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Maeki M, Kimura N, Okada Y, Shimizu K, Shibata K, Miyazaki Y, Ishida A, Yonezawa K, Shimizu N, Shinoda W, Tokeshi M. Understanding the effects of ethanol on the liposome bilayer structure using microfluidic-based time-resolved small-angle X-ray scattering and molecular dynamics simulations. NANOSCALE ADVANCES 2024; 6:2166-2176. [PMID: 38633055 PMCID: PMC11019499 DOI: 10.1039/d3na01073b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 02/29/2024] [Indexed: 04/19/2024]
Abstract
Lipid nanoparticles (LNPs) are essential carrier particles in drug delivery systems, particularly in ribonucleic acid delivery. In preparing lipid-based nanoparticles, microfluidic-based ethanol injection may produce precisely size-controlled nanoparticles. Ethanol is critical in LNP formation and post-treatment processes and affects liposome size, structure, lamellarity, and drug-loading efficiency. However, the effects of time-dependent changes in the ethanol concentration on the structural dynamics of liposomes are not clearly understood. Herein, we investigated ethanol-induced lipid bilayer changes in liposomes on a time scale from microseconds to tens of seconds using a microfluidic-based small-angle X-ray scattering (SAXS) measurement system coupled with molecular dynamics (MD) simulations. The time-resolved SAXS measurement system revealed that single unilamellar liposomes were converted to multilamellar liposomes within 0.8 s of contact with ethanol, and the d-spacing was decreased from 6.1 (w/o ethanol) to 4.4 nm (80% ethanol) with increasing ethanol concentration. We conducted 1 μs MD simulations to understand the molecular-level structural changes in the liposomes. The MD simulations revealed that the changes in the lamellar structure caused by ethanol at the molecular level could explain the structural changes in the liposomes observed via time-resolved SAXS. Therefore, the post-treatment process to remove residual ethanol is critical in liposome formation.
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Affiliation(s)
- Masatoshi Maeki
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University Kita 13 Nishi 8, Kita-ku Sapporo 060-8628 Japan +81-11-706-6745 +81-11-706-6773 +81-11-706-6744
- JST PRESTO 4-1-8 Honcho, Kawaguchi Saitama 332-0012 Japan
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) Tsukuba Ibaraki 305-0801 Japan
| | - Niko Kimura
- Graduate School of Chemical Sciences and Engineering, Hokkaido University Kita 13 Nishi 8, Kita-ku Sapporo 060-8628 Japan
| | - Yuto Okada
- Graduate School of Chemical Sciences and Engineering, Hokkaido University Kita 13 Nishi 8, Kita-ku Sapporo 060-8628 Japan
| | - Kazuki Shimizu
- Graduate School of Chemical Sciences and Engineering, Hokkaido University Kita 13 Nishi 8, Kita-ku Sapporo 060-8628 Japan
| | - Kana Shibata
- Department of Materials Chemistry, Nagoya University Chikusa-ku Nagoya 464-8603 Japan
| | - Yusuke Miyazaki
- Research Institute for Interdisciplinary Science, Okayama University Okayama 700-8530 Japan
| | - Akihiko Ishida
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University Kita 13 Nishi 8, Kita-ku Sapporo 060-8628 Japan +81-11-706-6745 +81-11-706-6773 +81-11-706-6744
| | - Kento Yonezawa
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) Tsukuba Ibaraki 305-0801 Japan
| | - Nobutaka Shimizu
- Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK) Tsukuba Ibaraki 305-0801 Japan
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University Okayama 700-8530 Japan
| | - Manabu Tokeshi
- Division of Applied Chemistry, Faculty of Engineering, Hokkaido University Kita 13 Nishi 8, Kita-ku Sapporo 060-8628 Japan +81-11-706-6745 +81-11-706-6773 +81-11-706-6744
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Li S, Wu B, Luo YL, Han W. Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model. J Chem Theory Comput 2024; 20:2228-2245. [PMID: 38374639 PMCID: PMC10938502 DOI: 10.1021/acs.jctc.3c01046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/18/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
Many large protein machines function through an interplay between large-scale movements and intricate conformational changes. Understanding functional motions of these proteins through simulations becomes challenging for both all-atom and coarse-grained (CG) modeling techniques because neither approach alone can readily capture the full details of these motions. In this study, we develop a multiscale model by employing the popular MARTINI CG model to represent a heterogeneous environment and structurally stable proteins and using the united-atom (UA) model PACE to describe proteins undergoing subtle conformational changes. PACE was previously developed to be compatible with the MARTINI solvent and membrane. Here, we couple the protein descriptions of the two models by directly mixing UA and CG interaction parameters to greatly simplify parameter determination. Through extensive validations with diverse protein systems in solution or membrane, we demonstrate that only additional parameter rescaling is needed to enable the resulting model to recover the stability of native structures of proteins under mixed representation. Moreover, we identify the optimal scaling factors that can be applied to various protein systems, rendering the model potentially transferable. To further demonstrate its applicability for realistic systems, we apply the model to a mechanosensitive ion channel Piezo1 that has peripheral arms for sensing membrane tension and a central pore for ion conductance. The model can reproduce the coupling between Piezo1's large-scale arm movement and subtle pore opening in response to membrane stress while consuming much less computational costs than all-atom models. Therefore, our model shows promise for studying functional motions of large protein machines.
