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Gonzalez BD, Forbrig E, Yao G, Kielb P, Mroginski MA, Hildebrandt P, Kozuch J. Cation Dependence of Enniatin B/Membrane-Interactions Assessed Using Surface-Enhanced Infrared Absorption (SEIRA) Spectroscopy. Chempluschem 2024; 89:e202400159. [PMID: 38700478 DOI: 10.1002/cplu.202400159] [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: 02/28/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
Enniatins are mycotoxins with well-known antibacterial, antifungal, antihelmintic and antiviral activity, which have recently come to attention as potential mitochondriotoxic anticancer agents. The cytotoxicity of enniatins is traced back to ionophoric properties, in which the cyclodepsipeptidic structure results in enniatin:cation-complexes of various stoichiometries proposed as membrane-active species. In this work, we employed a combination of surface-enhanced infrared absorption (SEIRA) spectroscopy, tethered bilayer lipid membranes (tBLMs) and density functional theory (DFT)-based computational spectroscopy to monitor the cation-dependence (Mz+=Na+, K+, Cs+, Li+, Mg2+, Ca2+) on the mechanism of enniatin B (EB) incorporation into membranes and identify the functionally relevant EBn : Mz+ complexes formed. We find that Na+ promotes a cooperative incorporation, modelled via an autocatalytic mechanism and mediated by a distorted 2 : 1-EB2 : Na+ complex. K+ (and Cs+) leads to a direct but less efficient insertion into membranes due to the adoption of "ideal" EB2 : K+ sandwich complexes. In contrast, the presence of Li+, Mg2+, and Ca2+ causes a (partial) extraction of EB from the membrane via the formation of "belted" 1 : 1-EB : Mz+ complexes, which screen the cationic charge less efficiently. Our results point to a relevance of the cation dependence for the transport into the malignant cells where the mitochondriotoxic anticancer activity is exerted.
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Affiliation(s)
- Barbara Daiana Gonzalez
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Enrico Forbrig
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Guiyang Yao
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 124, D-10623, Berlin, Germany
| | - Patrycja Kielb
- Clausius Institut für Physikalische und Theoretische Chemie, Universität Bonn, Wegelerstr. 12, D-53115, Bonn, Germany
- Transdisciplinary Research Area', Building Blocks of Matter and Fundamental Interactions (TRA Matter), Universität Bonn, D-53115, Bonn, Germany
| | - Maria Andrea Mroginski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin, Sekr. PC14, Straße des 17. Juni 135, D-10623, Berlin, Germany
| | - Jacek Kozuch
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, D-14195, Berlin, Germany
- Forschungsbau SupraFAB, Freie Universität Berlin, Altensteinstr. 23a, D-14195, Berlin, Germany
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2
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Cruz R, Ataka K, Heberle J, Kozuch J. Evaluating aliphatic CF, CF2, and CF3 groups as vibrational Stark effect reporters. J Chem Phys 2024; 160:204308. [PMID: 38814010 DOI: 10.1063/5.0198303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
Given the extensive use of fluorination in molecular design, it is imperative to understand the solvation properties of fluorinated compounds and the impact of the C-F bond on electrostatic interactions. Vibrational spectroscopy can provide direct insights into these interactions by using the C-F bond stretching [v(C-F)] as an electric field probe through the vibrational Stark effect (VSE). In this work, we explore the VSE of the three basic patterns of aliphatic fluorination, i.e., mono-, di-, and trifluorination in CF, CF2, and CF3 groups, respectively, and compare their response to the well-studied aromatic v(C-F). Magnitudes (i.e., Stark tuning rates) and orientations of the difference dipole vectors of the v(C-F)-containing normal modes were determined using density functional theory and a molecular dynamics (MD)-assisted solvatochromic analysis of model compounds in solvents of varying polarity. We obtain Stark tuning rates of 0.2-0.8 cm-1/(MV/cm), with smallest and largest electric field sensitivities for CFaliphatic and CF3,aliphatic, respectively. While average electric fields of solvation were oriented along the main symmetry axis of the CFn, and thus along its static dipole, the Stark tuning rate vectors were tilted by up to 87° potentially enabling to map electrostatics in multiple dimensions. We discuss the influence of conformational heterogeneity on spectral shifts and point out the importance of multipolar and/or polarizable MD force fields to describe the electrostatics of fluorinated molecules. The implications of this work are of direct relevance for studies of fluorinated molecules as found in pharmaceuticals, fluorinated peptides, and proteins.
