1
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Mahur P, Sharma A, Jahan G, S G A, Kumar Singh A, Muthukumaran J, Jain M. Understanding Genetic Risks: Computational Exploration of Human β-Synuclein nsSNPs and their Potential Impact on Structural Alteration. Neurosci Lett 2024; 833:137826. [PMID: 38768940 DOI: 10.1016/j.neulet.2024.137826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/16/2024] [Accepted: 05/17/2024] [Indexed: 05/22/2024]
Abstract
Synucleins are pivotal in neurodegenerative conditions. Beta-synuclein (β-synuclein) is part of the synuclein protein family alongside alpha-synuclein (α-synuclein) and gamma-synuclein (γ-synuclein). These proteins, found mainly in brain tissue and cancers, are soluble and unstructured. β-synuclein shares significant similarity with α-synuclein, especially in their N-terminus, with a 90% match. However, their aggregation tendencies differ significantly. While α-synuclein aggregation is believed to be counteracted by β-synuclein, which occurs in conditions like Parkinson's disease, β-synuclein may counteract α-synuclein's toxic effects on the nervous system, offering potential treatment for neurodegenerative diseases. Under normal circumstances, β-synuclein may guard against disease by interacting with α-synuclein. Yet, in pathological environments with heightened levels or toxic substances, it might contribute to disease. Our research aims to explore potential harmful mutations in the β-synuclein using computational tools to predict their destabilizing impact on protein structure. Consensus analysis revealed rs1207608813 (A63P), rs1340051870 (S72F), and rs1581178262 (G36C) as deleterious. These findings highlight the intricate relationship between nsSNPs and protein function, shedding light on their potential implications in disease pathways. Understanding the structural consequences of nsSNPs is crucial for elucidating their role in pathogenesis and developing targeted therapeutic interventions. Our results offer a robust computational framework for identifying neurodegenerative disorder-related mutations from SNP datasets, potentially reducing the costs associated with experimental characterization.
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Affiliation(s)
- Pragati Mahur
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Abhishek Sharma
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Gulnaz Jahan
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Adithya S G
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Amit Kumar Singh
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India.
| | - Monika Jain
- Department of Biotechnology, Sharda School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India.
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2
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Panconi L, Lorenz CD, May RC, Owen DM, Makarova M. Phospholipid tail asymmetry allows cellular adaptation to anoxic environments. J Biol Chem 2023; 299:105134. [PMID: 37562570 PMCID: PMC10482748 DOI: 10.1016/j.jbc.2023.105134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/24/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Membrane biophysical properties are critical to cell fitness and depend on unsaturated phospholipid acyl tails. These can only be produced in aerobic environments since eukaryotic desaturases require molecular oxygen. This raises the question of how cells maintain bilayer properties in anoxic environments. Using advanced microscopy, molecular dynamics simulations, and lipidomics by mass spectrometry we demonstrated the existence of an alternative pathway to regulate membrane fluidity that exploits phospholipid acyl tail length asymmetry, replacing unsaturated species in the membrane lipidome. We show that the fission yeast, Schizosaccharomyces japonicus, which can grow in aerobic and anaerobic conditions, is capable of utilizing this strategy, whereas its sister species, the well-known model organism Schizosaccharomyces pombe, cannot. The incorporation of asymmetric-tailed phospholipids might be a general adaptation to hypoxic environmental niches.
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Affiliation(s)
- Luca Panconi
- Institute of Immunology and immunotherapy, School of Mathematics and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Chris D Lorenz
- Department of Physics, King's College London, London, UK
| | - Robin C May
- Institute of Microbiology and Infection and School of Biosciences, University of Birmingham, Birmingham, UK
| | - Dylan M Owen
- Institute of Immunology and immunotherapy, School of Mathematics and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK
| | - Maria Makarova
- School of Biosciences, Institute of Metabolism and Systems Research and Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham, Birmingham, UK.
