1
|
Fu X, Diao W, Luo Y, Liu Y, Wang Z. Theoretical Insight into the Fluorescence Spectral Tuning Mechanism: A Case Study of Flavin-Dependent Bacterial Luciferase. J Chem Theory Comput 2024; 20:8652-8664. [PMID: 39298275 DOI: 10.1021/acs.jctc.4c00950] [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: 09/21/2024]
Abstract
Bioluminescence of bacteria is widely applied in biological imaging, environmental toxicant detection, and many other situations. Understanding the spectral tuning mechanism not only helps explain the diversity of colors observed in nature but also provides principles for bioengineering new color variants for practical applications. In this study, time-dependent density functional theory (TD-DFT) and quantum mechanics and molecular mechanics (QM/MM) calculations have been employed to understand the fluorescence spectral tuning mechanism of bacterial luciferase with a focus on the electrostatic effect. The spectrum can be tuned by both a homogeneous dielectric environment and oriented external electric fields (OEEFs). Increasing the solvent polarity leads to a redshift of the fluorescence emission maximum, λF, accompanied by a substantial increase in density. In contrast, applying an OEEF along the long axis of the isoalloxazine ring (X-axis) leads to a significant red- or blue-shift in λF, depending on the direction of the OEEF, yet with much smaller changes in intensity. The effect of polar solvents is directionless, and the red-shifts can be attributed to the larger dipole moment of the S1 state compared with that of the S0 state. However, the effect of OEEFs directly correlates with the difference dipole moment between the S1 and S0 states, which is directional and is determined by the charge redistribution upon deexcitation. Moreover, the electrostatic effect of bacterial luciferase is in line with the presence of an internal electric field (IEF) pointing in the negative X direction. Finally, the key residues that contribute to this IEF and strategies for modulating the spectrum through site-directed point mutations are discussed.
Collapse
Affiliation(s)
- Xiaodi Fu
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| | - Wenwen Diao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Wenzhou 325000, China
| | - Yanling Luo
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Yajun Liu
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Zhanfeng Wang
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
| |
Collapse
|
2
|
Lamm GHU, Zabelskii D, Balandin T, Gordeliy V, Wachtveitl J. Calcium-Sensitive Microbial Rhodopsin VirChR1: A Femtosecond to Second Photocycle Study. J Phys Chem Lett 2024; 15:5510-5516. [PMID: 38749015 DOI: 10.1021/acs.jpclett.4c00693] [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: 05/24/2024]
Abstract
Viral rhodopsins are light-gated cation channels representing a novel class of microbial rhodopsins. For viral rhodopsin 1 subfamily members VirChR1 and OLPVR1, channel activity is abolished above a certain calcium concentration. Here we present a calcium-dependent spectroscopic analysis of VirChR1 on the femtosecond to second time scale. Unlike channelrhodopsin-2, VirChR1 possesses two intermediate states P1 and P2 on the ultrafast time scale, similar to J and K in ion-pumping rhodopsins. Subsequently, we observe multifaceted photocycle kinetics with up to seven intermediate states. Calcium predominantly affects the last photocycle steps, including the appearance of additional intermediates P6Ca and P7 representing the blocked channel. Furthermore, the photocycle of the counterion variant D80N is drastically altered, yielding intermediates with different spectra and kinetics compared to those of the wt. These findings demonstrate the central role of the counterion within the defined reaction sequence of microbial rhodopsins that ultimately defines the protein function.
