1
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Mendanha K, Colherinhas G. Exploring How System Dimensions and Periodic Boundary Conditions Influence the Molecular Dynamics Simulation of A 6H Peptide Self-Assembly Nanostructures. J Phys Chem B 2024; 128:6853-6865. [PMID: 38981040 PMCID: PMC11264264 DOI: 10.1021/acs.jpcb.4c03043] [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: 05/08/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/11/2024]
Abstract
This work presents a study on the effects of periodic boundary conditions (PBC) on the energetic/structural properties and hydrogen bond dynamics (HB) using molecular dynamics (MD) simulations of peptide membranes composed of alanine and histidine. Our results highlight that simulations using small surface areas for the peptide membrane may result in nonconvergent values for membrane properties, which are only observed in regions simulated at a certain distance from the PBCs. Specifically, regarding hydrogen bonds, a property pervasive in peptide membranes, our findings indicate a significant increase in the lifetime of these interactions, reaching values ∼19% higher when observed in structures free from PBCs. For peptide mobility in these nanomembranes, our results compare regions simulated directly under the influence of PBCs with regions free from these conditions, emphasizing greater mobility of amino acid psi/phi angles in the latter model.
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Affiliation(s)
- Karinna Mendanha
- Instituto de Física, Universidade Federal de Goiás, Goiânia, GO 74690-900, Brazil
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2
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Maity S, Pahari S, Santra S, Jana M. Interfacial Glucose to Regulate Hydrated Lipid Bilayer Properties: Influence of Concentrations. J Chem Inf Model 2024; 64:3841-3854. [PMID: 38635679 DOI: 10.1021/acs.jcim.3c01991] [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: 04/20/2024]
Abstract
A series of atomistic molecular dynamics (MD) simulations were carried out with a hydrated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayer with the variation of glucose concentrations from 0 to 30 wt % in the presence of 0.3 M NaCl. The study suggested that although the thickness of the lipid bilayer dropped significantly with the increase in glucose concentration, it expanded laterally at high glucose levels due to the intercalation of glucose between the headgroups of adjacent lipids. We adopted the surface assessment via the grid evaluation method to compute the deviation of the bilayer's key structural features for the different amounts of glucose present. This suggested that the accumulation of glucose molecules near the headgroups influences the local lipid bilayer undulation and crimping of the lipid tails. We find that the area compressibility modulus increases with the glucose level, causing enhanced bilayer rigidity arising from the slow lateral diffusion of lipids. The restricted lipid motion at high glucose concentrations controls the sustainability of the curved bilayer surface. Calculations revealed that certain orientations of CO → of interfacial glucose with the PN → of lipid headgroups are preferred, which helps the glucose to form direct hydrogen bonds (HBs) with the lipid headgroups. Such lipid-glucose (LG) HBs relax slowly at low glucose concentrations and exhibit a higher lifetime, whereas fast structural relaxation of LG HBs with a shorter lifetime was noticed at a higher glucose level. In contrast, lipid-water (LW) HBs exhibited a higher lifetime at a higher glucose level, which gradually decreased with the glucose level lowering. The study interprets that the glucose concentration-driven LW and LG interactions are mutually inclusive. Our detailed analysis will exemplify small saccharide concentration-driven membrane stabilizing efficiency, which is, in general, helpful for drug delivery study.
