1
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Kumar A, Mishra B, Konar AD, Mylonakis E, Basu A. Molecular Dynamics Simulations Help Determine the Molecular Mechanisms of Lasioglossin-III and Its Variant Peptides' Membrane Interfacial Interactions. J Phys Chem B 2024; 128:6049-6058. [PMID: 38840325 DOI: 10.1021/acs.jpcb.4c02387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Lasioglossin-III (LL-III) is a potent broad-spectrum antimicrobial peptide used in diverse antimicrobial applications. In this work, coarse-grained and all-atom molecular dynamics simulation strategies were used in tandem to interpret the molecular mechanisms involved in the interfacial dynamics of LL-III and its recombinant variants during interactions with diverse cell membrane systems. Our results indicate that the membrane charges act as the driving force for initiating the membrane-peptide interactions, while the hydrophobic or van der Waals forces help to reinforce the membrane-peptide bindings. The optimized charge-hydrophobicity ratio of the LL-III peptides helps ensure their high specificity toward bacterial membranes compared to mammalian membrane systems, which also helps explain our experimental observations. Overall, we hope that our work gives new insight into the antimicrobial action of LL-III peptides and that the adopted simulation strategy will help other scientists and engineers extract maximal information from complex molecular simulations using minimal computational power.
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Affiliation(s)
- Atul Kumar
- School of Pharmaceutical Sciences, Rajiv Gandhi Technological University, Airport Bypass Road, Gandhinagar, Bhopal 462033, India
| | - Biswajit Mishra
- Department of Medicine, Houston Methodist Hospital, Houston, Texas 77030, United States
| | - Anita Dutt Konar
- School of Pharmaceutical Sciences, Rajiv Gandhi Technological University, Airport Bypass Road, Gandhinagar, Bhopal 462033, India
- Department of Applied Chemistry, Rajiv Gandhi Technological University, Bhopal 462033, India
| | - Eleftherios Mylonakis
- Department of Medicine, Houston Methodist Hospital, Houston, Texas 77030, United States
| | - Anindya Basu
- School of Pharmaceutical Sciences, Rajiv Gandhi Technological University, Airport Bypass Road, Gandhinagar, Bhopal 462033, India
- School of Biomolecular Engineering and Biotechnology, Rajiv Gandhi Technological University, Bhopal 462033, India
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2
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Metya S, Roy S, Mandal S, Huang QR, Kuo JL, Das A. Modulation of the strength of weak S-H⋯O hydrogen-bond: Spectroscopic study of the complexes of 2-flurothiophenol with methanol and ethanol. J Chem Phys 2024; 160:224302. [PMID: 38856058 DOI: 10.1063/5.0208086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024] Open
Abstract
Spectroscopic exploration of sulfur-centered hydrogen bonding involving a thiol group (S-H) as the hydrogen bond donor is scarce in the literature. Herein, we have investigated 1:1 complexes of 2-fluorothiophenol (2-FTP) with methanol (MeOH) and ethanol (EtOH) in the gas phase to examine the physical characteristics and strength of the S-H⋯O hydrogen bond. Structures, conformations, and the strength of the S-H⋯O interaction are investigated by measuring the electronic and Infrared (IR) spectra of the two complexes employing resonant two-photon ionization, UV-UV hole-burning, and IR-UV double resonance spectroscopic techniques combined with quantum chemical calculations. Three conformers of 2-FTP⋯MeOH and two conformers of 2-FTP⋯EtOH have been detected in the experiment. A comparison of the IR spectra obtained from the experiment with those of the low-energy conformers of 2-FTP⋯MeOH and 2-FTP⋯EtOH predicted from the theory confirms that all the observed conformers of the two complexes are primarily S-H⋯O hydrogen bonded. The IR red-shifts found in the S-H stretching frequencies in 2-FTP⋯MeOH and 2-FTP⋯EtOH concerning that in 2-FTP are ∼76 and ∼88 cm-1, respectively, which are much larger than that was reported earlier in the 2-FTP⋯H2O complex (30 cm-1). The strength and physical nature of different noncovalent interactions, including the S-H⋯O hydrogen bond existing in the complexes, are further analyzed using natural bond orbital analysis, quantum theory of atoms in molecules, and localized molecular orbital-energy decomposition analysis. The current investigation reveals that the S-H⋯O hydrogen bond can be strengthened by judicial choices of the hydrogen bond acceptors of higher proton affinities.
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Affiliation(s)
- Surajit Metya
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Supravat Roy
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sourav Mandal
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Qian-Rui Huang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Jer-Lai Kuo
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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3
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Torres-Hernández F, Pinillos P, Li W, Saragi RT, Camiruaga A, Juanes M, Usabiaga I, Lesarri A, Fernández JA. Competition between O-H and S-H Intermolecular Interactions in Conformationally Complex Systems: The 2-Phenylethanethiol and 2-Phenylethanol Dimers. J Phys Chem Lett 2024; 15:5674-5680. [PMID: 38767855 PMCID: PMC11145646 DOI: 10.1021/acs.jpclett.4c00903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/15/2024] [Accepted: 05/16/2024] [Indexed: 05/22/2024]
Abstract
Noncovalent interactions involving sulfur centers play a relevant role in biological and chemical environments. Yet, detailed molecular descriptions are scarce and limited to very simple model systems. Here we explore the formation of the elusive S-H···S hydrogen bond and the competition between S-H···O and O-H···S interactions in pure and mixed dimers of the conformationally flexible molecules 2-phenylethanethiol (PET) and 2-phenylethanol (PEAL), using the isolated and size-controlled environment of a jet expansion. The structure of both PET-PET and PET-PEAL dimers was unraveled through a comprehensive methodology that combined rotationally resolved microwave spectroscopy, mass-resolved isomer-specific infrared laser spectroscopy, and quantum chemical calculations. This synergic experimental-computational approach offered unique insights into the potential energy surface, conformational equilibria, molecular structure, and intermolecular interactions of the dimers. The results show a preferential order for establishing hydrogen bonds following the sequence S-H···S < S-H···O ≲ O-H···S < O-H···O, despite the hydrogen bond only accounting for a fraction of the total interaction energy.
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Affiliation(s)
- Fernando Torres-Hernández
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Paul Pinillos
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Wenqin Li
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias - I.U. CINQUIMA, Universidad
de Valladolid, Paseo de Belén, 7, E-47011 Valladolid, Spain
| | - Rizalina Tama Saragi
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias - I.U. CINQUIMA, Universidad
de Valladolid, Paseo de Belén, 7, E-47011 Valladolid, Spain
| | - Ander Camiruaga
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Marcos Juanes
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias - I.U. CINQUIMA, Universidad
de Valladolid, Paseo de Belén, 7, E-47011 Valladolid, Spain
| | - Imanol Usabiaga
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
| | - Alberto Lesarri
- Departamento
de Química Física y Química Inorgánica,
Facultad de Ciencias - I.U. CINQUIMA, Universidad
de Valladolid, Paseo de Belén, 7, E-47011 Valladolid, Spain
| | - José A. Fernández
- Departamento
de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco (UPV/EHU), Barrio Sarriena s/n, Leioa 48940, Spain
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4
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Botti G, Ceotto M, Conte R. Investigating the Spectroscopy of the Gas Phase Guanine-Cytosine Pair: Keto versus Enol Configurations. J Phys Chem Lett 2023; 14:8940-8947. [PMID: 37768143 PMCID: PMC10577776 DOI: 10.1021/acs.jpclett.3c02073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 09/26/2023] [Indexed: 09/29/2023]
Abstract
We report on a vibrational study of the guanine-cytosine dimer tautomers using state-of-the-art quasiclassical trajectory and semiclassical vibrational spectroscopy. The latter includes possible quantum mechanical effects. Through an accurate comparison to the experimental spectra, we are able to shine a light on the hydrogen bond network of one of the main subunits of DNA and put the experimental assignment on a solid footing. Our calculations corroborate the experimental conclusion that the global minimum Watson-and-Crick structure is not detected in the spectra, and there is no evidence of tunnel-effect-based double proton hopping. Our accurate assignment of the spectral features may also serve as a basis for the development of precise force fields to study the guanine-cytosine dimer.
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Affiliation(s)
- Giacomo Botti
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
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5
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Adhav V, Saikrishnan K. The Realm of Unconventional Noncovalent Interactions in Proteins: Their Significance in Structure and Function. ACS OMEGA 2023; 8:22268-22284. [PMID: 37396257 PMCID: PMC10308531 DOI: 10.1021/acsomega.3c00205] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/22/2023] [Indexed: 07/04/2023]
Abstract
Proteins and their assemblies are fundamental for living cells to function. Their complex three-dimensional architecture and its stability are attributed to the combined effect of various noncovalent interactions. It is critical to scrutinize these noncovalent interactions to understand their role in the energy landscape in folding, catalysis, and molecular recognition. This Review presents a comprehensive summary of unconventional noncovalent interactions, beyond conventional hydrogen bonds and hydrophobic interactions, which have gained prominence over the past decade. The noncovalent interactions discussed include low-barrier hydrogen bonds, C5 hydrogen bonds, C-H···π interactions, sulfur-mediated hydrogen bonds, n → π* interactions, London dispersion interactions, halogen bonds, chalcogen bonds, and tetrel bonds. This Review focuses on their chemical nature, interaction strength, and geometrical parameters obtained from X-ray crystallography, spectroscopy, bioinformatics, and computational chemistry. Also highlighted are their occurrence in proteins or their complexes and recent advances made toward understanding their role in biomolecular structure and function. Probing the chemical diversity of these interactions, we determined that the variable frequency of occurrence in proteins and the ability to synergize with one another are important not only for ab initio structure prediction but also to design proteins with new functionalities. A better understanding of these interactions will promote their utilization in designing and engineering ligands with potential therapeutic value.
