Indexed: 12/19/2022]
Abstract
Lipases are essential and widely used biocatalysts. Hence, the production of lipases requires a detailed understanding of the molecular mechanism of its folding and secretion. Lipase A from Pseudomonas aeruginosa, PaLipA, constitutes a prominent example that has additional relevance because of its role as a virulence factor in many diseases. PaLipA requires the assistance of a membrane-integrated steric chaperone, the lipase-specific foldase Lif, to achieve its enzymatically active state. However, the molecular mechanism of how Lif activates its cognate lipase has remained elusive. Here, we show by molecular dynamics simulations at the atomistic level and potential of mean force computations that Lif catalyzes the activation process of PaLipA by structurally stabilizing an intermediate PaLipA conformation, particularly a β-sheet in the region of residues 17-30, such that the opening of PaLipA's lid domain is facilitated. This opening allows substrate access to PaLipA's catalytic site. A surprising and so far not fully understood aspect of our study is that the open state of PaLipA is unstable compared to the closed one according to our computational and in vitro biochemical results. We thus speculate that further interactions of PaLipA with the Xcp secretion machinery and/or components of the extracellular matrix contribute to the remaining activity of secreted PaLipA. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Neha Verma
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätstr. 1, 40225, Düsseldorf, Germany
| | - Peter Dollinger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätstr. 1, 40225, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
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21
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Preising MN, Görg B, Friedburg C, Qvartskhava N, Budde BS, Bonus M, Toliat MR, Pfleger C, Altmüller J, Herebian D, Beyer M, Zöllner HJ, Wittsack HJ, Schaper J, Klee D, Zechner U, Nürnberg P, Schipper J, Schnitzler A, Gohlke H, Lorenz B, Häussinger D, Bolz HJ. Biallelic mutation of human SLC6A6 encoding the taurine transporter TAUT is linked to early retinal degeneration. FASEB J 2019; 33:11507-11527. [PMID: 31345061 DOI: 10.1096/fj.201900914rr] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We previously reported that inactivation of the transmembrane taurine transporter (TauT or solute carrier 6a6) causes early retinal degeneration in mice. Compatible with taurine's indispensability for cell volume homeostasis, protein stabilization, cytoprotection, antioxidation, and immuno- and neuromodulation, mice develop multisystemic dysfunctions (hearing loss; liver fibrosis; and behavioral, heart, and skeletal muscle abnormalities) later on. Here, by genetic, cell biologic, in vivo 1H-magnetic resonance spectroscopy and molecular dynamics simulation studies, we conducted in-depth characterization of a novel disorder: human TAUT deficiency. Loss of TAUT function due to a homozygous missense mutation caused panretinal degeneration in 2 brothers. TAUTp.A78E still localized in the plasma membrane but is predicted to impact structural stabilization. 3H-taurine uptake by peripheral blood mononuclear cells was reduced by 95%, and taurine levels were severely reduced in plasma, skeletal muscle, and brain. Extraocular dysfunctions were not yet detected, but significantly increased urinary excretion of 8-oxo-7,8-dihydroguanosine indicated generally enhanced (yet clinically unapparent) oxidative stress and RNA oxidation, warranting continuous broad surveillance.-Preising, M. N., Görg, B., Friedburg, C., Qvartskhava, N., Budde, B. S., Bonus, M., Toliat, M. R., Pfleger, C., Altmüller, J., Herebian, D., Beyer, M., Zöllner, H. J., Wittsack, H.-J., Schaper, J., Klee, D., Zechner, U., Nürnberg, P., Schipper, J., Schnitzler, A., Gohlke, H., Lorenz, B., Häussinger, D., Bolz, H. J. Biallelic mutation of human SLC6A6 encoding the taurine transporter TAUT is linked to early retinal degeneration.
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Affiliation(s)
- Markus N Preising
- Department of Ophthalmology, Justus-Liebig University Giessen, Giessen, Germany
| | - Boris Görg
- Department of Gastroenterology, Hepatology, and Infectious Diseases, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph Friedburg
- Department of Ophthalmology, Justus-Liebig University Giessen, Giessen, Germany
| | - Natalia Qvartskhava
- Department of Gastroenterology, Hepatology, and Infectious Diseases, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Birgit S Budde
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Michele Bonus
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mohammad R Toliat
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Diran Herebian
- Department of General Pediatrics, Neonatology, and Pediatric Cardiology, Medical Faculty, University Hospital Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Mila Beyer
- Department of Gastroenterology, Hepatology, and Infectious Diseases, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Helge J Zöllner
- Institute of Clinical Neuroscience and Medical Psychology, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Hans-Jörg Wittsack
- Department of Diagnostic and Interventional Radiology, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jörg Schaper
- Department of Diagnostic and Interventional Radiology, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Dirk Klee
- Department of Diagnostic and Interventional Radiology, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Ulrich Zechner
- Senckenberg Centre for Human Genetics, Frankfurt on the Main, Germany.,Institute of Human Genetics, Mainz University Medical Center, Mainz, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Jörg Schipper
- Klinik für Hals-Nasen-Ohren Heilkunde, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alfons Schnitzler
- Institute of Clinical Neuroscience and Medical Psychology, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC)-Jülich Supercomputing Centre (JSC)-Structural Biochemistry, Institute of Complex Systems (ICS 6), Research Centre Jülich, Jülich, Germany
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig University Giessen, Giessen, Germany
| | - Dieter Häussinger
- Department of Gastroenterology, Hepatology, and Infectious Diseases, University Hospital of Düsseldorf-Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Hanno J Bolz
- Institute of Human Genetics, University of Cologne, Cologne, Germany.,Senckenberg Centre for Human Genetics, Frankfurt on the Main, Germany
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22
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On the perturbation nature of allostery: sites, mutations, and signal modulation. Curr Opin Struct Biol 2019; 56:18-27. [DOI: 10.1016/j.sbi.2018.10.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 10/27/2018] [Accepted: 10/30/2018] [Indexed: 10/27/2022]
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23
