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Pérez-Mora S, Pérez-Ishiwara DG, Salgado-Hernández SV, Medel-Flores MO, Reyes-López CA, Rodríguez MA, Sánchez-Monroy V, Gómez-García MDC. Entamoeba histolytica: In Silico and In Vitro Oligomerization of EhHSTF5 Enhances Its Binding to the HSE of the EhPgp5 Gene Promoter. Int J Mol Sci 2024; 25:4218. [PMID: 38673804 PMCID: PMC11050682 DOI: 10.3390/ijms25084218] [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: 03/08/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Throughout its lifecycle, Entamoeba histolytica encounters a variety of stressful conditions. This parasite possesses Heat Shock Response Elements (HSEs) which are crucial for regulating the expression of various genes, aiding in its adaptation and survival. These HSEs are regulated by Heat Shock Transcription Factors (EhHSTFs). Our research has identified seven such factors in the parasite, designated as EhHSTF1 through to EhHSTF7. Significantly, under heat shock conditions and in the presence of the antiamoebic compound emetine, EhHSTF5, EhHSTF6, and EhHSTF7 show overexpression, highlighting their essential role in gene response to these stressors. Currently, only EhHSTF7 has been confirmed to recognize the HSE as a promoter of the EhPgp5 gene (HSE_EhPgp5), leaving the binding potential of the other EhHSTFs to HSEs yet to be explored. Consequently, our study aimed to examine, both in vitro and in silico, the oligomerization, and binding capabilities of the recombinant EhHSTF5 protein (rEhHSTF5) to HSE_EhPgp5. The in vitro results indicate that the oligomerization of rEhHSTF5 is concentration-dependent, with its dimeric conformation showing a higher affinity for HSE_EhPgp5 than its monomeric state. In silico analysis suggests that the alpha 3 α-helix (α3-helix) of the DNA-binding domain (DBD5) of EhHSTF5 is crucial in binding to the major groove of HSE, primarily through hydrogen bonding and salt-bridge interactions. In summary, our results highlight the importance of oligomerization in enhancing the affinity of rEhHSTF5 for HSE_EhPgp5 and demonstrate its ability to specifically recognize structural motifs within HSE_EhPgp5. These insights significantly contribute to our understanding of one of the potential molecular mechanisms employed by this parasite to efficiently respond to various stressors, thereby enabling successful adaptation and survival within its host environment.
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Affiliation(s)
- Salvador Pérez-Mora
- Laboratorio de Biomedicina Molecular 1, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (S.P.-M.); (D.G.P.-I.); (S.V.S.-H.); (M.O.M.-F.)
| | - David Guillermo Pérez-Ishiwara
- Laboratorio de Biomedicina Molecular 1, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (S.P.-M.); (D.G.P.-I.); (S.V.S.-H.); (M.O.M.-F.)
| | - Sandra Viridiana Salgado-Hernández
- Laboratorio de Biomedicina Molecular 1, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (S.P.-M.); (D.G.P.-I.); (S.V.S.-H.); (M.O.M.-F.)
| | - María Olivia Medel-Flores
- Laboratorio de Biomedicina Molecular 1, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (S.P.-M.); (D.G.P.-I.); (S.V.S.-H.); (M.O.M.-F.)
| | - César Augusto Reyes-López
- Laboratorio de Bioquímica Estructural, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico;
| | - Mario Alberto Rodríguez
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), Mexico City 07360, Mexico;
| | - Virginia Sánchez-Monroy
- Sección de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - María del Consuelo Gómez-García
- Laboratorio de Biomedicina Molecular 1, Escuela Nacional de Medicina y Homeopatía, Instituto Politécnico Nacional, Mexico City 07320, Mexico; (S.P.-M.); (D.G.P.-I.); (S.V.S.-H.); (M.O.M.-F.)
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Makki H, Burke CA, Troisi A. Microstructural Model of Indacenodithiophene- co-benzothiadiazole Polymer: π-Crossing Interactions and Their Potential Impact on Charge Transport. J Phys Chem Lett 2023; 14:8867-8873. [PMID: 37756473 PMCID: PMC10561260 DOI: 10.1021/acs.jpclett.3c02305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023]
Abstract
Morphological and electronic properties of indacenodithiophene-co-benzothiadiazole (IDTBT) copolymer with varying molecular weights are calculated through combined molecular dynamics (MD) and quantum chemical (QC) methods. Our study focuses on the polymer chain arrangements, interchain connectivity pathways, and interplay between morphological and electronic structure properties of IDTBT. Our models, which are verified against GIWAXS measurements, show a considerable number of BT-BT π-π interactions with a (preferential) perpendicular local orientation of polymer chains due to the steric hindrance of bulky side chains around IDT. Although our models predict a noncrystalline structure for IDTBT, the BT-BT (interchain) crossing points show a considerable degree of short-range order in spatial arrangement which most likely result in a mesh-like structure for the polymer and provide efficient pathways for interchain charge transport.
