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Loubet NA, Verde AR, Appignanesi GA. A structural determinant of the behavior of water at hydration and nanoconfinement conditions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2024; 47:61. [PMID: 39343851 DOI: 10.1140/epje/s10189-024-00454-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 09/13/2024] [Indexed: 10/01/2024]
Abstract
The molecular nature of the phases that conform the two-liquid scenario is elucidated in this work in the light of a molecular principle governing water structuring, which unveils the relevance of the contraction and reorientation of the second molecular shell to allow for the existence of coordination defects in water's hydrogen bond network. In turn, such principle is shown to also determine the behavior of hydration and nanoconfined water while enabling to define conditions for wettability (quantifying hydrophobicity and predicting drying transitions), thus opening the possibility to unravel the active role of water in central fields of research.
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Affiliation(s)
- Nicolás A Loubet
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Alejandro R Verde
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Gustavo A Appignanesi
- INQUISUR, Departamento de Química, Universidad Nacional del Sur (UNS)-CONICET, Avenida Alem 1253, 8000, Bahía Blanca, Argentina.
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2
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Barbero F, Michelini S, Moriones OH, Patarroyo J, Rosell J, F. Gusta M, Vitali M, Martín L, Canals F, Duschl A, Horejs-Hoeck J, Mondragón L, Bastús NG, Puntes V. Role of Common Cell Culture Media Supplements on Citrate-Stabilized Gold Nanoparticle Protein Corona Formation, Aggregation State, and the Consequent Impact on Cellular Uptake. Bioconjug Chem 2022; 33:1505-1514. [DOI: 10.1021/acs.bioconjchem.2c00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francesco Barbero
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Universitat Autònoma de Barcelona (UAB), Campus
UAB, Bellaterra, 08193 Barcelona, Spain
| | - Sara Michelini
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Oscar H. Moriones
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Universitat Autònoma de Barcelona (UAB), Campus
UAB, Bellaterra, 08193 Barcelona, Spain
| | - Javier Patarroyo
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Jordi Rosell
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
| | - Muriel F. Gusta
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
| | - Michele Vitali
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
| | - Luna Martín
- Proteomics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Francesc Canals
- Proteomics Laboratory, Vall d’Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Albert Duschl
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Jutta Horejs-Hoeck
- Department of Biosciences, University of Salzburg, Hellbrunner Str. 34, 5020 Salzburg, Austria
| | - Laura Mondragón
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
| | - Neus G. Bastús
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Víctor Puntes
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and BIST, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Universitat Autònoma de Barcelona (UAB), Campus
UAB, Bellaterra, 08193 Barcelona, Spain
- Vall d’Hebron Institut de Recerca (VHIR), 08035 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), P. Lluís Companys 23, 08010 Barcelona, Spain
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3
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Ngassam VN, Su WC, Gettel DL, Deng Y, Yang Z, Wang-Tomic N, Sharma VP, Purushothaman S, Parikh AN. Recurrent dynamics of rupture transitions of giant lipid vesicles at solid surfaces. Biophys J 2021; 120:586-597. [PMID: 33460597 DOI: 10.1016/j.bpj.2021.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/20/2020] [Accepted: 01/07/2021] [Indexed: 10/22/2022] Open
Abstract
Single giant unilamellar vesicles (GUVs) rupture spontaneously from their salt-laden suspension onto solid surfaces. At hydrophobic surfaces, the GUVs rupture via a recurrent, bouncing ball rhythm. During each contact, the GUVs, rendered tense by the substrate interactions, porate, and spread a molecularly transformed motif of a monomolecular layer on the hydrophobic surface from the point of contact in a symmetric manner. The competition from pore closure, however, limits the spreading and produces a daughter vesicle, which re-engages with the substrate. At solid hydrophilic surfaces, by contrast, GUVs rupture via a distinctly different recurrent burst-heal dynamics; during burst, single pores nucleate at the contact boundary of the adhering vesicles, facilitating asymmetric spreading and producing a "heart"-shaped membrane patch. During the healing phase, the competing pore closure produces a daughter vesicle. In both cases, the pattern of burst-reseal events repeats multiple times, splashing and spreading the vesicular fragments as bilayer patches at the solid surface in a pulsatory manner. These remarkable recurrent dynamics arise, not because of the elastic properties of the solid surface, but because the competition between membrane spreading and pore healing, prompted by the surface-energy-dependent adhesion, determine the course of the topological transition.