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Affiliation(s)
- Shu Li
- Centre
for Artificial Intelligence Driven Drug Discovery, Faculty of Applied
Sciences, Macao Polytechnic University, Macao 999078, China
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Bohua Wu
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Yun Lyna Luo
- Department
of Biotechnology and Pharmaceutical Sciences, Western University of Health Sciences, Pomona, California 91766, United States
| | - Wei Han
- State
Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key
Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
- Department
of Chemistry, Faculty of Science, Hong Kong
Baptist University, Hong Kong SAR 999077, China
- Shenzhen
Bay Laboratory, Institute of Chemical Biology, Shenzhen 518132, China
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Plazinski W, Lutsyk V, Plazinska A. Exploring Free Energies of Specific Protein Conformations Using the Martini Force Field. J Chem Theory Comput 2024; 20:2273-2283. [PMID: 38427574 PMCID: PMC10938637 DOI: 10.1021/acs.jctc.3c01155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 02/16/2024] [Accepted: 02/16/2024] [Indexed: 03/03/2024]
Abstract
Coarse-grained (CG) level molecular dynamics simulations are routinely used to study various biomolecular processes. The Martini force field is currently the most widely adopted parameter set for such simulations. The functional form of this and several other CG force fields enforces secondary protein structure support by employing a variety of harmonic potentials or restraints that favor the protein's native conformation. We propose a straightforward method to calculate the energetic consequences of transitions between predefined conformational states in systems in which multiple factors can affect protein conformational equilibria. This method is designed for use within the Martini force field and involves imposing conformational transitions by linking a Martini-inherent elastic network to the coupling parameter λ. We demonstrate the applicability of our method using the example of five biomolecular systems that undergo experimentally characterized conformational transitions between well-defined structures (Staphylococcal nuclease, C-terminal segment of surfactant protein B, LAH4 peptide, and β2-adrenergic receptor) as well as between folded and unfolded states (GCN4 leucine zipper protein). The results show that the relative free energy changes associated with protein conformational transitions, which are affected by various factors, such as pH, mutations, solvent, and lipid membrane composition, are correctly reproduced. The proposed method may be a valuable tool for understanding how different conditions and modifications affect conformational equilibria in proteins.