Collapse
Affiliation(s)
- Gerrit H U Lamm
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | | | - Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Valentin Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, 52428 Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, 52428 Jülich, Germany
- University Grenoble Alpes, CEA, CNRS, Institute de Biologie Structurale (IBS), 38000 Grenoble, France
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| |
Collapse
|
3
|
Li Y, Yang B, Wang Y, Huang Z, Wang J, Pu X, Wen J, Ao Q, Xiao K, Wu J, Yin G. Postoperatively Noninvasive Optogenetic Stimulation via Upconversion Nanoparticles Enhancing Sciatic Nerve Repair. NANO LETTERS 2024; 24:5403-5412. [PMID: 38669639 DOI: 10.1021/acs.nanolett.3c04619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The efficacy of electrical stimulation facilitating peripheral nerve regeneration is evidenced extensively, while the associated secondary damage resulting from repeated electrode invasion and indiscriminate stimulation is inevitable. Here, we present an optogenetics strategy that utilizes upconversion nanoparticles (UCNPs) to convert deeply penetrating near-infrared excitation into blue emission, which activates an adeno-associated virus-encoding ChR2 photoresponsive ion channel on cell membranes. The induced Ca2+ flux, similar to the ion flux in the electrical stimulation approach, efficiently regulates viability and proliferation, secretion of nerve growth factor, and neural function of RSC96 cells. Furthermore, deep near-infrared excitation is harnessed to stimulate autologous Schwann cells in situ via a UCNP-composited scaffold, which enhances nerve sprouting and myelination, consequently promoting functional recovery, electrophysiological restoration, and reinnervation of damaged nerves. This developed postoperatively noninvasive optogenetics strategy presents a novel, minimally traumatic, and enduring therapeutic stimulus to effectively promote peripheral nerve repair.
Collapse
Affiliation(s)
- Ya Li
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
- Institute of Regulatory Science for Medical Devices, Sichuan University, Chengdu 610065, China
| | - Bing Yang
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
- Precision Medicine Research Center of West China Hospital, Sichuan University, Chengdu 610093, China
| | - Yulin Wang
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
- Institute of Regulatory Science for Medical Devices, Sichuan University, Chengdu 610065, China
| | - Zhongbing Huang
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Juan Wang
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Ximing Pu
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| | - Jirui Wen
- Department of Otolaryngology Head and Neck Surgery/Deep Underground Space Medical Center West China Hospital, Sichuan University, No. 37 Guoxuexiang, Chengdu 610041, China
| | - Qiang Ao
- Institute of Regulatory Science for Medical Devices, Sichuan University, Chengdu 610065, China
| | - Kai Xiao
- Precision Medicine Research Center of West China Hospital, Sichuan University, Chengdu 610093, China
| | - Jiang Wu
- Department of Otolaryngology Head and Neck Surgery/Deep Underground Space Medical Center West China Hospital, Sichuan University, No. 37 Guoxuexiang, Chengdu 610041, China
| | - Guangfu Yin
- College of Biomedical Engineering, Sichuan University, Chengdu 610065, China
| |
Collapse
|
4
|
Lee IS, Filatov M, Min SK. Formulation of transition dipole gradients for non-adiabatic dynamics with polaritonic states. J Chem Phys 2024; 160:154103. [PMID: 38624116 DOI: 10.1063/5.0202095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/31/2024] [Indexed: 04/17/2024] Open
Abstract
A general formulation of the strong coupling between photons confined in a cavity and molecular electronic states is developed for the state-interaction state-average spin-restricted ensemble-referenced Kohn-Sham method. The light-matter interaction is included in the Jaynes-Cummings model, which requires the derivation and implementation of the analytical derivatives of the transition dipole moments between the molecular electronic states. The developed formalism is tested in the simulations of the nonadiabatic dynamics in the polaritonic states resulting from the strong coupling between the cavity photon mode and the ground and excited states of the penta-2,4-dieniminium cation, also known as PSB3. Comparison with the field-free simulations of the excited-state decay dynamics in PSB3 reveals that the light-matter coupling can considerably alter the decay dynamics by increasing the excited state lifetime and hindering photochemically induced torsion about the C=C double bonds of PSB3. The necessity of obtaining analytical transition dipole gradients for the accurate propagation of the dynamics is underlined.
