1
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Schmidt L, Tüting C, Kyrilis FL, Hamdi F, Semchonok DA, Hause G, Meister A, Ihling C, Stubbs MT, Sinz A, Kastritis PL. Delineating organizational principles of the endogenous L-A virus by cryo-EM and computational analysis of native cell extracts. Commun Biol 2024; 7:557. [PMID: 38730276 PMCID: PMC11087493 DOI: 10.1038/s42003-024-06204-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
The high abundance of most viruses in infected host cells benefits their structural characterization. However, endogenous viruses are present in low copy numbers and are therefore challenging to investigate. Here, we retrieve cell extracts enriched with an endogenous virus, the yeast L-A virus. The determined cryo-EM structure discloses capsid-stabilizing cation-π stacking, widespread across viruses and within the Totiviridae, and an interplay of non-covalent interactions from ten distinct capsomere interfaces. The capsid-embedded mRNA decapping active site trench is supported by a constricting movement of two flexible opposite-facing loops. tRNA-loaded polysomes and other biomacromolecules, presumably mRNA, are found in virus proximity within the cell extract. Mature viruses participate in larger viral communities resembling their rare in-cell equivalents in terms of size, composition, and inter-virus distances. Our results collectively describe a 3D-architecture of a viral milieu, opening the door to cell-extract-based high-resolution structural virology.
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Affiliation(s)
- Lisa Schmidt
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Technical Biogeochemistry, Helmholtz Centre for Environmental Research, Permoserstraße 15, Leipzig, Germany
| | - Christian Tüting
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany.
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany.
| | - Fotis L Kyrilis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Farzad Hamdi
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Dmitry A Semchonok
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
| | - Gerd Hause
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany
| | - Annette Meister
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Christian Ihling
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale), Germany
| | - Milton T Stubbs
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany
| | - Andrea Sinz
- Institute of Pharmacy, Center for Structural Mass Spectrometry, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Str. 3, Halle (Saale), Germany
| | - Panagiotis L Kastritis
- Interdisciplinary Research Center HALOmem, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3a, Halle/Saale, Germany.
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, Halle/Saale, Germany.
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.
- Biozentrum, Martin Luther University Halle-Wittenberg, Weinbergweg 22, Halle/Saale, Germany.
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2
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Grelska J, Jurkiewicz K, Nowok A, Pawlus S. Computer simulations as an effective way to distinguish supramolecular nanostructure in cyclic and phenyl alcohols. Phys Rev E 2023; 108:024603. [PMID: 37723707 DOI: 10.1103/physreve.108.024603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 07/02/2023] [Indexed: 09/20/2023]
Abstract
Molecular dynamics simulations supported by x-ray-diffraction experimental data were utilized to demonstrate how replacing the cyclic ring with the phenyl one in molecules of alcohols significantly differentiates their nanostructure by reducing the number of H-bonded clusters. Besides, molecules in the phenyl alcohols associate themselves in clusters via phenyl ring organization which likely is the result of OH⋯π and π⋯π interactions. Thus, at room temperature, the supramolecular structure of phenyl alcohols is more heterogeneous and governed by the formation of various clusters arising due to three types of interactions, while in cyclic alcohols, the H bonding controls the association of molecules. We believe that our methodology could be applied to better understand the fundamental process of association via H bonding and the competitive aggregation caused by phenyl rings.
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Affiliation(s)
- Joanna Grelska
- A. Chełkowski Institute of Physics, University of Silesia in Katowice, 75 Pułku Piechoty 1, 41-500 Chorzów, Poland
| | - Karolina Jurkiewicz
- A. Chełkowski Institute of Physics, University of Silesia in Katowice, 75 Pułku Piechoty 1, 41-500 Chorzów, Poland
| | - Andrzej Nowok
- Department of Experimental Physics, Wrocław University of Science and Technology, Wybrzeże Stanisława Wyspiańskiego 27, 50-370 Wrocław, Poland
- Laboratoire National des Champs Magnétiques Intenses, UPR 3228, CNRS-UGA-UPS-INSA, Grenoble and Toulouse, France
| | - Sebastian Pawlus
- A. Chełkowski Institute of Physics, University of Silesia in Katowice, 75 Pułku Piechoty 1, 41-500 Chorzów, Poland
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3
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Wagen CC, Jacobsen EN. Evidence for Oxonium Ions in Ethereal "Hydrogen Chloride". Org Lett 2022; 24:8826-8831. [PMID: 36450043 PMCID: PMC9879297 DOI: 10.1021/acs.orglett.2c03622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Although solutions of hydrogen chloride in ethereal solvents like diethyl ether or dioxane are commonly employed in the laboratory, the solution structure of these reagents has yet to be firmly established. Here, we analyze solutions of ethereal hydrogen chloride or deuterium chloride in toluene, in dichloromethane, or in the absence of a co-solvent by in situ infrared spectroscopy. The resulting spectra are inconsistent with free HCl or often-proposed 1:1 HCl-ether complexes but closely match the predicted spectra of oxonium ions generated via protonation of diethyl ether. Molecular dynamics simulation of the oxonium chloride complexes provides evidence for an outer-sphere contact ion pair. These results suggest new approaches for tuning the acidity of strong Brønsted acids in organic solvents and demonstrate the importance of conducting spectroscopic measurements under reaction-relevant conditions.