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Affiliation(s)
- Wojciech Plazinski
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow 30-239, Poland
- Department
of Biopharmacy, Medical University of Lublin, Chodzki 4a, Lublin 20-093, Poland
| | - Valery Lutsyk
- Jerzy
Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, Krakow 30-239, Poland
| | - Anita Plazinska
- Department
of Biopharmacy, Medical University of Lublin, Chodzki 4a, Lublin 20-093, Poland
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Dixit M, Hajari T, Meti MD, Srivastava S, Srivastava A, Daniel J. Ionic Pairing and Selective Solvation of Butylmethylimidazolium Chloride Ion Pairs in DMSO-Water Mixtures: A Comprehensive Examination via Molecular Dynamics Simulations and Potentials of Mean Force Analysis. J Phys Chem B 2024; 128:2168-2180. [PMID: 38415290 DOI: 10.1021/acs.jpcb.3c06876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/29/2024]
Abstract
Ionic liquids (ILs) with dimethyl sulfoxide (DMSO) and water act as a promising solvent medium for the dissolution of cellulose in an efficient manner. To develop a proper solvent system, it is really important to understand the thermodynamics of the molecular solutions consisting of ILs, DMSO, and water. The ion-pairing propensity of the ILs in the presence of DMSO and water plays a crucial role in governing the property of the solvent mixtures. Employing all-atom molecular dynamics simulations, we estimate the potentials of mean force between BMIM+ and Cl- ions in DMSO-water mixtures. Analysis reveals a significant increase in the thermodynamic stability of both contact ion pair (CIP) and solvent-assisted ion pair (SAIP) states with a rising DMSO mole fraction. Thermodynamic assessments highlight the entropic stabilization of CIP states and SAIP states in pure water, in DMSO-water mixtures, and in pure DMSO. The structural analysis reveals that in comparison to the DMSO local density, the local water density is relatively very high around ion pairs, more specifically in the solvation shell of a chloride ion. Preferential binding coefficients also consistently indicate exclusion of DMSO from the ion pair in DMSO-water mixtures. To enhance our understanding regarding the solvent molecules kinetics around the ion pairs, the survival probabilities of DMSO and water are computed. The calculations reveal that the water molecules prefer a prolonged stay in the solvation shell of Cl- ions.
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Affiliation(s)
- Mayank Dixit
- Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Timir Hajari
- Department of Chemistry, City College, 102/1, Raja Rammohan Sarani, Kolkata - 700009, India
| | - Manjunath D Meti
- Bio-physical Laboratory, Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India
| | - Srishti Srivastava
- Department of Zoology, Allahabad University, Prayagraj, Uttar Pradesh 211002, India
| | - Amar Srivastava
- Chemistry Department, Har Sahai (PG) College, Kanpur, Uttar Pradesh 208012, India
| | - Joseph Daniel
- Department of Chemistry, Christ Church College, Kanpur 208001, India
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5
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Xue Q, Jiao Z, Pan W, Liu X, Fu J, Zhang A. Multiscale computational simulation of pollutant behavior at water interfaces. WATER RESEARCH 2024; 250:121043. [PMID: 38154340 DOI: 10.1016/j.watres.2023.121043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 12/30/2023]
Abstract
The investigation of pollutant behavior at water interfaces is critical to understand pollution in aquatic systems. Computational methods allow us to overcome the limitations of experimental analysis, delivering valuable insights into the chemical mechanisms and structural characteristics of pollutant behavior at interfaces across a range of scales, from microscopic to mesoscopic. Quantum mechanics, all-atom molecular dynamics simulations, coarse-grained molecular dynamics simulations, and dissipative particle dynamics simulations represent diverse molecular interaction calculation methods that can effectively model pollutant behavior at environmental interfaces from atomic to mesoscopic scales. These methods provide a rich variety of information on pollutant interactions with water surfaces. This review synthesizes the advancements in applying typical computational methods to the formation, adsorption, binding, and catalytic conversion of pollutants at water interfaces. By drawing on recent advancements, we critically examine the current challenges and offer our perspective on future directions. This review seeks to advance our understanding of computational techniques for elucidating pollutant behavior at water interfaces, a critical aspect of water research.
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Affiliation(s)
- Qiao Xue
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Zhiyue Jiao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxiao Pan
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Xian Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; Institute of Environment and Health, Jianghan University, Wuhan 430056, China.
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; School of Environment, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China; Institute of Environment and Health, Jianghan University, Wuhan 430056, China.
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6
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Miyazaki Y, Shinoda W. pSPICA Force Field Extended for Proteins and Peptides. J Chem Inf Model 2024; 64:532-542. [PMID: 38156656 DOI: 10.1021/acs.jcim.3c01611] [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: 01/03/2024]
Abstract
Many coarse-grained (CG) molecular dynamics (MD) studies have been performed to investigate biological processes involving proteins and lipids. CG force fields (FFs) in these MD studies often use implicit or nonpolar water models to reduce computational costs. CG-MD using water models cannot properly describe electrostatic screening effects owing to the hydration of ionic segments and thus cannot appropriately describe molecular events involving water channels and pores through lipid membranes. To overcome this issue, we developed a protein model in the pSPICA FF, in which a polar CG water model showing the proper dielectric response was adopted. The developed CG model greatly improved the transfer free energy profiles of charged side chain analogues across the lipid membrane. Application studies on melittin-induced membrane pores and mechanosensitive channels in lipid membranes demonstrated that CG-MDs using the pSPICA FF correctly reproduced the structure and stability of the pores and channels. Furthermore, the adsorption behavior of the highly charged nona-arginine peptides on lipid membranes changed with salt concentration, indicating the pSPICA FF is also useful for simulating protein adsorption on membrane surfaces.