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Affiliation(s)
- Sankar Maity
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Somdev Pahari
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Santanu Santra
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
| | - Madhurima Jana
- Molecular Simulation Laboratory, Department of Chemistry, National Institute of Technology, Rourkela 769008, India
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3
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Park P, Matsubara DK, Barzotto DR, Lima FS, Chaimovich H, Marrink SJ, Cuccovia IM. Vesicle protrusion induced by antimicrobial peptides suggests common carpet mechanism for short antimicrobial peptides. Sci Rep 2024; 14:9701. [PMID: 38678109 PMCID: PMC11055889 DOI: 10.1038/s41598-024-60601-w] [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: 09/30/2023] [Accepted: 04/25/2024] [Indexed: 04/29/2024] Open
Abstract
Short-cationic alpha-helical antimicrobial peptides (SCHAMPs) are promising candidates to combat the growing global threat of antimicrobial resistance. They are short-sequenced, selective against bacteria, and have rapid action by destroying membranes. A full understanding of their mechanism of action will provide key information to design more potent and selective SCHAMPs. Molecular Dynamics (MD) simulations are invaluable tools that provide detailed insights into the peptide-membrane interaction at the atomic- and meso-scale level. We use atomistic and coarse-grained MD to look into the exact steps that four promising SCHAMPs-BP100, Decoralin, Neurokinin-1, and Temporin L-take when they interact with membranes. Following experimental set-ups, we explored the effects of SCHAMPs on anionic membranes and vesicles at multiple peptide concentrations. Our results showed all four peptides shared similar binding steps, initially binding to the membrane through electrostatic interactions and then flipping on their axes, dehydrating, and inserting their hydrophobic moieties into the membrane core. At higher concentrations, fully alpha-helical peptides induced membrane budding and protrusions. Our results suggest the carpet mode of action is fit for the description of SCHAMPs lysis activity and discuss the importance of large hydrophobic residues in SCHAMPs design and activity.
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Affiliation(s)
- Peter Park
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG, Groningen, the Netherlands
| | - Danilo K Matsubara
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Domenico R Barzotto
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Filipe S Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Brazil
| | - Hernan Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG, Groningen, the Netherlands.
| | - Iolanda M Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil.
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4
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van der Pol RI, Brinkmann BW, Sevink GJA. Analyzing Lipid Membrane Defects via a Coarse-Grained to Triangulated Surface Map: The Role of Lipid Order and Local Curvature in Molecular Binding. J Chem Theory Comput 2024; 20:2888-2900. [PMID: 38537131 PMCID: PMC11008102 DOI: 10.1021/acs.jctc.4c00082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 04/10/2024]
Abstract
Lipid packing defects are known to serve as quantitative indicators for protein binding to lipid membranes. This paper presents a protocol for mapping molecular lipid detail onto a triangulated continuum leaflet representation. Besides establishing the desired forward counterpart to the existing inverse TS2CG map, this coarse-grained to triangulated surface (CG2TS) map enables straightforward extraction of the defect characteristics for any membrane geometry found in nature. We have applied our protocol to investigate the role of local curvature and varying lipid packing on the defect constant π. We find that the defect size is greatly influenced by both factors, arguing strongly against the usual assignment of a single defect constant in the case of more realistic membrane conditions. An important discovery is that lipids in the gel phase produce larger defects, or a higher π, in domains of high (local) curvature than the same lipid in a liquid phase of any curvature. This finding suggests that membranes featuring very ordered lipid packing can bind proteins via large defects in curved regions. Finally, we propose a route for estimating defect constants directly from the standard membrane properties. Identifying the precise role of composition, lipid (tail) order, and (local) curvature in defects for the irregular lipid structures that are (temporally) present in many biological processes is instrumental for obtaining fundamental insight as well as for a rational design of membrane binding targets.
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Affiliation(s)
- Rianne
W. I. van der Pol
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - Bregje W. Brinkmann
- Institute
of Environmental Sciences, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - G. J. Agur Sevink
- Leiden
Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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5
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Frigini EN, Porasso RD, Beke-Somfai T, López Cascales JJ, Enriz RD, Pantano S. The Mechanism of Antimicrobial Small-Cationic Peptides from Coarse-Grained Simulations. J Chem Inf Model 2023; 63:6877-6889. [PMID: 37905818 DOI: 10.1021/acs.jcim.3c01348] [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: 11/02/2023]
Abstract
Antimicrobial cationic peptides (AMPs) are excellent candidates for use as therapeutic antimicrobial agents. Among them, short peptides possessing sequences of 9-11 amino acids have some advantages over long-sequence peptides. However, one of the main limitations of short peptides is that their mechanism of action at the molecular level is not well-known. In this article, we report a model based on multiscale molecular dynamics simulations of short peptides interacting with vesicles containing palmitoyl-oleoyl-phosphatidylglycerol (POPG)/palmitoyl-oleoyl-phosphatidylethanolamine (POPE). Simulations using this approach have allowed us to understand the different behaviors of peptides with antimicrobial activity with respect to those that do not produce this effect. We found remarkable agreement with a series of experimental results directly supporting our model. Moreover, these results allow us to understand the mechanism of action at the molecular level of these short peptides. Our simulations suggest that mechanical inhomogeneities appear in the membrane, promoting membrane rupture when a threshold concentration of peptides adsorbed on the membrane is achieved. These results explain the high structural demand for these peptides to maintain a delicate balance between the affinity for the bilayer surface, a low peptide-peptide repulsion (in order to reach the threshold concentration), and an acceptable tendency to penetrate into the bilayer. This mechanism is different from those proposed for peptides with long amino acid sequences. Such information is very useful from the medicinal chemistry point of view for the design of new small antimicrobial peptides.