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Affiliation(s)
- Corin C. Wagen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Eric N. Jacobsen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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4
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Complex investigation of H-bond in Water-N-methylacetamide system: Volumetric properties, DFT, IR, MD analysis. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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5
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Efficient Non-Volatile Organogold Complex for TiO2-Supported Gold Cluster Catalysts: Preparation and Catalytic Activity for CO Oxidation. J Catal 2022. [DOI: 10.1016/j.jcat.2022.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Pourabdi L, Küçükkılınç TT, Khoshtale F, Ayazgök B, Nadri H, Farokhi Alashti F, Forootanfar H, Akbari T, Shafiei M, Foroumadi A, Sharifzadeh M, Shafiee Ardestani M, Abaee MS, Firoozpour L, Khoobi M, Mojtahedi MM. Synthesis of New 3-Arylcoumarins Bearing N-Benzyl Triazole Moiety: Dual Lipoxygenase and Butyrylcholinesterase Inhibitors With Anti-Amyloid Aggregation and Neuroprotective Properties Against Alzheimer’s Disease. Front Chem 2022; 9:810233. [PMID: 35127652 PMCID: PMC8812461 DOI: 10.3389/fchem.2021.810233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
A novel series of coumarin derivatives linked to the N-benzyl triazole group were synthesized and evaluated against 15-lipoxygenase (15-LOX), and acetyl- and butyrylcholinesterase (AChE and BuChE) to find the most potent derivative against Alzheimer’s disease (AD). Most of the compounds showed weak to moderate activity against ChEs. Among the most active BuChE and 15-LOX inhibitors, 8l and 8n exhibited an excellent neuroprotective effect, higher than the standard drug (quercetin) on the PC12 cell model injured by H2O2 and significantly reduced aggregation of amyloid Aβ1-42, with potencies of 1.44 and 1.79 times higher than donepezil, respectively. Compound 8l also showed more activity than butylated hydroxytoluene (BHT) as the reference antioxidant agent in reducing the levels of H2O2 activated by amyloid β in BV2 microglial cells. Kinetic and ligand–enzyme docking studies were also performed for better understanding of the mode of interaction between the best BuChE inhibitor and the enzyme. Considering the acceptable BuChE and 15-LOX inhibition activities as well as significant neuroprotection, and anti-amyloid aggregation activities, 8l and 8n could be considered as potential MTDLs for further modification and studies against AD.
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Affiliation(s)
- Ladan Pourabdi
- Department of Organic Chemistry and Natural Products, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | | | - Fatemeh Khoshtale
- Department of Organic Chemistry and Natural Products, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Beyza Ayazgök
- Faculty of Pharmacy, Department of Biochemistry, Hacettepe University, Ankara, Turkey
| | - Hamid Nadri
- Department of Medicinal Chemistry, Faculty of Pharmacy and Pharmaceutical Sciences Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Farid Farokhi Alashti
- Department of Organic Chemistry and Natural Products, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Hamid Forootanfar
- Pharmaceutical Sciences and Cosmetic Products Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Tayebeh Akbari
- Department of Microbiology, Islamic Azad University, North Tehran Branch, Tehran, Iran
| | - Mohammad Shafiei
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Alireza Foroumadi
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Pharmaceutical Sciences Research Center, The institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Sharifzadeh
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Shafiee Ardestani
- Department of Radiopharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - M. Saeed Abaee
- Department of Organic Chemistry and Natural Products, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
| | - Loghman Firoozpour
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehdi Khoobi
- Pharmaceutical Sciences Research Center, The institute of Pharmaceutical Sciences (TIPS), Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiopharmacy, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Mohammad M. Mojtahedi, ; Mehdi Khoobi, ,
| | - Mohammad M. Mojtahedi
- Department of Organic Chemistry and Natural Products, Chemistry and Chemical Engineering Research Center of Iran, Tehran, Iran
- *Correspondence: Mohammad M. Mojtahedi, ; Mehdi Khoobi, ,
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7
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Walker DR, Alizadehmojarad AA, Kolomeisky AB, Hartgerink JD. Charge-Free, Stabilizing Amide-π Interactions Can Be Used to Control Collagen Triple-Helix Self-Assembly. Biomacromolecules 2021; 22:2137-2147. [PMID: 33881314 DOI: 10.1021/acs.biomac.1c00234] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
There is a noted lack of understood, controllable interactions for directing the organization of collagen triple helices. While the field has had success using charge-pair interactions and cation-π interactions in helix design, these alone are not adequate for achieving the degree of specificity desirable for these supramolecular structures. Furthermore, because of the reliance on electrostatic interactions, designed heterotrimeric systems have been heavily charged, a property undesirable in some applications. Amide-π interactions are a comparatively understudied class of charge-free interactions, which could potentially be harnessed for triple-helix design. Herein, we propose, validate, and utilize pairwise amino acid amide-π interactions in collagen triple-helix design. Glutamine-phenylalanine pairs, when arranged in an axial geometry, are found to exhibit a moderately stabilizing effect, while in the lateral geometry, this pair is destabilizing. Together this allows glutamine-phenylalanine pairs to effectively set the register of triple helices. In contrast, interactions between asparagine and phenylalanine appear to have little effect on triple-helical stability. After deconvoluting the contributions of these amino acids to triple-helix stability, we demonstrate these new glutamine-phenylalanine interactions in the successful design of a heterotrimeric triple helix. The results of all of these analyses are used to update our collagen triple-helix thermal stability prediction algorithm, Scoring function for Collagen Emulating Peptides' Temperature of Transition (SCEPTTr).
