1
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Banerjee KK, Maity P, Das S, Karmakar S. Effect of cholesterol on the ion-membrane interaction: Zeta potential and dynamic light scattering study. Chem Phys Lipids 2023; 254:105307. [PMID: 37182823 DOI: 10.1016/j.chemphyslip.2023.105307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/11/2023] [Indexed: 05/16/2023]
Abstract
Cholesterol in a bio-membrane plays a significant role in many cellular event and is known to regulate the functional activity of protein and ion channel. In this study we report a significant effect of cholesterol on the ion-membrane interaction. We prepare large unilamellar vesicles, composed of zwitterionic lipid DOPC and anionic lipid DOPG with different cholesterol concentration. Electrostatics of anionic membranes containing cholesterol in the presence of NaCl has systematically been explored using dynamic light scattering and zeta potential. Negative zeta potential of the membrane decreases its negative value with increasing ion concentration for all cholesterol concentrations. However, zeta potential itself decreases with increasing cholesterol content even in the absence of monovalent ions. Electrostatic behaviour of the membrane is determined from well-known Gouy Chapmann model. Negative surface charge density of the membrane decreases with increasing cholesterol content. Binding constant, estimated from the electrostatic double layer theory, is found to increase significantly in the presence of cholesterol. Comparison of electrostatic parameters of the membrane in the presence and absence of cholesterol suggests that cholesterol significantly alter the electrostatic behaviour of the membrane.
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Affiliation(s)
- Kalyan Kumar Banerjee
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Pabitra Maity
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Surajit Das
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India
| | - Sanat Karmakar
- Soft matter and Biophysics Laboratory, Department of Physics, Jadavpur University, 188, Raja S. C. Mallick Road, Kolkata 700032, India.
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2
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Wang X, Zhang Y, Xie M, Wang Z, Qiao H. Temperature-Promoted Giant Unilamellar Vesicle (GUV) Aggregation: A Way of Multicellular Formation. Curr Issues Mol Biol 2023; 45:3757-3771. [PMID: 37232711 DOI: 10.3390/cimb45050242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023] Open
Abstract
The evolution of unicellular to multicellular life is considered to be an important step in the origin of life, and it is crucial to study the influence of environmental factors on this process through cell models in the laboratory. In this paper, we used giant unilamellar vesicles (GUVs) as a cell model to investigate the relationship between environmental temperature changes and the evolution of unicellular to multicellular life. The zeta potential of GUVs and the conformation of the headgroup of phospholipid molecules at different temperatures were examined using phase analysis light scattering (PALS) and attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR), respectively. In addition, the effect of increasing temperature on the aggregation of GUVs was further investigated in ionic solutions, and the possible mechanisms involved were explored. The results showed that increasing temperature reduced the repulsive forces between cells models and promoted their aggregation. This study could effectively contribute to our understanding of the evolution of primitive unicellular to multicellular life.
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Affiliation(s)
- Xinmao Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Yangruizi Zhang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Maobin Xie
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Zhibiao Wang
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
| | - Hai Qiao
- State Key Laboratory of Ultrasound in Medicine and Engineering, College of Biomedical Engineering, Chongqing Medical University, Chongqing, 400016, China
- Chongqing Key Laboratory of Biomedical Engineering, Chongqing Medical University, Chongqing 400016, China
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3
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Jang J, Kim S, Eom K. NaCl increases the dielectric constant of nanoconfined water in phospholipid multilamellar vesicle by enhancing intermolecular orientation correlation rather than rotational freedom of individual molecules. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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4
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Duboué-Dijon E, Javanainen M, Delcroix P, Jungwirth P, Martinez-Seara H. A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization. J Chem Phys 2021; 153:050901. [PMID: 32770904 DOI: 10.1063/5.0017775] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Molecular simulations can elucidate atomistic-level mechanisms of key biological processes, which are often hardly accessible to experiment. However, the results of the simulations can only be as trustworthy as the underlying simulation model. In many of these processes, interactions between charged moieties play a critical role. Current empirical force fields tend to overestimate such interactions, often in a dramatic way, when polyvalent ions are involved. The source of this shortcoming is the missing electronic polarization in these models. Given the importance of such biomolecular systems, there is great interest in fixing this deficiency in a computationally inexpensive way without employing explicitly polarizable force fields. Here, we review the electronic continuum correction approach, which accounts for electronic polarization in a mean-field way, focusing on its charge scaling variant. We show that by pragmatically scaling only the charged molecular groups, we qualitatively improve the charge-charge interactions without extra computational costs and benefit from decades of force field development on biomolecular force fields.