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Affiliation(s)
- Yusuke Miyazaki
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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7
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Yamada T, Miyazaki Y, Harada S, Kumar A, Vanni S, Shinoda W. Improved Protein Model in SPICA Force Field. J Chem Theory Comput 2023; 19:8967-8977. [PMID: 37989551 DOI: 10.1021/acs.jctc.3c01016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
The previous version of the SPICA coarse-grained (CG) force field (FF) protein model focused primarily on membrane proteins and successfully reproduced the dimerization free energies of several transmembrane helices and the stable structures of various membrane protein assemblies. However, that model had limited accuracy when applied to other proteins, such as intrinsically disordered proteins (IDPs) and peripheral proteins, because the dimensions of the IDPs in an aqueous solution were too compact, and protein binding on the lipid membrane surface was overstabilized. To improve the accuracy of the SPICA FF model for the simulation of such systems, in this study, we introduce protein secondary structure-dependent nonbonded interaction parameters to the backbone segments and reoptimize almost all nonbonded parameters for amino acids. The improved FF proposed here successfully reproduces the radii of gyration of various IDPs, the binding sensitivity of several peripheral membrane proteins, and the dimerization free energies of several transmembrane helices. The new model also shows improved agreement with experiments on the free energy of peptide association in water. In addition, an extensive library of nonbonded interactions between proteins and lipids, including various glycerophospholipids, sphingolipids, and cholesterol, allows the study of specific interactions between lipids and peripheral and transmembrane proteins. Hence, the new SPICA FF (version 2) proposed herein is applicable with high accuracy for simulating a wide range of protein systems.
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Affiliation(s)
- Teppei Yamada
- Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yusuke Miyazaki
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Shogo Harada
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan
| | - Ashutosh Kumar
- Department of Biology and National Center of Competence in Research Bio-inspired Materials, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Stefano Vanni
- Department of Biology and National Center of Competence in Research Bio-inspired Materials, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
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Borges-Araújo L, Patmanidis I, Singh AP, Santos LHS, Sieradzan AK, Vanni S, Czaplewski C, Pantano S, Shinoda W, Monticelli L, Liwo A, Marrink SJ, Souza PCT. Pragmatic Coarse-Graining of Proteins: Models and Applications. J Chem Theory Comput 2023; 19:7112-7135. [PMID: 37788237 DOI: 10.1021/acs.jctc.3c00733] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing role in the field. However, biological processes involving large-scale protein assemblies or long time scale dynamics are still computationally expensive to study in atomistic detail. For these applications, employing coarse-grained (CG) modeling approaches has become a key strategy. In this Review, we provide an overview of what we call pragmatic CG protein models, which are strategies combining, at least in part, a physics-based implementation and a top-down experimental approach to their parametrization. In particular, we focus on CG models in which most protein residues are represented by at least two beads, allowing these models to retain some degree of chemical specificity. A description of the main modern pragmatic protein CG models is provided, including a review of the most recent applications and an outlook on future perspectives in the field.
