1
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Saavedra-Avila NA, Pigni NB, Caldwell DR, Chena-Becerra F, Intano J, Ng TW, Chennamadhavuni D, Porcelli SA, Gascón JA, Howell AR. A Humanized Mouse Model Coupled with Computational Analysis Identifies Potent Glycolipid Agonist of Invariant NKT Cells. ACS Chem Biol 2024; 19:926-937. [PMID: 38477945 PMCID: PMC11075374 DOI: 10.1021/acschembio.3c00736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Invariant natural killer T (iNKT) cells play an important role in many innate and adaptive immune responses, with potential applications in cancer immunotherapy. The glycolipid KRN7000, an α-galactosylceramide, potently activates iNKT cells but has shown limited anticancer effects in human clinical trials conducted so far. In spite of almost three decades of structure-activity relationship studies, no alternative glycolipid has yet emerged as a superior clinical candidate. One reason for the slow progress in this area is that standard mouse models do not accurately reflect the specific ligand recognition by human iNKT cells and their requirements for activation. Here we evaluated a series of KRN7000 analogues using a recently developed humanized mouse model that expresses a human αTCR chain sequence and human CD1d. In this process, a more stimulatory, previously reported but largely overlooked glycolipid was identified, and its activity was probed and rationalized via molecular simulations.
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Affiliation(s)
- Noemi A. Saavedra-Avila
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY USA 10461
| | - Natalia B. Pigni
- Department of Chemistry, University of Connecticut, Storrs CT USA 06269
- Instituto de Ciencia y Tecnología de Alimentos Córdoba (ICYTAC CONICET-UNC), Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | | | - Florencia Chena-Becerra
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY USA 10461
| | - Jose Intano
- Department of Chemistry, University of Connecticut, Storrs CT USA 06269
| | - Tony W. Ng
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY USA 10461
| | | | - Steven A. Porcelli
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY USA 10461
| | - José A. Gascón
- Department of Chemistry, University of Connecticut, Storrs CT USA 06269
| | - Amy R. Howell
- Department of Chemistry, University of Connecticut, Storrs CT USA 06269
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2
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Daniels R, Yassin OA, Toribio JM, Gascón JA, Sotzing G. Re-Examining Cannabidiol: Conversion to Tetrahydrocannabinol Using Only Heat. Cannabis Cannabinoid Res 2024; 9:486-494. [PMID: 36516105 DOI: 10.1089/can.2022.0235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Introduction: In the last decade, the market for Cannabidiol (CBD) has grown to become a near $2 billion dollar industry in the United States alone. This growth can be attributed to a growing social acceptance of marijuana, a more detailed understanding of many health benefits attributed to cannabinoids, and the low cost and wide availibility of hemp-derived cannabinoids. Due to the complex legal histories of marijuana and cannabinoids, the stability and safety of CBD is still an area of interest as research has been restricted globally. Conversion of CBD to its psychoactive isomers, most notably delta-9-Tetrahydrocannabinol (Δ9-THC), presents a significant safety issue for consumers and producers of CBD products. Methods: Previous studies investigating the stability of CBD have focused mainly on replicating conditions experienced during long-term storage at room temperature or lower. Here, we report the thermal stability of CBD at 175°C. Dynamic 1H-NMR experiments and computational electronic structure calculations were used to characterize possible reaction paths from CBD to THC. Results: After 30 minutes of heating, Δ9-THC was produced in detectable amounts in aerobic and anaerobic conditions without an acid catalyst. Conclusions: Our findings support an energetically feasible reaction route that is favorable due to both an increase in phenol acidity at high temperatures and the presence of intramolecular OH-π hydrogen bonding.
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Affiliation(s)
- Robert Daniels
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Omer A Yassin
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - John M Toribio
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Gregory Sotzing
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Polymer Program, University of Connecticut, Storrs, Connecticut, USA
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3
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Rose JB, Gascón JA, Sutter M, Sheppard DI, Kerfeld CA, Beck WF. Photoactivation of the orange carotenoid protein requires two light-driven reactions mediated by a metastable monomeric intermediate. Phys Chem Chem Phys 2023; 25:33000-33012. [PMID: 38032096 DOI: 10.1039/d3cp04484j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
The orange carotenoid protein (OCP) functions as a sensor of the ambient light intensity and as a quencher of bilin excitons when it binds to the core of the cyanobacterial phycobilisome. We show herein that the photoactivation mechanism that converts the resting, orange-colored state, OCPO, to the active red-colored state, OCPR, requires a sequence of two reactions, each requiring absorption of a single photon by an intrinsic ketocarotenoid chromophore. Global analysis of absorption spectra recorded during continuous illumination of OCPO preparations from Synechocystis sp. PCC 6803 detects the reversible formation of a metastable intermediate, OCPI, in which the ketocarotenoid canthaxanthin exhibits an absorption spectrum with a partial red shift and a broadened vibronic structure compared to that of the OCPO state. While the dark recovery from OCPR to OCPI is a first-order, unimolecular reaction, the subsequent conversion of OCPI to the resting OCPO state is bimolecular, involving association of two OCPO monomers to form the dark-stable OCPO dimer aggregate. These results indicate that photodissociation of the OCPO dimer to form the monomeric OCPO intermediate is the first step in the photoactivation mechanism. Formation of the OCPO monomer from the dimer increases the mean value and broadens the distribution of the solvent-accessible surface area of the canthaxanthin chromophore measured in molecular dynamics trajectories at 300 K. The second step in the photoactivation mechanism is initiated by absorption of a second photon, by canthaxanthin in the OCPO monomer, which obtains the fully red-shifted and broadened absorption spectrum detected in the OCPR product state owing to displacement of the C-terminal domain and the translocation of canthaxanthin more than 12 Å into the N-terminal domain. Both steps in the photoactivation reaction of OCP are likely to involve changes in the structure of the C-terminal domain elicited by excited-state conformational motions of the ketocarotenoid.
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Affiliation(s)
- Justin B Rose
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, USA.
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, USA
| | - Markus Sutter
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824-1322, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Damien I Sheppard
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824-1322, USA
| | - Cheryl A Kerfeld
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824-1322, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Warren F Beck
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, USA.
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4
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Hewage N, Guberman-Pfeffer MJ, Chaudhri N, Zeller M, Gascón JA, Brückner C. Syntheses and Aromaticity Parameters of Hexahydroxypyrrocorphin, Porphotrilactones, and Their Oxidation State Intermediates. J Org Chem 2022; 87:12096-12108. [PMID: 36066858 DOI: 10.1021/acs.joc.2c01202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triple OsO4-mediated dihydroxylation of meso-tetrakis(pentafluorophenyl)porphyrin formed a non-aromatic hexahydroxypyrrocorphin as a single stereo-isomer. A one-step oxidative conversion of all three diol functionalities to lactone moieties generated three out of the four possible porphotrilactone regioisomers that were spectroscopically and structurally characterized. This conversion recovered most of the porphyrinic macrocycle aromatic ring current, as seen in their 1H NMR spectra and modeled using DFT computations. Stepwise OsO4-mediated dihydroxylations of porpho-mono- and -di-lactones generated intermediate oxidation state compounds between the pyrrole-three pyrroline macrocycle of the pyrrocorphin and the pyrrole-three oxazolone chromophore of the trilactones. The aromaticity of these chromophores was reduced with increasing number of oxazolone to pyrroline replacements, showing the importance for the presence of three lactone moieties for the retention of the macrocycle aromaticity in the tris-β,β'-modified macrocycles. This work first describes hexahydoxypyrrocorphins, porphotrislactones, and the oxidation state intermediates between them; furthers the understanding of the roles of β-lactone moieties in the expression of porphyrinic macrocycle aromaticity; and generally broadens access to chemically stable pyrrocorphins and pyrrocorphin analogues.
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Affiliation(s)
- Nisansala Hewage
- Department of Chemistry, University of Connecticut, Unit 3060, Storrs, Connecticut 06269-3060, United States
| | - Matthew J Guberman-Pfeffer
- Department of Chemistry, University of Connecticut, Unit 3060, Storrs, Connecticut 06269-3060, United States
| | - Nivedita Chaudhri
- Department of Chemistry, University of Connecticut, Unit 3060, Storrs, Connecticut 06269-3060, United States
| | - Matthias Zeller
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Unit 3060, Storrs, Connecticut 06269-3060, United States
| | - Christian Brückner
- Department of Chemistry, University of Connecticut, Unit 3060, Storrs, Connecticut 06269-3060, United States
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5
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Wijesiri K, Gascón JA. Microsolvation Effects in the Spectral Tuning of Heliorhodopsin. J Phys Chem B 2022; 126:5803-5809. [PMID: 35894868 DOI: 10.1021/acs.jpcb.2c03672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Heliorhodopsins (HeR) are a new category of heptahelical transmembrane photoactive proteins with a covalently linked all-trans retinal. The protonated Schiff base (PSB) nitrogen in the retinal is stabilized by a negatively charged counterion. It is well-known that stronger or weaker electrostatic interactions with the counterion cause a significant spectral blue- or red-shift, respectively, in both microbial and animal rhodopsins. In HeR, however, while Glu107 acts as the counterion, mutations of this residue are not directly correlated with a spectral shift. A molecular dynamics analysis revealed that a water cluster pocket produces a microsolvation effect on the Schiff base, compensating to various extents the replacement of the native counterion. Using a combination of molecular dynamics and quantum mechanical/molecular mechanics (QM/MM), we study this microsolvation effect on the electronic absorption of the retinylidene Schiff base chromophore of HeR.