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8
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Petters L, Burger S, Kronawitter S, Drees M, Kieslich G. Linear negative thermal expansion in Pd(acac) 2. CrystEngComm 2021. [DOI: 10.1039/d1ce00534k] [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
We propose that chemical interactions in the coordination compound Pd(acac)2 can be mapped on a wine-rack network, explaining linear negative thermal expansion in a classic coordination compound based on concepts known from network materials.
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Affiliation(s)
- Ludwig Petters
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Stefan Burger
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Silva Kronawitter
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Markus Drees
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Gregor Kieslich
- Department of Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
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9
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Hema, Bhatt T, Pant T, Dhondiyal CC, Rana M, Chowdhury P, Joshi GC, Arya P, Tiwari H. Computational study of the intermolecular interactions and their effect on the UV-visible spectra of the ternary liquid mixture of benzene, ethanol and propylene glycol. J Mol Model 2020; 26:268. [PMID: 32926296 DOI: 10.1007/s00894-020-04533-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/03/2020] [Indexed: 11/30/2022]
Abstract
Quantum chemical calculations are well-equipped to provide answers to the questions regarding the different aspects of intermolecular interactions. We investigate the benzene, ethanol and 1,2 propanediol ternary mixture with theoretical as well as experimental UV-Vis spectroscopy. An extensive theoretical study on the molecular structure and UV-Vis spectral analysis was undertaken using density functional theory (DFT) method. Structural parameter analysis and the HOMO-LUMO (highest occupied molecular orbital-lowest unoccupied molecular orbital) energy gap help to describe the possible interaction between molecules in dimer and in combination. Interaction energy has been calculated from topological study. Time-dependent density functional theory (TDDFT) calculations on dimer/cluster in gas phase help to understand the effect of the molecular interaction on the overall spectral shift and related intensity variation. Our results show that in the ternary mixture, the interaction energies of the interactions are π-π interaction: 0.52-2.57 kcal/mol, Hp-π interaction: 1.15 kcal/mol and H-bonding: 2.49 to 4.46 kcal/mol. The π-π interaction and H-bonding cause red shift in absorption spectra while Hp-π interaction causes blue shift. In the ternary mixture, the strength of different kinds of interaction depends on the concentration, and as each interaction has its own effect on spectral shift, the overall experimental spectra get broader and distorted from the Gaussian shape.
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Affiliation(s)
- Hema
- Department of Physics, M. B. Govt. P. G. College, Haldwani, Uttarakhand, India
| | - Tara Bhatt
- Department of Physics, M. B. Govt. P. G. College, Haldwani, Uttarakhand, India.
| | - Tarun Pant
- Department of Physics, M. B. Govt. P. G. College, Haldwani, Uttarakhand, India
| | - Charu Ch Dhondiyal
- Department of Physics, M. B. Govt. P. G. College, Haldwani, Uttarakhand, India
| | - Meenakshi Rana
- Uttarakhand Open University, Haldwani, Uttarakhand, India
| | - Papia Chowdhury
- Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India
| | - G C Joshi
- G.B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India
| | - Pratibha Arya
- Department of Physics, M. B. Govt. P. G. College, Haldwani, Uttarakhand, India
| | - Himani Tiwari
- Department of Physics, M. B. Govt. P. G. College, Haldwani, Uttarakhand, India
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10
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Leisle L, Xu Y, Fortea E, Lee S, Galpin JD, Vien M, Ahern CA, Accardi A, Bernèche S. Divergent Cl - and H + pathways underlie transport coupling and gating in CLC exchangers and channels. eLife 2020; 9:51224. [PMID: 32343228 PMCID: PMC7274781 DOI: 10.7554/elife.51224] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/28/2020] [Indexed: 12/12/2022] Open
Abstract
The CLC family comprises H+-coupled exchangers and Cl- channels, and mutations causing their dysfunction lead to genetic disorders. The CLC exchangers, unlike canonical 'ping-pong' antiporters, simultaneously bind and translocate substrates through partially congruent pathways. How ions of opposite charge bypass each other while moving through a shared pathway remains unknown. Here, we use MD simulations, biochemical and electrophysiological measurements to identify two conserved phenylalanine residues that form an aromatic pathway whose dynamic rearrangements enable H+ movement outside the Cl- pore. These residues are important for H+ transport and voltage-dependent gating in the CLC exchangers. The aromatic pathway residues are evolutionarily conserved in CLC channels where their electrostatic properties and conformational flexibility determine gating. We propose that Cl- and H+ move through physically distinct and evolutionarily conserved routes through the CLC channels and transporters and suggest a unifying mechanism that describes the gating mechanism of both CLC subtypes.