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3
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Yee SM, Lorenz CD. On the Structure and Flip-flop of Free Docosahexaenoic Acid in a Model Human Brain Membrane. J Phys Chem B 2021; 125:8038-8047. [PMID: 34270235 DOI: 10.1021/acs.jpcb.1c03929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Among the omega-3 fatty acids, docosahexaenoic acid (DHA, sn22:6) is particularly vital in human brain cell membranes. There is considerable interest in DHA because low-level DHA has been associated with declined cognitive function and poor visual acuity. In this work, atomistic molecular dynamics simulations were used to investigate the effects of free protonated DHA (DHAP) in molar fractions of 0, 17, 30, and 38% in a realistic model of a healthy brain cell membrane comprising 26 lipid types. Numerous flip-flop events of DHAP were observed and categorized as successful or aborted. Novel use of the machine learning technique, density-based spatial clustering of applications with noise (DBSCAN), effectively identified flip-flop events by way of clustering. Our data show that increasing amounts of DHAP in the membrane disorder the bilayer packing, fluidize the membrane, and increase the rates of successful flip-flop from k = 0.2 μs-1 (17% DHAP) to 0.8 μs-1 (30% DHAP) and to 1.3 μs-1 (38% DHAP). In addition, we also provided a detailed understanding of the flip-flop mechanism of DHAP across this complex membrane. Interestingly, we noted the role of hydrogen bonds in two distinct coordinated flip-flop phenomena between two DHAP molecules: double flip-flop and assisted flip-flop. Understanding the effects of various concentrations of DHAP on the dynamics within a lipid membrane and the resulting structural properties of the membrane are important when considering the use of DHAP as a dietary supplement or as a potential therapeutic.
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Affiliation(s)
- Sze May Yee
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Christian D Lorenz
- Department of Physics, King's College London, London WC2R 2LS, United Kingdom
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4
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Smith P, Owen DM, Lorenz CD, Makarova M. Asymmetric glycerophospholipids impart distinctive biophysical properties to lipid bilayers. Biophys J 2021; 120:1746-1754. [PMID: 33705758 DOI: 10.1016/j.bpj.2021.02.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/23/2021] [Accepted: 02/24/2021] [Indexed: 01/25/2023] Open
Abstract
Phospholipids are a diverse group of biomolecules consisting of a hydrophilic headgroup and two hydrophobic acyl tails. The nature of the head and length and saturation of the acyl tails are important for defining the biophysical properties of lipid bilayers. It has recently been shown that the membranes of certain yeast species contain high levels of unusual asymmetric phospholipids consisting of one long and one medium-chain acyl moiety, a configuration not common in mammalian cells or other well-studied model yeast species. This raises the possibility that structurally asymmetric glycerophospholipids impart distinctive biophysical properties to the yeast membranes. Previously, it has been shown that lipids with asymmetric length tails form a mixed interdigitated gel phase and exhibit unusual endotherm behavior upon heating and cooling. Here, however, we address physiologically relevant temperature conditions and, using atomistic molecular dynamics simulations and environmentally sensitive fluorescent membrane probes, characterize key biophysical parameters (such as lipid packing, diffusion coefficient, membrane thickness, and area per lipid) in membranes composed of both length-asymmetric glycerophospholipids and ergosterol. Interestingly, we show that saturated but asymmetric glycerophospholipids maintain membrane lipid order across a wide range of temperatures. We also show that these asymmetric lipids can substiture of unsaturated symmetric lipids in the phase behaviour of ternary lipid bilayers. This may allow cells to maintain membrane fluidity, even in environments that lack oxygen, which is required for the synthesis of unsaturated lipids and sterols.
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Affiliation(s)
- Paul Smith
- Department of Physics, King's College London, London, United Kingdom
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences and School of Mathematics, College of Engineering and Physical Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | | | - Maria Makarova
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.
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5
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Suhaj A, Gowland D, Bonini N, Owen DM, Lorenz CD. Laurdan and Di-4-ANEPPDHQ Influence the Properties of Lipid Membranes: A Classical Molecular Dynamics and Fluorescence Study. J Phys Chem B 2020; 124:11419-11430. [PMID: 33275430 DOI: 10.1021/acs.jpcb.0c09496] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Environmentally sensitive (ES) dyes have been used for many decades to study the lipid order of cell membranes, as different lipid phases play a crucial role in a wide variety of cell processes. Yet, the understanding of how ES dyes behave, interact, and affect membranes at the atomistic scale is lacking, partially due to the lack of molecular dynamics (MD) models of these dyes. Here, we present ground- and excited-state MD models of commonly used ES dyes, Laurdan and di-4-ANEPPDHQ, and use MD simulations to study the behavior of these dyes in a disordered and an ordered membrane. We also investigate the effect that these two dyes have on the hydration and lipid order of the membranes, where we see a significant effect on the hydration of lipids proximal to the dyes. These findings are combined with experimental fluorescence experiments of ordered and disordered vesicles and live HeLa cells stained by the aforementioned dyes, where the generalized polarization (GP) values were measured at different concentrations of the dyes. We observe a small but significant decrease of GP at higher Laurdan concentrations in vesicles, while the same effect is not observed in cell membranes. The opposite effect is observed with di-4-ANEPPDHQ where no significant change in GP is seen for vesicles but a very substantial and significant decrease is seen in cell membranes. Together, our results show the profound effect that ES dyes have on membranes, and the presented MD models will be important for further understanding of these effects.