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Affiliation(s)
- E Duboué-Dijon
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - M Javanainen
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Delcroix
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - P Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
| | - H Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, Prague 6 166 10, Czech Republic
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5
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Gnopo YMD, Misra A, Hsu HL, DeLisa MP, Daniel S, Putnam D. Induced fusion and aggregation of bacterial outer membrane vesicles: Experimental and theoretical analysis. J Colloid Interface Sci 2020; 578:522-532. [PMID: 32540551 PMCID: PMC7487024 DOI: 10.1016/j.jcis.2020.04.068] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 11/15/2022]
Abstract
Recombinantly engineered bacterial outer membrane vesicles (OMVs) are promising vaccine delivery vehicles. The diversity of exogenous antigens delivered by OMVs can be enhanced by induced fusion of OMV populations. To date there are no reports of induced fusion of bacterial OMVs. Here we measure the pH and salt-induced aggregation and fusion of OMVs and analyze the processes against the Derjaguin-Landau-Verwey-Overbeek (DLVO) colloidal stability model. Vesicle aggregation and fusion kinetics were investigated for OMVs isolated from native E. coli (Nissle 1917) and lipopolysaccharide (LPS) modified E. coli (ClearColi) strains to evaluate the effect of lipid type on vesicle aggregation and fusion. Electrolytes and low pHs induced OMV aggregation for both native and modified LPS constructs, approaching a calculated fusion efficiency of ~25% (i.e. ~1/4 of collision events lead to fusion). However, high fusion efficiency was achieved for Nissle OMVs solely with decreased pH as opposed to a combination of low pH and increased divalent counterion concentration for ClearColi OMVs. The lipid composition of the OMVs from Nissle negatively impacted fusion in the presence of electrolytes, causing higher deviations from DLVO-predicted critical coagulation concentrations with monovalent counterions. The outcome of the work is a defined set of conditions under which investigators can induce OMVs to fuse and make various combinations of vesicle compositions.
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Affiliation(s)
- Yehou M D Gnopo
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Aditya Misra
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Hung-Lun Hsu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Susan Daniel
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - David Putnam
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.
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6
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De Mel JU, Gupta S, Perera RM, Ngo L, Zolnierczuk P, Bleuel M, Pingali SV, Schneider GJ. Influence of External NaCl Salt on Membrane Rigidity of Neutral DOPC Vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:9356-9367. [PMID: 32672981 DOI: 10.1021/acs.langmuir.0c01004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Sodium chloride (NaCl) is a very common molecule in biotic and abiotic aqueous environments. In both cases, variation of ionic strength is inevitable. In addition to the osmotic variation posed by such perturbations, the question of whether the interactions of monovalent ions Na+ and Cl-, especially with the neutral head groups of phospholipid membranes are impactful enough to change the membrane rigidity, is still not entirely understood. We investigated the dynamics of 1,2-di-(octadecenoyl)-sn-glycero-3-phosphocholine (DOPC) vesicles with zwitterionic neutral head groups in the fluid phase with increasing external salt concentration. At higher salt concentrations, we observe an increase in bending rigidity from neutron spin echo (NSE) spectroscopy and an increase in bilayer thickness from small-angle X-ray scattering (SAXS). We compared different models to distinguish membrane undulations, lipid tail motions, and the translational diffusion of the vesicles. All of the models indicate an increase in bending rigidity by a factor of 1.3-3.6. We demonstrate that even down to t > 10 ns and for Q > 0.07 Å-1, the observed NSE relaxation spectra are influenced by translational diffusion of the vesicles. For t < 5 ns, the lipid tail motion dominates the intermediate dynamic structure factor. As the salt concentration increases, this contribution diminishes. We introduced a time-dependent analysis for the bending rigidity that highlights only a limited Zilman-Granek time window in which the rigidity is physically meaningful.
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Affiliation(s)
- Judith U De Mel
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Sudipta Gupta
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Rasangi M Perera
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Ly Ngo
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Piotr Zolnierczuk
- Jülich Centre for Neutron Science (JCNS), Outstation at SNS, POB 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Markus Bleuel
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8562, United States
| | - Sai Venkatesh Pingali
- Neutron Sciences Directorate, Oak Ridge National Laboratory (ORNL), POB 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Gerald J Schneider
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Department of Physics & Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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7
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Li S, Wu L, Zhang X, Jiang X. The Structure of Water Bonded to Phosphate Groups at the Electrified Zwitterionic Phospholipid Membranes/Aqueous Interface. Angew Chem Int Ed Engl 2020; 59:6627-6630. [DOI: 10.1002/anie.202000511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Indexed: 12/17/2022]
Affiliation(s)
- Shanshan Li
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022, Jilin China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Lie Wu
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022, Jilin China
| | - Xiaofei Zhang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022, Jilin China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Xiue Jiang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022, Jilin China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
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8
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Li S, Wu L, Zhang X, Jiang X. The Structure of Water Bonded to Phosphate Groups at the Electrified Zwitterionic Phospholipid Membranes/Aqueous Interface. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202000511] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shanshan Li
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022, Jilin China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Lie Wu
