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Paul A, Chakrabarti J. Dynamics of an aqueous suspension of short hyaluronic acid chains near a DPPC bilayer. Phys Chem Chem Phys 2024. [PMID: 39021115 DOI: 10.1039/d4cp01088d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The synergy between hyaluronic acid (HA) and lipid molecules plays a crucial role in synovial fluids, cell coatings, etc. Diseased cells in cancer and arthritis show changes in HA concentration and chain size, impacting the viscoelastic and mechanical properties of the cells. Although the solution behavior of HA is known in experiments, a molecular-level understanding of the role of HA in the dynamics at the interface of HA-water and the cellular boundary is lacking. Here, we perform atomistic molecular dynamics simulation of short HA chains in an explicit water solvent in the presence of a DPPC bilayer, relevant in pathological cases. We identify a stable interface between HA-water and the bilayer where the water molecules are in contact with the bilayer and the HA chains are located away without any direct contact. Both translation and rotation of the interfacial waters in contact with the lipid bilayer and translation of the HA chains exhibit subdiffusive behavior. The diffusive behavior sets in slightly away from the bilayer, where the diffusion coefficients of water and HA decrease monotonically with increase in HA concentration. On the contrary, the dependence on HA chain size is only marginal due to enhanced chain flexibility as their size increases.
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Affiliation(s)
- Anirban Paul
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block JD, Sector - III, Salt Lake, Kolkata 700106, India.
| | - Jaydeb Chakrabarti
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block JD, Sector - III, Salt Lake, Kolkata 700106, India.
- Department of Chemical and Biological Sciences and the Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
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2
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Calderón JC, Plut E, Keller M, Cabrele C, Reiser O, Gervasio FL, Clark T. Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors. J Chem Inf Model 2024; 64:205-218. [PMID: 38150388 DOI: 10.1021/acs.jcim.3c01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
A metadynamics protocol is presented to characterize the binding and unbinding of peptide ligands to class A G-protein-coupled receptors (GPCRs). The protocol expands on the one previously presented for binding and unbinding small-molecule ligands to class A GPCRs and accounts for the more demanding nature of the peptide binding-unbinding process. It applies to almost all class A GPCRs. Exemplary simulations are described for subtypes Y1R, Y2R, and Y4R of the neuropeptide Y receptor family, vasopressin binding to the vasopressin V2 receptor (V2R), and oxytocin binding to the oxytocin receptor (OTR). Binding free energies and the positions of alternative binding sites are presented and, where possible, compared with the experiment.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, Erlangen 91052, Germany
| | - Eva Plut
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg D-93040, Germany
| | - Chiara Cabrele
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany
| | - Oliver Reiser
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Regensburg 93040, Germany
| | | | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, Erlangen 91052, Germany
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3
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Mai TL, Derreumaux P, Nguyen PH. Structure and Elasticity of Mitochondrial Membranes: A Molecular Dynamics Simulation Study. J Phys Chem B 2023; 127:10778-10791. [PMID: 38084584 DOI: 10.1021/acs.jpcb.3c05112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Mitochondria are known as the powerhouse of the cell because they produce energy in the form of adenosine triphosphate. They also have other crucial functions such as regulating apoptosis, calcium homeostasis, and reactive oxygen species production. To perform these diverse functions, mitochondria adopt specific structures and frequently undergo dynamic shape changes, indicating that their mechanical properties play an essential role in their functions. To gain a detailed understanding at the molecular level of the structure and mechanical properties of mitochondria, we carry out atomistic molecular dynamics simulations for three inner mitochondrial membranes and three outer mitochondrial membrane models. These models take into account variations in cardiolipin and cholesterol concentrations as well as the symmetry/asymmetry between the two leaflets. Our simulations allow us to calculate various structural quantities and the bending, twisting, and tilting elastic moduli of the membrane models. Our results indicate that the structures of the inner and outer mitochondrial membranes are quite similar and do not depend much on the variation in lipid compositions. However, the bending modulus of the membranes increases with increasing concentrations of cardiolipin or cholesterol but decreases with a membrane asymmetry. Notably, we found that the dipole potential of the membrane increases with an increasing cardiolipin concentration. Finally, possible roles of cardiolipin in regulating ion and proton currents and maintaining the cristate are discussed in some details.
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Affiliation(s)
- Thi Ly Mai
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, Institute de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris 75005, France
| | - Philippe Derreumaux
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, Institute de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris 75005, France
- Institut Universitaire de France (IUF), Paris 75005, France
| | - Phuong H Nguyen
- CNRS, Université Paris Cité, UPR9080, Laboratoire de Biochimie Théorique, Institute de Biologie Physico-Chimique, Fondation Edmond de Rothschild, 13 rue Pierre et Marie Curie, Paris 75005, France
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4
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Plut E, Calderón JC, Stanojlović V, Gattor AO, Höring C, Humphrys LJ, Konieczny A, Kerres S, Schubert M, Keller M, Cabrele C, Clark T, Reiser O. Stereochemistry-Driven Interactions of α,γ-Peptide Ligands with the Neuropeptide Y Y 4-Receptor. J Med Chem 2023. [PMID: 37440703 DOI: 10.1021/acs.jmedchem.3c00363] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
The G-protein-coupled Y4-receptor (Y4R) and its endogenous ligand, pancreatic polypeptide (PP), suppress appetite in response to food intake and, thus, are attractive drug targets for body-weight control. The C-terminus of human PP (hPP), T32-R33-P34-R35-Y36-NH2, penetrates deep into the binding pocket with its tyrosine-amide and di-arginine motif. Here, we present two C-terminally amidated α,γ-hexapeptides (1a/b) with sequence Ac-R31-γ-CBAA32-R33-L34-R35-Y36-NH2, where γ-CBAA is the (1R,2S,3R)-configured 2-(aminomethyl)-3-phenylcyclobutanecarboxyl moiety (1a) or its mirror image (1b). Both peptides bind the Y4R (Ki of 1a/b: 0.66/12 nM) and act as partial agonists (intrinsic activity of 1a/b: 50/39%). Their induced-fit binding poses in the Y4R pocket are unique and build ligand-receptor contacts distinct from those of the C-terminus of the endogenous ligand hPP. We conclude that energetically favorable interactions, although they do not match those of the native ligand hPP, still guarantee high binding affinity (with 1a rivaling hPP) but not the maximum receptor activation.
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Affiliation(s)
- Eva Plut
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Jacqueline C Calderón
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Vesna Stanojlović
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Albert O Gattor
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Carina Höring
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Laura J Humphrys
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Adam Konieczny
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Sabine Kerres
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Mario Schubert
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Chiara Cabrele
- Department of Biosciences and Medical Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, 91052 Erlangen, Germany
| | - Oliver Reiser
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
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5
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Greife P, Schönborn M, Capone M, Assunção R, Narzi D, Guidoni L, Dau H. The electron-proton bottleneck of photosynthetic oxygen evolution. Nature 2023; 617:623-628. [PMID: 37138082 PMCID: PMC10191853 DOI: 10.1038/s41586-023-06008-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/23/2023] [Indexed: 05/05/2023]
Abstract
Photosynthesis fuels life on Earth by storing solar energy in chemical form. Today's oxygen-rich atmosphere has resulted from the splitting of water at the protein-bound manganese cluster of photosystem II during photosynthesis. Formation of molecular oxygen starts from a state with four accumulated electron holes, the S4 state-which was postulated half a century ago1 and remains largely uncharacterized. Here we resolve this key stage of photosynthetic O2 formation and its crucial mechanistic role. We tracked 230,000 excitation cycles of dark-adapted photosystems with microsecond infrared spectroscopy. Combining these results with computational chemistry reveals that a crucial proton vacancy is initally created through gated sidechain deprotonation. Subsequently, a reactive oxygen radical is formed in a single-electron, multi-proton transfer event. This is the slowest step in photosynthetic O2 formation, with a moderate energetic barrier and marked entropic slowdown. We identify the S4 state as the oxygen-radical state; its formation is followed by fast O-O bonding and O2 release. In conjunction with previous breakthroughs in experimental and computational investigations, a compelling atomistic picture of photosynthetic O2 formation emerges. Our results provide insights into a biological process that is likely to have occurred unchanged for the past three billion years, which we expect to support the knowledge-based design of artificial water-splitting systems.
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Affiliation(s)
- Paul Greife
- Department of Physics, Freie Universität, Berlin, Germany
| | | | - Matteo Capone
- Department of Information Engineering, Computer Science and Mathematics, University of L'Aquila, L'Aquila, Italy
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | | | - Daniele Narzi
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Leonardo Guidoni
- Department of Physical and Chemical Sciences, University of L'Aquila, L'Aquila, Italy.
| | - Holger Dau
- Department of Physics, Freie Universität, Berlin, Germany.
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6
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Singh H, Sharma S. Hydration of Linear Alkanes is Governed by the Small Length-Scale Hydrophobic Effect. J Chem Theory Comput 2022; 18:3805-3813. [PMID: 35648114 DOI: 10.1021/acs.jctc.2c00219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Length-scale dependence of the hydrophobic effect is well understood for apolar spherical solutes: for small solutes (diameter, d ≲ 0.8 nm), the hydration free energy is entropically driven, while for larger solutes (d ≳ 2 nm), it is enthalpically driven. The nature of the hydrophobic effect in the case of anisotropic molecules such as linear alkanes is not understood yet. In this work, we have calculated the hydration free energy of linear alkanes going from methane to octadecane and of a spherical decane droplet of d ≈ 3 nm using molecular simulations. We show that the hydration free energies of alkanes, irrespective of their size, are governed by the small length-scale hydrophobic effect. That is, unlike the case of large spherical solutes, the hydration free energies of linear alkanes are entropically driven.
