51
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Göddeke H, Timachi MH, Hutter CAJ, Galazzo L, Seeger MA, Karttunen M, Bordignon E, Schäfer LV. Atomistic Mechanism of Large-Scale Conformational Transition in a Heterodimeric ABC Exporter. J Am Chem Soc 2018; 140:4543-4551. [DOI: 10.1021/jacs.7b12944] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Hendrik Göddeke
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - M. Hadi Timachi
- EPR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Cedric A. J. Hutter
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland
| | - Laura Galazzo
- EPR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Markus A. Seeger
- Institute of Medical Microbiology, University of Zürich, 8006 Zürich, Switzerland
| | - Mikko Karttunen
- Department of Chemistry and Department of Applied Mathematics, Western University, London, Ontario N6A 3K7, Canada
| | - Enrica Bordignon
- EPR Spectroscopy, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
| | - Lars V. Schäfer
- Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, 44780 Bochum, Germany
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52
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Hauwert NJ, Mocking TAM, Da Costa Pereira D, Kooistra AJ, Wijnen LM, Vreeker GCM, Verweij EWE, De Boer AH, Smit MJ, De Graaf C, Vischer HF, de Esch IJP, Wijtmans M, Leurs R. Synthesis and Characterization of a Bidirectional Photoswitchable Antagonist Toolbox for Real-Time GPCR Photopharmacology. J Am Chem Soc 2018; 140:4232-4243. [PMID: 29470065 PMCID: PMC5879491 DOI: 10.1021/jacs.7b11422] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Noninvasive methods
to modulate G protein-coupled receptors (GPCRs)
with temporal and spatial precision are in great demand. Photopharmacology
uses photons to control in situ the biological properties
of photoswitchable small-molecule ligands, which bodes well for chemical
biological precision approaches. Integrating the light-switchable
configurational properties of an azobenzene into the ligand core,
we developed a bidirectional antagonist toolbox for an archetypical
family A GPCR, the histamine H3 receptor (H3R). From 16 newly synthesized photoswitchable compounds, VUF14738
(28) and VUF14862 (33) were selected as
they swiftly and reversibly photoisomerize and show over 10-fold increased
or decreased H3R binding affinities, respectively, upon
illumination at 360 nm. Both ligands combine long thermal half-lives
with fast and high photochemical trans-/cis conversion, allowing their use in real-time electrophysiology experiments
with oocytes to confirm dynamic photomodulation of H3R
activation in repeated second-scale cycles. VUF14738 and VUF14862
are robust and fatigue-resistant photoswitchable GPCR antagonists
suitable for spatiotemporal studies of H3R signaling.
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Affiliation(s)
- Niels J Hauwert
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Tamara A M Mocking
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Daniel Da Costa Pereira
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Lisa M Wijnen
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Gerda C M Vreeker
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Eléonore W E Verweij
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Albertus H De Boer
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Martine J Smit
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Chris De Graaf
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Henry F Vischer
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Maikel Wijtmans
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
| | - Rob Leurs
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Faculty of Science , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ Amsterdam , The Netherlands
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53
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Srivastava A, Debnath A. Hydration dynamics of a lipid membrane: Hydrogen bond networks and lipid-lipid associations. J Chem Phys 2018. [DOI: 10.1063/1.5011803] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- Abhinav Srivastava
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
| | - Ananya Debnath
- Department of Chemistry, Indian Institute of Technology Jodhpur, Karwad, Rajasthan, India
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54
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Navarro G, Cordomí A, Brugarolas M, Moreno E, Aguinaga D, Pérez-Benito L, Ferre S, Cortés A, Casadó V, Mallol J, Canela EI, Lluís C, Pardo L, McCormick PJ, Franco R. Cross-communication between G i and G s in a G-protein-coupled receptor heterotetramer guided by a receptor C-terminal domain. BMC Biol 2018; 16:24. [PMID: 29486745 PMCID: PMC6389107 DOI: 10.1186/s12915-018-0491-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/22/2018] [Indexed: 12/02/2022] Open
Abstract
Background G-protein-coupled receptor (GPCR) heteromeric complexes have distinct properties from homomeric GPCRs, giving rise to new receptor functionalities. Adenosine receptors (A1R or A2AR) can form A1R-A2AR heteromers (A1-A2AHet), and their activation leads to canonical G-protein-dependent (adenylate cyclase mediated) and -independent (β-arrestin mediated) signaling. Adenosine has different affinities for A1R and A2AR, allowing the heteromeric receptor to detect its concentration by integrating the downstream Gi- and Gs-dependent signals. cAMP accumulation and β-arrestin recruitment assays have shown that, within the complex, activation of A2AR impedes signaling via A1R. Results We examined the mechanism by which A1-A2AHet integrates Gi- and Gs-dependent signals. A1R blockade by A2AR in the A1-A2AHet is not observed in the absence of A2AR activation by agonists, in the absence of the C-terminal domain of A2AR, or in the presence of synthetic peptides that disrupt the heteromer interface of A1-A2AHet, indicating that signaling mediated by A1R and A2AR is controlled by both Gi and Gs proteins. Conclusions We identified a new mechanism of signal transduction that implies a cross-communication between Gi and Gs proteins guided by the C-terminal tail of the A2AR. This mechanism provides the molecular basis for the operation of the A1-A2AHet as an adenosine concentration-sensing device that modulates the signals originating at both A1R and A2AR. Electronic supplementary material The online version of this article (10.1186/s12915-018-0491-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gemma Navarro
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Marc Brugarolas
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Estefanía Moreno
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - David Aguinaga
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Sergi Ferre
- Integrative Neurobiology Section, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Antoni Cortés
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Vicent Casadó
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Josefa Mallol
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Enric I Canela
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Carme Lluís
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain.,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain.,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Peter J McCormick
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain. .,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain. .,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain. .,School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, UK.
| | - Rafael Franco
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas, University of Barcelona, 08028, Barcelona, Spain. .,Institute of Biomedicine of the University of Barcelona (IBUB), University of Barcelona, 08028, Barcelona, Spain. .,Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, 08028, Barcelona, Spain.
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55
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Stoddart LA, Vernall AJ, Bouzo-Lorenzo M, Bosma R, Kooistra AJ, de Graaf C, Vischer HF, Leurs R, Briddon SJ, Kellam B, Hill SJ. Development of novel fluorescent histamine H 1-receptor antagonists to study ligand-binding kinetics in living cells. Sci Rep 2018; 8:1572. [PMID: 29371669 PMCID: PMC5785503 DOI: 10.1038/s41598-018-19714-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/03/2018] [Indexed: 01/01/2023] Open
Abstract
The histamine H1-receptor (H1R) is an important mediator of allergy and inflammation. H1R antagonists have particular clinical utility in allergic rhinitis and urticaria. Here we have developed six novel fluorescent probes for this receptor that are very effective for high resolution confocal imaging, alongside bioluminescence resonance energy transfer approaches to monitor H1R ligand binding kinetics in living cells. The latter technology exploits the opportunities provided by the recently described bright bioluminescent protein NanoLuc when it is fused to the N-terminus of a receptor. Two different pharmacophores (mepyramine or the fragment VUF13816) were used to generate fluorescent H1R antagonists conjugated via peptide linkers to the fluorophore BODIPY630/650. Kinetic properties of the probes showed wide variation, with the VUF13816 analogues having much longer H1R residence times relative to their mepyramine-based counterparts. The kinetics of these fluorescent ligands could also be monitored in membrane preparations providing new opportunities for future drug discovery applications.
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Affiliation(s)
- Leigh A Stoddart
- Division of Pharmacology Physiology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Midlands, UK
| | - Andrea J Vernall
- School of Pharmacy, Division of Biomolecular Science and Medicinal Chemistry, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Monica Bouzo-Lorenzo
- Division of Pharmacology Physiology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Midlands, UK
| | - Reggie Bosma
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, PO Box 7161, Amsterdam, The Netherlands
| | - Albert J Kooistra
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, PO Box 7161, Amsterdam, The Netherlands
| | - Chris de Graaf
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, PO Box 7161, Amsterdam, The Netherlands
| | - Henry F Vischer
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, PO Box 7161, Amsterdam, The Netherlands
| | - Rob Leurs
- Department of Chemistry and Pharmaceutical Sciences, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit, Amsterdam, PO Box 7161, Amsterdam, The Netherlands
| | - Stephen J Briddon
- Division of Pharmacology Physiology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Midlands, UK
| | - Barrie Kellam
- School of Pharmacy, Division of Biomolecular Science and Medicinal Chemistry, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, NG7 2RD, UK.
- Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Midlands, UK.
| | - Stephen J Hill
- Division of Pharmacology Physiology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK.
- Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, Midlands, UK.
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56
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Distinct modulation of inactivation by a residue in the pore domain of voltage-gated Na + channels: mechanistic insights from recent crystal structures. Sci Rep 2018; 8:631. [PMID: 29330525 PMCID: PMC5766632 DOI: 10.1038/s41598-017-18919-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/18/2017] [Indexed: 12/19/2022] Open
Abstract
Inactivation of voltage-gated Na+ channels (VGSC) is essential for the regulation of cellular excitability. The molecular rearrangement underlying inactivation is thought to involve the intracellular linker between domains III and IV serving as inactivation lid, the receptor for the lid (domain III S4-S5 linker) and the pore-lining S6 segements. To better understand the role of the domain IV S6 segment in inactivation we performed a cysteine scanning mutagenesis of this region in rNav 1.4 channels and screened the constructs for perturbations in the voltage-dependence of steady state inactivation. This screen was performed in the background of wild-type channels and in channels carrying the mutation K1237E, which profoundly alters both permeation and gating-properties. Of all tested constructs the mutation I1581C was unique in that the mutation-induced gating changes were strongly influenced by the mutational background. This suggests that I1581 is involved in specific short-range interactions during inactivation. In recently published crystal structures VGSCs the respective amino acids homologous to I1581 appear to control a bend of the S6 segment which is critical to the gating process. Furthermore, I1581 may be involved in the transmission of the movement of the DIII voltage-sensor to the domain IV S6 segment.