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Affiliation(s)
- Kithmini Wijesiri
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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6
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Sharawy M, Pigni NB, May ER, Gascón JA. A favorable path to domain separation in the orange carotenoid protein. Protein Sci 2022; 31:850-863. [PMID: 35000233 PMCID: PMC8927859 DOI: 10.1002/pro.4273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/24/2021] [Accepted: 01/03/2022] [Indexed: 11/10/2022]
Abstract
The orange carotenoid protein (OCP) is responsible for nonphotochemical quenching (NPQ) in cyanobacteria, a defense mechanism against potentially damaging effects of excess light conditions. This soluble two-domain protein undergoes profound conformational changes upon photoactivation, involving translocation of the ketocarotenoid inside the cavity followed by domain separation. Domain separation is a critical step in the photocycle of OCP because it exposes the N-terminal domain (NTD) to perform quenching of the phycobilisomes. Many details regarding the mechanism and energetics of OCP domain separation remain unknown. In this work, we apply metadynamics to elucidate the protein rearrangements that lead to the active, domain-separated, form of OCP. We find that translocation of the ketocarotenoid canthaxanthin has a profound effect on the energetic landscape and that domain separation only becomes favorable following translocation. We further explore, characterize, and validate the free energy surface (FES) using equilibrium simulations initiated from different states on the FES. Through pathway optimization methods, we characterize the most probable path to domain separation and reveal the barriers along that pathway. We find that the free energy barriers are relatively small (<5 kcal/mol), but the overall estimated kinetic rate is consistent with experimental measurements (>1 ms). Overall, our results provide detailed information on the requirement for canthaxanthin translocation to precede domain separation and an energetically feasible pathway to dissociation.
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Affiliation(s)
- Mahmoud Sharawy
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - Natalia B. Pigni
- Department of ChemistryUniversity of ConnecticutStorrsConnecticutUSA
- Instituto de Ciencia y Tecnología de Alimentos Córdoba (ICYTAC‐CONICET)Ciudad UniversitariaCórdobaArgentina
| | - Eric R. May
- Department of Molecular and Cell BiologyUniversity of ConnecticutStorrsConnecticutUSA
| | - José A. Gascón
- Department of ChemistryUniversity of ConnecticutStorrsConnecticutUSA
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7
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Sharawy M, Pigni NB, May ER, Gascón JA. A favorable path to domain separation in the orange carotenoid protein. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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8
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Wolf M, Ortiz-Garcia JJ, Guberman-Pfeffer MJ, Gascón JA, Quardokus RC. Electronic energy levels of porphyrins are influenced by the local chemical environment. RSC Adv 2022; 12:1361-1365. [PMID: 35425205 PMCID: PMC8978926 DOI: 10.1039/d1ra09116f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 12/23/2021] [Indexed: 11/26/2022] Open
Abstract
Self-assembled islands of 5,10,15,20-tetrakis(pentafluoro-phenyl)porphyrin (2HTFPP) on Au(111) contain two bistable molecular species that differ by shifted electronic energy levels. Interactions with the underlying gold herringbone reconstruction and neighboring 2HTFPP molecules cause approximately 60% of molecules to have shifted electronic energy levels. We observed the packing density decrease from 0.64 ± 0.04 molecules per nm2 to 0.38 ± 0.03 molecules per nm2 after annealing to 200 °C. The molecules with shifted electronic energy levels show longer-range hexagonal packing or are adjacent to molecular vacancies, indicating that molecule–molecule and molecule–substrate interactions contribute to the shifted energies. Multilayers of porphyrins do not exhibit the same shifting of electronic energy levels which strongly suggests that molecule–substrate interactions play a critical role in stabilization of two electronic species of 2HTFPP on Au(111). Self-assembled islands of 5,10,15,20-tetrakis(pentafluoro-phenyl)porphyrin (2HTFPP) on Au(111) contain two bistable molecular species that differ by shifted electronic energy levels.![]()
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Affiliation(s)
- Margaret Wolf
- Department of Chemistry, University of Connecticut, USA
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9
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An J, Intano J, Richard A, Kim T, Gascón JA, Howell AR. Easily accessible non-aromatic heterocycles with handles: 4-bromo-2,3-dihydrofurans from 1,2-dibromohomoallylic alcohols. Chem Sci 2021; 12:10347-10353. [PMID: 34377420 PMCID: PMC8336482 DOI: 10.1039/d1sc01013a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 06/28/2021] [Indexed: 11/21/2022] Open
Abstract
The first general preparation of 4-bromo-2,3-dihydrofurans is reported. These non-aromatic heterocycles containing a useful coupling handle are accessed via Cu-catalyzed intramolecular cyclization of 1,2-dibromohomoallylic alcohols, which are themselves available in just two steps from aromatic and aliphatic aldehydes and ketones. Molecular dynamics simulations using the simple substrates and key geometric parameters provide a rationale for the selectivities observed. The synthetic utility of the 4-bromodihydrofurans is also demonstrated.
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Affiliation(s)
- Jason An
- Department of Chemistry, University of Connecticut Storrs CT 06269 USA
| | - Jose Intano
- Department of Chemistry, University of Connecticut Storrs CT 06269 USA
| | - Alissa Richard
- Department of Chemistry, University of Connecticut Storrs CT 06269 USA
| | - Taehyun Kim
- Department of Chemistry, University of Connecticut Storrs CT 06269 USA
| | - José A Gascón
- Department of Chemistry, University of Connecticut Storrs CT 06269 USA
| | - Amy R Howell
- Department of Chemistry, University of Connecticut Storrs CT 06269 USA
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10
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Karunaratne E, Hill DW, Pracht P, Gascón JA, Grimme S, Grant DF. High-Throughput Non-targeted Chemical Structure Identification Using Gas-Phase Infrared Spectra. Anal Chem 2021; 93:10688-10696. [PMID: 34288660 PMCID: PMC8404482 DOI: 10.1021/acs.analchem.1c02244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The high-throughput identification of unknown metabolites in biological samples remains challenging. Most current non-targeted metabolomics studies rely on mass spectrometry, followed by computational methods that rank thousands of candidate structures based on how closely their predicted mass spectra match the experimental mass spectrum of an unknown. We reasoned that the infrared (IR) spectra could be used in an analogous manner and could add orthologous structure discrimination; however, this has never been evaluated on large data sets. Here, we present results of a high-throughput computational method for predicting IR spectra of candidate compounds obtained from the PubChem database. Predicted spectra were ranked based on their similarity to gas-phase experimental IR spectra of test compounds obtained from the NIST. Our computational workflow (IRdentify) consists of a fast semiempirical quantum mechanical method for initial IR spectra prediction, ranking, and triaging, followed by a final IR spectra prediction and ranking using density functional theory. This approach resulted in the correct identification of 47% of 258 test compounds. On average, there were 2152 candidate structures evaluated for each test compound, giving a total of approximately 555,200 candidate structures evaluated. We discuss several variables that influenced the identification accuracy and then demonstrate the potential application of this approach in three areas: (1) combining IR and mass spectra rankings into a single composite rank score, (2) identifying the precursor and fragment ions using cryogenic ion vibrational spectroscopy, and (3) the incorporation of a trimethylsilyl derivatization step to extend the method compatibility to less-volatile compounds. Overall, our results suggest that matching computational with experimental IR spectra is a potentially powerful orthogonal option for adding significant high-throughput chemical structure discrimination when used with other non-targeted chemical structure identification methods.
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Affiliation(s)
- Erandika Karunaratne
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Dennis W Hill
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Philipp Pracht
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269, United States
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstrasse 4, 53115 Bonn, Germany
| | - David F Grant
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, Connecticut 06269, United States
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11
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Gelpí-Domínguez S, Rossi AR, Gascón JA. Insights into diastereotopic effects in thiolated gold nanoclusters. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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12
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Saavedra-Avila NA, Keshipeddy S, Guberman-Pfeffer MJ, Pérez-Gallegos A, Saini NK, Schäfer C, Carreño LJ, Gascón JA, Porcelli SA, Howell AR. Amide-Linked C4″-Saccharide Modification of KRN7000 Provides Potent Stimulation of Human Invariant NKT Cells and Anti-Tumor Immunity in a Humanized Mouse Model. ACS Chem Biol 2020; 15:3176-3186. [PMID: 33296161 DOI: 10.1021/acschembio.0c00707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Activation of invariant natural killer T (iNKT) cells by α-galactosylceramides (α-GalCers) stimulates strong immune responses and potent anti-tumor immunity. Numerous modifications of the glycolipid structure have been assessed to derive activating ligands for these T cells with altered and potentially advantageous properties in the induction of immune responses. Here, we synthesized variants of the prototypical α-GalCer, KRN7000, with amide-linked phenyl alkane substitutions on the C4″-position of the galactose ring. We show that these variants have weak iNKT cell stimulating activity in mouse models but substantially greater activity for human iNKT cells. The most active of the C4″-amides in our study showed strong anti-tumor effects in a partially humanized mouse model for iNKT cell responses. In silico analysis suggested that the tether length and degree of flexibility of the amide substituent affected the recognition by iNKT cell antigen receptors of the C4″-amide substituted glycolipids in complex with their antigen presenting molecule CD1d. Our findings establish the use of stable C4″-amide linked additions to the sugar moiety for further exploration of the immunological effects of structural modifications of iNKT cell activating glycolipids and highlight the critical need for more accurate animal models to assess these compounds for immunotherapeutic potential in humans.