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Affiliation(s)
- R Cruz
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
| | - K Ataka
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
| | - J Heberle
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
- Forschungsbau SupraFAB, Freie Universität Berlin, Berlin 14195, Germany
| | - J Kozuch
- Fachbereich Physik, Freie Universität Berlin, Berlin 14195, Germany
- Forschungsbau SupraFAB, Freie Universität Berlin, Berlin 14195, Germany
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3
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Antila HS, Dixit S, Kav B, Madsen JJ, Miettinen MS, Ollila OHS. Evaluating Polarizable Biomembrane Simulations against Experiments. J Chem Theory Comput 2024; 20:4325-4337. [PMID: 38718349 PMCID: PMC11137822 DOI: 10.1021/acs.jctc.3c01333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/10/2024] [Accepted: 04/10/2024] [Indexed: 05/29/2024]
Abstract
Owing to the increase of available computational capabilities and the potential for providing a more accurate description, polarizable molecular dynamics force fields are gaining popularity in modeling biomolecular systems. It is, however, crucial to evaluate how much precision is truly gained with increasing cost and complexity of the simulation. Here, we leverage the NMRlipids open collaboration and Databank to assess the performance of available polarizable lipid models─the CHARMM-Drude and the AMOEBA-based parameters─against high-fidelity experimental data and compare them to the top-performing nonpolarizable models. While some improvement in the description of ion binding to membranes is observed in the most recent CHARMM-Drude parameters, and the conformational dynamics of AMOEBA-based parameters are excellent, the best nonpolarizable models tend to outperform their polarizable counterparts for each property we explored. The identified shortcomings range from inaccuracies in describing the conformational space of lipids to excessively slow conformational dynamics. Our results provide valuable insights for the further refinement of polarizable lipid force fields and for selecting the best simulation parameters for specific applications.
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Affiliation(s)
- Hanne S. Antila
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Department
of Biomedicine, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
| | - Sneha Dixit
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
| | - Batuhan Kav
- Institute
of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, Jïulich 52428, Germany
| | - Jesper J. Madsen
- Department
of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
- Center
for Global Health and Infectious Diseases Research, Global and Planetary
Health, College of Public Health, University
of South Florida, Tampa, Florida 33612, United States of America
| | - Markus S. Miettinen
- Department
of Theory and Bio-Systems, Max Planck Institute
of Colloids and Interfaces, Potsdam 14476, Germany
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5008, Norway
- Department
of Chemistry, University of Bergen, Bergen 5007, Norway
| | - O. H. Samuli Ollila
- VTT Technical
Research Centre of Finland, Espoo 02044, Finland
- Institute
of Biotechnology, University of Helsinki, Helsinki 00014, Finland
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Zhang Y, Fan Q, Liu K, Zhou L, Zhou Y, Ding M, Zhang Y. EFFECTS OF CORE RESISTANCE TRAINING ON PUGILISM IN BOXERS. REV BRAS MED ESPORTE 2023. [DOI: 10.1590/1517-8692202329012022_0589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
ABSTRACT Introduction: Resistance training aims to improve the physical fitness of an athlete by improving their balance, movement, and agility skills. Boxers should have complementary attention to the strength of the core, a key area for boxing skills. Objective: Examine the effects of core strength training on pugilism in boxers. Methods: Ten volunteer professional boxers were selected. All undergo three months of core strength training under the described protocol. The athletes' sport quality index was studied using mathematical statistics. Results: After 3 months of core strength training, the physical test result was significantly higher (P<0.01). Although in 400-meter runs, sandbag training and interval running scores were higher than before training, the difference was insignificant (P>0.05). Conclusion: The core strength exercises improve the body mass of a boxing athlete and the level of their boxing. Supplementing athletes with core resistance training during regular exercise is indicated. Level of evidence II; Therapeutic studies - investigation of treatment outcomes.
