1
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Konstantinovsky D, Perets EA, Santiago T, Velarde L, Hammes-Schiffer S, Yan ECY. Detecting the First Hydration Shell Structure around Biomolecules at Interfaces. ACS CENTRAL SCIENCE 2022; 8:1404-1414. [PMID: 36313165 PMCID: PMC9615115 DOI: 10.1021/acscentsci.2c00702] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Indexed: 05/15/2023]
Abstract
Understanding the role of water in biological processes remains a central challenge in the life sciences. Water structures in hydration shells of biomolecules are difficult to study in situ due to overwhelming background from aqueous environments. Biological interfaces introduce additional complexity because biomolecular hydration differs at interfaces compared to bulk solution. Here, we perform experimental and computational studies of chiral sum frequency generation (chiral SFG) spectroscopy to probe chirality transfer from a protein to the surrounding water molecules. This work reveals that chiral SFG probes the first hydration shell around the protein almost exclusively. We explain the selectivity to the first hydration shell in terms of the asymmetry induced by the protein structure and specific protein-water hydrogen-bonding interactions. This work establishes chiral SFG as a powerful technique for studying hydration shell structures around biomolecules at interfaces, presenting new possibilities to address grand research challenges in biology, including the molecular origins of life.
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Affiliation(s)
- Daniel Konstantinovsky
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
- Department
of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ethan A. Perets
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Ty Santiago
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | - Luis Velarde
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14260, United States
| | | | - Elsa C. Y. Yan
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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2
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Gagkayeva ZV, Gorshunov BP, Kachesov AY, Motovilov KA. Infrared fingerprints of water collective dynamics indicate proton transport in biological systems. Phys Rev E 2022; 105:044409. [PMID: 35590571 DOI: 10.1103/physreve.105.044409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/03/2022] [Indexed: 06/15/2023]
Abstract
Recent publications on spectroscopy of water layers in water bridge structures revealed a significant enhancement of the proton mobility and the dielectric contribution of translational vibrations of water molecules in the interfacial layers compared to bulk water. Herewith, the results of long-term studies of proton dynamics in solid-state acids have shown that proton mobility increases significantly with the predominance of hydronium, but not Zundel, cations in the aqueous phase. In the present work, in the light of these data, we reanalyzed our previously published results on broadband dielectric spectroscopy of bovine heart cytochrome c, bovine serum albumin, and the extracellular matrix and filaments of Shewanella oneidensis MR-1. We revealed that, just as in water bridges, an increase in electrical conductivity in these systems correlates with an increase in the dielectric contribution of water molecular translational vibrations. In addition, the appearance of spectral signatures of the hydronium cations was observed only in those cases when the system revealed noticeable electrical conductivity due to delocalized charge carriers.
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Affiliation(s)
- Z V Gagkayeva
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - B P Gorshunov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - A Ye Kachesov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
| | - K A Motovilov
- Center for Photonics and 2D Materials, Moscow Institute of Physics and Technology (National Research University), 9 Institutskiy per., Dolgoprudny, Moscow Region 141701, Russian Federation
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3
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Water Distribution on Protein Surface of the Lyophilized Proteins with Different Topography Studied by Molecular Dynamics Simulations. J Pharm Sci 2022; 111:2299-2311. [DOI: 10.1016/j.xphs.2022.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/04/2022] [Accepted: 03/04/2022] [Indexed: 11/30/2022]
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4
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Xiang L, Zhang P, Liu C, He X, Li HB, Li Y, Wang Z, Hihath J, Kim SH, Beratan DN, Tao N. Conductance and configuration of molecular gold-water-gold junctions under electric fields. MATTER 2020; 3:166-179. [PMID: 33103114 PMCID: PMC7584381 DOI: 10.1016/j.matt.2020.03.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Water molecules can mediate charge transfer in biological and chemical reactions by forming electronic coupling pathways. Understanding the mechanism requires a molecular-level electrical characterization of water. Here, we describe the measurement of single water molecular conductance at room temperature, characterize the structure of water molecules using infrared spectroscopy, and perform theoretical studies to assist in the interpretation of the experimental data. The study reveals two distinct states of water, corresponding to a parallel and perpendicular orientation of the molecules. Water molecules switch from parallel to perpendicular orientations on applying an electric field, producing switching from high to low conductance states, thus enabling the determination of single water molecular dipole moments. The work further shows that water-water interactions affect the atomic scale configuration and conductance of water molecules. These findings demonstrate the importance of the discrete nature of water molecules in electron transfer and set limits on water-mediated electron transfer rates.