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Affiliation(s)
- Himanshu Singh
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, Ohio 45701, United States
| | - Sumit Sharma
- Department of Chemical and Biomolecular Engineering, Ohio University, Athens, Ohio 45701, United States
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7
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Conde D, Garrido PF, Calvelo M, Piñeiro Á, Garcia-Fandino R. Molecular Dynamics Simulations of Transmembrane Cyclic Peptide Nanotubes Using Classical Force Fields, Hydrogen Mass Repartitioning, and Hydrogen Isotope Exchange Methods: A Critical Comparison. Int J Mol Sci 2022; 23:3158. [PMID: 35328578 PMCID: PMC8951607 DOI: 10.3390/ijms23063158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 12/04/2022] Open
Abstract
Self-assembled cyclic peptide nanotubes with alternating D- and L-amino acid residues in the sequence of each subunit have attracted a great deal of attention due to their potential for new nanotechnology and biomedical applications, mainly in the field of antimicrobial peptides. Molecular dynamics simulations can be used to characterize these systems with atomic resolution at different time scales, providing information that is difficult to obtain via wet lab experiments. However, the performance of classical force fields typically employed in the simulation of biomolecules has not yet been extensively tested with this kind of highly constrained peptide. Four different classical force fields (AMBER, CHARMM, OPLS, and GROMOS), using a nanotube formed by eight D,L-α-cyclic peptides inserted into a lipid bilayer as a model system, were employed here to fill this gap. Significant differences in the pseudo-cylindrical cavities formed by the nanotubes were observed, the most important being the diameter of the nanopores, the number and location of confined water molecules, and the density distribution of the solvent molecules. Furthermore, several modifications were performed on GROMOS54a7, aiming to explore acceleration strategies of the MD simulations. The hydrogen mass repartitioning (HMR) and hydrogen isotope exchange (HIE) methods were tested to slow down the fastest degrees of freedom. These approaches allowed a significant increase in the time step employed in the equation of the motion integration algorithm, from 2 fs up to 5-7 fs, with no serious changes in the structural and dynamical properties of the nanopores. Subtle differences with respect to the simulations with the unmodified force fields were observed in the concerted movements of the cyclic peptides, as well as in the lifetime of several H-bonds. All together, these results are expected to contribute to better understanding of the behavior of self-assembled cyclic peptide nanotubes, as well as to support the methods tested to speed up general MD simulations; additionally, they do provide a number of quantitative descriptors that are expected to be used as a reference to design new experiments intended to validate and complement computational studies of antimicrobial cyclic peptides.
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Affiliation(s)
- Daniel Conde
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain; (D.C.); (M.C.)
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Pablo F. Garrido
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Martín Calvelo
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain; (D.C.); (M.C.)
- Departament de Química Inorgánica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Ángel Piñeiro
- Departamento de Física Aplicada, Facultade de Física, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain;
| | - Rebeca Garcia-Fandino
- Center for Research in Biological Chemistry and Molecular Materials, Departamento de Química Orgánica, Universidade de Santiago de Compostela, Campus Vida s/n, 15782 Santiago de Compostela, Spain; (D.C.); (M.C.)
- CIQUP, Centro de Investigação em Química, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, 4196-007 Porto, Portugal
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8
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Kim AV, Shelepova EA, Evseenko VI, Dushkin AV, Medvedev NN, Polyakov NE. Mechanism of the enhancing effect of glycyrrhizin on nifedipine penetration through a lipid membrane. J Mol Liq 2021; 344:117759. [PMID: 34658466 PMCID: PMC8500845 DOI: 10.1016/j.molliq.2021.117759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/02/2021] [Indexed: 01/04/2023]
Abstract
The saponin glycyrrhizin from liquorice root shows the ability to enhance the therapeutic activity of other drugs when used as a drug delivery system. Due to its amphiphilic properties, glycyrrhizin can form self-associates (dimers, micelles) and supramolecular complexes with a wide range of hydrophobic drugs, which leads to an increase in their solubility, stability and bioavailability. That is why the mechanism of the biological activity of glycyrrhizin is of considerable interest and has been the subject of intensive physical and chemical research in the last decade. Two mechanisms have been proposed to explain the effect of glycyrrhizin on drug bioavailability, namely, the increase in drug solubility in water and enhancement of the membrane permeability. Interest in the membrane-modifying ability of glycyrrhizic acid (GA) is also growing at present due to its recently discovered antiviral activity against SARS-CoV-2 Bailly and Vergoten (2020) [1]. In the present study, the passive permeability of the DOPC lipid membrane for the calcium channel blocker nifedipine was elucidated by parallel artificial membrane permeability assay (PAMPA) and full atomistic molecular dynamics (MD) simulation with free energy calculations. PAMPA experiments show a remarkable increase in the amount of nifedipine (NF) permeated with glycyrrhizin compared to free NF. In previous studies, we have shown using MD techniques that glycyrrhizin molecules can integrate into the lipid bilayer. In this study, MD simulation demonstrates a significant decrease in the energy barrier of NF penetration through the lipid bilayer in the presence of glycyrrhizin both in the pure DOPC membrane and in the membrane with cholesterol. This effect can be explained by the formation of hydrogen bonds between NF and GA in the middle of the bilayer.
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Key Words
- CLR, cholesterol
- DDS, drug delivery system
- DOPC
- DOPC, dioleoylphosphatidylcholine
- Drug delivery
- GA, glycyrrhizic acid
- Glycyrrhizin
- Lipid bilayer
- MD, molecular dynamics
- Membrane penetration
- Molecular dynamics
- NF, nifedipine
- NMR
- NMR, nuclear magnetic resonance
- Nifedipine
- PAMPA
- PAMPA, parallel artificial membrane permeability assay
- PMF, potential of mean force
- TBK, tebuconazole
- VDW, Van der Waals
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Affiliation(s)
- A V Kim
- Institute of Chemical Kinetics and Combustion, Institutskaya St., 3, 630090 Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - E A Shelepova
- Institute of Chemical Kinetics and Combustion, Institutskaya St., 3, 630090 Novosibirsk, Russia
| | - V I Evseenko
- Institute of Solid State Chemistry and Mechanochemistry, Novosibirsk, Russia
| | - A V Dushkin
- Institute of Solid State Chemistry and Mechanochemistry, Novosibirsk, Russia
| | - N N Medvedev
- Institute of Chemical Kinetics and Combustion, Institutskaya St., 3, 630090 Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - N E Polyakov
- Institute of Chemical Kinetics and Combustion, Institutskaya St., 3, 630090 Novosibirsk, Russia.,Institute of Solid State Chemistry and Mechanochemistry, Novosibirsk, Russia
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9
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Konieczny A, Conrad M, Ertl FJ, Gleixner J, Gattor AO, Grätz L, Schmidt MF, Neu E, Horn AHC, Wifling D, Gmeiner P, Clark T, Sticht H, Keller M. N-Terminus to Arginine Side-Chain Cyclization of Linear Peptidic Neuropeptide Y Y 4 Receptor Ligands Results in Picomolar Binding Constants. J Med Chem 2021; 64:16746-16769. [PMID: 34748345 DOI: 10.1021/acs.jmedchem.1c01574] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The family of neuropeptide Y (NPY) receptors comprises four subtypes (Y1R, Y2R, Y4R, Y5R), which are addressed by at least three endogenous peptides, i.e., NPY, peptide YY, and pancreatic polypeptide (PP), the latter showing a preference for Y4R. A series of cyclic oligopeptidic Y4R ligands were prepared by applying a novel approach, i.e., N-terminus to arginine side-chain cyclization. Most peptides acted as Y4R partial agonists, showing up to 60-fold higher Y4R affinity compared to the linear precursor peptides. Two cyclic hexapeptides (18, 24) showed higher Y4R potency (Ca2+ aequorin assay) and, with pKi values >10, also higher Y4R affinity compared to human pancreatic polypeptide (hPP). Compounds such as 18 and 24, exhibiting considerably lower molecular weight and considerably more pronounced Y4R selectivity than PP and previously described dimeric peptidic ligands with high Y4R affinity, represent promising leads for the preparation of labeled tool compounds and might support the development of drug-like Y4R ligands.
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Affiliation(s)
- Adam Konieczny
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Marcus Conrad
- Institute of Biochemistry, Emil-Fischer-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - Fabian J Ertl
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Jakob Gleixner
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Albert O Gattor
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Lukas Grätz
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Maximilian F Schmidt
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Eduard Neu
- Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstraße 25, D-91052 Erlangen, Germany
| | - Anselm H C Horn
- Institute of Biochemistry, Emil-Fischer-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - David Wifling
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Timothy Clark
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany.,Department of Chemistry and Pharmacy, Computer-Chemistry-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Nägelsbachstraße 25, D-91052 Erlangen, Germany
| | - Heinrich Sticht
- Institute of Biochemistry, Emil-Fischer-Center, Friedrich-Alexander-University Erlangen-Nürnberg, Fahrstraße 17, D-91054 Erlangen, Germany
| | - Max Keller
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
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10
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Höring C, Conrad M, Söldner CA, Wang J, Sticht H, Strasser A, Miao Y. Specific Engineered G Protein Coupling to Histamine Receptors Revealed from Cellular Assay Experiments and Accelerated Molecular Dynamics Simulations. Int J Mol Sci 2021; 22:10047. [PMID: 34576210 PMCID: PMC8467750 DOI: 10.3390/ijms221810047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 01/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are targets of extracellular stimuli and hence occupy a key position in drug discovery. By specific and not yet fully elucidated coupling profiles with α subunits of distinct G protein families, they regulate cellular responses. The histamine H2 and H4 receptors (H2R and H4R) are prominent members of Gs- and Gi-coupled GPCRs. Nevertheless, promiscuous G protein and selective Gi signaling have been reported for the H2R and H4R, respectively, the molecular mechanism of which remained unclear. Using a combination of cellular experimental assays and Gaussian accelerated molecular dynamics (GaMD) simulations, we investigated the coupling profiles of the H2R and H4R to engineered mini-G proteins (mG). We obtained coupling profiles of the mGs, mGsi, or mGsq proteins to the H2R and H4R from the mini-G protein recruitment assays using HEK293T cells. Compared to H2R-mGs expressing cells, histamine responses were weaker (pEC50, Emax) for H2R-mGsi and -mGsq. By contrast, the H4R selectively bound to mGsi. Similarly, in all-atom GaMD simulations, we observed a preferential binding of H2R to mGs and H4R to mGsi revealed by the structural flexibility and free energy landscapes of the complexes. Although the mG α5 helices were consistently located within the HR binding cavity, alternative binding orientations were detected in the complexes. Due to the specific residue interactions, all mG α5 helices of the H2R complexes adopted the Gs-like orientation toward the receptor transmembrane (TM) 6 domain, whereas in H4R complexes, only mGsi was in the Gi-like orientation toward TM2, which was in agreement with Gs- and Gi-coupled GPCRs structures resolved by X-ray/cryo-EM. These cellular and molecular insights support (patho)physiological profiles of the histamine receptors, especially the hitherto little studied H2R function in the brain, as well as of the pharmacological potential of H4R selective drugs.