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Affiliation(s)
- Vishal
Annasaheb Adhav
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research, Pune 411008, India
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6
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Ogawa A, Ohira S, Kato Y, Ikuta T, Yanagida S, Mi X, Ishii Y, Kanda Y, Nishida M, Inoue A, Wei FY. Activation of the urotensin-II receptor by remdesivir induces cardiomyocyte dysfunction. Commun Biol 2023; 6:511. [PMID: 37173432 PMCID: PMC10175918 DOI: 10.1038/s42003-023-04888-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Remdesivir is an antiviral drug used for COVID-19 treatment worldwide. Cardiovascular side effects have been associated with remdesivir; however, the underlying molecular mechanism remains unknown. Here, we performed a large-scale G-protein-coupled receptor screening in combination with structural modeling and found that remdesivir is a selective, partial agonist for urotensin-II receptor (UTS2R) through the Gαi/o-dependent AKT/ERK axis. Functionally, remdesivir treatment induced prolonged field potential and APD90 in human induced pluripotent stem cell (iPS)-derived cardiomyocytes and impaired contractility in both neonatal and adult cardiomyocytes, all of which mirror the clinical pathology. Importantly, remdesivir-mediated cardiac malfunctions were effectively attenuated by antagonizing UTS2R signaling. Finally, we characterized the effect of 110 single-nucleotide variants in UTS2R gene reported in genome database and found four missense variants that show gain-of-function effects in the receptor sensitivity to remdesivir. Collectively, our study illuminates a previously unknown mechanism underlying remdesivir-related cardiovascular events and that genetic variations of UTS2R gene can be a potential risk factor for cardiovascular events during remdesivir treatment, which collectively paves the way for a therapeutic opportunity to prevent such events in the future.
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Affiliation(s)
- Akiko Ogawa
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Seiya Ohira
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, 980-8575, Japan
- Graduate School of Medicine, Tohoku University, Sendai, Miyagi, 980-8575, Japan
| | - Yuri Kato
- Department of Physiology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tatsuya Ikuta
- Laboratory of Molecular & Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Shota Yanagida
- Division of Pharmacology, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
- Division of Pharmaceutical Sciences, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Xinya Mi
- Department of Physiology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yukina Ishii
- Department of Physiology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Yasunari Kanda
- Division of Pharmacology, National Institute of Health Sciences, Kanagawa, 210-9501, Japan
| | - Motohiro Nishida
- Department of Physiology, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, 812-8582, Japan.
- National Institute for Physiological Sciences and Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, 444-8787, Japan.
| | - Asuka Inoue
- Laboratory of Molecular & Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
| | - Fan-Yan Wei
- Department of Modomics Biology and Medicine, Institute of Development, Aging and Cancer (IDAC), Tohoku University, Sendai, Miyagi, 980-8575, Japan.
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7
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Lu T, Zhang J, Xu Y, Wang Z, Feng G, Zeng Z. Hydrogen bond interactions between thioethers and amides: A joint rotational spectroscopic and theoretical study of the formamide⋯dimethyl sulfide adduct. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 288:122199. [PMID: 36473293 DOI: 10.1016/j.saa.2022.122199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/17/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
The rotational spectrum of the binary adduct of formamide (HCONH2) with dimethyl sulfide (DMS) has been investigated employing cavity-based Fourier transform microwave spectroscopy combined with theoretical computations. Experimentally, only one isomer of the adduct was unambiguously observed and assigned according to the theoretically predicted spectroscopic parameters, and its rotational spectrum displays the hyperfine splittings associated with the 14N nuclear quadrupole coupling effect. The observed isomer exhibits Cs symmetry, such that the ∠CSC angle of the DMS subunit is bisected by the ab-plane of the HCONH2 moiety. The two moieties in the detected isomer are connected via one primary NH···S and two secondary CH···O hydrogen bonds. Quantum theory of atoms in molecules (QTAIM), non-covalent interaction (NCI), natural bond orbital (NBO) and symmetry-adapted perturbation theory (SAPT) approaches were utilized for characterizing the intermolecular interactions occurring in the titled adduct. Additionally, the adduct of HCONH2 with dimethyl ether (DME) was also theoretically investigated to compare the difference in structure and energy characteristics between the NH···S and NH···O hydrogen bonds.
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Affiliation(s)
- Tao Lu
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China; School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China.
| | - Jiaqi Zhang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Yugao Xu
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Zhen Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, Chongqing 401331, China
| | - Zhu Zeng
- School of Biology and Engineering, Guizhou Medical University, Guiyang 550025, China.
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8
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Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
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9
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Metya S, Das A. S–H···O Hydrogen Bond Can Win over O–H···S Hydrogen Bond: Gas-Phase Spectroscopy of 2-Fluorothiophenol···H 2O Complex. J Phys Chem A 2022; 126:9178-9189. [DOI: 10.1021/acs.jpca.2c06083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Surajit Metya
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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10
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Jena S, Routray C, Dutta J, Biswal HS. Hydrogen Bonding Directed Reversal of
13
C NMR Chemical Shielding. Angew Chem Int Ed Engl 2022; 61:e202207521. [DOI: 10.1002/anie.202207521] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Indexed: 12/30/2022]
Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Chinmay Routray
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Juhi Dutta
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur Via-Jatni, District-Khurda PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute, Training School Complex Anushakti Nagar Mumbai 400094 India
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11
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Zhu D, Yu L, Luo H, Xue X, Chen Z. Atroposelective Electrophilic Sulfenylation of
N
‐Aryl Aminoquinone Derivatives Catalyzed by Chiral SPINOL‐Derived Sulfide. Angew Chem Int Ed Engl 2022; 61:e202211782. [DOI: 10.1002/anie.202211782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Indexed: 11/07/2022]
Affiliation(s)
- Deng Zhu
- School of Chemistry and Chemical Engineering Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Lu Yu
- College of Chemistry Nankai University Tianjin 300071 P. R. China
- Key Laboratory of Organofluorine Chemistry Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai 200032 P. R. China
| | - Hui‐Yun Luo
- School of Chemistry and Chemical Engineering Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University Shanghai 200240 P. R. China
| | - Xiao‐Song Xue
- Key Laboratory of Organofluorine Chemistry Shanghai Institute of Organic Chemistry University of Chinese Academy of Sciences Chinese Academy of Sciences Shanghai 200032 P. R. China
- School of Chemistry and Materials Science Hangzhou Institute for Advanced Study University of Chinese Academy of Sciences 1 Sub-lane Xiangshan Hangzhou 310024 P. R. China
| | - Zhi‐Min Chen
- School of Chemistry and Chemical Engineering Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs Shanghai Jiao Tong University Shanghai 200240 P. R. China
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12
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Kumar Konidala K, Bommu U, Pabbaraju N. Integration of in silico methods to determine endocrine-disrupting tobacco pollutants binding potency with steroidogenic genes: comprehensive QSAR modeling and ensemble docking strategies. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:65806-65825. [PMID: 35501431 DOI: 10.1007/s11356-022-20443-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/21/2022] [Indexed: 06/14/2023]
Abstract
A myriad of tobacco-associated chemicals may have possibilities to developmental/reproductive axis and endocrine-disruption impacts. Mostly they breach the biotransformation of cholesterol in mitochondria by interfering with steroidogenic pathway genes, prompting to adverse effects in steroid biosynthesis; however, studies are scanty. The quantitative structure-activity relationship (QSAR) modeling and comparative docking strategies were used to understand structural features of dataset compounds that influence developmental/reproductive toxicity and estrogen and androgen receptor-binding abilities, and to predict binding levels of toxicants with steroidogenic acute regulatory protein (StAR) and cholesterol side-chain cleavage enzyme (CYP11A1) active sites. Developed QSAR models presented good robustness and predictive ability that were determined from the applicability domain and, clustering and classification of chemicals by performing self-organizing maps. Accordingly, the exorbitant amount of polycyclic aromatic hydrocarbons (PAHs) and a limited number of other chemicals including N-nitrosamines and nicotine was represented as potential developmental/reproductive toxicants as well as estrogen and androgen receptor binders. From the docking analysis, hydrogen bonding, nonpolar, atomic π-stacking, and π-cation interactions were found between PAHs (bay and fjord structural pockets) and functional hotspot residues of StAR and CYP11A1, which strengthened the subtle structural changes at domains. These govern barrier effects to cholesterol binding and/or locking cholesterol to complicate its ejection from the Ω1 loop of StAR, and further mitigates steroid biosynthesis through cholesterol by CYP11A1; therefore, they are presumably considered as block-cluster mechanisms. These outcomes are significant to be hopeful to estimate developmental/reproductive toxicity and endocrine-disruption activities of other environmental pollutants, and could be useful for further assessment to discover binding mechanisms of PAHs with other steroidogenesis pathway genes.