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Affiliation(s)
- Limin Xiang
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Lead contact
| | - Peng Zhang
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Chaoren Liu
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Xin He
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Haipeng B. Li
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Yueqi Li
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Zixiao Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Joshua Hihath
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Seong H. Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David N. Beratan
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
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5
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Mobility of water and of protein atoms at the protein-water interface, monitored by anisotropic atomic displacement parameters, are largely uncorrelated. Amino Acids 2020; 52:435-443. [PMID: 32008094 DOI: 10.1007/s00726-020-02820-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/22/2020] [Indexed: 01/03/2023]
Abstract
A non-redundant set of 231 protein crystal structures refined at a resolution better than (or equal to) 1 Å was extracted from the Protein Data Bank and the degree of conformational rigidity at the protein-water interface was examined by means of the Hirshfeld test and by comparing the orientations of the anisotropic Us for contacting protein and water atoms. Contacts between protein and water atoms are more rigid that contacts between water atoms and the degree of rigidity increases for shorter contacts and for more hydrogen-bonded atoms. Nevertheless, water and protein atoms are not rigidly held together. On the contrary, they seem to have little influence on their mobility to such an extent that hydration water, different from the protein atoms, cannot be considered to be properly in the solid state.
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6
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Perets EA, Yan ECY. Chiral Water Superstructures around Antiparallel β-Sheets Observed by Chiral Vibrational Sum Frequency Generation Spectroscopy. J Phys Chem Lett 2019; 10:3395-3401. [PMID: 31070921 PMCID: PMC9059516 DOI: 10.1021/acs.jpclett.9b00878] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Hydration modulates every aspect of protein structure and function. However, studying water structures in hydration shells remains challenging mostly due to overwhelming background from bulk water. We used vibrational sum frequency generation (SFG) spectroscopy to characterize hydrated films of an antiparallel β-sheet peptide (LK7β) adsorbed on glass slides. The hydrated films give chiral SFG response from water only when the peptide self-assembles into antiparallel β-sheets. Experiments of isotopic labeling, isotopic dilution of water, and H2O-D2O exchange kinetics corroborate the assignments of the chiral SFG response to water stretching modes. Because individual water molecules are achiral, the chiral SFG response indicates formation of chiral superstructures of water around the antiparallel β-sheet, implying that a protein secondary structure can imprint its chirality onto the surrounding water. This result demonstrates chiral SFG spectroscopy as a promising tool for probing water structures in protein hydration and addressing fundamental questions of protein structure-function.
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Affiliation(s)
- Ethan A. Perets
- Department of Chemistry, Yale University, New Haven, Connecticut 06520 United States
| | - E. Chui-Ying Yan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520 United States
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7
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Kuroki S, Tsenkova R, Moyankova D, Muncan J, Morita H, Atanassova S, Djilianov D. Water molecular structure underpins extreme desiccation tolerance of the resurrection plant Haberlea rhodopensis. Sci Rep 2019; 9:3049. [PMID: 30816196 PMCID: PMC6395626 DOI: 10.1038/s41598-019-39443-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 01/21/2019] [Indexed: 11/29/2022] Open
Abstract
Haberlea rhodopensis is a resurrection plant with an extremely high desiccation tolerance. Even after long periods of almost full desiccation, its physiological functions are recovered shortly upon re-watering. In order to identify physiological strategies which contribute to its remarkable drought stress tolerance we used near infrared spectroscopy to investigate the state of water in the leaves of this plant and compared it to its relative, non-resurrection plant species Deinostigma eberhardtii. Here we show, using a novel aquaphotomics spectral analysis, that H. rhodopensis performs a dynamic regulation of water molecular structure during dehydration directed at drastic decrease of free water molecules, increase of water molecules with 4 hydrogen bonds, and a massive accumulation of water dimers in the full desiccation stage. Our findings suggest that changes in water structure mirror the changes in major metabolites and antioxidants which together constitute a robust defense system underlying the desiccation tolerance of the resurrection plant, while the water dimer may hold special importance for the “drying without dying” ability.