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Affiliation(s)
- Adam Suhaj
- Biological Physics and Soft Matter Group, Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Duncan Gowland
- Theory & Simulation of Condensed Matter Group, Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Nicola Bonini
- Theory & Simulation of Condensed Matter Group, Department of Physics, King's College London, London WC2R 2LS, United Kingdom
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, Department of Mathematics and Centre of Membrane Proteins and Receptors, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Christian D Lorenz
- Biological Physics and Soft Matter Group, Department of Physics, King's College London, London WC2R 2LS, United Kingdom
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6
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van der Spoel D, Henschel H, van Maaren PJ, Ghahremanpour MM, Costa LT. A potential for molecular simulation of compounds with linear moieties. J Chem Phys 2020; 153:084503. [PMID: 32872881 DOI: 10.1063/5.0015184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The harmonic angle bending potential is used in many force fields for (bio)molecular simulation. The force associated with this potential is discontinuous at angles close to 180°, which can lead to numeric instabilities. Angle bending of linear groups, such as alkynes or nitriles, or linear molecules, such as carbon dioxide, can be treated by a simple harmonic potential if we describe the fluctuations as a deviation from a reference position of the central atom, the position of which is determined by the flanking atoms. The force constant for the linear angle potential can be derived analytically from the corresponding force constant in the traditional potential. The new potential is tested on the properties of alkynes, nitriles, and carbon dioxide. We find that the angles of the linear groups remain about 2° closer to 180° using the new potential. The bond and angle force constants for carbon dioxide were tuned to reproduce the experimentally determined frequencies. An interesting finding was that simulations of liquid carbon dioxide under pressure with the new flexible model were stable only when explicitly modeling the long-range Lennard-Jones (LJ) interactions due to the very long-range nature of the LJ interactions (>1.7 nm). In the other tested liquids, we find that a Lennard-Jones cutoff of 1.1 nm yields similar results as the particle mesh Ewald algorithm for LJ interactions. Algorithmic factors influencing the stability of liquid simulations are discussed as well. Finally, we demonstrate that the linear angle potential can be used in free energy perturbation calculations.
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Affiliation(s)
- David van der Spoel
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - Henning Henschel
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | - Paul J van Maaren
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-75124 Uppsala, Sweden
| | | | - Luciano T Costa
- MolMod-CS - Instituto de Química, Universidade Federal Fluminense, Niterói, RJ CEP 24020-141, Brazil
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7
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Jain M, Muthukumaran J, Singh AK. Comparative structural and functional analysis of STL and SLL, chitin-binding lectins from Solanum spp. J Biomol Struct Dyn 2020; 39:4907-4922. [DOI: 10.1080/07391102.2020.1781693] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
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8
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Steinmark IE, Chung PH, Ziolek RM, Cornell B, Smith P, Levitt JA, Tregidgo C, Molteni C, Yahioglu G, Lorenz CD, Suhling K. Time-Resolved Fluorescence Anisotropy of a Molecular Rotor Resolves Microscopic Viscosity Parameters in Complex Environments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e1907139. [PMID: 32363742 DOI: 10.1002/smll.201907139] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 02/14/2020] [Accepted: 03/06/2020] [Indexed: 06/11/2023]
Abstract
Understanding viscosity in complex environments remains a largely unanswered question despite its importance in determining reaction rates in vivo. Here, time-resolved fluorescence anisotropy imaging (TR-FAIM) is combined with fluorescent molecular rotors (FMRs) to simultaneously determine two non-equivalent viscosity-related parameters in complex heterogeneous environments. The parameters, FMR rotational correlation time and lifetime, are extracted from fluorescence anisotropy decays, which in heterogeneous environments show dip-and-rise behavior due to multiple dye populations. Decays of this kind are found both in artificially constructed adiposomes and in live cell lipid droplet organelles. Molecular dynamics simulations are used to assign each population to nano-environments within the lipid systems. The less viscous population corresponds to the state showing an average 25° tilt to the lipid membrane normal, and the more viscous population to the state showing an average 55° tilt. This combined experimental and simulation approach enables a comprehensive description of the FMR probe behavior within viscous nano-environments in complex, biological systems.
