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Pieri E, Weingart O, Huix-Rotllant M, Ledentu V, Garavelli M, Ferré N. Modeling pH-Dependent Biomolecular Photochemistry. J Chem Theory Comput 2024; 20:842-855. [PMID: 38198619 DOI: 10.1021/acs.jctc.3c00980] [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: 01/12/2024]
Abstract
The tuning mechanism of pH can be extremely challenging to model computationally in complex biological systems, especially with respect to the photochemical properties. This article reports a protocol aimed at modeling pH-dependent photodynamics using a combination of constant-pH molecular dynamics and semiclassical nonadiabatic molecular dynamics simulations. With retinal photoisomerization in Anabaena sensory rhodopsin (ASR) as a testbed, we show that our protocol produces pH-dependent photochemical properties, such as the isomerization quantum yield or decay rates. We decompose our results into single-titrated residue contributions, identifying some key tuning amino acids. Additionally, we assess the validity of the single protonation state picture to represent the system at a given pH and propose the most populated protein charge state as a compromise between cost and accuracy.
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Affiliation(s)
- Elisa Pieri
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Oliver Weingart
- Faculty of Mathematics and Natural Sciences, Institute for Theoretical and Computational Chemistry, Heinrich Heine University, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Miquel Huix-Rotllant
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Vincent Ledentu
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
| | - Marco Garavelli
- Dipartimento di Chimica Industriale "Toso Montanari", Università degli Studi di Bologna, Viale del Risorgimento, 4, 40136 Bologna, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, Institut de Chimie Radicalaire, 13013 Marseille, France
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Cárdenas G, Ledentu V, Huix-Rotllant M, Olivucci M, Ferré N. Automatic Rhodopsin Modeling with Multiple Protonation Microstates. J Phys Chem A 2023; 127:9365-9380. [PMID: 37877699 DOI: 10.1021/acs.jpca.3c05413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Automatic Rhodopsin Modeling (ARM) is a simulation protocol providing QM/MM models of rhodopsins capable of reproducing experimental electronic absorption and emission trends. Currently, ARM is restricted to a single protonation microstate for each rhodopsin model. Herein, we incorporate an extension of the minimal electrostatic model (MEM) into the ARM protocol to account for all relevant protonation microstates at a given pH. The new ARM+MEM protocol determines the most important microstates contributing to the description of the absorption spectrum. As a test case, we have applied this methodology to simulate the pH-dependent absorption spectrum of a toy model, showing that the single-microstate picture breaks down at certain pH values. Subsequently, we applied ARM+MEM toAnabaenasensory rhodopsin, confirming an improved description of its absorption spectrum when the titration of several key residues is considered.
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Affiliation(s)
| | | | | | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, 53100 Siena, Italy
| | - Nicolas Ferré
- Aix-Marseille Univ, CNRS, ICR, 13013 Marseille, France
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Maity A, Kumar A. Higher-order assembly of BSA gold nanoclusters using supramolecular host-guest chemistry: a 40% absolute fluorescence quantum yield. NANOSCALE ADVANCES 2022; 4:2988-2991. [PMID: 36133515 PMCID: PMC9417410 DOI: 10.1039/d2na00123c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/31/2022] [Indexed: 06/02/2023]
Abstract
Herein, we report for the first time a highly emissive higher-order assembled structure of BSA-Au NCs in the presence of cucurbit[7]uril, which enhances the absolute fluorescence quantum yield of BSA-Au NCs up to 40%. Cucurbit[7]uril neutralizes the surface charge of BSA-Au NCs, and hence aggregation happens. This aggregation shows reversible disaggregation in the presence of adamantylamine.
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Affiliation(s)
- Anjan Maity
- Materials Research Centre, Indian Institute of Science Bangalore 560012 India
| | - Atul Kumar
- Department of Inorganic and Physical Chemistry, Indian Institute of Science Bangalore 560012 India
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de Almeida Barbosa NM, Gosset P, Réal E, Ledentu V, Didier P, Ferré N. pH-Dependent absorption spectrum of oxyluciferin analogues in the active site of firefly luciferase. Phys Chem Chem Phys 2020; 22:21731-21740. [PMID: 32985625 DOI: 10.1039/d0cp02514c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the quest for the identification of the light emitter(s) responsible for the firefly bioluminescence, the study of oxyluciferin analogues with controlled chemical and electronic structures is of particular importance. In this article, we report the results of our experimental and computational investigation of the pH-dependent absorption spectra characterizing three analogues bound into the luciferase cavity, together with adenosine-monophosphate (AMP). While the analogue microscopic pKa values do not differ much from their reference values, it turns out that the AMP protonation state is analogue-dependent and never doubly-deprotonated. A careful analysis of the interactions evidences the main role of E344 glutamic acid, as well as the flexibility of the cavity which can accommodate any oxyluciferin analogue. The consideration of the absorption spectra suggests that the oxyluciferin enolate form has to be excluded from the list of the bioluminescence reaction products.
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Affiliation(s)
| | - Pauline Gosset
- Université de Strasbourg, UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Strasbourg, France
| | - Eléonore Réal
- Université de Strasbourg, UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Strasbourg, France
| | | | - Pascal Didier
- Université de Strasbourg, UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Strasbourg, France
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Pieri E, Ledentu V, Sahlin M, Dehez F, Olivucci M, Ferré N. CpHMD-Then-QM/MM Identification of the Amino Acids Responsible for the Anabaena Sensory Rhodopsin pH-Dependent Electronic Absorption Spectrum. J Chem Theory Comput 2019; 15:4535-4546. [PMID: 31264415 DOI: 10.1021/acs.jctc.9b00221] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Anabaena Sensory Rhodopsin (ASR), a microbial photoactive protein featuring the retinal chromophore in two different conformations, exhibits a pH-dependent electronic absorption spectrum. Using the recently developed CpHMD-then-QM/MM multiscale protocol applied to ASR embedded in a membrane model, the pH-induced changes in its maximum absorption wavelength have been reproduced and analyzed. While the acidic tiny red-shift is essentially correlated with the deprotonation of an aspartic acid located on the ASR extracellular side, the larger blue-shift experimentally reported at pH values larger than 5 involves a cluster of titrating residues sitting on the cytoplasmic side. The ASR pH-dependent spectrum is the consequence of the competitive stabilization of retinal ground and excited states by the protein electrostatic potential.
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Affiliation(s)
- Elisa Pieri
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | | | - Michael Sahlin
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
| | - François Dehez
- Laboratoire de Physique et Chimie Théorique , UMR 7019, Faculté des Sciences et Technique , Campus Aiguillettes , 54506 Vandoeuvre-les-Nancy , France
| | - Massimo Olivucci
- Department of Chemistry , Bowling Green State University , Bowling Green , Ohio 43403 , United States.,Dipartimento di Biotecnologie, Chimica e Farmacia , Università degli Studi di Siena , via A. Moro 2 , 53100 Siena , Italy
| | - Nicolas Ferré
- Aix-Marseille Univ , CNRS, ICR , 13013 Marseille , France
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Collette F, Renger T, Müh F, Schmidt am Busch M. Red/Green Color Tuning of Visual Rhodopsins: Electrostatic Theory Provides a Quantitative Explanation. J Phys Chem B 2018; 122:4828-4837. [DOI: 10.1021/acs.jpcb.8b02702] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Florimond Collette
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Marcel Schmidt am Busch
- Institut für Theoretische Physik, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
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