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Affiliation(s)
- Shinichiro Kuroki
- Laboratory for Information Engineering of Bioproduction, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan
| | - Roumiana Tsenkova
- Biomeasurement Technology Laboratory, Graduate School of Agricultural Science, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657-8501, Japan.
| | - Daniela Moyankova
- Abiotic stress, AgroBioInstitute, Agricultural Academy, 8 Dragan Tzankov Blvd., 1164, Sofia, Bulgaria
| | - Jelena Muncan
- Nanolab, Biomedical Engineering, Faculty of Mechanical Engineering, University of Belgrade, Kraljice Marije 16, Belgrade, 11120, Serbia
| | - Hiroyuki Morita
- NIRECO CORPORATION, 2951-4, Ishikawa machi, Hachioji, Tokyo, Japan
| | - Stefka Atanassova
- Department of Biochemistry, Microbiology and Physics, Faculty of Agriculture, Trakia University, Stara Zagora, Bulgaria
| | - Dimitar Djilianov
- Abiotic stress, AgroBioInstitute, Agricultural Academy, 8 Dragan Tzankov Blvd., 1164, Sofia, Bulgaria.
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8
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Gropp C, Husch T, Trapp N, Reiher M, Diederich F. Wasserstoffbrücken-Netzwerke: molekulare Erkennung zyklischer Alkohole in enantiomerenreinen alleno-acetylenischen Käfigrezeptoren. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Cornelius Gropp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Tamara Husch
- Laboratorium für Physikalische Chemie; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Schweiz
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
| | - Markus Reiher
- Laboratorium für Physikalische Chemie; ETH Zürich; Vladimir-Prelog-Weg 2 8093 Zürich Schweiz
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Schweiz
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9
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Gropp C, Husch T, Trapp N, Reiher M, Diederich F. Hydrogen-Bonded Networks: Molecular Recognition of Cyclic Alcohols in Enantiopure Alleno-Acetylenic Cage Receptors. Angew Chem Int Ed Engl 2018; 57:16296-16301. [DOI: 10.1002/anie.201810562] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Indexed: 12/19/2022]
Affiliation(s)
- Cornelius Gropp
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Tamara Husch
- Laboratorium für Physikalische Chemie; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie; ETH Zurich; Vladimir-Prelog-Weg 2 8093 Zurich Switzerland
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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10
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Movsisyan LD, Schäfer E, Nguyen A, Ehrmann FR, Schwab A, Rossolini T, Zimmerli D, Wagner B, Daff H, Heine A, Klebe G, Diederich F. Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase. Chemistry 2018; 24:9957-9967. [PMID: 29939431 DOI: 10.1002/chem.201801756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/10/2018] [Indexed: 11/09/2022]
Abstract
The intestinal disease shigellosis caused by Shigella bacteria affects over 120 million people annually. There is an urgent demand for new drugs as resistance against common antibiotics emerges. Bacterial tRNA-guanine transglycosylase (TGT) is a druggable target and controls the pathogenicity of Shigella flexneri. We report the synthesis of sugar-functionalized lin-benzoguanines addressing the ribose-33 pocket of TGT from Zymomonas mobilis. Ligand binding was analyzed by isothermal titration calorimetry and X-ray crystallography. Pocket occupancy was optimized by variation of size and protective groups of the sugars. The participation of a polycyclic water-cluster in the recognition of the sugar moiety was revealed. Acetonide-protected ribo- and psicofuranosyl derivatives are highly potent, benefiting from structural rigidity, good solubility, and metabolic stability. We conclude that sugar acetonides have a significant but not yet broadly recognized value in drug development.