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Affiliation(s)
| | - Umadevi Bommu
- Department of Zoology, Sri Venkateswara University, Tirupati, 517502 AP, India
| | - Neeraja Pabbaraju
- Department of Zoology, Sri Venkateswara University, Tirupati, 517502 AP, India.
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13
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Zhu D, Yu L, Luo HY, Xue XS, Chen ZM. Atroposelective Electrophilic Sulfenylation of N‐Aryl Aminoquinone Derivatives Catalyzed by Chiral SPINOL‐Derived Sulfide. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Deng Zhu
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Lu Yu
- Nankai University college of chemistry 94 Weijin Road, Nankai District 300071 CHINA
| | - Hui-Yun Luo
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Xiao-Song Xue
- Shanghai Institute of Organic Chemistry Key Laboratory of Organofluorine Chemistry CHINA
| | - Zhi-Min Chen
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 800 Dongchuan RD. Minhang District 200240 Shanghai CHINA
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14
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Jena S, Routray C, Dutta J, Biswal HS. Hydrogen‐Bonding Directed Reversal of 13C NMR Chemical Shielding. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202207521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Subhrakant Jena
- National Institute of Science Education and Research School of Chemical Sciences INDIA
| | - Chinmay Routray
- National Institute of Science Education and Research School of Chemical Sciences INDIA
| | - Juhi Dutta
- National Institute of Science Education and Research School of Chemical Sciences INDIA
| | - Himansu Sekhar Biswal
- National Institute of Science Education and Research School of Chemical Sciences Jatani 752050 Bhubaneswar INDIA
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15
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Chandra S, Bag S. Attochemistry of hydrogen bonded amide and thioamide model complexes in protein following vertical ionization. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M. Selenium in Proteins: Conformational Changes Induced by Se Substitution on Methionine, as Studied in Isolated Model Peptides by Optical Spectroscopy and Quantum Chemistry. Molecules 2022; 27:molecules27103163. [PMID: 35630640 PMCID: PMC9144663 DOI: 10.3390/molecules27103163] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/09/2022] [Accepted: 05/11/2022] [Indexed: 02/01/2023] Open
Abstract
The side-chain of methionine residues is long enough to establish NH⋯S H-bonds with neighboring carbonyl groups of the backbone, giving rise to so-called intra-residue 6δ and inter-residue 7δ H-bonds. The aim of the present article is to document how the substitution of sulfur with a selenium atom affects the H-bonding of the Met system. This was investigated both experimentally and theoretically by conformation-resolved optical spectroscopy, following an isolated molecule approach. The present work emphasizes the similarities of the Met and Sem residues in terms of conformational structures, energetics, NH⋯Se/S H-bond strength and NH stretch spectral shifts, but also reveals subtle behavior differences between them. It provides evidence for the sensitivity of the H-bonding network with the folding type of the Sem/Met side-chains, where a simple flip of the terminal part of the side-chain can induce an extra 50 cm−1 spectral shift of the NH stretch engaged in a 7δ NH⋯S/Se bond.
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17
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Bridging H2O and H2S homomeric clusters via H2O-H2S mixed clusters: Impact of the changing ratio of H2O and H2S moieties. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Ma X, Zhu Y, Yu J, Zhao G, Duanmu J, Yuan Y, Chang XP, Xu D, Zhou Q. Unprecedented observation and characterization of sulfur-centred bifurcated hydrogen bonds. Phys Chem Chem Phys 2021; 23:26519-26523. [PMID: 34807205 DOI: 10.1039/d1cp04601b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Owing to the small electronegativity of the sulfur atom, it is commonly supposed that at most one weak H-bond can be formed between a sulfur atom and an H-bond donor. In this paper, an unprecedented 2 : 1 binding species generated from two molecules of phenol and a molecule of thioether was observed and characterized by various nuclear magnetic resonance (NMR) techniques, Fourier transform-infrared (FT-IR) techniques and density functional theory (DFT) calculations, revealing the formation of sulfur-centred O-H⋯S⋯H-O bifurcated H-bonds. This work may provide a simple and efficient method for the quantitative analysis of weak H-bonds between small organic molecules.
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Affiliation(s)
- Xiantao Ma
- College of Chemistry and Chemical Engineering, Green Catalysis & Synthesis Key Laboratory of Xinyang City, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Yingying Zhu
- College of Chemistry and Chemical Engineering, Green Catalysis & Synthesis Key Laboratory of Xinyang City, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Jing Yu
- College of Chemistry and Chemical Engineering, Green Catalysis & Synthesis Key Laboratory of Xinyang City, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Geng Zhao
- College of Chemistry and Chemical Engineering, Green Catalysis & Synthesis Key Laboratory of Xinyang City, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Jiaxin Duanmu
- College of Chemistry and Chemical Engineering, Green Catalysis & Synthesis Key Laboratory of Xinyang City, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Yiyun Yuan
- College of Chemistry and Chemical Engineering, Green Catalysis & Synthesis Key Laboratory of Xinyang City, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Xue-Ping Chang
- College of Chemistry and Chemical Engineering, Green Catalysis & Synthesis Key Laboratory of Xinyang City, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Dongli Xu
- College of Chemistry and Chemical Engineering, Green Catalysis & Synthesis Key Laboratory of Xinyang City, Xinyang Normal University, Xinyang, Henan 464000, China.
| | - Qiuju Zhou
- College of Chemistry and Chemical Engineering, Green Catalysis & Synthesis Key Laboratory of Xinyang City, Xinyang Normal University, Xinyang, Henan 464000, China.
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19
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Gandolfi M, Ceotto M. Unsupervised Machine Learning Neural Gas Algorithm for Accurate Evaluations of the Hessian Matrix in Molecular Dynamics. J Chem Theory Comput 2021; 17:6733-6746. [PMID: 34705463 PMCID: PMC8582248 DOI: 10.1021/acs.jctc.1c00707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Indexed: 11/29/2022]
Abstract
The Hessian matrix of the potential energy of molecular systems is employed not only in geometry optimizations or high-order molecular dynamics integrators but also in many other molecular procedures, such as instantaneous normal mode analysis, force field construction, instanton calculations, and semiclassical initial value representation molecular dynamics, to name a few. Here, we present an algorithm for the calculation of the approximated Hessian in molecular dynamics. The algorithm belongs to the family of unsupervised machine learning methods, and it is based on the neural gas idea, where neurons are molecular configurations whose Hessians are adopted for groups of molecular dynamics configurations with similar geometries. The method is tested on several molecular systems of different dimensionalities both in terms of accuracy and computational time versus calculating the Hessian matrix at each time-step, that is, without any approximation, and other Hessian approximation schemes. Finally, the method is applied to the on-the-fly, full-dimensional simulation of a small synthetic peptide (the 46 atom N-acetyl-l-phenylalaninyl-l-methionine amide) at the level of DFT-B3LYP-D/6-31G* theory, from which the semiclassical vibrational power spectrum is calculated.
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Affiliation(s)
- Michele Gandolfi
- Dipartimento di Chimica, Università
degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Michele Ceotto
- Dipartimento di Chimica, Università
degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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20
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Zhang Y, Wang J, Zhao S, Serdechnova M, Blawert C, Wang H, Zheludkevich ML, Chen F. Double-Ligand Strategy to Construct an Inhibitor-Loaded Zn-MOF and Its Corrosion Protection Ability for Aluminum Alloy 2A12. ACS APPLIED MATERIALS & INTERFACES 2021; 13:51685-51694. [PMID: 34670367 DOI: 10.1021/acsami.1c13738] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A promising double-ligand strategy for the delivery of active corrosion inhibitors by a Zn(II)-based metal-organic framework (Zn-MOF) is developed. Zn-MOF compounds were synthesized by a facile one-pot solvothermal method and characterized. The Zn-MOF is based on the corrosion inhibitor benzotriazole (BTA) and 2,5-furandicarboxylic acid (H2FDA) ligand, which is a promising renewable building block alternative to terephthalic or isophthalic acid. The crystal structure and morphology are characterized by single-crystal X-ray diffraction analysis, powder X-ray diffraction analysis (PXRD), Fourier transform infrared spectroscopy (FT-IR), and scanning electron microscopy (SEM). The synthesized MOF crystallites are in the trigonal space group R3c with the cell parameters in a three-dimensional (3D) anionic framework. Their ability to inhibit the corrosion process of aluminum alloy 2A12 in NaCl solution was also evaluated by immersion tests in solutions with and without a MOF. The postcorrosion analysis was performed by SEM and X-ray photoelectron spectroscopy (XPS). Additional information about the inhibition efficiency was obtained by electrochemical impedance spectroscopy (EIS). The results suggest that the as-synthesized MOF can release the inhibitors and form protective layers effectively on the surface of the aluminum alloy. The use of inhibitor-loaded MOF nanocontainers provides promising opportunities for the smart delivery of inhibitors and effective corrosion protection of 2A12 aluminum alloys.
