1
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Basu K, Brielle ES, Arkin IT. Hydrogen Bond Strengthens Acceptor Group: The Curious Case of the C-H···O=C Bond. Int J Mol Sci 2024; 25:8606. [PMID: 39201293 PMCID: PMC11354782 DOI: 10.3390/ijms25168606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 08/03/2024] [Accepted: 08/04/2024] [Indexed: 09/02/2024] Open
Abstract
An H-bond involves the sharing of a hydrogen atom between an electronegative atom to which it is covalently bound (the donor) and another electronegative atom serving as an acceptor. Such bonds represent a critically important geometrical force in biological macromolecules and, as such, have been characterized extensively. H-bond formation invariably leads to a weakening within the acceptor moiety due to the pulling exerted by the donor hydrogen. This phenomenon can be compared to a spring connecting two masses; pulling one mass stretches the spring, similarly affecting the bond between the two masses. Herein, we describe the opposite phenomenon when investigating the energetics of the C-H···O=C bond. This bond underpins the most prevalent protein transmembrane dimerization motif (GxxxG) in which a glycine Cα-H on one helix forms a hydrogen bond with a carbonyl in a nearby helix. We use isotope-edited FT-IR spectroscopy and corroborating computational approaches to demonstrate a surprising strengthening of the acceptor C=O bond upon binding with the glycine Cα-H. We show that electronic factors associated with the Cα-H bond strengthen the C=O oscillator by increasing the s-character of the σ-bond, lowering the hyperconjugative disruption of the π-bond. In addition, a reduction of the acceptor C=O bond's polarity is observed upon the formation of the C-H···O=C bond. Our findings challenge the conventional understanding of H-bond dynamics and provide new insights into the structural stability of inter-helical protein interactions.
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Affiliation(s)
- Kingshuk Basu
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190400, Israel;
| | - Esther S. Brielle
- The Alexander Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190400, Israel;
| | - Isaiah T. Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190400, Israel;
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2
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Shekhar S, Meena R, Lal J, Yadav M, Kant R, Reddy DN. Stabilizing Bifurcated Hydrogen Bond in 8-Aminoquinoline Appended Peptides. Chem Asian J 2024; 19:e202400248. [PMID: 38701035 DOI: 10.1002/asia.202400248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/21/2024] [Accepted: 05/03/2024] [Indexed: 05/05/2024]
Abstract
The hydrogen bonding interaction between an amide N-H and the amide N of the preceding residue is prevalent in proline-containing proteins and peptides. However, the N-H⋅⋅⋅N hydrogen bonding interaction is rare in non-prolyl natural peptides due to restricted dihedral angles. Herein, we stabilize this type of interaction in 8-aminoquinoline appended non-prolyl peptides through bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bond. The 8-aminoquinoline-incorporated model peptides 2 a-i were designed, synthesized, and the crystal structures of 2 a-c and 2 i were solved. Analysis of crystal data reveals that the amide N-H of aminoquinoline is involved in bifurcated hydrogen bonding interaction with the nitrogen of the preceding amino acid residue and the nitrogen in quinoline. Analysis of crystal packing, Hirshfeld surface and fingerprint plots confirms that the intermolecular O⋅⋅⋅H contacts significantly contribute to stabilizing bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bonding interaction. Furthermore, NMR experiments and CD spectroscopy were conducted to examine the preferred conformation in solution, and the data corroborate with the crystal structure conformation.