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Affiliation(s)
- Levon D Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Frederik R Ehrmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Anatol Schwab
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Thomas Rossolini
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Daniel Zimmerli
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Björn Wagner
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Hamina Daff
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
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11
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Basak S, Gicheru Y, Samanta A, Molugu SK, Huang W, Fuente MLD, Hughes T, Taylor DJ, Nieman MT, Moiseenkova-Bell V, Chakrapani S. Cryo-EM structure of 5-HT 3A receptor in its resting conformation. Nat Commun 2018; 9:514. [PMID: 29410406 PMCID: PMC5802770 DOI: 10.1038/s41467-018-02997-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 01/10/2018] [Indexed: 11/24/2022] Open
Abstract
Serotonin receptors (5-HT3AR) directly regulate gut movement, and drugs that inhibit 5-HT3AR function are used to control emetic reflexes associated with gastrointestinal pathologies and cancer therapies. The 5-HT3AR function involves a finely tuned orchestration of three domain movements that include the ligand-binding domain, the pore domain, and the intracellular domain. Here, we present the structure from the full-length 5-HT3AR channel in the apo-state determined by single-particle cryo-electron microscopy at a nominal resolution of 4.3 Å. In this conformation, the ligand-binding domain adopts a conformation reminiscent of the unliganded state with the pore domain captured in a closed conformation. In comparison to the 5-HT3AR crystal structure, the full-length channel in the apo-conformation adopts a more expanded conformation of all the three domains with a characteristic twist that is implicated in gating. Serotonin receptor (5-HT3AR), a pentameric ligand-gated ion channel, regulates numerous gastrointestinal functions. Here the authors provide a cryo-electron microscopic structure from the full-length 5-HT3AR in the apo-state which corresponds to a resting conformation of the channel.
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Affiliation(s)
- Sandip Basak
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Yvonne Gicheru
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Amrita Samanta
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Sudheer Kumar Molugu
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Wei Huang
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Maria la de Fuente
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Taylor Hughes
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Derek J Taylor
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Marvin T Nieman
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Vera Moiseenkova-Bell
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.,Department of Pharmacology, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA. .,Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
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12
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Protein hydration: Investigation of globular protein crystal structures. Int J Biol Macromol 2017; 99:160-165. [DOI: 10.1016/j.ijbiomac.2017.02.073] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 02/10/2017] [Indexed: 01/06/2023]
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13
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Brader ML, Baker EN, Dunn MF, Laue TM, Carpenter JF. Using X-Ray Crystallography to Simplify and Accelerate Biologics Drug Development. J Pharm Sci 2017; 106:477-494. [DOI: 10.1016/j.xphs.2016.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/11/2016] [Accepted: 10/13/2016] [Indexed: 02/08/2023]
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14
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The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability. Methods Mol Biol 2017; 1607:77-115. [PMID: 28573570 DOI: 10.1007/978-1-4939-7000-1_4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.