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Affiliation(s)
- Lilia Leisle
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Yanyan Xu
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
| | - Eva Fortea
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States
| | - Sangyun Lee
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Malvin Vien
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, United States
| | - Alessio Accardi
- Department of Anesthesiology, Weill Cornell Medical College, New York, United States.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Department of Biochemistry, Weill Cornell Medical College, New York, United States
| | - Simon Bernèche
- SIB Swiss Institute of Bioinformatics, University of Basel, Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
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11
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Hema, Bhatt T. Comparative thermo-acoustic study of ternary mixture of polar and nonpolar solvents with benzene and ethanol system. SN APPLIED SCIENCES 2020. [DOI: 10.1007/s42452-019-1777-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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12
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Chatzimitakos TG, Karali KK, Stalikas CD. Magnetic graphene oxide as a convenient nanosorbent to streamline matrix solid-phase dispersion towards the extraction of pesticides from vegetables and their determination by GC–MS. Microchem J 2019. [DOI: 10.1016/j.microc.2019.104247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Enhancing Stability and Reducing Viscosity of a Monoclonal Antibody With Cosolutes by Weakening Protein-Protein Interactions. J Pharm Sci 2019; 108:2517-2526. [DOI: 10.1016/j.xphs.2019.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 02/12/2019] [Accepted: 03/01/2019] [Indexed: 12/22/2022]
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14
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Zabelin AA, Fufina TY, Khristin AM, Khatypov RA, Shkuropatova VA, Shuvalov VA, Vasilieva LG, Shkuropatov AY. Effect of Leucine M196 Substitution by Histidine on Electronic Structure of the Primary Electron Donor and Electron Transfer in Reaction Centers from Rhodobacter sphaeroides. BIOCHEMISTRY (MOSCOW) 2019; 84:520-528. [PMID: 31234766 DOI: 10.1134/s0006297919050067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In our recent X-ray study, we demonstrated that substitution of the natural leucine residue M196 with histidine in the reaction center (RC) from Rhodobacter (Rba.) sphaeroides leads to formation of a close contact between the genetically introduced histidine and the primary electron donor P (bacteriochlorophylls (BChls) PA and PB dimer) creating a novel pigment-protein interaction that is not observed in native RCs. In the present work, the possible nature of this novel interaction and its effects on the electronic properties of P and the photochemical charge separation in isolated mutant RCs L(M196)H are investigated at room temperature using steady-state absorption spectroscopy, light-induced difference FTIR spectroscopy, and femtosecond transient absorption spectroscopy. The results are compared with the data obtained for the RCs from Rba. sphaeroides pseudo-wild type strain. It is shown that the L(M196)H mutation results in a decrease in intensity and broadening of the long-wavelength Qy absorption band of P at ~865 nm. Due to the mutation, there is also weakening of the electronic coupling between BChls in the radical cation P+ and increase in the positive charge localization on the PA molecule. Despite the significant perturbations of the electronic structure of P, the mutant RCs retain high electron transfer rates and quantum yield of the P+QA- state (QA is the primary quinone acceptor), which is close to the one observed in the native RCs. Comparison of our results with the literature data suggests that the imidazole group of histidine M196 forms a π-hydrogen bond with the π-electron system of the PB molecule in the P dimer. It is likely that the specific (T-shaped) spatial organization of the π-hydrogen interaction and its potential heterogeneity in relation to the bonding energy is, at least partially, the reason that this type of interaction between the protein and the pigment and quinone cofactors is not realized in the native RCs.
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Affiliation(s)
- A A Zabelin
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - T Yu Fufina
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - A M Khristin
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - R A Khatypov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - V A Shkuropatova
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - V A Shuvalov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - L G Vasilieva
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - A Ya Shkuropatov
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
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15
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Carmona-Negrón JA, Flores-Rivera MM, Santana A, Rheingold AL, Meléndez E. Synthesis, crystal structure, Hirshfeld Surface analysis, and DFT studies of 16-ferrocenylidene-17β-estra-1,3,5-triene-3,17-diol: Towards the application of ferrocene-hormone conjugates to target hormone dependent breast cancer. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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The Widely Conserved ebo Cluster Is Involved in Precursor Transport to the Periplasm during Scytonemin Synthesis in Nostoc punctiforme. mBio 2018; 9:mBio.02266-18. [PMID: 30482833 PMCID: PMC6282210 DOI: 10.1128/mbio.02266-18] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Scytonemin is a dimeric indole-phenol sunscreen synthesized by some cyanobacteria under conditions of exposure to UVA radiation. While its biosynthetic pathway has been elucidated only partially, comparative genomics reveals that the scytonemin operon often contains a cluster of five highly conserved genes (ebo cluster) of unknown function that is widespread and conserved among several bacterial and algal phyla. We sought to elucidate the function of the ebo cluster in the cyanobacterium Nostoc punctiforme by constructing and analyzing in-frame deletion mutants (one for each ebo gene and one for the entire cluster). Under conditions of UVA induction, all ebo mutants were scytoneminless, and all accumulated a single compound, the scytonemin monomer, clearly implicating all ebo genes in scytonemin production. We showed that the scytonemin monomer also accumulated in an induced deletion mutant of scyE, a non-ebo scytonemin gene whose product is demonstrably targeted to the periplasm. Confocal autofluorescence microscopy revealed that the accumulation was confined to the cytoplasm in all ebo mutants but that that was not the case in the scyE deletion, with an intact ebo cluster, where the scytonemin monomer was also excreted to the periplasm. The results implicate the ebo cluster in the export of the scytonemin monomer to the periplasm for final oxidative dimerization by ScyE. By extension, the ebo gene cluster may play similar roles in metabolite translocation across many bacterial phyla. We discuss potential mechanisms for such a role on the basis of structural and phylogenetic considerations of the ebo proteins.IMPORTANCE Elucidating the biochemical and genetic basis of scytonemin constitutes an interesting challenge because of its unique structure and the unusual fact that it is partially synthesized in the periplasmic space. Our work points to the ebo gene cluster, associated with the scytonemin operon of cyanobacteria, as being responsible for the excretion of scytonemin intermediates from the cytoplasm into the periplasm during biosynthesis. Few conserved systems have been described that facilitate the membrane translocation of small molecules. Because the ebo cluster is well conserved among a large diversity of bacteria and algae and yet insights into its potential function are lacking, our findings suggest that translocation of small molecules across the plasma membrane may be its generic role across microbes.