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57
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Izquierdo C, Gómez-Tamayo JC, Nebel JC, Pardo L, Gonzalez A. Identifying human diamine sensors for death related putrescine and cadaverine molecules. PLoS Comput Biol 2018; 14:e1005945. [PMID: 29324768 PMCID: PMC5783396 DOI: 10.1371/journal.pcbi.1005945] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/24/2018] [Accepted: 12/28/2017] [Indexed: 12/21/2022] Open
Abstract
Pungent chemical compounds originating from decaying tissue are strong drivers of animal behavior. Two of the best-characterized death smell components are putrescine (PUT) and cadaverine (CAD), foul-smelling molecules produced by decarboxylation of amino acids during decomposition. These volatile polyamines act as ‘necromones’, triggering avoidance or attractive responses, which are fundamental for the survival of a wide range of species. The few studies that have attempted to identify the cognate receptors for these molecules have suggested the involvement of the seven-helix trace amine-associated receptors (TAARs), localized in the olfactory epithelium. However, very little is known about the precise chemosensory receptors that sense these compounds in the majority of organisms and the molecular basis of their interactions. In this work, we have used computational strategies to characterize the binding between PUT and CAD with the TAAR6 and TAAR8 human receptors. Sequence analysis, homology modeling, docking and molecular dynamics studies suggest a tandem of negatively charged aspartates in the binding pocket of these receptors which are likely to be involved in the recognition of these small biogenic diamines. The distinctive dead smell comes largely from molecules like cadaverine and putrescine that are produced during decomposition of organic tissues. These volatile compounds act as powerful chemical signals important for the survival of a wide range of species. Previous studies have identified the trace amine-associated receptor 13c (or TAAR13c) in zebrafish as the cognate receptor of cadaverine in bony fishes. In this work, we employed computational strategies to disclose the human TAAR6 and TAAR8 receptors as sensors of the putrescine and cadaverine molecules. Our results indicate that several negatively charged residues in the ligand binding pocket of these receptors constitute the molecular basis for recognition of these necromones in humans.
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Affiliation(s)
- Cristina Izquierdo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - José C. Gómez-Tamayo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Jean-Christophe Nebel
- Faculty of Science, Engineering and Computing, Kingston University, London, United Kingdom
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Angel Gonzalez
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
- * E-mail:
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58
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Vickery ON, Carvalheda CA, Zaidi SA, Pisliakov AV, Katritch V, Zachariae U. Intracellular Transfer of Na + in an Active-State G-Protein-Coupled Receptor. Structure 2018; 26:171-180.e2. [PMID: 29249607 PMCID: PMC5805466 DOI: 10.1016/j.str.2017.11.013] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Revised: 10/13/2017] [Accepted: 11/15/2017] [Indexed: 01/01/2023]
Abstract
Playing a central role in cell signaling, G-protein-coupled receptors (GPCRs) are the largest superfamily of membrane proteins and form the majority of drug targets in humans. How extracellular agonist binding triggers the activation of GPCRs and associated intracellular effector proteins remains, however, poorly understood. Structural studies have revealed that inactive class A GPCRs harbor a conserved binding site for Na+ ions in the center of their transmembrane domain, accessible from the extracellular space. Here, we show that the opening of a conserved hydrated channel in the activated state receptors allows the Na+ ion to egress from its binding site into the cytosol. Coupled with protonation changes, this ion movement occurs without significant energy barriers, and can be driven by physiological transmembrane ion and voltage gradients. We propose that Na+ ion exchange with the cytosol is a key step in GPCR activation. Further, we hypothesize that this transition locks receptors in long-lived active-state conformations.
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Affiliation(s)
- Owen N Vickery
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK
| | - Catarina A Carvalheda
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK
| | - Saheem A Zaidi
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrei V Pisliakov
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK
| | - Vsevolod Katritch
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA; Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Ulrich Zachariae
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK; School of Science and Engineering, University of Dundee, Dundee DD1 4NH, UK.
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59
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Dourado DFAR, Swart M, Carvalho ATP. Why the Flavin Adenine Dinucleotide (FAD) Cofactor Needs To Be Covalently Linked to Complex II of the Electron-Transport Chain for the Conversion of FADH 2 into FAD. Chemistry 2017; 24:5246-5252. [PMID: 29124817 PMCID: PMC5969107 DOI: 10.1002/chem.201704622] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/07/2017] [Indexed: 11/10/2022]
Abstract
A covalently bound flavin cofactor is predominant in the succinate‐ubiquinone oxidoreductase (SQR; Complex II), an essential component of aerobic electron transport, and in the menaquinol‐fumarate oxidoreductase (QFR), the anaerobic counterpart, although it is only present in approximately 10 % of the known flavoenzymes. This work investigates the role of this 8α‐N3‐histidyl linkage between the flavin adenine dinucleotide (FAD) cofactor and the respiratory Complex II. After parameterization with DFT calculations, classical molecular‐dynamics simulations and quantum‐mechanics calculations for Complex II:FAD and Complex II:FADH2, with and without the covalent bond, were performed. It was observed that the covalent bond is essential for the active‐center arrangement of the FADH2/FAD cofactor. Removal of this bond causes a displacement of the isoalloxazine group, which influences interactions with the protein, flavin solvation, and possible proton‐transfer pathways. Specifically, for the noncovalently bound FADH2 cofactor, the N1 atom moves away from the His‐A365 and His‐A254 residues and the N5 atom moves away from the glutamine‐62A residue. Both of the histidine and glutamine residues interact with a chain of water molecules that cross the enzyme, which is most likely involved in proton transfer. Breaking this chain of water molecules could thereby compromise proton transfer across the two active sites of Complex II.
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Affiliation(s)
- Daniel F A R Dourado
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Stranmillis Road, Belfast, BT9 5AG, Northern Ireland, UK.,Almac Sciences, Department of Biocatalysis and Isotope Chemistry, Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, Northern Ireland, UK
| | - Marcel Swart
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, 17003, Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Alexandra T P Carvalho
- CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504, Coimbra, Portugal
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60
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Tamburrino G, Llabrés S, Vickery ON, Pitt SJ, Zachariae U. Modulation of the Neisseria gonorrhoeae drug efflux conduit MtrE. Sci Rep 2017; 7:17091. [PMID: 29213101 PMCID: PMC5719041 DOI: 10.1038/s41598-017-16995-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 11/21/2017] [Indexed: 11/09/2022] Open
Abstract
Widespread antibiotic resistance, especially of Gram-negative bacteria, has become a severe concern for human health. Tripartite efflux pumps are one of the major contributors to resistance in Gram-negative pathogens, by efficiently expelling a broad spectrum of antibiotics from the organism. In Neisseria gonorrhoeae, one of the first bacteria for which pan-resistance has been reported, the most expressed efflux complex is MtrCDE. Here we present the electrophysiological characterisation of the outer membrane component MtrE and the membrane fusion protein MtrC, obtained by a combination of planar lipid bilayer recordings and in silico techniques. Our in vitro results show that MtrE can be regulated by periplasmic binding events and that the interaction between MtrE and MtrC is sufficient to stabilize this complex in an open state. In contrast to other efflux conduits, the open complex only displays a slight preference for cations. The maximum conductance we obtain in the in vitro recordings is comparable to that seen in our computational electrophysiology simulations conducted on the MtrE crystal structure, indicating that this state may reflect a physiologically relevant open conformation of MtrE. Our results suggest that the MtrC/E binding interface is an important modulator of MtrE function, which could potentially be targeted by new efflux inhibitors.
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Affiliation(s)
- Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Physics, School of Science and Engineering, University of Dundee, Dundee, DD1 4NH, UK
| | - Salomé Llabrés
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Physics, School of Science and Engineering, University of Dundee, Dundee, DD1 4NH, UK
| | - Owen N Vickery
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Physics, School of Science and Engineering, University of Dundee, Dundee, DD1 4NH, UK
| | - Samantha J Pitt
- School of Medicine, University of St Andrews, St Andrews, KY16 9TF, UK.
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
- Physics, School of Science and Engineering, University of Dundee, Dundee, DD1 4NH, UK.
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Chaudhary A, Yadav BS, Singh S, Maurya PK, Mishra A, Srivastva S, Varadwaj PK, Singh NK, Mani A. Docking-based Screening of Ficus religiosa Phytochemicals as Inhibitors of Human Histamine H2 Receptor. Pharmacogn Mag 2017; 13:S706-S714. [PMID: 29142437 PMCID: PMC5669120 DOI: 10.4103/pm.pm_49_17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/21/2017] [Indexed: 11/11/2022] Open
Abstract
Background: Ficus religiosa L. is generally known as Peepal and belongs to family Moraceae. The tree is a source of many compounds having high medicinal value. In gastrointestinal tract, histamine H2 receptors have key role in histamine-stimulated gastric acid secretion. Their over stimulation causes its excessive production which is responsible for gastric ulcer. Objective: This study aims to screen the range of phytochemicals present in F. religiosa for binding with human histamine H2 and identify therapeutics for a gastric ulcer from the plant. Materials and Methods: In this work, a 3D-structure of human histamine H2 receptor was modeled by using homology modeling and the predicted model was validated using PROCHECK. Docking studies were also performed to assess binding affinities between modeled receptor and 34 compounds. Molecular dynamics simulations were done to identify most stable receptor-ligand complexes. Absorption, distribution, metabolism, excretion, and screening was done to evaluate pharmacokinetic properties of compounds. Results: The results suggest that seven ligands, namely, germacrene, bergaptol, lanosterol, Ergost-5-en-3beta-ol, α-amyrin acetate, bergapten, and γ-cadinene showed better binding affinities. Conclusion: Among seven phytochemicals, lanosterol and α-amyrin acetate were found to have greater stability during simulation studies. These two compounds may be a suitable therapeutic agent against histamine H2 receptor. SUMMARY This study was performed to screen antiulcer compounds from F. religiosa. Molecular modeling, molecular docking and MD simulation studies were performed with selected phytochemicals from F. religiosa. The analysis suggests that Lanosterol and α-amyrin may be a suitable therapeutic agent against histamine H2 receptor. This study facilitates initiation of the herbal drug discovery process for the antiulcer activity.