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Affiliation(s)
- You Zhang
- College of New Materials and Chemical Engineering, Beijing Key Lab of Special Elastomeric Composite Materials, Beijing Institute of Petrochemical Technology, Beijing 102617, China
- Institute of Surface Science, Helmholtz-Zentrum Hereon, Geesthacht 21502, Germany
| | - Juping Wang
- College of New Materials and Chemical Engineering, Beijing Key Lab of Special Elastomeric Composite Materials, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Shuai Zhao
- College of New Materials and Chemical Engineering, Beijing Key Lab of Special Elastomeric Composite Materials, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Maria Serdechnova
- Institute of Surface Science, Helmholtz-Zentrum Hereon, Geesthacht 21502, Germany
| | - Carsten Blawert
- Institute of Surface Science, Helmholtz-Zentrum Hereon, Geesthacht 21502, Germany
| | - Hao Wang
- College of New Materials and Chemical Engineering, Beijing Key Lab of Special Elastomeric Composite Materials, Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Mikhail L Zheludkevich
- Institute of Surface Science, Helmholtz-Zentrum Hereon, Geesthacht 21502, Germany
- Faculty of Engineering, Kiel University, Kiel 24143, Germany
| | - Fei Chen
- College of New Materials and Chemical Engineering, Beijing Key Lab of Special Elastomeric Composite Materials, Beijing Institute of Petrochemical Technology, Beijing 102617, China
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21
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Monu, Oram BK, Bandyopadhyay B. A unified cost-effective method for the construction of reliable potential energy surfaces for H 2S and H 2O clusters. Phys Chem Chem Phys 2021; 23:18044-18057. [PMID: 34387290 DOI: 10.1039/d1cp01544c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A DFT-based methodology has been used to construct the potential energy surface of H2S clusters up to pentamers. Geometrical parameters and energetics show very good agreement with the existing experimental and high-level theoretical results. Distinct stable conformers of three dimers, six trimers, eleven tetramers and twenty-three pentamers have been identified. Both S-HS H-bond and SS interactions are identified in dimers, trimers and pentamers, while no SS interactions could be found in any of the 11 tetramer conformers. The binding energies of the most stable dimer, trimer, tetramer and pentamer are -1.66, -5.21, -8.57 and -12.54 kcal mol-1, respectively. The PES has been found to be exceedingly flat and the energy gap between the most and the least stable conformers was found to be only 0.09, 2.13, 1.65 and 1.13 kcal mol-1, from the dimer to the pentamer, respectively. The proposed method has also been used for water clusters up to the pentamer. The results obtained were found to agree closely with the existing results. Only one conformer was found for the water dimer, whereas four, five and fifteen conformers were obtained for the trimer, tetramer and pentamer, respectively. Atoms in molecular calculations were found to corroborate with the geometric and energetic results for both clusters.
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Affiliation(s)
- Monu
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, JLN Marg, Jaipur - 302017, India.
| | - Binod Kumar Oram
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, JLN Marg, Jaipur - 302017, India.
| | - Biman Bandyopadhyay
- Department of Chemistry, Malaviya National Institute of Technology Jaipur, JLN Marg, Jaipur - 302017, India.
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22
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Mundlapati VR, Imani Z, Goldsztejn G, Gloaguen E, Brenner V, Le Barbu-Debus K, Zehnacker-Rentien A, Baltaze JP, Robin S, Mons M, Aitken DJ. A theoretical and experimental case study of the hydrogen bonding predilection of S-methylcysteine. Amino Acids 2021; 53:621-633. [PMID: 33743071 DOI: 10.1007/s00726-021-02967-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/12/2021] [Indexed: 12/17/2022]
Abstract
S-containing amino acids can lead to two types of local NH···S interactions which bridge backbone NH sites to the side chain to form either intra- or inter-residue H-bonds. The present work reports on the conformational preferences of S-methyl-L-cysteine, Cys(Me), using a variety of investigating tools, ranging from quantum chemistry simulations, gas-phase UV and IR laser spectroscopy, and solution state IR and NMR spectroscopies, on model compounds comprising one or two Cys(Me) residues. We demonstrate that in gas phase and in low polarity solution, the C- and N-capped model compound for one Cys(Me) residue adopts a preferred C5-C6γ conformation which combines an intra-residue N-H···O=C backbone interaction (C5) and an inter-residue N-H···S interaction implicating the side-chain sulfur atom (C6γ). In contrast, the dominant conformation of the C- and N-capped model compound featuring two consecutive Cys(Me) residues is a regular type I β-turn. This structure is incompatible with concomitant C6γ interactions, which are no longer in evidence. Instead, C5γ interactions occur, that are fully consistent with the turn geometry and additionally stabilize the structure. Comparison with the thietane amino acid Attc, which exhibits a rigid cyclic side chain, pinpoints the significance of side chain flexibility for the specific conformational behavior of Cys(Me).
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Affiliation(s)
- Venkateswara Rao Mundlapati
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
- Institut de Recherche en Astrophysique Et Planétologie (IRAP), Université de Toulouse (UPS), CNRS, CNES, 9 Avenue du Colonel Roche, 31028, Toulouse, France
| | - Zeynab Imani
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Gildas Goldsztejn
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
- Institut Des Sciences Moléculaires D'Orsay (ISMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Eric Gloaguen
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Valérie Brenner
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France
| | - Katia Le Barbu-Debus
- Institut Des Sciences Moléculaires D'Orsay (ISMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Anne Zehnacker-Rentien
- Institut Des Sciences Moléculaires D'Orsay (ISMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Jean-Pierre Baltaze
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
| | - Sylvie Robin
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France
- Faculté de Pharmacie, Université de Paris, 75006, Paris, France
| | - Michel Mons
- Laboratoire Interactions, Dynamiques Et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay, 91191, Gif-sur-Yvette, France.
| | - David J Aitken
- Institut de Chimie Moléculaire Et Des Matériaux D'Orsay (ICMMO), Université Paris-Saclay, CNRS, 91405, Orsay, France.
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23
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Bhattacharyya S, Ghosh S, Wategaonkar S. O-H stretching frequency red shifts do not correlate with the dissociation energies in the dimethylether and dimethylsulfide complexes of phenol derivatives. Phys Chem Chem Phys 2021; 23:5718-5739. [PMID: 33662068 DOI: 10.1039/d0cp01589j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this perspective, we present a comprehensive report on the spectroscopic and computational investigations of the hydrogen bonded (H-bonded) complexes of Me2O and Me2S with seven para-substituted H-bond donor phenols. The salient finding was that although the dissociation energies, D0, of the Me2O complexes were consistently higher than those of the analogous Me2S complexes, the red-shifts in phenolic O-H frequencies, Δν(O-H), showed the exactly opposite trend. This is in contravention of the general perception that the red shift in the X-H stretching frequency in the X-HY hydrogen bonded complexes is a reliable indicator of H-bond strength (D0), a concept popularly known as the Badger-Bauer rule. This is also in contrast to the trend reported for the H-bonded complexes of H2S/H2O with several para substituted phenols of different pKa values wherein the oxygen centered hydrogen bonded (OCHB) complexes consistently showed higher Δν(O-H) and D0 compared to those of the analogous sulfur centered hydrogen bonded (SCHB) complexes. Our effort was to understand these intriguing observations based on the spectroscopic investigations of 1 : 1 complexes in combination with a variety of high level quantum chemical calculations. Ab initio calculations at the MP2 level and the DFT calculations using various dispersion corrected density functionals (including DFT-D3) were performed on counterpoise corrected surfaces to compute the dissociation energy, D0, of the H-bonded complexes. The importance of anharmonic frequency computations is underscored as they were able to correctly reproduce the observed trend in the relative OH frequency shifts unlike the harmonic frequency computations. We have attempted to find a unified correlation that would globally fit the observed red shifts in the O-H frequency with the H-bonding strength for the four bases, namely, H2S, H2O, Me2O, and Me2S, in this set of H-bond donors. It was found that the proton affinity normalized Δν(O-H) values scale very well with the H-bond strength.
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Affiliation(s)
- Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanat Ghosh
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India.