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15
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Krimmer SG, Cramer J, Betz M, Fridh V, Karlsson R, Heine A, Klebe G. Rational Design of Thermodynamic and Kinetic Binding Profiles by Optimizing Surface Water Networks Coating Protein-Bound Ligands. J Med Chem 2016; 59:10530-10548. [DOI: 10.1021/acs.jmedchem.6b00998] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Stefan G. Krimmer
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Jonathan Cramer
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Michael Betz
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Veronica Fridh
- GE Healthcare Bio-Sciences AB, SE-751 84 Uppsala, Sweden
| | | | - Andreas Heine
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institute
of Pharmaceutical Chemistry, University of Marburg, Marbacher
Weg 6, 35032 Marburg, Germany
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16
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Quantitative assessment of kinase selectivity based the water-ring network in protein binding sites using molecular dynamics simulations. J Mol Liq 2016. [DOI: 10.1016/j.molliq.2016.06.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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When proteins are completely hydrated in crystals. Int J Biol Macromol 2016; 89:137-43. [DOI: 10.1016/j.ijbiomac.2016.04.061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/15/2016] [Accepted: 04/21/2016] [Indexed: 12/16/2022]
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18
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Bellissent-Funel MC, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia AE. Water Determines the Structure and Dynamics of Proteins. Chem Rev 2016; 116:7673-97. [PMID: 27186992 DOI: 10.1021/acs.chemrev.5b00664] [Citation(s) in RCA: 540] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
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Affiliation(s)
| | - Ali Hassanali
- International Center for Theoretical Physics, Condensed Matter and Statistical Physics 34151 Trieste, Italy
| | - Martina Havenith
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Richard Henchman
- Manchester Institute of Biotechnology The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Pohl
- Johannes Kepler University , Gruberstrasse, 40 4020 Linz, Austria
| | - Fabio Sterpone
- Institut de Biologie Physico-Chimique Laboratoire de Biochimie Théorique 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - David van der Spoel
- Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University , 751 24 Uppsala, Sweden
| | - Yao Xu
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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Nikonov O, Kravchenko O, Arkhipova V, Stolboushkina E, Nikonov S, Garber M. Water clusters in the nucleotide-binding pocket of the protein aIF2γ from the archaeon Sulfolobus solfataricus: Proton transmission. Biochimie 2015; 121:197-203. [PMID: 26700147 DOI: 10.1016/j.biochi.2015.11.029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 11/30/2015] [Indexed: 10/22/2022]
Abstract
In Archaea and Eukaryotes, the binding of Met-tRNAi(Met) to the P-site of the ribosome is mediated by translation initiation factor 2 (a/eIF2) which consists of three subunits: α, β and γ. Here, we present the high-resolution structure of intact aIF2γ from Sulfolobus solfataricus (SsoIF2γ) in complex with GTP analog, GDPCP. The comparison of the nucleotide-binding pockets in this structure and in the structure of the ribosome-bound form of EF-Tu reveals their close conformation similarity. The nucleotide-binding pocket conformation observed in this structure could be consider as corresponding to intermediate conformation of EF-Tu nucleotide-binding pocket in its transition from the GTP-bound form to the GDP-bound one. Three clusters of well defined water molecules are associated with amino acid residues of the SsoIF2γ nucleotide-binding pocket and stabilize its conformation. We suppose that two water bridges between the oxygen atoms of the GTP γ-phosphate and negatively charged residues of the pocket can serve as ways to transmit protons arising from the catalytic reaction.
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Affiliation(s)
- Oleg Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation.