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Affiliation(s)
| | | | | | | | - Paul Smith
- Department of Physics, King's College London, UK
| | - James A Levitt
- Randall Centre for Cell & Molecular Biophysics, King's College London, UK
| | - Carolyn Tregidgo
- Department of Physics, King's College London, UK
- Genomics England, London, EC1M 6BQ, UK
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9
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Jain M, Muthukumaran J, Singh AK. Structural and functional characterization of chitin binding lectin from Datura stramonium: insights from phylogenetic analysis, protein structure prediction, molecular docking and molecular dynamics simulation. J Biomol Struct Dyn 2020; 39:1698-1716. [DOI: 10.1080/07391102.2020.1737234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Monika Jain
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Jayaraman Muthukumaran
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
| | - Amit Kumar Singh
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, Uttar Pradesh, India
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10
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Jász Á, Rák Á, Ladjánszki I, Cserey G. Classical molecular dynamics on graphics processing unit architectures. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2020. [DOI: 10.1002/wcms.1444] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Ádám Jász
- StreamNovation Ltd. Budapest Hungary
| | - Ádám Rák
- StreamNovation Ltd. Budapest Hungary
| | | | - György Cserey
- Faculty of Information Technology and Bionics Pázmány Péter Catholic University Budapest Hungary
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11
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Morrison AF, Epifanovsky E, Herbert JM. Double-buffered, heterogeneous CPU + GPU integral digestion algorithm for single-excitation calculations involving a large number of excited states. J Comput Chem 2018; 39:2173-2182. [PMID: 30368836 DOI: 10.1002/jcc.25531] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/12/2018] [Accepted: 06/14/2018] [Indexed: 01/29/2023]
Abstract
The most widely used quantum-chemical models for excited states are single-excitation theories, a category that includes configuration interaction with single substitutions, time-dependent density functional theory, and also a recently developed ab initio exciton model. When a large number of excited states are desired, these calculations incur a significant bottleneck in the "digestion" step in which two-electron integrals are contracted with density or density-like matrices. We present an implementation that moves this step onto graphical processing units (GPUs), and introduce a double-buffer scheme that minimizes latency by computing integrals on the central processing units (CPUs) concurrently with their digestion on the GPUs. An automatic code generation scheme simplifies the implementation of high-performance GPU kernels. For the exciton model, which requires separate excited-state calculations on each electronically coupled chromophore, the heterogeneous implementation described here results in speedups of 2-6× versus a CPU-only implementation. For traditional time-dependent density functional theory calculations, we obtain speedups of up to 5× when a large number of excited states is computed. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Adrian F Morrison
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio.,Q-Chem Inc., Pleasanton, California
| | | | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
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12
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Pascoini AL, Federico LB, Arêas ALF, Verde BA, Freitas PG, Camps I. In silico development of new acetylcholinesterase inhibitors. J Biomol Struct Dyn 2018; 37:1007-1021. [DOI: 10.1080/07391102.2018.1447513] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- A. L. Pascoini
- Laboratory of Computational Modeling-LaModel, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - L. B. Federico
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - A. L. F. Arêas
- Laboratory of Computational Modeling-LaModel, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - B. A. Verde
- Laboratory of Computational Modeling-LaModel, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - P. G. Freitas
- Laboratory of Molecular Modeling and Computer Simulations-MolMod-CS, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - I. Camps
- Laboratory of Computational Modeling-LaModel, Institute of Exact Sciences, Federal University of Alfenas, Alfenas, Brazil
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13
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Rauschenbach S, Rinke G, Gutzler R, Abb S, Albarghash A, Le D, Rahman TS, Dürr M, Harnau L, Kern K. Two-Dimensional Folding of Polypeptides into Molecular Nanostructures at Surfaces. ACS NANO 2017; 11:2420-2427. [PMID: 28122181 DOI: 10.1021/acsnano.6b06145] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Herein we report the fabrication of molecular nanostructures on surfaces via two-dimensional (2D) folding of the nine amino acid peptide bradykinin. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy is used to fabricate and investigate the molecular nanostructures. Subnanometer resolved images evidence the large conformational freedom of the molecules if thermal motion is inhibited and the formation of stable uniform dimers of only one specific conformation when diffusion can take place. Molecular dynamics modeling supported by density functional theory calculations give atomically precise insight into the induced-fit binding scheme when the folded dimer is formed. In the absence of solvent, we find a hierarchy of binding strength from polar to nonpolar, manifested in an inverted polar-nonpolar segregation which suppresses unspecific interactions at the rim of the nanostructure. The demonstrated 2D-folding scheme resembles many key properties of its native 3D counterpart and shows that functional, molecular nanostructures on surfaces fabricated by folding could be just as versatile and specific.