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24
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Jena S, Tulsiyan KD, Kar RK, Kisan HK, Biswal HS. Doubling Förster Resonance Energy Transfer Efficiency in Proteins with Extrinsic Thioamide Probes: Implications for Thiomodified Nucleobases. Chemistry 2021; 27:4373-4383. [PMID: 33210381 DOI: 10.1002/chem.202004627] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Indexed: 12/29/2022]
Abstract
Designing a potential protein-ligand pair is pivotal, not only to track the protein structure dynamics, but also to assist in an atomistic understanding of drug delivery. Herein, the potential of a small model thioamide probe being used to study albumin proteins is reported. By monitoring the Förster resonance energy transfer (FRET) dynamics with the help of fluorescence spectroscopic techniques, a twofold enhancement in the FRET efficiency of 2-thiopyridone (2TPY), relative to that of its amide analogue, is observed. Molecular dynamics simulations depict the relative position of the free energy minimum to be quite stable in the case of 2TPY through noncovalent interactions with sulfur, which help to enhance the FRET efficiency. Finally, its application is shown by pairing thiouracils with protein. It is found that the site-selective sulfur atom substitution approach and noncovalent interactions with sulfur can substantially enhance the FRET efficiency, which could be a potential avenue to explore in the design of FRET probes to study the structure and dynamics of biomolecules.
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Affiliation(s)
- Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Kiran Devi Tulsiyan
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Hemanta K Kisan
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel.,Department of Chemistry, Utkal University, 751004, Bhubaneswar, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO-Bhimpur-Padanpur, Jatni, Khurda, Bhubaneswar, 752050, India.,Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, 400094, India
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25
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Mishra KK, Borish K, Singh G, Panwaria P, Metya S, Madhusudhan MS, Das A. Observation of an Unusually Large IR Red-Shift in an Unconventional S-H···S Hydrogen-Bond. J Phys Chem Lett 2021; 12:1228-1235. [PMID: 33492971 DOI: 10.1021/acs.jpclett.0c03183] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The S-H···S non-covalent interaction is generally known as an extremely unconventional weak hydrogen-bond in the literature. The present gas-phase spectroscopic investigation shows that the S-H···S hydrogen-bond can be as strong as any conventional hydrogen-bond in terms of the IR red-shift in the stretching frequency of the hydrogen-bond donor group. Herein, the strength of the S-H···S hydrogen-bond has been determined by measuring the red-shift (∼150 cm-1) of the S-H stretching frequency in a model complex of 2-chlorothiophenol and dimethyl sulfide using isolated gas-phase IR spectroscopy coupled with quantum chemistry calculations. The observation of an unusually large IR red-shift in the S-H···S hydrogen-bond is explained in terms of the presence of a significant amount of charge-transfer interactions in addition to the usual electrostatic interactions. The existence of ∼750 S-H···S interactions between the cysteine and methionine residues in 642 protein structures determined from an extensive Protein Data Bank analysis also indicates that this interaction is important for the structures of proteins.
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Affiliation(s)
- Kamal K Mishra
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Kshetrimayum Borish
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Gulzar Singh
- Department of Biology, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Prakash Panwaria
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Surajit Metya
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - M S Madhusudhan
- Department of Biology, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune-411008, India
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26
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Goldsztejn G, Mundlapati VR, Brenner V, Gloaguen E, Mons M, Cabezas C, León I, Alonso JL. Intrinsic folding of the cysteine residue: competition between folded and extended forms mediated by the -SH group. Phys Chem Chem Phys 2021; 22:20284-20294. [PMID: 32966425 DOI: 10.1039/d0cp03136d] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A dual microwave and optical spectroscopic study of a capped cysteine amino acid isolated in a supersonic expansion, combined with quantum chemistry modelling, enabled us to characterize the conformational preferences of Cys embedded in a protein chain. IR/UV double resonance spectroscopy provided evidence for the coexistence of two conformers, assigned to folded and extended backbones (with classical C7 and C5 backbone H-bonding respectively), each of them additionally stabilized by specific main-chain/side-chain H-bonding, where the sulfur atom essentially plays the role of H-bond acceptor. The folded structure was confirmed by microwave spectroscopy, which demonstrated the validity of the DFT-D methods currently used in the field. These structural and spectroscopic results, complemented by a theoretical Natural Bond Orbital analysis, enabled us to document the capacity of the weakly polar -CH2-SH side chain of Cys to adapt itself to the intrinsic local preferences of the peptide backbone, i.e., a γ-turn or a β-sheet extended secondary structure. The corresponding local H-bonding bridges the side chain acceptor S atom to the backbone NH donor site of the same or the next residue along the chain, through a 5- or a 6-membered ring respectively.
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Affiliation(s)
- Gildas Goldsztejn
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | | | - Valérie Brenner
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Eric Gloaguen
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Michel Mons
- LIDYL, CEA, CNRS, Université Paris-Saclay, bât 522, CEA Paris-Saclay, 9119 Gif-sur-Yvette, France.
| | - Carlos Cabezas
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - Iker León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - José Luis Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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27
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Abstract
The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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28
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Chopra N, Chopra G, Kaur D. Modeling the protein-nucleic acid base interactions through hydrogen-bonded complexes of N-heterocyclic analogs of Indene with amino acid side-chain mimics. Struct Chem 2020. [DOI: 10.1007/s11224-020-01600-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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29
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Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
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Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
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Chand A, Sahoo DK, Rana A, Jena S, Biswal HS. The Prodigious Hydrogen Bonds with Sulfur and Selenium in Molecular Assemblies, Structural Biology, and Functional Materials. Acc Chem Res 2020; 53:1580-1592. [PMID: 32677432 DOI: 10.1021/acs.accounts.0c00289] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Hydrogen bonds (H-bonds) play important roles in imparting functionality to the basic molecules of life by stabilizing their structures and directing their interactions. Numerous studies have been devoted to understanding H-bonds involving highly electronegative atoms like nitrogen, oxygen, and halogens and consequences of those H-bonds in chemical reactions, catalysis, and structure and function of biomolecules; but the involvement of less electronegative atoms like sulfur and selenium in H-bond formation establishes the concept of noncanonical H-bonds. Initially belittled for the "weak" nature of their interactions, these perceptions have gradually evolved over time through dedicated efforts by several research groups. This has been facilitated by advancements in experimental methods for their detection through gas-phase laser spectroscopy and solution NMR spectroscopy, as well as through theoretical predictions from high level quantum chemical calculations.In this Account, we present insights into the versatility of the sulfur and selenium centered H-bonds (S/SeCHBs) by highlighting their multifarious applications in various fields from chemical reactions to optoelectronic properties to structural biology. Our group has highlighted the significance and strength of such H-bonds in natural and modified biomolecules. Here, we have reviewed several molecular assemblies, biomolecules, and functional materials, where the role of these H-bonds is pivotal in influencing biological functions. It is worth mentioning here that the precise experimental data obtained from gas-phase laser spectroscopy have contributed considerably to changing the existing perceptions toward S/SeCHBs. Thus, molecular beam experiments, though difficult to perform on smaller model thio- or seleno-substituted Molecules, etc. (amides, nucleobases, drug molecules), are inevitable to gather elementary knowledge and convincing concepts on S/SeCHBs that can be extended from a small four-atom sulfanyl dimer to a large 14 kDa iron-sulfur protein, ferredoxin. These H-bonds can also tailor a fascinating array of molecular frameworks and design supramolecular assemblies by inter- and intralinking of individual "molecular Lego-like" units.The discussion is indeed intriguing when it turns to the usage of S/SeCHBs in facile synthetic strategies like tuning regioselectivity in reactions, as well as invoking phenomena like dual phosphorescence and chemiluminescence. This is in addition to our investigations of the dispersive nature of the hydrogen bond between metal hydrides and sulfur or selenium as acceptor, which we anticipate would lead to progress in the areas of proton and hydride transfer, as well as force-field design. This Account demonstrates how ease of fabrication, enhanced efficiency, and alteration of physicochemical properties of several functional materials is facilitated owing to the presence of S/SeCHBs. Our efforts have been instrumental in the evaluation of various S/SeCHBs in flue gas capture, as well as design of organic energy harvesting materials, where dipole moment and polarizability have important roles to play. We hope this Account invokes newer perspectives with regard to how H-bonds with sulfur and selenium can be adequately adopted for crystal engineering, for more photo- and biophysical studies with different spectroscopic methods, and for developing next-generation field-effect transistors, batteries, superconductors, and organic thin-film transistors, among many other multifunctional materials for the future.
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Affiliation(s)
- Apramita Chand
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Abhijit Rana
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Subhrakant Jena
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S. Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), PO Bhimpur-Padanpur, Via-Jatni, District Khurda, 752050 Bhubaneswar, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
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31
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Imani Z, Mundlapati VR, Goldsztejn G, Brenner V, Gloaguen E, Guillot R, Baltaze JP, Le Barbu-Debus K, Robin S, Zehnacker A, Mons M, Aitken DJ. Conformation control through concurrent N-H⋯S and N-H⋯O[double bond, length as m-dash]C hydrogen bonding and hyperconjugation effects. Chem Sci 2020; 11:9191-9197. [PMID: 34123167 PMCID: PMC8163419 DOI: 10.1039/d0sc03339a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
In addition to the classical N-H⋯O[double bond, length as m-dash]C non-covalent interaction, less conventional types of hydrogen bonding, such as N-H⋯S, may play a key role in determining the molecular structure. In this work, using theoretical calculations in combination with spectroscopic analysis in both gas phase and solution phase, we demonstrate that both these H-bonding modes exist simultaneously in low-energy conformers of capped derivatives of Attc, a thietane α-amino acid. 6-Membered ring inter-residue N-H⋯S interactions (C6γ), assisted by hyperconjugation between the thietane ring and the backbone, combine with 5-membered ring intra-residue backbone N-H⋯O[double bond, length as m-dash]C interactions (C5) to provide a C5-C6γ feature that stabilizes a planar geometry in the monomer unit. Two contiguous C5-C6γ features in the planar dimer implicate an unprecedented three-centre H-bond of the type C[double bond, length as m-dash]O⋯H(N)⋯SR2, while the trimer adopts two C5-C6γ features separated by a Ramachandran α-type backbone configuration. These low-energy conformers are fully characterized in the gas phase and support is presented for their existence in solution state.