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Abdolmaleki A, Dadsetani M, Zabardasti A. Improving the first hyperpolarizability of anthracene through interaction with HX molecules (XF, Cl, Br): A theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 196:353-365. [PMID: 29475184 DOI: 10.1016/j.saa.2018.02.042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 01/28/2018] [Accepted: 02/12/2018] [Indexed: 06/08/2023]
Abstract
The variations in nonlinear optical activity (NLO) of anthracene (C14H10) was investigated via intermolecular interactions between C14H10 and HX molecules (XF, Cl and Br) using B3LYP-D3 method at 6-311++G(d,p) basis set. The stabilization of those complexes was investigated via vibrational analysis, quantum theory of atoms in molecules, molecular electrostatic potential, natural bond orbitals and symmetry-adapted perturbation theory (SAPT) analysis. Furthermore, the optical spectra and the first hyperpolarizabilities of C14H10⋯HX complexes were computed. The adsorption of hydrogen halide through C14H10⋯HX complex formation, didn't change much the linear optical activities of C14H10 molecule, but the magnitude of the first hyperpolarizability of the C14H10⋯HX complexes to be as much as that of urea.
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Wierzchowski M, Dutkiewicz Z, Gielara-Korzańska A, Korzański A, Teubert A, Teżyk A, Stefański T, Baer-Dubowska W, Mikstacka R. Synthesis, biological evaluation and docking studies of trans-stilbene methylthio derivatives as cytochromes P450 family 1 inhibitors. Chem Biol Drug Des 2017. [PMID: 28632937 DOI: 10.1111/cbdd.13042] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Cytochromes P450 family 1 (CYP1) are responsible for the metabolism of procarcinogens, for example polycyclic aromatic hydrocarbons and aromatic and heterocyclic amines. The inhibition of CYP1 activity is examined in terms of chemoprevention and cancer chemotherapy. We designed and synthesized a series of trans-stilbene derivatives possessing a combination of methoxy and methylthio functional groups attached in different positions to the trans-stilbene skeleton. We determined the effects of synthesized compounds on the activities of human recombinant CYP1A1, CYP1A2 and CYP1B1 and, to explain the variation of inhibitory potency of methoxystilbene derivatives and their methylthio analogues, we employed computational analysis. The compounds were docked to CYP1A1, CYP1A2 and CYP1B1 binding sites with the use of Accelrys Discovery Studio 4.0 by the CDOCKER procedure. For CYP1A2 and CYP1B1, values of scoring functions correlated well with inhibitory potency of stilbene derivatives. All compounds were relatively poor inhibitors of CYP1A2 that possess the most narrow and flat enzyme cavity among CYP1s. For the most active CYP1A1 inhibitor, 2-methoxy-4'-methylthio-trans-stilbene, a high number of molecular interactions was observed, although the interaction energies were not distinctive.
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Affiliation(s)
- Marcin Wierzchowski
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Poznan University of Medical Sciences, Poznań, Poland
| | - Zbigniew Dutkiewicz
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Poznan University of Medical Sciences, Poznań, Poland
| | - Agnieszka Gielara-Korzańska
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Poznan University of Medical Sciences, Poznań, Poland
| | - Artur Korzański
- Department of Crystallography, Adam Mickiewicz University, Poznań, Poland
| | - Anna Teubert
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Artur Teżyk
- Department of Forensic Medicine, Poznan University of Medical Sciences, Poznań, Poland
| | - Tomasz Stefański
- Department of Chemical Technology of Drugs, Faculty of Pharmacy, Poznan University of Medical Sciences, Poznań, Poland
| | - Wanda Baer-Dubowska
- Department of Pharmaceutical Biochemistry, Poznan University of Medical Sciences, Poznań, Poland
| | - Renata Mikstacka
- Department of Inorganic and Analytical Chemistry, Ludwik Rydygier Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
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19
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Silva DS, Oliveira BG. New insights about the hydrogen bonds formed between acetylene and hydrogen fluoride: π⋯H, C⋯H and F⋯H. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:160-169. [PMID: 27636326 DOI: 10.1016/j.saa.2016.08.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 08/26/2016] [Accepted: 08/28/2016] [Indexed: 06/06/2023]
Abstract
A theoretical study of hydrogen bond strength and bond properties in the C2H2⋯(HF)-T, C2H2⋯2(HF)-T, C2H2⋯2(HF), C2H2⋯3(HF) and C2H2⋯4(HF) complexes was carried out at the B3LYP/6-311++G(d,p) theory level. In these systems, a strength competition between the π⋯H and C⋯H interactions was examined. Specifically the F⋯H hydrogen bond, its properties were studied through a comparison between the hydrogen fluoride and the higher-order complexes (trimer, tetramer and pentamer). Regarding the electronic properties, the hydrogen bond strength could not be determined by the supermolecule approach. Thus, the hydrogen bond energies were computed via NBO calculations. Additionally to NBO, the ChelpG charge calculations were used to interpret the intermolecular charge transfer. The QTAIM integrations were useful to predict the covalent character of the π⋯H, C⋯H and F⋯H hydrogen bonds. Moreover, values of hybrid orbitals (s and p) and atomic radii were also determined in order to justify the red shifts in the stretch frequencies of the HF bonds.
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Affiliation(s)
- Denize S Silva
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual de Santa Cruz, 45662-900 Ilhéus, BA, Brazil; Instituto de Ciências Ambientais e Desenvolvimento Sustentável, Universidade Federal da Bahia, 47801-100 Barreiras, Brazil
| | - Boaz G Oliveira
- Departamento de Ciências Exatas e Tecnológicas, Universidade Estadual de Santa Cruz, 45662-900 Ilhéus, BA, Brazil; Instituto de Ciências Ambientais e Desenvolvimento Sustentável, Universidade Federal da Bahia, 47801-100 Barreiras, Brazil.