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Affiliation(s)
- Ezequiel N Frigini
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
| | - Rodolfo D Porasso
- Instituto de Matemáticas Aplicada San Luis (IMASL), CONICET, Facultad de Ciencias Físico Matemáticas y Naturales, Universidad Nacional de San Luis, Av. Ejército de los Andes 950, San Luis 5700, Argentina
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, H-1117 Budapest, Hungary
| | - José Javier López Cascales
- Universidad Politécnica de Cartagena, Grupo de Bioinformática y Macromoleculas (BioMac), Area de Química Física, Aulario II, Campus de Alfonso XIII, 30203 Cartagena, Murcia, Spain
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Instituto Multidisciplinario de Investigaciones Biológicas (IMIBIO-SL), Universidad Nacional de San Luis, Ejército de los Andes 950, San Luis 5700, Argentina
| | - Sergio Pantano
- Biomolecular Simulations Group, Institut Pasteur de Montevideo, Mataojo 2020, Montevideo 11400, Uruguay
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6
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Carrer M, Nielsen JE, Cezar HM, Lund R, Cascella M, Soares TA. Accelerating Lipid Flip-Flop at Low Concentrations: A General Mechanism for Membrane Binding Peptides. J Phys Chem Lett 2023; 14:7014-7019. [PMID: 37523748 PMCID: PMC10424232 DOI: 10.1021/acs.jpclett.3c01284] [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: 05/11/2023] [Accepted: 07/27/2023] [Indexed: 08/02/2023]
Abstract
We report a physicochemical investigation of the lipid transport properties of model lipid membranes in the presence of the antimicrobial peptide indolicidin through comparisons of experimental SANS/SAXS scattering techniques to fully atomistic molecular dynamics simulations. In agreement with the experiment, we show that upon peripheral binding of the peptides, even at low concentrations, lipid flip-flop dynamics is greatly accelerated. Computer modeling elucidates the interplay between structural changes and lipid dynamics induced by peptides and proposes a mechanism for the mode of action of antimicrobial peptides, assessing the major role of entropy for the catalysis of the flipping events. The mechanism introduced here is universal for all peptides with preferential peripheral binding to the membrane as it does not depend on the specific amino acid sequence.
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Affiliation(s)
- Manuel Carrer
- Department
of Chemistry, University of Oslo, Postboks 1033 Blindern, 0315 Oslo, Norway
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, 0315 Oslo, Norway
| | | | - Henrique Musseli Cezar
- Department
of Chemistry, University of Oslo, Postboks 1033 Blindern, 0315 Oslo, Norway
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, 0315 Oslo, Norway
| | - Reidar Lund
- Department
of Chemistry, University of Oslo, Postboks 1033 Blindern, 0315 Oslo, Norway
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, 0315 Oslo, Norway
| | - Michele Cascella
- Department
of Chemistry, University of Oslo, Postboks 1033 Blindern, 0315 Oslo, Norway
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, 0315 Oslo, Norway
| | - Thereza A. Soares
- Department
of Chemistry, University of Oslo, Postboks 1033 Blindern, 0315 Oslo, Norway
- Department
of Chemistry, University of São Paulo, 055508−090 Ribeirão Preto, Brazil
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, 0315 Oslo, Norway
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7
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Santos DS, De Nicola A, dos Santos VF, Milano G, Soares TA. Exploring the Molecular Dynamics of a Lipid-A Vesicle at the Atom Level: Morphology and Permeation Mechanism. J Phys Chem B 2023; 127:6694-6702. [PMID: 37467380 PMCID: PMC10405212 DOI: 10.1021/acs.jpcb.3c02848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/18/2023] [Indexed: 07/21/2023]
Abstract
Lipid-A was previously shown to spontaneously aggregate into a vesicle via the hybrid particle field approach. We assess the validity of the proposed vesiculation mechanism by simulating the resulting lipid-A vesicle at the atom level. The spatial confinement imposed by the vesicle geometry on the conformation and packing of lipid-A induces significant heterogeneity of physical properties in the inner and outer leaflets. It also induces tighter molecular packing and lower acyl chain order compared to the lamellar arrangement. Around 5% of water molecules passively permeates the vesicle membrane inward and outward. The permeation is facilitated by interactions with water molecules that are transported across the membrane by a network of electrostatic interactions with the hydrogen bond donors/acceptors in the N-acetylglucosamine ring and upper region of the acyl chains of lipid-A. The permeation process takes place at low rates but still at higher frequencies than observed for the lamellar arrangement of lipid-A. These findings not only substantiate the proposed lipid-A vesiculation mechanism but also reveal the complex structural dynamics of an important nonlamellar arrangement of lipid-A.