Abbreviations used: ADMET: Absorption, distribution, metabolism, excretion and toxicity, DOPE: Discrete Optimized Potential Energy, OPLS: Optimized potential for liquid simulations, RMSD: Root-mean-square deviation, HOA: Human oral absorption, MW: Molecular weight, SP: Standard-precision, XP: Extra-precision, GPCRs: G protein-coupled receptors, SASA: Solvent accessible surface area, Rg: Radius of gyration, NHB: Number of hydrogen bond
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Affiliation(s)
- Amit Chaudhary
- Department of Biotechnology, MNNIT, Allahabad, Uttar Pradesh, India
| | | | - Swati Singh
- Center of Bioinformatics, University of Allahabad, Allahabad, Uttar Pradesh, India
| | | | - Alok Mishra
- Department of Biotechnology, MNNIT, Allahabad, Uttar Pradesh, India
| | - Shweta Srivastva
- Department of Biotechnology, MNNIT, Allahabad, Uttar Pradesh, India
| | | | - Nand Kumar Singh
- Department of Biotechnology, MNNIT, Allahabad, Uttar Pradesh, India
| | - Ashutosh Mani
- Department of Biotechnology, MNNIT, Allahabad, Uttar Pradesh, India
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Qaradakhi T, Matsoukas MT, Hayes A, Rybalka E, Caprnda M, Rimarova K, Sepsi M, Büsselberg D, Kruzliak P, Matsoukas J, Apostolopoulos V, Zulli A. Alamandine reverses hyperhomocysteinemia-induced vascular dysfunction via PKA-dependent mechanisms. Cardiovasc Ther 2017; 35. [PMID: 28901725 DOI: 10.1111/1755-5922.12306] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 08/30/2017] [Accepted: 09/08/2017] [Indexed: 11/29/2022] Open
Abstract
INTRODUCTION Hyperhomocysteinemia (HHcy) impairs nitric oxide endothelium-dependent vasodilation, consequently leading to atherosclerosis, a risk factor for cardiovascular disease. Novel treatments for HHcy are necessary. AIM We tested the hypothesis that alamandine, a vasoactive peptide of the renin-angiotensin system (RAS), could reverse HHcy-induced vascular dysfunction through the MrgD receptor and that this is mediated by the protein kinase A (PKA) pathway. Furthermore, we sought to determine a putative binding model of alamandine to the MrgD receptor through docking and molecular dynamics simulations. METHOD The abdominal aorta was excised from New Zealand white rabbits (n = 15) and incubated with 3 mmol/L Hcy (to mimic HHcy) to induce vascular dysfunction in vitro. Vascular function was assessed by vasodilatory responses to cumulative doses of acetylcholine. RESULT Vasodilation was significantly impaired in HHcy-incubated aortic rings while alamandine reversed this effect (control, 74.2 ± 5.0%; Hcy, 30.3 ± 9.8%; alamandine + Hcy, 59.7 ± 4.8%, P < .0001). KT5720 (PKA inhibitor) significantly inhibited the ability of alamandine to attenuate the impaired vasodilation caused by HHcy (KT5720 + Hcy + alamandine, 27.1 ± 24.1, P < .01). Following immunohistochemistry analysis, the MrgD receptor was highly expressed within the media and endothelial layer of aortic rings in HHcy compared to control (media: 0.23 ± 0.003 vs control 0.16 ± 0.01, P < .05 and endothelium: 0.68 ± 0.07 vs control 0.13 ± 0.02, P < .01, in PA/I (A.U) units). Computational studies also propose certain interactions of alamandine within the MrgD transmembrane domain. CONCLUSION This study shows that alamandine is effective in reversing HHcy-induced vascular dysfunction, possibly through the PKA signaling pathway via MrgD. Our results indicate a therapeutic potential of alamandine in reversing the detrimental effects of HHcy.
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Affiliation(s)
- Tawar Qaradakhi
- Centre for Chronic Disease, College of Health and Biomedicine, Victoria University, Melbourne, Vic., Australia
| | | | - Alan Hayes
- Centre for Chronic Disease, College of Health and Biomedicine, Victoria University, Melbourne, Vic., Australia
| | - Emma Rybalka
- Centre for Chronic Disease, College of Health and Biomedicine, Victoria University, Melbourne, Vic., Australia
| | - Martin Caprnda
- 2nd Department of Internal Medicine, Faculty of Medicine, Comenius University, Bratislava, Slovakia
| | - Kvetoslava Rimarova
- Department of Public Health and Hygiene, Faculty of Medicine, Pavol Jozef Safarik University, Kosice, Slovakia
| | - Milan Sepsi
- Department of Internal Medicine and Cardiology, University Hospital, Brno, Czech Republic
| | - Dietrich Büsselberg
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Qatar Foundation - Education City, Doha, Qatar
| | - Peter Kruzliak
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
| | | | - Vasso Apostolopoulos
- Centre for Chronic Disease, College of Health and Biomedicine, Victoria University, Melbourne, Vic., Australia
| | - Anthony Zulli
- Centre for Chronic Disease, College of Health and Biomedicine, Victoria University, Melbourne, Vic., Australia
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Zhu W, Khalifa I, Peng J, Li C. Position and orientation of gallated proanthocyanidins in lipid bilayer membranes: influence of polymerization degree and linkage type. J Biomol Struct Dyn 2017; 36:2862-2875. [DOI: 10.1080/07391102.2017.1369163] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Wei Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Ibrahim Khalifa
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinming Peng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Chunmei Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Environment Correlative Food Science, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
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Zhu W, Deng X, Peng J, Zou B, Li C. A-type ECG and EGCG dimers inhibit 3T3-L1 differentiation by binding to cholesterol in lipid rafts. J Nutr Biochem 2017; 48:62-73. [PMID: 28772148 DOI: 10.1016/j.jnutbio.2017.06.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 04/26/2017] [Accepted: 06/21/2017] [Indexed: 12/21/2022]
Abstract
The present study aimed to explore the underlying mechanisms of epicatechin-3-gallate-(4β→8, 2β→O→7)-epicatechin-3-gallate (A-type ECG dimer) and epigallocatechin-3-gallate-(4β→8, 2β→O→7)-epigallocatechin-3-gallate (A-type EGCG dimer) involved in their strong inhibitory effects on 3T3-L1 preadipocytes differentiation. In the synthetic "lipid raft-like" liposome, A-type ECG and EGCG dimers incorporated into the liposome with high affinity and decreased the fluidity of the liposome. In 3T3-L1 preadipocytes, A-type ECG and EGCG dimers possibly bonded to lipid rafts cholesterol and disrupted the integrity of lipid rafts, thus exerting their notable inhibitory effects on 3T3-L1 preadipocytes differentiation by suppressing mitotic clonal expansion process and mRNA levels of PPARγ, C/EBPα and SREBP1C. A highly positive correlation between the cholesterol binding capacity of the two dimers and their inhibitory effect on 3T3-L1 preadipocytes differentiation (R2=0.9328) was observed. Molecular dynamics simulation further verified that A-type ECG and EGCG dimers could bond to cholesterol via hydrogen bonding. The results of this study suggested that the disruption of A-type ECG and EGCG dimers on membrane lipid rafts by targeting cholesterol in the lipid rafts was involved in the underlying mechanisms of their strong inhibitory effects on 3T3-L1 preadipocytes differentiation. This broadens the understanding of the molecular mechanisms of polyphenols on modulating and controlling of metabolic dysregulation, particularly adipocyte differentiation, which is a significant risk factor associated with the development of cardiovascular disease.
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Affiliation(s)
- Wei Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China, 430070
| | - Xiangyi Deng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China, 430070
| | - Jinming Peng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China, 430070
| | - Bo Zou
- Sericultural & Agri-food Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China, 510610
| | - Chunmei Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China, 430070; Key Laboratory of Environment Correlative Food Science (Huazhong Agricultural University), Ministry of Education.
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Abstract
The 97 amino acid bitopic membrane protein M2 of influenza A forms a tetrameric bundle in which two of the monomers are covalently linked via a cysteine bridge. In its tetrameric assembly the protein conducts protons across the viral envelope and within intracellular compartments during the infectivity cycle of the virus. A key residue in the translocation of the protons is His-37 which forms a planar tetrad in the configuration of the bundle accepting and translocating the incoming protons from the N terminal side, exterior of the virus, to the C terminal side, inside the virus. With experimentally available data from NMR spectroscopy of the transmembrane domains of the tetrameric M2 bundle classical MD simulations are conducted with the protein bundle in different protonation stages in respect to His-37. A full correlation analysis (FCA) of the data sets with the His-37 tetrad either in a fully four times unprotonated or protonated state, assumed to mimic high and low pH in vivo, respectively, in both cases reveal asymmetric backbone dynamics. His-37 side chain rotation dynamics is increased at full protonation of the tetrad compared to the dynamics in the fully unprotonated state. The data suggest that proton translocation can be achieved by decoupled side chain or backbone dynamics. Graphical abstract Visualization of the tetrameric bundle of the transmembrane domains of M2 of influenza A after 200 ns of MD simulations (upper left). The four histidine residues 37 are either not protonated as in M20 or fully protonated is in M24+. The asymmetric dynamics of the backbones are shown after a full correlation analysis (FCA) in blue (lower left). The rotational dynamics of the χ2 dihedral angles of the histidines in M20 (upper right) are less than those in M24+ (lower right).
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Affiliation(s)
- Monoj Mon Kalita
- Institute of Biophotonics and Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, 155, Li-Nong St., Sec. 2, Taipei, 112, Taiwan
| | - Wolfgang B Fischer
- Institute of Biophotonics and Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, 155, Li-Nong St., Sec. 2, Taipei, 112, Taiwan.
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Aponte-Santamaría C, Fischer G, Båth P, Neutze R, de Groot BL. Temperature dependence of protein-water interactions in a gated yeast aquaporin. Sci Rep 2017; 7:4016. [PMID: 28638135 PMCID: PMC5479825 DOI: 10.1038/s41598-017-04180-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/10/2017] [Indexed: 11/18/2022] Open
Abstract
Regulation of aquaporins is a key process of living organisms to counteract sudden osmotic changes. Aqy1, which is a water transporting aquaporin of the yeast Pichia pastoris, is suggested to be gated by chemo-mechanical stimuli as a protective regulatory-response against rapid freezing. Here, we tested the influence of temperature by determining the X-ray structure of Aqy1 at room temperature (RT) at 1.3 Å resolution, and by exploring the structural dynamics of Aqy1 during freezing through molecular dynamics simulations. At ambient temperature and in a lipid bilayer, Aqy1 adopts a closed conformation that is globally better described by the RT than by the low-temperature (LT) crystal structure. Locally, for the blocking-residue Tyr31 and the water molecules inside the pore, both LT and RT data sets are consistent with the positions observed in the simulations at room-temperature. Moreover, as the temperature was lowered, Tyr31 adopted a conformation that more effectively blocked the channel, and its motion was accompanied by a temperature-driven rearrangement of the water molecules inside the channel. We therefore speculate that temperature drives Aqy1 from a loosely- to a tightly-blocked state. This analysis provides high-resolution structural evidence of the influence of temperature on membrane-transport channels.