| | - Olesya Kravchenko
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation
| | - Valentina Arkhipova
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation
| | - Elena Stolboushkina
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation
| | - Stanislav Nikonov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation
| | - Maria Garber
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290, Pushchino, Moscow Region, Russian Federation
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Talon R, Coquelle N, Madern D, Girard E. An experimental point of view on hydration/solvation in halophilic proteins. Front Microbiol 2014; 5:66. [PMID: 24600446 PMCID: PMC3930881 DOI: 10.3389/fmicb.2014.00066] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/04/2014] [Indexed: 11/23/2022] Open
Abstract
Protein-solvent interactions govern the behaviors of proteins isolated from extreme halophiles. In this work, we compared the solvent envelopes of two orthologous tetrameric malate dehydrogenases (MalDHs) from halophilic and non-halophilic bacteria. The crystal structure of the MalDH from the non-halophilic bacterium Chloroflexus aurantiacus (Ca MalDH) solved, de novo, at 1.7 Å resolution exhibits numerous water molecules in its solvation shell. We observed that a large number of these water molecules are arranged in pentagonal polygons in the first hydration shell of Ca MalDH. Some of them are clustered in large networks, which cover non-polar amino acid surface. The crystal structure of MalDH from the extreme halophilic bacterium Salinibacter ruber (Sr) solved at 1.55 Å resolution shows that its surface is strongly enriched in acidic amino acids. The structural comparison of these two models is the first direct observation of the relative impact of acidic surface enrichment on the water structure organization between a halophilic protein and its non-adapted counterpart. The data show that surface acidic amino acids disrupt pentagonal water networks in the hydration shell. These crystallographic observations are discussed with respect to halophilic protein behaviors in solution
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Affiliation(s)
- Romain Talon
- Institut de Biologie Structurale, Université Grenoble Alpes Grenoble, France ; CEA, DSV, Institut de Biologie Structurale Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique Grenoble, France
| | - Nicolas Coquelle
- Institut de Biologie Structurale, Université Grenoble Alpes Grenoble, France ; CEA, DSV, Institut de Biologie Structurale Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique Grenoble, France
| | - Dominique Madern
- Institut de Biologie Structurale, Université Grenoble Alpes Grenoble, France ; CEA, DSV, Institut de Biologie Structurale Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique Grenoble, France
| | - Eric Girard
- Institut de Biologie Structurale, Université Grenoble Alpes Grenoble, France ; CEA, DSV, Institut de Biologie Structurale Grenoble, France ; Institut de Biologie Structurale, Centre National de la Recherche Scientifique Grenoble, France
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Structural basis for ion permeation mechanism in pentameric ligand-gated ion channels. EMBO J 2013; 32:728-41. [PMID: 23403925 PMCID: PMC3590989 DOI: 10.1038/emboj.2013.17] [Citation(s) in RCA: 116] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 01/07/2013] [Indexed: 12/14/2022] Open
Abstract
To understand the molecular mechanism of ion permeation in pentameric ligand-gated ion channels (pLGIC), we solved the structure of an open form of GLIC, a prokaryotic pLGIC, at 2.4 Å. Anomalous diffraction data were used to place bound anions and cations. This reveals ordered water molecules at the level of two rings of hydroxylated residues (named Ser6' and Thr2') that contribute to the ion selectivity filter. Two water pentagons are observed, a self-stabilized ice-like water pentagon and a second wider water pentagon, with one sodium ion between them. Single-channel electrophysiology shows that the side-chain hydroxyl of Ser6' is crucial for ion translocation. Simulations and electrostatics calculations complemented the description of hydration in the pore and suggest that the water pentagons observed in the crystal are important for the ion to cross hydrophobic constriction barriers. Simulations that pull a cation through the pore reveal that residue Ser6' actively contributes to ion translocation by reorienting its side chain when the ion is going through the pore. Generalization of these findings to the pLGIC family is proposed.
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Oliete R, Pous J, Rodríguez-Puente S, Abad-Zapatero C, Guasch A. Elastic and inelastic diffraction changes upon variation of the relative humidity environment of PurE crystals. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:194-212. [DOI: 10.1107/s090744491204454x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Accepted: 10/27/2012] [Indexed: 11/11/2022]
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Nasief NN, Tan H, Kong J, Hangauer D. Water mediated ligand functional group cooperativity: the contribution of a methyl group to binding affinity is enhanced by a COO(-) group through changes in the structure and thermodynamics of the hydration waters of ligand-thermolysin complexes. J Med Chem 2012; 55:8283-302. [PMID: 22894131 DOI: 10.1021/jm300472k] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Ligand functional groups can modulate the contributions of one another to the ligand-protein binding thermodynamics, producing either positive or negative cooperativity. Data presented for four thermolysin phosphonamidate inhibitors demonstrate that the differential binding free energy and enthalpy caused by replacement of a H with a Me group, which binds in the well-hydrated S2' pocket, are more favorable in presence of a ligand carboxylate. The differential entropy is however less favorable. Dissection of these differential thermodynamic parameters, X-ray crystallography, and density-functional theory calculations suggest that these cooperativities are caused by variations in the thermodynamics of the complex hydration shell changes accompanying the H→Me replacement. Specifically, the COO(-) reduces both the enthalpic penalty and the entropic advantage of displacing water molecules from the S2' pocket and causes a subsequent acquisition of a more enthalpically, less entropically, favorable water network. This study contributes to understanding the important role water plays in ligand-protein binding.