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Affiliation(s)
- Zeynab Imani
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Venkateswara Rao Mundlapati
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Gildas Goldsztejn
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Valérie Brenner
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Eric Gloaguen
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Jean-Pierre Baltaze
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Sylvie Robin
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France .,Faculté de Pharmacie, Université de Paris 75006 Paris France
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay 91405 Orsay France
| | - Michel Mons
- Laboratoire Interactions, Dynamiques et Lasers (LIDYL), CEA, CNRS, Université Paris-Saclay 91191 Gif-sur-Yvette France
| | - David J Aitken
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS, Université Paris-Saclay 91405 Orsay France
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32
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Chand A, Biswal HS. Hydrogen Bonds with Chalcogens: Looking Beyond the Second Row of the Periodic Table. J Indian Inst Sci 2019. [DOI: 10.1007/s41745-019-00140-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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33
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Biological Effects of Single-Nucleotide Polymorphisms in the Drosophila melanogaster Malic Enzyme Locus. Biochem Genet 2019; 58:129-156. [PMID: 31302799 DOI: 10.1007/s10528-019-09932-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
Abstract
A pair of amino acid polymorphisms within the Drosophila melanogaster Malic enzyme (Men) locus presents an interesting case of genetic variation that appears to be under selection. The two alleles at each site are biochemically distinct, but their biological effects are unknown. One polymorphic site is near the active site and the other is buried within the protein. Strikingly, in twelve different populations, the first polymorphism is always found at approximately a 50:50 allelic frequency, whereas the second polymorphism is always found at approximately 90:10. The consistency of the frequencies between populations suggests that the polymorphisms are under selection and it is possible that balancing selection is at play. We used 16 lines of flies to create the nine genotypes needed to quantify both effects of the polymorphic sites and possible genetic background effects, which we found to be widespread. The alleles at each site differ, but in different biochemical characteristics. The first site significantly influences MEN Km and Vmax, whereas the second site affects the Km and the Vmax/Km ratio (relative activity). Interestingly, the rarest allele is the most biochemically distinct. We also assayed three more distal phenotypes, triglyceride concentration, carbohydrate concentration, and longevity. In all cases, the phenotypes of the heterozygous genotypes are intermediate between those of the respective homozygotes suggesting that if balancing selection is maintaining the observed allele frequencies it is not through non-linear combinations of the biochemical phenotypes.
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34
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Conte R, Gabas F, Botti G, Zhuang Y, Ceotto M. Semiclassical vibrational spectroscopy with Hessian databases. J Chem Phys 2019; 150:244118. [PMID: 31255076 DOI: 10.1063/1.5109086] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We report on a new approach to ease the computational overhead of ab initio "on-the-fly" semiclassical dynamics simulations for vibrational spectroscopy. The well known bottleneck of such computations lies in the necessity to estimate the Hessian matrix for propagating the semiclassical pre-exponential factor at each step along the dynamics. The procedure proposed here is based on the creation of a dynamical database of Hessians and associated molecular geometries able to speed up calculations while preserving the accuracy of results at a satisfactory level. This new approach can be interfaced to both analytical potential energy surfaces and on-the-fly dynamics, allowing one to study even large systems previously not achievable. We present results obtained for semiclassical vibrational power spectra of methane, glycine, and N-acetyl-L-phenylalaninyl-L-methionine-amide, a molecule of biological interest made of 46 atoms.
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Affiliation(s)
- Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Fabio Gabas
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Giacomo Botti
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Yu Zhuang
- Department of Computer Science, Texas Tech University, Lubbock, Texas 79409-3104, USA
| | - Michele Ceotto
- Dipartimento di Chimica, Università degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
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35
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Gupta S, Sutter M, Remesh SG, Dominguez-Martin MA, Bao H, Feng XA, Chan LJG, Petzold CJ, Kerfeld CA, Ralston CY. X-ray radiolytic labeling reveals the molecular basis of orange carotenoid protein photoprotection and its interactions with fluorescence recovery protein. J Biol Chem 2019; 294:8848-8860. [PMID: 30979724 DOI: 10.1074/jbc.ra119.007592] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/05/2019] [Indexed: 11/06/2022] Open
Abstract
In cyanobacterial photoprotection, the orange carotenoid protein (OCP) is photoactivated under excess light conditions and binds to the light-harvesting antenna, triggering the dissipation of captured light energy. In low light, the OCP relaxes to the native state, a process that is accelerated in the presence of fluorescence recovery protein (FRP). Despite the importance of the OCP in photoprotection, the precise mechanism of photoactivation by this protein is not well-understood. Using time-resolved X-ray-mediated in situ hydroxyl radical labeling, we probed real-time solvent accessibility (SA) changes at key OCP residues during photoactivation and relaxation. We observed a biphasic photoactivation process in which carotenoid migration preceded domain dissociation. We also observed a multiphasic relaxation process, with collapsed domain association preceding the final conformational rearrangement of the carotenoid. Using steady-state hydroxyl radical labeling, we identified sites of interaction between the FRP and OCP. In combination, the findings in this study provide molecular-level insights into the factors driving structural changes during OCP-mediated photoprotection in cyanobacteria, and furnish a basis for understanding the physiological relevance of the FRP-mediated relaxation process.
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Affiliation(s)
- Sayan Gupta
- From the Molecular Biophysics and Integrated Bioimaging Division
| | - Markus Sutter
- From the Molecular Biophysics and Integrated Bioimaging Division.,the MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.,the Environmental Genomics and Systems Biology Division, and
| | - Soumya G Remesh
- From the Molecular Biophysics and Integrated Bioimaging Division
| | - Maria Agustina Dominguez-Martin
- the MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Han Bao
- the MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Xinyu A Feng
- From the Molecular Biophysics and Integrated Bioimaging Division
| | - Leanne-Jade G Chan
- the Biological Systems and Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720 and
| | - Christopher J Petzold
- the Biological Systems and Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720 and
| | - Cheryl A Kerfeld
- From the Molecular Biophysics and Integrated Bioimaging Division, .,the MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.,the Environmental Genomics and Systems Biology Division, and
| | - Corie Y Ralston
- From the Molecular Biophysics and Integrated Bioimaging Division,
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36
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Sahoo DK, Jena S, Dutta J, Rana A, Biswal HS. Nature and Strength of M-H···S and M-H···Se (M = Mn, Fe, & Co) Hydrogen Bond. J Phys Chem A 2019; 123:2227-2236. [PMID: 30802055 DOI: 10.1021/acs.jpca.8b12003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The significance of dispersion contribution in the formation of strong hydrogen bonds (H-bonds) can no more be ignored. It was illustrated that less electronegative and electropositive H-bond acceptors such as S, Se, and Te are also capable of forming strong N-H···Y H-bonds, mostly due to the high polarizabilities of H-bond acceptor atoms. Herein, for the first time, we report the evidence of formation of nonconventional M-H···Y H-bonds between metal hydrides (M-H, M = Mn, Fe, Co) and chalcogen H-bond acceptors (Y = O, S, or Se). The nature and the strength of unusual M-H···Y H-bonds were revealed by several quantum chemical calculations and H-bond descriptors. The structural parameters, electron density topology, donor-acceptor natural bond orbital (NBO) interaction energies, and spectroscopic observables such as M-H stretching frequencies and 1H chemical shifts are well-correlated to manifest the existence and strength of M-H···Y H-bonding. The M-H···Y H-bonds are dispersive in nature, and the computed H-bond energies are found to be in the range from ∼5 to 30 kJ/mol, which can be compared to those of the conventional H-bonds such as O-H···O, N-H···O, and N-H···O═C H-bonds, etc.