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Affiliation(s)
- Viviane N Ngassam
- Department of Biomedical Engineering, University of California, Davis, California
| | - Wan-Chih Su
- Department of Chemistry, University of California, Davis, California
| | - Douglas L Gettel
- Department of Chemical Engineering, University of California, Davis, California
| | - Yawen Deng
- Department of Biomedical Engineering, University of California, Davis, California
| | - Zexu Yang
- Department of Biomedical Engineering, University of California, Davis, California
| | - Neven Wang-Tomic
- Department of Biomedical Engineering, University of California, Davis, California
| | - Varun P Sharma
- Department of Biomedical Engineering, University of California, Davis, California
| | - Sowmya Purushothaman
- Department of Biomedical Engineering, University of California, Davis, California
| | - Atul N Parikh
- Department of Biomedical Engineering, University of California, Davis, California; Department of Chemistry, University of California, Davis, California; Department of Chemical Engineering, University of California, Davis, California; Department of Materials Science and Engineering, University of California, Davis, California.
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4
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Fernández A. Artificial Intelligence Steering Molecular Therapy in the Absence of Information on Target Structure and Regulation. J Chem Inf Model 2020; 60:460-466. [PMID: 31738539 DOI: 10.1021/acs.jcim.9b00651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protein associations are at the core of biological activity, and the drug-based disruption of dysfunctional associations poses a major challenge to targeted therapy. The problem becomes daunting when the structure and regulated modulation of the complex are unknown. To address the challenge, we leverage an artificial intelligence platform that learns from structural and epistructural data and infers regulation-susceptible regions that also generate interfacial tension between protein and water, thereby promoting protein associations. The input consists of sequence-derived 1D-features. The network is configured with evolutionarily coupled residues and taught to search for phosphorylation-modulated binding epitopes. The discovery platform is benchmarked against a PDB-derived testing set and validated against experimental data on a therapeutic disruptor designed according to the inferred epitope for a large deregulated complex known to be recruited in heart failure. Thus, dysfunctional "molecular brakes" of cardiac contractility get released through a therapeutic intervention guided by artificial intelligence.
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Affiliation(s)
- Ariel Fernández
- National Research Council (CONICET) , Rivadavia 1917 , Buenos Aires 1033 , INQUISUR /UNS-CONICET, Bahia Blanca 8000, Argentina.,AF Innovation Pharma Consultancy, GmbH , 4000 Pemberton Court , Winston-Salem , North Carolina 27106 , United States
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5
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Fernández A, Scott LR. Advanced Modeling Reconciles Counterintuitive Decisions in Lead Optimization. Trends Biotechnol 2017; 35:490-497. [DOI: 10.1016/j.tibtech.2016.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/24/2016] [Accepted: 12/07/2016] [Indexed: 12/21/2022]
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Fernández A. Acid-base chemistry of frustrated water at protein interfaces. FEBS Lett 2016; 590:215-23. [PMID: 26762189 DOI: 10.1002/1873-3468.12047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/20/2015] [Accepted: 12/15/2015] [Indexed: 11/07/2022]
Abstract
Water molecules at a protein interface are often frustrated in hydrogen-bonding opportunities due to subnanoscale confinement. As shown, this condition makes them behave as a general base that may titrate side-chain ammonium and guanidinium cations. Frustration-based chemistry is captured by a quantum mechanical treatment of proton transference and shown to remove same-charge uncompensated anticontacts at the interface found in the crystallographic record and in other spectroscopic information on the aqueous interface. Such observations are untenable within classical arguments, as hydronium is a stronger acid than ammonium or guanidinium. Frustration enables a directed Grotthuss mechanism for proton transference stabilizing same-charge anticontacts.
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Affiliation(s)
- Ariel Fernández
- Argentine Institute of Mathematics (I. A. M.), National Research Council (CONICET), Buenos Aires, Argentina.,Collegium Basilea, Institute for Advanced Study, Basel, Schweiz
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7
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Fernández A, Scott LR. Drug leads for interactive protein targets with unknown structure. Drug Discov Today 2015; 21:531-5. [PMID: 26484433 DOI: 10.1016/j.drudis.2015.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/29/2015] [Accepted: 10/12/2015] [Indexed: 11/24/2022]
Abstract
The disruption of protein-protein interfaces (PPIs) remains a challenge in drug discovery. The problem becomes daunting when the structure of the target protein is unknown and is even further complicated when the interface is susceptible to disruptive phosphorylation. Based solely on protein sequence and information about phosphorylation-susceptible sites within the PPI, a new technology has been developed to identify drug leads to inhibit protein associations. Here we reveal this technology and contrast it with current structure-based technologies for the generation of drug leads. The novel technology is illustrated by a patented invention to treat heart failure. The success of this technology shows that it is possible to generate drug leads in the absence of target structure.