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Affiliation(s)
- Stephan Rauschenbach
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Gordon Rinke
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Rico Gutzler
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Sabine Abb
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Alyazan Albarghash
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
| | - Duy Le
- University of Central Florida , Orlando, Florida 32816, United States
| | - Talat S Rahman
- University of Central Florida , Orlando, Florida 32816, United States
| | - Michael Dürr
- Justus Liebig University Giessen, Institute of Applied Physics , Heinrich-Buff-Ring 16, Giessen DE-35392, Germany
| | - Ludger Harnau
- University of Stuttgart , Bernhäuserstr. 75, Leinfelden-Echterdingen DE-70771, Germany
| | - Klaus Kern
- Max Planck Institute for Solid State Research , Heisenbergstr. 1, Stuttgart DE-70569, Germany
- Ecole Polytechnique Fédérale de Lausanne, Institut de Physique , Lausanne CH-1015, Switzerland
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14
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Mona CE, Besserer-Offroy É, Cabana J, Lefrançois M, Boulais PE, Lefebvre MR, Leduc R, Lavigne P, Heveker N, Marsault É, Escher E. Structure–Activity Relationship and Signaling of New Chimeric CXCR4 Agonists. J Med Chem 2016; 59:7512-24. [DOI: 10.1021/acs.jmedchem.6b00566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Christine E. Mona
- Department
of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Élie Besserer-Offroy
- Department
of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Jérôme Cabana
- Department
of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Marilou Lefrançois
- Department
of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Philip E. Boulais
- Department
of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Marie-Reine Lefebvre
- Department
of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Richard Leduc
- Department
of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Pierre Lavigne
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Nikolaus Heveker
- Department of Biochemistry and Molecular
Medicine, Centre de recherche du CHU Sainte-Justine, Université de Montréal, Montréal, QC H3T 1C4, Canada
| | - Éric Marsault
- Department
of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Emanuel Escher
- Department
of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
- Institut
de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
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15
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Hall BA, Piterman N, Hajnal A, Fisher J. Emergent stem cell homeostasis in the C. elegans germline is revealed by hybrid modeling. Biophys J 2016. [PMID: 26200879 PMCID: PMC4621618 DOI: 10.1016/j.bpj.2015.06.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The establishment of homeostasis among cell growth, differentiation, and apoptosis is of key importance for organogenesis. Stem cells respond to temporally and spatially regulated signals by switching from mitotic proliferation to asymmetric cell division and differentiation. Executable computer models of signaling pathways can accurately reproduce a wide range of biological phenomena by reducing detailed chemical kinetics to a discrete, finite form. Moreover, coordinated cell movements and physical cell-cell interactions are required for the formation of three-dimensional structures that are the building blocks of organs. To capture all these aspects, we have developed a hybrid executable/physical model describing stem cell proliferation, differentiation, and homeostasis in the Caenorhabditis elegans germline. Using this hybrid model, we are able to track cell lineages and dynamic cell movements during germ cell differentiation. We further show how apoptosis regulates germ cell homeostasis in the gonad, and propose a role for intercellular pressure in developmental control. Finally, we use the model to demonstrate how an executable model can be developed from the hybrid system, identifying a mechanism that ensures invariance in fate patterns in the presence of instability.
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Affiliation(s)
- Benjamin A Hall
- Medical Research Council Cancer Unit, Hutchison/Medical Research Council Research Centre, University of Cambridge, Cambridge, United Kingdom; Microsoft Research Cambridge, Cambridge, UK.
| | - Nir Piterman
- Department of Computer Science, University of Leicester, Leicester, UK
| | - Alex Hajnal
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Jasmin Fisher
- Microsoft Research Cambridge, Cambridge, UK; Department of Biochemistry, University of Cambridge, Cambridge, UK.
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16
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Khruschev SS, Abaturova AM, Fedorov VA, Kovalenko IB, Riznichenko GY, Rubin AB. The identification of intermediate states of the electron-transfer proteins plastocyanin and cytochrome f diffusional encounters. Biophysics (Nagoya-shi) 2015. [DOI: 10.1134/s0006350915040156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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17
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Cabana J, Holleran B, Leduc R, Escher E, Guillemette G, Lavigne P. Identification of Distinct Conformations of the Angiotensin-II Type 1 Receptor Associated with the Gq/11 Protein Pathway and the β-Arrestin Pathway Using Molecular Dynamics Simulations. J Biol Chem 2015; 290:15835-15854. [PMID: 25934394 DOI: 10.1074/jbc.m114.627356] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 01/14/2023] Open
Abstract
Biased signaling represents the ability of G protein-coupled receptors to engage distinct pathways with various efficacies depending on the ligand used or on mutations in the receptor. The angiotensin-II type 1 (AT1) receptor, a prototypical class A G protein-coupled receptor, can activate various effectors upon stimulation with the endogenous ligand angiotensin-II (AngII), including the Gq/11 protein and β-arrestins. It is believed that the activation of those two pathways can be associated with distinct conformations of the AT1 receptor. To verify this hypothesis, microseconds of molecular dynamics simulations were computed to explore the conformational landscape sampled by the WT-AT1 receptor, the N111G-AT1 receptor (constitutively active and biased for the Gq/11 pathway), and the D74N-AT1 receptor (biased for the β-arrestin1 and -2 pathways) in their apo-forms and in complex with AngII. The molecular dynamics simulations of the AngII-WT-AT1, N111G-AT1, and AngII-N111G-AT1 receptors revealed specific structural rearrangements compared with the initial and ground state of the receptor. Simulations of the D74N-AT1 receptor revealed that the mutation stabilizes the receptor in the initial ground state. The presence of AngII further stabilized the ground state of the D74N-AT1 receptor. The biased agonist [Sar(1),Ile(8)]AngII also showed a preference for the ground state of the WT-AT1 receptor compared with AngII. These results suggest that activation of the Gq/11 pathway is associated with a specific conformational transition stabilized by the agonist, whereas the activation of the β-arrestin pathway is linked to the stabilization of the ground state of the receptor.