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022, Jilin China
| | - Xiaofei Zhang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022, Jilin China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
| | - Xiue Jiang
- State Key Laboratory of Electroanalytical ChemistryChangchun Institute of Applied ChemistryChinese Academy of Sciences Changchun 130022, Jilin China
- University of Science and Technology of China Hefei Anhui 230029 P. R. China
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9
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Oh MI, Gupta M, Weaver DF. Understanding Water Structure in an Ion-Pair Solvation Shell in the Vicinity of a Water/Membrane Interface. J Phys Chem B 2019; 123:3945-3954. [DOI: 10.1021/acs.jpcb.9b01331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Myong In Oh
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Mayuri Gupta
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
| | - Donald F. Weaver
- Krembil Research Institute, University Health Network, Toronto, Ontario M5T 0S8, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario M5G 2C4, Canada
- Department of Pharmaceutical Sciences, University of Toronto, Toronto, Ontario M5S 3M2, Canada
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10
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Maity P, Saha B, Suresh Kumar G, Karmakar S. Effect of Zwitterionic Phospholipid on the Interaction of Cationic Membranes with Monovalent Sodium Salts. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:9810-9817. [PMID: 30056708 DOI: 10.1021/acs.langmuir.8b01792] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cationic lipids have attracted much attention because of their potential for biomedical applications, such as gene delivery. The gene transfection efficiency of cationic lipids is greatly influenced by the counterions as well as salt ions. We have systematically investigated the interaction of different monovalent sodium salts with positively charged membrane, composed of 1,2-dioleoyl- sn-glycero-3-phosphocholine (DOPC)/1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and DOTAP, using dynamic light scattering, zeta potential, isothermal titration calorimetry (ITC), and fluorescence spectroscopy techniques. Our results reveal that the affinity of anions with cationic membranes follows the sequence I- ≫ Br- > Cl- according to descending order of their sizes and is consistent with the Hofmeister series. Interestingly, the electrostatic behavior of the DOTAP membrane in the presence of monovalent anions differs significantly from the DOPC/DOTAP membrane. This difference is due to the strong interplay between phosphocholine and trimethylammonium-propane (TAP) headgroups leading to the reorientation of the TAP group in the membrane. The binding constant of anions, derived from zeta potential and ITC is in agreement with the affinity of anions mentioned above. Among all anions, I- shows strongest affinity, as evidenced from the rapid increase in hydrodynamic radius which eventually leads to the formation of large aggregates. The fluorescence spectroscopy of a lypophilic probe Nile red in the presence of cationic vesicles containing ions complements the I- adsorption onto the membrane. Nonlinear Stern-Volmer plot, consisting of accessible and inaccessible Nile red to I- is consistent with the zeta potential as well as ITC results.
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Affiliation(s)
- Pabitra Maity
- Soft Matter and Biophysics Laboratory, Department of Physics , Jadavpur University , 188, Raja S. C. Mallick Road , Kolkata 700032 , India
| | - Baishakhi Saha
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700 032 , India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mallick Road , Kolkata 700 032 , India
| | - Sanat Karmakar
- Soft Matter and Biophysics Laboratory, Department of Physics , Jadavpur University , 188, Raja S. C. Mallick Road , Kolkata 700032 , India
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11
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Melcr J, Martinez-Seara H, Nencini R, Kolafa J, Jungwirth P, Ollila OHS. Accurate Binding of Sodium and Calcium to a POPC Bilayer by Effective Inclusion of Electronic Polarization. J Phys Chem B 2018; 122:4546-4557. [DOI: 10.1021/acs.jpcb.7b12510] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Josef Melcr
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 117 20 Prague 6, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 117 20 Prague 6, Czech Republic
| | - Ricky Nencini
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 117 20 Prague 6, Czech Republic
| | - Jiří Kolafa
- Department of Physical Chemistry, Institute of Chemical Technology, 166 28 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 117 20 Prague 6, Czech Republic
- Department of Physics, Tampere University of Technology, P.O. Box 692, FI-33101 Tampere, Finland
| | - O. H. Samuli Ollila
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 117 20 Prague 6, Czech Republic
- Institute of Biotechnology, University of Helsinki, 00100 Helsinki, Finland
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12
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Reis PPS, Vila-Viçosa D, Campos SRR, Baptista A, Machuqueiro M. Role of Counterions in Constant-pH Molecular Dynamics Simulations of PAMAM Dendrimers. ACS OMEGA 2018; 3:2001-2009. [PMID: 30023821 PMCID: PMC6045380 DOI: 10.1021/acsomega.7b01708] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/08/2018] [Indexed: 05/25/2023]
Abstract
Electrostatic interactions play a pivotal role in the structure and mechanism of action of most biomolecules. There are several conceptually different methods to deal with electrostatics in molecular dynamics simulations. Ionic strength effects are usually introduced using such methodologies and can have a significant impact on the quality of the final conformation space obtained. We have previously shown that full system neutralization can lead to wrong lipidic phases in the 25% PA/PC bilayer (J. Chem. Theory Comput. 2014,10, 5483-5492). In this work, we investigate how two limit approaches to the ionic strength treatment (implicitly with GRF or using full system neutralization with either GRF or PME) can influence the conformational space of the second-generation PAMAM dendrimer. Constant-pH MD simulations were used to map PAMAM's conformational space at its full pH range (from 2.5 to 12.5). Our simulations clearly captured the coupling between protonation and conformation in PAMAM. Interestingly, the dendrimer conformational distribution was almost independent of the ionic strength treatment methods, which is in contrast to what we have observed in charged lipid bilayers. Overall, our results confirm that both GRF with implicit ionic strength and a fully neutralized system with PME are valid approaches to model charged globular systems, using the GROMOS 54A7 force field.