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Affiliation(s)
- Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Ilias Patmanidis
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Akhil P Singh
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
| | - Lucianna H S Santos
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Adam K Sieradzan
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, Fribourg CH-1700, Switzerland
- Institut de Pharmacologie Moléculaire et Cellulaire, Université Côte d'Azur, Inserm, CNRS, 06560 Valbonne, France
| | - Cezary Czaplewski
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Montevideo 11400, Uruguay
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita, Okayama 700-8530, Japan
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
| | - Adam Liwo
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry (MMSB, UMR 5086), CNRS, University of Lyon, 7 Passage du Vercors, 69007 Lyon, France
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Dixit M, Taniguchi T. Role of Terminal Groups of cis-1,4-Polyisoprene Chains in the Formation of Physical Junction Points in Natural Rubber. Biomacromolecules 2023; 24:3589-3602. [PMID: 37527033 DOI: 10.1021/acs.biomac.3c00355] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
The terminal structures of cis-1,4-polyisoprene (PI) chains play a vital role in the excellent comprehensive performance of Hevea natural rubber (NR) with properties such as high toughness, tear-resistance, and wet skid resistance. The cis-1,4-polyisoprene chain constituting NR exhibits a distinct composition of terminal groups comprising two distinct types, namely, the ω and α terminal groups. The structures of the ω terminal [dimethyl allyl (DMA)-(trans-1,4-isoprene)2] and six kinds of α end groups of the polymer chain of NR have been explored by utilizing a newly developed 2D NMR method. In the present work, we examine different kinds of PI melt systems, and we choose various combinations of terminal groups: Hydrogen, one DMA unit with two trans isoprene units as ω end groups and ester-terminated isopentene (α1), hydroxy-terminated isopentene (α2), ester-terminated isobutane (α3), hydroxy-terminated isobutane (α4), ester-terminated 1,4-cis-isoprene (α5), and hydroxy-terminated 1,4-cis-isoprene (α6), i.e., HPIH (PI0)-pure PI (Hydrogen terminal), ωPIα1 (PII), ωPIα2 (PIII), ωPIα3 (PIIII), ωPIα4 (PIIV), ωPIα5 (PIV), and ωPIα6 (PIVI). We evaluated dynamic and static properties of PI chains such as the end-to-end vector autocorrelation function (C(t)), its average relaxation time (τ), end-to-end distance (Ree), and radius of gyration (Rg). We also estimated the diffusion coefficients of polyisoprene chains and pair correlation functions [radial distribution functions (RDFs)], potentials of mean force (PMFs) in between end residues, and survival probability (P(τ)) of end groups around the end group by analyzing the equilibrated trajectories of full-atom MD simulations. As per the examination of C(t), rotational relaxation time τ, and RDFs, we discovered that the existence of a strong hydrogen bond in α2-α2, α4-α4, and α6-α6 residues makes the dynamics of hydroxy-terminated polyisoprene chains in ωPIα2,α4,α6 melt systems slower. From the analyses of RDFs and PMFs (W(r)), the association between [α2]-[α2], [α4]-[α4], and [α6]-[α6] terminals in ωPIα2,α4,α6 melt systems is significantly stronger than in [ISO]-[ISO] [Hydrogen terminated 1,4-cis-isoprene:(ISO)] in HPIH and ω-ω, [α1]-[α1], [α3]-[α3], and [α5]-[α5] in ωPIα1,α3,α5 systems. We quantified the fraction of cluster formation of terminal groups of a given size in the seven PI melt systems by employing the criteria of PMFs. It is revealed that no stable cluster exists in the HPIH, ωPIα1, ωPIα3, and ωPIα5 melt systems. Conversely, in the ωPIα2, ωPIα4, and ωPIα6 systems, we perceived stable clusters of [(α2)p] [(α4)p] and [(α6)p] end groups where p (2 ≤ x ≤ 6). These stable clusters validate the presence of physical junction points in between hydroxy-terminated polyisoprene chains through their α2, α4, and α6 terminals. These physical junction points might be crucial for superior properties of NR such as high toughness, crack growth resistance, and strain-induced crystallization.
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Affiliation(s)
- Mayank Dixit
- Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takashi Taniguchi
- Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
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10
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Petretto E, Campomanes P, Vanni S. Development of a coarse-grained model for surface-functionalized gold nanoparticles: towards an accurate description of their aggregation behavior. SOFT MATTER 2023; 19:3290-3300. [PMID: 37092690 PMCID: PMC10170483 DOI: 10.1039/d3sm00094j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Understanding the dispersion stability and aggregation propensity of self-assembled monolayer gold NPs at a molecular level is crucial to guide their rational design and to inform about the optimal surface functionalization for specific applications. To reach this goal, in silico modeling via coarse-grained (CG) molecular dynamics (MD) simulations is a fundamental tool to complement the information acquired from experimental studies since CG modeling allows to get a deep knowledge of the molecular interactions that take place at the nanoscale in this kind of systems. Unfortunately, current CG models of monolayer-protected AuNPs present several drawbacks that limit their accuracy in certain scenarios. We here develop a CG model that is fully compatible and extends the SPICA/SDK (Shinoda-DeVane-Klein) force field. Our model allows reproducing the behavior of AuNPs functionalized with hydrophobic as well as charged and more hydrophilic ligands. This model improves upon results obtained with previously derived CG force fields and successfully describes NPs aggregation and self-assembly in aqueous solution.