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Affiliation(s)
- Ariel Fernández
- Argentine Institute of Mathematics (IAM), National Research Council (CONICET), Buenos Aires 1083, Argentina; AF Innovation, Avenida del Libertador 1092, Buenos Aires 1112, Argentina.
| | - L Ridgway Scott
- Department of Computer Science, The University of Chicago, Chicago, IL 60637, USA; Department of Mathematics, The University of Chicago, Chicago, IL 60637, USA
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8
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Bayden AS, Moustakas DT, Joseph-McCarthy D, Lamb ML. Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP. J Chem Inf Model 2015; 55:1552-65. [DOI: 10.1021/ci500746d] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alexander S. Bayden
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Demetri T. Moustakas
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Diane Joseph-McCarthy
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Michelle L. Lamb
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
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9
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Fernández A. Communication: Chemical functionality of interfacial water enveloping nanoscale structural defects in proteins. J Chem Phys 2015; 140:221102. [PMID: 24929366 DOI: 10.1063/1.4882895] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Building upon a non-Debye multiscale treatment of water dielectrics, this work reveals the biochemical role of interfacial water enveloping nanoscale structural defects in soluble proteins, asserting its role as a chemical base. This quasi-reactant status is already implied by the significant concentration of structural defects in the vicinity of an enzymatically active site, delineating their role as promoters or enhancers of catalytic activity.
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Affiliation(s)
- Ariel Fernández
- Instituto Argentino de Matemática, National Research Council (CONICET), Saavedra 15, Buenos Aires 1083, Argentina
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Arthur EJ, King JT, Kubarych KJ, Brooks CL. Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes. J Phys Chem B 2014; 118:8118-27. [PMID: 24823618 PMCID: PMC4216199 DOI: 10.1021/jp501132z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
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Cytoplasmic
osmolytes can significantly alter the thermodynamic
and kinetic properties of proteins relative to those under dilute
solution conditions. Spectroscopic experiments of lysozymes in cosolvents
indicate that such changes may arise from the heterogeneous, site-specific
hydrophobic interactions between protein surface residues and individual
solvent molecules. In pursuit of an accurate and predictive model
for explaining biomolecular interactions, we study the averaged structural
characteristics of mixed solvents with homologous lysozyme solutes
using all-atom molecular dynamics. By observing the time-averaged
densities of different aqueous solutions of trifluoroethanol, we deduce
trends in the heterogeneous solvent interactions over each protein’s
surface, and investigate how the homology of protein structure does
not necessarily translate to similarities in solvent structure and
composition—even when observing identical side chains.
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Affiliation(s)
- Evan J Arthur
- Department of Chemistry and ‡Biophysics Program, University of Michigan , 930 N. University Avenue , Ann Arbor, Michigan 48109-1055, USA
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Kapoor K, Patil S. Viscoelasticity and shear thinning of nanoconfined water. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:013004. [PMID: 24580317 DOI: 10.1103/physreve.89.013004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Indexed: 06/03/2023]
Abstract
Understanding flow properties and phase behavior of water confined to nanometer-sized pores and slits is central to a wide range of problems in science, such as percolation in geology, lubrication of future nano-machines, self-assembly and interactions of biomolecules, and transport through porous media in filtration processes. Experiments with different techniques in the past have reported that viscosity of nanoconfined water increases, decreases, or remains close to bulk water. Here we show that water confined to less than 20-nm-thick films exhibits both viscoelasticity and shear thinning. Typically viscoelasticity and shear thinning appear due to shearing of complex non-Newtonian mixtures possessing a slowly relaxing microstructure. The shear response of nanoconfined water in a range of shear frequencies (5 to 25 KHz) reveals that relaxation time diverges with reducing film thickness. It suggests that slow relaxation under confinement possibly arises due to existence of a critical point with respect to slit width. This criticality is similar to the capillary condensation in porous media.