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Affiliation(s)
- Pedro
B. P. S. Reis
- Centro
de Química e Bioquímica, Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Diogo Vila-Viçosa
- Centro
de Química e Bioquímica, Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Sara R. R. Campos
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - António
M. Baptista
- Instituto
de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica, Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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13
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Venâncio C, Pereira R, Freitas AC, Rocha-Santos TAP, da Costa JP, Duarte AC, Lopes I. Salinity induced effects on the growth rates and mycelia composition of basidiomycete and zygomycete fungi. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 231:1633-1641. [PMID: 28964607 DOI: 10.1016/j.envpol.2017.09.075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/08/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
Soil salinization, as the combination of primary and secondary events, can adversely affect organisms inhabiting this compartment. In the present study, the effects of increased salinity were assessed in four species of terrestrial fungi: Lentinus sajor caju, Phanerochaete chrysosporium, Rhizopus oryzae and Trametes versicolor. The mycelial growth and biochemical composition of the four fungi were determined under three exposure scenarios: 1) exposure to serial dilutions of natural seawater (SW), 2) exposure to serial concentrations of NaCl (potential surrogate of SW); and 3) exposure to serial concentrations of NaCl after a period of pre-exposure to low levels of NaCl. The toxicity of NaCl was slightly higher than that of SW, for all fungi species: the conductivities causing 50% of growth inhibition (EC50) were within 14.9 and 22.0 mScm-1 for NaCl and within 20.2 and 34.1 mScm-1 for SW. Phanerochaete chrysosporium showed to be the less sensitive species, both for NaCl and SW. Exposure to NaCl caused changes in the biochemical composition of fungi, mainly increasing the production of polysaccharides. When fungi were exposed to SW this pattern of biochemical response was not observed. Fungi pre-exposed to low levels of salinity presented higher EC50 than fungi non-pre-exposed, though 95% confidence limits overlapped, with the exception of P. chrysosporium. Pre-exposure to low levels of NaCl also induced changes in the biochemical composition of the mycelia of L. sajor caju and R. oryzae, relatively to the respective control. These results suggest that some terrestrial fungi may acquire an increased tolerance to NaCl after being pre-exposed to low levels of this salt, thus, suggesting their capacity to persist in environments that will undergo salinization. Furthermore, NaCl could be used as a protective surrogate of SW to derive safe salinity levels for soils, since it induced toxicity similar or higher than that of SW.
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Affiliation(s)
- C Venâncio
- Department of Biology & CESAM, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - R Pereira
- Department of Biology, Faculty of Sciences of the University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - A C Freitas
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Rua Arquiteto Lobão Vital, Apartado 2511, 45202-401 Porto, Portugal
| | - T A P Rocha-Santos
- Department of Chemistry & CESAM, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - J P da Costa
- Department of Chemistry & CESAM, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - A C Duarte
- Department of Chemistry & CESAM, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
| | - I Lopes
- Department of Biology & CESAM, Campus de Santiago, University of Aveiro, 3810-193 Aveiro, Portugal
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14
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The Charge Properties of Phospholipid Nanodiscs. Biophys J 2017; 111:989-98. [PMID: 27602726 DOI: 10.1016/j.bpj.2016.06.041] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/22/2016] [Accepted: 06/15/2016] [Indexed: 11/23/2022] Open
Abstract
Phospholipids (PLs) are a major, diverse constituent of cell membranes. PL diversity arises from the nature of the fatty acid chains, as well as the headgroup structure. The headgroup charge is thought to contribute to both the strength and specificity of protein-membrane interactions. Because it has been difficult to measure membrane charge, ascertaining the role charge plays in these interactions has been challenging. Presented here are charge measurements on lipid Nanodiscs at 20°C in 100 mM NaCl, 50 mM Tris, at pH 7.4. Values are also reported for measurements made in the presence of Ca(2+) and Mg(2+) as a function of NaCl concentration, pH, and temperature, and in solvents containing other types of cations and anions. Measurements were made for neutral (phosphatidylcholine and phosphatidylethanolamine) and anionic (phosphatidylserine, phosphatidic acid, cardiolipin, and phosphatidylinositol 4,5-bisphosphate (PIP2)) PLs containing palmitoyl-oleoyl and dimyristoyl fatty acid chains. In addition, charge measurements were made on Nanodiscs containing an Escherichia coli lipid extract. The data collected reveal that 1) POPE is anionic and not neutral at pH 7.4; 2) high-anionic-content Nanodiscs exhibit polyelectrolyte behavior; 3) 3 mM Ca(2+) neutralizes a constant fraction of the charge, but not a constant amount of charge, for POPS and POPC Nanodiscs; 4) in contrast to some previous work, POPC only interacts weakly with Ca(2+); 5) divalent cations interact with lipids in a lipid- and ion-specific manner for POPA and PIP2 lipids; and 6) the monovalent anion type has little influence on the lipid charge. These results should help eliminate inconsistencies among data obtained using different techniques, membrane systems, and experimental conditions, and they provide foundational data for developing an accurate view of membranes and membrane-protein interactions.