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Affiliation(s)
| | - Santosh Keshipeddy
- Department of Chemistry, The University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | | | | | | | - Carolina Schäfer
- Millennium Institute on Immunology and Immunotherapy, Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - Leandro J. Carreño
- Millennium Institute on Immunology and Immunotherapy, Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago 8380453, Chile
| | - José A Gascón
- Department of Chemistry, The University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | | | - Amy R. Howell
- Department of Chemistry, The University of Connecticut, Storrs, Connecticut 06269-3060, United States
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13
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Abstract
The orange carotenoid protein (OCP) is involved in the photoprotective processes in cyanobacteria via nonphotochemical quenching. Triggered by blue-green light absorption, the carotenoid chromophore undergoes translocation, displacing around 12 Å from the C-terminal domain (CTD) to the N-terminal domain (NTD). The detailed molecular rearrangements that occur within the carotenoid and the protein during this process remain largely elusive. By using a combination of molecular dynamics, well-tempered metadynamics, and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations, we were able to mimic the translocation of the carotenoid from the inactive OCPO and obtain metastable red-shifted states in the photoactivation mechanism, replicating the λmax values of reference experimental spectra. In addition, our simulations give insight into the structure of the red-shifted form of the inactive state of OCP.
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Affiliation(s)
- Natalia B Pigni
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States.,Instituto de Ciencia y Tecnología de Alimentos Córdoba (ICYTAC-CONICET), Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | - Kevin L Clark
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Warren F Beck
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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14
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Gurchiek JK, Rose JB, Guberman-Pfeffer MJ, Tilluck RW, Ghosh S, Gascón JA, Beck WF. Fluorescence Anisotropy Detection of Barrier Crossing and Ultrafast Conformational Dynamics in the S 2 State of β-Carotene. J Phys Chem B 2020; 124:9029-9046. [PMID: 32955881 DOI: 10.1021/acs.jpcb.0c06961] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carotenoids are usually only weakly fluorescent despite being very strong absorbers in the mid-visible region because their first two excited singlet states, S1 and S2, have very short lifetimes. To probe the structural mechanisms that promote the nonradiative decay of the S2 state to the S1 state, we have carried out a series of fluorescence lineshape and anisotropy measurements with a prototype carotenoid, β-carotene, in four aprotic solvents. The anisotropy values observed in the fluorescence emission bands originating from the S2 and S1 states reveal that the large internal rotations of the emission transition dipole moment, as much as 50° relative to that of the absorption transition dipole moment, are initiated during ultrafast evolution on the S2 state potential energy surface and persist upon nonradiative decay to the S1 state. Electronic structure calculations of the orientation of the transition dipole moment account for the anisotropy results in terms of torsional and pyramidal distortions near the center of the isoprenoid backbone. The excitation wavelength dependence of the fluorescence anisotropy indicates that these out-of-plane conformational motions are initiated by passage over a low-activation energy barrier from the Franck-Condon S2 structure. This conclusion is consistent with detection over the 80-200 K range of a broad, red-shifted fluorescence band from a dynamic intermediate evolving on a steep gradient of the S2 state potential energy surface after crossing the activation barrier. The temperature dependence of the oscillator strength and anisotropy indicate that nonadiabatic passage from S2 through a conical intersection seam to S1 is promoted by the out-of-plane motions of the isoprenoid backbone with strong hindrance by solvent friction.
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Affiliation(s)
- J K Gurchiek
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Justin B Rose
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Matthew J Guberman-Pfeffer
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06268-1712, United States
| | - Ryan W Tilluck
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - Soumen Ghosh
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci, 32, Milan, Lombardy 20133, Italy
| | - José A Gascón
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06268-1712, United States
| | - Warren F Beck
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
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15
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Jolin WC, Richard A, Vasudevan D, Gascón JA, MacKay AA. Aluminosilicate Mineralogy and the Sorption of Organic Cations: Interplay between Electrostatic Barriers and Compound Structural Features. Environ Sci Technol 2020; 54:1623-1633. [PMID: 31909596 DOI: 10.1021/acs.est.9b06121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Current predictive models of organic cation sorption assume that sorbates interact with all sites on aluminosilicate minerals in the same manner. To examine whether differences in aluminosilicate structure and the resultant changes in electrostatic potential influence the sorption of organic cations, seven smectites were chosen with different proportions of isomorphic substitutions (origin of clay charge) located in octahedral versus tetrahedral layers and with the presence or absence of aluminosilicate interlayers. Sorption coefficients for 14 benzylamine derivatives with systematic differences in compound structures were collected to understand the possible influence of aluminosilicate mineralogy. Benzylamine compounds with methyl group substitution on the charged amine or with electron-donating or -withdrawing ring substituents displayed decreases in cation exchange-normalized sorption coefficients (KCEC), by up to one order of magnitude, between hectorite (100% isomorphic substitution in the octahedral layer) and nontronite (100% isomorphic substitution in the tetrahedral layer). To understand this difference across aluminosilicates, stochastic molecular models of the various aluminosilicate minerals with interlayers were performed. These models showed that negative charge density associated with tetrahedral sites results in high positive electrostatic energy barriers within the interlayer, creating a penalty for compounds with positive charge spread over a larger compound surface area as occurs from primary to quaternary amines. Conversely, clays with charge originating from octahedral sites produce low electrostatic potential barriers within the interlayer, decreasing the penalty for quaternary amine sorption. Trends for nine cationic pharmaceutical compounds, which varied in size, group alkylation, and/or polar substituents, demonstrated similar decreases in KCEC values to aluminosilicate minerals with high electrostatic energy barriers. Overall, aluminosilicate mineralogy was found to exert a large influence (0.5-1 order of magnitude in sorption coefficients) on organic cation sorption. The application of atomistic electrostatic potential mapping of both sorbent and sorbate structures provided insights to explain trends in sorption coefficients that could not be described by the basic electrostatic potential theory or by assuming that sorbate structure moieties yielded additive sorption contributions.
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Affiliation(s)
- William C Jolin
- Department of Civil and Environmental Engineering , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Alissa Richard
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Dharni Vasudevan
- Department of Chemistry , Bowdoin College , Brunswick , Maine 04011 , United States
| | - José A Gascón
- Department of Chemistry , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Allison A MacKay
- Department of Civil, Environmental and Geodetic Engineering , The Ohio State University , Columbus , Ohio 43210 , United States
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16
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Hassan DM, Guberman-Pfeffer M, Gascón JA. Finite Temperature Analysis of Inter-Chromophore Electronic Couplings in Different Forms of the Peridinin-Chlorophyll a Protein. Biophys J 2020. [DOI: 10.1016/j.bpj.2019.11.854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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17
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Guberman-Pfeffer MJ, Lalisse RF, Hewage N, Brückner C, Gascón JA. Origins of the Electronic Modulations of Bacterio- and Isobacteriodilactone Regioisomers. J Phys Chem A 2019; 123:7470-7485. [PMID: 31361130 DOI: 10.1021/acs.jpca.9b05656] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Advances in the utilization of porphyrinoids for photomedicine, catalysis, and artificial photosynthesis require a fundamental understanding of the relationships between their molecular connectivity and resulting electronic structures. Herein, we analyze how the replacement of two pyrrolic Cβ═Cβ bonds of a porphyrin by two lactone (O═C-O) moieties modulates the ground-state thermodynamic stability and electronic structure of the resulting five possible pyrrole-modified porphyrin isomers. We made these determinations based on density functional theory (DFT) and time-dependent DFT computations of the optical spectra of all regioisomers. We also analyzed the computed magnetically induced currents of their aromatic π-systems. All regioisomers adopt the tautomeric state that maximizes aromaticity, whether or not transannular steric strains are incurred. In all isomers, the O═Cβ-Oβ bonds were found to support a macrocycle diatropic ring current. We attributed this to the delocalization of nonbonding electrons from the ring oxa- and oxo-atoms into the macrocycle. As a consequence of this delocalization, the dilactone regioisomers are as-or even more-aromatic than their hydroporphyrin congeners. The electronic structures follow different trends for the bacteriochlorin- and isobacteriochlorin-type isomers. The presence of either oxo- or oxa-oxygens conjugated with the macrocyclic π-system was found to be the minimal structural requirement for the regioisomers to exhibit distinct electronic properties. Our computational methods and mechanistic insights provide a basis for the systematic exploration of the physicochemical properties of porphyrinoids as a function of the number, relative orientation, and degree of macrocycle-π-conjugation of β-substituents, in general, and for dilactone-based porphyrinic chromophores, in particular.