Collapse
Affiliation(s)
- In Seong Lee
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Michael Filatov
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
| | - Seung Kyu Min
- Center for Multidimensional Carbon Materials (CMCM), Institute for Basic Science (IBS), Ulsan 44919, Republic of Korea
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), 50 UNIST-gil, Ulju-gun, Ulsan 44919, Republic of Korea
| |
Collapse
|
5
|
Malakar P, Gholami S, Aarabi M, Rivalta I, Sheves M, Garavelli M, Ruhman S. Retinal photoisomerization versus counterion protonation in light and dark-adapted bacteriorhodopsin and its primary photoproduct. Nat Commun 2024; 15:2136. [PMID: 38459010 PMCID: PMC10923925 DOI: 10.1038/s41467-024-46061-w] [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: 09/20/2023] [Accepted: 02/08/2024] [Indexed: 03/10/2024] Open
Abstract
Discovered over 50 years ago, bacteriorhodopsin is the first recognized and most widely studied microbial retinal protein. Serving as a light-activated proton pump, it represents the archetypal ion-pumping system. Here we compare the photochemical dynamics of bacteriorhodopsin light and dark-adapted forms with that of the first metastable photocycle intermediate known as "K". We observe that following thermal double isomerization of retinal in the dark from bio-active all-trans 15-anti to 13-cis, 15-syn, photochemistry proceeds even faster than the ~0.5 ps decay of the former, exhibiting ballistic wave packet curve crossing to the ground state. In contrast, photoexcitation of K containing a 13-cis, 15-anti chromophore leads to markedly multi-exponential excited state decay including much slower stages. QM/MM calculations, aimed to interpret these results, highlight the crucial role of protonation, showing that the classic quadrupole counterion model poorly reproduces spectral data and dynamics. Single protonation of ASP212 rectifies discrepancies and predicts triple ground state structural heterogeneity aligning with experimental observations. These findings prompt a reevaluation of counter ion protonation in bacteriorhodopsin and contribute to the broader understanding of its photochemical dynamics.
Collapse
Affiliation(s)
- Partha Malakar
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Samira Gholami
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Mohammad Aarabi
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
| | - Ivan Rivalta
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, 46 allée d'Italie, 69364, Lyon, France
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, The Weizmann Institute of Science, Rehovot, 7610001, Israel.
| | - Marco Garavelli
- Dipartimento di Chimica industriale "Toso Montanari", Università di Bologna, Viale del Risorgimento 4, 40136, Bologna, Italy.
| | - Sanford Ruhman
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
| |
Collapse
|
6
|
Salvadori G, Mazzeo P, Accomasso D, Cupellini L, Mennucci B. Deciphering Photoreceptors Through Atomistic Modeling from Light Absorption to Conformational Response. J Mol Biol 2024; 436:168358. [PMID: 37944793 DOI: 10.1016/j.jmb.2023.168358] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/28/2023] [Accepted: 11/02/2023] [Indexed: 11/12/2023]
Abstract
In this review, we discuss the successes and challenges of the atomistic modeling of photoreceptors. Throughout our presentation, we integrate explanations of the primary methodological approaches, ranging from quantum mechanical descriptions to classical enhanced sampling methods, all while providing illustrative examples of their practical application to specific systems. To enhance the effectiveness of our analysis, our primary focus has been directed towards the examination of applications across three distinct photoreceptors. These include an example of Blue Light-Using Flavin (BLUF) domains, a bacteriophytochrome, and the orange carotenoid protein (OCP) employed by cyanobacteria for photoprotection. Particular emphasis will be placed on the pivotal role played by the protein matrix in fine-tuning the initial photochemical event within the embedded chromophore. Furthermore, we will investigate how this localized perturbation initiates a cascade of events propagating from the binding pocket throughout the entire protein structure, thanks to the intricate network of interactions between the chromophore and the protein.