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15
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Effect of Sodium and Chloride Binding on a Lecithin Bilayer. A Molecular Dynamics Study. MEMBRANES 2017; 7:membranes7010005. [PMID: 28125062 PMCID: PMC5371966 DOI: 10.3390/membranes7010005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/12/2017] [Accepted: 01/14/2017] [Indexed: 01/17/2023]
Abstract
The effect of ion binding on the structural, mechanical, dynamic and electrostatic properties of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer in a 0.5 M aqueous NaCl solution is investigated using classical atomistic molecular dynamics simulation with different force-field descriptions for ion-ion and ion-lipid interactions. Most importantly, the repulsive Lennard-Jones parameters for the latter were modified, such that approximately similar binding of cations and anions to the lipid membrane is achieved. This was done to qualitatively improve the apparent ion-lipid binding constants obtained from simulations with the original force field (Berger lipids and GROMOS87 ions in combination with the SPC water model) in comparison to experimental data. Furthermore, various parameters characterizing membrane structure, elasticity, order and dynamics are analyzed. It is found that ion binding as observed in simulations involving the modified in comparison to the original force-field description leads to: (i) a smaller salt-induced change in the area per lipid, which is in closer agreement with the experiment; (ii) a decrease in the area compressibility and bilayer thickness to values comparable to a bilayer in pure water; (iii) lipid deuterium order parameters and lipid diffusion coefficients on nanosecond timescales that are very similar to the values for a membrane in pure water. In general, salt effects on the structural properties of a POPC bilayer in an aqueous sodium-chloride solution appear to be reproduced reasonably well by the new force-field description. An analysis of membrane-membrane disjoining pressure suggests that the smaller salt-induced change in area per lipid induced by the new force-field description is not due to the alteration of membrane-associated net charge, but must rather be understood as a consequence of ion-specific effects on the arrangement of lipid molecules.
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16
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Fugit KD, Anderson BD. Ion-Pairing Contribution to the Liposomal Transport of Topotecan as Revealed by Mechanistic Modeling. J Pharm Sci 2016; 106:1149-1161. [PMID: 28007561 DOI: 10.1016/j.xphs.2016.12.011] [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: 09/09/2016] [Revised: 12/07/2016] [Accepted: 12/09/2016] [Indexed: 11/18/2022]
Abstract
Actively loaded liposomal formulations of anticancer agents have been widely explored due to their high drug encapsulation efficiencies and prolonged drug retention. Mathematical models to predict and optimize drug loading and release kinetics from these nanoparticle formulations would be useful in their development and may allow researchers to tune release profiles. Such models must account for the driving forces as influenced by the physicochemical properties of the drug and the microenvironment, and the liposomal barrier properties. This study employed mechanistic modeling to describe the active liposomal loading and release kinetics of the anticancer agent topotecan (TPT). The model incorporates ammonia transport resulting in generation of a pH gradient, TPT dimerization, TPT lactone ring-opening and -closing interconversion kinetics, chloride transport, and transport of TPT-chloride ion-pairs to describe the active loading and release kinetics of TPT in the presence of varying chloride concentrations. Model-based predictions of the kinetics of active loading at varying loading concentrations of TPT and release under dynamic dialysis conditions were in reasonable agreement with experiments. These findings identify key attributes to consider in optimizing and predicting loading and release of liposomal TPT that may also be applicable to liposomal formulations of other weakly basic pharmaceuticals.
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Affiliation(s)
- Kyle D Fugit
- Department of Pharmaceutical Development, Metrics Contract Services, Greenville, NC 27834
| | - Bradley D Anderson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536.
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17
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Ge Z, Wang Y. Estimation of Nanodiamond Surface Charge Density from Zeta Potential and Molecular Dynamics Simulations. J Phys Chem B 2016; 121:3394-3402. [PMID: 28423901 DOI: 10.1021/acs.jpcb.6b08589] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Molecular dynamics simulations of nanoparticles (NPs) are increasingly used to study their interactions with various biological macromolecules. Such simulations generally require detailed knowledge of the surface composition of the NP under investigation. Even for some well-characterized nanoparticles, however, this knowledge is not always available. An example is nanodiamond, a nanoscale diamond particle with surface dominated by oxygen-containing functional groups. In this work, we explore using the harmonic restraint method developed by Venable et al., to estimate the surface charge density (σ) of nanodiamonds. Based on the Gouy-Chapman theory, we convert the experimentally determined zeta potential of a nanodiamond to an effective charge density (σeff), and then use the latter to estimate σ via molecular dynamics simulations. Through scanning a series of nanodiamond models, we show that the above method provides a straightforward protocol to determine the surface charge density of relatively large (> ∼100 nm) NPs. Overall, our results suggest that despite certain limitation, the above protocol can be readily employed to guide the model construction for MD simulations, which is particularly useful when only limited experimental information on the NP surface composition is available to a modeler.
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Affiliation(s)
- Zhenpeng Ge
- Department of Physics, The Chinese University of Hong Kong , Shatin, N.T., Hong Kong
| | - Yi Wang
- Department of Physics, The Chinese University of Hong Kong , Shatin, N.T., Hong Kong
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18
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Rems L, Tarek M, Casciola M, Miklavčič D. Properties of lipid electropores II: Comparison of continuum-level modeling of pore conductance to molecular dynamics simulations. Bioelectrochemistry 2016; 112:112-24. [DOI: 10.1016/j.bioelechem.2016.03.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/24/2016] [Accepted: 03/27/2016] [Indexed: 12/18/2022]
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19
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do Canto AMTM, Robalo JR, Santos PD, Carvalho AJP, Ramalho JPP, Loura LMS. Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2647-2661. [PMID: 27475296 DOI: 10.1016/j.bbamem.2016.07.013] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 07/05/2016] [Accepted: 07/25/2016] [Indexed: 10/21/2022]
Abstract
Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3-4Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters.