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Affiliation(s)
- Dipak Kumar Sahoo
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
| | - Subhrakant Jena
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
| | - Juhi Dutta
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
| | - Abhijit Rana
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
| | - Himansu S Biswal
- School of Chemical Sciences , National Institute of Science Education and Research , 752050 Bhubaneswar , India.,Homi Bhabha National Institute , Training School Complex , Anushakti Nagar, Mumbai 400094 , India
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37
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Mundlapati VR, Sahoo DK, Bhaumik S, Jena S, Chandrakar A, Biswal HS. Noncovalent Carbon-Bonding Interactions in Proteins. Angew Chem Int Ed Engl 2018; 57:16496-16500. [DOI: 10.1002/anie.201811171] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Indexed: 12/14/2022]
Affiliation(s)
- V. Rao Mundlapati
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Suman Bhaumik
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Amol Chandrakar
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
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38
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Mundlapati VR, Sahoo DK, Bhaumik S, Jena S, Chandrakar A, Biswal HS. Noncovalent Carbon-Bonding Interactions in Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811171] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- V. Rao Mundlapati
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Suman Bhaumik
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Amol Chandrakar
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER); PO- Bhimpur-Padanpur, Via-Jatni, District- Khurda, PIN - 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
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39
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Wategaonkar S, Bhattacherjee A. N–H···S Interaction Continues To Be an Enigma: Experimental and Computational Investigations of Hydrogen-Bonded Complexes of Benzimidazole with Thioethers. J Phys Chem A 2018; 122:4313-4321. [DOI: 10.1021/acs.jpca.8b01943] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
| | - Aditi Bhattacherjee
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai 400 005, India
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40
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Taylor ZW, Raushel FM. Cytidine Diphosphoramidate Kinase: An Enzyme Required for the Biosynthesis of the O-Methyl Phosphoramidate Modification in the Capsular Polysaccharides of Campylobacter jejuni. Biochemistry 2018; 57:2238-2244. [PMID: 29578334 DOI: 10.1021/acs.biochem.8b00279] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Campylobacter jejuni, a leading cause of gastroenteritis, produces a capsular polysaccharide that is derivatized with a unique O-methyl phosphoramidate (MeOPN) modification. This modification contributes to serum resistance and invasion of epithelial cells. Previously, the first three biosynthetic steps for the formation of MeOPN were elucidated. The first step is catalyzed by a novel glutamine kinase (Cj1418), which catalyzes the adenosine triphosphate (ATP)-dependent phosphorylation of the amide nitrogen of l-glutamine. l-Glutamine phosphate is used by cytidine triphosphate (CTP):phosphoglutamine cytidylyltransferase (Cj1416) to displace pyrophosphate from CTP to generate cytidine diphosphate (CDP)-l-glutamine, which is then hydrolyzed by γ-glutamyl-CDP-amidate hydrolase (Cj1417) to form cytidine diphosphoramidate (CDP-NH2). Here, we show that Cj1415 catalyzes the ATP-dependent phosphorylation of CDP-NH2 to form 3'-phospho-cytidine-5'-diphosphoramidate. Cj1415 will also catalyze the phosphorylation of adenosine diphosphoramidate (ADP-NH2) and uridine diphosphoramidate (UDP-NH2) but at significantly reduced rates. It is proposed that Cj1415 be named cytidine diphosphoramidate kinase.
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Affiliation(s)
- Zane W Taylor
- Department of Biochemistry & Biophysics , Texas A&M University , College Station , Texas 77843 , United States
| | - Frank M Raushel
- Department of Biochemistry & Biophysics , Texas A&M University , College Station , Texas 77843 , United States.,Department of Chemistry , Texas A&M University , College Station , Texas 77843 , United States
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41
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Mishra KK, Singh SK, Ghosh P, Ghosh D, Das A. The nature of selenium hydrogen bonding: gas phase spectroscopy and quantum chemistry calculations. Phys Chem Chem Phys 2018; 19:24179-24187. [PMID: 28840208 DOI: 10.1039/c7cp05265k] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Subsequent to the recent re-definition of hydrogen bonding by the IUPAC committee, there has been a growing search for finding the presence of this ever interesting non-covalent interaction between a hydrogen atom in an X-H group and any other atom in the periodic table. In recent gas phase experiments, it has been observed that hydrogen bonding interactions involving S and Se are of similar strength to those with an O atom. However, there is no clear explanation for the unusual strength of this interaction in the case of hydrogen bond acceptors which are not conventional electronegative atoms. In this work, we have explored the nature of Se hydrogen bonding by studying indoledimethyl selenide (indmse) and phenoldimethyl selenide (phdmse) complexes using gas phase IR spectroscopy and quantum chemistry calculations. We have found through various energy decomposition analysis (EDA) methods and natural bond orbital (NBO) calculations that, along with electrostatics and polarization, charge transfer interactions are important to understand Se/S hydrogen bonding and there is a delicate balance between the various interactions that plays the crucial role rather than a single component of the interaction energy. An in-depth understanding of this type of non-covalent interaction has immense significance in biology as amino acids containing S and Se are widely present in proteins and hence hydrogen bonding interactions involving S and Se atoms contribute to the folding of proteins.
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Affiliation(s)
- Kamal K Mishra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr Homi Bhabha Road, Pune-411008, India.
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42
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Habka S, Sohn WY, Vaquero-Vara V, Géléoc M, Tardivel B, Brenner V, Gloaguen E, Mons M. On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins. Phys Chem Chem Phys 2018; 20:3411-3423. [DOI: 10.1039/c7cp07605c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The anchoring properties of an asparagine (Asn) residue to its local backbone environment in turn model peptides is characterized using gas phase laser spectroscopy and compared to crystallized protein structures.
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Affiliation(s)
- S. Habka
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - W. Y. Sohn
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | | | - M. Géléoc
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - B. Tardivel
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - V. Brenner
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - E. Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - M. Mons
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
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43
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BenNasr F, Pérez-Mellor A, Alata I, Lepere V, Jaïdane NE, Zehnacker A. Stereochemistry-dependent hydrogen bonds stabilise stacked conformations in jet-cooled cyclic dipeptides: (LD) vs. (LL) cyclo tyrosine-tyrosine. Faraday Discuss 2018; 212:399-419. [PMID: 30229773 DOI: 10.1039/c8fd00079d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Tyrosine-containing cyclic dipeptides based on a diketopiperazine (DKP) ring are studied under jet-cooled conditions using resonance-enhanced multi-photon ionisation (REMPI), conformer-selective IR-UV double resonance vibrational spectroscopy and quantum chemical calculations. The conformational landscape of the dipeptide containing natural L tyrosine (Tyr), namely c-LTyr-LTyr strongly differs from that of its diastereomer c-LTyr-DTyr. A similar family of conformers exists in both systems, with one aromatic ring folded on the dipeptide DKP ring and the other one extended. Weak NHπ and CHπ interactions are observed, which are slightly different in c-LTyr-LTyr and c-LTyr-DTyr. These structures are identical to those of LL and LD cyclo diphenylalanine, which only differ from c-Tyr-Tyr by the absence of hydroxyl on the benzene rings. While this is the only conformation observed for c-LTyr-DTyr, c-LTyr-LTyr exhibits an additional form stabilised by the interaction of the two hydroxyls, in which the two aromatic rings are in a stacked geometry. Stereochemical effects are still visible in the radical cation, for which one structure is observed for c-LTyr-DTyr, while the spectrum of the c-LTyr-LTyr radical cation is explained in terms of two co-existing structures.
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Affiliation(s)
- Feriel BenNasr
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France. and Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ivan Alata
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valeria Lepere
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
| | - Nejm-Eddine Jaïdane
- Laboratoire de Spectroscopie Atomique, Moléculaire et Applications (LSAMA), Université de Tunis El Manar, Tunis 1060, Tunisia
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay, France.
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44
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Vidal-Vidal Á, Faza ON, Silva López C. CO 2 Complexes with Five-Membered Heterocycles: Structure, Topology, and Spectroscopic Characterization. J Phys Chem A 2017; 121:9118-9130. [PMID: 29052989 DOI: 10.1021/acs.jpca.7b09394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In a first step toward the rational design of macrocyclic structures optimized for CO2 capture, we systematically explored the potential of 30 five-membered aromatic heterocycles to establish coordinating complexes with this pollutant. The interactions between the two moieties were studied in several orientations, and the obtained complexes were analyzed in terms of electron density and vibrational fingerprint. The former is an aid to provide an in-depth knowledge of the interaction, whereas the latter should help to select structural motifs that have not only good complexation properties but also diagnostic spectroscopic signals.