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Affiliation(s)
- Carina Höring
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Marcus Conrad
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany
| | - Christian A Söldner
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany
| | - Jinan Wang
- Department of Computational Biology and Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Fahrstraße 17, 91054 Erlangen, Germany
- Erlangen National High Performance Computing Center (NHR@FAU), Friedrich-Alexander-University Erlangen-Nürnberg (FAU), 91058 Erlangen, Germany
| | - Andrea Strasser
- Institute of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, 93040 Regensburg, Germany
| | - Yinglong Miao
- Department of Computational Biology and Molecular Biosciences, University of Kansas, Lawrence, KS 66047, USA
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11
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Bouquiaux C, Castet F, Champagne B. Unravelling the Effects of Cholesterol on the Second-Order Nonlinear Optical Responses of Di-8-ANEPPS Dye Embedded in Phosphatidylcholine Lipid Bilayers. J Phys Chem B 2021; 125:10195-10212. [PMID: 34491062 DOI: 10.1021/acs.jpcb.1c05630] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cholesterol is known for its role in maintaining the correct fluidity and rigidity of the animals cell membranes and thus their functions. Assessing the content and the role of cholesterol in lipid bilayers is therefore of crucial importance for a deeper understanding and control of membrane functioning. In this computational work, we investigate bilayers built from three types of glycerophospholipid phosphatidylcholine (PC) lipids, namely dipalmitoylphosphatidylcholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and dioleoylphosphatidylcholine (DOPC), and containing different amounts of cholesterol by analyzing the second-harmonic generation (SHG) nonlinear optical (NLO) response of a probe molecule, di-8-ANEPPS, inserted into the membranes. This molecular property presents the advantage to be specific to interfacial regions such as lipid bilayers. To unravel these effects, Molecular Dynamics (MD) simulations have been performed on both DPPC and DOPC lipids by varying the cholesterol mole fraction (from 0 to 0.66), while POPC was only considered as a pure bilayer. In the case of the structural properties of the bilayers, all the analyses converge toward the same conclusion: as the mole fraction of cholesterol increases, the systems become more rigid, confirming the condensing effect of cholesterol. In addition, the chromophore is progressively more aligned with respect to the normal to the bilayer. On the contrary, addition of unsaturation disorders the lipid bilayers, with barely no impact on the alignment of the chromophore. Then, using the frames obtained from the MD simulations, the first hyperpolarizability β of the dye in its environment has been computed at the TDDFT level. On the one hand, the addition of cholesterol induces a progressive increase of the diagonal component the β tensor parallel to the bilayer normal. On the other hand, larger β values have been calculated for the unsaturated than for the saturated lipid systems. In summary, this study illustrates the relationship between the composition and structure of the bilayers and the NLO responses of the embedded dye.
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Affiliation(s)
- Charlotte Bouquiaux
- Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
| | - Frédéric Castet
- , Institut des Sciences Moléculaires, UMR 5255 CNRS, University of Bordeaux, cours de la Libération 351, F-33405 Talence Cedex, France
| | - Benoît Champagne
- Theoretical Chemistry Lab, Unit of Theoretical and Structural Physical Chemistry, Namur Institute of Structured Matter, University of Namur, rue de Bruxelles, 61, B-5000 Namur, Belgium
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12
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Shen H, Wu Z, Lu C. Extension of the CAVS model to the simulation of helical peptides in a membrane environment. Phys Chem Chem Phys 2021; 23:12850-12863. [PMID: 34060579 DOI: 10.1039/d1cp01238j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Considering the effect of peptide insertion on the dipole potential of the lipid membrane, we extend the CAVS coarse-grained (CG) model to the simulation of helical peptides in a membrane environment. In this approach, the CG scheme for a peptide backbone is similar to the treatment in the united-atom model, while we treated the side chain of an amino acid by grouping 1-3 heavy atoms into a CG unit. The CAVS CG force field for peptides is optimized by reproducing the experimental results for the backbone (φ, ψ) distribution and predicting the PMF profiles of transferring organic molecules in a lipid bilayer membrane obtained from all-atom simulations. The CAVS simulation of a helical peptide in a phosphatidylcholine (PC) lipid bilayer revealed that the insertion of a peptide increases the dipole potential of the PC lipid bilayer, in which the peptide and its neutralized ions make a significant contribution. Finally, we carried out the CAVS simulation for five different helical peptides in the PC lipid bilayer to explore the behavior of peptide tilt, showing excellent agreement with the all-atom simulations. Our work suggests that the peptide tilt should relieve the deformation stress from the lipid bilayer, and the peptide aggregation could reduce the peptide tilt by resisting the deformation stress from the surrounding lipids.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, Guizhou 550018, P. R. China.
| | - Zhenhua Wu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, P. R. China
| | - Chan Lu
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Education University, Guiyang, Guizhou 550018, P. R. China.
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13
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Capelli R, Gardin A, Empereur-mot C, Doni G, Pavan GM. A Data-Driven Dimensionality Reduction Approach to Compare and Classify Lipid Force Fields. J Phys Chem B 2021; 125:7785-7796. [PMID: 34254518 PMCID: PMC8311647 DOI: 10.1021/acs.jpcb.1c02503] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/30/2021] [Indexed: 01/05/2023]
Abstract
Molecular dynamics simulations of all-atom and coarse-grained lipid bilayer models are increasingly used to obtain useful insights for understanding the structural dynamics of these assemblies. In this context, one crucial point concerns the comparison of the performance and accuracy of classical force fields (FFs), which sometimes remains elusive. To date, the assessments performed on different classical potentials are mostly based on the comparison with experimental observables, which typically regard average properties. However, local differences of the structure and dynamics, which are poorly captured by average measurements, can make a difference, but these are nontrivial to catch. Here, we propose an agnostic way to compare different FFs at different resolutions (atomistic, united-atom, and coarse-grained), by means of a high-dimensional similarity metrics built on the framework of Smooth Overlap of Atomic Position (SOAP). We compare and classify a set of 13 FFs, modeling 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers. Our SOAP kernel-based metrics allows us to compare, discriminate, and correlate different FFs at different model resolutions in an unbiased, high-dimensional way. This also captures differences between FFs in modeling nonaverage events (originating from local transitions), for example, the liquid-to-gel phase transition in dipalmitoylphosphatidylcholine (DPPC) bilayers, for which our metrics allows us to identify nucleation centers for the phase transition, highlighting some intrinsic resolution limitations in implicit versus explicit solvent FFs.
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Affiliation(s)
- Riccardo Capelli
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca Degli Abruzzi 24, I-10129 Torino, Italy
| | - Andrea Gardin
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca Degli Abruzzi 24, I-10129 Torino, Italy
| | - Charly Empereur-mot
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario
Lugano, Campus Est, Via
la Santa 1, CH-6962 Lugano-Viganello, Switzerland
| | - Giovanni Doni
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario
Lugano, Campus Est, Via
la Santa 1, CH-6962 Lugano-Viganello, Switzerland
| | - Giovanni M. Pavan
- Department
of Applied Science and Technology, Politecnico
di Torino, Corso Duca Degli Abruzzi 24, I-10129 Torino, Italy
- Department
of Innovative Technologies, University of
Applied Sciences and Arts of Southern Switzerland, Polo Universitario
Lugano, Campus Est, Via
la Santa 1, CH-6962 Lugano-Viganello, Switzerland
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14
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Borocci S, Bozzuto G, Bombelli C, Ceccacci F, Formisano G, Stringaro A, Molinari A, Mancini G. How stereochemistry of lipid components can affect lipid organization and the route of liposome internalization into cells. NANOSCALE 2021; 13:11976-11993. [PMID: 34212969 DOI: 10.1039/d1nr02175c] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Though liposome-based drugs are in clinical use, the mechanism of cell internalization of liposomes is yet an object of controversy. The present experimental investigation, carried out on human glioblastoma cells, indicated different internalization routes for two diastereomeric liposomes. Molecular dynamics simulations of the lipid bilayers of the two formulations indicated that the different stereochemistry of a lipid component controls some parameters such as area per lipid molecule and fluidity of lipid membranes, surface potential and water organization at the lipid/water interface, all of which affect the interaction with biomolecules and cell components.
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Affiliation(s)
- Stefano Borocci
- Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, L.go dell'Università, s.n.c., 01100 Viterbo, Italy.