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Affiliation(s)
- Emanuele Petretto
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| | - Stefano Vanni
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
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11
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Gao A, Remsing RC, Weeks JD. Local Molecular Field Theory for Coulomb Interactions in Aqueous Solutions. J Phys Chem B 2023; 127:809-821. [PMID: 36669139 DOI: 10.1021/acs.jpcb.2c06988] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Coulomb interactions play a crucial role in a wide array of processes in aqueous solutions but present conceptual and computational challenges to both theory and simulations. We review recent developments in an approach addressing these challenges─local molecular field (LMF) theory. LMF theory exploits an exact and physically suggestive separation of intermolecular Coulomb interactions into strong short-range and uniformly slowly varying long-range components. This allows us to accurately determine the averaged effects of the long-range components on the short-range structure using effective single particle fields and analytical corrections, greatly reducing the need for complex lattice summation techniques used in most standard approaches. The simplest use of these ideas in aqueous solutions leads to the short solvent (SS) model, where both solvent-solvent and solute-solvent Coulomb interactions have only short-range components. Here we use the SS model to give a simple description of pairing of nucleobases and biologically relevant ions in water.
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Affiliation(s)
- Ang Gao
- Department of Physics, Beijing University of Posts and Telecommunications, Beijing, China 100876
| | - Richard C Remsing
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - John D Weeks
- Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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Dixit M, Taniguchi T. Substantial Effect of Terminal Groups in cis-Polyisoprene: A Multiscale Molecular Dynamics Simulation Study. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mayank Dixit
- Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takashi Taniguchi
- Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan
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13
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Miyazaki Y, Shinoda W. Cooperative antimicrobial action of melittin on lipid membranes: A coarse-grained molecular dynamics study. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183955. [PMID: 35526599 DOI: 10.1016/j.bbamem.2022.183955] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/09/2022] [Accepted: 04/29/2022] [Indexed: 12/29/2022]
Abstract
We conducted a series of coarse-grained molecular dynamics (CG-MD) simulations to investigate the complicated actions of melittin, which is an antimicrobial peptide (AMP) derived from honey bee venom, on a lipid membrane. To accurately simulate the AMP action, we developed and used a protein CG model as an extension of the pSPICA force field (FF), which was designed to reproduce several thermodynamic quantities and structural properties. At a low peptide-to-lipid (P/L) ratio (1/102), no defect was detected. At P/L = 1/51, toroidal pore formation was observed due to collective insertion of multiple melittin peptides from the N-termini. The pore formation was initiated by a local increase in membrane curvature in the vicinity of the peptide aggregate. At a higher P/L ratio (1/26), two more modes were detected, seemingly not controlled by the P/L ratio but by a local arrangement of melittin peptides: 1. Pore formation accompanied by lipid extraction by melittin peptides:a detergent-like mechanism. 2. A rapidly formed large pore in a significantly curved membrane: bursting. Thus, we observed three pore formation modes (toroidal pore formation, lipid extraction, and bursting) depending on the peptide concentration and local arrangement. These observations were consistent with experimental observations and hypothesized melittin modes. Through this study, we found that the local arrangements and population of melittin peptides and the area expansion rate by membrane deformation were key to the initiation of and competition among the multiple pore formation mechanisms.
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Affiliation(s)
- Yusuke Miyazaki
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Wataru Shinoda
- Department of Materials Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan; Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan; Department of Chemistry, Faculty of Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
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Marrink SJ, Monticelli L, Melo MN, Alessandri R, Tieleman DP, Souza PCT. Two decades of Martini: Better beads, broader scope. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1620] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siewert J. Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials University of Groningen Groningen The Netherlands
| | - Luca Monticelli
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
| | - Manuel N. Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa Oeiras Portugal
| | - Riccardo Alessandri
- Pritzker School of Molecular Engineering University of Chicago Chicago Illinois USA
| | - D. Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences University of Calgary Alberta Canada
| | - Paulo C. T. Souza
- Molecular Microbiology and Structural Biochemistry (MMSB ‐ UMR 5086) CNRS & University of Lyon Lyon France
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