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Affiliation(s)
- Ángel Vidal-Vidal
- Departamento de Quı́mica Orgánica, Universidade de Vigo , Campus Lagoas-Marcosende, 36310 Vigo, Spain
| | - Olalla Nieto Faza
- Departamento de Quı́mica Orgánica, Facultade de Ciencias, Universidade de Vigo , Campus As Lagoas, 32004 Ourense, Spain
| | - Carlos Silva López
- Departamento de Quı́mica Orgánica, Universidade de Vigo , Campus Lagoas-Marcosende, 36310 Vigo, Spain
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45
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Singh A, Sahoo DK, Sethi SK, Jena S, Biswal HS. Nature and Strength of the Inner-Core H⋅⋅⋅H Interactions in Porphyrinoids. Chemphyschem 2017; 18:3625-3633. [DOI: 10.1002/cphc.201700742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Ankit Singh
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Srikant Kumar Sethi
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Subhrakant Jena
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
| | - Himansu S. Biswal
- School of Chemical Sciences; National Institute of Science Education and Research (NISER), PO- Bhimpur-Padanpur; Via-Jatni, District- Khurda, PIN 752050 Bhubaneswar India
- Homi Bhabha National Institute; Training School Complex; Anushakti Nagar Mumbai 400094 India
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46
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Mundlapati VR, Gautam S, Sahoo DK, Ghosh A, Biswal HS. Thioamide, a Hydrogen Bond Acceptor in Proteins and Nucleic Acids. J Phys Chem Lett 2017; 8:4573-4579. [PMID: 28876948 DOI: 10.1021/acs.jpclett.7b01810] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Thioamides are used as potential surrogates of amides to study the structure and dynamics of proteins and nucleic acids. However, incorporation of thioamides in biomolecules leads to changes in their structures and conformations mostly attributed to the strength of the amide-N-H···S═C hydrogen bond. In most cases, it is considered weak owing to the small electronegativity of sulfur, and in some cases, it is as strong as conventional H-bonds. Herein, adopting PDB structure analysis, NMR spectroscopy, and quantum chemistry calculations, we have shown that thioamides in a geometrical and structural constraint-free environment are capable of forming strong H-bonds like their amide counterparts. These studies also enabled us to determine the amide-N-H···S═C H-bond enthalpy (ΔH) very precisely. The estimated ΔH for the amide-N-H···S═C H-bond is ∼-30 kJ/mol, which suggests that the amide-N-H···S═C H-bond is a strong H-bond and merits its inclusion in computational force fields for biomolecular structure simulations to explore the role of amide-N-H···S═C H-bonds in nucleobase pairing and protein folding.
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Affiliation(s)
- V Rao Mundlapati
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Sanjeev Gautam
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Dipak Kumar Sahoo
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Arindam Ghosh
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Himansu S Biswal
- School of Chemical Sciences, National Institute of Science Education and Research (NISER) , PO-Bhimpur-Padanpur, Via-Jatni, District-Khurda, PIN-752050 Bhubaneswar, India
- Homi Bhabha National Institute , Training School Complex, Anushakti Nagar, Mumbai 400094, India
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47
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Shimizu A, Nagasaki K, Inoue Y, Mori T. Chiroptical properties of dithia[3.3]cyclophanes composed of anthracene and pyridine/pyridinium moieties: A combined experimental and theoretical study. Chirality 2017; 29:677-683. [PMID: 28833559 DOI: 10.1002/chir.22740] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/06/2017] [Accepted: 07/10/2017] [Indexed: 11/12/2022]
Abstract
Circular dichroisms (CDs) of neutral and protonated [3.3]anthracenopyridinophane (1 and 1-H+ ) were investigated experimentally and theoretically. Introducing an anthracene moiety with extended conjugation affected the cyclophane structure with the bent angles being appreciably reduced from those of parent [3.3]pyridinophane. The Cotton effects (CEs) observed at the 1 Bb band for both 1 and 1-H+ were fairly strong and apparently bisignate, which, however, turned out not to be a simple exciton couplet but to be composed of multiple transitions. In contrast, the CEs were much weaker in the 1 La band region. The spectral changes upon protonation were less significant compared with the parent pyridinophane, being dominated by the local transitions of anthracene. Nevertheless, the CD spectra of 1 and 1-H+ were well reproduced by theoretical calculations to allow us an unambiguous absolute configuration determination of the first high-performance liquid chromatography (HPLC) elute (from Chiralcel IB column) as Sp . The transannular interactions between the anthracene and pyridine/pyridinium units were examined by UV-vis and fluorescence spectroscopy to reveal a charge-transfer (CT) band in the low-energy region, particularly for 1-H+ . Despite the comparable CT interactions, the CE at the CT band was much stronger for the anthracenopyridinophane than for the parent pyridinophane, affording an anisotropy (g) factor as large as 4 × 10-3 .
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Affiliation(s)
- Akinori Shimizu
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Keisuke Nagasaki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Yoshihisa Inoue
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Tadashi Mori
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, Japan
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48
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Yan XC, Robertson MJ, Tirado-Rives J, Jorgensen WL. Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization. J Phys Chem B 2017. [PMID: 28627890 DOI: 10.1021/acs.jpcb.7b04233] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The atomic point-charge model used in most molecular mechanics force fields does not represent well the electronic anisotropy that is featured in many directional noncovalent interactions. Sulfur participates in several types of such interactions with its lone pairs and σ-holes. The current study develops a new model, via the addition of off-atom charged sites, for a variety of sulfur compounds in the OPLS-AA and OPLS/CM5 force fields to address the lack of charge anisotropy. Parameter optimization is carried out to reproduce liquid-state properties, torsional and noncovalent energetics from reliable quantum mechanical calculations, and electrostatic potentials. Significant improvements are obtained for computed free energies of hydration, reducing the mean unsigned errors from ca. 1.4 to 0.4-0.7 kcal/mol. Enhanced accuracy in directionality and energetics is also obtained for molecular complexes with sulfur-containing hydrogen and halogen bonds. Moreover, the new model reproduces the unusual conformational preferences of sulfur-containing compounds with 1,4-intramolecular chalcogen bonds. Transferability of the new force field parameters to cysteine and methionine is verified via molecular dynamic simulations of blocked dipeptides. The study demonstrates the effectiveness of using off-atom charge sites to address electronic anisotropy, and provides a parametrization methodology that can be applied to other systems.
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Affiliation(s)
- Xin Cindy Yan
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Michael J Robertson
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - Julian Tirado-Rives
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
| | - William L Jorgensen
- Department of Chemistry, Yale University , New Haven, Connecticut 06520-8107, United States
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49
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Comparison of metal-binding strength between methionine and cysteine residues: Implications for the design of metal-binding motifs in proteins. Biophys Chem 2017; 224:32-39. [DOI: 10.1016/j.bpc.2017.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/01/2017] [Accepted: 02/15/2017] [Indexed: 11/18/2022]
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50
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Huang R, Chen Z, Dolan S, Schetz JA, Dillon GH. The dual modulatory effects of efavirenz on GABA A receptors are mediated via two distinct sites. Neuropharmacology 2017; 121:167-178. [PMID: 28456686 DOI: 10.1016/j.neuropharm.2017.04.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 03/27/2017] [Accepted: 04/24/2017] [Indexed: 11/20/2022]
Abstract
Efavirenz is a widely prescribed medicine used to treat type 1 human immunodeficiency virus (HIV-1), the most prevalent pathogenic strain of the virus responsible for the acquired immune deficiency syndrome (AIDS) pandemic. Under prescribed dosing conditions, either alone or in combination therapy, efavirenz-induced CNS disturbances are frequently reported. Efavirenz was recently reported to interact in a similar concentration range with a number of receptors, transporters and ion channels including recombinant rat α1β2γ2 GABAA receptors whose actions were potentiated (Gatch et al., 2013; Dalwadi et al., 2016). Now we report on the molecular mechanism of efavirenz on GABAA receptors as a function of concentration and subunit composition via whole-cell recordings of GABA-activated currents from HEK293 cells expressing varying subunit configurations of GABAA receptors. Efavirenz elicited dual effects on the GABA response; it allosterically potentiated currents at low concentrations, whereas it inhibited currents at higher concentrations. The allosteric potentiating action on GABAA receptors was pronounced in the α1β2γ2, α2β2γ2 and α4β2γ2 configurations, greatly diminished in the α6β2γ2 configuration, and completely absent in the α3β2γ2 or α5β2γ2 configuration. In stark contrast, the inhibitory modulation of efavirenz at higher concentrations was evident in all subunit configurations examined. Moreover, efavirenz-induced modulatory effects were dependent on GABA concentration ([GABA]), with a pronounced impact on currents activated by low [GABA] but little effect at saturating [GABA]. Mutation of a highly-conserved threonine to phenylalanine in transmembrane domain 2 of the α1 subunit abolished the inhibitory effect of efavirenz in α1β2 receptors. Finally, mutations of any of the three conserved extracellular residues in α1/2/4 subunits to the conserved residues at the corresponding positions in α3/5 subunits (i.e., R84P, M89L or I120L) completely eliminated the potentiating effect of efavirenz in α1β2γ2 configuration. These findings demonstrate that efavirenz's positive allosteric modulation of the GABAA receptor is mediated via a novel allosteric site associated with the extracellular domain of the receptor.
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Affiliation(s)
- Renqi Huang
- Center for Neuroscience Discovery, Institute for Healthy Aging, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX 76107, United States.
| | - Zhenglan Chen
- Center for Neuroscience Discovery, Institute for Healthy Aging, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX 76107, United States
| | - Sean Dolan
- Center for Neuroscience Discovery, Institute for Healthy Aging, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX 76107, United States
| | - John A Schetz
- Center for Neuroscience Discovery, Institute for Healthy Aging, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX 76107, United States
| | - Glenn H Dillon
- Center for Neuroscience Discovery, Institute for Healthy Aging, University of North Texas Health Science Center at Fort Worth, Fort Worth, TX 76107, United States
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