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15
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Shen H, Zou X, Yang H, Zhong W, Wang Y, Wang S, Deng M. Adsorption of Organic Molecules and Surfactants on Graphene: A Coarse-Grained Study. J Phys Chem A 2021; 125:700-711. [PMID: 33432811 DOI: 10.1021/acs.jpca.0c11111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The research studies on the adsorption of surfactants on graphene help us to know how to use surfactants to exfoliate graphene from graphite or functionalize the graphene surface. Among them, molecular dynamics (MD) simulation has been widely used to investigate the adsorption of organic molecules and surfactants on graphene. In particular, coarse-grained (CG) MD simulation greatly improves the computational efficiency by simplifying the complexity of the studied systems, allowing us to explore the structure and dynamics of complex systems on larger spatial scales and longer time scales. However, an accurate prediction of the adsorption of surfactants on graphene is required by optimizing the interaction between surfactants and graphene, which is often overlooked by some CG models. In this work, we found that an accurate prediction of the adsorption enthalpies of organic molecules on graphene can be achieved by optimizing the interactions between organic molecules and benzene. Meanwhile, we simulated the adsorption of a surfactant on single-layer and double-layer graphene nanosheets, respectively. Our results revealed that increasing the temperature would favor the interactions between hydrophilic groups of surfactants. In addition, we discovered that the surfactant prefers to be adsorbed on the inner surfaces of double-layer graphene compared with the outer surfaces, and this is owing to the dehydration in the middle of double-layer graphene, which is beneficial to the hydrophilic interactions between surfactant molecules inside the double-layer graphene.
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Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Xuefeng Zou
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Hengxiu Yang
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Wenhui Zhong
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Yu Wang
- School of Chemistry and Materials Sciences, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Shuiyi Wang
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Mingsen Deng
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
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16
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Moqadam M, Tubiana T, Moutoussamy EE, Reuter N. Membrane models for molecular simulations of peripheral membrane proteins. ADVANCES IN PHYSICS: X 2021. [DOI: 10.1080/23746149.2021.1932589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Affiliation(s)
- Mahmoud Moqadam
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Thibault Tubiana
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Nathalie Reuter
- Department of Chemistry, University of Bergen, Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
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17
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Shen H, Wu Z, Zou X. Interfacial Water Structure at Zwitterionic Membrane/Water Interface: The Importance of Interactions between Water and Lipid Carbonyl Groups. ACS OMEGA 2020; 5:18080-18090. [PMID: 32743182 PMCID: PMC7391366 DOI: 10.1021/acsomega.0c01633] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/07/2020] [Indexed: 06/11/2023]
Abstract
In this work, atomistic molecular dynamics (MD) simulations of palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer were carried out to investigate the effect of water models on membrane dipole potential, which is primarily associated with the preferential orientation of molecular dipoles at the membrane-water interface. We discovered that the overestimation of the dipole potential by the TIPS3P water model can be effectively reduced by the TIP4P water model. On the one hand, the TIP4P water model decreases the negative contribution of lipid to the dipole potential through influencing the orientation of lipid headgroups. On the other hand, the TIP4P water model reduces the positive contribution of water to the dipole potential by increasing the preference of H-down orientation (the water dipole orients toward the bilayer center). Interestingly, the TIP4P water model affects the orientation of interfacial water molecules more obviously than that of lipid headgroups, leading to the decrease in the dipole potential. Furthermore, the MD results revealed that the water close to the positively charged choline (namely, N-associated water) prefers the H-down orientation while the water around the negatively charged phosphate (namely, P-associated water) favors the H-up orientation, in support of recent experimental and MD studies. However, interfacial water molecules are more strongly influenced by the phosphate groups than by the choline groups, resulting in the net H-up orientation (the water dipole orients toward the bilayer center) in the region of lipid headgroups. In addition, it is intriguing that the preference of H-up orientation decreases when water molecules penetrate more deeply into the lipid bilayer. This is attributed to the counteracting effect of lipid carbonyl groups, and the effect varies with the lipid chains (oleoyl and palmitoyl chains), suggesting the important role of lipid carbonyl groups.
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Affiliation(s)
- Hujun Shen
- Guizhou
Provincial Key Laboratory of Computational Nano-Material Science,
Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced
Manufacturing Technology, Guizhou Education
University, No. 115,
Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
- Guizhou
University of Finance and Economics, School of Information, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Zhenhua Wu
- Guizhou
University of Finance and Economics, School of Information, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Xuefeng Zou
- Guizhou
Provincial Key Laboratory of Computational Nano-Material Science,
Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced
Manufacturing Technology, Guizhou Education
University, No. 115,
Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
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18
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Thai NQ, Theodorakis PE, Li MS. Fast Estimation of the Blood-Brain Barrier Permeability by Pulling a Ligand through a Lipid Membrane. J Chem Inf Model 2020; 60:3057-3067. [PMID: 32469527 PMCID: PMC7588033 DOI: 10.1021/acs.jcim.9b00834] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The blood–brain barrier (BBB)
is a physical barrier that
regulates the homeostasis of the neural microenvironment. A relative
estimate of the BBB permeability, which is important for drug design,
may be experimentally provided by the logBB (the blood–brain
concentration ratio) and the logPS (permeability–surface-area
product), while many computational methods aim to identify key properties
that correlate well with these quantities. Although currently existing
computational methods (e.g., quantitative structure activity relation)
have made a significant contribution in screening various compounds
that could potentially translocate through the BBB, they are unable
to provide a physical explanation of the underlying processes and
they can often be computationally demanding. Here, we use steered
molecular dynamics simulation to estimate the BBB permeability of
various compounds on the basis of simple lipid–membrane models
by computing the nonequilibrium work, Wneq, produced by pulling the compounds through the membrane. We found
that the values of Wneq correlate remarkably
well with logBB and logPS for a range of compounds and different membrane
types and pulling speeds, independently of the choice of force field.
Moreover, our results provide insight into the role of hydrogen bonds,
the energetic barriers, and the forces exerted on the ligands during
their pulling. Our method is computationally easy to implement and
fast. Therefore, we anticipate that it could provide a reliable prescreening
tool for estimating the relative permeability of the BBB to various
substances.
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Affiliation(s)
- Nguyen Quoc Thai
- Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 700000, Vietnam.,Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City 870000, Dong Thap, Vietnam
| | | | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, 02-668 Warsaw, Poland
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19
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Mustafa G, Nandekar PP, Mukherjee G, Bruce NJ, Wade RC. The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics. Sci Rep 2020; 10:7284. [PMID: 32350331 PMCID: PMC7190701 DOI: 10.1038/s41598-020-64129-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 04/13/2020] [Indexed: 11/24/2022] Open
Abstract
The simulation of membrane proteins requires compatible protein and lipid force fields that reproduce the properties of both the protein and the lipid bilayer. Cytochrome P450 enzymes are bitopic membrane proteins with a transmembrane helical anchor and a large cytosolic globular domain that dips into the membrane. As such, they are representative and challenging examples of membrane proteins for simulations, displaying features of both peripheral and integral membrane proteins. We performed molecular dynamics simulations of three cytochrome P450 isoforms (2C9, 2C19 and 1A1) in a 2-oleoyl-1-palmitoyl-sn-glycerol-3-phosphocholine bilayer using two AMBER force field combinations: GAFF-LIPID with ff99SB for the protein, and LIPID14 with ff14SB for the protein. Comparison of the structural and dynamic properties of the proteins, the lipids and the protein-membrane interactions shows differing sensitivity of the cytochrome P450 isoforms to the choice of force field, with generally better agreement with experiment for the LIPID14 + ff14SB combination.
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Affiliation(s)
- Ghulam Mustafa
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,B-Zell-Immunologie (D130), German Cancer Research Center, Deutsches Krebsforschungszentrum (DKF), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Prajwal P Nandekar
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120, Heidelberg, Germany.,Schrodinger Inc. #147, 3rd Floor, Jawaharlal Nehru main road, Above State Bank of India, Channasandra, 5th Stage, RR Nagar, Bengaluru, 560098, India
| | - Goutam Mukherjee
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120, Heidelberg, Germany
| | - Neil J Bruce
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Heidelberg, Germany. .,Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, INF 282, 69120, Heidelberg, Germany. .,Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, INF 368, 69120, Heidelberg, Germany.
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20
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Loschwitz J, Olubiyi OO, Hub JS, Strodel B, Poojari CS. Computer simulations of protein-membrane systems. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 170:273-403. [PMID: 32145948 PMCID: PMC7109768 DOI: 10.1016/bs.pmbts.2020.01.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The interactions between proteins and membranes play critical roles in signal transduction, cell motility, and transport, and they are involved in many types of diseases. Molecular dynamics (MD) simulations have greatly contributed to our understanding of protein-membrane interactions, promoted by a dramatic development of MD-related software, increasingly accurate force fields, and available computer power. In this chapter, we present available methods for studying protein-membrane systems with MD simulations, including an overview about the various all-atom and coarse-grained force fields for lipids, and useful software for membrane simulation setup and analysis. A large set of case studies is discussed.
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Affiliation(s)
- Jennifer Loschwitz
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Olujide O Olubiyi
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Jochen S Hub
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany
| | - Birgit Strodel
- Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
| | - Chetan S Poojari
- Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany.
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21
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Li C, Qin Z, Han W. Bottom-up derived flexible water model with dipole and quadrupole moments for coarse-grained molecular simulations. Phys Chem Chem Phys 2020; 22:27394-27412. [DOI: 10.1039/d0cp04185h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A bottom-up CG water model is developed to capture the electrostatic multipoles, structural correlation and thermodynamics of water.