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Affiliation(s)
- Hesam Makki
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Liverpool L69 7ZD, U.K.
| | - Colm A. Burke
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Liverpool L69 7ZD, U.K.
| | - Alessandro Troisi
- Department
of Chemistry and Materials Innovation Factory, University of Liverpool, Liverpool L69 7ZD, U.K.
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Bhat V, Callaway CP, Risko C. Computational Approaches for Organic Semiconductors: From Chemical and Physical Understanding to Predicting New Materials. Chem Rev 2023. [PMID: 37141497 DOI: 10.1021/acs.chemrev.2c00704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
While a complete understanding of organic semiconductor (OSC) design principles remains elusive, computational methods─ranging from techniques based in classical and quantum mechanics to more recent data-enabled models─can complement experimental observations and provide deep physicochemical insights into OSC structure-processing-property relationships, offering new capabilities for in silico OSC discovery and design. In this Review, we trace the evolution of these computational methods and their application to OSCs, beginning with early quantum-chemical methods to investigate resonance in benzene and building to recent machine-learning (ML) techniques and their application to ever more sophisticated OSC scientific and engineering challenges. Along the way, we highlight the limitations of the methods and how sophisticated physical and mathematical frameworks have been created to overcome those limitations. We illustrate applications of these methods to a range of specific challenges in OSCs derived from π-conjugated polymers and molecules, including predicting charge-carrier transport, modeling chain conformations and bulk morphology, estimating thermomechanical properties, and describing phonons and thermal transport, to name a few. Through these examples, we demonstrate how advances in computational methods accelerate the deployment of OSCsin wide-ranging technologies, such as organic photovoltaics (OPVs), organic light-emitting diodes (OLEDs), organic thermoelectrics, organic batteries, and organic (bio)sensors. We conclude by providing an outlook for the future development of computational techniques to discover and assess the properties of high-performing OSCs with greater accuracy.
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Affiliation(s)
- Vinayak Bhat
- Department of Chemistry & Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Connor P Callaway
- Department of Chemistry & Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506-0055, United States
| | - Chad Risko
- Department of Chemistry & Center for Applied Energy Research, University of Kentucky, Lexington, Kentucky 40506-0055, United States
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Makki H, Troisi A. Morphology of conducting polymer blends at the interface of conducting and insulating phases: insight from PEDOT:PSS atomistic simulations. JOURNAL OF MATERIALS CHEMISTRY. C 2022; 10:16126-16137. [PMID: 36387833 PMCID: PMC9632246 DOI: 10.1039/d2tc03158b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/30/2022] [Indexed: 06/12/2023]
Abstract
Having phase-separated conductive and less-conductive domains is a common morphology in semiconducting polymer blends as it exists in the case of PEDOT:PSS, which is a representative example with a wide range of applications. In this paper, we constructed atomistic models for the interface between the PEDOT-rich (conductive) grains and the PSS-rich (less-conductive) phase through molecular dynamics simulations. Our models are obtained from experimentally relevant compositions, based on precise force field parameters, and through a robust relaxation procedure. We show that both PEDOT-rich and PSS-rich phases consist of PEDOT lamellae embedded in PSS chains. The size of these lamellae depends on the PEDOT concentration in each phase and our model predictions are in quantitative agreement with the experimental data. Furthermore, our models suggest that neither the phases nor the interfaces are entirely connected by π-π stacking. Thus, inter-lamellae tunnelling is essential for both intra- and inter-grain charge transport. We also show that a small increase (≈8 wt%) in the PEDOT concentration results in rather larger lamellae sizes, considerably more oriented lamellae, and slightly better inter-lamellae connectivity, which result in enhanced intra-grain conductivity. Moreover, we show how enhancing phase separation between PEDOT-rich and PSS-rich domains (similar to the effect of polar co-solvents), i.e., pulling out PEDOT from the PSS-rich phase and adding it in the PEDOT-rich phase, highly enhances the intra-grain connectivity but decreases the inter-grain conduction paths through the interface. Our results explain how the marginal extra degree of phase separation (based on experimentally obtained values) could result in a great enhancement in the overall film conductivity.
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Affiliation(s)
- Hesam Makki
- Department of Chemistry, University of Liverpool Liverpool L69 3BX UK
| | - Alessandro Troisi
- Department of Chemistry, University of Liverpool Liverpool L69 3BX UK
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Ziolek RM, Santana-Bonilla A, López-Ríos de Castro R, Kühn R, Green M, Lorenz CD. Conformational Heterogeneity and Interchain Percolation Revealed in an Amorphous Conjugated Polymer. ACS NANO 2022; 16:14432-14442. [PMID: 36103148 PMCID: PMC9527807 DOI: 10.1021/acsnano.2c04794] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Conjugated polymers are employed in a variety of application areas due to their bright fluorescence and strong biocompatibility. However, understanding the structure of amorphous conjugated polymers on the nanoscale is extremely challenging compared to their related crystalline phases. Using a bespoke classical force field, we study amorphous poly(9,9-di-n-octylfluorene-alt-benzothiadiazole) (F8BT) with molecular dynamics simulations to investigate the role that its nanoscale structure plays in controlling its emergent (and all-important) optical properties. Notably, we show that a giant percolating cluster exists within amorphous F8BT, which has ramifications in understanding the nature of interchain species that drive the quantum yield reduction and bathochromic shift observed in conjugated polymer-based devices and nanostructures. We also show that distinct conformations can be unravelled from within the disordered structure of amorphous F8BT using a two-stage machine learning protocol, highlighting a link between molecular conformation and ring stacking propensity. This work provides predictive understanding by which to enhance the optical properties of next-generation conjugated polymer-based devices and materials by rational, simulation-led design principles.