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Haldar T, Chatterjee S, Alam MN, Maity P, Bagchi S. Blue Fluorescence of Cyano-tryptophan Predicts Local Electrostatics and Hydrogen Bonding in Biomolecules. J Phys Chem B 2022; 126:10732-10740. [PMID: 36511763 DOI: 10.1021/acs.jpcb.2c05848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Cyano-tryptophan is an unnatural fluorescent amino acid that emits in the visible region. Along with the structural similarity with tryptophan, the unique photophysical properties of this fluorophore make it an ideal probe for biophysical research. Herein, combining fluorescence spectroscopy, infrared spectroscopy, and molecular dynamics simulations, we show that the cyano-tryptophan's emission energy quantifies the underlying bond-specific noncovalent interactions in terms of the electric field. We further report the use of fluorophore's emission energy to predict its hydrogen bond characteristics. We demonstrate that combining experiments with molecular dynamics simulations can provide the hydrogen bonding status of the nitrile moiety. In addition, we report a method to differentiate between aqueous and nonaqueous hydrogen-bonding partners. Using a phenomenological approach, we demonstrate that the presence of the cyano-indole moiety is responsible for the distinct correlations between the fluorophore's emission and the electrostatic forces on the nitrile bond. As indole is a privileged scaffold for both native amino acids and nucleobases, cyano-indoles will have many multifaceted applications.
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Affiliation(s)
- Tapas Haldar
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Srijan Chatterjee
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Md Nirshad Alam
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Pradip Maity
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad201002, India
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Lin YC, Ren P, Webb LJ. AMOEBA Force Field Trajectories Improve Predictions of Accurate p Ka Values of the GFP Fluorophore: The Importance of Polarizability and Water Interactions. J Phys Chem B 2022; 126:7806-7817. [PMID: 36194474 PMCID: PMC10851343 DOI: 10.1021/acs.jpcb.2c03642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Precisely quantifying the magnitude, direction, and biological functions of electric fields in proteins has long been an outstanding challenge in the field. The most widely implemented experimental method to measure such electric fields at a particular residue in a protein has been through changes in pKa of titratable residues. While many computational strategies exist to predict these values, it has been difficult to do this accurately or connect predicted results to key structural or mechanistic features of the molecule. Here, we used experimentally determined pKa values of the fluorophore in superfolder green fluorescent protein (GFP) with amino acid mutations made at position Thr 203 to evaluate the pKa prediction ability of molecular dynamics (MD) simulations using a polarizable force field, AMOEBA. Structure ensembles from AMOEBA were used to calculate pKa values of the GFP fluorophore. The calculated pKa values were then compared to trajectories using a conventional fixed charge force field (Amber03 ff). We found that the position of water molecules included in the pKa calculation had opposite effects on the pKa values between the trajectories from AMOEBA and Amber03 force fields. In AMOEBA trajectories, the inclusion of water molecules within 35 Å of the fluorophore decreased the difference between the predicted and experimental values, resulting in calculated pKa values that were within an average of 0.8 pKa unit from the experimental results. On the other hand, in Amber03 trajectories, including water molecules that were more than 5 Å from the fluorophore increased the differences between the calculated and experimental pKa values. The inaccuracy of pKa predictions determined from Amber03 trajectories was caused by a significant stabilization of the deprotonated chromophore's free energy compared to the result in AMOEBA. We rationalize the cutoffs for explicit water molecules when calculating pKa to better predict the electrostatic environment surrounding the fluorophore buried in GFP. We discuss how the results from this work will assist the prospective prediction of pKa values or other electrostatic effects in a wide variety of folded proteins.
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Affiliation(s)
- Yu-Chun Lin
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX 78712-1224
| | - Pengyu Ren
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX 78712-1224
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX 78712-1224
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7
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A two-directional vibrational probe reveals different electric field orientations in solution and an enzyme active site. Nat Chem 2022; 14:891-897. [PMID: 35513508 PMCID: PMC10082611 DOI: 10.1038/s41557-022-00937-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/25/2022] [Indexed: 12/26/2022]
Abstract
The catalytic power of an electric field depends on its magnitude and orientation with respect to the reactive chemical species. Understanding and designing new catalysts for electrostatic catalysis thus requires methods to measure the electric field orientation and magnitude at the molecular scale. We demonstrate that electric field orientations can be extracted using a two-directional vibrational probe by exploiting the vibrational Stark effect of both the C=O and C-D stretches of a deuterated aldehyde. Combining spectroscopy with molecular dynamics and electronic structure partitioning methods, we demonstrate that, despite distinct polarities, solvents act similarly in their preference for electrostatically stabilizing large bond dipoles at the expense of destabilizing small ones. In contrast, we find that for an active-site aldehyde inhibitor of liver alcohol dehydrogenase, the electric field orientation deviates markedly from that found in solvents, which provides direct evidence for the fundamental difference between the electrostatic environment of solvents and that of a preorganized enzyme active site.