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Affiliation(s)
- Denys
E. S. Santos
- Departmento
de Química Fundamental, Universidade
Federal de Pernambuco, Recife 50740-560, Brazil
| | - Antonio De Nicola
- Scuola
Superiore Meridionale, Largo S. Marcellino 10, Napoli 80138, Italy
- Graduate
School of Organic Materials Science, Yamagata
University, Yonezawa 992-8510, Yamagata, Japan
| | - Vinicius F. dos Santos
- Departamento
de Química, Faculdade de Filosofia, Ciências e Letras
de Ribeirão Preto, Universidade de
São Paulo, Ribeirão
Preto 14040-901, Brazil
| | - Giuseppe Milano
- Department
of Chemical, Materials and Production Engineering, University of Naples Federico II, Piazzale Tecchio 80, Napoli 80125, Italy
| | - Thereza A. Soares
- Departamento
de Química, Faculdade de Filosofia, Ciências e Letras
de Ribeirão Preto, Universidade de
São Paulo, Ribeirão
Preto 14040-901, Brazil
- Hylleraas
Centre for Quantum Molecular Sciences, University
of Oslo, Oslo 0315, Norway
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8
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Corey RA, Baaden M, Chavent M. A brief history of visualizing membrane systems in molecular dynamics simulations. FRONTIERS IN BIOINFORMATICS 2023; 3:1149744. [PMID: 37213533 PMCID: PMC10196259 DOI: 10.3389/fbinf.2023.1149744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/13/2023] [Indexed: 05/23/2023] Open
Abstract
Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.
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Affiliation(s)
- R. A. Corey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - M. Baaden
- Centre Nationale de la Recherche Scientifique, Laboratoire de Biochimie Théorique, Université Paris Cité, Paris, France
| | - M. Chavent
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de Toulouse, Toulouse, France
- *Correspondence: M. Chavent,
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9
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EF4K bola-amphiphilic peptide nanomembrane: structural, energetic and dynamic properties using molecular dynamics. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Mendanha K, Bruno Assis Oliveira L, Colherinhas G. Modeling, energetic and structural analysis of peptide membranes formed by arginine and phenylalanine (R2F4R2) using fully atomistic molecular dynamics. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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11
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Santos DES, Coutinho K, Soares TA. Surface Assessment via Grid Evaluation (SuAVE) for Every Surface Curvature and Cavity Shape. J Chem Inf Model 2022; 62:4690-4701. [PMID: 35946873 PMCID: PMC9554907 DOI: 10.1021/acs.jcim.2c00673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The surface assessment via grid evaluation
(SuAVE)
software was developed to account for the effect of curvature in the
calculations of structural properties of chemical interfaces regardless
of the chemical composition, asymmetry, and level of atom coarseness.
It employs differential geometry techniques, enabling the representation
of chemical surfaces as fully differentiable. In this article, we
present novel developments of SuAVE to treat closed surfaces and complex
cavity shapes. These developments expand the repertoire of curvature-dependent
analyses already available in the previous version of SuAVE (e.g., area per lipid, density profiles, membrane thickness,
deuterium-order parameters, volume per lipid, and surface curvature
angle) to include new functionalities applicable to soft matter (e.g., sphericity, average radius, principal moment of inertia,
and roundness) and crystalline porous materials (e.g., pore diameter, internal void volume, total area, and the total
void volume of the unit cell structure). SuAVE can accurately handle
chemical systems with high and low atom density as demonstrated for
two distinct chemical systems: the lipid A vesicle and a set of selected
metal–organic frameworks. The SuAVE software v2.0 is fully
parallel and benefits from a compiler that supports OpenMP. SuAVE
is freely available from https://github.com/SuAVE-Software/source and https://www.biomatsite.net/.