Collapse
Affiliation(s)
- Giacomo Salvadori
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Patrizia Mazzeo
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Davide Accomasso
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Lorenzo Cupellini
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Benedetta Mennucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| |
Collapse
|
7
|
Singh NK, Ramamourthy B, Hage N, Kappagantu KM. Optogenetics: Illuminating the Future of Hearing Restoration and Understanding Auditory Perception. Curr Gene Ther 2024; 24:208-216. [PMID: 38676313 DOI: 10.2174/0115665232269742231213110937] [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: 06/29/2023] [Revised: 10/07/2023] [Accepted: 10/25/2023] [Indexed: 04/28/2024]
Abstract
Hearing loss is a prevalent sensory impairment significantly affecting communication and quality of life. Traditional approaches for hearing restoration, such as cochlear implants, have limitations in frequency resolution and spatial selectivity. Optogenetics, an emerging field utilizing light-sensitive proteins, offers a promising avenue for addressing these limitations and revolutionizing hearing rehabilitation. This review explores the methods of introducing Channelrhodopsin- 2 (ChR2), a key light-sensitive protein, into cochlear cells to enable optogenetic stimulation. Viral- mediated gene delivery is a widely employed technique in optogenetics. Selecting a suitable viral vector, such as adeno-associated viruses (AAV), is crucial in efficient gene delivery to cochlear cells. The ChR2 gene is inserted into the viral vector through molecular cloning techniques, and the resulting viral vector is introduced into cochlear cells via direct injection or round window membrane delivery. This allows for the expression of ChR2 and subsequent light sensitivity in targeted cells. Alternatively, direct cell transfection offers a non-viral approach for ChR2 delivery. The ChR2 gene is cloned into a plasmid vector, which is then combined with transfection agents like liposomes or nanoparticles. This mixture is applied to cochlear cells, facilitating the entry of the plasmid DNA into the target cells and enabling ChR2 expression. Optogenetic stimulation using ChR2 allows for precise and selective activation of specific neurons in response to light, potentially overcoming the limitations of current auditory prostheses. Moreover, optogenetics has broader implications in understanding the neural circuits involved in auditory processing and behavior. The combination of optogenetics and gene delivery techniques provides a promising avenue for improving hearing restoration strategies, offering the potential for enhanced frequency resolution, spatial selectivity, and improved auditory perception.
Collapse
Affiliation(s)
- Namit Kant Singh
- Department of Otorhinolaryngology and Head and Neck Surgery, All India institute of Medical Sciences, Bibinagar, Hyderabad, India
| | - Balaji Ramamourthy
- Department of Otorhinolaryngology and Head and Neck Surgery, All India institute of Medical Sciences, Bibinagar, Hyderabad, India
| | - Neemu Hage
- Department of Otorhinolaryngology and Head and Neck Surgery, All India institute of Medical Sciences, Bibinagar, Hyderabad, India
| | - Krishna Medha Kappagantu
- Department of Otorhinolaryngology and Head and Neck Surgery, All India institute of Medical Sciences, Bibinagar, Hyderabad, India
| |
Collapse
|
8
|
Costa GJ, Egbemhenghe A, Liang R. Computational Characterization of the Reactivity of Compound I in Unspecific Peroxygenases. J Phys Chem B 2023; 127:10987-10999. [PMID: 38096487 DOI: 10.1021/acs.jpcb.3c06311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Unspecific peroxygenases (UPOs) are emerging as promising biocatalysts for selective oxyfunctionalization of unactivated C-H bonds. However, their potential in large-scale synthesis is currently constrained by suboptimal chemical selectivity. Improving the selectivity of UPOs requires a deep understanding of the molecular basis of their catalysis. Recent molecular simulations have sought to unravel UPO's selectivity and inform their design principles. However, most of these studies focused on substrate-binding poses. Few researchers have investigated how the reactivity of CpdI, the principal oxidizing intermediate in the catalytic cycle, influences selectivity in a realistic protein environment. Moreover, the influence of protein electrostatics on the reaction kinetics of CpdI has also been largely overlooked. To bridge this gap, we used multiscale simulations to interpret the regio- and enantioselective hydroxylation of the n-heptane substrate catalyzed by Agrocybe aegerita UPO (AaeUPO). We comprehensively characterized the energetics and kinetics of the hydrogen atom-transfer (HAT) step, initiated by CpdI, and the subsequent oxygen rebound step forming the product. Notably, our approach involved both free energy and potential energy evaluations in a quantum mechanics/molecular mechanics (QM/MM) setting, mitigating the dependence of results on the choice of initial conditions. These calculations illuminate the thermodynamics and kinetics of the HAT and oxygen rebound steps. Our findings highlight that both the conformational selection and the distinct chemical reactivity of different substrate hydrogen atoms together dictate the regio- and enantio-selectivity. Building on our previous study of CpdI's formation in AaeUPO, our results indicate that the HAT step is the rate-limiting step in the overall catalytic cycle. The subsequent oxygen rebound step is swift and retains the selectivity determined by the HAT step. We also pinpointed several polar and charged amino acid residues whose electrostatic potentials considerably influence the reaction barrier of the HAT step. Notably, the Glu196 residue is pivotal for both the CpdI's formation and participation in the HAT step. Our research offers in-depth insights into the catalytic cycle of AaeUPO, which will be instrumental in the rational design of UPOs with enhanced properties.