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Affiliation(s)
- António M T M do Canto
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - João R Robalo
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal; Theory and Bio-Systems Department, Max Planck Institute of Colloids and Interfaces, Wissenschaftspark Golm, D-14424 Potsdam, Germany
| | - Patrícia D Santos
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - Alfredo J Palace Carvalho
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - J P Prates Ramalho
- Centro de Química de Évora e Departamento de Química, Escola de Ciências e Tecnologia, Colégio Luís Verney, Rua Romão Ramalho 59, P-7002-554 Évora, Portugal
| | - Luís M S Loura
- Faculdade de Farmácia, Universidade de Coimbra, Pólo das Ciências da Saúde, Azinhaga de Santa Comba, P-3000-548 Coimbra, Portugal; Centro de Química de Coimbra, Largo D. Dinis, Rua Larga, P-3004-535 Coimbra, Portugal.
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20
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Casper CB, Verreault D, Adams EM, Hua W, Allen HC. Surface Potential of DPPC Monolayers on Concentrated Aqueous Salt Solutions. J Phys Chem B 2016; 120:2043-52. [PMID: 26761608 DOI: 10.1021/acs.jpcb.5b10483] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Clayton B. Casper
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dominique Verreault
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Ellen M. Adams
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Wei Hua
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Heather C. Allen
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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21
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Pasenkiewicz-Gierula M, Baczynski K, Markiewicz M, Murzyn K. Computer modelling studies of the bilayer/water interface. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2305-2321. [PMID: 26825705 DOI: 10.1016/j.bbamem.2016.01.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/18/2016] [Accepted: 01/21/2016] [Indexed: 01/24/2023]
Abstract
This review summarises high resolution studies on the interface of lamellar lipid bilayers composed of the most typical lipid molecules which constitute the lipid matrix of biomembranes. The presented results were obtained predominantly by computer modelling methods. Whenever possible, the results were compared with experimental results obtained for similar systems. The first and main section of the review is concerned with the bilayer-water interface and is divided into four subsections. The first describes the simplest case, where the interface consists only of lipid head groups and water molecules and focuses on interactions between the lipid heads and water molecules; the second describes the interface containing also mono- and divalent ions and concentrates on lipid-ion interactions; the third describes direct inter-lipid interactions. These three subsections are followed by a discussion on the network of direct and indirect inter-lipid interactions at the bilayer interface. The second section summarises recent computer simulation studies on the interactions of antibacterial membrane active compounds with various models of the bacterial outer membrane. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg.
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Affiliation(s)
- Marta Pasenkiewicz-Gierula
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.
| | - Krzysztof Baczynski
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Michal Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Krzysztof Murzyn
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
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22
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Maity P, Saha B, Kumar GS, Karmakar S. Effect of counterions on the binding affinity of Na+ ions with phospholipid membranes. RSC Adv 2016. [DOI: 10.1039/c6ra17056k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
We have systematically investigated the effect of counterions on the interaction of the Na+ ion with phospholipid membranes using dynamic light scattering, zeta potential, isothermal titration calorimetry and fluorescence spectroscopy techniques.
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Affiliation(s)
- Pabitra Maity
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
| | - Baishakhi Saha
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Sanat Karmakar
- Department of Physics
- Jadavpur University
- Kolkata 700032
- India
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23
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Catte A, Girych M, Javanainen M, Loison C, Melcr J, Miettinen MS, Monticelli L, Määttä J, Oganesyan VS, Ollila OHS, Tynkkynen J, Vilov S. Molecular electrometer and binding of cations to phospholipid bilayers. Phys Chem Chem Phys 2016; 18:32560-32569. [DOI: 10.1039/c6cp04883h] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The molecular electrometer – reorientation of lipid head due to bound charge – allows direct quantitative vetting of simulations against noninvasive NMR experiments; most simulation models overestimated lipid–cation affinities.
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24
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Dzikovski B, Livshits V, Freed J. Interaction of Spin-Labeled Lipid Membranes with Transition Metal Ions. J Phys Chem B 2015; 119:13330-46. [PMID: 26490692 PMCID: PMC4762260 DOI: 10.1021/acs.jpcb.5b08165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The large values of spin relaxation
enhancement (RE) for PC spin-labels
in the phospholipid membrane induced by paramagnetic metal salts dissolved
in the aqueous phase can be explained by Heisenberg spin exchange
due to conformational fluctuations of the nitroxide group as a result
of membrane fluidity, flexibility of lipid chains, and, possibly,
amphiphilic nature of the nitroxide label. Whether the magnetic interaction
occurs predominantly via Heisenberg spin exchange (Ni) or by the dipole–dipole
(Gd) mechanism, it is essential for the paramagnetic ion to get into
close proximity to the nitroxide moiety for efficient RE. For different
salts of Ni the RE in phosphatidylcholine membranes follows the anionic
Hofmeister series and reflects anion adsorption followed by anion-driven
attraction of paramagnetic cations on the choline groups. This adsorption
is higher for chaotropic ions, e.g., perchlorate. (A chaotropic agent
is a molecule in water solution that can disrupt the hydrogen bonding
network between water molecules.) However, there is no anionic dependence
of RE for model membranes made from negatively charged lipids devoid
of choline groups. We used Ni-induced RE to study the thermodynamics
and electrostatics of ion/membrane interactions. We also studied the
effect of membrane composition and the phase state on the RE values.