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Affiliation(s)
- Denys E S Santos
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, Cidade Universitária, Recife 50740-560, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil
| | - Thereza A Soares
- Instituto de Física, Universidade de São Paulo, Cidade Universitária, São Paulo 05508-090, Brazil.,Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, 0315 Oslo, Norway
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12
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Sun L, Pan F, Li S. Self-Assembly of Lipid Mixtures in Solutions: Structures, Dynamics Processes and Mechanical Properties. MEMBRANES 2022; 12:membranes12080730. [PMID: 35893448 PMCID: PMC9394357 DOI: 10.3390/membranes12080730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023]
Abstract
The self-assembly of lipid mixtures in aqueous solution was investigated by dissipative particle dynamics simulation. Two types of lipid molecules were modelled, where three mixed structures, i.e., the membrane, perforated membrane and vesicle, were determined in the self-assembly processes. Phase behaviour was investigated by using the phase diagrams based on the tail chain lengths for the two types of lipids. Several parameters, such as chain number and average radius of gyration, were employed to explore the structural formations of the membrane and perforated membrane in the dynamic processes. Interface tension was used to demonstrate the mechanical properties of the membrane and perforated membrane in the equilibrium state and dynamics processes. Results help us to understand the self-assembly mechanism of the biomolecule mixtures, which has a potential application for designing the lipid molecule-based bio-membranes in solutions.
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Affiliation(s)
| | - Fan Pan
- Correspondence: (F.P.); (S.L.)
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13
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Domingos Alves E, de Andrade DX, de Almeida AR, Colherinhas G. Molecular dynamics study of hydrogen bond in peptide membrane at 150–300 K. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118165] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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Zhang J, Wang Y, Wang J, Yan Y, Li J, Li Z. Self-assembly of an in silico designed dipeptide derivative to obtain photo-responsive vesicles. Phys Chem Chem Phys 2022; 24:27751-27758. [DOI: 10.1039/d2cp03258a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Photo-responsive vesicles self-assembled from in silico designed peptide derivatives were investigated using coarse-grained molecular dynamics simulations.
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Affiliation(s)
- Jun Zhang
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Yining Wang
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Junfeng Wang
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Youguo Yan
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Jiawei Li
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
| | - Zhen Li
- School of Materials Science and Engineering, China University of Petroleum (East China), Qingdao 266580, China
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15
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Franco LR, Park P, Chaimovich H, Coutinho K, Cuccovia IM, Lima FS. Simulations reveal that antimicrobial BP100 induces local membrane thinning, slows lipid dynamics and favors water penetration. RSC Adv 2022; 12:4573-4588. [PMID: 35425494 PMCID: PMC8981376 DOI: 10.1039/d1ra06267k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/26/2022] [Indexed: 11/21/2022] Open
Abstract
MD simulations reveal that BP100 peptide induces local membrane thinning and negative curvature, slows lipid dynamics and increases the water life time in the lipid hydrophobic core and transmembrane water transport in the direction of the peptide.
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Affiliation(s)
| | - Peter Park
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Hernan Chaimovich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, São Paulo, Brazil
| | - Iolanda M. Cuccovia
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Filipe S. Lima
- Departamento de Química Fundamental, Centro de Ciências Exatas e da Natureza, Universidade Federal de Pernambuco, Recife, Brazil
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16
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Cruz VL, Ramos J, Martinez-Salazar J, Montalban-Lopez M, Maqueda M. The Role of Key Amino Acids in the Antimicrobial Mechanism of a Bacteriocin Model Revealed by Molecular Simulations. J Chem Inf Model 2021; 61:6066-6078. [PMID: 34874722 PMCID: PMC9178794 DOI: 10.1021/acs.jcim.1c00838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
![]()
The AS-48 bacteriocin is a potent
antimicrobial polypeptide with
enhanced stability due to its circular sequence of peptidic bonds.