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Affiliation(s)
- Matthew J Guberman-Pfeffer
- Department of Chemistry , University of Connecticut , Unit 3060 , Storrs , Connecticut 06269-3060 , United States
| | - Remy F Lalisse
- Department of Chemistry , University of Connecticut , Unit 3060 , Storrs , Connecticut 06269-3060 , United States
| | - Nisansala Hewage
- Department of Chemistry , University of Connecticut , Unit 3060 , Storrs , Connecticut 06269-3060 , United States
| | - Christian Brückner
- Department of Chemistry , University of Connecticut , Unit 3060 , Storrs , Connecticut 06269-3060 , United States
| | - José A Gascón
- Department of Chemistry , University of Connecticut , Unit 3060 , Storrs , Connecticut 06269-3060 , United States
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18
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Hewage N, Daddario P, Lau KSF, Guberman-Pfeffer MJ, Gascón JA, Zeller M, Lee CO, Khalil GE, Gouterman M, Brückner C. Bacterio- and Isobacteriodilactones by Stepwise or Direct Oxidations of meso-Tetrakis(pentafluorophenyl)porphyrin. J Org Chem 2019; 84:239-256. [PMID: 30484650 DOI: 10.1021/acs.joc.8b02628] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Porpholactones are porphyrinoids in which one or more β,β'-bonds of the parent chromophore were replaced by lactone moieties. Accessible to varying degrees by direct and nonselective oxidations of porphyrins, the rational syntheses of all five dilactone isomers along stepwise, controlled, and high-yielding routes via porphyrin → tetrahydroxyisobacteriochlorin metal complexes → isobacteriochlorindilactone metal complexes or porphyrin → tetrahydroxybacteriochlorin → bacteriochlorindilactone (and related) pathways, respectively, are described. A major benefit of these complementary routes over established methods is the simplicity of the isolation of the dilactones because of the reduced number of side products formed. In an alternative approach we report the direct and selective conversion of free base meso-tetrakis(pentafluorophenyl)porphyrin to all isomers of free base isobacteriodilactones using the oxidant cetyltrimethylN+MnO4-. The solid-state structures of some of the isomers and their precursors are reported, providing data on the conformational modulation induced by the derivatizations. We also rationalize computationally their differing thermodynamic stability and electronic properties. In making new efficient routes toward these dilactone isomers available, we enable the further study of this diverse class of porphyrinoids.
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Affiliation(s)
- Nisansala Hewage
- Department of Chemistry , University of Connecticut , Unit 3060, Storrs , Connecticut 06269-3060 , United States
| | - Pedro Daddario
- Department of Chemistry , University of Connecticut , Unit 3060, Storrs , Connecticut 06269-3060 , United States
| | - Kimberly S F Lau
- Department of Chemistry , University of Connecticut , Unit 3060, Storrs , Connecticut 06269-3060 , United States.,Department of Chemistry , University of Washington , Box 351700, Seattle , Washington 98195 , United States
| | - Matthew J Guberman-Pfeffer
- Department of Chemistry , University of Connecticut , Unit 3060, Storrs , Connecticut 06269-3060 , United States
| | - José A Gascón
- Department of Chemistry , University of Connecticut , Unit 3060, Storrs , Connecticut 06269-3060 , United States
| | - Matthias Zeller
- Department of Chemistry , Purdue University , 101 Wetherill Hall, 560 Oval Drive , West Lafayette , Indiana 47907-2084 , United States
| | - Christal O Lee
- Department of Chemistry , University of Washington , Box 351700, Seattle , Washington 98195 , United States
| | - Gamal E Khalil
- Department of Chemistry , University of Washington , Box 351700, Seattle , Washington 98195 , United States
| | - Martin Gouterman
- Department of Chemistry , University of Washington , Box 351700, Seattle , Washington 98195 , United States
| | - Christian Brückner
- Department of Chemistry , University of Connecticut , Unit 3060, Storrs , Connecticut 06269-3060 , United States
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19
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Dainese T, Agrachev M, Antonello S, Badocco D, Black DM, Fortunelli A, Gascón JA, Stener M, Venzo A, Whetten RL, Maran F. Atomically precise Au 144(SR) 60 nanoclusters (R = Et, Pr) are capped by 12 distinct ligand types of 5-fold equivalence and display gigantic diastereotopic effects. Chem Sci 2018; 9:8796-8805. [PMID: 30647884 PMCID: PMC6301266 DOI: 10.1039/c8sc04092c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/06/2018] [Indexed: 01/28/2023] Open
Abstract
For two decades, Au144(SR)60 has been one of the most studied and used thiolate (SR) protected gold nanoclusters. In many ways, however, it proved to be a challenging and elusive case, also because of the difficulties in solving its structure by single-crystal X-ray crystallography. We used very short thiols and could prepare Au144(SC2H5)60 and Au144(SC3H7)60 in a very pure form, which was confirmed by UV-vis absorption spectroscopy and very regular electrochemistry patterns. Inductively coupled plasma and electrospray ionization mass spectrometries gave definite proof of the Au144(SR)60 stoichiometry. High-resolution 1D and 2D NMR spectroscopy in the solution phase provided the result of assessing the presence of 12 ligand types in exactly the same amount (5-fold equivalence). Equally important, we found that the two protons belonging to each methylene group along the thiolate chain are diastereotopic. For the α-CH2 protons, the diastereotopic effect can be indeed gigantic, as it reaches chemical-shift differences of 2.9 ppm. DFT calculations provided insights into the relationship between structure and NMR results. In particular, the 12 ligand types and corresponding diastereotopic effects may be explained by considering the presence of C-H···S hydrogen bonds. These results thus provide fundamental insights into the structure of the thiolate layer capping this long-studied gold nanocluster.
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Affiliation(s)
- Tiziano Dainese
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy .
| | - Mikhail Agrachev
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy .
| | - Sabrina Antonello
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy .
| | - Denis Badocco
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy .
| | - David M Black
- Department of Physics and Astronomy , University of Texas at San Antonio , One UTSA Circle , San Antonio , Texas 78249 , USA
| | | | - José A Gascón
- Department of Chemistry , University of Connecticut , 55 North Eagleville Road , Storrs , 06269 Connecticut , USA
| | - Mauro Stener
- Department of Chemical and Pharmaceutical Sciences , University of Trieste , 34127 Trieste , Italy
| | - Alfonso Venzo
- National Research Council , CNR-ICMATE , Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy
| | - Robert L Whetten
- Department of Physics and Astronomy , University of Texas at San Antonio , One UTSA Circle , San Antonio , Texas 78249 , USA
| | - Flavio Maran
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy .
- Department of Chemistry , University of Connecticut , 55 North Eagleville Road , Storrs , 06269 Connecticut , USA
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20
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Guberman-Pfeffer MJ, Gascón JA. Carotenoid-Chlorophyll Interactions in a Photosynthetic Antenna Protein: A Supramolecular QM/MM Approach. Molecules 2018; 23:molecules23102589. [PMID: 30308965 PMCID: PMC6222738 DOI: 10.3390/molecules23102589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 11/16/2022] Open
Abstract
Multichromophoric interactions control the initial events of energy capture and transfer in the light harvesting peridinin-chlorophyll a protein (PCP) from marine algae dinoflagellates. Due to the van der Waals association of the carotenoid peridinin (Per) with chlorophyll a in a unique 4:1 stoichiometric ratio, supramolecular quantum mechanical/molecular mechanical (QM/MM) calculations are essential to accurately describe structure, spectroscopy, and electronic coupling. We show that, by enabling inter-chromophore electronic coupling, substantial effects arise in the nature of the transition dipole moment and the absorption spectrum. We further hypothesize that inter-protein domain Per-Per interactions are not negligible, and are needed to explain the experimental reconstruction features of the spectrum in wild-type PCP.
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Affiliation(s)
| | - José A Gascón
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, USA.
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21
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Yang B, Hewage N, Guberman-Pfeffer MJ, Wax T, Gascón JA, Zhao J, Agrios AG, Brückner C. The limited extent of the electronic modulation of chlorins and bacteriochlorins through chromene-annulation. Phys Chem Chem Phys 2018; 20:18233-18240. [PMID: 29942972 DOI: 10.1039/c8cp02712a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Optical data (UV-vis absorption and fluorescence emission spectra, including fluorescence yields and lifetimes) and electrochemical measurements are used to quantify the modulation of the electronic properties of meso-tetrakis(pentafluorophenyl)-chlorin diol and -bacteriochlorin tetraols upon intramolecular chromene-annulation, including the investigation of regio- and stereoisomers. The small modulations of the frontier orbitals of the porphyrinoids are rationalized using DFT computations and can be traced to small electronic effects due to the co-planarized meso-aryl groups in combination with conformational effects.
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Affiliation(s)
- Bowen Yang
- Department of Civil and Environmental Engineering, University of Connecticut, Storrs, Connecticut 06269-3037, USA.