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Affiliation(s)
- Shashank Shekhar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Rachana Meena
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Jhajan Lal
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Mukul Yadav
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
| | - Ruchir Kant
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, 226031, Lucknow, India
| | - Damodara N Reddy
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
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3
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Pantelopulos GA, Abraham CB, Straub JE. Cholesterol and Lipid Rafts in the Biogenesis of Amyloid-β Protein and Alzheimer's Disease. Annu Rev Biophys 2024; 53:455-486. [PMID: 38382114 DOI: 10.1146/annurev-biophys-062823-023436] [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] [Indexed: 02/23/2024]
Abstract
Cholesterol has been conjectured to be a modulator of the amyloid cascade, the mechanism that produces the amyloid-β (Aβ) peptides implicated in the onset of Alzheimer's disease. We propose that cholesterol impacts the genesis of Aβ not through direct interaction with proteins in the bilayer, but indirectly by inducing the liquid-ordered phase and accompanying liquid-liquid phase separations, which partition proteins in the amyloid cascade to different lipid domains and ultimately to different endocytotic pathways. We explore the full process of Aβ genesis in the context of liquid-ordered phases induced by cholesterol, including protein partitioning into lipid domains, mechanisms of endocytosis experienced by lipid domains and secretases, and pH-controlled activation of amyloid precursor protein secretases in specific endocytotic environments. Outstanding questions on the essential role of cholesterol in the amyloid cascade are identified for future studies.
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Affiliation(s)
| | - Conor B Abraham
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
| | - John E Straub
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
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4
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Yamamoto H, Hattori M, Ito K, Shikano M, Yoshii K. Fluoride-Based Deep Eutectic Solvents with Amide Dual-Hydrogen-Bond Donors. J Phys Chem Lett 2024; 15:6249-6255. [PMID: 38842330 DOI: 10.1021/acs.jpclett.4c01085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
Abstract
Developing F--containing electrolytes is crucial for electrochemical and chemical fluorination. However, balancing the F- concentration and electrochemical stability of the electrolytes remains a challenge. In this study, fluoride-based deep eutectic solvents (F-DESs) were obtained by using amide hydrogen-bond donors (HBDs) containing dual N-H bonds. The obtained F-DES, [TMA]F·3.5[1,3-DMU], was prepared by facilely mixing solid compounds of tetramethylammonium fluoride ([TMA]F) and 1,3-dimethylurea (1,3-DMU), resulting in a high F- concentration (2.6 mol dm-3) and a wide electrochemical window (3.1 V) at room temperature. The electrochemical window was much wider than that of [TMA]F·3.5[EG] (EG, ethylene glycol) as another F-DES with an alcohol HBD (1.9 V). Moreover, [TMA]F·3.5[1,3-DMU] exhibited an ionic conductivity that was 2 orders of magnitude higher than that of [TMA]F·3.5[1,3-DMTU] (1,3-DMTU, 1,3-dimethylthiourea) around room temperature because of the bifurcated hydrogen bonds between the dual N-H bonds of 1,3-DMU and one F-. Thus, [TMA]F·3.5[1,3-DMU] was demonstrated to be applicable to electrochemical fluorination.
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Affiliation(s)
- Hiroki Yamamoto
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Mineyuki Hattori
- Research Institute for Material and Chemical Measurement, National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Kenji Ito
- Research Institute for Material and Chemical Measurement, National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Masahiro Shikano
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
- Fukushima Renewable Energy Institute, National Institute of Advanced Industrial Science and Technology, 2-2-9 Machiikedai, Koriyama, Fukushima 963-0298, Japan
| | - Kazuki Yoshii
- Research Institute of Electrochemical Energy, Department of Energy and Environment, National Institute of Advanced Industrial Science and Technology, 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
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5
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Chiari C, Batista PR, Viesser RV, Schenberg LA, Ducati LC, Linclau B, Tormena CF. Molecular dynamics and NMR reveal the coexistence of H-bond-assisted and through-space JFH coupling in fluorinated amino alcohols. Org Biomol Chem 2024; 22:2580-2595. [PMID: 38441115 DOI: 10.1039/d4ob00049h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024]
Abstract
The JFH coupling constants in fluorinated amino alcohols were investigated through experimental and theoretical approaches. The experimental JFH couplings were only reproduced theoretically when explicit solvation through molecular dynamics (MD) simulations was conducted in DMSO as the solvent. The combination of MD conformation sampling and DFT NMR spin-spin coupling calculations for these compounds reveals the simultaneous presence of through-space (TS) and hydrogen bond (H-bond) assisted JFH coupling between fluorine and hydrogen of the NH group. Furthermore, MD simulations indicate that the hydrogen in the amino group participates in both an intermolecular bifurcated H-bond with DMSO and in transmitting the observed JFH coupling. The contribution of TS to the JFH coupling is due to the spatial proximity of the fluorine and the NH group, aided by a combination of the non-bonding transmission pathway and the hydrogen bonding pathway. The experimental JFH coupling observed for the molecules studied should be represented as 4TS/1hJFH coupling.