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8
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Weaver JB, Kozuch J, Kirsh JM, Boxer SG. Nitrile Infrared Intensities Characterize Electric Fields and Hydrogen Bonding in Protic, Aprotic, and Protein Environments. J Am Chem Soc 2022; 144:7562-7567. [PMID: 35467853 PMCID: PMC10082610 DOI: 10.1021/jacs.2c00675] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitriles are widely used vibrational probes; however, the interpretation of their IR frequencies is complicated by hydrogen bonding (H-bonding) in protic environments. We report a new vibrational Stark effect (VSE) that correlates the electric field projected on the -C≡N bond to the transition dipole moment and, by extension, the nitrile peak area or integrated intensity. This linear VSE applies to both H-bonding and non-H-bonding interactions. It can therefore be generally applied to determine electric fields in all environments. Additionally, it allows for semiempirical extraction of the H-bonding contribution to the blueshift of the nitrile frequency. Nitriles were incorporated at H-bonding and non-H-bonding protein sites using amber suppression, and each nitrile variant was structurally characterized at high resolution. We exploited the combined information available from variations in frequency and integrated intensity and demonstrate that nitriles are a generally useful probe for electric fields.
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Affiliation(s)
- Jared Bryce Weaver
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Jacek Kozuch
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Jacob M Kirsh
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
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Schneider S, Kozuch J, Boxer SG. The Interplay of Electrostatics and Chemical Positioning in the Evolution of Antibiotic Resistance in TEM β-Lactamases. ACS CENTRAL SCIENCE 2021; 7:1996-2008. [PMID: 34963893 PMCID: PMC8704030 DOI: 10.1021/acscentsci.1c00880] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Indexed: 05/25/2023]
Abstract
The interplay of enzyme active site electrostatics and chemical positioning is important for understanding the origin(s) of enzyme catalysis and the design of novel catalysts. We reconstruct the evolutionary trajectory of TEM-1 β-lactamase to TEM-52 toward extended-spectrum activity to better understand the emergence of antibiotic resistance and to provide insights into the structure-function paradigm and noncovalent interactions involved in catalysis. Utilizing a detailed kinetic analysis and the vibrational Stark effect, we quantify the changes in rates and electric fields in the Michaelis and acyl-enzyme complexes for penicillin G and cefotaxime to ascertain the evolutionary role of electric fields to modulate function. These data are combined with MD simulations to interpret and quantify the substrate-dependent structural changes during evolution. We observe that this evolutionary trajectory utilizes a large preorganized electric field and substrate-dependent chemical positioning to facilitate catalysis. This governs the evolvability, substrate promiscuity, and protein fitness landscape in TEM β-lactamase antibiotic resistance.
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Affiliation(s)
| | | | - Steven G. Boxer
- Chemistry Department, Stanford University, Stanford, California 94305, United States
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10
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Matyushov DV. Ewald sum corrections in simulations of ion and dipole solvation and electron transfer. J Chem Phys 2021; 155:114110. [PMID: 34551535 DOI: 10.1063/5.0061644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Periodic boundary conditions and Ewald sums used in standard simulation protocols require finite-size corrections when the total charge of the simulated system is nonzero. Corrections for ion solvation were introduced by Hummer, Pratt, and García, [J. Chem. Phys. 107, 9275 (1997)]. The latter approach is extended here to derive finite-size correction for the Stokes-shift and reorganization energy applied to electron-transfer reactions. The same correction term, scaling inversely with the box size, adds to the reorganization energy from the energy-gap variance but is subtracted from the reorganization energy calculated from the Stokes shift. Finite-size corrections thus widen the gap between these two quantities, which were recently found to diverge for protein electron transfer. Corrections to the free energy of dipole solvation and the variance of the electric field scale as m2/L3 with the solute dipole m and the box size L.
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Affiliation(s)
- Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, USA
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