1
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Carter BM, Day GJ, Zhang WH, Sessions RB, Jackson CJ, Perriman AW. Partitioning of an Enzyme-Polymer Surfactant Nanocomplex into Lipid-Rich Cellular Compartments Drives In Situ Hydrolysis of Organophosphates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401982. [PMID: 38992997 DOI: 10.1002/smll.202401982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/30/2024] [Indexed: 07/13/2024]
Abstract
Most organophosphates (OPs) are hydrophobic, and after exposure, can sequester into lipophilic regions within the body, such as adipose tissue, resulting in long term chronic effects. Consequently, there is an urgent need for therapeutic agents that can decontaminate OPs in these hydrophobic regions. Accordingly, an enzyme-polymer surfactant nanocomplex is designed and tested comprising chemically supercharged phosphotriesterase (Agrobacterium radiobacter; arPTE) electrostatically conjugated to amphiphilic polymer surfactant chains ([cat.arPTE][S-]). Experimentally-derived structural data are combined with molecular dynamics (MD) simulations to provide atomic level detail on conformational ensembles of the nanocomplex using dielectric constants relevant to aqueous and lipidic microenvironments. These show the formation of a compact admicelle pseudophase surfactant corona under aqueous conditions, which reconfigures to yield an extended conformation at a low dielectric constant, providing insight into the mechanism underpinning cell membrane binding. Significantly, it demonstrated that [cat.arPTE][S-] spontaneously binds to human mesenchymal stem cell membranes (hMSCs), resulting in on-cell OP hydrolysis. Moreover, the nanoconstruct can endocytose and partition into the intracellular fatty vacuoles of adipocytes and hydrolyze sequestered OP.
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Affiliation(s)
- Benjamin M Carter
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - Graham J Day
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | - William H Zhang
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
| | | | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Australian National University, Canberra, ACT, 2601, Australia
| | - Adam W Perriman
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, BS8 1TD, UK
- Research School of Chemistry, Australian National University, Canberra, ACT, 2601, Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia
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2
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Johnson TG, Sadeghi-Kelishadi A, Langton MJ. Length dependent reversible off-on activation of photo-switchable relay anion transporters. Chem Commun (Camb) 2024; 60:7160-7163. [PMID: 38910566 DOI: 10.1039/d4cc02603a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
A homologous series of azobenzene-derived photo-switchable ion relay transporters is reported. We reveal that both the length and geometry of the relay strongly affect transport rate, allowing the relative activity of the E and Z isomers to be reversed and hence the wavelengths of light used for on and off switching to be exchanged.
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Affiliation(s)
- Toby G Johnson
- Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK.
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3
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Livernois W, Cao PS, Saha S, Ding Q, Gopinath A, Anantram MP. Ion detection in a DNA nanopore FET device. NANOTECHNOLOGY 2024; 35:325202. [PMID: 38692268 DOI: 10.1088/1361-6528/ad460b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/01/2024] [Indexed: 05/03/2024]
Abstract
An ion detection device that combines a DNA-origami nanopore and a field-effect transistor (FET) was designed and modeled to determine sensitivity of the nanodevice to the local cellular environment. Such devices could be integrated into a live cell, creating an abiotic-biotic interface integrated with semiconductor electronics. A continuum model is used to describe the behavior of ions in an electrolyte solution. The drift-diffusion equations are employed to model the ion distribution, taking into account the electric fields and concentration gradients. This was matched to the results from electric double layer theory to verify applicability of the model to a bio-sensing environment. The FET device combined with the nanopore is shown to have high sensitivity to ion concentration and nanopore geometry, with the electrical double layer behavior governing the device characteristics. A logarithmic relationship was found between ion concentration and a single FET current, generating up to 200 nA of current difference with a small applied bias.
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Affiliation(s)
- William Livernois
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, United States of America
| | - Purunc Simon Cao
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, United States of America
| | - Soumyadeep Saha
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON, CA, Canada
| | - Quanchen Ding
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, United States of America
- Department of Electrical and Computer Engineering, Carnegie Mellon University, Pittsburgh, PA, United States of America
| | - Ashwin Gopinath
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States of America
| | - M P Anantram
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, United States of America
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4
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Huang HC, Lin CJ, Sheng YJ, Tsao HK. Instability of membranes containing ionizable cationic lipids: Effects of the repulsive range of headgroups and tail structures. Colloids Surf B Biointerfaces 2024; 236:113807. [PMID: 38417348 DOI: 10.1016/j.colsurfb.2024.113807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/13/2024] [Accepted: 02/18/2024] [Indexed: 03/01/2024]
Abstract
The stability of membranes formed by ionizable cationic lipids, which constitute the primary components in lipid nanoparticles capable of endosomal escape, is explored using coarse-grained dissipative particle dynamics. Three types of ionizable model lipids with different tail structures are considered. Endosome acidification causes the ionization of lipids, leading to an increased repulsive range between their headgroups. When electrostatic repulsion is modeled as a conservative force with a long-range cutoff distance (rc,HH), the membrane and vesicle experience a loss of structural integrity and develop holes as rc,HH is beyond a critical value, which varies with the tail structure. When Coulombic repulsion is explicitly incorporated and intensified, a fully ionized lipid membrane undergoes a loss of structural integrity, displaying a qualitative similarity to the effect observed with the increase in rc,HH on the membrane stability. Qualitatively similar results are obtained for partially ionized membranes as the fraction of charged lipids increases. The stability of a mixed lipid membrane containing both ionizable and conventional lipids is also investigated. The disruption of the bilayer structure occurs for a sufficiently high charged fraction. The membrane instability can be attributed to the decrease in the packing parameter, which significantly deviates from unity as the interaction range increases.
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Affiliation(s)
- Hao-Chun Huang
- Department of Chemical and Materials Engineering, National Central University, Jhongli 320, Taiwan
| | - Chih-Jung Lin
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan
| | - Yu-Jane Sheng
- Department of Chemical Engineering, National Taiwan University, Taipei 106, Taiwan.
| | - Heng-Kwong Tsao
- Department of Chemical and Materials Engineering, National Central University, Jhongli 320, Taiwan.
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5
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Apprato G, Poongavanam V, Garcia Jimenez D, Atilaw Y, Erdelyi M, Ermondi G, Caron G, Kihlberg J. Exploring the chemical space of orally bioavailable PROTACs. Drug Discov Today 2024; 29:103917. [PMID: 38360147 DOI: 10.1016/j.drudis.2024.103917] [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: 10/08/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
A principal challenge in the discovery of proteolysis targeting chimeras (PROTACs) as oral medications is their bioavailability. To facilitate drug design, it is therefore essential to identify the chemical space where orally bioavailable PROTACs are more likely to be situated. To this aim, we extracted structure-bioavailability insights from published data using traditional 2D descriptors, thereby shedding light on their potential and limitations as drug design tools. Subsequently, we describe cutting-edge experimental, computational and hybrid design strategies based on 3D descriptors, which show promise for enhancing the probability of discovering PROTACs with high oral bioavailability.
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Affiliation(s)
- Giulia Apprato
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | | | - Diego Garcia Jimenez
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy.
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden.
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6
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Polita A, Žvirblis R, Dodonova-Vaitkūnienė J, Shivabalan AP, Maleckaitė K, Valinčius G. Bimodal effects on lipid droplets induced in cancer and non-cancer cells by chemotherapy drugs as revealed with a green-emitting BODIPY fluorescent probe. J Mater Chem B 2024; 12:3022-3030. [PMID: 38426244 DOI: 10.1039/d3tb02979d] [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: 03/02/2024]
Abstract
Lipid droplets (LDs) are cytoplasmic lipid-rich organelles with important roles in lipid storage and metabolism, cell signaling and membrane biosynthesis. Additionally, multiple diseases, such as obesity, fatty liver, cardiovascular diseases and cancer, are related to the metabolic disorders of LDs. In various cancer cells, LD accumulation is associated with resistance to cell death, reduced effectiveness of chemotherapeutic drugs, and increased proliferation and aggressiveness. In this work, we present a new viscosity-sensitive, green-emitting BODIPY probe capable of distinguishing between ordered and disordered lipid phases and selectively internalising into LDs of live cells. Through the use of fluorescence lifetime imaging microscopy (FLIM), we demonstrate that LDs in live cancer (A549) and non-cancer (HEK 293T) cells have vastly different microviscosities. Additionally, we quantify the microviscosity changes in LDs under the influence of DNA-damaging chemotherapy drugs doxorubicin and etoposide. Finally, we show that doxorubicin and etoposide have different effects on the microviscosities of LDs in chemotherapy-resistant A549 cancer cells.
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Affiliation(s)
- Artūras Polita
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius, LT-10257, Lithuania.
| | - Rokas Žvirblis
- Life Sciences Center, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, Vilnius, LT-10257, Lithuania
| | - Jelena Dodonova-Vaitkūnienė
- Institute of Chemistry, Faculty of Chemistry and Geosciences, Vilnius University, Naugarduko st. 24, Vilnius, LT-03225, Lithuania
| | - Arun Prabha Shivabalan
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius, LT-10257, Lithuania.
| | - Karolina Maleckaitė
- Center of Physical Sciences and Technology, Saulėtekio av. 3, Vilnius, LT-10257, Lithuania
| | - Gintaras Valinčius
- Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio av. 7, Vilnius, LT-10257, Lithuania.
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7
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Poongavanam V, Wieske LHE, Peintner S, Erdélyi M, Kihlberg J. Molecular chameleons in drug discovery. Nat Rev Chem 2024; 8:45-60. [PMID: 38123688 DOI: 10.1038/s41570-023-00563-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Molecular chameleons possess a flexibility that allows them to dynamically shield or expose polar functionalities in response to the properties of the environment. Although the concept of molecular chameleons was introduced already in 1970, interest in them has grown considerably since the 2010s, when drug discovery has focused to an increased extent on new chemical modalities. Such modalities include cyclic peptides, macrocycles and proteolysis-targeting chimeras, all of which reside in a chemical space far from that of traditional small-molecule drugs. Both cell permeability and aqueous solubility are required for the oral absorption of drugs. Engineering these properties, and potent target binding, into the larger new modalities is a more daunting task than for traditional small-molecule drugs. The ability of chameleons to adapt to different environments may be essential for success. In this Review, we provide both general and theoretical insights into the realm of molecular chameleons. We discuss why chameleons have come into fashion and provide a do-it-yourself toolbox for their design; we then provide a glimpse of how advanced in silico methods can support molecular chameleon design.
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Affiliation(s)
| | | | - Stefan Peintner
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden.