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Affiliation(s)
- Cassia Chiari
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
| | - Patrick R Batista
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
| | - Renan V Viesser
- Department of Chemistry, University of Houston, Houston, TX 77024, USA
| | - Leonardo A Schenberg
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
| | - Lucas C Ducati
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes, 748, 05508-000, São Paulo, SP, Brazil
| | - Bruno Linclau
- Department of Organic and Macromolecular Chemistry, Ghent University, Ghent 9000, Belgium
| | - Cláudio F Tormena
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box 6154, 13083-970, Campinas, São Paulo, Brazil.
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6
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Sahoo A, Das G, Ghosh A, Shivappa Bagale S, Kumar Choudhary N, Harikrishna S, Sinha S, Gore KR. N 3-Methyluridine and 2'-O-Alkyl/2'-Fluoro-N 3-methyluridine functionalized nucleic acids improve nuclease resistance while maintaining duplex geometry. Bioorg Med Chem 2024; 100:117616. [PMID: 38295488 DOI: 10.1016/j.bmc.2024.117616] [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: 12/06/2023] [Revised: 01/16/2024] [Accepted: 01/26/2024] [Indexed: 02/02/2024]
Abstract
Herein, we report the synthesis of 2'-O-alkyl/2'-fluoro-N3-methyluridine (2'-O-alkyl/2'-F-m3U) phosphoramidites and their incorporation in DNA and RNA oligonucleotides. The duplex binding affinity and base discrimination studies showed that all 2'-O-alkyl/2'-F-m3U modifications significantly decreased the thermal stability and base-pairing discrimination ability. Serum stability study of dT20 with 2'-O-alkyl-m3U modification exhibited excellent nuclease resistance when incubated with 3'-exonucleases (SVPD) or 5'-exonucleases (PDE-II) as compared to m3U, 2'-F, 2'-OMe modified oligonucleotides. MD simulation studies with RNA tetradecamer duplexes illustrated that the m3U and 2'-O-methyl-m3U modifications reduce the duplex stabilities by disrupting the Watson-Crick hydrogen bonding and base-stacking interactions. Further molecular modelling investigations demonstrated that the 2'-O-propyl-m3U modification exhibits steric interactions with amino acid residues in the active site of 3'- and 5'-exonuclease, leading to enhanced stability. These combined data indicate that the 2'-modified-m3U nucleotides can be used as a promising tool to enhance the stability, silencing efficiency, and drug-like properties of antisense/siRNA-based therapeutics.
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Affiliation(s)
- Avijit Sahoo
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Gourav Das
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | | | - Nishant Kumar Choudhary
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India
| | - S Harikrishna
- Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, United States
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Kiran R Gore
- Department of Chemistry, Indian Institute of Technology Kharagpur, West Bengal 721302, India.