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Affiliation(s)
- Camilo Aponte-Santamaría
- Molecular Biomechanics Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Heidelberg, Germany.
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia.
| | - Gerhard Fischer
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petra Båth
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Richard Neutze
- Department of Chemistry & Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
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Kumari S, Chowdhury J, Sikka M, Verma P, Jha P, Mishra AK, Saluja D, Chopra M. Identification of potent cholecystokinin-B receptor antagonists: synthesis, molecular modeling and anti-cancer activity against pancreatic cancer cells. MEDCHEMCOMM 2017; 8:1561-1574. [PMID: 30108868 DOI: 10.1039/c7md00171a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 06/02/2017] [Indexed: 12/12/2022]
Abstract
Advanced malignant stages of pancreatic cancer have poor prognosis and very few treatment strategies are available. Pancreatic cancer is known to possess unique growth-related receptors that when activated, stimulate tumour proliferation. Gastrin and its related peptide cholecystokinin (CCK) are also significantly involved in the growth of this cancer type as well as other malignancies through activation of the cholecystokinin-B receptor (CCK-BR). New treatment strategies with CCK-BR antagonists are being suggested that suppress the growth promoting effects of gastrin. In this paper, we report the development of two series of quinazolinone derivatives incorporating hydrazinecarbothioamide (compounds 3a-g) and the hydrazino group (compounds 4a-e) as linkers for developing CCK-BR antagonists. The affinities of the compounds were determined using docking into the CCK-BR homology modeled structure. The compounds were tested for in vitro CCK-BR binding and gastric acid secretion in an isolated lumen-perfused mouse stomach assay. The compounds exhibited CCK-BR binding activity (IC50) in the range of 0.2-975 nM and showed good gastric acid secretion inhibitory activity. Molecular modeling of the compounds was done and pharmacophore mapping results showed good prediction of in vitro activity which correlated well with the experimental antagonistic activity. The compounds were further tested for their cytotoxicity on CCK-BR expressing pancreatic cancer cells. The results of the study provided two potent CCK-BR antagonists which also possess good to moderate growth inhibitory activities against pancreatic cancer cells.
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Affiliation(s)
- Saroj Kumari
- Laboratory of Anticancer Drug Development , Dr. B. R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi 110007 , India . ;
| | - Joyita Chowdhury
- Laboratory of Anticancer Drug Development , Dr. B. R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi 110007 , India . ;
| | - Manisha Sikka
- Laboratory of Anticancer Drug Development , Dr. B. R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi 110007 , India . ;
| | - Priyanka Verma
- Laboratory of Anticancer Drug Development , Dr. B. R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi 110007 , India . ;
| | - Prakash Jha
- Laboratory of Anticancer Drug Development , Dr. B. R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi 110007 , India . ;
| | - Anil K Mishra
- Institute of Nuclear Medicine and Allied Sciences , Brig. S. K. Majumdar Road , Delhi 110054 , India
| | - Daman Saluja
- Laboratory of Anticancer Drug Development , Dr. B. R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi 110007 , India . ;
| | - Madhu Chopra
- Laboratory of Anticancer Drug Development , Dr. B. R. Ambedkar Center for Biomedical Research , University of Delhi , Delhi 110007 , India . ;
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Marsango S, Caltabiano G, Jiménez-Rosés M, Millan MJ, Pediani JD, Ward RJ, Milligan G. A Molecular Basis for Selective Antagonist Destabilization of Dopamine D 3 Receptor Quaternary Organization. Sci Rep 2017; 7:2134. [PMID: 28522847 PMCID: PMC5437050 DOI: 10.1038/s41598-017-02249-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/07/2017] [Indexed: 12/17/2022] Open
Abstract
The dopamine D3 receptor (D3R) is a molecular target for both first-generation and several recently-developed antipsychotic agents. Following stable expression of this mEGFP-tagged receptor, Spatial Intensity Distribution Analysis indicated that a substantial proportion of the receptor was present within dimeric/oligomeric complexes and that increased expression levels of the receptor favored a greater dimer to monomer ratio. Addition of the antipsychotics, spiperone or haloperidol, resulted in re-organization of D3R quaternary structure to promote monomerization. This action was dependent on ligand concentration and reversed upon drug washout. By contrast, a number of other antagonists with high affinity at the D3R, did not alter the dimer/monomer ratio. Molecular dynamics simulations following docking of each of the ligands into a model of the D3R derived from the available atomic level structure, and comparisons to the receptor in the absence of ligand, were undertaken. They showed that, in contrast to the other antagonists, spiperone and haloperidol respectively increased the atomic distance between reference α carbon atoms of transmembrane domains IV and V and I and II, both of which provide key interfaces for D3R dimerization. These results offer a molecular explanation for the distinctive ability of spiperone and haloperidol to disrupt D3R dimerization.
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Affiliation(s)
- Sara Marsango
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
| | - Gianluigi Caltabiano
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Mireia Jiménez-Rosés
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Mark J Millan
- Institut de Recherches Servier, Centre for Innovation in Neuropsychiatry, 125 Chemin de Ronde, Croissy sur Seine, France, 78290
| | - John D Pediani
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Richard J Ward
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK.
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Troupiotis-Tsaïlaki A, Zachmann J, González-Gil I, Gonzalez A, Ortega-Gutiérrez S, López-Rodríguez ML, Pardo L, Govaerts C. Ligand chain length drives activation of lipid G protein-coupled receptors. Sci Rep 2017; 7:2020. [PMID: 28515494 PMCID: PMC5435731 DOI: 10.1038/s41598-017-02104-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/07/2017] [Indexed: 01/20/2023] Open
Abstract
Sphingosine-1-phosphate (S1P) is a lipid mediator that can activate five cell membrane G protein-coupled receptors (GPCRs) which carry a variety of essential functions and are promising drug targets. S1P is composed of a polar zwitterionic head-group and a hydrophobic alkyl chain. This implies an activation mechanism of its cognate receptor that must be significantly different from what is known for prototypical GPCRs (ie receptor to small hydrophilic ligands). Here we aim to identify the structural features responsible for S1P agonism by combining molecular dynamics simulations and functional assays using S1P analogs of different alkyl chain lengths. We propose that high affinity binding involves polar interactions between the lipid head-group and receptor side chains while activation is due to hydrophobic interactions between the lipid tail and residues in a distinct binding site. We observe that ligand efficacy is directly related to alkyl chain length but also varies with receptor subtypes in correlation with the size of this binding pocket. Integrating experimental and computational data, we propose an activation mechanism for the S1P receptors involving agonist-induced conformational events that are conserved throughout class A GPCRs.
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Affiliation(s)
| | - Julian Zachmann
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Inés González-Gil
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Angel Gonzalez
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Maria L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Cedric Govaerts
- Laboratoire de Structure et Fonction des Membranes Biologiques, Université Libre de Bruxelles, Brussels, Belgium.
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Zhang L, Kang H, Vázquez FX, Toledo-Sherman L, Luan B, Zhou R. Molecular Mechanism of Stabilizing the Helical Structure of Huntingtin N17 in a Micellar Environment. J Phys Chem B 2017; 121:4713-4721. [DOI: 10.1021/acs.jpcb.7b01476] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leili Zhang
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | - Hongsuk Kang
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | - Francisco X. Vázquez
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | | | - Binquan Luan
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
| | - Ruhong Zhou
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown
Heights, New York 10598, United States
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Brandani GB, Vance SJ, Schor M, Cooper A, Kennedy MW, Smith BO, MacPhee CE, Cheung DL. Adsorption of the natural protein surfactant Rsn-2 onto liquid interfaces. Phys Chem Chem Phys 2017; 19:8584-8594. [PMID: 28289744 DOI: 10.1039/c6cp07261e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
To stabilize foams, droplets and films at liquid interfaces a range of protein biosurfactants have evolved in nature. Compared to synthetic surfactants, these combine surface activity with biocompatibility and low solution aggregation. One recently studied example is Rsn-2, a component of the foam nest of the frog Engystomops pustulosus, which has been predicted to undergo a clamshell-like opening transition at the air-water interface. Using atomistic molecular dynamics simulations and surface tension measurements we study the adsorption of Rsn-2 onto air-water and cyclohexane-water interfaces. The protein adsorbs readily at both interfaces, with adsorption mediated by the hydrophobic N-terminus. At the cyclohexane-water interface the clamshell opens, due to the favourable interaction between hydrophobic residues and cyclohexane molecules and the penetration of cyclohexane molecules into the protein core. Simulations of deletion mutants showed that removal of the N-terminus inhibits interfacial adsorption, which is consistent with the surface tension measurements. Deletion of the hydrophilic C-terminus also affects adsorption, suggesting that this plays a role in orienting the protein at the interface. The characterisation of the interfacial behaviour gives insight into the factors that control the interfacial adsorption of proteins, which may inform new applications of this and similar proteins in areas including drug delivery and food technology and may also be used in the design of synthetic molecules showing similar changes in conformation at interfaces.
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Affiliation(s)
- Giovanni B Brandani
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, UK.
| | - Steven J Vance
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Marieke Schor
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, UK.
| | - Alan Cooper
- School of Chemistry, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Malcolm W Kennedy
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Brian O Smith
- Institute of Molecular, Cell, and Systems Biology, University of Glasgow, G12 8QQ, UK.
| | - Cait E MacPhee
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, UK.
| | - David L Cheung
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, G1 1XL, UK and School of Chemistry, National University of Ireland Galway, Galway, Ireland.