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Affiliation(s)
- Chen Li
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Zhongyuan Qin
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
| | - Wei Han
- State Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Peking University Shenzhen Graduate School
- Shenzhen
- China
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22
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Ilyina MG, Khamitov EM, Galiakhmetov RN, Mustafin IA, Akhmetov AF, Shayakhmetova RK, Mustafin AG. Light gasoil of catalytic cracking: A quantitative description of the physical properties by joint use of chromato‐mass‐spectrometry and molecular dynamics. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.201800342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Margarita G. Ilyina
- Faculty of Chemistry, Chair of Physical Chemistry and Chemical Ecology, Bashkir State University Ufa Russia
| | - Edward M. Khamitov
- Laboratory of Quantum Chemistry and Molecular Dynamics of the Department of Chemistry and Technology, Institute of Petroleum Refining and Petrochemistry Ufa Russia
- Russian Academy of Sciences, Laboratory of Chemical PhysicsUfa Institute of Chemistry Ufa Russia
| | | | - Ildar A. Mustafin
- Technological Faculty, Department of Oil and Gas Technology, Ufa State Petroleum Technological University Ufa Russia
| | - Arslan F. Akhmetov
- Technological Faculty, Department of Oil and Gas Technology, Ufa State Petroleum Technological University Ufa Russia
| | - Regina Kh. Shayakhmetova
- Faculty of Chemistry, Chair of Physical Chemistry and Chemical Ecology, Bashkir State University Ufa Russia
| | - Akhat G. Mustafin
- Faculty of Chemistry, Chair of Physical Chemistry and Chemical Ecology, Bashkir State University Ufa Russia
- Russian Academy of Sciences, Laboratory of Chemical PhysicsUfa Institute of Chemistry Ufa Russia
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23
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Wifling D, Pfleger C, Kaindl J, Ibrahim P, Kling RC, Buschauer A, Gohlke H, Clark T. Basal Histamine H 4 Receptor Activation: Agonist Mimicry by the Diphenylalanine Motif. Chemistry 2019; 25:14613-14624. [PMID: 31498478 PMCID: PMC7687114 DOI: 10.1002/chem.201902801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/08/2019] [Indexed: 12/20/2022]
Abstract
Histamine H4 receptor (H4 R) orthologues are G-protein-coupled receptors (GPCRs) that exhibit species-dependent basal activity. In contrast to the basally inactive mouse H4 R (mH4 R), human H4 R (hH4 R) shows a high degree of basal activity. We have performed long-timescale molecular dynamics simulations and rigidity analyses on wild-type hH4 R, the experimentally characterized hH4 R variants S179M, F169V, F169V+S179M, F168A, and on mH4 R to investigate the molecular nature of the differential basal activity. H4 R variant-dependent differences between essential motifs of GPCR activation and structural stabilities correlate with experimentally determined basal activities and provide a molecular explanation for the differences in basal activation. Strikingly, during the MD simulations, F16945.55 dips into the orthosteric binding pocket only in the case of hH4 R, thus adopting the role of an agonist and contributing to the stabilization of the active state. The results shed new light on the molecular mechanism of basal H4 R activation that are of importance for other GPCRs.
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Affiliation(s)
- David Wifling
- Department of Pharmaceutical/Medicinal Chemistry IIInstitute of PharmacyUniversity of RegensburgUniversitätsstr. 3193053RegensburgGermany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Jonas Kaindl
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Passainte Ibrahim
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Ralf C. Kling
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Armin Buschauer
- Department of Pharmaceutical/Medicinal Chemistry IIInstitute of PharmacyUniversity of RegensburgUniversitätsstr. 3193053RegensburgGermany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
- John von Neumann Institute for Computing (NIC)Jülich Supercomputing Centre (JSC) &Institute for Complex Systems—Structural Biochemistry (ICS 6)Forschungszentrum Jülich GmbHWilhelm-Johnen-Str.52425JülichGermany
| | - Timothy Clark
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
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24
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Sumikama T, Oiki S. Queueing arrival and release mechanism for K + permeation through a potassium channel. J Physiol Sci 2019; 69:919-930. [PMID: 31456113 PMCID: PMC10717923 DOI: 10.1007/s12576-019-00706-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 08/18/2019] [Indexed: 01/26/2023]
Abstract
The mechanism underlying ion permeation through potassium channels still remains controversial. K+ ions permeate across a narrow selectivity filter (SF) in a single file. Conventional scenarios assume that K+ ions are tightly bound in the SF, and, thus, they are displaced from their energy well by ion-ion repulsion with an incoming ion. This tight coupling between entering and exiting ions has been called the "knock-on" mechanism. However, this paradigm is contradicted by experimental data measuring the water-ion flux coupling ratio, demonstrating fewer ion occupancies. Here, the results of molecular dynamics simulations of permeation through the KcsA potassium channel revealed an alternative mechanism. In the aligned ions in the SF (an ion queue), the outermost K+ was readily and spontaneously released toward the extracellular space, and the affinity of the relevant ion was ~ 50 mM. Based on this low-affinity regime, a simple queueing mechanism described by loose coupling of entering and exiting ions is proposed.
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Affiliation(s)
- Takashi Sumikama
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan
| | - Shigetoshi Oiki
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan.
- Biomedical Imaging Research Center, University of Fukui, Fukui, 910-1193, Japan.
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25
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Hakobyan D, Heuer A. Comparing an All-Atom and a Coarse-Grained Description of Lipid Bilayers in Terms of Enthalpies and Entropies: From MD Simulations to 2D Lattice Models. J Chem Theory Comput 2019; 15:6393-6402. [DOI: 10.1021/acs.jctc.9b00390] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Davit Hakobyan
- Institute of Physical Chemistry, WWU Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
- Center for Multiscale Theory and Computation (CMTC), WWU Muenster, 48149 Muenster, Germany
| | - Andreas Heuer
- Institute of Physical Chemistry, WWU Muenster, Corrensstr. 28/30, 48149 Muenster, Germany
- Center for Multiscale Theory and Computation (CMTC), WWU Muenster, 48149 Muenster, Germany
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26
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Münzberg E, Stein M. Structure and Dynamics of Mono- vs. Doubly Lipidated Rab5 in Membranes. Int J Mol Sci 2019; 20:ijms20194773. [PMID: 31561436 PMCID: PMC6801778 DOI: 10.3390/ijms20194773] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/25/2019] [Accepted: 09/25/2019] [Indexed: 01/13/2023] Open
Abstract
The Rab5 small GTPase is a regulator of endosomal trafficking and vesicle fusion. It possesses two adjacent cysteine residues for post-translational geranylgeranylation at its C-terminus for the protein to associate with the early endosome membrane. We compare the effect of mono-lipidification of only one cysteine residue with the doubly modified, fully functional Rab protein in both guanosine diphosphate (GDP)- and guanosine triphosphate (GTP)-bound states and in different membranes (one, three, and six-component membranes). Molecular simulations show that the mono-geranylgeranylated protein is less strongly associated with the membranes and diffuses faster than the doubly lipidated protein. The geranylgeranyl anchor membrane insertion depth is smaller and the protein–membrane distance distribution is broad and uncharacteristic for the membrane composition. The mono-geranylgeranylated protein reveals an unspecific association with the membrane and an orientation at the membrane that does not allow a nucleotide-specific recruitment of further effector proteins. This work shows that double-lipidification is critical for Rab5 to perform its physiological function and mono-geranylgeranylation renders it membrane-associated but non-functional.
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Affiliation(s)
- Eileen Münzberg
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany.
| | - Matthias Stein
- Max Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany.
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27
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Calvelo M, Granja JR, Garcia-Fandino R. Competitive double-switched self-assembled cyclic peptide nanotubes: a dual internal and external control. Phys Chem Chem Phys 2019; 21:20750-20756. [PMID: 31513191 DOI: 10.1039/c9cp02327e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
"Intelligent" materials based on synthetic small molecules that become functional only under specific conditions provide new opportunities for developing regulated systems aimed at a large number of applications. For instance, biologically active supramolecular entities that are sensitive to environmental conditions, such as the presence of bacterial membranes, are extremely interesting in biomedicine. In this work, we have designed and investigated, using molecular dynamics simulations, a doubly modulable nanotube formed by the self-assembly of cyclic peptides sensitive to both the presence of a lipid membrane and the pH of the aqueous media. The cyclic peptides were designed to self-assemble into peptide nanotubes in the presence of a lipid bilayer and at low pH values. Under these conditions, the residual side chains point outside the cyclic peptides, being exposed to the lipid bilayer, and the inner groups (carboxylic acids) are protonated, thus allowing the permeation of water and preventing that of ions. Higher pH values are expected to create carboxylate groups at the lumen of the peptides, leading to the disassembly of the nanotube, the attraction and translocation of ions towards the hydrophobic core of the bilayer, and eventually killing the target malignant cells. Our results suggest that by introducing a second switch in a membrane sensitive system, it is possible to modulate its interaction with the lipid bilayer. This opens the door to new strategies for the preparation of antimicrobial peptides that interact at the membrane level.
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Affiliation(s)
- Martín Calvelo
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Juan R Granja
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
| | - Rebeca Garcia-Fandino
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain.
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28
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Barrera EE, Machado MR, Pantano S. Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane-Protein Dynamics. J Chem Theory Comput 2019; 15:5674-5688. [PMID: 31433946 DOI: 10.1021/acs.jctc.9b00435] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The capability to handle highly heterogeneous molecular assemblies in a consistent manner is among the greatest challenges faced when deriving simulation parameters. This is particularly the case for coarse-grained (CG) simulations in which chemical functional groups are lumped into effective interaction centers for which transferability between different chemical environments is not guaranteed. Here, we introduce the parametrization of a set of CG phospholipids compatible with the latest version of the SIRAH force field for proteins. The newly introduced lipid species include different acylic chain lengths and partial unsaturation, as well as polar and acidic head groups that show a very good reproduction of structural membrane determinants, such as areas per lipid, thickness, order parameter, etc., and their dependence with temperature. Simulation of membrane proteins showed unprecedented accuracy in the unbiased description of the thickness-dependent membrane-protein orientation in systems where this information is experimentally available (namely, the SarcoEndoplasmic Reticulum Calcium-SERCA-pump and its regulator Phospholamban). The interactions that lead to this faithful reproduction can be traced down to the single amino acid-lipid interaction level and show full agreement with biochemical data present in the literature. Finally, the present parametrization is implemented in the GROMACS and AMBER simulation packages facilitating its use by a wide portion of the biocomputing community.