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8
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Samanta R, Gray JJ. Implicit model to capture electrostatic features of membrane environment. PLoS Comput Biol 2024; 20:e1011296. [PMID: 38252688 PMCID: PMC10833867 DOI: 10.1371/journal.pcbi.1011296] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 02/01/2024] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Membrane protein structure prediction and design are challenging due to the complexity of capturing the interactions in the lipid layer, such as those arising from electrostatics. Accurately capturing electrostatic energies in the low-dielectric membrane often requires expensive Poisson-Boltzmann calculations that are not scalable for membrane protein structure prediction and design. In this work, we have developed a fast-to-compute implicit energy function that considers the realistic characteristics of different lipid bilayers, making design calculations tractable. This method captures the impact of the lipid head group using a mean-field-based approach and uses a depth-dependent dielectric constant to characterize the membrane environment. This energy function Franklin2023 (F23) is built upon Franklin2019 (F19), which is based on experimentally derived hydrophobicity scales in the membrane bilayer. We evaluated the performance of F23 on five different tests probing (1) protein orientation in the bilayer, (2) stability, and (3) sequence recovery. Relative to F19, F23 has improved the calculation of the tilt angle of membrane proteins for 90% of WALP peptides, 15% of TM-peptides, and 25% of the adsorbed peptides. The performances for stability and design tests were equivalent for F19 and F23. The speed and calibration of the implicit model will help F23 access biophysical phenomena at long time and length scales and accelerate the membrane protein design pipeline.
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Affiliation(s)
- Rituparna Samanta
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland, United States of America
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
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9
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Takechi-Haraya Y, Ohgita T, Usui A, Nishitsuji K, Uchimura K, Abe Y, Kawano R, Konaklieva MI, Reimund M, Remaley AT, Sato Y, Izutsu KI, Saito H. Structural flexibility of apolipoprotein E-derived arginine-rich peptides improves their cell penetration capability. Sci Rep 2023; 13:19396. [PMID: 37938626 PMCID: PMC10632520 DOI: 10.1038/s41598-023-46754-0] [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: 08/17/2023] [Accepted: 11/04/2023] [Indexed: 11/09/2023] Open
Abstract
Amphipathic arginine-rich peptide, A2-17, exhibits moderate perturbation of lipid membranes and the highest cell penetration among its structural isomers. We investigated the direct cell-membrane penetration mechanism of the A2-17 peptide while focusing on structural flexibility. We designed conformationally constrained versions of A2-17, stapled (StpA2-17) and stitched (StchA2-17), whose α-helical conformations were stabilized by chemical crosslinking. Circular dichroism confirmed that StpA2-17 and StchA2-17 had higher α-helix content than A2-17 in aqueous solution. Upon liposome binding, only A2-17 exhibited a coil-to-helix transition. Confocal microscopy revealed that A2-17 had higher cell penetration efficiency than StpA2-17, whereas StchA2-17 remained on the cell membrane without cell penetration. Although the tryptophan fluorescence analysis suggested that A2-17 and its analogs had similar membrane-insertion positions between the interface and hydrophobic core, StchA2-17 exhibited a higher membrane affinity than A2-17 or StpA2-17. Atomic force microscopy demonstrated that A2-17 reduced the mechanical rigidity of liposomes to a greater extent than StpA2-17 and StchA2-17. Finally, electrophysiological analysis showed that A2-17 induced a higher charge influx through transient pores in a planer lipid bilayer than StpA2-17 and StchA2-17. These findings indicate that structural flexibility, which enables diverse conformations of A2-17, leads to a membrane perturbation mode that contributes to cell membrane penetration.
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Affiliation(s)
- Yuki Takechi-Haraya
- Division of Drugs, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, 210-9501, Japan.
| | - Takashi Ohgita
- Center for Instrumental Analysis, Kyoto Pharmaceutical University, 1 Misasagi-Shichono-cho, Yamashina-ku, Kyoto, 607-8412, Japan
| | - Akiko Usui
- Division of Drugs, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, 210-9501, Japan
| | - Kazuchika Nishitsuji
- Department of Biochemistry, Wakayama Medical University, 811-1 Kimiidera, Wakayama, 641-8509, Japan
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, Université de Lille, 59655, Villeneuve d'Ascq, France
| | - Kenji Uchimura
- Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576 CNRS, Université de Lille, 59655, Villeneuve d'Ascq, France
| | - Yasuhiro Abe
- Division of Drugs, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, 210-9501, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Monika I Konaklieva
- Department of Chemistry, American University, 4400 Massachusetts Avenue NW, Washington, DC, 20016-8014, USA
| | - Mart Reimund
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Alan T Remaley
- Lipoprotein Metabolism Laboratory, Translational Vascular Medicine Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yoji Sato
- Division of Drugs, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki, 210-9501, Japan
| | - Ken-Ichi Izutsu
- School of Pharmacy Department of Pharmaceutical Sciences, International University of Health and Welfare, 2600-1 Kitakanemaru, Otawara, Tochigi, 324-8501, Japan
| | - Hiroyuki Saito
- Department of Biophysical Chemistry, Kyoto Pharmaceutical University, 5 Misasagi-Nakauchi-cho, Yamashina-ku, Kyoto, 607-8414, Japan
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10
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Trewby W, Voïtchovsky K. Nanoscale probing of local dielectric changes at the interface between solids and aqueous saline solutions. Faraday Discuss 2023; 246:387-406. [PMID: 37449374 DOI: 10.1039/d3fd00021d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The mobility of dissolved ions and charged molecules at interfaces underpins countless processes in science and technology. Experimentally, this is typically measured from the averaged response of the charges to an electrical potential. High-resolution Atomic Force Microscopy (AFM) can image single adsorbed ions and molecules at solid-liquid interfaces, but probing the associated dynamics remains highly challenging. One possible strategy is to investigate the response of the species of interest to a highly localized AC electric field in an approach analogous to dielectric spectroscopy. The dielectric force experienced by the AFM tip apex is modulated by the dielectric properties of the sample probed, itself sensitive to the mobilities of solvated charges and dipoles. Previous work successfully used this approach to quantify the dielectric constant of thin samples, but with limited spatial resolution. Here we propose a strategy to simultaneously map the nanoscale topography and local dielectric variations across a range of interfaces by conducting high-resolution AFM imaging concomitantly with electrical AC measurements in a multifrequency approach. The strategy is tested over a 500 MHz bandwidth in pure liquids with different dielectric constants and in saline aqueous solutions. In liquids with higher dielectric constants, the system behaves as inductive-resistive-capacitive but the adjunction of ions removes the inductive resonances and precludes measurements at higher frequencies. High-resolution imaging is demonstrated over single graphene oxide (GrO) flakes with simultaneous but decoupled dielectric measurements. The dielectric constant is consistent and reproducible across liquids, except at higher salt concentrations where frequency-dependent effects occur. The results suggest the strategy is suitable for nanometre-level mapping of the dielectric properties of solid-liquid interfaces, but more work is needed to fully understand the different physical effects underpinning the measurements.
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Affiliation(s)
- William Trewby
- Physics Department, Durham University, Durham DH1 3LE, UK.
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11
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Vargas-Rosales P, D’Addio A, Zhang Y, Caflisch A. Disrupting Dimeric β-Amyloid by Electric Fields. ACS PHYSICAL CHEMISTRY AU 2023; 3:456-466. [PMID: 37780539 PMCID: PMC10540290 DOI: 10.1021/acsphyschemau.3c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/26/2023] [Accepted: 06/26/2023] [Indexed: 10/03/2023]
Abstract
The early oligomers of the amyloid Aβ peptide are implicated in Alzheimer's disease, but their transient nature complicates the characterization of their structure and toxicity. Here, we investigate the stability of the minimal toxic species, i.e., β-amyloid dimers, in the presence of an oscillating electric field. We first use deep learning (AlphaFold-multimer) for generating initial models of Aβ42 dimers. The flexibility and secondary structure content of the models are then analyzed by multiple runs of molecular dynamics (MD). Structurally stable models are similar to ensemble representatives from microsecond-long MD sampling. Finally, we employ the validated model as the starting structure of MD simulations in the presence of an external oscillating electric field and observe a fast decay of β-sheet content at high field strengths. Control simulations using the helical dimer of the 42-residue leucine zipper peptide show higher structural stability than the Aβ42 dimer. The simulation results provide evidence that an external electric field (oscillating at 1 GHz) can disrupt amyloid oligomers which should be further investigated by experiments with brain organoids in vitro and eventually in vivo.
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Affiliation(s)
| | - Alessio D’Addio
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Yang Zhang
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zürich, Switzerland
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12
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Samanta R, Gray JJ. Implicit model to capture electrostatic features of membrane environment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546486. [PMID: 37425950 PMCID: PMC10327106 DOI: 10.1101/2023.06.26.546486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Membrane protein structure prediction and design are challenging due to the complexity of capturing the interactions in the lipid layer, such as those arising from electrostatics. Accurately capturing electrostatic energies in the low-dielectric membrane often requires expensive Poisson-Boltzmann calculations that are not scalable for membrane protein structure prediction and design. In this work, we have developed a fast-to-compute implicit energy function that considers the realistic characteristics of different lipid bilayers, making design calculations tractable. This method captures the impact of the lipid head group using a mean-field-based approach and uses a depth-dependent dielectric constant to characterize the membrane environment. This energy function Franklin2023 (F23) is built upon Franklin2019 (F19), which is based on experimentally derived hydrophobicity scales in the membrane bilayer. We evaluated the performance of F23 on five different tests probing (1) protein orientation in the bilayer, (2) stability, and (3) sequence recovery. Relative to F19, F23 has improved the calculation of the tilt angle of membrane proteins for 90% of WALP peptides, 15% of TM-peptides, and 25% of the adsorbed peptides. The performances for stability and design tests were equivalent for F19 and F23. The speed and calibration of the implicit model will help F23 access biophysical phenomena at long time and length scales and accelerate the membrane protein design pipeline.
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Affiliation(s)
- Rituparna Samanta
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, Maryland, United States
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13
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Johnson TG, Docker A, Sadeghi-Kelishadi A, Langton MJ. Halogen bonding relay and mobile anion transporters with kinetically controlled chloride selectivity. Chem Sci 2023; 14:5006-5013. [PMID: 37206385 PMCID: PMC10189858 DOI: 10.1039/d3sc01170d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/03/2023] [Indexed: 05/21/2023] Open
Abstract
Selective transmembrane transport of chloride over competing proton or hydroxide transport is key for the therapeutic application of anionophores, but remains a significant challenge. Current approaches rely on enhancing chloride anion encapsulation within synthetic anionophores. Here we report the first example of a halogen bonding ion relay in which transport is facilitated by the exchange of ions between lipid-anchored receptors on opposite sides of the membrane. The system exhibits non-protonophoric chloride selectivity, uniquely arising from the lower kinetic barrier to chloride exchange between transporters within the membrane, compared to hydroxide, with selectivity maintained across membranes with different hydrophobic thicknesses. In contrast, we demonstrate that for a range of mobile carriers with known high chloride over hydroxide/proton selectivity, the discrimination is strongly dependent on membrane thickness. These results demonstrate that the selectivity of non-protonophoric mobile carriers does not arise from ion binding discrimination at the interface, but rather through a kinetic bias in transport rates, arising from differing membrane translocation rates of the anion-transporter complexes.