Collapse
Affiliation(s)
- Gustavo J Costa
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Abel Egbemhenghe
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| |
Collapse
|
9
|
Misra R, Das I, Dér A, Steinbach G, Shim JG, Busse W, Jung KH, Zimányi L, Sheves M. Impact of protein-chromophore interaction on the retinal excited state and photocycle of Gloeobacter rhodopsin: role of conserved tryptophan residues. Chem Sci 2023; 14:9951-9958. [PMID: 37736621 PMCID: PMC10510653 DOI: 10.1039/d3sc02961a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/25/2023] [Indexed: 09/23/2023] Open
Abstract
The function of microbial as well as mammalian retinal proteins (aka rhodopsins) is associated with a photocycle initiated by light excitation of the retinal chromophore of the protein, covalently bound through a protonated Schiff base linkage. Although electrostatics controls chemical reactions of many organic molecules, attempt to understand its role in controlling excited state reactivity of rhodopsins and, thereby, their photocycle is scarce. Here, we investigate the effect of highly conserved tryptophan residues, between which the all-trans retinal chromophore of the protein is sandwiched in microbial rhodopsins, on the charge distribution along the retinal excited state, quantum yield and nature of the light-induced photocycle and absorption properties of Gloeobacter rhodopsin (GR). Replacement of these tryptophan residues by non-aromatic leucine (W222L and W122L) or phenylalanine (W222F) does not significantly affect the absorption maximum of the protein, while all the mutants showed higher sensitivity to photobleaching, compared to wild-type GR. Flash photolysis studies revealed lower quantum yield of trans-cis photoisomerization in W222L as well as W222F mutants relative to wild-type. The photocycle kinetics are also controlled by these tryptophan residues, resulting in altered accumulation and lifetime of the intermediates in the W222L and W222F mutants. We propose that protein-retinal interactions facilitated by conserved tryptophan residues are crucial for achieving high quantum yield of the light-induced retinal isomerization, and affect the thermal retinal re-isomerization to the resting state.
Collapse
Affiliation(s)
- Ramprasad Misra
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science Rehovot 76100 Israel
| | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science Rehovot 76100 Israel
| | - András Dér
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network Szeged H-6726 Hungary
| | - Gábor Steinbach
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network Szeged H-6726 Hungary
- Cellular Imaging Laboratory, Biological Research Centre, Eötvös Loránd Research Network Szeged H-6726 Hungary
| | - Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University Seoul 04107 South Korea
| | - Wayne Busse
- Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin Berlin 10115 Germany
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University Seoul 04107 South Korea
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre, Eötvös Loránd Research Network Szeged H-6726 Hungary
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science Rehovot 76100 Israel
| |
Collapse
|
10
|
Zhao X, Li J, Luo J, Liu J. Significant Acceleration of E-Z Photoisomerization induced by Molecular Planarity Breaking. Chem Phys Lett 2023. [DOI: 10.1016/j.cplett.2023.140480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
|
11
|
Boeije Y, Olivucci M. From a one-mode to a multi-mode understanding of conical intersection mediated ultrafast organic photochemical reactions. Chem Soc Rev 2023; 52:2643-2687. [PMID: 36970950 DOI: 10.1039/d2cs00719c] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
This review discusses how ultrafast organic photochemical reactions are controlled by conical intersections, highlighting that decay to the ground-state at multiple points of the intersection space results in their multi-mode character.