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Affiliation(s)
- Exequiel E Barrera
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Matías R Machado
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay
| | - Sergio Pantano
- Biomolecular Simulations Group , Institut Pasteur de Montevideo , Mataojo 2020 , CP 11400 Montevideo , Uruguay.,Shanghai Institute for Advanced Immunochemical Studies , ShanghaiTech University , Shanghai 201210 , China
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29
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Temperature Dependence of the Structure and Dynamics of a Dye-Labeled Lipid in a Planar Phospholipid Bilayer: A Computational Study. J Membr Biol 2019; 252:227-240. [PMID: 31332471 DOI: 10.1007/s00232-019-00081-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
Fluorescent probes are widely employed to label lipids for the investigation of structural and dynamic properties of model and cell membranes through optical microscopy techniques. Although the effect of tagging a lipid with an organic dye is generally assumed to be negligible, optically modified lipids can nonetheless affect the local lipid structure and, in turn, the lipid lateral mobility. To better assess this potential issue, all-atom (MD) molecular dynamics simulations have been performed to study structural and dynamic effects in a model DOPC membrane in the presence of a standard Rhodamine B-labeled DOPE lipid (RHB) as a function of temperature, i.e., 293 K, 303 K, and 320 K. As the temperature is increased, we observe similar changes in the structural properties of both pure DOPC and RHB-DOPC lipid bilayers: an increase of the area per lipid, a reduction of the membrane thickness and a decrease of lipid order parameters. The partial density profile of the RHB headgroups and their orientation within the lipid bilayer confirm the amphiphilic nature of the RHB fluorescent moiety, which mainly partitions in the DOPC glycerol backbone region at each temperature. Moreover, at all temperatures, our results on lipid lateral diffusion support a non-neutral role of the dye with respect to the unlabeled lipid mobility, thus suggesting important implications for optical microscopy studies of lipid membranes.
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30
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Kim AV, Shelepova EA, Selyutina OY, Meteleva ES, Dushkin AV, Medvedev NN, Polyakov NE, Lyakhov NZ. Glycyrrhizin-Assisted Transport of Praziquantel Anthelmintic Drug through the Lipid Membrane: An Experiment and MD Simulation. Mol Pharm 2019; 16:3188-3198. [PMID: 31198045 DOI: 10.1021/acs.molpharmaceut.9b00390] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Praziquantel (PZQ) is one of the most widespread anthelmintic drugs. However, the frequent insufficient application of PZQ after oral administration is associated with its low solubility, penetration rate, and bioavailability. In the present study, the permeation of PZQ through a 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC) membrane was investigated to probe glycyrrhizin-assisted transport. Glycyrrhizin (or glycyrrhizic acid, GA), a natural saponin, shows the ability to enhance the therapeutic activity of various drugs when it is used as a drug delivery system. However, the molecular mechanism of this effect is still under debate. In the present study, the transport rate was measured experimentally by a parallel artificial membrane permeation assay (PAMPA) and molecular dynamics (MD) simulation with DOPC lipid bilayers. The formation of the noncovalent supramolecular complex of PZQ with disodium salt of GA (Na2GA) in an aqueous solution was proved by the NMR relaxation technique. PAMPA experiments show a strong increase in the amount of the penetrating praziquantel molecules in comparison with a saturated aqueous solution of pure drug used as a control. MD simulation of PZQ penetration through the bilayer demonstrates an increase in permeability into the membrane in the presence of a glycyrrhizin molecule. A decrease in the free energy barrier in the middle of the lipid bilayer was obtained, associated with the hydrogen bond between PZQ and GA. Also, GA reduces the local bilayer surface resistance to penetration of PZQ by rearranging the surface lipid headgroups. This study clarifies the mechanism of increasing the drug's bioavailability in the presence of glycyrrhizin.
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Affiliation(s)
- Alexandra V Kim
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Ekaterina A Shelepova
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Olga Yu Selyutina
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia
| | - Elizaveta S Meteleva
- Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
| | - Alexander V Dushkin
- Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
| | - Nikolai N Medvedev
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Novosibirsk State University , 630090 Novosibirsk , Russia
| | - Nikolay E Polyakov
- Institute of Chemical Kinetics and Combustion , Institutskaya Street, 3 , 630090 , Novosibirsk , Russia.,Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
| | - Nikolay Z Lyakhov
- Institute of Solid State Chemistry and Mechanochemistry , 630128 Novosibirsk , Russia
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31
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A Metadynamics-Based Protocol for the Determination of GPCR-Ligand Binding Modes. Int J Mol Sci 2019; 20:ijms20081970. [PMID: 31013635 PMCID: PMC6514967 DOI: 10.3390/ijms20081970] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/12/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are a main drug target and therefore a hot topic in pharmaceutical research. One important prerequisite to understand how a certain ligand affects a GPCR is precise knowledge about its binding mode and the specific underlying interactions. If no crystal structure of the respective complex is available, computational methods can be used to deduce the binding site. One of them are metadynamics simulations which have the advantage of an enhanced sampling compared to conventional molecular dynamics simulations. However, the enhanced sampling of higher-energy states hampers identification of the preferred binding mode. Here, we present a novel protocol based on clustering of multiple walker metadynamics simulations which allows identifying the preferential binding mode from such conformational ensembles. We tested this strategy for three different model systems namely the histamine H1 receptor in combination with its physiological ligand histamine, as well as the β2 adrenoceptor with its agonist adrenaline and its antagonist alprenolol. For all three systems, the proposed protocol was able to reproduce the correct binding mode known from the literature suggesting that the approach can more generally be applied to the prediction of GPCR ligand binding in future.
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32
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Cardenas AE, Anderson CM, Elber R, Webb LJ. Partition of Positively and Negatively Charged Tryptophan Ions in Membranes with Inverted Phospholipid Heads: Simulations and Experiments. J Phys Chem B 2019; 123:3272-3281. [PMID: 30912653 DOI: 10.1021/acs.jpcb.9b00754] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A joint experimental and computational study illustrates that the partitioning of positively and negatively charged tryptophan in a phospholipid bilayer is significantly altered by a reversal in the head group dipole arrangement. Experiments were conducted using tryptophan as a fluorescent reporter of its local environment. Based on the experimental design in a recent publication ( Anderson , C. M. ; Cardenas , A. ; Elber , R. ; Webb , L. J. J. Phys. Chem. B 2018 , 123 , 170 - 179 ), we were able to determine that the arrangement of the head group dipole altered the degree of partitioning of charged tryptophan in the lipid bilayer. In parallel, atomically detailed simulations were performed for the two membrane systems. The simulation results are in accord with the experimental findings and support a simple molecular partition mechanism of electrostatic interactions with the head groups, glycerol linkers, and interfacial water dipoles.
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33
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Shahane G, Ding W, Palaiokostas M, Orsi M. Physical properties of model biological lipid bilayers: insights from all-atom molecular dynamics simulations. J Mol Model 2019; 25:76. [PMID: 30806797 DOI: 10.1007/s00894-019-3964-0] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 02/07/2019] [Indexed: 02/04/2023]
Abstract
The physical properties of lipid bilayers are sensitive to the specific type and composition of the lipids that make up the many different types of cell membranes. Studying model bilayers of representative heterogeneous compositions can provide key insights into membrane functionality. In this work, we use atomistic molecular dynamics simulations to characterize key properties in a number of bilayer membranes of varying composition. We first examine basic properties, such as lipid area, volume, and bilayer thickness, of simple, homogeneous bilayers comprising several lipid types, which are prevalent in biological membranes. Such lipids are then used in simulations of heterogeneous systems representative of bacterial, mammalian, and cancer membranes. Our analysis is especially focused on depth-dependent, transmembrane profiles; in particular, we calculate lateral pressure and dipole potential profiles, two fundamental properties which play key roles in a large number of biological functions.
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Affiliation(s)
- Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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34
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Brukhno AV, Grant J, Underwood TL, Stratford K, Parker SC, Purton JA, Wilding NB. DL_MONTE: a multipurpose code for Monte Carlo simulation. MOLECULAR SIMULATION 2019. [DOI: 10.1080/08927022.2019.1569760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- A. V. Brukhno
- Scientific Computing Department, STFC, Daresbury Laboratory, Warrington, UK
| | - J. Grant
- Department of Chemistry, University of Bath, Bath, UK
- Computing Services, University of Bath, Bath, UK
| | | | | | - S. C. Parker
- Department of Chemistry, University of Bath, Bath, UK
| | - J. A. Purton
- Scientific Computing Department, STFC, Daresbury Laboratory, Warrington, UK
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35
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Söldner CA, Horn AHC, Sticht H. Binding of histamine to the H1 receptor-a molecular dynamics study. J Mol Model 2018; 24:346. [PMID: 30498974 DOI: 10.1007/s00894-018-3873-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/05/2018] [Indexed: 02/06/2023]
Abstract
Binding of histamine to the G-protein coupled histamine H1 receptor plays an important role in the context of allergic reactions; however, no crystal structure of the resulting complex is available yet. To deduce the histamine binding site, we performed unbiased molecular dynamics (MD) simulations on a microsecond time scale, which allowed to monitor one binding event, in which particularly the residues of the extracellular loop 2 were involved in the initial recognition process. The final histamine binding pose in the orthosteric pocket is characterized by interactions with Asp1073.32, Tyr1083.33, Thr1945.43, Asn1985.46, Trp4286.48, Tyr4316.51, Phe4326.52, and Phe4356.55, which is in agreement with existing mutational data. The conformational stability of the obtained complex structure was subsequently confirmed in 2 μs equilibrium MD simulations, and a metadynamics simulation proved that the detected binding site represents an energy minimum. A complementary investigation of a D107A mutant, which has experimentally been shown to abolish ligand binding, revealed that this exchange results in a significantly weaker interaction and enhanced ligand dynamics. This finding underlines the importance of the electrostatic interaction between the histamine ammonium group and the side chain of Asp1073.32 for histamine binding.