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Affiliation(s)
- Toby G Johnson
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Andrew Docker
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Amir Sadeghi-Kelishadi
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
| | - Matthew J Langton
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford 12 Mansfield Road Oxford OX1 3TA UK
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14
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Andersson J, Kleinheinz D, Ramach U, Kiesenhofer N, Ashenden A, Valtiner M, Holt S, Koeper I, Schmidpeter PAM, Knoll W. Native Function of the Bacterial Ion Channel SthK in a Sparsely Tethered Lipid Bilayer Membrane Architecture. J Phys Chem B 2023; 127:3641-3650. [PMID: 37072125 PMCID: PMC10150356 DOI: 10.1021/acs.jpcb.2c07252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
The plasma membrane protects the interiors of cells from their surroundings and also plays a critical role in communication, sensing, and nutrient import. As a result, the cell membrane and its constituents are among the most important drug targets. Studying the cell membrane and the processes it facilitates is therefore crucial, but it is a highly complex environment that is difficult to access experimentally. Various model membrane systems have been developed to provide an environment in which membrane proteins can be studied in isolation. Among them, tethered bilayer lipid membranes (tBLMs) are a promising model system providing a solvent-free membrane environment which can be prepared by self-assembly, is resistant to mechanical disturbances and has a high electrical resistance. tBLMs are therefore uniquely suitable to study ion channels and charge transport processes. However, ion channels are often large, complex, multimeric structures and their function requires a particular lipid environment. In this paper, we show that SthK, a bacterial cyclic nucleotide gated (CNG) ion channel that is strongly dependent on the surrounding lipid composition, functions normally when embedded into a sparsely tethered lipid bilayer. As SthK has been very well characterized in terms of structure and function, it is well-suited to demonstrate the utility of tethered membrane systems. A model membrane system suitable for studying CNG ion channels would be useful, as this type of ion channel performs a wide range of physiological functions in bacteria, plants, and mammals and is therefore of fundamental scientific interest as well as being highly relevant to medicine.
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Affiliation(s)
- Jakob Andersson
- Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - David Kleinheinz
- Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
| | - Ulrich Ramach
- Technische Universität Wien, Wiedner Hauptstr. 8-10/134, 1040 Wien, Austria
- CEST Kompetenzzentrum für Oberflächentechnologie, Viktor Kaplan-Straße 2, 2700 Wiener Neustadt, Austria
| | | | - Alex Ashenden
- Flinders University of South Australia, Bedford Park SA, 5042 Adelaide, Australia
| | - Markus Valtiner
- Technische Universität Wien, Wiedner Hauptstr. 8-10/134, 1040 Wien, Austria
- CEST Kompetenzzentrum für Oberflächentechnologie, Viktor Kaplan-Straße 2, 2700 Wiener Neustadt, Austria
| | - Stephen Holt
- Australian Nuclear Science and Technology Organization, New Illawarra Rd, Lucas Heights, NSW 2234, Australia
| | - Ingo Koeper
- Flinders University of South Australia, Bedford Park SA, 5042 Adelaide, Australia
| | - Philipp A M Schmidpeter
- Weill Cornell Medicine, Department of Anesthesiology, 1300 York Avenue, New York, New York 10065, United States
| | - Wolfgang Knoll
- Austrian Institute of Technology GmbH, Giefinggasse 4, 1210 Vienna, Austria
- Danube Private University, Steiner Landstraße 124, 3500 Krems an der Donau, Austria
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15
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Da A, Chu Y, Krach J, Liu Y, Park Y, Lee SE. Optical Penetration of Shape-Controlled Metallic Nanosensors across Membrane Barriers. SENSORS (BASEL, SWITZERLAND) 2023; 23:2824. [PMID: 36905027 PMCID: PMC10007193 DOI: 10.3390/s23052824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Precise nanostructure geometry that enables the optical biomolecular delivery of nanosensors to the living intracellular environment is highly desirable for precision biological and clinical therapies. However, the optical delivery through membrane barriers utilizing nanosensors remains difficult due to a lack of design guidelines to avoid inherent conflict between optical force and photothermal heat generation in metallic nanosensors during the process. Here, we present a numerical study reporting significantly enhanced optical penetration of nanosensors by engineering nanostructure geometry with minimized photothermal heating generation for penetrating across membrane barriers. We show that by varying the nanosensor geometry, penetration depths can be maximized while heat generated during the penetration process can be minimized. We demonstrate the effect of lateral stress induced by an angularly rotating nanosensor on a membrane barrier by theoretical analysis. Furthermore, we show that by varying the nanosensor geometry, maximized local stress fields at the nanoparticle-membrane interface enhanced the optical penetration process by four-fold. Owing to the high efficiency and stability, we anticipate that precise optical penetration of nanosensors to specific intracellular locations will be beneficial for biological and therapeutic applications.
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Affiliation(s)
- Ancheng Da
- Department of Electrical & Computer Engineering, Biomedical Engineering, Biointerfaces Institute, Applied Physics, Macromolecular Science & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yanan Chu
- Department of Electrical & Computer Engineering, Biomedical Engineering, Biointerfaces Institute, Applied Physics, Macromolecular Science & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jacob Krach
- Department of Electrical & Computer Engineering, Biomedical Engineering, Biointerfaces Institute, Applied Physics, Macromolecular Science & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yunbo Liu
- Department of Electrical & Computer Engineering, Biomedical Engineering, Biointerfaces Institute, Applied Physics, Macromolecular Science & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Younggeun Park
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Somin Eunice Lee
- Department of Electrical & Computer Engineering, Biomedical Engineering, Biointerfaces Institute, Applied Physics, Macromolecular Science & Engineering, University of Michigan, Ann Arbor, MI 48109, USA
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16
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Chen X, Chen W, Zhang X, Cheng D, Ren Y. The study on the dielectric properties of structural changes of surfactant aqueous solution by molecular dynamics simulation. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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17
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Vallaro M, Ermondi G, Saame J, Leito I, Caron G. Ionization and lipophilicity in nonpolar media mimicking the cell membrane interior. Bioorg Med Chem 2023; 81:117203. [PMID: 36796127 DOI: 10.1016/j.bmc.2023.117203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/25/2023] [Accepted: 02/03/2023] [Indexed: 02/09/2023]
Abstract
Ionization and lipophilicity may vary with the environment. Therefore, in this study we provide some insight in the performances of different experimental techniques (potentiometry, UV-vis, shake-flask and chromatography) to determine ionization and lipophilicity in more nonpolar systems than those commonly used in drug discovery. To this purpose a pool of 11 compounds of pharmaceutical interest was firstly submitted to a few experimental techniques to measure pKa in water, water/acetonitrile mixtures and pure acetonitrile. Then we measured logP/logD with shake-flask and potentiometry in octanol/water and toluene/water and also determined a chromatographic lipophilicity index (log k'80 PLRP-S) in a nonpolar system. Results show that ionization decreases for both acids and bases in a coherent, significant but not dramatical extent when water is present in the system, but the picture is completely different in pure acetonitrile. Lipophilicity may vary or not with the environment according to the chemical structure of the investigated compounds as also revealed by electrostatic potential maps. Since the internal core of cell membranes is largely nonpolar, our results support the need of extending the pool of physicochemical descriptors to be determined in the various stages of drug discovery programs and indicate some experimental strategies for their determination.
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Affiliation(s)
- Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy
| | - Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy
| | - Jaan Saame
- University of Tartu, Institute of Chemistry, Ravila 14a, Tartu 50411, Estonia
| | - Ivo Leito
- University of Tartu, Institute of Chemistry, Ravila 14a, Tartu 50411, Estonia
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, 10135 Torino, Italy.
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18
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Vyas V, Kotla NG, Rochev Y, Poudel A, Biggs M. Multifrequency dielectric mapping of fixed mice colon tissues in cell culture media via scanning electrochemical microscopy. Front Bioeng Biotechnol 2023; 11:1063063. [PMID: 36845172 PMCID: PMC9947134 DOI: 10.3389/fbioe.2023.1063063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Alternating current scanning electrochemical microscopy (AC-SECM) is a powerful tool for characterizing the electrochemical reactivity of surfaces. Here, perturbation in the sample is induced by the alternating current and altered local potential is measured by the SECM probe. This technique has been used to investigate many exotic a range of biological interfaces including live cells and tissues, as well as the corrosive degradation of various metallic surfaces, etc. In principle, AC-SECM imaging is derived from electrochemical impedance spectroscopy (EIS) which has been used for a century to describe interfacial and diffusive behaviour of molecules in solution or on a surface. Increasingly bioimpedance centric medical devices have become an important tool to detect evolution of tissue biochemistry. Predictive implications of measuring electrochemical changes within a tissue is one of the core concepts in developing minimally invasive and smart medical devices. In this study, cross sections of mice colon tissue were used for AC-SECM imaging. A 10 micron sized platinum probe was used for two-dimensional (2D) tan δ mapping of histological sections at a frequency of 10 kHz, Thereafter, multifrequency scans were performed at 100 Hz, 10 kHz, 300 kHz, and 900 kHz. Loss tangent (tan δ) mapping of mice colon revealed microscale regions within a tissue possessing a discrete tan δ signature. This tan δ map may be an immediate measure of physiological conditions in biological tissues. Multifrequency scans highlight subtle changes in protein or lipid composition as a function of frequency which was recorded as loss tangent maps. Impedance profile at different frequencies could also be used to identify optimal contrast for imaging and extracting the electrochemical signature specific for a tissue and its electrolyte.
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Affiliation(s)
- Varun Vyas
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland,CNRS, LIEC, Université de Lorraine, Nancy, France,*Correspondence: Varun Vyas, ; Manus Biggs,
| | - Niranjan G. Kotla
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
| | - Yury Rochev
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
| | - Anup Poudel
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland
| | - Manus Biggs
- CÚRAM, SFI Research Centre for Medical Devices, University of Galway, Galway, Ireland,*Correspondence: Varun Vyas, ; Manus Biggs,
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19
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Wieske LHE, Atilaw Y, Poongavanam V, Erdélyi M, Kihlberg J. Going Viral: An Investigation into the Chameleonic Behaviour of Antiviral Compounds. Chemistry 2023; 29:e202202798. [PMID: 36286339 PMCID: PMC10107787 DOI: 10.1002/chem.202202798] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 10/23/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022]
Abstract
The ability to adjust conformations in response to the polarity of the environment, i.e. molecular chameleonicity, is considered to be important for conferring both high aqueous solubility and high cell permeability to drugs in chemical space beyond Lipinski's rule of 5. We determined the conformational ensembles populated by the antiviral drugs asunaprevir, simeprevir, atazanavir and daclatasvir in polar (DMSO-d6 ) and non-polar (chloroform) environments with NMR spectroscopy. Daclatasvir was fairly rigid, whereas the first three showed large flexibility in both environments, that translated into major differences in solvent accessible 3D polar surface area within each conformational ensemble. No significant differences in size and polar surface area were observed between the DMSO-d6 and chloroform ensembles of these three drugs. We propose that such flexible compounds are characterized as "partial molecular chameleons" and hypothesize that their ability to adopt conformations with low polar surface area contributes to their membrane permeability and oral absorption.