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7
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Essert A, Castiglione K. Dimer Stabilization by SpyTag/SpyCatcher Coupling of the Reductase Domains of a Chimeric P450 BM3 Monooxygenase from Bacillus spp. Improves its Stability, Activity, and Purification. Chembiochem 2024; 25:e202300650. [PMID: 37994193 DOI: 10.1002/cbic.202300650] [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: 09/26/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 11/24/2023]
Abstract
The vast majority of known enzymes exist as oligomers, which often gives them high catalytic performance but at the same time imposes constraints on structural conformations and environmental conditions. An example of an enzyme with a complex architecture is the P450 BM3 monooxygenase CYP102A1 from Bacillus megaterium. Only active as a dimer, it is highly sensitive to dilution or common immobilization techniques. In this study, we engineered a thermostable P450BM3 chimera consisting of the heme domain of a CYP102A1 variant and the reductase domain of the homologous CYP102A3. The dimerization of the hybrid was even weaker compared to the corresponding CYP102A1 variant. To create a stable dimer, we covalently coupled the C-termini of two monomers of the chimera via SpyTag003/SpyCatcher003 interaction. As a result, purification, thermostability, pH stability, and catalytic activity were improved. Via a bioorthogonal two-step affinity purification, we obtained high purity (94 %) of the dimer-stabilized variant being robust against heme depletion. Long-term stability was increased with a half-life of over 2 months at 20 °C and 80-90 % residual activity after 2 months at 5 °C. Most catalytic features were retained with even an enhancement of the overall activity by ~2-fold compared to the P450BM3 chimera without SpyTag003/SpyCatcher003.
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Affiliation(s)
- Arabella Essert
- Institute of Bioprocess Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Straße 3, 91052, Erlangen, Germany
| | - Kathrin Castiglione
- Institute of Bioprocess Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg, Paul-Gordan-Straße 3, 91052, Erlangen, Germany
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8
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Almuhana ARY, Orton GRF, Rosenberg C, Champness NR. Photoinduced radical formation in hydrogen-bonded organic frameworks. Chem Commun (Camb) 2024; 60:452-455. [PMID: 38088086 DOI: 10.1039/d3cc05236b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Hydrogen-bonded organic frameworks (HOFs) constructed from naphthalene-diimide bearing tectons undergo photochromic changes whilst forming radical bearing species within the framework structure.
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Affiliation(s)
- Asia R Y Almuhana
- School of Chemistry, The University of Birmingham, Birmingham, UK.
- King Faisal University, P.O. 380, Al-Ahsa 31982, Saudi Arabia
| | | | - Callum Rosenberg
- School of Chemistry, The University of Birmingham, Birmingham, UK.
| | - Neil R Champness
- School of Chemistry, The University of Birmingham, Birmingham, UK.
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9
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Yang Z, Stein RA, Pink M, Madzelan P, Ngendahimana T, Rajca S, Wilson MA, Eaton SS, Eaton GR, Mchaourab HS, Rajca A. Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins. J Am Chem Soc 2023; 145:25726-25736. [PMID: 37963181 PMCID: PMC10961179 DOI: 10.1021/jacs.3c09184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least 1 order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase in the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of interspin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4-9, compared to the common spin label such as MTSL, which is not affected by CB-7. Interspin distances of 3 nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating an undisturbed structure and conformation of the protein.
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Affiliation(s)
- Zhimin Yang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Richard A. Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Maren Pink
- IUMSC, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Peter Madzelan
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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10
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Wang H, Caminati W, Li M, Chen J, Tian X, Grabow JU, Gou Q. n → π* Interaction Enabling Transient Inversion of Chirality. J Phys Chem Lett 2023; 14:8874-8879. [PMID: 37756497 DOI: 10.1021/acs.jpclett.3c02264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
This study reports the observation and characterization of two isomers of the acrolein dimer by using high-resolution rotational spectroscopy in pulsed jets. The first isomer is stabilized by two hydrogen bonds, adopting a planar configuration, and is energetically favored over the second isomer, which exhibits a dominant n → π* interaction in a nearly orthogonal arrangement. Surprisingly, the n → π* interaction was revealed to enable a concerted tunneling motion of two moieties along the carbonyl group. This motion leads to the inversion of transient chirality associated with the exchange of donor-acceptor roles, as revealed by the spectral feature of quadruplets. Inversion of transient chirality is a fundamental phenomenon in quantum mechanics and commonly observed for only inversional motions of protons. It is the first discovery, to the best of our knowledge, that such heavy moieties can also undergo chirality inversion.