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Affiliation(s)
- Robert M. Ziolek
- Biological
Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, United Kingdom
| | | | - Raquel López-Ríos de Castro
- Biological
Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, United Kingdom
- Department
of Chemistry, King’s College London, London, SE1 1DB, United Kingdom
| | - Reimer Kühn
- Department
of Mathematics, King’s College London, London WC2R 2LS, United Kingdom
| | - Mark Green
- Photonics
and Nanotechnology Group, Department of Physics, King’s College London, London WC2R 2LS, United
Kingdom
| | - Christian D. Lorenz
- Biological
Physics and Soft Matter Group, Department of Physics, King’s College London, London WC2R 2LS, United Kingdom
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Reisjalali M, Manurung R, Carbone P, Troisi A. Development of hybrid coarse-grained atomistic models for rapid assessment of local structuring of polymeric semiconductors. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2022; 7:294-305. [PMID: 35646391 PMCID: PMC9074845 DOI: 10.1039/d1me00165e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/06/2022] [Indexed: 05/05/2023]
Abstract
Decades of work in the field of computational study of semiconducting polymers using atomistic models illustrate the challenges of generating equilibrated models for this class of materials. While adopting a coarse-grained model can be helpful, the process of developing a suitable model is particularly non-trivial and time-consuming for semiconducting polymers due to a large number of different interactions with some having an anisotropic nature. This work introduces a procedure for the rapid generation of a hybrid model for semiconducting polymers where atoms of secondary importance (those in the alkyl side chains) are transformed into coarse-grained beads to reduce the computational cost of generating an equilibrated structure. The parameters are determined from easy-to-equilibrate simulations of very short oligomers and the model is constructed to enable a very simple back-mapping procedure to reconstruct geometries with atomistic resolution. The model is illustrated for three related polymers containing DPP (diketopyrrolopyrrole) to evaluate the transferability of the potential across different families of polymers. The accuracy of the model, determined by comparison with the results of fully equilibrated simulations of the same material before and after back-mapping, is fully satisfactory for two out of the three cases considered. We noticed that accuracy can be determined very early in the workflow so that it is easy to assess when the deployment of this method is advantageous. The hybrid representation can be used to evaluate directly the electronic properties of structures sampled by the simulations.
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Affiliation(s)
- Maryam Reisjalali
- Department of Chemistry, University of Liverpool Crown St L69 7ZD Liverpool UK
| | - Rex Manurung
- Department of Chemistry, University of Liverpool Crown St L69 7ZD Liverpool UK
| | - Paola Carbone
- Department of Chemical Engineering and Analytical Science Oxford Road M13 9PL Manchester UK
| | - Alessandro Troisi
- Department of Chemistry, University of Liverpool Crown St L69 7ZD Liverpool UK
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Dilmurat R, Prodhan S, Wang L, Beljonne D. Thermally activated intra-chain charge transport in high charge-carrier mobility copolymers. J Chem Phys 2022; 156:084115. [DOI: 10.1063/5.0082569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Disordered or even seemingly amorphous, donor–acceptor type, conjugated copolymers with high charge-carrier mobility have emerged as a new class of functional materials, where transport along the conjugated backbone is key. Here, we report on non-adiabatic molecular dynamics simulations of charge-carrier transport along chains of poly (indacenodithiophene-co-benzothiadiazole), within a model Hamiltonian parameterized against first-principles calculations. We predict thermally activated charge transport associated with a slightly twisted ground-state conformation, on par with experimental results. Our results also demonstrate that the energy mismatch between the hole on the donor vs the acceptor units of the copolymer drives localization of the charge carriers and limits the intra-chain charge-carrier mobility. We predict that room-temperature mobility values in excess of 10 cm2 V−1 s−1 can be achieved through proper chemical tuning of the component monomer units.
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Affiliation(s)
- Rishat Dilmurat
- Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc, 20, 7000 Mons, Belgium
| | - Suryoday Prodhan
- Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc, 20, 7000 Mons, Belgium
| | - Linjun Wang
- Key Laboratory of Excited-State Materials of Zhejiang Province, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - David Beljonne
- Laboratory for Chemistry of Novel Materials, University of Mons, Place du Parc, 20, 7000 Mons, Belgium
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