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Affiliation(s)
- Lianne H E Wieske
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | | | - Máté Erdélyi
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, SE-751 23, Uppsala, Sweden
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20
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Boahen F, Doyon N, Deteix J. Sensitivity of the electrical response of a node of Ranvier model to alterations of the myelin sheath geometry. J Math Biol 2022; 86:17. [PMID: 36534161 DOI: 10.1007/s00285-022-01841-0] [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: 04/12/2021] [Revised: 08/31/2022] [Accepted: 11/21/2022] [Indexed: 12/23/2022]
Abstract
Nodes of Ranvier play critical roles in the generation and transmission of action potentials. Alterations in node properties during pathology and/or development are known to affect the speed and quality of electrical transmission. From a modelling standpoint, nodes of Ranvier are often described by systems of ordinary differential equations neglecting or greatly simplifying their geometric structure. These approaches fail to accurately describe how fine scale alteration in the node geometry or in myelin thickness in the paranode region will impact action potential generation and transmission. Here, we rely on a finite element approximation to describe the three dimensional geometry of a node of Ranvier. With this, we are able to investigate how sensitive is the electrical response to alterations in the myelin sheath and paranode geometry. We could in particular investigate irregular loss of myelin, which might be more physiologically relevant than the uniform loss often described through simpler modelling approaches.
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Affiliation(s)
- Frank Boahen
- Groupe Interdisciplinaire de Recherche en Éléments Finis (GIREF), Département de mathématiques et statistique, Université Laval Pavillon Vachon, 1045 Avenue de la médecine, Université Laval, Québec, QC, Canada
| | - Nicolas Doyon
- Groupe Interdisciplinaire de Recherche en Éléments Finis (GIREF), Département de mathématiques et statistique, Université Laval Pavillon Vachon, 1045 Avenue de la médecine, Université Laval, Québec, QC, Canada.
| | - Jean Deteix
- Groupe Interdisciplinaire de Recherche en Éléments Finis (GIREF), Département de mathématiques et statistique, Université Laval Pavillon Vachon, 1045 Avenue de la médecine, Université Laval, Québec, QC, Canada
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21
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Vergilio J, Lockhart C, Klimov DK. De Novo Transmembrane Aggregation of Aβ10-40 Peptides in an Anionic Lipid Bilayer. J Chem Inf Model 2022; 62:6228-6241. [PMID: 36455155 DOI: 10.1021/acs.jcim.2c01192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Using the all-atom model and 10 μs serial replica-exchange molecular dynamics (SREMD), we investigated the binding of Alzheimer's Aβ10-40 peptides to the anionic dimyristoylphosphatidylcholine/dimyristoylphosphatidylglycerol (DMPC/DMPG) lipid bilayer. Our objective was to probe de novo transmembrane Aβ10-40 aggregation and to test the utility of SREMD. Our results are threefold. First, upon binding, Aβ10-40 adopts a helical structure in the C-terminus and deeply inserts into the bilayer. Binding is primarily controlled by electrostatic interactions of the peptides with water, ions, and lipids, particularly, anionic DMPG. Second, Aβ-bilayer interactions reorganize lipids in the proximity of the bound peptides, causing an influx of DMPG lipids into the Aβ binding footprint. Third and most important, computed free energy landscapes reveal that Aβ10-40 peptides partition into monomeric and dimeric species. The dimers result from transmembrane aggregation of the peptides and induce a striking lipid density void throughout both leaflets in the bilayer. There are multiple factors stabilizing transmembrane dimers, including van der Waals and steric interactions, electrostatic interactions, and hydrogen bonding, hydration, and entropic gains originating from dimer conformations and lipid disorder. We argue that helix dipole-dipole interactions underestimated in the all-atom force field must be a contributing factor to stabilizing antiparallel transmembrane dimers. We propose that transmembrane aggregates serve as mechanistic links between the populations of extra- and intracellular Aβ peptides. From the computational perspective, SREMD is found to be a viable alternative to traditional replica-exchange simulations.
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Affiliation(s)
- James Vergilio
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Christopher Lockhart
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
| | - Dmitri K Klimov
- School of Systems Biology, George Mason University, Manassas, Virginia 20110, United States
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22
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Saha A, Yi R, Fahrenbach AC, Wang A, Jia TZ. A Physicochemical Consideration of Prebiotic Microenvironments for Self-Assembly and Prebiotic Chemistry. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101595. [PMID: 36295030 PMCID: PMC9604842 DOI: 10.3390/life12101595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
The origin of life on Earth required myriads of chemical and physical processes. These include the formation of the planet and its geological structures, the formation of the first primitive chemicals, reaction, and assembly of these primitive chemicals to form more complex or functional products and assemblies, and finally the formation of the first cells (or protocells) on early Earth, which eventually evolved into modern cells. Each of these processes presumably occurred within specific prebiotic reaction environments, which could have been diverse in physical and chemical properties. While there are resources that describe prebiotically plausible environments or nutrient availability, here, we attempt to aggregate the literature for the various physicochemical properties of different prebiotic reaction microenvironments on early Earth. We introduce a handful of properties that can be quantified through physical or chemical techniques. The values for these physicochemical properties, if they are known, are then presented for each reaction environment, giving the reader a sense of the environmental variability of such properties. Such a resource may be useful for prebiotic chemists to understand the range of conditions in each reaction environment, or to select the medium most applicable for their targeted reaction of interest for exploratory studies.
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Affiliation(s)
- Arpita Saha
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Amity Institute of Applied Sciences, Amity University, Kolkata 700135, India
| | - Ruiqin Yi
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Albert C. Fahrenbach
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Anna Wang
- School of Chemistry, UNSW Sydney, Sydney, NSW 2052, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, NSW 2052, Australia
- UNSW RNA Institute, UNSW Sydney, Sydney, NSW 2052, Australia
- Correspondence: (A.W.); (T.Z.J.)
| | - Tony Z. Jia
- Blue Marble Space Institute of Science, 600 1st Ave, Floor 1, Seattle, WA 98104, USA
- Earth-Life Science Institute, Tokyo Institute of Technology, 2-12-1-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Correspondence: (A.W.); (T.Z.J.)
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23
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Poongavanam V, Atilaw Y, Siegel S, Giese A, Lehmann L, Meibom D, Erdelyi M, Kihlberg J. Linker-Dependent Folding Rationalizes PROTAC Cell Permeability. J Med Chem 2022; 65:13029-13040. [PMID: 36170570 PMCID: PMC9574858 DOI: 10.1021/acs.jmedchem.2c00877] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteolysis-targeting chimeras (PROTACs) must be cell permeable to reach their target proteins. This is challenging as the bivalent structure of PROTACs puts them in chemical space at, or beyond, the outer limits of oral druggable space. We used NMR spectroscopy and molecular dynamics (MD) simulations independently to gain insights into the origin of the differences in cell permeability displayed by three flexible cereblon PROTACs having closely related structures. Both methods revealed that the propensity of the PROTACs to adopt folded conformations with a low solvent-accessible 3D polar surface area in an apolar environment is correlated to high cell permeability. The chemical nature and the flexibility of the linker were essential for the PROTACs to populate folded conformations stabilized by intramolecular hydrogen bonds, π-π interactions, and van der Waals interactions. We conclude that MD simulations may be used for the prospective ranking of cell permeability in the design of cereblon PROTACs.
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Affiliation(s)
| | - Yoseph Atilaw
- Department of Chemistry─BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Stephan Siegel
- Drug Discovery Sciences, Bayer AG, 13342 Berlin, Germany
| | - Anja Giese
- Drug Discovery Sciences, Bayer AG, 13342 Berlin, Germany
| | - Lutz Lehmann
- Drug Discovery Sciences, Bayer AG, 42113 Wuppertal, Germany
| | - Daniel Meibom
- Drug Discovery Sciences, Bayer AG, 42113 Wuppertal, Germany
| | - Mate Erdelyi
- Department of Chemistry─BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry─BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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24
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Johnson TG, Sadeghi-Kelishadi A, Langton MJ. A Photo-responsive Transmembrane Anion Transporter Relay. J Am Chem Soc 2022; 144:10455-10461. [PMID: 35652660 PMCID: PMC9204766 DOI: 10.1021/jacs.2c02612] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Indexed: 01/17/2023]
Abstract
Ion transport across lipid membranes in biology is controlled by stimuli-responsive membrane channels and molecular machine ion pumps such as ATPases. Here, we report a synthetic molecular machine-like ion transport relay, in which transporters on opposite sides of a lipid bilayer membrane facilitate transport by passing ions between them. By incorporating a photo-responsive telescopic arm into the relay design, this process is reversibly controlled in response to irradiation with blue and green light. Transport occurs only in the extended state when the length of the arm is sufficient to pass the anion between transporters located on opposite sides of the membrane. In contrast, the contracted state of the telescopic arm is too short to mediate effective transport. The system acts as a stimuli-responsive ensemble of machine-like components, reminiscent of robotic arms in a factory assembly line, working cooperatively to mediate ion transport. This work points to new prospects for using lipid bilayer membranes as scaffolds for confining, orientating, and controlling the relative positions of molecular machines, thus enabling multiple components to work in concert and opening up new applications in biological contexts.
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Affiliation(s)
- Toby G. Johnson
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Amir Sadeghi-Kelishadi
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Matthew J. Langton
- Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
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25
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Caniglia G, Tezcan G, Meloni GN, Unwin PR, Kranz C. Probing and Visualizing Interfacial Charge at Surfaces in Aqueous Solution. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:247-267. [PMID: 35259914 DOI: 10.1146/annurev-anchem-121521-122615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Surface charge density and distribution play an important role in almost all interfacial processes, influencing, for example, adsorption, colloidal stability, functional material activity, electrochemical processes, corrosion, nanoparticle toxicity, and cellular processes such as signaling, absorption, and adhesion. Understanding the heterogeneity in, and distribution of, surface and interfacial charge is key to elucidating the mechanisms underlying reactivity, the stability of materials, and biophysical processes. Atomic force microscopy (AFM) and scanning ion conductance microscopy (SICM) are highly suitable for probing the material/electrolyte interface at the nanoscale through recent advances in probe design, significant instrumental (hardware and software) developments, and the evolution of multifunctional imaging protocols. Here, we assess the capability of AFM and SICM for surface charge mapping, covering the basic underpinning principles alongside experimental considerations. We illustrate and compare the use of AFM and SICM for visualizing surface and interfacial charge with examples from materials science, geochemistry, and the life sciences.