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Affiliation(s)
- Hao Wang
- Department of Chemistry School of Chemistry and Chemical Engineering, Chongqing University, No. 55 Daxuecheng South Road Shapingba, Chongqing 401331, China
| | - Walther Caminati
- Dipartimento di Chimica "G. Ciamician", Università di Bologna, Via Selmi 2, Bologna I-40126, Italy
| | - Meng Li
- Institut für Physikalische Chemie & Elektrochemie, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Junhua Chen
- School of Pharmacy, Guizhou Medical University, Guiyang 550025, Guizhou, China
| | - Xiao Tian
- Department of Chemistry School of Chemistry and Chemical Engineering, Chongqing University, No. 55 Daxuecheng South Road Shapingba, Chongqing 401331, China
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie & Elektrochemie, Leibniz Universität Hannover, 30167 Hannover, Germany
| | - Qian Gou
- Department of Chemistry School of Chemistry and Chemical Engineering, Chongqing University, No. 55 Daxuecheng South Road Shapingba, Chongqing 401331, China
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11
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Rezaie F, Noorizadeh S. Theoretical investigation of tube-like supramolecular structures formed through bifurcated lithium bonds. Sci Rep 2023; 13:15260. [PMID: 37709798 PMCID: PMC10502010 DOI: 10.1038/s41598-023-41979-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
The stability of three supramolecular naostructures, which are formed through the aggregation of identical belts of [12] arene containing p-nitrophenyllithium, 1,4-dilithiatedbenzene and 1,4-dinitrobenzene units, is investigated by density functional theory. The electrostatic potential calculations indicate the ability of these belts in forming bifurcated lithium bonds (BLBs) between the Li atoms of one belt and the oxygen atoms of the NO2 groups in the other belt, which is also confirmed by deformation density maps and quantum theory of atoms in molecules (QTAIM) analysis. Topological analysis and natural bond analysis (NBO) imply to ionic character for these BLBs with binding energies up to approximately - 60 kcal mol-1. The many-body interaction energy analysis shows the strong cooperativity belongs to the configuration with the highest symmetry (C4v) containing p-nitrophenyllithium fragments as the building unit. Therefore, it seems that this configuration could be a good candidate for designing a BLB-based supramolecular nanotube with infinite size in this study.
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Affiliation(s)
- Forough Rezaie
- Chemistry Department, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Siamak Noorizadeh
- Chemistry Department, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
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12
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Müller E, Hackney CM, Ellgaard L, Morth JP. High-resolution crystal structure of the Mu8.1 conotoxin from Conus mucronatus. Acta Crystallogr F Struct Biol Commun 2023; 79:240-246. [PMID: 37642664 PMCID: PMC10478764 DOI: 10.1107/s2053230x23007070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/10/2023] [Indexed: 08/31/2023] Open
Abstract
Marine cone snails produce a wealth of peptide toxins (conotoxins) that bind their molecular targets with high selectivity and potency. Therefore, conotoxins constitute valuable biomolecular tools with a variety of biomedical purposes. The Mu8.1 conotoxin from Conus mucronatus is the founding member of the newly identified saposin-like conotoxin class of conotoxins and has been shown to target Cav2.3, a voltage-gated calcium channel. Two crystal structures have recently been determined of Mu8.1 at 2.3 and 2.1 Å resolution. Here, a high-resolution crystal structure of Mu8.1 was determined at 1.67 Å resolution in the high-symmetry space group I4122. The asymmetric unit contained one molecule, with a symmetry-related molecule generating a dimer equivalent to that observed in the two previously determined structures. The high resolution allows a detailed atomic analysis of a water-filled cavity buried at the dimer interface, revealing a tightly coordinated network of waters that shield a lysine residue (Lys55) with a predicted unusually low side-chain pKa value. These findings are discussed in terms of a potential functional role of Lys55 in target interaction.