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73
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Ariz-Extreme I, Hub JS. Potential of Mean Force Calculations of Solute Permeation Across UT-B and AQP1: A Comparison between Molecular Dynamics and 3D-RISM. J Phys Chem B 2017; 121:1506-1519. [PMID: 28128570 DOI: 10.1021/acs.jpcb.6b11279] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Membrane channels facilitate the efficient and selective flux of various solutes across biological membranes. A common approach to investigate the selectivity of a channel has been the calculation of potentials of mean force (PMFs) for solute permeation across the pore. PMFs have been frequently computed from molecular dynamics (MD) simulations, yet the three-dimensional reference interaction site model (3D-RISM) has been suggested as a computationally efficient alternative to MD. Whether the two methods yield comparable PMFs for solute permeation has remained unclear. In this study, we calculated potentials of mean force for water, ammonia, urea, molecular oxygen, and methanol across the urea transporter B (UT-B) and aquaporin-1 (AQP1), using 3D-RISM, as well as using MD simulations and umbrella sampling. To allow direct comparison between the PMFs from 3D-RISM and MD, we ensure that all PMFs refer to a well-defined reference area in the bulk or, equivalently, to a well-defined density of channels in the membrane. For PMFs of water permeation, we found reasonable agreement between the two methods, with differences of ≲3 kJ mol-1. In contrast, we found stark discrepancies for the PMFs for all other solutes. Additional calculations confirm that discrepancies between MD and 3D-RISM are not explained by the choice for the closure relation, the definition the reaction coordinate (center of mass-based versus atomic site-based), details of the molecule force field, or fluctuations of the protein. Comparison of the PMFs suggests that 3D-RISM may underestimate effects from hydrophobic solute-channel interactions, thereby, for instance, missing the urea binding sites in UT-B. Furthermore, we speculate that the orientational averages inherent to 3D-RISM might lead to discrepancies in the narrow channel lumen. These findings suggest that current 3D-RISM solvers provide reasonable estimates for the PMF for water permeation, but that they are not suitable to study the selectivity of membrane channels with respect to uncharged nonwater solutes.
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Affiliation(s)
- Igor Ariz-Extreme
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
| | - Jochen S Hub
- Institute for Microbiology and Genetics, Georg-August-Universität , 37077 Göttingen, Germany
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74
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González-Vera JA, Medina RA, Martín-Fontecha M, Gonzalez A, de la Fuente T, Vázquez-Villa H, García-Cárceles J, Botta J, McCormick PJ, Benhamú B, Pardo L, López-Rodríguez ML. A new serotonin 5-HT 6 receptor antagonist with procognitive activity - Importance of a halogen bond interaction to stabilize the binding. Sci Rep 2017; 7:41293. [PMID: 28117458 PMCID: PMC5259792 DOI: 10.1038/srep41293] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/16/2016] [Indexed: 12/13/2022] Open
Abstract
Serotonin 5-HT6 receptor has been proposed as a promising therapeutic target for cognition enhancement though the development of new antagonists is still needed to validate these molecules as a drug class for the treatment of Alzheimer's disease and other pathologies associated with memory deficiency. As part of our efforts to target the 5-HT6 receptor, new benzimidazole-based compounds have been designed and synthesized. Site-directed mutagenesis and homology models show the importance of a halogen bond interaction between a chlorine atom of the new class of 5-HT6 receptor antagonists identified herein and a backbone carbonyl group in transmembrane domain 4. In vitro pharmacological characterization of 5-HT6 receptor antagonist 7 indicates high affinity and selectivity over a panel of receptors including 5-HT2B subtype and hERG channel, which suggests no major cardiac issues. Compound 7 exhibited in vivo procognitive activity (1 mg/kg, ip) in the novel object recognition task as a model of memory deficit.
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Affiliation(s)
- Juan A. González-Vera
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Rocío A. Medina
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Mar Martín-Fontecha
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Angel Gonzalez
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - Tania de la Fuente
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Javier García-Cárceles
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Joaquín Botta
- School of Pharmacy, University of East Anglia, NR4 7TJ Norwich, UK
| | | | - Bellinda Benhamú
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain
| | - María L. López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain
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75
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Bernsteiner H, Bründl M, Stary-Weinzinger A. Dynamics of the EAG1 K + channel selectivity filter assessed by molecular dynamics simulations. Biochem Biophys Res Commun 2017; 484:107-112. [PMID: 28109880 PMCID: PMC6531291 DOI: 10.1016/j.bbrc.2017.01.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 01/13/2017] [Indexed: 01/14/2023]
Abstract
EAG1 channels belong to the KCNH family of voltage gated potassium channels. They are expressed in several brain regions and increased expression is linked to certain cancer types. Recent cryo-EM structure determination finally revealed the structure of these channels in atomic detail, allowing computational investigations. In this study, we performed molecular dynamics simulations to investigate the ion binding sites and the dynamical behavior of the selectivity filter. Our simulations suggest that sites S2 and S4 form stable ion binding sites, while ions placed at sites S1 and S3 rapidly switched to sites S2 and S4. Further, ions tended to dissociate away from S0 within less than 20 ns, due to increased filter flexibility. This was followed by water influx from the extracellular side, leading to a widening of the filter in this region, and likely non-conductive filter configurations. Simulations with the inactivation-enhancing mutant Y464A or Na+ ions lead to trapped water molecules behind the SF, suggesting that these simulations captured early conformational changes linked to C-type inactivation.
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Affiliation(s)
- Harald Bernsteiner
- Department of Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Michael Bründl
- Department of Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Anna Stary-Weinzinger
- Department of Pharmacology and Toxicology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
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76
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Matsoukas MT, Spyroulias GA. Dynamic properties of the growth hormone releasing hormone receptor (GHRHR) and molecular determinants of GHRH binding. ACTA ACUST UNITED AC 2017; 13:1313-1322. [DOI: 10.1039/c7mb00130d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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77
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Zhu W, Xiong L, Peng J, Deng X, Gao J, Li CM. Molecular Insight into Affinities of Gallated and Nongallated Proanthocyanidins Dimers to Lipid Bilayers. Sci Rep 2016; 6:37680. [PMID: 27874097 PMCID: PMC5118708 DOI: 10.1038/srep37680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 11/01/2016] [Indexed: 12/22/2022] Open
Abstract
Experimental studies have proved the beneficial effects of proanthocyanidins (Pas) relating to interaction with the cell membrane. But the detailed mechanisms and structure-function relationship was unclear. In present study, molecular dynamics (MD) simulations were used to study the interactions of four PA dimers with a lipid bilayer composed of 1:1 mixed 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) and 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE). The results showed that the gallated PA dimers had much higher affinities to the bilayer with lower binding free energies compared with nongallated PA dimers. The gallated PA dimers penetrated deeper into the bilayer and formed more hydrogen bonds (H-bonds) with bilayer oxygen atoms, especially the deeper oxygen atoms of the lipids simultaneously, thus inducing stronger lateral expansion of the membrane and lipid tails disorder. The present results provided molecular insights into the interactions between PA dimers and bio-membranes and agreed with our experimental results well. These molecular interactions helped to elucidate the structure-function relationship of the PA dimers and provided a foundation for a better understanding of the underlying mechanisms of the bioactivities of PA oligomers.
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Affiliation(s)
- Wei Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Le Xiong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jinming Peng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiangyi Deng
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jun Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chun-Mei Li
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.,Key Laboratory of Environment Correlative Food Science, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
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78
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Hou J, Charron CL, Fowkes MM, Luyt LG. Bridging computational modeling with amino acid replacements to investigate GHS-R1a-peptidomimetic recognition. Eur J Med Chem 2016; 123:822-833. [DOI: 10.1016/j.ejmech.2016.07.078] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/13/2016] [Accepted: 07/31/2016] [Indexed: 12/26/2022]
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79
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Cid JM, Tresadern G, Vega JA, de Lucas AI, Del Cerro A, Matesanz E, Linares ML, García A, Iturrino L, Pérez-Benito L, Macdonald GJ, Oehlrich D, Lavreysen H, Peeters L, Ceusters M, Ahnaou A, Drinkenburg W, Mackie C, Somers M, Trabanco AA. Discovery of 8-Trifluoromethyl-3-cyclopropylmethyl-7-[(4-(2,4-difluorophenyl)-1-piperazinyl)methyl]-1,2,4-triazolo[4,3-a]pyridine (JNJ-46356479), a Selective and Orally Bioavailable mGlu2 Receptor Positive Allosteric Modulator (PAM). J Med Chem 2016; 59:8495-507. [PMID: 27579727 DOI: 10.1021/acs.jmedchem.6b00913] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Positive allosteric modulators of the metabotropic glutamate 2 receptor have generated great interest in the past decade. There is mounting evidence of their potential as therapeutic agents in the treatment of multiple central nervous system disorders. We have previously reported substantial efforts leading to potent and selective mGlu2 PAMs. However, finding compounds with the optimal combination of in vitro potency and good druglike properties has remained elusive, in part because of the hydrophobic nature of the allosteric binding site. Herein, we report on the lead optimization process to overcome the poor solubility inherent to the advanced lead 6. Initial prototypes already showed significant improvements in solubility while retaining good functional activity but displayed new liabilities associated with metabolism and hERG inhibition. Subsequent subtle modifications efficiently addressed those issues leading to the identification of compound 27 (JNJ-46356479). This new lead represents a more balanced profile that offers a significant improvement on the druglike attributes compared to previously reported leads.