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Affiliation(s)
- Karan Kapoor
- Physics Division, Indian Institute of Science Education and Research, Pune 411008, Maharashtra, India
| | - Shivprasad Patil
- Physics Division, Indian Institute of Science Education and Research, Pune 411008, Maharashtra, India
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12
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Biological Water Dynamics and Entropy: A Biophysical Origin of Cancer and Other Diseases. ENTROPY 2013. [DOI: 10.3390/e15093822] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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13
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Fernández A. The principle of minimal episteric distortion of the water matrix and its steering role in protein folding. J Chem Phys 2013; 139:085101. [DOI: 10.1063/1.4818874] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Fernández Stigliano A. Breakdown of the Debye polarization ansatz at protein-water interfaces. J Chem Phys 2013; 138:225103. [DOI: 10.1063/1.4810867] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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15
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Fernández A. Communication: Nanoscale electrostatic theory of epistructural fields at the protein-water interface. J Chem Phys 2012; 137:231101. [PMID: 23267464 DOI: 10.1063/1.4772603] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Nanoscale solvent confinement at the protein-water interface promotes dipole orientations that are not aligned with the internal electrostatic field of a protein, yielding what we term epistructural polarization. To quantify this effect, an equation is derived from first principles relating epistructural polarization with the magnitude of local distortions in water coordination causative of interfacial tension. The equation defines a nanoscale electrostatic model of water and enables an estimation of protein denaturation free energies and the inference of hot spots for protein associations. The theoretical results are validated vis-à-vis calorimetric data, revealing the destabilizing effect of epistructural polarization and its molecular origin.
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Affiliation(s)
- Ariel Fernández
- Instituto Argentino de Matemática Alberto P. Calderón, CONICET (National Research Council), Saavedra 15, Buenos Aires 1083, Argentina.
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Tayebi L, Ma Y, Vashaee D, Chen G, Sinha SK, Parikh AN. Long-range interlayer alignment of intralayer domains in stacked lipid bilayers. NATURE MATERIALS 2012; 11:1074-1080. [PMID: 23085566 DOI: 10.1038/nmat3451] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 09/11/2012] [Indexed: 05/28/2023]
Abstract
Liquid-crystalline phases of stacked lipid bilayers represent a pervasive motif in biomolecular assemblies. Here we report that, in addition to the usual smectic order, multicomponent multilayer membranes can exhibit columnar order arising from the coupling of two-dimensional intralayer phase separation and interlayer smectic ordering. This coupling propagates across hundreds of membrane lamellae, producing long-range alignment of phase-separated domains. Quantitative analysis of real-time dynamical experiments reveals that there is an interplay between intralayer domain growth and interlayer coupling, suggesting the existence of cooperative multilayer epitaxy. We postulate that such long-range epitaxy is solvent-assisted, and that it originates from the surface tension associated with differences in the network of hydrogen-bonded water molecules at the hydrated interfaces between the domains and the surrounding phase. Our findings might inspire the development of self-assembly-based strategies for the long-range alignment of functional lipid domains.
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Affiliation(s)
- Lobat Tayebi
- Department of Applied Science, University of California, Davis, California 95616, USA
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Caliandro R, Rossetti G, Carloni P. Local Fluctuations and Conformational Transitions in Proteins. J Chem Theory Comput 2012; 8:4775-85. [DOI: 10.1021/ct300610y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Rocco Caliandro
- CNR—Institute of Crystallography,
via Amendola 122/o, I-70126, Bari, Italy
| | - Giulia Rossetti
- Institute for Research in Biomedicine
and Barcelona Supercomputing Center, Joint Research Program on Computational
Biology, Baldiri I Reixac 10, 08028, Barcelona, Spain
- Jülich Supercomputing Centre,
Institute for Advanced Simulation, Forschungszentrum Jülich,
D-52425 Jülich, Germany
- Computational Biophysics, German
Research School for Simulation Sciences 1, D-52425 Jülich,
Germany, and Institute for Advanced Simulation, Forschungszentrum
Jülich, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German
Research School for Simulation Sciences 1, D-52425 Jülich,
Germany, and Institute for Advanced Simulation, Forschungszentrum
Jülich, D-52425 Jülich, Germany
- Statistical and Biological Physics
Sector, International School for Advanced Studies (SISSA), Trieste,
Italy
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