The mechanism of biological action is still not well understood in
spite of both the elucidation of the molecular structure some years
ago and several experiments performed that yielded valuable information
about the AS-48 bacterial membrane poration activity. In this work,
we present a computational study at an atomistic scale to analyze
the membrane disruption mechanism. The process is based on the two-stage
model: (1) peptide binding to the bilayer surface and (2) membrane
poration due to the surface tension exerted by the peptide. Indeed,
the induced membrane tension mechanism is able to explain stable formation
of pores leading to membrane disruption. The atomistic detail obtained
from the simulations allows one to envisage the contribution of the
different amino acids during the poration process. Clustering of cationic
residues and hydrophobic interactions between peptide and lipids seem
to be essential ingredients in the process. GLU amino acids have shown
to enhance the membrane disrupting ability of the bacteriocin. TRP24–TRP24
interactions make also an important contribution in the initial stages
of the poration mechanism. The detailed atomistic information obtained
from the simulations can serve to better understand bacteriocin structural
characteristics to design more potent antimicrobial therapies.
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Affiliation(s)
- Víctor L Cruz
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, Madrid 28006, Spain
| | - Javier Ramos
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, Madrid 28006, Spain
| | - Javier Martinez-Salazar
- BIOPHYM, Department of Macromolecular Physics, Instituto de Estructura de la Materia, IEM-CSIC, C/ Serrano 113 bis, Madrid 28006, Spain
| | - Manuel Montalban-Lopez
- Department of Microbiology, University of Granada, C/ Fuentenueva s/n, Granada 18071, Spain
| | - Mercedes Maqueda
- Department of Microbiology, University of Granada, C/ Fuentenueva s/n, Granada 18071, Spain
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17
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de Andrade DX, Alves ED, de Almeida AR, Colherinhas G. Laminar peptide structure: Energetic and structural evaluation using molecular dynamics. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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18
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Messias A, Santos DES, Pontes FJS, Soares TA. The tug of war between Al 3+ and Na + for order-disorder transitions in lipid-A membranes. Phys Chem Chem Phys 2021; 23:15127-15137. [PMID: 34254086 DOI: 10.1039/d1cp02173g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Cations play a critical role in the stability and morphology of lipid-A aggregates by neutralizing, hydrating and cross-linking these glycolipid molecules. Monophosphorylated lipid-A is the major immunostimulatory principle in commercially available adjuvants containing Al3+ such as adjuvant system 04 (AS04). The antagonist/agonist immunomodulatory properties of lipid-A are associated with chemical variations (e.g. the number of acyl chains and phosphate groups) and their aggregate arrangements (e.g. lamellar, nonlamellar or mixed). Therefore, the identification of the active form of lipid-A can provide valuable guidance in the development of vaccine adjuvants capable of boosting the immune system with decreased reactogenicity. Although the effect of mono and divalent cations on the structural polymorphism and endotoxicity of LPS has been previously investigated, much less is known about the effect of trivalent cations. We have investigated the effect of NaCl and AlCl3 salt solutions on the structural dynamics and stability of mono and diphosphorylated lipid-A membranes via atomistic MD simulations. The Al3+ ion exerts two major effects on the structural dynamics of lipid-A membranes. It acts as an efficient cross-linker of mono or diphosphorylated lipid-A molecules, thus stabilizing the lamellar arrangement of these glycolipids. It also alters the lipid-A packing and membrane fluidity, inducing disorder → order structural transitions of the membrane. This effect is promptly reversed upon the addition of NaCl solution, which promotes a nearly threefold increase in the amount of water in the carbohydrate moiety of the Al3+-containing lipid-A membranes. The exchange dynamics and residence times of cation-coordinated water molecules in these membranes provide insights into the molecular mechanism for the Na+-induced transition from a densely packed ordered phase to a disordered one. Al3+ counter-ions favor ordered lamellar aggregates, which has been previously associated with the lack of endotoxic activity and cytokine-inducing action. The resulting microscopic understanding of the structure and dynamics of lipid-A aggregates in the presence of Al3+ and Na+ salts can provide valuable guidance in the development of vaccine adjuvants capable of boosting the immune system with decreased reactogenicity.