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Affiliation(s)
- Emilie Müller
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | | | - Lars Ellgaard
- Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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13
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Yang Z, Stein RA, Pink M, Madzelan P, Ngendahimana T, Rajca S, Wilson MA, Eaton SS, Eaton GR, Mchaourab HS, Rajca A. Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.22.554361. [PMID: 37662277 PMCID: PMC10473685 DOI: 10.1101/2023.08.22.554361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
We report complex formation between the chloroacetamide 2,6-diazaadamantane nitroxide radical (ClA-DZD) and cucurbit[7]uril (CB-7), for which the association constant in water, Ka = 1.9 × 106 M-1, is at least one order of magnitude higher than the previously studied organic radicals. The radical is highly immobilized by CB-7, as indicated by the increase of the rotational correlation time, τrot, by a factor of 36, relative to that in the buffer solution. The X-ray structure of ClA-DZD@CB-7 shows the encapsulated DZD guest inside the undistorted CB-7 host, with the pendant group protruding outside. Upon addition of CB-7 to T4 Lysozyme (T4L) doubly spin-labeled with the iodoacetamide derivative of DZD, we observe the increase in τrot and electron spin coherence time, Tm, along with the narrowing of inter-spin distance distributions. Sensitivity of the DEER measurements at 83 K increases by a factor 4 - 9, compared to the common spin label such as MTSL, which is not affected by CB-7. Inter-spin distances of 3-nm could be reliably measured in water/glycerol up to temperatures near the glass transition/melting temperature of the matrix at 200 K, thus bringing us closer to the goal of supramolecular recognition-enabled long-distance DEER measurements at near physiological temperatures. The X-ray structure of DZD-T4L 65 at 1.12 Å resolution allows for unambiguous modeling of the DZD label (0.88 occupancy), indicating undisturbed structure and conformation of the protein.
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Affiliation(s)
- Zhimin Yang
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Richard A. Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Maren Pink
- IUMSC, Department of Chemistry, Indiana University, Bloomington, Indiana 47405-7102, United States
| | - Peter Madzelan
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Thacien Ngendahimana
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Suchada Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Mark A. Wilson
- Department of Biochemistry and Redox Biology Center, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
| | - Sandra S. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Gareth R. Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, Colorado 80208, United States
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Andrzej Rajca
- Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588-0304, United States
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14
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Rahimi R, Saban N, Bar I. Synergistic Spectroscopic and Computational Characterization Evidencing the Preservation or Flipping of the Hydroxyl Group of 2-Phenylethyl Alcohol upon Single and Double Hydration. J Am Chem Soc 2023; 145:18455-18467. [PMID: 37561882 DOI: 10.1021/jacs.3c04762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
Even apparently simple, obtaining and analyzing observations on molecules and clusters and unambiguously assigning their structures is challenging. We report here the first ionization-loss Raman spectra compared to quantum chemical predictions for establishing the structural preferences of hydrates of the neurotransmitters hydroxy analogue, 2-phenylethyl alcohol (PEAL). The spectra encode two monohydrates and two previously unnoticed dihydrates, consequences of water insertion and sidewise attachment to the O-H group of gauche PEALs, in PEAL-H2O and PEAL-(H2O)2, or the higher-energy gauche-trans PEAL in the latter. The electronic structures retain the stable PEAL or flip its O-H to convert the gauche-trans PEAL conformer to the global minimum-energy dihydrate. We disclose conventional and bifurcated hydrogen bonds and electron steric repulsions by noncovalent interaction analysis and correlations between the experimental O-H stretching vibrational frequencies and the O-H and H···X bond lengths and electron densities, pointing to implications on hydrate forms and our approach virtue.