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Ledesma J, Pisano PL, Martino DM, Boschetti CE, Bortolato SA. Thymine based copolymers: feasible sensors for the detection of persistent organic pollutants in water. RSC Adv 2017. [DOI: 10.1039/c7ra08868j] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A multidisciplinary approach for understanding properties of thymine-based copolymer sensors.
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Affiliation(s)
- J. Ledesma
- Instituto de Procesos Biotecnológicos y Químicos de Rosario
- CONICET
- Rosario 2000
- Argentina
| | - P. L. Pisano
- Instituto de Química de Rosario
- CONICET
- Rosario 2000
- Argentina
| | - D. M. Martino
- Instituto de Física del Litoral
- CONICET
- Güemes 3450
- Argentina
| | - C. E. Boschetti
- Instituto de Procesos Biotecnológicos y Químicos de Rosario
- CONICET
- Rosario 2000
- Argentina
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21
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Anion–π interactions in complexes of proteins and halogen-containing amino acids. J Biol Inorg Chem 2016; 21:357-68. [DOI: 10.1007/s00775-016-1346-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 02/08/2016] [Indexed: 10/22/2022]
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22
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Wichapong K, Alard JE, Ortega-Gomez A, Weber C, Hackeng TM, Soehnlein O, Nicolaes GAF. Structure-Based Design of Peptidic Inhibitors of the Interaction between CC Chemokine Ligand 5 (CCL5) and Human Neutrophil Peptides 1 (HNP1). J Med Chem 2016; 59:4289-301. [PMID: 26871718 DOI: 10.1021/acs.jmedchem.5b01952] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Protein-protein interactions (PPIs) are receiving increasing interest, much sparked by the realization that they represent druggable targets. Recently, we successfully developed a peptidic inhibitor, RRYGTSKYQ ("SKY" peptide), that shows high potential in vitro and in vivo to interrupt a PPI between the platelet-borne chemokine CCL5 and the neutrophil-derived granule protein HNP1. This PPI plays a vital role in monocyte adhesion, representing a key mechanism in acute and chronic inflammatory diseases. Here, we present extensive and detailed computational methods applied to develop the SKY peptide. We combined experimentally determined binding affinities (KD) of several orthologs of CCL5 with HNP1 with in silico studies to identify the most likely heterodimeric CCL5-HNP1 complex which was subsequently used as a starting structure to rationally design peptidic inhibitors. Our method represents a fast and simple approach that can be widely applied to determine other protein-protein complexes and moreover to design inhibitors or stabilizers of protein-protein interaction.
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Affiliation(s)
- Kanin Wichapong
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University , 6200 MD Maastricht, The Netherlands
| | - Jean-Eric Alard
- Institute for Cardiovascular Prevention, Ludwig Maximilians University Munich , 80336 Munich, Germany
| | - Almudena Ortega-Gomez
- Institute for Cardiovascular Prevention, Ludwig Maximilians University Munich , 80336 Munich, Germany
| | - Christian Weber
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University , 6200 MD Maastricht, The Netherlands.,Institute for Cardiovascular Prevention, Ludwig Maximilians University Munich , 80336 Munich, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80336 Munich, Germany
| | - Tilman M Hackeng
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University , 6200 MD Maastricht, The Netherlands
| | - Oliver Soehnlein
- Institute for Cardiovascular Prevention, Ludwig Maximilians University Munich , 80336 Munich, Germany.,German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, 80336 Munich, Germany.,Department of Pathology, Academic Medical Center (AMC), University of Amsterdam , 1105 AZ Amsterdam, The Netherlands
| | - Gerry A F Nicolaes
- Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University , 6200 MD Maastricht, The Netherlands
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Chang YP, Huang CC, Shen CC, Tsai KC, Ueng YF. Differential inhibition of CYP1-catalyzed regioselective hydroxylation of estradiol by berberine and its oxidative metabolites. Drug Metab Pharmacokinet 2015; 30:374-83. [DOI: 10.1016/j.dmpk.2015.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/17/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
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24
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Du QS, Chen D, Xie NZ, Huang RB, Chou KC. Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding. J Biomol Struct Dyn 2015; 33:1957-72. [PMID: 25375237 PMCID: PMC4536944 DOI: 10.1080/07391102.2014.984333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/02/2014] [Indexed: 11/20/2022]
Abstract
Although not being classified as the most fundamental protein structural elements like α-helices and β-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-π interaction (Hp-π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp-π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding.