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Affiliation(s)
- Giada Caniglia
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Ulm, Germany;
| | - Gözde Tezcan
- Department of Chemistry, University of Warwick, Coventry, United Kingdom;
| | - Gabriel N Meloni
- Department of Chemistry, University of Warwick, Coventry, United Kingdom;
| | - Patrick R Unwin
- Department of Chemistry, University of Warwick, Coventry, United Kingdom;
| | - Christine Kranz
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Ulm, Germany;
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26
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Heterogeneous Heat Absorption Is Complementary to Radiotherapy. Cancers (Basel) 2022; 14:cancers14040901. [PMID: 35205649 PMCID: PMC8870118 DOI: 10.3390/cancers14040901] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/20/2022] [Accepted: 01/30/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary This review shows the advantages of heterogeneous heating of selected malignant cells in harmonic synergy with radiotherapy. The main clinical achievement of this complementary therapy is its extreme safety and minimal adverse effects. Combining the two methods opens a bright perspective, transforming the local radiotherapy to the antitumoral impact on the whole body, destroying the distant metastases by “teaching” the immune system about the overall danger of malignancy. Abstract (1) Background: Hyperthermia in oncology conventionally seeks the homogeneous heating of the tumor mass. The expected isothermal condition is the basis of the dose calculation in clinical practice. My objective is to study and apply a heterogenic temperature pattern during the heating process and show how it supports radiotherapy. (2) Methods: The targeted tissue’s natural electric and thermal heterogeneity is used for the selective heating of the cancer cells. The amplitude-modulated radiofrequency current focuses the energy absorption on the membrane rafts of the malignant cells. The energy partly “nonthermally” excites and partly heats the absorbing protein complexes. (3) Results: The excitation of the transmembrane proteins induces an extrinsic caspase-dependent apoptotic pathway, while the heat stress promotes the intrinsic caspase-dependent and independent apoptotic signals generated by mitochondria. The molecular changes synergize the method with radiotherapy and promote the abscopal effect. The mild average temperature (39–41 °C) intensifies the blood flow for promoting oxygenation in combination with radiotherapy. The preclinical experiences verify, and the clinical studies validate the method. (4) Conclusions: The heterogenic, molecular targeting has similarities with DNA strand-breaking in radiotherapy. The controlled energy absorption allows using a similar energy dose to radiotherapy (J/kg). The two therapies are synergistically combined.
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27
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Lozano H, Millan-Solsona R, Blanco-Cabra N, Fabregas R, Torrents E, Gomila G. Electrical properties of outer membrane extensions from Shewanella oneidensis MR-1. NANOSCALE 2021; 13:18754-18762. [PMID: 34747424 DOI: 10.1039/d1nr04689f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Shewanella oneidensis MR-1 is a metal-reducing bacterium that is able to exchange electrons with solid-phase minerals outside the cell. These bacterial cells can produce outer membrane extensions (OMEs) that are tens of nanometers wide and several microns long. The capability of these OMEs to transport electrons is currently under investigation. Tubular chemically fixed OMEs from S. oneidensis have shown good dc conducting properties when measured in an air environment. However, no direct demonstration of the conductivity of the more common bubble-like OMEs has been provided yet, due to the inherent difficulties in measuring it. In the present work, we measured the electrical properties of bubble-like OMEs in a dry air environment by Scanning Dielectric Microscopy (SDM) in force detection mode. We found that at the frequency of the measurements (∼2 kHz), OMEs show an insulating behavior, with an equivalent homogeneous dielectric constant εOME = 3.7 ± 0.7 and no dephasing between the applied ac voltage and the measured ac electric force. The dielectric constant measured for the OMEs is comparable to that obtained for insulating supramolecular protein structures (εprotein = 3-4), pointing towards a rich protein composition of the OMEs, probably coming from the periplasm. Based on the detection sensitivity of the measuring instrument, the upper limit for the ac longitudinal conductivity of bubble-like OMEs in a dry air environment has been set to σOME,ac < 10-5 S m-1, a value several orders of magnitude smaller than the dc conductivity measured in tubular chemically fixed OMEs. The lack of conductivity of bubble-like OMEs can be attributed to the relatively large separation between cytochromes in these larger OMEs and to the suppression of cytochrome mobility due to the dry environmental conditions.
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Affiliation(s)
- Helena Lozano
- Nanoscale bioelectric characterization, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain.
| | - Ruben Millan-Solsona
- Nanoscale bioelectric characterization, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain.
- Departament d'Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, c/Martí i Franqués 1, 08028, Barcelona, Spain
| | - Nuria Blanco-Cabra
- Bacterial infections and antimicrobial therapies, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain
| | - Rene Fabregas
- Department of Physics and Astronomy, University of Manchester, Manchester M13 9PL, UK
| | - Eduard Torrents
- Bacterial infections and antimicrobial therapies, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain
- Departament de Genètica, Microbiologia i Estadística, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain
| | - Gabriel Gomila
- Nanoscale bioelectric characterization, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain.
- Departament d'Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, c/Martí i Franqués 1, 08028, Barcelona, Spain
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Sheikh AY, Mattei A, Miglani Bhardwaj R, Hong RS, Abraham NS, Schneider-Rauber G, Engstrom KM, Diwan M, Henry RF, Gao Y, Juarez V, Jordan E, DeGoey DA, Hutchins CW. Implications of the Conformationally Flexible, Macrocyclic Structure of the First-Generation, Direct-Acting Anti-Viral Paritaprevir on Its Solid Form Complexity and Chameleonic Behavior. J Am Chem Soc 2021; 143:17479-17491. [PMID: 34637297 DOI: 10.1021/jacs.1c06837] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Direct-acting antiviral regimens have transformed therapeutic management of hepatitis C across all prevalent genotypes. Most of the chemical matter in these regimens comprises molecules well outside the traditional drug development chemical space and presents significant challenges. Herein, the implications of high conformational flexibility and the presence of a 15-membered macrocyclic ring in paritaprevir are studied through a combination of advanced computational and experimental methods with focus on molecular chameleonicity and crystal form complexity. The ability of the molecule to toggle between high and low 3D polar surface area (PSA) conformations is underpinned by intramolecular hydrogen bonding (IMHB) interactions and intramolecular steric effects. Computational studies consequently show a very significant difference of over 75 Å2 in 3D PSA between polar and apolar environments and provide the structural basis for the perplexingly favorable passive permeability of the molecule. Crystal packing and protein binding resulting in strong intermolecular interactions disrupt these intramolecular interactions. Crystalline Form I benefits from strong intermolecular interactions, whereas the weaker intermolecular interactions in Form II are partially compensated by the energetic advantage of an IMHB. Like Form I, no IMHB is observed within the receptor-bound conformation; instead, an intermolecular H-bond contributes to the potency of the molecule. The choice of metastable Form II is derisked through strategies accounting for crystal surface and packing features to manage higher form specific solid-state chemical reactivity and specific processing requirements. Overall, the results show an unambiguous link between structural features and derived properties from crystallization to dissolution, permeation, and docking into the protein pocket.
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Affiliation(s)
- Ahmad Y Sheikh
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alessandra Mattei
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rajni Miglani Bhardwaj
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Richard S Hong
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Nathan S Abraham
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Gabriela Schneider-Rauber
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Kenneth M Engstrom
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Moiz Diwan
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rodger F Henry
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Yi Gao
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Vivian Juarez
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Erin Jordan
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - David A DeGoey
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Charles W Hutchins
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
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29
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Mahapatra P, Ohshima H, Gopmandal PP. Electrophoresis of Liquid-Layer Coated Particles: Impact of Ion Partitioning and Ion Steric Effects. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11316-11329. [PMID: 34529445 DOI: 10.1021/acs.langmuir.1c01875] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The biomimetic core-shell nanoparticles coated with membranes of various biological cells have attracted significant research interest, because of their extensive applications in targeted drug delivery systems. The cell membrane consists of a lipid bilayer, which can be regarded as a two-dimensional oriented viscous liquid with low dielectric permittivity, compared to a bulk aqueous medium. Such a liquid layer comprised of cell membrane may bear additional mobile charges, because of the presence of free lipid molecules or charged surfactant molecules, which further results in nonzero charge along the surface of the peripheral layer. In this article, we present an analytical theory for electrophoresis of such cell membrane coated functionalized nanoparticles in the extent of electrolyte solution, considering the combined effects of finite ion size and of ion partitioning. Going beyond the Debye-Huckel approximations, we propose an analytical theory for Donnan potential and electrophoretic mobility. The derived expressions are applicable for moderate to highly charged undertaken core-shell particles when the thickness of the peripheral liquid layer greatly exceeds the electric double layer thickness. The impact of pertinent parameters on the electrophoretic response of such a particle is further discussed.
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Affiliation(s)
- Paramita Mahapatra
- Department of Mathematics, National Institute of Technology Durgapur Durgapur-713209, India
| | - H Ohshima
- Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Partha P Gopmandal
- Department of Mathematics, National Institute of Technology Durgapur Durgapur-713209, India
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30
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Checa M, Millan-Solsona R, Mares AG, Pujals S, Gomila G. Fast Label-Free Nanoscale Composition Mapping of Eukaryotic Cells Via Scanning Dielectric Force Volume Microscopy and Machine Learning. SMALL METHODS 2021; 5:e2100279. [PMID: 34928004 DOI: 10.1002/smtd.202100279] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/28/2021] [Indexed: 06/14/2023]
Abstract
Mapping the biochemical composition of eukaryotic cells without the use of exogenous labels is a long-sought objective in cell biology. Recently, it has been shown that composition maps on dry single bacterial cells with nanoscale spatial resolution can be inferred from quantitative nanoscale dielectric constant maps obtained with the scanning dielectric microscope. Here, it is shown that this approach can also be applied to the much more challenging case of fixed and dry eukaryotic cells, which are highly heterogeneous and show micrometric topographic variations. More importantly, it is demonstrated that the main bottleneck of the technique (the long computation times required to extract the nanoscale dielectric constant maps) can be shortcut by using supervised neural networks, decreasing them from weeks to seconds in a wokstation computer. This easy-to-use data-driven approach opens the door for in situ and on-the-fly label free nanoscale composition mapping of eukaryotic cells with scanning dielectric microscopy.
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Affiliation(s)
- Martí Checa
- Nanoscale Bioelectrical Characterization Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 11-15, Barcelona, 08028, Spain
| | - Ruben Millan-Solsona
- Nanoscale Bioelectrical Characterization Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 11-15, Barcelona, 08028, Spain
- Departament d'Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, Carrer Martí i Franquès 1, Barcelona, 08028, Spain
| | - Adrianna Glinkowska Mares
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 11-15, Barcelona, 08028, Spain
| | - Silvia Pujals
- Departament d'Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, Carrer Martí i Franquès 1, Barcelona, 08028, Spain
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 11-15, Barcelona, 08028, Spain
| | - Gabriel Gomila
- Nanoscale Bioelectrical Characterization Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Carrer Baldiri i Reixac 11-15, Barcelona, 08028, Spain
- Departament d'Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, Carrer Martí i Franquès 1, Barcelona, 08028, Spain
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31
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Hayashi K, Sugimura H, Kamei T, Shimanouchi T, Nakamura H, Umakoshi H. Quantitative Determination of Relative Permittivity Based on the Fluorescence Property of Pyrene Derivatives: An Interpretation of Hydrophobicity in Self-Assembled Aggregates of Nonionic Amphiphiles. J Phys Chem B 2021; 125:6192-6200. [PMID: 34077661 DOI: 10.1021/acs.jpcb.1c00170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Aggregates in aqueous solutions can embed hydrophobic molecules, and their interactions depend on the properties of the aggregates. The electric surface potential, molecular mobility, and gradual hydrophobicity are the properties that regulate the interactions, and it is essential to understand these to quantify the properties. Electric surface potential and molecular mobility are quantified using the zeta potential and NMR measurements. In this study, the quantification of gradual hydrophobicity within the aggregate based on the relative permittivity, also called the dielectric constant, has been estimated from fluorescence spectra of pyrene-dicarboxylic acid conjugates. The localization of the pyrene moiety was modified by conjugation with succinic acid, suberic acid, or dodecanedioic acid, and the conjugates were evaluated in the shallow, middle, and deep regions of the aggregates. Span and Tween surfactants have been employed to prepare these aggregates, because they form various kinds of aggregates such as micelles and vesicles. It was realized that the hydrophobicity gradually increased from the interface to the hydrophobic core. Alternatively, a comparison of hydrophobicity within the aggregates showed no remarkable difference. Moreover, the analyses suggested that there are a few water molecules in the deep region. These results support the idea of the localization of embedded molecules in aggregates.