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Affiliation(s)
- Jérôme Cabana
- Departments of Pharmacology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4; PROTEO (Quebec Network on Protein Structure, Function, and Engineering), Université Laval, Québec, Québec G1V 0A6, Canada
| | - Brian Holleran
- Departments of Pharmacology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4
| | - Richard Leduc
- Departments of Pharmacology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4
| | - Emanuel Escher
- Departments of Pharmacology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4
| | - Gaétan Guillemette
- Departments of Pharmacology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4
| | - Pierre Lavigne
- PROTEO (Quebec Network on Protein Structure, Function, and Engineering), Université Laval, Québec, Québec G1V 0A6, Canada; Biochemistry, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4.
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18
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 738] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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19
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Affiliation(s)
- Vitaly V. Chaban
- MEMPHYS − Center for Biomembrane Physics, Syddansk Universitet, Odense M., 5230, Denmark
| | - Himanshu Khandelia
- MEMPHYS − Center for Biomembrane Physics, Syddansk Universitet, Odense M., 5230, Denmark
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20
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Chaban VV, Nielsen MB, Kopec W, Khandelia H. Insights into the role of cyclic ladderane lipids in bacteria from computer simulations. Chem Phys Lipids 2014; 181:76-82. [DOI: 10.1016/j.chemphyslip.2014.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 03/18/2014] [Accepted: 04/03/2014] [Indexed: 11/29/2022]
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21
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LeBard DN. Advancing simulations of biological materials: applications of coarse-grained models on graphics processing unit hardware. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.899700] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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22
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Gonzalez HC, Darré L, Pantano S. Transferable Mixing of Atomistic and Coarse-Grained Water Models. J Phys Chem B 2013; 117:14438-48. [DOI: 10.1021/jp4079579] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Leonardo Darré
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
- Department
of Chemistry, King’s College London, London, United Kingdom
| | - Sergio Pantano
- Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
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23
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A prospective overview of the essential requirements in molecular modeling for nanomedicine design. Future Med Chem 2013; 5:929-46. [PMID: 23682569 DOI: 10.4155/fmc.13.67] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Nanotechnology has presented many new challenges and opportunities in the area of nanomedicine design. The issues related to nanoconjugation, nanosystem-mediated targeted drug delivery, transitional stability of nanovehicles, the integrity of drug transport, drug-delivery mechanisms and chemical structural design require a pre-estimated and determined course of assumptive actions with property and characteristic estimations for optimal nanomedicine design. Molecular modeling in nanomedicine encompasses these pre-estimations and predictions of pertinent design data via interactive computographic software. Recently, an increasing amount of research has been reported where specialized software is being developed and employed in an attempt to bridge the gap between drug discovery, materials science and biology. This review provides an assimilative and concise incursion into the current and future strategies of molecular-modeling applications in nanomedicine design and aims to describe the utilization of molecular models and theoretical-chemistry computographic techniques for expansive nanomedicine design and development.
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24
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Létourneau D, Lorin A, Lefebvre A, Cabana J, Lavigne P, LeHoux JG. Thermodynamic and solution state NMR characterization of the binding of secondary and conjugated bile acids to STARD5. Biochim Biophys Acta Mol Cell Biol Lipids 2013; 1831:1589-99. [PMID: 23872533 DOI: 10.1016/j.bbalip.2013.07.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 07/04/2013] [Accepted: 07/09/2013] [Indexed: 12/21/2022]
Abstract
STARD5 is a member of the STARD4 sub-family of START domain containing proteins specialized in the non-vesicular transport of lipids and sterols. We recently reported that STARD5 binds primary bile acids. Herein, we report on the biophysical and structural characterization of the binding of secondary and conjugated bile acids by STARD5 at physiological concentrations. We found that the absence of the 7α-OH group and its epimerization increase the affinity of secondary bile acids for STARD5. According to NMR titration and molecular modeling, the affinity depends mainly on the number and positions of the steroid ring hydroxyl groups and to a lesser extent on the presence or type of bile acid side-chain conjugation. Primary and secondary bile acids have different binding modes and display different positioning within the STARD5 binding pocket. The relative STARD5 affinity for the different bile acids studied is: DCA>LCA>CDCA>GDCA>TDCA>CA>UDCA. TCA and GCA do not bind significantly to STARD5. The impact of the ligand chemical structure on the thermodynamics of binding is discussed. The discovery of these new ligands suggests that STARD5 is involved in the cellular response elicited by bile acids and offers many entry points to decipher its physiological role.