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Affiliation(s)
- Qi-Shi Du
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi530007, China
- Nanning Fermentation and Enzyme Engineering Research Center, Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi530004, China
- Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA02478, USA
| | - Dong Chen
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi530007, China
- Nanning Fermentation and Enzyme Engineering Research Center, Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi530004, China
| | - Neng-Zhong Xie
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi530007, China
| | - Ri-Bo Huang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, 98 Daling Road, Nanning, Guangxi530007, China
- Nanning Fermentation and Enzyme Engineering Research Center, Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi530004, China
| | - Kuo-Chen Chou
- Center of Excellence in Genomic Medicine Research (CEGMR), King Abdulaziz University, Jeddah21589, Saudi Arabia
- Gordon Life Science Institute, 53 South Cottage Road, Belmont, MA02478, USA
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Iwashita K, Shiraki K, Ishii R, Tanaka T, Hirano A. Liquid Chromatographic Analysis of the Interaction between Amino Acids and Aromatic Surfaces Using Single-Wall Carbon Nanotubes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015. [PMID: 26208035 DOI: 10.1021/acs.langmuir.5b02500] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Proteins have nonspecific adsorption capacities for solid surfaces. Although the nonspecific adsorption capacities are generally understood to be related to the hydrophobicity or charge density of the surfaces, little is known at the amino acid level about the interaction between proteins and polyaromatic surfaces such as carbon nanotubes, which have recently been used for biotechnology applications. In this study, we investigated the interaction between proteinogenic amino acids and carbon nanotubes using high-performance liquid chromatography on silica matrices coated by single-wall carbon nanotubes (SWCNTs). Among the amino acids used in this study, tryptophan, tyrosine, and phenylalanine showed exceptional affinity for the matrices. The characteristic affinities of these amino acids were ascribed to their unique interactions with the large polyaromatic surfaces of the SWCNTs. These results are useful for understanding and controlling protein adsorption onto aromatic surfaces.
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Affiliation(s)
- Kazuki Iwashita
- †Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Kentaro Shiraki
- †Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8573, Japan
| | - Rieko Ishii
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Takeshi Tanaka
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
| | - Atsushi Hirano
- ‡Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8562, Japan
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26
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Fufina TY, Vasilieva LG, Gabdulkhakov AG, Shuvalov VA. The L(M196)H mutation in Rhodobacter sphaeroides reaction center results in new electrostatic interactions. PHOTOSYNTHESIS RESEARCH 2015; 125:23-29. [PMID: 25480338 DOI: 10.1007/s11120-014-0062-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 11/20/2014] [Indexed: 06/04/2023]
Abstract
New histidine residue was introduced in M196 position in the reaction center of Rhodobacter sphaeroides in order to alter polarity of the BChl dimer's protein environment and to study how it affects properties and structure of the primary electron donor P. It was shown that in the absorption spectrum of the mutant RC the 6 nm red shift of the Q Y P band was observed together with considerable decrease of its amplitude. The mid-point potential of P/P (+) in the mutant RC was increased by +65 (±15) mV as compared to the E m P/P (+) value in the wild-type RC suggesting that the mutation resulted in new pigment-protein interactions. Crystal structure of RC L(M196)H determined at 2.4 Å resolution implies that BChl Р В and introduced histidine-M196 organize new electrostatic contact that may be specified either as π-π staking or as hydrogen-π interaction. Besides, the structure of the mutants RC shows that His-M196 apparently became involved in hydrogen bond network existing in BChl Р В vicinity that may favor stability of the mutant RC.
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Affiliation(s)
- Tatiana Y Fufina
- Institute of Basic Biological Problems, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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Jovanović M, Gruden-Pavlović M, Zlatović M. Stabilizing non-covalent interactions of ligand aromatic moieties and proline in ligand–protein systems. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-014-1357-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Hussain HB, Wilson KA, Wetmore SD. Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur. Aust J Chem 2015. [DOI: 10.1071/ch14598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.
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Cadel S, Darmon C, Pernier J, Hervé G, Foulon T. The M1 family of vertebrate aminopeptidases: role of evolutionarily conserved tyrosines in the enzymatic mechanism of aminopeptidase B. Biochimie 2014; 109:67-77. [PMID: 25530263 DOI: 10.1016/j.biochi.2014.12.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/11/2014] [Indexed: 01/15/2023]
Abstract
Aminopeptidase B (Ap-B), a member of the M1 family of Zn(2+)-aminopeptidases, removes basic residues at the NH2-terminus of peptides and is involved in the in vivo proteolytic processing of miniglucagon and cholecystokinin-8. M1 enzymes hydrolyze numerous different peptides and are implicated in many physiological functions. As these enzymes have similar catalytic mechanisms, their respective substrate specificity and/or catalytic efficiency must be based on subtle structural differences at or near the catalytic site. This leads to the hypothesis that each primary structure contains a consensus structural template, strictly necessary for aminopeptidase activity, and a specific amino acid environment localized in or outside the catalytic pocket that finely tunes the substrate specificity and catalytic efficiency of each enzyme. A multiple sequence alignment of M1 peptidases from vertebrates allowed to identify conserved tyrosine amino acids, which are members of this catalytic backbone. In the present work, site-directed mutagenesis and 3D molecular modeling of Ap-B were used to specify the role of four fully (Y281, Y229, Y414, and Y441) and one partially (Y409) conserved residues. Tyrosine to phenylalanine mutations allowed confirming the influence of the hydroxyl groups on the enzyme activity. These groups are implicated in the reaction mechanism (Y414), in substrate specificity and/or catalytic efficiency (Y409), in stabilization of essential amino acids of the active site (Y229, Y409) and potentially in the maintenance of its structural integrity (Y281, Y441). The importance of hydrogen bonds is verified by the Y229H substitution, which preserves the enzyme activity. These data provide new insights into the catalytic mechanism of Ap-B in the M1 family of aminopeptidases.