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22
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Chennamadhavuni D, Saavedra-Avila NA, Carreño LJ, Guberman-Pfeffer MJ, Arora P, Yongqing T, Pryce R, Koay HF, Godfrey DI, Keshipeddy S, Richardson SK, Sundararaj S, Lo JH, Wen X, Gascón JA, Yuan W, Rossjohn J, Le Nours J, Porcelli SA, Howell AR. Dual Modifications of α-Galactosylceramide Synergize to Promote Activation of Human Invariant Natural Killer T Cells and Stimulate Anti-tumor Immunity. Cell Chem Biol 2018; 25:571-584.e8. [PMID: 29576533 PMCID: PMC6025895 DOI: 10.1016/j.chembiol.2018.02.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Revised: 01/11/2018] [Accepted: 02/16/2018] [Indexed: 12/13/2022]
Abstract
Glycosylceramides that activate CD1d-restricted invariant natural killer T (iNKT) cells have potential therapeutic applications for augmenting immune responses against cancer and infections. Previous studies using mouse models identified sphinganine variants of α-galactosylceramide as promising iNKT cell activators that stimulate cytokine responses with a strongly proinflammatory bias. However, the activities of sphinganine variants in mice have generally not translated well to studies of human iNKT cell responses. Here, we show that strongly proinflammatory and anti-tumor iNKT cell responses were achieved in mice by a variant of α-galactosylceramide that combines a sphinganine base with a hydrocinnamoyl ester on C6″ of the sugar. Importantly, the activities observed with this variant were largely preserved for human iNKT cell responses. Structural and in silico modeling studies provided a mechanistic basis for these findings and suggested basic principles for capturing useful properties of sphinganine analogs of synthetic iNKT cell activators in the design of immunotherapeutic agents.
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Affiliation(s)
| | | | - Leandro J Carreño
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Millennium Institute on Immunology and Immunotherapy, Programa de Inmunologia, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Pooja Arora
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Tang Yongqing
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Rhys Pryce
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Hui-Fern Koay
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Dale I Godfrey
- Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging at the University of Melbourne, Melbourne, Australia
| | - Santosh Keshipeddy
- Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA
| | - Stewart K Richardson
- Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA
| | - Srinivasan Sundararaj
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia
| | - Jae Ho Lo
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Xiangshu Wen
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - José A Gascón
- Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA
| | - Weiming Yuan
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jamie Rossjohn
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK
| | - Jérôme Le Nours
- Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia.
| | - Steven A Porcelli
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Amy R Howell
- Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA.
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23
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Guberman-Pfeffer MJ, Greco JA, Birge RR, Frank HA, Gascón JA. Light Harvesting by Equally Contributing Mechanisms in a Photosynthetic Antenna Protein. J Phys Chem Lett 2018; 9:563-568. [PMID: 29337581 DOI: 10.1021/acs.jpclett.7b03211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We report supramolecular quantum mechanics/molecular mechanics simulations on the peridinin-chlorophyll a protein (PCP) complex from the causative algal species of red tides. These calculations reproduce for the first time quantitatively the distinct peridinin absorptions, identify multichromophoric molecular excitations, and elucidate the mechanisms regulating the strongly allowed S0 (11Ag-) → S2 (11Bu+) absorptions of the bound peridinins that span a 58 nm spectral range in the region of maximal solar irradiance. We discovered that protein binding site-imposed conformations, local electrostatics, and electronic coupling contribute equally to the spectral inhomogeneity. Electronic coupling causes coherent excitations among the densely packed pigments. Complementary pairing of tuning mechanisms is the result of a competition between pigment-pigment and pigment-environment interactions. We found that the aqueous solvent works in concert with the charge distribution of PCP to produce a strong correlation between peridinin spectral bathochromism and the local dielectric environment.
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Affiliation(s)
| | - Jordan A Greco
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060, United States
| | - Robert R Birge
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060, United States
| | - Harry A Frank
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060, United States
| | - José A Gascón
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060, United States
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24
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Guberman-Pfeffer MJ, Greco JA, Samankumara LP, Zeller M, Birge RR, Gascón JA, Brückner C. Bacteriochlorins with a Twist: Discovery of a Unique Mechanism to Red-Shift the Optical Spectra of Bacteriochlorins. J Am Chem Soc 2016; 139:548-560. [DOI: 10.1021/jacs.6b12419] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
| | - Jordan A. Greco
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Lalith P. Samankumara
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Matthias Zeller
- Department
of Chemistry, Youngstown State University, One University Plaza, Youngstown, Ohio 44555-3663, United States
| | - Robert R. Birge
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
- Department
of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut 06269-3125, United States
| | - José A. Gascón
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Christian Brückner
- Department
of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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25
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Agrachev M, Antonello S, Dainese T, Gascón JA, Pan F, Rissanen K, Ruzzi M, Venzo A, Zoleo A, Maran F. A magnetic look into the protecting layer of Au 25 clusters. Chem Sci 2016; 7:6910-6918. [PMID: 28567262 PMCID: PMC5450596 DOI: 10.1039/c6sc03691k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/18/2016] [Indexed: 12/18/2022] Open
Abstract
The field of molecular metal clusters protected by organothiolates is experiencing a very rapid growth. So far, however, a clear understanding of the fine interactions between the cluster core and the capping monolayer has remained elusive, despite the importance of the latter in interfacing the former to the surrounding medium. Here, we describe a very sensitive methodology that enables comprehensive assessment of these interactions. Pulse electron nuclear double resonance (ENDOR) was employed to study the interaction of the unpaired electron with the protons of the alkanethiolate ligands in four structurally related paramagnetic Au25(SR)018 clusters (R = ethyl, propyl, butyl, 2-methylpropyl). Whereas some of these structures were known, we present the first structural description of the highly symmetric Au25(SPr)018 cluster. Through knowledge of the structural data, the ENDOR signals could be successfully related to the types of ligand and the distance of the relevant protons from the central gold core. We found that orbital distribution affects atoms that can be as far as 6 Å from the icosahedral core. Simulations of the spectra provided the values of the hyperfine coupling constants. The resulting information was compared with that provided by 1H NMR spectroscopy, and molecular dynamics calculations provided useful hints to understanding differences between the ENDOR and NMR results. It is shown that the unpaired electron can be used as a very precise probe of the main structural features of the interface between the metal core and the capping ligands.
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Affiliation(s)
- Mikhail Agrachev
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy . ;
| | - Sabrina Antonello
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy . ;
| | - Tiziano Dainese
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy . ;
| | - José A Gascón
- Department of Chemistry , University of Connecticut , 55 North Eagleville Road, Storrs , 06269 Connecticut , USA
| | - Fangfang Pan
- Department of Chemistry , Nanoscience Center , University of Jyväskylä , P.O. Box 35 , 40014 JYU , Finland
| | - Kari Rissanen
- Department of Chemistry , Nanoscience Center , University of Jyväskylä , P.O. Box 35 , 40014 JYU , Finland
| | - Marco Ruzzi
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy . ;
| | - Alfonso Venzo
- National Research Council , ICMATE c/o Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy
| | - Alfonso Zoleo
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy . ;
| | - Flavio Maran
- Department of Chemistry , University of Padova , via Marzolo 1 , 35131 Padova , Italy . ;
- Department of Chemistry , University of Connecticut , 55 North Eagleville Road, Storrs , 06269 Connecticut , USA
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Askerka M, Ho J, Batista ER, Gascón JA, Batista VS. The MOD-QM/MM Method: Applications to Studies of Photosystem II and DNA G-Quadruplexes. Methods Enzymol 2016; 577:443-81. [PMID: 27498648 PMCID: PMC5304415 DOI: 10.1016/bs.mie.2016.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and catalytic sites embedded in macrobiomolecules (eg, proteins and nucleic acids). QM/MM methodologies are highly efficient since they implement quantum chemistry methods for modeling only the portion of the system involving bond-breaking/forming processes (QM layer), as influenced by the surrounding molecular environment described in terms of molecular mechanics force fields (MM layer). Some of the limitations of QM/MM methods when polarization effects are not explicitly considered include the approximate treatment of electrostatic interactions between QM and MM layers. Here, we review recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in biomacromolecules and structural refinement, beyond the common limitations of QM/MM hybrid methods. We focus on photosystem II (PSII) with emphasis on the description of the oxygen-evolving complex (OEC) and its high-resolution extended X-ray absorption fine structure spectra (EXAFS) in conjunction with Monte Carlo structural refinement. Furthermore, we review QM/MM structural refinement studies of DNA G4 quadruplexes with embedded monovalent cations and direct comparisons to NMR data.
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Affiliation(s)
- M Askerka
- Yale University, New Haven, CT, United States
| | - J Ho
- Yale University, New Haven, CT, United States
| | - E R Batista
- Los Alamos National Laboratory, Los Alamos, NM, United States
| | - J A Gascón
- University of Connecticut, Storrs, CT, United States
| | - V S Batista
- Yale University, New Haven, CT, United States.
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27
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Abstract
This paper introduces structural models of the oxygen-evolving complex of photosystem II (PSII) in the dark-stable S1 state, as well as in the reduced S0 and oxidized S2 states, with complete ligation of the metal-oxo cluster by amino acid residues, water, hydroxide, and chloride. The models are developed according to state-of-the-art quantum mechanics/molecular mechanics (QM/MM) hybrid methods, applied in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus, recently reported at 3.5 Å resolution. Manganese and calcium ions are ligated consistently with standard coordination chemistry assumptions, supported by biochemical and spectroscopic data. Furthermore, the calcium-bound chloride ligand is found to be bound in a position consistent with pulsed electron paramagnetic resonance data obtained from acetate-substituted PSII. The ligation of protein ligands includes monodentate coordination of D1-D342, CP43-E354, and D1-D170 to Mn(1), Mn(3), and Mn(4), respectively; η(2) coordination of D1-E333 to both Mn(3) and Mn(2); and ligation of D1-E189 and D1-H332 to Mn(2). The resulting QM/MM structural models are consistent with available mechanistic data and also are compatible with X-ray diffraction models and extended X-ray absorption fine structure measurements of PSII. It is, therefore, conjectured that the proposed QM/MM models are particularly relevant to the development and validation of catalytic water-oxidation intermediates.