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Affiliation(s)
- Christian A Söldner
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), , Fahrstraße 17, 91054, Erlangen, Germany
| | - Anselm H C Horn
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), , Fahrstraße 17, 91054, Erlangen, Germany
| | - Heinrich Sticht
- Bioinformatik, Institut für Biochemie, Emil-Fischer-Centrum, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), , Fahrstraße 17, 91054, Erlangen, Germany.
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36
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Shen H, Wu Z, Deng M, Wen S, Gao C, Li S, Wu X. Molecular Dynamics Simulations of Ether- and Ester-Linked Phospholipid Bilayers: A Comparative Study of Water Models. J Phys Chem B 2018; 122:9399-9408. [DOI: 10.1021/acs.jpcb.8b06726] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hujun Shen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
- School of Information, Guizhou University of Finance and Economics, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Zhenhua Wu
- School of Information, Guizhou University of Finance and Economics, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Mingsen Deng
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
- School of Information, Guizhou University of Finance and Economics, University City of Huaxi District, Guiyang, Guizhou 550025, P. R. China
| | - Shuiguo Wen
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Chenggui Gao
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Shixiong Li
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
| | - Xupu Wu
- Guizhou Provincial Key Laboratory of Computational Nano-Material Science, Guizhou Synergetic Innovation Center of Scientific Big Data for Advanced Manufacturing Technology, Guizhou Education University, No. 115, Gaoxin Road, Guiyang, Guizhou 550018, P. R. China
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37
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Tang J, Yin H, Ma J, Bo W, Yang Y, Xu J, Liu Y, Gong Y. Terahertz Electric Field-Induced Membrane Electroporation by Molecular Dynamics Simulations. J Membr Biol 2018; 251:681-693. [PMID: 30094474 DOI: 10.1007/s00232-018-0045-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/02/2018] [Indexed: 10/28/2022]
Abstract
In this paper, the membrane electroporation induced by the terahertz electric field is simulated by means of the molecular dynamics method. The influences of the waveform and frequency of the applied terahertz electric field on the electroporation and the unique features of the process of the electroporation with the applied terahertz electric field are given. It shows that whether the electroporation can happen depends on the waveform of the applied terahertz electric field when the magnitude is not large enough. No pore appears if the terahertz electric field direction periodically reverses, and dipole moments of the interfacial water and the bulk water keep reversing. The nm-scale single pore forms with the applied terahertz trapezoidal electric field. It is found that the average pore formation time is strongly influenced by the terahertz electric field frequency. An abnormal variation region that shows decline exists on the correlation curve of the average pore formation time and the trapezoidal electric field frequency, whereas the overall trend of the curve is increasing. The decrease of the water oriented polarization degree results in the increase of the electroporation time, and the abnormal variation region appearance may be related to the drastic change of average water hydrogen bond number that is resulted from the resonance of water hydrogen bond network and the applied electric field. Compared to the nanosecond electric pulse and constant electric field, the numbers of the water protrusions and the water bridges are smaller and the pore formation time is relatively longer with the applied terahertz electric field.
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Affiliation(s)
- Jingchao Tang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.,Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Hairong Yin
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.,Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jialu Ma
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.,Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Wenfei Bo
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.,Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yang Yang
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.,Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jin Xu
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.,Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yiyao Liu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yubin Gong
- School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, Sichuan, China. .,Center for Information in Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China.
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38
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Rezaei Sani SM, Akhavan M, Jalili S. Salt-induced effects on natural and inverse DPPC lipid membranes: Molecular dynamics simulation. Biophys Chem 2018; 239:7-15. [DOI: 10.1016/j.bpc.2018.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/22/2018] [Accepted: 04/22/2018] [Indexed: 11/29/2022]
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39
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Voloshin VP, Kim AV, Shelepova EA, Medvedev NN. Determination of the Boundary Surface Between the Lipid Bilayer and Water. J STRUCT CHEM+ 2018. [DOI: 10.1134/s0022476618010146] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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40
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Nguyen TH, Zhang C, Weichselbaum E, Knyazev DG, Pohl P, Carloni P. Interfacial water molecules at biological membranes: Structural features and role for lateral proton diffusion. PLoS One 2018; 13:e0193454. [PMID: 29474432 PMCID: PMC5825111 DOI: 10.1371/journal.pone.0193454] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/26/2018] [Indexed: 11/19/2022] Open
Abstract
Proton transport at water/membrane interfaces plays a fundamental role for a myriad of bioenergetic processes. Here we have performed ab initio molecular dynamics simulations of proton transfer along two phosphatidylcholine bilayers. As found in previous theoretical studies, the excess proton is preferably located at the water/membrane interface. Further, our simulations indicate that it interacts not only with phosphate head groups, but also with water molecules at the interfaces. Interfacial water molecules turn out to be oriented relative to the lipid bilayers, consistently with experimental evidence. Hence, the specific water-proton interaction may help explain the proton mobility experimentally observed at the membrane interface.
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Affiliation(s)
- Trung Hai Nguyen
- Computational Biomedicine (IAS-5 / INM-9) Forschungszentrum Jülich, Jülich, Germany, RWTH Aachen University, Aachen, Germany
| | - Chao Zhang
- Computational Biomedicine (IAS-5 / INM-9) Forschungszentrum Jülich, Jülich, Germany, RWTH Aachen University, Aachen, Germany
- * E-mail: (CZ); (PC)
| | | | - Denis G. Knyazev
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Peter Pohl
- Institute of Biophysics, Johannes Kepler University Linz, Linz, Austria
| | - Paolo Carloni
- Computational Biomedicine (IAS-5 / INM-9) Forschungszentrum Jülich, Jülich, Germany, RWTH Aachen University, Aachen, Germany
- * E-mail: (CZ); (PC)
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41
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Chu H, Peng X, Li Y, Zhang Y, Min H, Li G. Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1436201] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Huiying Chu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
| | - Xiangda Peng
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
| | - Yuebin Zhang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
| | - Hanyi Min
- Chinese Academy of Medical Science & Peking Union Medical College Hospital, Ophthalmology, Beijing, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Liaoning, China
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42
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A Polarizable Atomic Multipole-Based Force Field for Molecular Dynamics Simulations of Anionic Lipids. Molecules 2017; 23:molecules23010077. [PMID: 29301229 PMCID: PMC6017617 DOI: 10.3390/molecules23010077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 12/26/2017] [Accepted: 12/28/2017] [Indexed: 11/18/2022] Open
Abstract
In all of the classical force fields, electrostatic interaction is simply treated and explicit electronic polarizability is neglected. The condensed-phase polarization, relative to the gas-phase charge distributions, is commonly accounted for in an average way by increasing the atomic charges, which remain fixed throughout simulations. Based on the lipid polarizable force field DMPC and following the same framework as Atomic Multipole Optimized Energetics for BiomoleculAr (AMOEBA) simulation, the present effort expands the force field to new anionic lipid models, in which the new lipids contain DMPG and POPS. The parameters are compatible with the AMOEBA force field, which includes water, ions, proteins, etc. The charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments, which are derived from the ab initio gas phase calculations. Many-body polarization including the inter- and intramolecular polarization is modeled in a consistent manner with distributed atomic polarizabilities. Molecular dynamics simulations of the two aqueous DMPG and POPS membrane bilayer systems, consisting of 72 lipids with water molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, electrostatic potential difference between the center of the bilayer and water are all calculated, and compared with limited experimental data.
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43
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Ding W, Palaiokostas M, Shahane G, Wang W, Orsi M. Effects of High Pressure on Phospholipid Bilayers. J Phys Chem B 2017; 121:9597-9606. [PMID: 28926699 DOI: 10.1021/acs.jpcb.7b07119] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The response of lipid membranes to changes in external pressure is important for many biological processes, and it can also be exploited for technological applications. In this work, we employ all-atom molecular dynamics simulations to characterize the changes in the physical properties of phospholipid bilayers brought about by high pressure (1000 bar). In particular, we study how the response differs, in relation to different chain unsaturation levels, by comparing monounsaturated 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) and biunsaturated dioleoyl-phosphatidylcholine (DOPC) bilayers. Various structural, mechanical, and dynamical features are found to be altered by the pressure increase in both bilayers. Notably, for most properties, including bilayer area and thickness, lipid order parameters, lateral pressure profile, and curvature frustration energy, we observe significantly more pronounced effects for monounsaturated POPC than biunsaturated DOPC. Possible biological implications of the results obtained are discussed, especially in relation to how different lipids can control the structure and function of membrane proteins.
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Affiliation(s)
- Wei Ding
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London E1 4NS, U.K
| | - Michail Palaiokostas
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London E1 4NS, U.K
| | - Ganesh Shahane
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London E1 4NS, U.K
| | - Wen Wang
- School of Engineering & Materials Science, Queen Mary University of London , Mile End Road, London E1 4NS, U.K
| | - Mario Orsi
- Department of Applied Sciences, University of the West of England , Coldharbour Lane, Bristol BS16 1QY, U.K
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44
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Piggot TJ, Allison JR, Sessions RB, Essex JW. On the Calculation of Acyl Chain Order Parameters from Lipid Simulations. J Chem Theory Comput 2017; 13:5683-5696. [PMID: 28876925 DOI: 10.1021/acs.jctc.7b00643] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
For molecular dynamics simulations of biological membrane systems to live up to the potential of providing accurate atomic level detail into membrane properties and functions, it is essential that the force fields used to model such systems are as accurate as possible. One membrane property that is often used to assess force field accuracy is the carbon-hydrogen (or carbon-deuterium) order parameters of the lipid tails, which can be accurately measured using experimental NMR techniques. There are a variety of analysis tools available to calculate these order parameters from simulations and it is essential that these computational tools work correctly to ensure the accurate assessment of the simulation force fields. In this work we compare many of these computational tools for calculating the order parameters of POPC membranes. While tools that work on all-atom systems and tools that work on saturated lipid tails in general work extremely well, we demonstrate that the majority of the tested tools that calculate the order parameters for unsaturated united-atom lipid tails do so incorrectly. We identify tools that do perform accurate calculations and include one such program with this work, enabling rapid and accurate calculation of united-atom lipid order parameters. Furthermore, we discuss cases in which it is nontrivial to appropriately predict the unsaturated carbon order parameters in united-atom systems. Finally, we examine order parameter splitting for carbon 2 in sn-2 lipid chains, demonstrating substantial deviations from experimental values in several all-atom and united-atom lipid force fields.