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Affiliation(s)
- Andresa Messias
- Department of Fundamental Chemistry, Universidade Federal de Pernambuco, 50740-560 Recife, Brazil.
| | - Denys E S Santos
- Department of Fundamental Chemistry, Universidade Federal de Pernambuco, 50740-560 Recife, Brazil.
| | - Frederico J S Pontes
- Department of Fundamental Chemistry, Universidade Federal de Pernambuco, 50740-560 Recife, Brazil.
| | - Thereza A Soares
- Department of Fundamental Chemistry, Universidade Federal de Pernambuco, 50740-560 Recife, Brazil. and Instituto de Fisica, Universidade de São Paulo, 05508-090 São Paulo, Brazil
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19
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Weigle AT, Carr M, Shukla D. Impact of Increased Membrane Realism on Conformational Sampling of Proteins. J Chem Theory Comput 2021; 17:5342-5357. [PMID: 34339605 DOI: 10.1021/acs.jctc.1c00276] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The realism and accuracy of lipid bilayer simulations through molecular dynamics (MD) are heavily dependent on the lipid composition. While the field is pushing toward implementing more heterogeneous and realistic membrane compositions, a lack of high-resolution lipidomic data prevents some membrane protein systems from being modeled with the highest level of realism. Given the additional diversity of real-world cellular membranes and protein-lipid interactions, it is still not fully understood how altering membrane complexity affects modeled membrane protein functions or if it matters over long-timescale simulations. This is especially true for organisms whose membrane environments have little to no computational study, such as the plant plasma membrane. Tackling these issues in tandem, a generalized, realistic, and asymmetric plant plasma membrane with more than 10 different lipid species is constructed herein. Classical MD simulations of pure membrane constructs were performed to evaluate how altering the compositional complexity of the membrane impacted the plant membrane properties. The apo form of a plant sugar transporter, OsSWEET2b, was inserted into membrane models where lipid diversity was calculated in either a size-dependent or size-independent manner. An adaptive sampling simulation regime validated by Markov-state models was performed to capture the gating dynamics of OsSWEET2b in each of these membrane constructs. In comparison to previous OsSWEET2b simulations performed in a pure POPC bilayer, we confirm that simulations performed within a native-like membrane composition alter the stabilization of apo OsSWEET2b conformational states by ∼1 kcal/mol. The free-energy barriers of intermediate conformational states decrease when realistic membrane complexity is simplified, albeit roughly within sampling error, suggesting that protein-specific responses to membranes differ due to altered packing caused by compositional fluctuations. This work serves as a case study where a more realistic bilayer composition makes unbiased conformational sampling easier to achieve than with simplified bilayers.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Matthew Carr
- Independent Software Development Provider310 East Marlette Avenue, Phoenix, Arizona 85012, United States
| | - Diwakar Shukla
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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20
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Freire RV, Pillco-Valencia Y, da Hora GC, Ramstedt M, Sandblad L, Soares TA, Salentinig S. Antimicrobial peptide induced colloidal transformations in bacteria-mimetic vesicles: Combining in silico tools and experimental methods. J Colloid Interface Sci 2021; 596:352-363. [DOI: 10.1016/j.jcis.2021.03.060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 01/21/2023]
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21
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Oliveira MC, Yusupov M, Bogaerts A, Cordeiro RM. Lipid Oxidation: Role of Membrane Phase-Separated Domains. J Chem Inf Model 2021; 61:2857-2868. [PMID: 34080860 DOI: 10.1021/acs.jcim.1c00104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Lipid oxidation is associated with several inflammatory and neurodegenerative diseases, but many questions to unravel its effects on biomembranes are still open due to the complexity of the topic. For instance, recent studies indicated that phase-separated domains can have a significant effect on membrane function. It is reported that domain interfaces are "hot spots" for pore formation, but the underlying mechanisms and the effect of oxidation-induced phase separation on membranes remain elusive. Thus, to evaluate the permeability of the membrane coexisting of liquid-ordered (Lo) and liquid-disordered (Ld) domains, we performed atomistic molecular dynamics simulations. Specifically, we studied the membrane permeability of nonoxidized or oxidized homogeneous membranes (single-phase) and at the Lo/Ld domain interfaces of heterogeneous membranes, where the Ld domain is composed of either oxidized or nonoxidized lipids. Our simulation results reveal that the addition of only 1.5% of lipid aldehyde molecules at the Lo/Ld domain interfaces of heterogeneous membranes increases the membrane permeability, whereas their addition at homogeneous membranes does not have any effect. This study is of interest for a better understanding of cancer treatment methods based on oxidative stress (causing among others lipid oxidation), such as plasma medicine and photodynamic therapy.