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Affiliation(s)
- Eduardo M Sproviero
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - José A Gascón
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - James P McEvoy
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - Gary W Brudvig
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - Victor S Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
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Sharifi R, Samaraweera M, Gascón JA, Papadimitrakopoulos F. Thermodynamics of the Quasi-Epitaxial Flavin Assembly around Various-Chirality Carbon Nanotubes. J Am Chem Soc 2014; 136:7452-63. [DOI: 10.1021/ja502714z] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Roholah Sharifi
- Nanomaterials Optoelectronics Laboratory (NOEL), Polymer Program,
Institute of Materials Science and ‡Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3136, United States
| | - Milinda Samaraweera
- Nanomaterials Optoelectronics Laboratory (NOEL), Polymer Program,
Institute of Materials Science and ‡Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3136, United States
| | - José A. Gascón
- Nanomaterials Optoelectronics Laboratory (NOEL), Polymer Program,
Institute of Materials Science and ‡Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3136, United States
| | - Fotios Papadimitrakopoulos
- Nanomaterials Optoelectronics Laboratory (NOEL), Polymer Program,
Institute of Materials Science and ‡Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3136, United States
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29
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Dainese T, Antonello S, Gascón JA, Pan F, Perera NV, Ruzzi M, Venzo A, Zoleo A, Rissanen K, Maran F. Au₂₅(SEt)₁₈, a nearly naked thiolate-protected Au₂₅ cluster: structural analysis by single crystal X-ray crystallography and electron nuclear double resonance. ACS Nano 2014; 8:3904-3912. [PMID: 24628268 DOI: 10.1021/nn500805n] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
X-ray crystallography has been fundamental in discovering fine structural features of ultrasmall gold clusters capped by thiolated ligands. For still unknown structures, however, new tools capable of providing relevant structural information are sought. We prepared a 25-gold atom nanocluster protected by the smallest ligand ever used, ethanethiol. This cluster displays the electrochemistry, mass spectrometry, and UV-vis absorption spectroscopy features of similar Au25 clusters protected by 18 thiolated ligands. The anionic and the neutral form of Au25(SEt)18 were fully characterized by (1)H and (13)C NMR spectroscopy, which confirmed the monolayer's properties and the paramagnetism of neutral Au25(SEt)18(0). X-ray crystallography analysis of the latter provided the first known structure of a gold cluster protected by a simple, linear alkanethiolate. Here, we also report the direct observation by electron nuclear double resonance (ENDOR) of hyperfine interactions between a surface-delocalized unpaired electron and the gold atoms of a nanocluster. The advantages of knowing the exact molecular structure and having used such a small ligand allowed us to compare the experimental values of hyperfine couplings with DFT calculations unaffected by structure's approximations or omissions.
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Affiliation(s)
- Tiziano Dainese
- Department of Chemistry, University of Padova , via Marzolo 1, 35131 Padova, Italy
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30
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Garbuio L, Li Y, Antonello S, Gascón JA, Lawler RG, Lei X, Murata Y, Turro NJ, Maran F. Interaction of H2@C60and Nitroxide through Conformationally Constrained Peptide Bridges. Photochem Photobiol 2013; 90:439-47. [DOI: 10.1111/php.12191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 10/11/2013] [Indexed: 01/22/2023]
Affiliation(s)
- Luca Garbuio
- Department of Chemistry; University of Padova; Padova Italy
| | - Yongjun Li
- Department of Chemistry; Columbia University; New York NY
| | | | - José A. Gascón
- Department of Chemistry; University of Connecticut; Storrs CT
| | | | - Xuegong Lei
- Department of Chemistry; Columbia University; New York NY
| | - Yasujiro Murata
- Institute for Chemical Research; Kyoto University; Kyoto Japan
| | | | - Flavio Maran
- Department of Chemistry; University of Padova; Padova Italy
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31
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Farber E, Rudnitskaya A, Keshipeddy S, Lao KS, Gascón JA, Howell AR. Silicon Acceleration of a Tandem Alkene Isomerization/Electrocyclic Ring-opening of 2-Methyleneoxetanes to α,β-Unsaturated Methylketones. J Org Chem 2013; 78:11213-20. [DOI: 10.1021/jo4014645] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elisa Farber
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Aleksandra Rudnitskaya
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Santosh Keshipeddy
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Kendricks S. Lao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - José A. Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Amy R. Howell
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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32
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Antonello S, Perera NV, Ruzzi M, Gascón JA, Maran F. Interplay of Charge State, Lability, and Magnetism in the Molecule-like Au25(SR)18 Cluster. J Am Chem Soc 2013; 135:15585-94. [DOI: 10.1021/ja407887d] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Sabrina Antonello
- Department of
Chemistry, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - Neranjan V. Perera
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269 United States
| | - Marco Ruzzi
- Department of
Chemistry, University of Padova, via Marzolo 1, 35131 Padova, Italy
| | - José A. Gascón
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269 United States
| | - Flavio Maran
- Department of
Chemistry, University of Padova, via Marzolo 1, 35131 Padova, Italy
- Department of Chemistry, University of Connecticut, 55 North Eagleville Road, Storrs, Connecticut 06269 United States
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Abstract
8,5'-Cyclopurine deoxynucleosides are unique tandem lesions containing an additional covalent bond between the base and the sugar. These mutagenic and genotoxic lesions are repaired only by nucleotide excision repair. The N-glycosidic (or C1'-N9) bond of 2'-deoxyguanosine (dG) derivatives is usually susceptible to acid hydrolysis, but even after cleavage of this bond of the cyclopurine lesions, the base would remain attached to the sugar. Here, the stability of the N-glycosidic bond and the products formed by formic acid hydrolysis of (5'S)-8,5'-cyclo-2'-deoxyguanosine (S-cdG) were investigated. For comparison, the stability of the N-glycosidic bond of 8,5'-cyclo-2',5'-dideoxyguanosine (ddcdG), 8-methyl-2'-deoxyguanosine (8-Me-dG), 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-Oxo-dG), and dG was also studied. In various acid conditions, S-cdG and ddcdG exhibited similar stability to hydrolysis. Likewise, 8-Me-dG and dG showed comparable stability, but the half-lives of the cyclic dG lesions were at least 5-fold higher than those of dG or 8-Me-dG. NMR studies were carried out to investigate the products formed after the cleavage of the C1'-N9 bond. 2-Deoxyribose generated α and β anomers of deoxyribopyranose and deoxyribopyranose oligomers following acid treatment. S-cdG gave α- and β-deoxyribopyranose linked guanine as the major products, but α and β anomers of deoxyribofuranose linked guanine and other products were also detected. The N-glycosidic bond of 8-Oxo-dG was found exceptionally stable in acid. Computational studies determined that both the protonation of the N7 atom and the rate constant in the bond breaking step control the overall kinetics of hydrolysis, but both varied for the molecules studied indicating a delicate balance between the two steps. Nevertheless, the computational approach successfully predicted the trend observed experimentally. For 8-Oxo-dG, the low pK(a) of O(8) and N3 prevented appreciable protonation, making the free energy for N-glycosidic bond cleavage in the subsequent step very high.
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Affiliation(s)
- Rajat S Das
- Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
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Rudnitskaya AN, Eddy NA, Fenteany G, Gascón JA. Recognition and reactivity in the binding between Raf kinase inhibitor protein and its small-molecule inhibitor locostatin. J Phys Chem B 2012; 116:10176-81. [PMID: 22861375 DOI: 10.1021/jp303140j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The present work is aimed to provide detail on the binding process between Raf kinase inhibitor protein (RKIP) and locostatin, the only exogenous compound known to alter the function of RKIP. Understanding the basis of RKIP inhibition for use in pharmacological applications is of considerable interest, as dysregulated RKIP expression has the potential to contribute to pathophysiological processes. Herein, we report a series of atomistic models to describe the protein-ligand recognition step and the subsequent reactivity steps. Modeling approaches include ligand docking, molecular dynamics, and quantum mechanics/molecular mechanics calculations. We expect that such a computational assay will serve to study similar complexes in which potency is associated with recognition and reactivity. Although previous data suggested a single amino acid residue (His86) to be involved in the binding of locostatin, the actual ligand conformation and the steps involved in the reactivity process remain elusive from a detailed atomistic description. We show that the first reaction step, consisting of a nucleophilic attack of the nitrogen (Nε) of His86 at the sp(2)-hybridized carbon (C2) of locostatin, presents a late transition state (almost identical to the product). The reaction is followed by a hydrogen abstraction and hydrolysis. The theoretically predicted overall rate constant (6 M(-1) s(-1)) is in a very good agreement with the experimentally determined rate constant (13 M(-1) s(-1)).