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Affiliation(s)
- Thomas J Piggot
- Chemical, Biological and Radiological Sciences, Defence Science and Technology Laboratory , Porton Down, Salisbury, Wiltshire SP4 0JQ, U.K.,Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
| | - Jane R Allison
- Centre for Theoretical Chemistry and Physics, Institute of Natural and Mathematical Sciences, Massey University , Auckland 0632, New Zealand
| | - Richard B Sessions
- School of Biochemistry, University of Bristol , University Walk, Bristol BS8 1TD, U.K
| | - Jonathan W Essex
- Chemistry, University of Southampton , Highfield, Southampton SO17 1BJ, U.K
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45
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Narzi D, Coccia E, Manzoli M, Guidoni L. Impact of molecular flexibility on the site energy shift of chlorophylls in Photosystem II. Biophys Chem 2017; 229:93-98. [DOI: 10.1016/j.bpc.2017.06.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/26/2017] [Accepted: 06/26/2017] [Indexed: 01/31/2023]
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46
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Buslaev P, Gushchin I. Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules. Sci Rep 2017; 7:11476. [PMID: 28904383 PMCID: PMC5597592 DOI: 10.1038/s41598-017-11761-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/25/2017] [Indexed: 12/14/2022] Open
Abstract
Molecular dynamics simulations are used extensively to study the processes on biological membranes. The simulations can be conducted at different levels of resolution: all atom (AA), where all atomistic details are provided; united atom (UA), where hydrogen atoms are treated inseparably of corresponding heavy atoms; and coarse grained (CG), where atoms are grouped into larger particles. Here, we study the behavior of model bilayers consisting of saturated and unsaturated lipids DOPC, SOPC, OSPC and DSPC in simulations performed using all atom CHARMM36 and coarse grained Martini force fields. Using principal components analysis, we show that the structural and dynamical properties of the lipids are similar, both in AA and CG simulations, although the unsaturated molecules are more dynamic and favor more extended conformations. We find that CG simulations capture 75 to 100% of the major collective motions, overestimate short range ordering, result in more flexible molecules and 5–7 fold faster sampling. We expect that the results reported here will be useful for comprehensive quantitative comparisons of simulations conducted at different resolution levels and for further development and improvement of CG force fields.
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Affiliation(s)
- Pavel Buslaev
- Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia.
| | - Ivan Gushchin
- Moscow Institute of Physics and Technology, 141700, Dolgoprudny, Russia. .,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, 52425, Jülich, Germany.
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47
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Rabinovich AL, Lyubartsev AP, Zhurkin DV. Unperturbed hydrocarbon chains and liquid phase bilayer lipid chains: a computer simulation study. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2017; 47:109-130. [PMID: 28698919 PMCID: PMC5834621 DOI: 10.1007/s00249-017-1231-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 04/13/2017] [Accepted: 06/07/2017] [Indexed: 11/24/2022]
Abstract
In this work, the properties of saturated and unsaturated fatty acid acyl chains 16:0, 18:0, 18:1(n-9)cis, 18:2(n-6)cis, 18:3(n-3)cis, 18:4(n-3)cis, 18:5(n-3)cis, 20:4(n-6)cis, 20:5(n-3)cis and 22:6(n-3)cis in a bilayer liquid crystalline state and similar hydrocarbon chains (with CH[Formula: see text] terminal groups instead of C=O groups) in the unperturbed state characterised by a lack of long-range interaction were investigated. The unperturbed hydrocarbon chains were modelled by Monte Carlo simulations at temperature [Formula: see text] K; sixteen fully hydrated homogeneous liquid crystalline phosphatidylcholine bilayers containing these chains were studied by molecular dynamics simulations at the same temperature. To eliminate effects of the simulation parameters, the molecular dynamics and Monte Carlo simulations were carried out using the same structural data and force field coefficients. From these computer simulations, the average distances between terminal carbon atoms of the chains (end-to-end distances) were calculated and compared. The trends in the end-to-end distances obtained for the unperturbed chains were found to be qualitatively similar to those obtained for the same lipid chains in the bilayers. So, for understanding of a number of processes in biological membranes (e.g., changes in fatty acid composition caused by environmental changes such as temperature and pressure), it is possible to use, at least as a first approximation, the relationships between the structure and properties for unperturbed or isolated hydrocarbon chains.
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Affiliation(s)
- Alexander L Rabinovich
- Institute of Biology, Karelian Research Center, Russian Academy of Sciences, Pushkinskaya 11, Petrozavodsk, 185910, Russian Federation
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 106 91, Stockholm, Sweden.
| | - Dmitrii V Zhurkin
- Physics and Technology Department, Petrozavodsk State University, Universitetskaya 10, Petrozavodsk, 185910, Russian Federation
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48
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Rocco P, Cilurzo F, Minghetti P, Vistoli G, Pedretti A. Molecular Dynamics as a tool for in silico screening of skin permeability. Eur J Pharm Sci 2017. [PMID: 28627472 DOI: 10.1016/j.ejps.2017.06.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Prediction of skin permeability can have manifold applications ranging from drug delivery to toxicity prediction. Along with the semi-empirical or mechanistic models proposed in the last decades, Molecular Dynamics simulations have recently become a fruitful tool for investigating membrane permeability, in particular as they allow the involved mechanisms to be modelled at a molecular level. Despite their significant structural complexity, Molecular Dynamics simulations can also be utilized to study permeation through the lipid matrix that characterizes the stratum corneum. In this work, Steered Molecular Dynamics simulations are performed on a suitably developed stratum corneum lipid matrix model. Regardless of their actual tortuous path within the stratum corneum, the permeants, taken from a Fully Validated dataset of 80 compounds of known permeability coefficient, are moved through the bilayer along its normal. This allows the exploration of all the possible conformational and physicochemical constraints the molecule experiences when moving through the bilayer. The so performed Steered Molecular Dynamics simulations are then utilized to extract the corresponding lipophilicity and diffusion parameters as computed by subdividing the entire path in 18 regions of different polarity and composition. Correlative analyses showed that the water-lipids interface is the best performing region and that significant enhancements can be gained by including parameters accounting for the temperature effect. Taken together, the developed models possess an enhanced predictive power compared to the existing equations and statistics are approaching the best possible results, given the uncertainty in the utilized permeability data.
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Affiliation(s)
- Paolo Rocco
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via G. Colombo, 71, I-20133 Milan, Italy.
| | - Francesco Cilurzo
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via G. Colombo, 71, I-20133 Milan, Italy
| | - Paola Minghetti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via G. Colombo, 71, I-20133 Milan, Italy
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milan, Italy
| | - Alessandro Pedretti
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Via Mangiagalli, 25, I-20133 Milan, Italy
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49
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Saleh N, Ibrahim P, Saladino G, Gervasio FL, Clark T. An Efficient Metadynamics-Based Protocol To Model the Binding Affinity and the Transition State Ensemble of G-Protein-Coupled Receptor Ligands. J Chem Inf Model 2017; 57:1210-1217. [PMID: 28453271 DOI: 10.1021/acs.jcim.6b00772] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A generally applicable metadynamics scheme for predicting the free energy profile of ligand binding to G-protein-coupled receptors (GPCRs) is described. A common and effective collective variable (CV) has been defined using the ideally placed and highly conserved Trp6.48 as a reference point for ligand-GPCR distance measurement and the common orientation of GPCRs in the cell membrane. Using this single CV together with well-tempered multiple-walker metadynamics with a funnel-like boundary allows an efficient exploration of the entire ligand binding path from the extracellular medium to the orthosteric binding site, including vestibule and intermediate sites. The protocol can be used with X-ray structures or high-quality homology models (based on a high-quality template and after thorough refinement) for the receptor and is universally applicable to agonists, antagonists, and partial and reverse agonists. The root-mean-square error (RMSE) in predicted binding free energies for 12 diverse ligands in five receptors (a total of 23 data points) is surprisingly small (less than 1 kcal mol-1). The RMSEs for simulations that use receptor X-ray structures and homology models are very similar.
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Affiliation(s)
- Noureldin Saleh
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials Friedrich-Alexander-Universität Erlangen-Nürnberg , Nägelsbachstraße 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials Friedrich-Alexander-Universität Erlangen-Nürnberg , Nägelsbachstraße 25, 91052 Erlangen, Germany
| | - Giorgio Saladino
- Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom
| | - Francesco Luigi Gervasio
- Department of Chemistry, University College London , London WC1H 0AJ, United Kingdom.,Institute of Structural and Molecular Biology, University College London , London WC1E 6BT, United Kingdom
| | - Timothy Clark
- Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials Friedrich-Alexander-Universität Erlangen-Nürnberg , Nägelsbachstraße 25, 91052 Erlangen, Germany
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50
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Vosahlikova M, Ujcikova H, Chernyavskiy O, Brejchova J, Roubalova L, Alda M, Svoboda P. Effect of therapeutic concentration of lithium on live HEK293 cells; increase of Na + /K + -ATPase, change of overall protein composition and alteration of surface layer of plasma membrane. Biochim Biophys Acta Gen Subj 2017; 1861:1099-1112. [DOI: 10.1016/j.bbagen.2017.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 01/20/2017] [Accepted: 02/10/2017] [Indexed: 12/19/2022]
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