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Affiliation(s)
- Rami Rahimi
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Noga Saban
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Ilana Bar
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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15
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Kenneth C, Anugrah DSB, Julianus J, Junedi S. Molecular insights into the inhibitory potential of anthocyanidins on glucokinase regulatory protein. PLoS One 2023; 18:e0288810. [PMID: 37467274 DOI: 10.1371/journal.pone.0288810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 07/05/2023] [Indexed: 07/21/2023] Open
Abstract
Computational methods were used to investigate six anthocyanidins exhibiting antidiabetic activity by inhibiting glucokinase regulatory protein (GKRP) activity. Density functional theory was used to optimise the geometry of anthocyanidins and calculate their quantum chemical properties. A blind docking method was employed to conduct a molecular docking study, which revealed that delphinidin (Del), cyanidin (Cya), and pelargonidin (Pel) as potential GKRP inhibitors with the lowest binding free energy of -8.7, -8.6, and -8.6 kcal/mol, corresponding to high binding affinity. The molecular dynamics study further verified the blind docking results by showing high GKRP-F1P complex stability and high binding affinity calculated through the MM/GBSA method, upon the binding of pelargonidin. The lower RMSF values of pivotal GK-interacting residues for GKRP-F1P-Pel compared to GKRP-F1P, as a positive control, indicating pelargonidin ability to maintain the inactive conformation of GKRP through the inhibition of GK binding. The key residues that control the binding of the F1P to GKRP and anthocyanidin to GKRP-F1P were also identified in this study. Altogether, pelargonidin is anthocyanidins-derived natural products that have the most potential to act as inhibitors of GKRP and as antidiabetic nutraceuticals.
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Affiliation(s)
- Christian Kenneth
- Biotechnology Study Program, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Daru Seto Bagus Anugrah
- Biotechnology Study Program, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta, Indonesia
| | - Jeffry Julianus
- Faculty of Pharmacy, Sanata Dharma University, Yogyakarta, Indonesia
| | - Sendy Junedi
- Faculty of Biotechnology, Universitas Atma Jaya Yogyakarta, Yogyakarta, Indonesia
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16
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Zhang J, Shao Y, Zheng H, Xue XS. Transition State Stabilization by SCF 2 -H⋅⋅⋅O Bifurcated Hydrogen Bond. Chem Asian J 2023; 18:e202201244. [PMID: 36635229 DOI: 10.1002/asia.202201244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/10/2023] [Accepted: 01/12/2023] [Indexed: 01/14/2023]
Abstract
The difluoromethylthio group (SCF2 H), which is generally considered a highly lipophilic weak hydrogen bonding donor, has attracted special interest from the pharmaceutical and agrochemical industry. Remarkably, there have been relatively few literature investigations of SCF2 H hydrogen bonding interactions. Here, we report the determination of the hydrogen bond acidity parameter A of the SCF2 H in the most popularly used electrophilic difluoromethylthiolating reagent. We present kinetic and computational evidence of the RSCF2 -H⋅⋅⋅O2 bifurcated hydrogen bond for stabilizing the SCF2 H-transferring transition state, which could cause a reversal of apparent electrophilic reactivity of difluoromethylthiolating and trifluoromethylthiolating reagents. Solvent effects on the RSCF2 -H⋅⋅⋅O2 bifurcated hydrogen bonds will also be discussed.
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Affiliation(s)
- Jingjing Zhang
- Center of Basic Molecular Science, Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yingbo Shao
- College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Hanliang Zheng
- College of Chemistry, Nankai University, Tianjin, 300071, P. R. China
| | - Xiao-Song Xue
- College of Chemistry, Nankai University, Tianjin, 300071, P. R. China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, P. R. China.,School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Sub-lane Xiangshan, Hangzhou, 310024, P. R. China
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17
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Kojasoy V, Tantillo DJ. Impacts of noncovalent interactions involving sulfur atoms on protein stability, structure, folding, and bioactivity. Org Biomol Chem 2022; 21:11-23. [PMID: 36345987 DOI: 10.1039/d2ob01602h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This review discusses the various types of noncovalent interactions in which sulfur atoms participate and their effects on protein stability, structure, folding and bioactivity. Current approaches and recommendations for modelling these noncovalent interactions (in terms of both geometries and interaction energies) are highlighted.