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Affiliation(s)
- Aleksandra N Rudnitskaya
- Department of Chemistry, The University of Connecticut , 55 North Eagleville Road, Storrs, Connecticut 06269, United States
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35
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Ju SY, Abanulo DC, Badalucco CA, Gascón JA, Papadimitrakopoulos F. Handedness enantioselection of carbon nanotubes using helical assemblies of flavin mononucleotide. J Am Chem Soc 2012; 134:13196-9. [PMID: 22871052 DOI: 10.1021/ja305250g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In order to truly unlock advanced applications of single-walled carbon nanotubes (SWNTs), one needs to separate them according to both chirality and handedness. Here we show that the chiral D-ribityl phosphate chain of flavin mononucleotide (FMN) induces a right-handed helix that enriches the left-handed SWNTs for all suspended (n,m) species. Such enantioselectivity stems from the sp(3) hybridization of the N atom anchoring the sugar moiety to the flavin ring. This produces two FMN conformations (syn and anti) analogous to DNA. Electrostatic interactions between the neighboring uracil moiety and the 2'-OH group of the side chain provide greater stability to the anti-FMN conformation that leads to a right-handed FMN helix. The right-handed twist that the FMN helix imposes to the underlying nanotube, similar to "Indian burn", causes diameter dilation of only the left-handed SWNTs, whose improved intermolecular interactions with the overlaying FMN helix, impart enantioselection.
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Affiliation(s)
- Sang-Yong Ju
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3136, USA
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36
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Abstract
Recent developments in the biophysical characterization of proteins have provided a means of directly measuring electrostatic fields by introducing a probe molecule to the system of interest and interpreting photon absorption in the context of the Stark effect. To fully account for this effect, the development of accurate atomistic models is of paramount importance. However, suitable computational protocols for evaluating Stark shifts in proteins are yet to be established. In this work, we present a comprehensive computational method to predict the change in absorption frequency of a probe functional group as a direct result of a perturbation in its surrounding electrostatic field created by a protein environment, i.e., the Stark shift. We apply the method to human aldose reductase, a key protein enzyme that catalyzes the reduction of monosaccharides. We develop a protocol based on a combination of molecular dynamics and moving-domain QM/MM methods, which achieves quantitative agreement with experiment. We outline the difficulties in predicting localized electrostatic field changes within a protein environment, and by extension the Stark shift, due to a protein site mutation. Furthermore, the combined use of Stark effect spectroscopy and computational modeling is used to predict the protonation state of ionizable residues in the vicinity of the electrostatic probe.
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Affiliation(s)
- Daniel J Sandberg
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
| | | | - José A Gascón
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269, United States
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37
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Venzo A, Antonello S, Gascón JA, Guryanov I, Leapman RD, Perera NV, Sousa A, Zamuner M, Zanella A, Maran F. Effect of the charge state (z = -1, 0, +1) on the nuclear magnetic resonance of monodisperse Au25[S(CH2)2Ph]18(z) clusters. Anal Chem 2011; 83:6355-62. [PMID: 21718063 DOI: 10.1021/ac2012653] [Citation(s) in RCA: 110] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monodisperse Au(25)L(18)(0) (L = S(CH(2))(2)Ph) and [n-Oct(4)N(+)][Au(25)L(18)(-)] clusters were synthesized in tetrahydrofuran. An original strategy was then devised to oxidize them: in the presence of bis(pentafluorobenzoyl) peroxide, the neutral or the negatively charged clusters react as efficient electron donors in a dissociative electron-transfer (ET) process, in the former case yielding [Au(25)L(18)(+)][C(6)F(5)CO(2)(-)]. As opposed to other reported redox methods, this dissociative ET approach is irreversible, easily controllable, and clean, particularly for NMR purposes, as no hydrogen atoms are introduced. By using this approach, the -1, 0, and +1 charge states of Au(25)L(18) could be fully characterized by (1)H and (13)C NMR spectroscopy, using one- and two-dimensional techniques, in various solvents, and as a function of temperature. For all charge states, the NMR results and analysis nicely match recent structural findings about the presence of two different ligand populations in the capping monolayer, each resonance of the two ligand families displaying distinct NMR patterns. The radical nature of Au(25)L(18)(0) is particularly evident in the (1)H and (13)C NMR patterns of the inner ligands. The NMR behavior of radical Au(25)L(18)(0) was also simulated by DFT calculations, and the interplay between theory and experiments revealed a fundamental paramagnetic contribution coming from Fermi contact shifts. Interestingly, the NMR patterns of Au(25)L(18)(-) and Au(25)L(18)(+) were found to be quite similar, pointing to the latter cluster form as a diamagnetic species.
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Affiliation(s)
- Alfonso Venzo
- Department of Chemistry, University of Padova, Padova, Italy
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38
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Menikarachchi LC, Gascón JA. An extrapolation method for computing protein solvation energies based on density fragmentation of a graphical surface tessellation. J Mol Graph Model 2011; 30:38-45. [PMID: 21715202 DOI: 10.1016/j.jmgm.2011.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/26/2011] [Accepted: 06/02/2011] [Indexed: 11/28/2022]
Abstract
Modeling chemical events inside proteins often require the incorporation of solvent effects via continuum polarizable models. One of these approaches is based on the assumption that the interface between solute and solvent acts as a conductor. Image charges are added on the molecular surface to satisfy the appropriate conductor boundary conditions in the presence of solute charges. As in the case of other polarizable continuum models that are based on surface tessellation, the simplest implementation of this approach is often limited to several hundred atoms due to a matrix inversion, which scales as the cube of the number or tesserae. For larger systems, approaches that use iterative matrix solvers coupled to fast summation methods must be used. In the present work, we develop a self-consistent approach to obtain conductor-like screening charges suitable for applications in proteins. The approach is based on a density fragmentation of a graphical surface tessellation. This method, although approximate, provides a straightforward scheme of parallelization, which can in principle be added to existing linear scaling implementations of conductor-like models. We implement this method in conjunction with a fixed charge model for the protein, as well as with a moving domain QM/MM description of the protein. In the latter case, the overall result leads to a charge distribution within the protein determined by self-polarization and polarization due to solvent.
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Affiliation(s)
- Lochana C Menikarachchi
- Department of Chemistry, University of Connecticut, 55 North Eagleville Rd., Unit 3060, Storrs, CT 06269, USA
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Beshir AB, Argueta CE, Menikarachchi LC, Gascón JA, Fenteany G. Locostatin Disrupts Association of Raf Kinase Inhibitor Protein With Binding Proteins by Modifying a Conserved Histidine Residue in the Ligand-Binding Pocket. ACTA ACUST UNITED AC 2011; 2:47-58. [PMID: 21709760 DOI: 10.1615/forumimmundisther.v2.i1.60] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Raf kinase inhibitor protein (RKIP) interacts with a number of different proteins and regulates multiple signaling pathways. Here, we show that locostatin, a small molecule that covalently binds RKIP, not only disrupts interactions of RKIP with Raf-1 kinase, but also with G protein-coupled receptor kinase 2. In contrast, we found that locostatin does not disrupt binding of RKIP to two other proteins: inhibitor of κB kinase α and transforming growth factor β-activated kinase 1. These results thus imply that different proteins interact with different regions of RKIP. Locostatin's mechanism of action involves modification of a nucleophilic residue on RKIP. We observed that after binding RKIP, part of locostatin is slowly hydrolyzed, leaving a smaller RKIP-butyrate adduct. We identified the residue alkylated by locostatin as His86, a highly conserved residue in RKIP's ligand-binding pocket. Computational modeling of the binding of locostatin to RKIP suggested that the recognition interaction between small molecule and protein ensures that locostatin's electrophilic site is poised to react with His86. Furthermore, binding of locostatin would sterically hinder binding of other ligands in the pocket. These data provide a basis for understanding how locostatin disrupts particular interactions of RKIP with RKIP-binding proteins and demonstrate its utility as a probe of specific RKIP interactions and functions.
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Affiliation(s)
- Anwar B Beshir
- Department of Chemistry, University of Connecticut, Storrs, Connecticut
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40
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Duff MR, Fyvie WS, Markad SD, Frankel AE, Kumar CV, Gascón JA, Peczuh MW. Computational and experimental investigations of mono-septanoside binding by Concanavalin A: correlation of ligand stereochemistry to enthalpies of binding. Org Biomol Chem 2010; 9:154-64. [PMID: 21085738 DOI: 10.1039/c0ob00425a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Structure-energy relationships for a small group of pyranose and septanose mono-saccharide ligands are developed for binding to Concanavalin A (ConA). The affinity of ConA for methyl "manno"β-septanoside 7 was found to be higher than any of the previously reported mono-septanoside ligands. Isothermal titration calorimetry (ITC) in conjunction with docking simulations and quantum mechanics/molecular mechanics (QM/MM) modeling established the specific role of binding enthalpy in the structure-energy relations of ConA bound to natural mono-saccharides and unnatural mono-septanosides. An important aspect in the differential binding among ligands is the deformation energy required to reorganize internal hydroxyl groups upon binding of the ligand to ConA.
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Affiliation(s)
- Michael R Duff
- Department of Chemistry, The University of Connecticut, 55 North Eagleville Road, Storrs, CT 06269, USA
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41
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Farber E, Herget J, Gascón JA, Howell AR. Unexpected Cleavage of 2-Azido-2-(hydroxymethyl)oxetanes: Conformation Determines Reaction Pathway? J Org Chem 2010; 75:7565-72. [DOI: 10.1021/jo101328c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Elisa Farber
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Jackson Herget
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - José A. Gascón
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
| | - Amy R. Howell
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060, United States
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42
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Abstract
One of the goals of medicinal chemistry concerns the ability to compute protein-ligand interactions based on the structural knowledge of the receptor. To this end, the majority of current approaches incorporate classical force field potentials to describe receptor-ligand interactions. One of the most critical problems of standard molecular mechanics (MM) force fields is their fixed-charge treatment of electrostatic interactions. Two problems are derived from this approximation, polarization and charge transfer. As an immediate step in computational complexity, it seems natural to incorporate Quantum Mechanics (QM) within a hybrid QM/MM approach, which has shown to be a useful tool to describe structural and mechanistic aspects of chromophores and prosthetic residues in proteins. In this review, we describe specifically the role of QM/MM methods and their various applications to computational drug design and medicinal chemistry research in general.