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Affiliation(s)
- Nader N Nasief
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA.
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Biela A, Betz M, Heine A, Klebe G. Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding. ChemMedChem 2012; 7:1423-34. [PMID: 22733601 DOI: 10.1002/cmdc.201200206] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 05/21/2012] [Indexed: 12/18/2022]
Abstract
The binding of four congeneric peptide-like thermolysin inhibitors has been studied by high-resolution crystal structure analysis and isothermal titration calorimetry. The ligands differ only by a terminal carboxylate and/or methyl group. A surprising non-additivity of functional group contributions for the carboxylate and/or methyl groups is detected. Adding the methyl first and then the carboxylate group results in a small Gibbs free energy increase and minor enthalpy/entropy partitioning for the first modification, whereas the second involves a strong affinity increase combined with large enthalpy/entropy changes. However, first adding the carboxylate and then the methyl group yields reverse effects: the acidic group attachment now causes minor effects, whereas the added methyl group provokes large changes. As all crystal structures show virtually identical binding modes, affinity changes are related to rearrangements of the first solvation layer next to the S(2)' pocket. About 20-25 water molecules are visible next to the studied complexes. The added COO(-) groups perturb the local water network in both carboxylated complexes, and the attached methyl groups provide favorable interaction sites for water molecules. Apart from one example, a contiguously connected water network between protein and ligand functional groups is observed in all complexes. In the complex with the carboxylated ligand, which still lacks the terminal methyl group, the water network is unfavorably ruptured. This results in a surprising thermodynamic signature showing only a minor affinity increase upon COO(-) group attachment. Because the further added methyl group provides a favorable interaction site for water, the network can be reestablished, and a strong affinity increase with a large enthalpy/entropy signature is then detected.
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Affiliation(s)
- Adam Biela
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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Xu KM, Liu YJ, Liu HS. A 3D Water Network Confined in 3D Pure Inorganic Framework Constructed by [SiW12O40]4- and Potassium Ions. Z Anorg Allg Chem 2012. [DOI: 10.1002/zaac.201200023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Affiliation(s)
- Caterina Bissantz
- Discovery Chemistry, F. Hoffmann-La Roche AG, CH-4070 Basel, Switzerland
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Saeed MA, Wong BM, Fronczek FR, Venkatraman R, Hossain MA. Formation of an Amine-Water Cyclic Pentamer: A New Type of Water Cluster in a Polyazacryptand. CRYSTAL GROWTH & DESIGN 2010; 10:1486-1488. [PMID: 20495666 PMCID: PMC2873190 DOI: 10.1021/cg100161a] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Structural analysis of an adduct of a thiophene-based cryptand with tosylic acid shows the formation of a hybrid amine-water cyclic pentamer composed of four water molecules and one protonated amine in the charged hydrophobic cavity. The bulky tosylate groups remain outside the cavity, making the ligand favorable for hosting water molecules. Ab initio calculations based on density functional theory (DFT) confirm that the hybrid amine-water pentamer is stabilized inside the hydrophobic cavity of the cryptand.
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Affiliation(s)
- Musabbir A. Saeed
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212
| | - Bryan M. Wong
- Materials Chemistry Department, Sandia National Laboratories, Livermore, CA 94551
| | - Frank R. Fronczek
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803
| | - Ramaiyer Venkatraman
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212
| | - Md. Alamgir Hossain
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212
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