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Affiliation(s)
- Keita Hayashi
- Department of Chemical Engineering, National Institute of Technology, Nara College, 22 Yata-cho, Yamatokoriyama, Nara 639-1080, Japan
| | - Haruna Sugimura
- Department of Chemical Engineering, National Institute of Technology, Nara College, 22 Yata-cho, Yamatokoriyama, Nara 639-1080, Japan
| | - Toshiyuki Kamei
- Department of Chemical Engineering, National Institute of Technology, Nara College, 22 Yata-cho, Yamatokoriyama, Nara 639-1080, Japan
| | - Toshinori Shimanouchi
- Graduate School of Environmental and Life Science, Okayama University, 3-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hidemi Nakamura
- Department of Chemical Engineering, National Institute of Technology, Nara College, 22 Yata-cho, Yamatokoriyama, Nara 639-1080, Japan
| | - Hiroshi Umakoshi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama-cho, Toyonaka, Osaka 560-8531, Japan
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32
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Begnini F, Poongavanam V, Atilaw Y, Erdelyi M, Schiesser S, Kihlberg J. Cell Permeability of Isomeric Macrocycles: Predictions and NMR Studies. ACS Med Chem Lett 2021; 12:983-990. [PMID: 34136079 PMCID: PMC8201747 DOI: 10.1021/acsmedchemlett.1c00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 05/13/2021] [Indexed: 12/22/2022] Open
Abstract
![]()
Conformation-dependent 3D descriptors
have been shown to provide
better predictions of the physicochemical properties of macrocycles
than 2D descriptors. However, the computational identification of
relevant conformations for macrocycles is nontrivial. Herein, we report
that the Caco-2 cell permeability difference between a pair of diastereomeric
macrocycles correlated with their solvent accessible 3D polar surface
area and radius of gyration. The descriptors were calculated from
the macrocycles’ solution-phase conformational ensembles and
independently from ensembles obtained by conformational sampling.
Calculation of the two descriptors for three other stereo- and regioisomeric
macrocycles also allowed the correct ranking of their cell permeability.
Methods for conformational sampling may thus allow ranking of passive
permeability for moderately flexible macrocycles, thereby contributing
to the prioritization of macrocycles for synthesis in lead optimization.
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Affiliation(s)
- Fabio Begnini
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | | | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
| | - Stefan Schiesser
- Department of Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43183 Mölndal, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, Box 576, 75123 Uppsala, Sweden
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33
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Di Muzio M, Millan-Solsona R, Dols-Perez A, Borrell JH, Fumagalli L, Gomila G. Dielectric properties and lamellarity of single liposomes measured by in-liquid scanning dielectric microscopy. J Nanobiotechnology 2021; 19:167. [PMID: 34082783 PMCID: PMC8176598 DOI: 10.1186/s12951-021-00912-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 05/25/2021] [Indexed: 12/31/2022] Open
Abstract
Liposomes are widely used as drug delivery carriers and as cell model systems. Here, we measure the dielectric properties of individual liposomes adsorbed on a metal electrode by in-liquid scanning dielectric microscopy in force detection mode. From the measurements the lamellarity of the liposomes, the separation between the lamellae and the specific capacitance of the lipid bilayer can be obtained. As application we considered the case of non-extruded DOPC liposomes with radii in the range ~ 100-800 nm. Uni-, bi- and tri-lamellar liposomes have been identified, with the largest population corresponding to bi-lamellar liposomes. The interlamellar separation in the bi-lamellar liposomes is found to be below ~ 10 nm in most instances. The specific capacitance of the DOPC lipid bilayer is found to be ~ 0.75 µF/cm2 in excellent agreement with the value determined on solid supported planar lipid bilayers. The lamellarity of the DOPC liposomes shows the usual correlation with the liposome's size. No correlation is found, instead, with the shape of the adsorbed liposomes. The proposed approach offers a powerful label-free and non-invasive method to determine the lamellarity and dielectric properties of single liposomes.
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Affiliation(s)
- Martina Di Muzio
- Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain
| | - Ruben Millan-Solsona
- Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain.,Departament D'Enginyeria Electrònica I Biomèdica, Universitat de Barcelona, C/Martí i Franqués 1, 08028, Barcelona, Spain
| | - Aurora Dols-Perez
- Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain
| | - Jordi H Borrell
- Secció de Fisicoquímica, Facultat de Farmàcia I Ciències de L'Alimentació, Universitat de Barcelona, Av. Diagonal, 643, 08028, Barcelona, Spain
| | - Laura Fumagalli
- Department of Physics and Astronomy, University of Manchester, Manchester, M13 9PL, UK.,National Graphene Institute, University of Manchester, Manchester, M13 9PL, UK
| | - Gabriel Gomila
- Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain. .,Departament D'Enginyeria Electrònica I Biomèdica, Universitat de Barcelona, C/Martí i Franqués 1, 08028, Barcelona, Spain.
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34
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Checa M, Millan-Solsona R, Glinkowska Mares A, Pujals S, Gomila G. Dielectric Imaging of Fixed HeLa Cells by In-Liquid Scanning Dielectric Force Volume Microscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1402. [PMID: 34070690 PMCID: PMC8226567 DOI: 10.3390/nano11061402] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/21/2021] [Accepted: 05/23/2021] [Indexed: 01/16/2023]
Abstract
Mapping the dielectric properties of cells with nanoscale spatial resolution can be an important tool in nanomedicine and nanotoxicity analysis, which can complement structural and mechanical nanoscale measurements. Recently we have shown that dielectric constant maps can be obtained on dried fixed cells in air environment by means of scanning dielectric force volume microscopy. Here, we demonstrate that such measurements can also be performed in the much more challenging case of fixed cells in liquid environment. Performing the measurements in liquid media contributes to preserve better the structure of the fixed cells, while also enabling accessing the local dielectric properties under fully hydrated conditions. The results shown in this work pave the way to address the nanoscale dielectric imaging of living cells, for which still further developments are required, as discussed here.
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Affiliation(s)
- Martí Checa
- Nanoscale Bioelectric Characterization, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri I Reixac 11-15, 08028 Barcelona, Spain;
| | - Ruben Millan-Solsona
- Nanoscale Bioelectric Characterization, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri I Reixac 11-15, 08028 Barcelona, Spain;
- Departament d’Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, c/Martí i Franquès 1, 08028 Barcelona, Spain;
| | - Adrianna Glinkowska Mares
- Nanoscopy for Nanomedicine, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri I Reixac 11-15, 08028 Barcelona, Spain;
| | - Silvia Pujals
- Departament d’Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, c/Martí i Franquès 1, 08028 Barcelona, Spain;
- Nanoscopy for Nanomedicine, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri I Reixac 11-15, 08028 Barcelona, Spain;
| | - Gabriel Gomila
- Nanoscale Bioelectric Characterization, Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology (BIST), c/Baldiri I Reixac 11-15, 08028 Barcelona, Spain;
- Departament d’Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, c/Martí i Franquès 1, 08028 Barcelona, Spain;
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35
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Javidpour L, BoŽič A, Naji A, Podgornik R. Electrostatic interactions between the SARS-CoV-2 virus and a charged electret fibre. SOFT MATTER 2021; 17:4296-4303. [PMID: 33908595 DOI: 10.1039/d1sm00232e] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
While almost any kind of face mask offers some protection against particles and pathogens of different sizes, the most efficient ones make use of a layered structure where one or more layers are electrically charged. These electret layers are essential for the efficient filtration of difficult-to-capture small particles, yet the exact nature of electrostatic capture with respect to the charge on both the particles and the electret fibres as well as the effect of the immediate environment remain unclear. Here, we explore in detail the electrostatic interactions between the surface of a single charged electret fibre and a model of the SARS-CoV-2 virus. Using Poisson-Boltzmann electrostatics coupled to a detailed spike protein charge regulation model, we show how pH and salt concentration drastically change both the scale and the sign of the interaction. Furthermore, the configuration of the few spike proteins closest to the electret fibre turns out to be as important for the strength of the interaction as their total number on the virus envelope, a direct consequence of spike protein charge regulation. The results of our work elucidate the details of virus electrostatics and contribute to the general understanding of efficient virus filtration mechanisms.
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Affiliation(s)
- Leili Javidpour
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran, 19395-5531, Iran
| | - AnŽe BoŽič
- Department of Theoretical Physics, JoŽef Stefan Institute, SI-1000 Ljubljana, Slovenia
| | - Ali Naji
- School of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran, 19395-5531, Iran and School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran, 19395-5531, Iran
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. and Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325000, China
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36
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Kundu R, Chandra A, Datta A. Fluorescent Chemical Tools for Tracking Anionic Phospholipids. Isr J Chem 2021. [DOI: 10.1002/ijch.202100003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Rajasree Kundu
- Department of Chemical Sciences Tata Institute of Fundamental Research 1 Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Amitava Chandra
- Department of Chemical Sciences Tata Institute of Fundamental Research 1 Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Ankona Datta
- Department of Chemical Sciences Tata Institute of Fundamental Research 1 Homi Bhabha Road, Colaba Mumbai 400005 India
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37
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Grauffel C, Dudev T, Lim C. Metal Affinity/Selectivity of Monophosphate-Containing Signaling/Lipid Molecules. J Chem Theory Comput 2021; 17:2444-2456. [PMID: 33818070 DOI: 10.1021/acs.jctc.0c01007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Monophosphate, an essential component of nucleic acids, as well as cell membranes and signaling molecules, is often bound to metal cations. Despite the biological importance of monophosphate-containing cell-signaling or lipid molecules, their propensity to bind the two most abundant cellular dications, Mg2+ and Ca2+, in a particular mode (inner/outer shell, mono/bidentate) is not well understood. Whether they prefer binding to Mg2+ than to Ca2+ and if they can outcompete the carboxylates of excitatory Asp/Glu and inhibitory gamma-aminobutyric acid (GABA) neurotransmitters in binding to Mg2+/Ca2+ remain unclear. To address these questions, we modeled cyclic adenosine/guanosine monophosphate (cAMP/cGMP), nucleoside 2',3'-cyclic phosphate, phosphatidylinositol (PI), phosphatidylserine (PS), and phosphatidylethanolamine (PEA) and determined their most stable metal-binding modes, including those of Asp/Glu and GABA, as well as their selectivity for Mg2+/Ca2+ using density functional theory combined with the polarizable continuum model. The results obtained, which are consistent with the available experimental findings, reveal that the structurally and functionally diverse monophosphate-containing ligands studied prefer monodentate coordination of Mg2+ because of the greater strain encountered upon bidentate coordination, whereas the larger Ca2+ imposes less strain upon bidentate binding and has reduced/no preference for monodentate coordination. We further show that in a low-dielectric environment, negatively charged monophosphate-containing ligands favor the better charge-accepting dication, that is, Mg2+ rather than Ca2+. By promoting Mg2+ over Ca2+ binding, signaling monophosphates (cAMP/cGMP) do not entrap cellular Ca2+ and interfere with signal transduction processes employing Ca2+ as a second messenger. In regions with high glutamate cytoplasmic concentration, glutamate may sequester Mg2+ bound to isolated five-/six-membered ring phosphates, PI, or neutral PEA, but not anionic phospholipids constituting the inner leaflet of the cell membrane.