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Schmidt D, Boehm M, McClendon CL, Torella R, Gohlke H. Cosolvent-Enhanced Sampling and Unbiased Identification of Cryptic Pockets Suitable for Structure-Based Drug Design. J Chem Theory Comput 2019; 15:3331-3343. [PMID: 30998331 DOI: 10.1021/acs.jctc.8b01295] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Modulating protein activity with small-molecules binding to cryptic pockets offers great opportunities to overcome hurdles in drug design. Cryptic sites are atypical binding sites in proteins that are closed in the absence of a stabilizing ligand and are thus inherently difficult to identify. Many studies have proposed methods to predict cryptic sites. However, a general approach to prospectively sample open conformations of these sites and to identify cryptic pockets in an unbiased manner suitable for structure-based drug design remains elusive. Here, we describe an all-atom, explicit cosolvent, molecular dynamics (MD) simulations-based workflow to sample the open states of cryptic sites and identify opened pockets, in a manner that does not require a priori knowledge about these sites. Furthermore, the workflow relies on a target-independent parametrization that only distinguishes between binding pockets for peptides or small molecules. We validated our approach on a diverse test set of seven proteins with crystallographically determined cryptic sites. The known cryptic sites were found among the three highest-ranked predicted cryptic sites, and an open site conformation was sampled and selected for most of the systems. Crystallographic ligand poses were well reproduced by docking into these identified open conformations for five of the systems. When the fully open state could not be reproduced, we were still able to predict the location of the cryptic site, or identify other cryptic sites that could be retrospectively validated with knowledge of the protein target. These characteristics render our approach valuable for investigating novel protein targets without any prior information.
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Affiliation(s)
- Denis Schmidt
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany
| | - Markus Boehm
- Medicinal Sciences , Pfizer Inc. , Cambridge , Massachusetts 02139 , United States
| | | | - Rubben Torella
- Medicinal Sciences , Pfizer Inc. , Cambridge , Massachusetts 02139 , United States
| | - Holger Gohlke
- Mathematisch-Naturwissenschaftliche Fakultät, Institut für Pharmazeutische und Medizinische Chemie , Heinrich-Heine-Universität Düsseldorf , 40225 Düsseldorf , Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems-Structural Biochemistry (ICS 6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany
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24
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Daura X. Advances in the Computational Identification of Allosteric Sites and Pathways in Proteins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:141-169. [PMID: 31707703 DOI: 10.1007/978-981-13-8719-7_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With the increasing difficulty to develop new drugs and the emergence of resistance to traditional orthosteric-site inhibitors, the search for alternatives is finally approaching the focus on allosteric sites. Allosteric sites offer opportunities to regulate many pharmacologically targeted pathways by inhibition or activation. In addition, allosteric sites tend to be less conserved than the functional site, which may facilitate the design of specific effectors in the protein families for which specific orthosteric inhibitors have proved difficult to design. Furthermore, recent evidence suggests that all proteins might be susceptible of allosteric regulation, increasing the space of druggable targets. Computational identification of allosteric sites has therefore become an active field of research. The problem can be approached from two sides: (1) the identification of allosteric-communication pathways between the functional site and potential allosteric sites and (2) the functional-site-independent identification of allosteric sites. While the first approach tends to be more laborious and thus restricted to a single protein, the second tends to be more amenable to larger-scale analysis, thus providing tools for the two drug discovery scenarios: the analysis of known targets and the screening for new potential targets. Here, I show some basic concepts and methods useful to the identification of allosteric sites and pathways, in line with these two approaches. I describe them in some detail to build a clear framework, at the risk of losing the interest of experts. Examples of recent studies involving these methods are also illustrated, focusing on the techniques rather than on their findings on allosterism.
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Affiliation(s)
- Xavier Daura
- Catalan Institution for Research and Advanced Studies (ICREA) and Institute of Biotechnology and Biomedicine, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.
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25
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Milić D, Dick M, Mulnaes D, Pfleger C, Kinnen A, Gohlke H, Groth G. Recognition motif and mechanism of ripening inhibitory peptides in plant hormone receptor ETR1. Sci Rep 2018; 8:3890. [PMID: 29497085 PMCID: PMC5832771 DOI: 10.1038/s41598-018-21952-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 02/13/2018] [Indexed: 12/21/2022] Open
Abstract
Synthetic peptides derived from ethylene-insensitive protein 2 (EIN2), a central regulator of ethylene signalling, were recently shown to delay fruit ripening by interrupting protein-protein interactions in the ethylene signalling pathway. Here, we show that the inhibitory peptide NOP-1 binds to the GAF domain of ETR1 - the prototype of the plant ethylene receptor family. Site-directed mutagenesis and computational studies reveal the peptide interaction site and a plausible molecular mechanism for the ripening inhibition.
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Affiliation(s)
- Dalibor Milić
- Institute of Biochemical Plant Physiology and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Department of Structural and Computational Biology, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Vienna, Austria
| | - Markus Dick
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, USA
| | - Daniel Mulnaes
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christopher Pfleger
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Anna Kinnen
- Institute of Biochemical Plant Physiology and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Holger Gohlke
- Institute of Pharmaceutical and Medicinal Chemistry and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) & Institute for Complex Systems - Structural Biochemistry (ICS 6), Forschungszentrum Jülich GmbH, Jülich, Germany.
| | - Georg Groth
- Institute of Biochemical Plant Physiology and Bioeconomy Science Center (BioSC), Heinrich Heine University Düsseldorf, Düsseldorf, Germany.
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