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Affiliation(s)
- Danny Létourneau
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - Aurélien Lorin
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - Andrée Lefebvre
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - Jérôme Cabana
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - Pierre Lavigne
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
| | - Jean-Guy LeHoux
- Département de Biochimie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada.
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25
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Lourenço TC, Coelho MFC, Ramalho TC, van der Spoel D, Costa LT. Insights on the solubility of CO2 in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide from the microscopic point of view. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2013; 47:7421-7429. [PMID: 23718214 DOI: 10.1021/es4020986] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Emissions of greenhouse gases due to human activities have been well documented as well as the effects on global warming resulting from it. Efforts to reduce greenhouse gases at the source are crucial to curb climate change, but due to insignificant economic incentives to reduce usage of fossil fuels, not a lot of progress has been made by this route. This necessitates additional measures to reduce the occurrence of greenhouse gases in the atmosphere. Here we used theoretical methods to study the solubility of carbon dioxide in ionic liquids (ILs) since sequestration of CO2 in ILs has been proposed as a possible technology for reducing the emissions of CO2 to the atmosphere. Ionic liquids form a class of solvents with melting temperatures below 100 °C and, due to very low vapor pressures, which are not volatile. We have performed molecular dynamics (MD) simulations of 1-ethyl-3-methylimidazolium (C2mim) bis(trifluoromethylsulfonyl)imide (Tf2N) and its mixtures with carbon dioxide in order to investigate the CO2 concentration effect on the CO2-cation and CO2-anion interactions. A systematic investigation of CO2 concentration effects on resulting equilibrium liquid structure, and the local environment of the ions is provided. The Quantum Theory of Atoms in Molecules (QTAIM) was used to determine the interaction energy for CO2-cation and CO2-anion complexes from uncorrelated structures derived from MD simulations. A spatial distribution function analysis demonstrates the specific interactions between CO2 and the ionic liquid. Our findings indicate that the total volume of the system increases with the CO2 concentration, with a molar volume of CO2 of about 0.038 L/mol, corresponding to liquid CO2 under a pressure of 100 bar. In other words, the IL effectively pressurizes the CO2 inside its matrix. The thermodynamics of CO2 solvation in C2 min-Tf2N were computed using free energy techniques, and the solubility of CO2 is found to be higher in this IL (-3.7 ± 1 kcal/mol) than in water (+0.2 kJ/mol), predominantly due to anion-CO2 interactions.
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Affiliation(s)
- Tuanan C Lourenço
- Instituto de Química, Universidade Federal de Alfenas, Rua Gabriel Monteiro da Silva, 700 Alfenas-MGCEP:37130-000, Brazil
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26
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Chaban VV, Verspeek B, Khandelia H. Novel Ultrathin Membranes Composed of Organic Ions. J Phys Chem Lett 2013; 4:1216-1220. [PMID: 26282045 DOI: 10.1021/jz400424f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Until recently, construction of bilayers was an exclusive mission of nature. It requires careful choice of compounds, whose delicate interplay between head group attraction and chain repulsion engenders a truly unique balance over a narrow temperature range. We report the investigation of artificial bilayers composed of long-chained organic ions, such as dodecyltrimethylammonium (DMA(+)) and perfluorooctaonate (PFO(-)). Various ratios of DMA/PFO surfactants result in bilayers of different stability, thickness, area per molecule, and density profiles. In our quest for water filtration, we incorporated aquaporin protein into the DMA/PFO bilayer but did not observe sufficient stability of the system. We discuss further steps to utilize these surfactant bilayers as highly selective, salt-impermeable membranes.