In membranes with cholesterol a significant difference is observed
between PC labels with nitroxide tethers long enough vs not long enough
to reach deep into the membrane hydrophobic core behind the area of
fused cholesterol rings. This study indicates one must be cautious
in interpreting data obtained by PC labels in fluid membranes in terms
of probing membrane properties at different immersion depths when
it can be affected by paramagnetic species at the membrane surface.
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Affiliation(s)
- Boris Dzikovski
- National Biomedical Center for Advanced ESR Technology (ACERT), Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University , Ithaca, New York 14853, United States.,Centre of Photochemistry, Russian Academy of Sciences , ul. Novatorov 7a, 117427 Moscow, Russia
| | - Vsevolod Livshits
- Centre of Photochemistry, Russian Academy of Sciences , ul. Novatorov 7a, 117427 Moscow, Russia
| | - Jack Freed
- National Biomedical Center for Advanced ESR Technology (ACERT), Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University , Ithaca, New York 14853, United States
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25
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Cardenas AE, Shrestha R, Webb LJ, Elber R. Membrane permeation of a peptide: it is better to be positive. J Phys Chem B 2015; 119:6412-20. [PMID: 25941740 DOI: 10.1021/acs.jpcb.5b02122] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A joint experimental and computational study investigates the translocation of a tryptophan molecule through a phospholipid membrane. Time dependent spectroscopy of the tryptophan side chain determines the rate of permeation into 150 nm phospholipid vesicles. Atomically detailed simulations are conducted to calculate the free energy profiles and the permeation coefficient. Different charging conditions of the peptide (positive, negative, or zwitterion) are considered. Both experiment and simulation reproduce the qualitative trend and suggest that the fastest permeation is when the tryptophan is positively charged. The permeation mechanism, which is revealed by molecular dynamics simulations, is of a translocation assisted by a local defect. The influence of long-range electrostatic interactions, such as the membrane dipole potential on the permeation process, is not significant.
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Affiliation(s)
- Alfredo E Cardenas
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Rebika Shrestha
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Lauren J Webb
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Ron Elber
- †Institute for Computational Engineering and Sciences and ‡Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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26
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Vila-Viçosa D, Teixeira VH, Santos HAF, Baptista AM, Machuqueiro M. Treatment of Ionic Strength in Biomolecular Simulations of Charged Lipid Bilayers. J Chem Theory Comput 2014; 10:5483-92. [DOI: 10.1021/ct500680q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Diogo Vila-Viçosa
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Vitor H. Teixeira
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Hugo A. F. Santos
- Faculty
of Sciences, BioFIG−Centre for Biodiversity, Functional and
Integrative Genomics, University of Lisboa, 1649-004 Lisboa, Portugal
| | - António M. Baptista
- Instituto
de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | - Miguel Machuqueiro
- Centro
de Química e Bioquímica and Departamento de Química
e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
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27
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Polak A, Tarek M, Tomšič M, Valant J, Ulrih NP, Jamnik A, Kramar P, Miklavčič D. Structural properties of archaeal lipid bilayers: small-angle X-ray scattering and molecular dynamics simulation study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8308-8315. [PMID: 25000416 DOI: 10.1021/la5014208] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Aeropyrum pernix is an aerobic hyperthermophilic archaeon that grows in harsh environmental conditions and as such possesses unique structural and metabolic features. Its membrane interfaces with the extreme environment and is the first line of defense from external factors. Therefore, lipids composing this membrane have special moieties that increase its stability. The membrane of A. pernix is composed predominantly of two polar lipids 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-1'(2'-O-α-D-glucosyl)-myo-inositol (AGI) and 2,3-di-O-sesterterpanyl-sn-glicerol-1-phospho-myo-inositol (AI). Both have methyl branches in their lipid tails and ether linkages and carbohydrates in their headgroup. These moieties significantly affect the structure and dynamics of the bilayer. To provide a molecular level insight into these characteristics, we used here Molecular Dynamics (MD) simulations of lipid bilayers of composition similar to those of the archaeal membranes. First, we show that the electron density profiles along the normal to the bilayers derived from the simulations are in good agreement with the profiles obtained by the small-angle X-ray scattering (SAXS) technique, which provides confidence in the force fields used. Analyses of the simulation data show that the archaeal lipid bilayers are less hydrated than conventional phosphatidylcholine (PC) lipids and that their structure is not affected by the salt present in the surrounding solution. Furthermore, the lateral pressure in their hydrophobic core, due to the presence of the branched tails, is much higher than that at PC-based lipid bilayers. Both the methyl branched tails and the special headgroup moieties contribute to slow drastically the lateral diffusion of the lipids. Furthermore, we found that the lipid head groups associate via hydrogen bonding, which affects their reorientational dynamics. All together, our data provide links between the microscopic properties of these membranes and their overall stability in harsh environments.