Collapse
Affiliation(s)
- Yorrick Boeije
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Massimo Olivucci
- Chemistry Department, University of Siena, Via Aldo Moro n. 2, 53100 Siena, Italy
- Chemistry Department, Bowling Green State University, Overman Hall, Bowling Green, Ohio 43403, USA
| |
Collapse
|
12
|
Tu H, Han Y, Wang Z, Li J. Clustered tree regression to learn protein energy change with mutated amino acid. Brief Bioinform 2022; 23:6702668. [PMID: 36124753 DOI: 10.1093/bib/bbac374] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 12/14/2022] Open
Abstract
Accurate and effective prediction of mutation-induced protein energy change remains a great challenge and of great interest in computational biology. However, high resource consumption and insufficient structural information of proteins severely limit the experimental techniques and structure-based prediction methods. Here, we design a structure-independent protocol to accurately and effectively predict the mutation-induced protein folding free energy change with only sequence, physicochemical and evolutionary features. The proposed clustered tree regression protocol is capable of effectively exploiting the inherent data patterns by integrating unsupervised feature clustering by K-means and supervised tree regression using XGBoost, and thus enabling fast and accurate protein predictions with different mutations, with an average Pearson correlation coefficient of 0.83 and an average root-mean-square error of 0.94kcal/mol. The proposed sequence-based method not only eliminates the dependence on protein structures, but also has potential applications in protein predictions with rare structural information.
Collapse
Affiliation(s)
- Hongwei Tu
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yanqiang Han
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zhilong Wang
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jinjin Li
- Key Laboratory of Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
13
|
Retinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin. Nat Commun 2022; 13:6652. [PMID: 36333283 PMCID: PMC9636224 DOI: 10.1038/s41467-022-33953-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
The understanding of how the rhodopsin sequence can be modified to exactly modulate the spectroscopic properties of its retinal chromophore, is a prerequisite for the rational design of more effective optogenetic tools. One key problem is that of establishing the rules to be satisfied for achieving highly fluorescent rhodopsins with a near infrared absorption. In the present paper we use multi-configurational quantum chemistry to construct a computer model of a recently discovered natural rhodopsin, Neorhodopsin, displaying exactly such properties. We show that the model, that successfully replicates the relevant experimental observables, unveils a geometrical and electronic structure of the chromophore featuring a highly diffuse charge distribution along its conjugated chain. The same model reveals that a charge confinement process occurring along the chromophore excited state isomerization coordinate, is the primary cause of the observed fluorescence enhancement.
Collapse
|
14
|
Towards the engineering of a photon-only two-stroke rotary molecular motor. Nat Commun 2022; 13:6433. [PMID: 36307476 PMCID: PMC9616945 DOI: 10.1038/s41467-022-33695-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 09/27/2022] [Indexed: 12/25/2022] Open
Abstract
The rational engineering of photoresponsive materials, e.g., light-driven molecular motors, is a challenging task. Here, we use structure-related design rules to prepare a prototype molecular rotary motor capable of completing an entire revolution using, exclusively, the sequential absorption of two photons; i.e., a photon-only two-stroke motor. The mechanism of rotation is then characterised using a combination of non-adiabatic dynamics simulations and transient absorption spectroscopy measurements. The results show that the rotor moiety rotates axially relative to the stator and produces, within a few picoseconds at ambient T, an intermediate with the same helicity as the starting structure. We discuss how such properties, that include a 0.25 quantum efficiency, can help overcome the operational limitations of the classical overcrowded alkene designs.