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Affiliation(s)
- Vitaly V Chaban
- †MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, Odense M. 5230, Denmark
| | - Bram Verspeek
- ‡Department of Biomedical Engineering, University of Technology Eindhoven, The Netherlands
| | - Himanshu Khandelia
- †MEMPHYS - Center for Biomembrane Physics, University of Southern Denmark, Campusvej 55, Odense M. 5230, Denmark
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27
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Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, Shirts MR, Smith JC, Kasson PM, van der Spoel D, Hess B, Lindahl E. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics 2013; 29:845-54. [PMID: 23407358 PMCID: PMC3605599 DOI: 10.1093/bioinformatics/btt055] [Citation(s) in RCA: 5009] [Impact Index Per Article: 455.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 01/28/2013] [Accepted: 01/29/2013] [Indexed: 01/27/2023] Open
Abstract
MOTIVATION Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. RESULTS Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. AVAILABILITY GROMACS is an open source and free software available from http://www.gromacs.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sander Pronk
- Science for Life Laboratory, Stockholm and Uppsala, 171 21 Stockholm, Sweden
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28
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Cabana J, Holleran B, Beaulieu MÈ, Leduc R, Escher E, Guillemette G, Lavigne P. Critical hydrogen bond formation for activation of the angiotensin II type 1 receptor. J Biol Chem 2012; 288:2593-604. [PMID: 23223579 DOI: 10.1074/jbc.m112.395939] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptors contain selectively important residues that play central roles in the conformational changes that occur during receptor activation. Asparagine 111 (N111(3.35)) is such a residue within the angiotensin II type 1 (AT(1)) receptor. Substitution of N111(3.35) for glycine leads to a constitutively active receptor, whereas substitution for tryptophan leads to an inactivable receptor. Here, we analyzed the AT(1) receptor and two mutants (N111G and N111W) by molecular dynamics simulations, which revealed a novel molecular switch involving the strictly conserved residue D74(2.50). Indeed, D74(2.50) forms a stable hydrogen bond (H-bond) with the residue in position 111(3.35) in the wild-type and the inactivable receptor. However, in the constitutively active mutant N111G-AT(1) receptor, residue D74 is reoriented to form a new H-bond with another strictly conserved residue, N46(1.50). When expressed in HEK293 cells, the mutant N46G-AT(1) receptor was poorly activable, although it retained a high binding affinity. Interestingly, the mutant N46G/N111G-AT(1) receptor was also inactivable. Molecular dynamics simulations also revealed the presence of a cluster of hydrophobic residues from transmembrane domains 2, 3, and 7 that appears to stabilize the inactive form of the receptor. Whereas this hydrophobic cluster and the H-bond between D74(2.50) and W111(3.35) are more stable in the inactivable N111W-AT(1) receptor, the mutant N111W/F77A-AT(1) receptor, designed to weaken the hydrophobic core, showed significant agonist-induced signaling. These results support the potential for the formation of an H-bond between residues D74(2.50) and N46(1.50) in the activation of the AT(1) receptor.
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Affiliation(s)
- Jérôme Cabana
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quecec J1H 5N4, Canada
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29
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Darré L, Tek A, Baaden M, Pantano S. Mixing Atomistic and Coarse Grain Solvation Models for MD Simulations: Let WT4 Handle the Bulk. J Chem Theory Comput 2012; 8:3880-94. [DOI: 10.1021/ct3001816] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Leonardo Darré
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
| | - Alex Tek
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
- Université Pierre et Marie
Curie, UPMC Sorbonne Universités, 4 place Jussieu 75005 Paris,
France
| | - Marc Baaden
- Laboratoire de Biochimie Théorique,
CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité. 13
rue Pierre et Marie Curie, 75005, Paris, France
| | - Sergio Pantano
- Institut Pasteur de Montevideo,
Mataojo 2020, CP 11400, Uruguay
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30
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Wu X, Koslowski A, Thiel W. Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU–GPU Computing Platform. J Chem Theory Comput 2012; 8:2272-81. [DOI: 10.1021/ct3001798] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Xin Wu
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilheim-Platz
1, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilheim-Platz
1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilheim-Platz
1, 45470 Mülheim an der Ruhr, Germany
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31
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32
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Caleman C, van Maaren PJ, Hong M, Hub JS, Costa LT, van der Spoel D. Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant. J Chem Theory Comput 2012; 8:61-74. [PMID: 22241968 PMCID: PMC3254193 DOI: 10.1021/ct200731v] [Citation(s) in RCA: 453] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Indexed: 12/15/2022]
Abstract
The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.
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Affiliation(s)
- Carl Caleman
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron Notkestraße 85, DE-22607 Hamburg, Germany
| | - Paul J. van Maaren
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Minyan Hong
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Jochen S. Hub
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
| | - Luciano T. Costa
- Departamento de Ciências Exatas, Federal University of Alfenas—MG Rua Gabriel Monteiro da Silva, 700 Alfenas—MG CEP:37130-000, Brazil
| | - David van der Spoel
- Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, SE-75124 Uppsala, Sweden
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