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Affiliation(s)
- Maria C Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André, SP, Brazil.,Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Maksudbek Yusupov
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Annemie Bogaerts
- Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Rodrigo M Cordeiro
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Avenida dos Estados 5001, CEP 09210-580 Santo André, SP, Brazil
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22
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Out of Sight, Out of Mind: The Effect of the Equilibration Protocol on the Structural Ensembles of Charged Glycolipid Bilayers. Molecules 2020; 25:molecules25215120. [PMID: 33158044 PMCID: PMC7663769 DOI: 10.3390/molecules25215120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022] Open
Abstract
Molecular dynamics (MD) simulations represent an essential tool in the toolbox of modern chemistry, enabling the prediction of experimental observables for a variety of chemical systems and processes and majorly impacting the study of biological membranes. However, the chemical diversity of complex lipids beyond phospholipids brings new challenges to well-established protocols used in MD simulations of soft matter and requires continuous assessment to ensure simulation reproducibility and minimize unphysical behavior. Lipopolysaccharides (LPS) are highly charged glycolipids whose aggregation in a lamellar arrangement requires the binding of numerous cations to oppositely charged groups deep inside the membrane. The delicate balance between the fully hydrated carbohydrate region and the smaller hydrophobic core makes LPS membranes very sensitive to the choice of equilibration protocol. In this work, we show that the protocol successfully used to equilibrate phospholipid bilayers when applied to complex lipopolysaccharide membranes occasionally leads to a small expansion of the simulation box very early in the equilibration phase. Although the use of a barostat algorithm controls the system dimension and particle distances according to the target pressure, fluctuation in the fleeting pressure occasionally enables a few water molecules to trickle into the hydrophobic region of the membrane, with spurious solvent buildup. We show that this effect stems from the initial steps of NPT equilibration, where initial pressure can be fairly high. This can be solved with the use of a stepwise-thermalization NVT/NPT protocol, as demonstrated for atomistic MD simulations of LPS/DPPE and lipid-A membranes in the presence of different salts using an extension of the GROMOS forcefield within the GROMACS software. This equilibration protocol should be standard procedure for the generation of consistent structural ensembles of charged glycolipids starting from atomic coordinates not previously pre-equilibrated. Although different ways to deal with this issue can be envisioned, we investigated one alternative that could be readily available in major MD engines with general users in mind.
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23
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Soares TA, Wahab HA. Outlook on the Development and Application of Molecular Simulations in Latin America. J Chem Inf Model 2020; 60:435-438. [PMID: 32009389 DOI: 10.1021/acs.jcim.0c00112] [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]
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24
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Fornasier F, Souza LMP, Souza FR, Reynaud F, Pimentel AS. Lipophilicity of Coarse-Grained Cholesterol Models. J Chem Inf Model 2020; 60:569-577. [DOI: 10.1021/acs.jcim.9b00830] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Franccesca Fornasier
- Departamento de Quı́mica, Pontifı́cia Universidade Católica do Rio de Janeiro Rio de Janeiro, RJ 22453-900, Brazil
| | - Lucas M. P. Souza
- Departamento de Quı́mica, Pontifı́cia Universidade Católica do Rio de Janeiro Rio de Janeiro, RJ 22453-900, Brazil
| | - Felipe R. Souza
- Departamento de Quı́mica, Pontifı́cia Universidade Católica do Rio de Janeiro Rio de Janeiro, RJ 22453-900, Brazil
| | - Franceline Reynaud
- Institut Galien Paris-Sud, CNRS 8612, Université Paris-Saclay, 92290 Châtenay, Malabry, France
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | - Andre S. Pimentel
- Departamento de Quı́mica, Pontifı́cia Universidade Católica do Rio de Janeiro Rio de Janeiro, RJ 22453-900, Brazil
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