Collapse
|
15
|
Walter M, Schubert L, Heberle J, Schlesinger R, Losi A. Time-resolved photoacoustics of channelrhodopsins: early energetics and light-driven volume changes. Photochem Photobiol Sci 2022; 22:477-486. [PMID: 36273368 DOI: 10.1007/s43630-022-00327-8] [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: 09/16/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022]
Abstract
AbstractIn biological photoreceptors, the energy stored in early transient species is a key feature to drive the photocycle or a chain of reactions. Time-resolved photoacoustics (PA) can explore the energy landscape of transient species formed within few ns after photoexcitation, as well as volumetric changes (ΔV) of these intermediates with respect to the parental state. In this work, PA identified these important parameters for several channelrhodopsins, namely CaChR1 from Chlamydomonas augustae and CrChR2 from Chlamydomonas reinhardtii and various variants. PA has access to the sub-ns formation of the early photoproduct P1 and to its relaxation, provided that this latter process occurs within a few μs. We found that ΔVP1 for CaChR1 is ca. 12 mL/mol, while it is much smaller for CrChR2 (4.7 mL/mol) and for H. salinarum bacteriorhodopsin (HsBR, ΔVK = 2.8 mL/mol). PA experiments on variants strongly indicate that part of this large ΔVP1 value for CaChR1 is caused by the protonation dynamics of the Schiff base counterion complex involving E169 and D299. PA data further show that the energy level of P1 is higher in CrChR2 (ca. 96 kJ/mol) than in CaChr1 (ca. 46 kJ/mol), comparable to the energy level of the K state of HsBR (60 kJ/mol). Instrumental to gain these molecular values from the raw PA data was the estimation of the quantum yield (Φ) for P1 formation via transient spectroscopy; for both channelrhodopsins, ΦP2 was evaluated as ca. 0.4.
Graphical Abstract
Collapse
Affiliation(s)
- Maria Walter
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Luiz Schubert
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Ramona Schlesinger
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Aba Losi
- Department of Mathematical, Physical and Computer Sciences, University of Parma, Parco Area Delle Scienze 7/A, 43124, Parma, Italy.
| |
Collapse
|
16
|
Zhu H, Li Q. Understanding of Photo‐Induced Reversible Rearrangement from Borepin to Borirane. Chemistry 2022; 28:e202201360. [DOI: 10.1002/chem.202201360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Hong‐Yang Zhu
- Key Laboratory of Cluster Science of Ministry of Education Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials School of Chemistry and Chemical Engineering Beijing Institute of Technology 5 South Zhongguancun Street Beijing 100081 P. R. China
| | - Quan‐Song Li
- Key Laboratory of Cluster Science of Ministry of Education Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials School of Chemistry and Chemical Engineering Beijing Institute of Technology 5 South Zhongguancun Street Beijing 100081 P. R. China
| |
Collapse
|
17
|
Schmerwitz YLA, Ivanov AV, Jónsson EÖ, Jónsson H, Levi G. Variational Density Functional Calculations of Excited States: Conical Intersection and Avoided Crossing in Ethylene Bond Twisting. J Phys Chem Lett 2022; 13:3990-3999. [PMID: 35481754 DOI: 10.1021/acs.jpclett.2c00741] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Theoretical studies of photochemical processes require a description of the energy surfaces of excited electronic states, especially near degeneracies, where transitions between states are most likely. Systems relevant to photochemical applications are typically too large for high-level multireference methods, and while time-dependent density functional theory (TDDFT) is efficient, it can fail to provide the required accuracy. A variational, time-independent density functional approach is applied to the twisting of the double bond and pyramidal distortion in ethylene, the quintessential model for photochemical studies. By allowing for symmetry breaking, the calculated energy surfaces exhibit the correct topology around the twisted-pyramidalized conical intersection even when using a semilocal functional approximation, and by including explicit self-interaction correction, the torsional energy curves are in close agreement with published multireference results. The findings of the present work point to the possibility of using a single determinant time-independent density functional approach to simulate nonadiabatic dynamics, even for large systems where multireference methods are impractical and TDDFT is often not accurate enough.