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Affiliation(s)
- Jose María Cid
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Gary Tresadern
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Juan Antonio Vega
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Ana Isabel de Lucas
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Alcira Del Cerro
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Encarnación Matesanz
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - María Lourdes Linares
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Aránzazu García
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Laura Iturrino
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona , Bellaterra 08193, Spain
| | - Gregor J Macdonald
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Daniel Oehlrich
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Hilde Lavreysen
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Luc Peeters
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Marc Ceusters
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Abdellah Ahnaou
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | | | - Claire Mackie
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Marijke Somers
- Janssen Research & Development, Janssen Pharmaceutica NV, Beerse B-2340, Belgium
| | - Andrés A Trabanco
- Janssen Research & Development, a Division of Janssen-Cilag, S.A., Toledo 45007, Spain
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80
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Exploring new scaffolds for angiotensin II receptor antagonism. Bioorg Med Chem 2016; 24:4444-4451. [DOI: 10.1016/j.bmc.2016.07.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/19/2016] [Accepted: 07/20/2016] [Indexed: 11/21/2022]
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81
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Lee SJ, Ren F, Zangerl-Plessl EM, Heyman S, Stary-Weinzinger A, Yuan P, Nichols CG. Structural basis of control of inward rectifier Kir2 channel gating by bulk anionic phospholipids. J Gen Physiol 2016; 148:227-37. [PMID: 27527100 PMCID: PMC5004336 DOI: 10.1085/jgp.201611616] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 07/12/2016] [Indexed: 01/11/2023] Open
Abstract
Phospholipids are required to bind to two distinct sites on the inward rectifier potassium channel for maximal efficacy. Lee et al. show that a membrane-associating tryptophan residue in the second site can mimic the effect of phospholipid binding and cause a conformational change to reveal the primary binding site. Inward rectifier potassium (Kir) channel activity is controlled by plasma membrane lipids. Phosphatidylinositol-4,5-bisphosphate (PIP2) binding to a primary site is required for opening of classic inward rectifier Kir2.1 and Kir2.2 channels, but interaction of bulk anionic phospholipid (PL−) with a distinct second site is required for high PIP2 sensitivity. Here we show that introduction of a lipid-partitioning tryptophan at the second site (K62W) generates high PIP2 sensitivity, even in the absence of PL−. Furthermore, high-resolution x-ray crystal structures of Kir2.2[K62W], with or without added PIP2 (2.8- and 2.0-Å resolution, respectively), reveal tight tethering of the C-terminal domain (CTD) to the transmembrane domain (TMD) in each condition. Our results suggest a refined model for phospholipid gating in which PL− binding at the second site pulls the CTD toward the membrane, inducing the formation of the high-affinity primary PIP2 site and explaining the positive allostery between PL− binding and PIP2 sensitivity.
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Affiliation(s)
- Sun-Joo Lee
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Feifei Ren
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | | | - Sarah Heyman
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Anna Stary-Weinzinger
- Department of Pharmacology and Toxicology, University of Vienna, A-1090 Vienna, Austria
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
| | - Colin G Nichols
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110 Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO 63110
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82
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Prieß M, Schäfer LV. Release of Entropic Spring Reveals Conformational Coupling Mechanism in the ABC Transporter BtuCD-F. Biophys J 2016; 110:2407-2418. [PMID: 27276259 PMCID: PMC4906252 DOI: 10.1016/j.bpj.2016.04.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/30/2016] [Accepted: 04/20/2016] [Indexed: 01/14/2023] Open
Abstract
Substrate translocation by ATP-binding cassette (ABC) transporters involves coupling of ATP binding and hydrolysis in the nucleotide-binding domains (NBDs) to conformational changes in the transmembrane domains. We used molecular dynamics simulations to investigate the atomic-level mechanism of conformational coupling in the ABC transporter BtuCD-F, which imports vitamin B12 across the inner membrane of Escherichia coli. Our simulations show how an engineered disulfide bond across the NBD dimer interface reduces conformational fluctuations and hence configurational entropy. As a result, the disulfide bond is under substantial mechanical stress. Releasing this entropic spring, as is the case in the wild-type transporter, combined with analyzing the pairwise forces between individual residues, unravels the coupling mechanism. The identified pathways along which force is propagated from the NBDs via the coupling helix to the transmembrane domains are composed of highly conserved residues, underlining their functional relevance. This study not only reveals the details of conformational coupling in BtuCD-F, it also provides a promising approach to other long-range conformational couplings, e.g., in ABC exporters or other ATP-driven molecular machines.
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Affiliation(s)
- Marten Prieß
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany
| | - Lars V Schäfer
- Center for Theoretical Chemistry, Faculty of Chemistry and Biochemistry, Ruhr-University, Bochum, Germany.
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83
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Vickery ON, Machtens JP, Tamburrino G, Seeliger D, Zachariae U. Structural Mechanisms of Voltage Sensing in G Protein-Coupled Receptors. Structure 2016; 24:997-1007. [PMID: 27210286 PMCID: PMC4906246 DOI: 10.1016/j.str.2016.04.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 12/01/2022]
Abstract
G-protein-coupled receptors (GPCRs) form the largest superfamily of membrane proteins and one-third of all drug targets in humans. A number of recent studies have reported evidence for substantial voltage regulation of GPCRs. However, the structural basis of GPCR voltage sensing has remained enigmatic. Here, we present atomistic simulations on the δ-opioid and M2 muscarinic receptors, which suggest a structural and mechanistic explanation for the observed voltage-induced functional effects. The simulations reveal that the position of an internal Na(+) ion, recently detected to bind to a highly conserved aqueous pocket in receptor crystal structures, strongly responds to voltage changes. The movements give rise to gating charges in excellent agreement with previous experimental recordings. Furthermore, free energy calculations show that these rearrangements of Na(+) can be induced by physiological membrane voltages. Due to its role in receptor function and signal bias, the repositioning of Na(+) has important general implications for signal transduction in GPCRs.
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MESH Headings
- Animals
- Crystallography, X-Ray
- Humans
- Ion Channel Gating
- Models, Molecular
- Molecular Dynamics Simulation
- Protein Binding
- Protein Structure, Secondary
- Receptor, Muscarinic M2/chemistry
- Receptor, Muscarinic M2/metabolism
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Opioid, delta/chemistry
- Receptors, Opioid, delta/metabolism
- Sodium/metabolism
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Affiliation(s)
- Owen N Vickery
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK
| | - Jan-Philipp Machtens
- Forschungszentrum Jülich GmbH, Institute of Complex Systems, Zelluläre Biophysik (ICS-4), Leo-Brandt-Strasse, 52428 Jülich, Germany
| | - Giulia Tamburrino
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK
| | - Daniel Seeliger
- Lead Identification and Optimization Support, Boehringer Ingelheim Pharma GmbH & Co KG, 88397 Biberach an der Riss, Germany
| | - Ulrich Zachariae
- Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK; Physics, School of Science and Engineering, University of Dundee, Nethergate, Dundee DD1 4NH, UK.
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84
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Kalita MM, Fischer WB. Asymmetric dynamics of ion channel forming proteins - Hepatitis C virus (HCV) p7 bundles. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1462-70. [PMID: 27079148 DOI: 10.1016/j.bbamem.2016.04.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 01/01/2023]
Abstract
Protein p7 of hepatitis C virus (HCV) is a short 63 amino acid membrane protein which homo-oligomerises in the lipid membrane to form ion and proton conducting bundles. Two different genotypes (GTs) of p7, 1a and 5a, are used to simulate hexameric bundles of the protein embedded in a fully hydrated lipid bilayer during 400 ns molecular dynamics (MD) simulations. Whilst the bundle of GT 1a is based on a fully computational derived structure, the bundle of GT 5a is based on NMR spectroscopic data. Results of a full correlation analysis (FCA) reveal that albeit structural differences both bundles screen local minima during the simulation. The collective motion of the protein domains is asymmetric. No 'breathing-mode'-like dynamics is observed. The presence of divalent ions, such as Ca-ions affects the dynamics of especially solvent exposed parts of the protein, but leaves the asymmetric domain motion unaffected.
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Affiliation(s)
- Monoj Mon Kalita
- Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC
| | - Wolfgang B Fischer
- Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC.
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85
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Quaternary structure of a G-protein-coupled receptor heterotetramer in complex with Gi and Gs. BMC Biol 2016; 14:26. [PMID: 27048449 PMCID: PMC4822319 DOI: 10.1186/s12915-016-0247-4] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 03/16/2016] [Indexed: 12/04/2022] Open
Abstract
Background G-protein-coupled receptors (GPCRs), in the form of monomers or homodimers that bind heterotrimeric G proteins, are fundamental in the transfer of extracellular stimuli to intracellular signaling pathways. Different GPCRs may also interact to form heteromers that are novel signaling units. Despite the exponential growth in the number of solved GPCR crystal structures, the structural properties of heteromers remain unknown. Results We used single-particle tracking experiments in cells expressing functional adenosine A1-A2A receptors fused to fluorescent proteins to show the loss of Brownian movement of the A1 receptor in the presence of the A2A receptor, and a preponderance of cell surface 2:2 receptor heteromers (dimer of dimers). Using computer modeling, aided by bioluminescence resonance energy transfer assays to monitor receptor homomerization and heteromerization and G-protein coupling, we predict the interacting interfaces and propose a quaternary structure of the GPCR tetramer in complex with two G proteins. Conclusions The combination of results points to a molecular architecture formed by a rhombus-shaped heterotetramer, which is bound to two different interacting heterotrimeric G proteins (Gi and Gs). These novel results constitute an important advance in understanding the molecular intricacies involved in GPCR function. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0247-4) contains supplementary material, which is available to authorized users.
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86
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Cardenas AE, Elber R. Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning. J Phys Chem B 2016; 120:8208-16. [PMID: 27016332 DOI: 10.1021/acs.jpcb.6b01890] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We exploit atomically detailed simulations and the milestoning theory to extract coarse grained models of membrane kinetics and thermodynamics. Non-Markovian and Markovian theories for the phosphate group displacements are used to coarsely represent membrane motions. The construction of the two models makes it possible to examine their consistency and accuracy. The equilibrium and fluctuations of the phosphate groups along the normal to the membrane plane are estimated, and milestoning equations are constructed and solved. An optimal Markovian model is constructed that reproduces exactly the equilibrium and mean first passage time (MFPT) of the non-Markovian model. The equilibrium solution of both models is favorably compared to distributions obtained from straightforward molecular dynamics simulations. The picture for the kinetics is complex. Multiple local relaxation times of the mass density are illustrated emphasizing the non-Markovian characteristics of the process. In Markovian modeling, only a single relaxation time is assumed for a state. Mapping of particle dynamics to the dynamics of a field density offers a new way of coarse graining complex systems as membranes that may bridge between atomically detailed models and phenomenological descriptions of macroscopic membranes.