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Affiliation(s)
- Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan
| | - Todor Dudev
- Faculty of Chemistry and Pharmacy, Sofia University, Sofia 1164, Bulgaria
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
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38
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Low-molecular components of colostrum as a regulator of the organism redox-system and biological antidote. EUREKA: LIFE SCIENCES 2021. [DOI: 10.21303/2504-5695.2021.001738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The protein composition in the diapason of molecular masses from 4800 to 9500 Dа has been studied in colostrum, taken from different cows, and manifested the expressed biological activity. For this aim, an influence of low-molecular components of colostrum on some physiological parameters (change of body mass and temperature) at intoxication of animals (Wistar rats) by blue stone has been studied. An influence of colostrum low-molecular components on parameters of the organism redox-system (content of hyperperoxides of lipids and activity of glutathione peroxidase) in the blood serum of animals has been studied. For determining integral characteristics of colostrum components, electric conductivity of skim colostrum and one of colostrum with low-molecular proteins (less than 10 000 Dа), taken from different cows, were used. The aim of this work is to study interconnections of an influence of colostrum low-molecular proteins on models of organism intoxication by cooper ions.
It is demonstrated, that the colostrum composition includes 25–35 different proteins with a molecular mass from 4800 to 9500 Dа. The number and ratio between protein fractions depend on individual physiological-biochemical characteristics of producers. It has been revealed, that there is no direct dependence between the protein content in a measuring cell (2 mg/ml, 4 mg/ml and 10 mg/ml) with skim colostrum and electric conductivity change, and this dependence is different for skim colostrum, taken from different cows. Individual differences are manifested both at electric conductivity change and by the content of colostrum low-molecular proteins in a measuring cell. It is demonstrated, that colostrum low-molecular components can eliminate the toxic effect of blue stone on the organism, which mechanisms are connected with a balance shift in the system “prooxidants↔antioxidants” towards antioxidants. The electric conductivity of colostrum components may be used as an express-method for evaluating biologically active substances of colostrum
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39
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Ermondi G, Vallaro M, Saame J, Toom L, Leito I, Ruiz R, Caron G. Rifampicin as an example of beyond-rule-of-5 compound: Ionization beyond water and lipophilicity beyond octanol/water. Eur J Pharm Sci 2021; 161:105802. [PMID: 33716188 DOI: 10.1016/j.ejps.2021.105802] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 10/21/2022]
Abstract
Ionization and lipophilicity in early drug discovery are commonly characterized in water and octanol/water, respectively and thus do not consider the non-polar features of the biomembrane core. This is particularly limiting for bRo5 compounds which may adapt their properties (e.g. ionization and lipophilicity) to the environment. In this paper we used experimental methods to characterize rifampicin for its ionization properties in various water/cosolvent mixtures and in pure MeCN and its lipophilicity in octanol/water and toluene/water systems. Moreover, we also measured log k'80 PLRP-S, a chromatographic index of lipophilicity in non-polar media. Results show that the existence domain of neutral rifampicin is limited compared to the zwitterion, but the lipophilic cationic species is extremely relevant in non-polar environments.
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Affiliation(s)
- Giuseppe Ermondi
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, Torino 10135, Italy
| | - Maura Vallaro
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, Torino 10135, Italy
| | - Jaan Saame
- University of Tartu, Institute of Chemistry, Ravila 14a, Tartu 50411, Estonia
| | - Lauri Toom
- University of Tartu, Institute of Chemistry, Ravila 14a, Tartu 50411, Estonia
| | - Ivo Leito
- University of Tartu, Institute of Chemistry, Ravila 14a, Tartu 50411, Estonia
| | - Rebeca Ruiz
- Pion Inc., Forest Row Business Park, Forest Row RH18 5DW, UK
| | - Giulia Caron
- Molecular Biotechnology and Health Sciences Dept., Università degli Studi di Torino, via Quarello 15, Torino 10135, Italy.
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40
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Clarke RW. Theory of cell membrane interaction with glass. Phys Rev E 2021; 103:032401. [PMID: 33862714 DOI: 10.1103/physreve.103.032401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/19/2021] [Indexed: 11/07/2022]
Abstract
There are three regimes of cell membrane interaction with glass: Tight and loose adhesion, separated by repulsion. Explicitly including hydration, this paper evaluates the pressure between the surfaces as functions of distance for ion correlation and ion-screened electrostatics and electromagnetic fluctuations. The results agree with data for tight adhesion energy (0.5-3 vs 0.4-4 mJ/m^{2}), detachment pressure (7.9 vs. 9 MPa), and peak repulsion (3.4-7.5 vs. 5-10 kPa), also matching the repulsion's distance dependence on renormalization by steric pressure mainly from undulations.
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Affiliation(s)
- Richard W Clarke
- National Physical Laboratory, Teddington, TW11 0LW, United Kingdom
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41
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Valentine ML, Waterland MK, Fathizadeh A, Elber R, Baiz CR. Interfacial Dynamics in Lipid Membranes: The Effects of Headgroup Structures. J Phys Chem B 2021; 125:1343-1350. [DOI: 10.1021/acs.jpcb.0c08755] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mason L. Valentine
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Maya K. Waterland
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Arman Fathizadeh
- Oden Institute for Computational Science and Engineering, Austin, Texas 78712, United States
| | - Ron Elber
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, United States
- Oden Institute for Computational Science and Engineering, Austin, Texas 78712, United States
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, United States
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42
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Atilaw Y, Poongavanam V, Svensson Nilsson C, Nguyen D, Giese A, Meibom D, Erdelyi M, Kihlberg J. Solution Conformations Shed Light on PROTAC Cell Permeability. ACS Med Chem Lett 2021; 12:107-114. [PMID: 33488971 PMCID: PMC7812666 DOI: 10.1021/acsmedchemlett.0c00556] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/18/2020] [Indexed: 12/18/2022] Open
Abstract
![]()
Proteolysis
targeting chimeras (PROTACs) induce intracellular degradation
of target proteins. Their bifunctional structure puts degraders in
a chemical space where ADME properties often complicate drug discovery.
Herein we provide the first structural insight into PROTAC cell permeability
obtained by NMR studies of a VHL-based PROTAC (1), which
is cell permeable despite having a high molecular weight and polarity
and a large number of rotatable bonds. We found that 1 populates elongated and polar conformations in solutions that mimic
extra- and intracellular compartments. Conformations were folded and
had a smaller polar surface area in chloroform, mimicking a cell membrane
interior. Formation of intramolecular and nonclassical hydrogen bonds,
π–π interactions, and shielding of amide groups
from solvent all facilitate cell permeability by minimization of size
and polarity. We conclude that molecular chameleonicity appears to
be of major importance for 1 to enter into target cells.
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Affiliation(s)
- Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | | | | | - Duy Nguyen
- Nuvisan Innovation Campus Berlin GmbH, Muellerstrasse 178, 13353 Berlin, Germany
| | - Anja Giese
- Drug Discovery Sciences, Bayer AG, 13342 Berlin, Germany
| | - Daniel Meibom
- Drug Discovery Sciences, Bayer AG, 42113 Wuppertal, Germany
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
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43
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Choi Y, Kim SM, Heo Y, Lee G, Kang JY, Yoon DS. Nanoelectrical characterization of individual exosomes secreted by Aβ 42-ingested cells using electrostatic force microscopy. NANOTECHNOLOGY 2021; 32:025705. [PMID: 32957091 DOI: 10.1088/1361-6528/abba58] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Quantifying the physical properties of individual exosomes containing amyloid-β42 (Aβ42) is crucial for a better understanding of an underpinning mechanism of Alzheimer's disease expression which is associated with the Aβ42 transfer. Because of the lack of proper tools, however, there have been very few studies on how the amount of Aβ42 affects the physical properties of exosomes. To answer the question, we investigated the physical properties of exosomes secreted by neuroblastoma by probing individual exosomes using electrostatic force microscopy. Interestingly, we observed that when the higher concentration of Aβ42 oligomers was fed to cells, the higher surface charge of the exosomes appeared. This result indicates that the exosomes contain more Aβ42 with the increase in Aβ42 concentration in cell media, implying that they serve as transport vesicles for Aβ42. Our approach could help to better understand how the neuronal exosomes are related to the propagation of neurodegenerative diseases and to seek how to make an early diagnosis of those diseases.
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Affiliation(s)
- Yeseong Choi
- Bio-convergence Engineering, Korea University, Seoul, Republic of Korea
- Center for BioMicrosystems, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Su-Mi Kim
- Center for BioMicrosystems, Korea Institute of Science and Technology, Seoul, Republic of Korea
- R&D Team, Public CMO for Microbial-based Vaccine, Hwasun, Republic of Korea
| | - Youhee Heo
- Center for BioMicrosystems, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Department of Biomedical Engineering, Sogang University, Seoul, Republic of Korea
| | - Gyudo Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea
| | - Ji Yoon Kang
- Center for BioMicrosystems, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Biomedical Engineering, KIST School, Korea University of Science and Technology, Seoul, Republic of Korea
| | - Dae Sung Yoon
- Bio-convergence Engineering, Korea University, Seoul, Republic of Korea
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44
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Chinappi M, Yamaji M, Kawano R, Cecconi F. Analytical Model for Particle Capture in Nanopores Elucidates Competition among Electrophoresis, Electroosmosis, and Dielectrophoresis. ACS NANO 2020; 14:15816-15828. [PMID: 33170650 PMCID: PMC8016366 DOI: 10.1021/acsnano.0c06981] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 11/02/2020] [Indexed: 05/15/2023]
Abstract
The interaction between nanoparticles dispersed in a fluid and nanopores is governed by the interplay of hydrodynamical, electrical, and chemical effects. We developed a theory for particle capture in nanopores and derived analytical expressions for the capture rate under the concurrent action of electrical forces, fluid advection, and Brownian motion. Our approach naturally splits the average capture time in two terms, an approaching time due to the migration of particles from the bulk to the pore mouth and an entrance time associated with a free-energy barrier at the pore entrance. Within this theoretical framework, we described the standard experimental condition where a particle concentration is driven into the pore by an applied voltage, with specific focus on different capture mechanisms: under pure electrophoretic force, in the presence of a competition between electrophoresis and electroosmosis, and finally under dielectrophoretic reorientation of dipolar particles. Our theory predicts that dielectrophoresis is able to induce capture for both positive and negative voltages. We performed a dedicated experiment involving a biological nanopore (α-hemolysin) and a rigid dipolar dumbbell (realized with a β-hairpin peptide) that confirms the theoretically proposed capture mechanism.