Collapse
Affiliation(s)
| | - Aleksei V Ivanov
- Science Institute of the University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Elvar Ö Jónsson
- Science Institute of the University of Iceland, VR-III, 107 Reykjavík, Iceland
| | - Hannes Jónsson
- Faculty of Physical Sciences, University of Iceland, VR-III, 107 Reykjavík, Iceland
- Department of Applied Physics, Aalto University, FI-00076 Espoo, Finland
| | - Gianluca Levi
- Science Institute of the University of Iceland, VR-III, 107 Reykjavík, Iceland
| |
Collapse
|
18
|
Liang R, Bakhtiiari A. Effects of Enzyme-Ligand Interactions on the Photoisomerization of a Light-Regulated Chemotherapeutic Drug. J Phys Chem B 2022; 126:2382-2393. [PMID: 35297246 DOI: 10.1021/acs.jpcb.1c10819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular photoswitches permit using light to control protein activity with high spatiotemporal resolutions, thereby alleviating the side effects of conventional chemotherapy. However, due to the challenges in probing ultrafast photoisomerization reactions in biological environments, it remains elusive how the protein influences the photochemistry of the photoswitches, which hampers the rational design of light-regulated therapeutics. To overcome this challenge, we employed first-principles nonadiabatic dynamics simulations to characterize the photodynamics of the phototrexate (PTX), a recently developed photoswitchable anticancer chemotherapeutic that reversibly inhibits its target enzyme dihydrofolate reductase (DHFR). Our simulations show that the protein environment impedes the trans to cis photoisomerization of the PTX. The confinement in the ligand-binding cavity slows down the isomerization kinetics and quantum yield of the photoswitch by reshaping its conical intersection, increasing its excited-state free-energy barrier and quenching its local density fluctuations. Also, the protein environment results in a suboptimal binding mode of the photoproduct that needs to undergo large structural rearrangement to effectively inhibit the enzyme. Therefore, we predict that the PTX's trans → cis photoisomerization in solution precedes its binding with the protein, despite the favorable binding energy of the trans isomer. Our findings highlight the importance of the protein environment on the photochemical reactions of the molecular photoswitches. As such, our work represents an important step toward the rational design of light-regulated drugs in photopharmacology.
Collapse
Affiliation(s)
- Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Amirhossein Bakhtiiari
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| |
Collapse
|
19
|
Sirohiwal A, Pantazis DA. Electrostatic profiling of photosynthetic pigments: implications for directed spectral tuning. Phys Chem Chem Phys 2021; 23:24677-24684. [PMID: 34708851 DOI: 10.1039/d1cp02580e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photosynthetic pigment-protein complexes harvest solar energy with a high quantum efficiency. Protein scaffolds are known to tune the spectral properties of embedded pigments principally through structured electrostatic environments. Although the physical nature of electrostatic tuning is straightforward, the precise spatial principles of electrostatic preorganization remain poorly explored for different protein matrices and incompletely characterized with respect to the intrinsic properties of different photosynthetic pigments. In this work, we study the electronic structure features associated with the lowest excited state of a series of eight naturally occurring (bacterio)chlorophylls and pheophytins to describe the precise topological differences in electrostatic potentials and hence determine intrinsic differences in the expected mode and impact of electrostatic tuning. The difference electrostatic potentials between the ground and first excited states are used as fingerprints. Both the spatial profile and the propensity for spectral tuning are found to be unique for each pigment, indicating spatially and directionally distinct modes of electrostatic tuning. The results define a specific partitioning of the protein matrix around each pigment as an aid to identify regions with a maximal impact on spectral tuning and have direct implications for dimensionality reduction in protein design and engineering. Thus, a quantum mechanical basis is provided for understanding, predicting, and ultimately designing sequence-modified or pigment-exchanged biological systems, as suggested for selected examples of pigment-reconstituted proteins.
Collapse
Affiliation(s)
- Abhishek Sirohiwal
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| |
Collapse
|
20
|
Lee S, Park W, Nakata H, Filatov M, Choi CH. Recent advances in ensemble density functional theory and linear response theory for strong correlation. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12429] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Seunghoon Lee
- Division of Chemistry and Chemical Engineering California Institute of Technology Pasadena California USA
| | - Woojin Park
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Hiroya Nakata
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Michael Filatov
- Department of Chemistry Kyungpook National University Daegu South Korea
| | - Cheol Ho Choi
- Department of Chemistry Kyungpook National University Daegu South Korea
| |
Collapse
|