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Affiliation(s)
- Alfredo E Cardenas
- Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Ron Elber
- Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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87
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Karakas E, Taveneau C, Bressanelli S, Marchi M, Robert B, Abel S. Derivation of original RESP atomic partial charges for MD simulations of the LDAO surfactant with AMBER: applications to a model of micelle and a fragment of the lipid kinase PI4KA. J Biomol Struct Dyn 2016; 35:159-181. [DOI: 10.1080/07391102.2015.1135822] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Esra Karakas
- Maison de la Simulation, USR 3441, CEA – CNRS – INRIA – Univ. Paris-Sud – Univ. de Versailles, 91191, Gif sur Yvette, France
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DRF/IBITECS/SB2SM/LBMS & CNRS UMR 9198, Saclay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Cyntia Taveneau
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Stéphane Bressanelli
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Massimo Marchi
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DRF/IBITECS/SB2SM/LBMS & CNRS UMR 9198, Saclay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Bruno Robert
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DRF/IBITECS/SB2SM/LBMS & CNRS UMR 9198, Saclay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
| | - Stéphane Abel
- Commissariat à l'Energie Atomique et aux Energies Alternatives, DRF/IBITECS/SB2SM/LBMS & CNRS UMR 9198, Saclay, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris Sud, Université Paris-Saclay, 91198 Gif sur Yvette, France
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88
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Oakes V, Furini S, Domene C. Voltage-Gated Sodium Channels: Mechanistic Insights From Atomistic Molecular Dynamics Simulations. CURRENT TOPICS IN MEMBRANES 2016; 78:183-214. [PMID: 27586285 DOI: 10.1016/bs.ctm.2015.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The permeation of ions and other molecules across biological membranes is an inherent requirement of all cellular organisms. Ion channels, in particular, are responsible for the conduction of charged species, hence modulating the propagation of electrical signals. Despite the universal physiological implications of this property, the molecular functioning of ion channels remains ambiguous. The combination of atomistic structural data with computational methodologies, such as molecular dynamics (MD) simulations, is now considered routine to investigate structure-function relationships in biological systems. A fuller understanding of conduction, selectivity, and gating, therefore, is steadily emerging due to the applicability of these techniques to ion channels. However, because their structure is known at atomic resolution, studies have consistently been biased toward K(+) channels, thus the molecular determinants of ionic selectivity, activation, and drug blockage in Na(+) channels are often overlooked. The recent increase of available crystallographic data has eminently encouraged the investigation of voltage-gated sodium (NaV) channels via computational methods. Here, we present an overview of simulation studies that have contributed to our understanding of key principles that underlie ionic conduction and selectivity in Na(+) channels, in comparison to the K(+) channel analogs.
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Affiliation(s)
- V Oakes
- King's College London, London, United Kingdom
| | - S Furini
- University of Siena, Siena, Italy
| | - C Domene
- King's College London, London, United Kingdom; University of Oxford, Oxford, United Kingdom
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89
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Javanainen M, Martinez-Seara H. Efficient preparation and analysis of membrane and membrane protein systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2468-2482. [PMID: 26947184 DOI: 10.1016/j.bbamem.2016.02.036] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 02/23/2016] [Accepted: 02/25/2016] [Indexed: 11/25/2022]
Abstract
Molecular dynamics (MD) simulations have become a highly important technique to consider lipid membrane systems, and quite often they provide considerable added value to laboratory experiments. Rapid development of both software and hardware has enabled the increase of time and size scales reachable by MD simulations to match those attainable by several accurate experimental techniques. However, until recently, the quality and maturity of software tools available for building membrane models for simulations as well as analyzing the results of these simulations have seriously lagged behind. Here, we discuss the recent developments of such tools from the end-users' point of view. In particular, we review the software that can be employed to build lipid bilayers and other related structures with or without embedded membrane proteins to be employed in MD simulations. Additionally, we provide a brief critical insight into force fields and MD packages commonly used for membrane and membrane protein simulations. Finally, we list analysis tools that can be used to study the properties of membrane and membrane protein systems. In all these points we comment on the respective compatibility of the covered tools. We also share our opinion on the current state of the available software. We briefly discuss the most commonly employed tools and platforms on which new software can be built. We conclude the review by providing a few ideas and guidelines on how the development of tools can be further boosted to catch up with the rapid pace at which the field of membrane simulation progresses. This includes improving the compatibility between software tools and promoting the openness of the codes on which these applications rely. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Matti Javanainen
- Department of Physics, Tampere University of Technology, Tampere, Finland.
| | - Hector Martinez-Seara
- Department of Physics, Tampere University of Technology, Tampere, Finland; Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
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90
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Doornbos MLJ, Pérez-Benito L, Tresadern G, Mulder-Krieger T, Biesmans I, Trabanco AA, Cid JM, Lavreysen H, IJzerman AP, Heitman LH. Molecular mechanism of positive allosteric modulation of the metabotropic glutamate receptor 2 by JNJ-46281222. Br J Pharmacol 2016; 173:588-600. [PMID: 26589404 DOI: 10.1111/bph.13390] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/09/2015] [Accepted: 11/10/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND AND PURPOSE Allosteric modulation of the mGlu2 receptor is a potential strategy for treatment of various neurological and psychiatric disorders. Here, we describe the in vitro characterization of the mGlu2 positive allosteric modulator (PAM) JNJ-46281222 and its radiolabelled counterpart [(3) H]-JNJ-46281222. Using this novel tool, we also describe the allosteric effect of orthosteric glutamate binding and the presence of a bound G protein on PAM binding and use computational approaches to further investigate the binding mode. EXPERIMENTAL APPROACH We have used radioligand binding studies, functional assays, site-directed mutagenesis, homology modelling and molecular dynamics to study the binding of JNJ-46281222. KEY RESULTS JNJ-46281222 is an mGlu2 -selective, highly potent PAM with nanomolar affinity (KD = 1.7 nM). Binding of [(3) H]-JNJ-46281222 was increased by the presence of glutamate and greatly reduced by the presence of GTP, indicating the preference for a G protein bound state of the receptor for PAM binding. Its allosteric binding site was visualized and analysed by a computational docking and molecular dynamics study. The simulations revealed amino acid movements in regions expected to be important for activation. The binding mode was supported by [(3) H]-JNJ-46281222 binding experiments on mutant receptors. CONCLUSION AND IMPLICATIONS Our results obtained with JNJ-46281222 in unlabelled and tritiated form further contribute to our understanding of mGlu2 allosteric modulation. The computational simulations and mutagenesis provide a plausible binding mode with indications of how the ligand permits allosteric activation. This study is therefore of interest for mGlu2 and class C receptor drug discovery.
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Affiliation(s)
- Maarten L J Doornbos
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Laura Pérez-Benito
- Janssen Research and Development, Toledo, Spain.,Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autonoma de Barcelona, Bellaterra, Spain
| | | | - Thea Mulder-Krieger
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | | | | | | | | | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, Leiden, The Netherlands
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91
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Côté S, Binette V, Salnikov ES, Bechinger B, Mousseau N. Probing the Huntingtin 1-17 membrane anchor on a phospholipid bilayer by using all-atom simulations. Biophys J 2016; 108:1187-98. [PMID: 25762330 DOI: 10.1016/j.bpj.2015.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 01/18/2015] [Accepted: 02/02/2015] [Indexed: 12/12/2022] Open
Abstract
Mislocalization and aggregation of the huntingtin protein are related to Huntington's disease. Its first exon-more specifically the first 17 amino acids (Htt17)-is crucial for the physiological and pathological functions of huntingtin. It regulates huntingtin's activity through posttranslational modifications and serves as an anchor to membrane-containing organelles of the cell. Recently, structure and orientation of the Htt17 membrane anchor were determined using a combined solution and solid-state NMR approach. This prompted us to refine this model by investigating the dynamics and thermodynamics of this membrane anchor on a POPC bilayer using all-atom, explicit solvent molecular dynamics and Hamiltonian replica exchange. Our simulations are combined with various experimental measurements to generate a high-resolution atomistic model for the huntingtin Htt17 membrane anchor on a POPC bilayer. More precisely, we observe that the single α-helix structure is more stable in the phospholipid membrane than the NMR model obtained in the presence of dodecylphosphocholine detergent micelles. The resulting Htt17 monomer has its hydrophobic plane oriented parallel to the bilayer surface. Our results further unveil the key residues interacting with the membrane in terms of hydrogen bonds, salt-bridges, and nonpolar contributions. We also observe that Htt17 equilibrates at a well-defined insertion depth and that it perturbs the physical properties-order parameter, thickness, and area per lipid-of the bilayer in a manner that could favor its dimerization. Overall, our observations reinforce and refine the NMR measurements on the Htt17 membrane anchor segment of huntingtin that is of fundamental importance to its biological functions.
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Affiliation(s)
- Sébastien Côté
- Département de Physique and Groupe de Recherche sur les Protéines Membranaires, Université de Montréal, Montréal, Québec, Canada.
| | - Vincent Binette
- Département de Physique and Groupe de Recherche sur les Protéines Membranaires, Université de Montréal, Montréal, Québec, Canada
| | - Evgeniy S Salnikov
- Université de Strasbourg/Centre National de la Recherche Scientifique, UMR7177, Institut de Chimie, Strasbourg, France
| | - Burkhard Bechinger
- Université de Strasbourg/Centre National de la Recherche Scientifique, UMR7177, Institut de Chimie, Strasbourg, France
| | - Normand Mousseau
- Département de Physique and Groupe de Recherche sur les Protéines Membranaires, Université de Montréal, Montréal, Québec, Canada.
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92
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Yue T, Sun M, Zhang S, Ren H, Ge B, Huang F. How transmembrane peptides insert and orientate in biomembranes: a combined experimental and simulation study. Phys Chem Chem Phys 2016; 18:17483-94. [DOI: 10.1039/c6cp01133k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
After the synthesis of transmembrane peptides/proteins (TMPs), their insertion into a lipid bilayer is a fundamental biophysical process.
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Affiliation(s)
- Tongtao Yue
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Mingbin Sun
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Shuai Zhang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Hao Ren
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing
- Center for Bioengineering and Biotechnology
- China University of Petroleum (East China)
- Qingdao
- China
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93
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Bisha I, Magistrato A. The molecular mechanism of secondary sodium symporters elucidated through the lens of the computational microscope. RSC Adv 2016. [DOI: 10.1039/c5ra22131e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Transport of molecules across cellular membranes is a key biological process for normal cell function. In this review we describe current state-of-the-art knowledge on molecular mechanism of secondary active transporters obtained by molecular simulations studies.