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Affiliation(s)
- Lochana C Menikarachchi
- Department of Chemistry, University of Connecticut, 55 North Eagleville Rd, Unit 3060, Storrs, CT 06269, USA
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43
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Sproviero EM, Newcomer MB, Gascón JA, Batista ER, Brudvig GW, Batista VS. The MoD-QM/MM methodology for structural refinement of photosystem II and other biological macromolecules. Photosynth Res 2009; 102:455-470. [PMID: 19633920 PMCID: PMC2954272 DOI: 10.1007/s11120-009-9467-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 06/25/2009] [Indexed: 05/28/2023]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) hybrid methods are currently the most powerful computational tools for studies of structure/function relations and structural refinement of macrobiomolecules (e.g., proteins and nucleic acids). These methods are highly efficient, since they implement quantum chemistry techniques for modeling only the small part of the system (QM layer) that undergoes chemical modifications, charge transfer, etc., under the influence of the surrounding environment. The rest of the system (MM layer) is described in terms of molecular mechanics force fields, assuming that its influence on the QM layer can be roughly decomposed in terms of electrostatic interactions and steric hindrance. Common limitations of QM/MM methods include inaccuracies in the MM force fields, when polarization effects are not explicitly considered, and the approximate treatment of electrostatic interactions at the boundaries between QM and MM layers. This article reviews recent advances in the development of computational protocols that allow for rigorous modeling of electrostatic interactions in extended systems beyond the common limitations of QM/MM hybrid methods. We focus on the moving-domain QM/MM (MoD-QM/MM) methodology that partitions the system into many molecular domains and obtains the electrostatic and structural properties of the whole system from an iterative self-consistent treatment of the constituent molecular fragments. We illustrate the MoD-QM/MM method as applied to the description of photosystem II as well as in conjunction with the application of spectroscopically constrained QM/MM optimization methods, based on high-resolution spectroscopic data (extended X-ray absorption fine structure spectra, and exchange coupling constants).
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Affiliation(s)
- Eduardo M. Sproviero
- Yale University, Department of Chemistry, P. O. Box 208107, New Haven Connecticut 06520-8107 USA
| | - Michael B. Newcomer
- Yale University, Department of Chemistry, P. O. Box 208107, New Haven Connecticut 06520-8107 USA
| | | | - Enrique R. Batista
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
| | - Gary W. Brudvig
- Yale University, Department of Chemistry, P. O. Box 208107, New Haven Connecticut 06520-8107 USA
| | - Victor S. Batista
- Yale University, Department of Chemistry, P. O. Box 208107, New Haven Connecticut 06520-8107 USA
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Zhang Y, Gascón JA. QM/MM investigation of structure and spectroscopic properties of a vanadium-containing peroxidase. J Inorg Biochem 2008; 102:1684-90. [DOI: 10.1016/j.jinorgbio.2008.04.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2008] [Revised: 04/09/2008] [Accepted: 04/21/2008] [Indexed: 11/25/2022]
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Sproviero EM, McEvoy JP, Gascón JA, Brudvig GW, Batista VS. Computational insights into the O2-evolving complex of photosystem II. Photosynth Res 2008; 97:91-114. [PMID: 18483777 PMCID: PMC2728911 DOI: 10.1007/s11120-008-9307-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2007] [Accepted: 04/10/2008] [Indexed: 05/04/2023]
Abstract
Mechanistic investigations of the water-splitting reaction of the oxygen-evolving complex (OEC) of photosystem II (PSII) are fundamentally informed by structural studies. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy, and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the exact configuration of the catalytic metal cluster and its ligation scheme. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein, have proposed chemically satisfactory models of the fully ligated OEC within PSII that are maximally consistent with experimental results. The inorganic core of these models is similar to the crystallographic model upon which they were based, but comprises important modifications due to structural refinement, hydration, and proteinaceous ligation which improve agreement with a wide range of experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting in PSII as described by the intermediate oxidation states of the OEC. This review summarizes these recent advances in QM/MM modeling of PSII within the context of recent experimental studies.
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Sproviero EM, Shinopoulos K, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. QM/MM computational studies of substrate water binding to the oxygen-evolving centre of photosystem II. Philos Trans R Soc Lond B Biol Sci 2008; 363:1149-56; discussion 1156. [PMID: 17971333 DOI: 10.1098/rstb.2007.2210] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
This paper reports computational studies of substrate water binding to the oxygen-evolving centre (OEC) of photosystem II (PSII), completely ligated by amino acid residues, water, hydroxide and chloride. The calculations are based on quantum mechanics/molecular mechanics hybrid models of the OEC of PSII, recently developed in conjunction with the X-ray crystal structure of PSII from the cyanobacterium Thermosynechococcus elongatus. The model OEC involves a cuboidal Mn3CaO4Mn metal cluster with three closely associated manganese ions linked to a single mu4-oxo-ligated Mn ion, often called the 'dangling manganese'. Two water molecules bound to calcium and the dangling manganese are postulated to be substrate molecules, responsible for dioxygen formation. It is found that the energy barriers for the Mn(4)-bound water agree nicely with those of model complexes. However, the barriers for Ca-bound waters are substantially larger. Water binding is not simply correlated to the formal oxidation states of the metal centres but rather to their corresponding electrostatic potential atomic charges as modulated by charge-transfer interactions. The calculations of structural rearrangements during water exchange provide support for the experimental finding that the exchange rates with bulk 18 O-labelled water should be smaller for water molecules coordinated to calcium than for water molecules attached to the dangling manganese. The models also predict that the S1-->S2 transition should produce opposite effects on the two water-exchange rates.
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Affiliation(s)
- Eduardo M Sproviero
- Department of Chemistry, Yale University, PO Box 208107, New Haven, CT 06520-8107, USA
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Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. A model of the oxygen-evolving center of photosystem II predicted by structural refinement based on EXAFS simulations. J Am Chem Soc 2008; 130:6728-30. [PMID: 18457397 DOI: 10.1021/ja801979n] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A refined computational structural model of the oxygen-evolving complex (OEC) of photosystem II (PSII) is introduced. The model shows that the cuboidal core Mn3CaO4 with a "dangler" Mn ligated to a corner mu4-oxide ion is maximally consistent with the positioning of the amino acids around the metal cluster as characterized by XRD models and high-resolution spectroscopic data, including polarized EXAFS of oriented single crystals and isotropic EXAFS. It is, therefore, natural to expect that the proposed structural model should be particularly useful to establish the structure of the OEC, consistently with high-resolution spectroscopic data, and for elucidating the mechanism of water-splitting in PSII as described by the intermediate oxidation states of the EC along the catalytic cycle.
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Affiliation(s)
- Eduardo M Sproviero
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
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Menikarachchi LC, Gascón JA. Optimization of cutting schemes for the evaluation of molecular electrostatic potentials in proteins via Moving-Domain QM/MM. J Mol Model 2008; 14:479-87. [DOI: 10.1007/s00894-008-0306-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 03/19/2008] [Indexed: 11/29/2022]
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Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. Quantum Mechanics/Molecular Mechanics Study of the Catalytic Cycle of Water Splitting in Photosystem II. J Am Chem Soc 2008; 130:3428-42. [DOI: 10.1021/ja076130q] [Citation(s) in RCA: 311] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Eduardo M. Sproviero
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - José A. Gascón
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - James P. McEvoy
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - Gary W. Brudvig
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut 06520-8107
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Sproviero EM, Gascón JA, McEvoy JP, Brudvig GW, Batista VS. Quantum mechanics/molecular mechanics structural models of the oxygen-evolving complex of photosystem II. Curr Opin Struct Biol 2007; 17:173-80. [PMID: 17395452 DOI: 10.1016/j.sbi.2007.03.015] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2006] [Revised: 01/18/2007] [Accepted: 03/16/2007] [Indexed: 11/23/2022]
Abstract
The annual production of 260 Gtonnes of oxygen, during the process of photosynthesis, sustains life on earth. Oxygen is produced in the thylakoid membranes of green-plant chloroplasts and the internal membranes of cyanobacteria by photocatalytic water oxidation at the oxygen-evolving complex (OEC) of photosystem II (PSII). Recent breakthroughs in X-ray crystallography and advances in quantum mechanics/molecular mechanics (QM/MM) hybrid methods have enabled the construction of chemically sensible models of the OEC of PSII. The resulting computational structural models suggest the complete ligation of the catalytic center by amino acid residues, water, hydroxide and chloride, as determined from the intrinsic electronic properties of the oxomanganese core and the perturbational influence of the surrounding protein environment. These structures are found to be consistent with available mechanistic data, and are also compatible with X-ray diffraction models and extended X-ray absorption fine structure measurements. It is therefore conjectured that these OEC models are particularly relevant for the elucidation of the catalytic mechanism of water oxidation.
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