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Affiliation(s)
- Andraž Polak
- Faculty of Electrical Engineering, University of Ljubljana , Tržaška cesta 25, SI-1000 Ljubljana, Slovenia
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28
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Manzini MC, Perez KR, Riske KA, Bozelli JC, Santos TL, da Silva MA, Saraiva GK, Politi MJ, Valente AP, Almeida FC, Chaimovich H, Rodrigues MA, Bemquerer MP, Schreier S, Cuccovia IM. Peptide:lipid ratio and membrane surface charge determine the mechanism of action of the antimicrobial peptide BP100. Conformational and functional studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:1985-99. [DOI: 10.1016/j.bbamem.2014.04.004] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 03/21/2014] [Accepted: 04/05/2014] [Indexed: 02/06/2023]
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29
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Latorraca NR, Callenberg KM, Boyle JP, Grabe M. Continuum approaches to understanding ion and peptide interactions with the membrane. J Membr Biol 2014; 247:395-408. [PMID: 24652510 PMCID: PMC4096575 DOI: 10.1007/s00232-014-9646-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2013] [Accepted: 02/22/2014] [Indexed: 12/22/2022]
Abstract
Experimental and computational studies have shown that cellular membranes deform to stabilize the inclusion of transmembrane (TM) proteins harboring charge. Recent analysis suggests that membrane bending helps to expose charged and polar residues to the aqueous environment and polar head groups. We previously used elasticity theory to identify membrane distortions that minimize the insertion of charged TM peptides into the membrane. Here, we extend our work by showing that it also provides a novel, computationally efficient method for exploring the energetics of ion and small peptide penetration into membranes. First, we show that the continuum method accurately reproduces energy profiles and membrane shapes generated from molecular simulations of bare ion permeation at a fraction of the computational cost. Next, we demonstrate that the dependence of the ion insertion energy on the membrane thickness arises primarily from the elastic properties of the membrane. Moreover, the continuum model readily provides a free energy decomposition into components not easily determined from molecular dynamics. Finally, we show that the energetics of membrane deformation strongly depend on membrane patch size both for ions and peptides. This dependence is particularly strong for peptides based on simulations of a known amphipathic, membrane binding peptide from the human pathogen Toxoplasma gondii. In total, we address shortcomings and advantages that arise from using a variety of computational methods in distinct biological contexts.
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Affiliation(s)
- Naomi R Latorraca
- Department of Biological Sciences, University of Pittsburgh, 4249 Fifth Avenue, Pittsburgh, PA, 15260, USA
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30
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Electrophoretic mobility of weakly-charged (dipolar) hydrogels in water: Contribution of hydrogen-bonding in the solvent dipole layer. J Colloid Interface Sci 2014; 416:294-305. [DOI: 10.1016/j.jcis.2013.10.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/30/2013] [Accepted: 10/31/2013] [Indexed: 11/21/2022]
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Huynh L, Perrot N, Beswick V, Rosilio V, Curmi PA, Sanson A, Jamin N. Structural properties of POPC monolayers under lateral compression: computer simulations analysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:564-573. [PMID: 24397263 DOI: 10.1021/la4043809] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
1-Palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), a lipid comprising a saturated and an unsaturated acyl chain, belongs to the class of glycerophosphatidylcholines, major lipids in eukaryotic cell membranes. To get insight into the structural properties of this lipid within monolayers as membrane models, we performed molecular dynamics (MD) simulations of POPC monolayers under compression at the air/water interface. MD simulations were carried out at 300 K and at different surface pressures using the all-atom general Amber force field (GAFF). A good agreement was found between the simulated data and experimental isotherms. At surface pressures greater than 15 mN/m, two orientations of the head groups clearly appear: one nearly parallel to the monolayer interface and another one pointing toward the water. On the basis of the analysis of headgroup dihedral angles, we propose that the conformational variations around the bonds connecting the phosphorus atom to the adjacent oxygens are involved in these two orientations of the headgroup. The glycerol group orientation is characterized by a large distribution centered around 50° with respect to the monolayer normal. The acyl chains are predominantly in trans configuration from 7.5 to 43 mN/m surface pressures. Moreover, the calculated order parameter profiles of both chains suggest an independent behavior of the saturated and unsaturated chains that could be correlated with the formation of chain-type clusters observed along the simulated trajectories.
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Affiliation(s)
- Lucie Huynh
- INSERM, U829, Laboratoire Structure - Activité des Biomolécules Normales et Pathologiques, Université d'Evry-Val-d'Essonne , F-91025 Evry, France
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A tale of two ions and their membrane interactions: clearly the same or clearly different? Biophys J 2013; 104:746-7. [PMID: 23442952 DOI: 10.1016/j.bpj.2013.01.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/10/2013] [Indexed: 11/24/2022] Open
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Knecht V, Klasczyk B, Dimova R. Macro- versus microscopic view on the electrokinetics of a water-membrane interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:7939-7948. [PMID: 23697333 DOI: 10.1021/la400342m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Electrophoresis is an experimental method widely used to study electrostatic properties of interfaces. Here, we question the validity of the macroscopic theory for the planar geometry by Helmholtz and Smoluchowski by considering a POPC bilayer in an aqueous solution with 500 mM NaCl, using molecular dynamics simulations. We find that POPC shows positive electrophoretic mobility due to adsorption of sodium ions at the lipid headgroups. The theory assumes that the region in which the water density undergoes a transition from the bulk value to zero (interfacial width) is small compared to the Debye screening length. This separation of length scale is not fullfilled in the present case. Hence, contrasting the theory, we observe that the surface is not sharply defined, continuum hydrodynamics is not applicable, the effective viscosity in the double layer is increased compared to the bulk, and the zeta potential is dominated by the dipole potential. Our results might have widespread implications for interpretation of electrokinetic studies in general.
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Affiliation(s)
- Volker Knecht
- Theory & Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, D-14424 Potsdam, Germany.
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