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Affiliation(s)
- Mauro Chinappi
- Dipartimento
di Ingegneria Industriale, Università
di Roma Tor Vergata, Via del Politecnico 1, 00133 Rome, Italy
| | - Misa Yamaji
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Ryuji Kawano
- Department
of Biotechnology and Life Science, Tokyo
University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Fabio Cecconi
- CNR-Istituto
dei Sistemi Complessi, Via dei Taurini 19, I-00185 Rome, Italy
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45
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Alshaibi HF, Al-shehri B, Hassan B, Al-zahrani R, Assiss T. Modulated Electrohyperthermia: A New Hope for Cancer Patients. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8814878. [PMID: 33274226 PMCID: PMC7683119 DOI: 10.1155/2020/8814878] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/14/2020] [Accepted: 10/31/2020] [Indexed: 12/26/2022]
Abstract
According to the World Health Organization, the prevalence of cancer has increased worldwide. Oncological hyperthermia is a group of methods that overheat the malignant tissues locally or systematically. Nevertheless, hyperthermia is not widely accepted, primarily because of the lack of selectivity for cancer cells and because the temperature-triggered higher blood flow increases the nutrient supply to the tumor, raising the risk of metastases. These problems with classical hyperthermia led to the development of modulated electrohyperthermia (mEHT). The biophysical differences of the cancer cells and their healthy hosts allow for selective energy absorption on the membrane rafts of the plasma membrane of the tumor cells, triggering immunogenic cell death. Currently, this method is used in only 34 countries. The effectiveness of conventional oncotherapies increases when it is applied in combination with mEHT. In silico, in vitro, and in vivo preclinical research studies have all shown the extraordinary ability of mEHT to kill malignant cells. Clinical applications have improved the quality of life and the survival of patients. For these reasons, many other research studies are presently in progress worldwide. Thus, the objective of this review is to highlight the capabilities and advantages of mEHT and provide new hopes for cancer patients worldwide.
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Affiliation(s)
- Huda F. Alshaibi
- Faculty of Science Biochemistry Department, King Abdulaziz University, Saudi Arabia P.O. Box 52502, Jeddah 21573
| | - Bashayr Al-shehri
- Faculty of Science Biochemistry Department, Undergraduate Students at King Abdulaziz University, Saudi Arabia
| | - Basmah Hassan
- Faculty of Science Biochemistry Department, Undergraduate Students at King Abdulaziz University, Saudi Arabia
| | - Raghad Al-zahrani
- Faculty of Science Biochemistry Department, Undergraduate Students at King Abdulaziz University, Saudi Arabia
| | - Taghreed Assiss
- Faculty of Science Biochemistry Department, Undergraduate Students at King Abdulaziz University, Saudi Arabia
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46
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Muzio MD, Millan-Solsona R, Borrell JH, Fumagalli L, Gomila G. Cholesterol Effect on the Specific Capacitance of Submicrometric DOPC Bilayer Patches Measured by in-Liquid Scanning Dielectric Microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:12963-12972. [PMID: 33084346 DOI: 10.1021/acs.langmuir.0c02251] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The specific capacitance of biological membranes is a key physical parameter in bioelectricity that also provides valuable physicochemical information on composition, phase, or hydration properties. Cholesterol is known to modulate the physicochemical properties of biomembranes, but its effect on the specific capacitance has not been fully established yet. Here we use the high spatial resolution capabilities of in-liquid scanning dielectric microscopy in force detection mode to directly demonstrate that DOPC bilayer patches at 50% cholesterol concentration show a strong reduction of their specific capacitance with respect to pure DOPC bilayer patches. The reduction observed (∼35%) cannot be explained by the small increase in bilayer thickness (∼16%). We suggest that the reduction of the specific capacitance might be due to the dehydration of the polar head groups caused by the insertion of cholesterol molecules in the bilayer. The results reported confirm the potential of in-liquid SDM to study the electrical and physicochemical properties of lipid bilayers at very small scales (down to ∼200 nm here), with implications in fields such as biophysics, bioelectricity, biochemistry, and biosensing.
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Affiliation(s)
- Martina Di Muzio
- Nanoscale Bioelectrical Characterization, Institut de Bioenginyeria de Catalunya, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Ruben Millan-Solsona
- Nanoscale Bioelectrical Characterization, Institut de Bioenginyeria de Catalunya, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | | | | | - Gabriel Gomila
- Nanoscale Bioelectrical Characterization, Institut de Bioenginyeria de Catalunya, The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
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47
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Modeling the mechanobioelectricity of cell clusters. Biomech Model Mechanobiol 2020; 20:535-554. [PMID: 33145723 PMCID: PMC7979637 DOI: 10.1007/s10237-020-01399-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/16/2020] [Indexed: 10/31/2022]
Abstract
We propose a continuum finite strain theory for the interplay between the bioelectricity and the poromechanics of a cell cluster. Specifically, we refer to a cluster of closely packed cells, whose mechanics is governed by a polymer network of cytoskeletal filaments joined by anchoring junctions, modeled through compressible hyperelasticity. The cluster is saturated with a solution of water and ions. We account for water and ion transport in the intercellular spaces, between cells through gap junctions, and across cell membranes through aquaporins and ion channels. Water fluxes result from the contributions due to osmosis, electro-osmosis, and water pressure, while ion fluxes encompass electro-diffusive and convective terms. We consider both the cases of permeable and impermeable cluster boundary, the latter simulating the presence of sealing tight junctions. We solve the coupled governing equations for a one-dimensional axisymmetric benchmark through finite elements, thus determining the spatiotemporal evolution of the intracellular and extracellular ion concentrations, setting the membrane potential, and water concentrations, establishing the cluster deformation. When suitably complemented with genetic, biochemical, and growth dynamics, we expect this model to become a useful instrument for investigating specific aspects of developmental mechanobioelectricity.
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48
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Millan-Solsona R, Checa M, Fumagalli L, Gomila G. Mapping the capacitance of self-assembled monolayers at metal/electrolyte interfaces at the nanoscale by in-liquid scanning dielectric microscopy. NANOSCALE 2020; 12:20658-20668. [PMID: 33043923 DOI: 10.1039/d0nr05723a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Organic self-assembled monolayers (SAMs) at metal/electrolyte interfaces have been thoroughly investigated both from fundamental and applied points of view. A relevant figure of merit of metal/SAM/electrolyte interfaces is the specific capacitance, which determines the charge that can be accumulated at the metal electrode. Here, we show that the specific capacitance of non-uniform alkanethiol SAMs at gold/electrolyte interfaces can be quantitatively measured and mapped at the nanoscale by in-liquid scanning dielectric microscopy in force detection mode. We show that sub-100 nm spatial resolution in ultrathin (<1 nm) SAMs can be achieved, largely improving the performance of current sensing characterization techniques. The present results provide access to study the dielectric properties of metal/SAM/electrolyte interfaces at scales that have remained unexplored until now.
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Affiliation(s)
- Ruben Millan-Solsona
- Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology, c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain. and Departament d'Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain
| | - Martí Checa
- Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology, c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain.
| | - Laura Fumagalli
- Department of Physics and Astronomy, University of Manchester, Manchester M13 9PL, UK and National Graphene Institute, University of Manchester, Manchester M13 9PL, UK
| | - Gabriel Gomila
- Institut de Bioenginyeria de Catalunya (IBEC), The Barcelona Institute of Science and Technology, c/Baldiri i Reixac 11-15, 08028, Barcelona, Spain. and Departament d'Enginyeria Electrònica i Biomèdica, Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain
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49
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Osella S, Paloncýová M, Sahi M, Knippenberg S. Influence of Membrane Phase on the Optical Properties of DPH. Molecules 2020; 25:E4264. [PMID: 32957614 PMCID: PMC7570797 DOI: 10.3390/molecules25184264] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/05/2020] [Accepted: 09/14/2020] [Indexed: 11/24/2022] Open
Abstract
The fluorescent molecule diphenylhexatriene (DPH) has been often used in combination with fluorescence anisotropy measurements, yet little is known regarding the non-linear optical properties. In the current work, we focus on them and extend the application to fluorescence, while paying attention to the conformational versatility of DPH when it is embedded in different membrane phases. Extensive hybrid quantum mechanics/molecular mechanics calculations were performed to investigate the influence of the phase- and temperature-dependent lipid environment on the probe. Already, the transition dipole moments and one-photon absorption spectra obtained in the liquid ordered mixture of sphingomyelin (SM)-cholesterol (Chol) (2:1) differ largely from the ones calculated in the liquid disordered DOPC and solid gel DPPC membranes. Throughout the work, the molecular conformation in SM:Chol is found to differ from the other environments. The two-photon absorption spectra and the ones obtained by hyper-Rayleigh scattering depend strongly on the environment. Finally, a stringent comparison of the fluorescence anisotropy decay and the fluorescence lifetime confirm the use of DPH to gain information upon the surrounding lipids and lipid phases. DPH might thus open the possibility to detect and analyze different biological environments based on its absorption and emission properties.
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Affiliation(s)
- Silvio Osella
- Chemical and Biological Systems Simulation Lab, Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Markéta Paloncýová
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic;
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden;
| | - Maryam Sahi
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden;
| | - Stefan Knippenberg
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 12, 771 46 Olomouc, Czech Republic;
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-10691 Stockholm, Sweden;
- Theory Lab, Hasselt University, Agoralaan Building D, 3590 Diepenbeek, Belgium
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50
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Ardham VR, Zoni V, Adamowicz S, Campomanes P, Vanni S. Accurate Estimation of Membrane Capacitance from Atomistic Molecular Dynamics Simulations of Zwitterionic Lipid Bilayers. J Phys Chem B 2020; 124:8278-8286. [PMID: 32856913 DOI: 10.1021/acs.jpcb.0c03145] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lipid membranes are indispensable to life, and they regulate countless cellular processes. To investigate the properties of membranes under controlled conditions, numerous reconstitution methods have been developed over the last few decades. Several of these methods result in the formation of lipid bilayers containing residual hydrophobic molecules between the two monolayers. These contaminants might alter membrane properties, including bilayer thickness, that is usually inferred from measurements of membrane capacitance assuming a simple slab model. However, recent measurements on solvent-free bilayers raised significant questions on the reliability of this approach. To reconcile the observed discrepancies, we developed a protocol to predict membrane capacitance from the dielectric profile of lipid bilayers computed from molecular dynamics simulations. Our methodology shows excellent agreement against available data on solvent-free noncharged bilayers, and it confirms that the uniform slab model is a reliable approximation from which to infer membrane capacitance. We find that the effective electrical thickness contributing to membrane capacitance is different from the hydrophobic thickness inferred from X-ray scattering form factors. We apply our model to estimate the concentration of residual solvent in reconstituted systems, and we propose that our protocol could be used to infer membrane properties in the presence of hydrophobic solvents.
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Affiliation(s)
- Vikram Reddy Ardham
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Valeria Zoni
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Sylvain Adamowicz
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Pablo Campomanes
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
| | - Stefano Vanni
- Chemin du Musée 10, Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
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