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Affiliation(s)
- Sandrine Cadel
- Sorbonne universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), FR 3631 UPMC-CNRS, BIOSIPE, BIOgenèse des SIgnaux PEptidiques, Paris, France.
| | - Cécile Darmon
- Sorbonne universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), FR 3631 UPMC-CNRS, BIOSIPE, BIOgenèse des SIgnaux PEptidiques, Paris, France.
| | - Julien Pernier
- Cytoskeleton Dynamics and Motility Group, Laboratoire d'Enzymologie et Biochimie Structurale [LEBS], UPR 3082 - CNRS, Gif-sur-Yvette, France.
| | - Guy Hervé
- Sorbonne universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), FR 3631 UPMC-CNRS, BIOSIPE, BIOgenèse des SIgnaux PEptidiques, Paris, France.
| | - Thierry Foulon
- Sorbonne universités, UPMC Univ Paris 06, Institut de Biologie Paris-Seine (IBPS), FR 3631 UPMC-CNRS, BIOSIPE, BIOgenèse des SIgnaux PEptidiques, Paris, France.
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Garneau L, Klein H, Lavoie MF, Brochiero E, Parent L, Sauvé R. Aromatic-aromatic interactions between residues in KCa3.1 pore helix and S5 transmembrane segment control the channel gating process. ACTA ACUST UNITED AC 2014; 143:289-307. [PMID: 24470490 PMCID: PMC4001770 DOI: 10.1085/jgp.201311097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Interactions between aromatic amino acid residues in the pore helix and S5 transmembrane domain control gating of the Ca2+-activated potassium channel KCa3.1. The Ca2+-activated potassium channel KCa3.1 is emerging as a therapeutic target for a large variety of health disorders. One distinguishing feature of KCa3.1 is that the channel open probability at saturating Ca2+ concentrations (Pomax) is low, typically 0.1–0.2 for KCa3.1 wild type. This observation argues for the binding of Ca2+ to the calmodulin (CaM)–KCa3.1 complex, promoting the formation of a preopen closed-state configuration leading to channel opening. We have previously shown that the KCa3.1 active gate is most likely located at the level of the selectivity filter. As Ca2+-dependent gating of KCa3.1 originates from the binding of Ca2+ to CaM in the C terminus, the hypothesis of a gate located at the level of the selectivity filter requires that the conformational change initiated in the C terminus be transmitted to the S5 and S6 transmembrane helices, with a resulting effect on the channel pore helix directly connected to the selectivity filter. A study was thus undertaken to determine to what extent the interactions between the channel pore helix with the S5 and S6 transmembrane segments contribute to KCa3.1 gating. Molecular dynamics simulations first revealed that the largest contact area between the pore helix and the S5 plus S6 transmembrane helices involves residue F248 at the C-terminal end of the pore helix. Unitary current recordings next confirmed that modulating aromatic–aromatic interactions between F248 and W216 of the S5 transmembrane helical segment and/or perturbing the interactions between F248 and residues in S6 surrounding the glycine hinge G274 cause important changes in Pomax. This work thus provides the first evidence for a key contribution of the pore helix in setting Pomax by stabilizing the channel closed configuration through aromatic–aromatic interactions involving F248 of the pore helix. We propose that the interface pore helix/S5 constitutes a promising site for designing KCa3.1 potentiators.
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Affiliation(s)
- Line Garneau
- Department of Physiology and Membrane Protein Research Group, 2 Centre de recherche du Centre hospitalier de l'Université de Montréal, and 3 Department of Medicine, Université de Montréal, Montréal, Quebec H3C 3J7, Canada
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Du QS, Wang SQ, Chen D, Meng JZ, Huang RB. In depth analysis on the binding sites of adamantane derivatives in HCV (hepatitis C virus) p7 channel based on the NMR structure. PLoS One 2014; 9:e93613. [PMID: 24714586 PMCID: PMC3979700 DOI: 10.1371/journal.pone.0093613] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 03/07/2014] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The recently solved solution structure of HCV (hepatitis C virus) p7 ion channel provides a solid structure basis for drug design against HCV infection. In the p7 channel the ligand amantadine (or rimantadine) was determined in a hydrophobic pocket. However the pharmocophore (-NH2) of the ligand was not assigned a specific binding site. RESULTS The possible binding sites for amino group of adamantane derivatives is studied based on the NMR structure of p7 channel using QM calculation and molecular modeling. In the hydrophobic cavity and nearby three possible binding sites are proposed: His17, Phe20, and Trp21. The ligand binding energies at the three binding sites are studied using high level QM method CCSD(T)/6-311+G(d,p) and AutoDock calculations, and the interaction details are analyzed. The potential application of the binding sites for rational inhibitor design are discussed. CONCLUSIONS Some useful viewpoints are concluded as follows. (1) The amino group (-NH2) of adamantane derivatives is protonated (-NH3+), and the positively charged cation may form cation-π interactions with aromatic amino acids. (2) The aromatic amino acids (His17, Phe20, and Trp21) are the possible binding sites for the protonated amino group (-NH3+) of adamantane derivatives, and the cation-π bond energies are 3 to 5 times stronger than the energies of common hydrogen bonds. (3) The higher inhibition potent of rimantadine than amantadine probably because of its higher pKa value (pKa = 10.40) and the higher positive charge in the amino group. The potential application of p7 channel structure for inhibitor design is discussed.
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Affiliation(s)
- Qi-Shi Du
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail:
| | - Shu-Qing Wang
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics (Theranostics), School of Pharmacy, Tianjin Medical University, Tianjin, China
| | - Dong Chen
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, China
| | - Jian-Zong Meng
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, China
| | - Ri-Bo Huang
- State Key Laboratory of Non-food Biomass and Enzyme Technology, National Engineering Research Center for Non-food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
- Life Science and Biotechnology College, Guangxi University, Nanning, Guangxi, China
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