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Affiliation(s)
- Ina Bisha
- Theoretical Chemical Biology and Protein Modelling Group
- Technische Universität München
- 85354 Freising
- Germany
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94
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Ing C, Pomès R. Simulation Studies of Ion Permeation and Selectivity in Voltage-Gated Sodium Channels. CURRENT TOPICS IN MEMBRANES 2016; 78:215-60. [DOI: 10.1016/bs.ctm.2016.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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95
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Blees A, Reichel K, Trowitzsch S, Fisette O, Bock C, Abele R, Hummer G, Schäfer LV, Tampé R. Assembly of the MHC I peptide-loading complex determined by a conserved ionic lock-switch. Sci Rep 2015; 5:17341. [PMID: 26611325 PMCID: PMC4661472 DOI: 10.1038/srep17341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 10/15/2015] [Indexed: 01/14/2023] Open
Abstract
Salt bridges in lipid bilayers play a decisive role in the dynamic assembly and downstream signaling of the natural killer and T-cell receptors. Here, we describe the identification of an inter-subunit salt bridge in the membrane within yet another key component of the immune system, the peptide-loading complex (PLC). The PLC regulates cell surface presentation of self-antigens and antigenic peptides via molecules of the major histocompatibility complex class I. We demonstrate that a single salt bridge in the membrane between the transporter associated with antigen processing TAP and the MHC I-specific chaperone tapasin is essential for the assembly of the PLC and for efficient MHC I antigen presentation. Molecular modeling and all-atom molecular dynamics simulations suggest an ionic lock-switch mechanism for the binding of TAP to tapasin, in which an unfavorable uncompensated charge in the ER-membrane is prevented through complex formation. Our findings not only deepen the understanding of the interaction network within the PLC, but also provide evidence for a general interaction principle of dynamic multiprotein membrane complexes in immunity.
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Affiliation(s)
- Andreas Blees
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Katrin Reichel
- Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, D-44780 Bochum, Germany
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Simon Trowitzsch
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Olivier Fisette
- Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Christoph Bock
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Rupert Abele
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Max Planck Institute of Biophysics, Max-von-Laue-Str. 3, D-60438 Frankfurt am Main, Germany
| | - Lars V. Schäfer
- Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, D-44780 Bochum, Germany
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
- Cluster of Excellence–Macromolecular Complexes, Goethe-University Frankfurt am Main, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
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96
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Nishizawa M, Nishizawa K. Free energy of helical transmembrane peptide dimerization in OPLS-AA/Berger force field simulations: inaccuracy and implications for partner-specific Lennard-Jones parameters between peptides and lipids. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1112006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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97
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Nishizawa K, Nishizawa M, Gnanasambandam R, Sachs F, Sukharev SI, Suchyna TM. Effects of Lys to Glu mutations in GsMTx4 on membrane binding, peptide orientation, and self-association propensity, as analyzed by molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:2767-78. [PMID: 26342676 DOI: 10.1016/j.bbamem.2015.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/27/2015] [Accepted: 09/01/2015] [Indexed: 10/23/2022]
Abstract
GsMTx4, a gating modifier peptide acting on cationic mechanosensitive channels, has a positive charge (+5e) due to six Lys residues. The peptide does not have a stereospecific binding site on the channel but acts from the boundary lipids within a Debye length of the pore probably by changing local stress. To gain insight into how these Lys residues interact with membranes, we performed molecular dynamics simulations of Lys to Glu mutants in parallel with our experimental work. In silico, K15E had higher affinity for 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine bilayers than wild-type (WT) peptide or any other mutant tested, and showed deeper penetration than WT, a finding consistent with the experimental data. Experimentally, the inhibitory activities of K15E and K25E were most compromised, whereas K8E and K28E inhibitory activities remained similar to WT peptide. Binding of WT in an interfacial mode did not influence membrane thickness. With interfacial binding, the direction of the dipole moments of K15E and K25E was predicted to differ from WT, whereas those of K8E and K28E oriented similarly to that of WT. These results support a model in which binding of GsMTx4 to the membrane acts like an immersible wedge that serves as a membrane expansion buffer reducing local stress and thus inhibiting channel activity. In simulations, membrane-bound WT attracted other WT peptides to form aggregates. This may account for the positive cooperativity observed in the ion channel experiments. The Lys residues seem to fine-tune the depth of membrane binding, the tilt angle, and the dipole moments.
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Affiliation(s)
| | | | | | - Frederick Sachs
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Sergei I Sukharev
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Thomas M Suchyna
- Department of Physiology and Biophysics, State University of New York at Buffalo, Buffalo, NY, USA
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98
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Pluhackova K, Böckmann RA. Biomembranes in atomistic and coarse-grained simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015. [PMID: 26194872 DOI: 10.1088/0953-8984/27/32/323103] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The architecture of biological membranes is tightly coupled to the localization, organization, and function of membrane proteins. The organelle-specific distribution of lipids allows for the formation of functional microdomains (also called rafts) that facilitate the segregation and aggregation of membrane proteins and thus shape their function. Molecular dynamics simulations enable to directly access the formation, structure, and dynamics of membrane microdomains at the molecular scale and the specific interactions among lipids and proteins on timescales from picoseconds to microseconds. This review focuses on the latest developments of biomembrane force fields for both atomistic and coarse-grained molecular dynamics (MD) simulations, and the different levels of coarsening of biomolecular structures. It also briefly introduces scale-bridging methods applicable to biomembrane studies, and highlights selected recent applications.
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Affiliation(s)
- Kristyna Pluhackova
- Computational Biology, Department of Biology, Friedrich-Alexander Universität Erlangen-Nürnberg, Staudtstr. 5, 91058 Erlangen, Germany
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99
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Rosa M, Caltabiano G, Barreto-Valer K, Gonzalez-Nunez V, Gómez-Tamayo JC, Ardá A, Jiménez-Barbero J, Pardo L, Rodríguez RE, Arsequell G, Valencia G. Modulation of the Interaction between a Peptide Ligand and a G Protein-Coupled Receptor by Halogen Atoms. ACS Med Chem Lett 2015; 6:872-6. [PMID: 26288687 DOI: 10.1021/acsmedchemlett.5b00126] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/16/2015] [Indexed: 12/25/2022] Open
Abstract
Systematic halogenation of two native opioid peptides has shown that halogen atoms can modulate peptide-receptor interactions in different manners. First, halogens may produce a steric hindrance that reduces the binding of the peptide to the receptor. Second, chlorine, bromine, or iodine may improve peptide binding if their positive σ-hole forms a halogen bond interaction with negatively charged atoms of the protein. Lastly, the negative electrostatic potential of fluorine can interact with positively charged atoms of the protein to improve peptide binding.
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Affiliation(s)
- Mònica Rosa
- Institut de Química Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), E-08034 Barcelona, Spain
| | - Gianluigi Caltabiano
- Laboratori
de Medicina Computacional, Unitat de Bioestadística, Facultat
de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Katy Barreto-Valer
- Department
of Biochemistry and Molecular Biology, Faculty of Medicine, Instituto
de Neurociencias de Castilla y León (INCyL), University of Salamanca, 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), E-37007 Salamanca, Spain
| | - Verónica Gonzalez-Nunez
- Department
of Biochemistry and Molecular Biology, Faculty of Medicine, Instituto
de Neurociencias de Castilla y León (INCyL), University of Salamanca, 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), E-37007 Salamanca, Spain
| | - José C. Gómez-Tamayo
- Laboratori
de Medicina Computacional, Unitat de Bioestadística, Facultat
de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Ana Ardá
- CIC
bioGUNE, Bizkaia Technological Park, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, E-48013 Bilbao, Spain
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Bizkaia Technological Park, 48160 Derio, Spain
- Ikerbasque, Basque Foundation for Science, E-48013 Bilbao, Spain
| | - Leonardo Pardo
- Laboratori
de Medicina Computacional, Unitat de Bioestadística, Facultat
de Medicina, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Raquel E. Rodríguez
- Department
of Biochemistry and Molecular Biology, Faculty of Medicine, Instituto
de Neurociencias de Castilla y León (INCyL), University of Salamanca, 37008 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), E-37007 Salamanca, Spain
| | - Gemma Arsequell
- Institut de Química Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), E-08034 Barcelona, Spain
| | - Gregorio Valencia
- Institut de Química Avançada de Catalunya (I.Q.A.C.-C.S.I.C.), E-08034 Barcelona, Spain
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Debnath A, Schäfer LV. Structure and Dynamics of Phospholipid Nanodiscs from All-Atom and Coarse-Grained Simulations. J Phys Chem B 2015; 119:6991-7002. [PMID: 25978497 DOI: 10.1021/acs.jpcb.5b02101] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We investigated structural and dynamical properties of nanodiscs comprising dimyristoylphosphatidylcholine (DMPC) lipids and major scaffold protein MSP1Δ(1-22) from human apolipoprotein A-1 using combined all-atom and coarse-grained (CG) molecular dynamics (MD) simulations. The computational efficiency of the Martini-CG force field enables the spontaneous self-assembly of lipids and scaffold proteins into stable nanodisc structures on time scales up to tens of microseconds. Subsequent all-atom and CG-MD simulations reveal that the lipids in the nanodisc have lower configurational entropy and higher acyl tail order than in a lamellar bilayer phase. These altered average properties arise from rather differential behavior of lipids, depending on their location in the nanodisc. Since the scaffold proteins exert constrictive forces from the outer rim of the disc toward its center, lipids at the center of the nanodisc are highly ordered, whereas annular lipids that are in contact with the MSP proteins are remarkably disordered due to perturbed packing. Although specific differences between all-atom and CG simulations are also evident, the results obtained at both levels of resolution are in overall good agreement with each other and provide atomic level interpretations of recent experiments. Thus, the present study highlights the applicability of multiscale simulation approaches for nanodisc systems and opens the way for future applications, including the study of nanodisc-embedded membrane proteins.
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Affiliation(s)
- Ananya Debnath
- †Department of Chemistry, Indian Institute of Technology Jodhpur, Jodhpur 342 011, India
| | - Lars V Schäfer
- ‡Lehrstuhl für Theoretische Chemie, Ruhr-University Bochum, D-44780 Bochum, Germany
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