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Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, 1 Shields Avenue, Davis, CA, 95616, USA.
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18
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Kolocouris A, Arkin I, Glykos NM. A proof-of-concept study of the secondary structure of influenza A, B M2 and MERS- and SARS-CoV E transmembrane peptides using folding molecular dynamics simulations in a membrane mimetic solvent. Phys Chem Chem Phys 2022; 24:25391-25402. [PMID: 36239696 DOI: 10.1039/d2cp02881f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Here, we have carried out a proof-of-concept molecular dynamics (MD) simulation with adaptive tempering in a membrane mimetic environment to study the folding of single-pass membrane peptides. We tested the influenza A M2 viroporin, influenza B M2 viroporin, and protein E from coronaviruses MERS-Cov-2 and SARS-CoV-2 peptides with known experimental secondary structures in membrane bilayers. The two influenza-derived peptides are significantly different in the peptide sequence and secondary structure and more polar than the two coronavirus-derived peptides. Through a total of more than 50 μs of simulation time that could be accomplished in trifluoroethanol (TFE), as a membrane model, we characterized comparatively the folding behavior, helical stability, and helical propensity of these transmembrane peptides that match perfectly their experimental secondary structures, and we identified common motifs that reflect their quaternary organization and known (or not) biochemical function. We showed that BM2 is organized into two structurally distinct parts: a significantly more stable N-terminal half, and a fast-converting C-terminal half that continuously folds and unfolds between α-helical structures and non-canonical structures, which are mostly turns. In AM2, both the N-terminal half and C-terminal half are very flexible. In contrast, the two coronavirus-derived transmembrane peptides are much more stable and fast helix-formers when compared with the influenza ones. In particular, the SARS-derived peptide E appears to be the fastest and most stable helix-former of all the four viral peptides studied, with a helical structure that persists almost without disruption for the whole of its 10 μs simulation. By comparing the results with experimental observations, we benchmarked TFE in studying the conformation of membrane and hydrophobic peptides. This work provided accurate results suggesting a methodology to run long MD simulations and predict structural properties of biologically important membrane peptides.
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Affiliation(s)
- Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis, 15771, Greece.
| | - Isaiah Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, 91904, Israel
| | - Nicholas M Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece.
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19
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Van Guyse JFR, Leiske MN, Verjans J, Bernhard Y, Hoogenboom R. Accelerated Post‐Polymerization Amidation of Polymers with Side‐Chain Ester Groups by Intramolecular Activation. Angew Chem Int Ed Engl 2022; 61:e202201781. [DOI: 10.1002/anie.202201781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Joachim F. R. Van Guyse
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
- Present address: Innovation Center of NanoMedicine Kawasaki Institute of Industrial Promotion 3-25-14, Tonomachi, Kawasaki-ku Kawasaki 210-0821 Japan
| | - Meike N. Leiske
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Jente Verjans
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Yann Bernhard
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
- Present address: Université de Lorraine, UMR CNRS 7053 L2CM Faculté des Sciences et Technologies, BP 70239 54506 Vandoeuvre-lès-Nancy Cedex France
| | - Richard Hoogenboom
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
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20
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Lee AG. The role of cholesterol binding in the control of cholesterol by the Scap-Insig system. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2022; 51:385-399. [PMID: 35717507 PMCID: PMC9233655 DOI: 10.1007/s00249-022-01606-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 05/26/2022] [Accepted: 06/05/2022] [Indexed: 12/02/2022]
Abstract
Scap and Insig, two proteins embedded in the membrane of the endoplasmic reticulum (ER), regulate the synthesis of cholesterol in animal cells by forming a dimer in the presence of high concentrations of cholesterol. Cryo-electron microscopic structures for the Scap-Insig dimer show a sterol-binding site at the dimer interface, but none of the structures include cholesterol itself. Here, a molecular docking approach developed to characterise cholesterol binding to the transmembrane (TM) regions of membrane proteins is used to characterise cholesterol binding to sites on the TM surface of the dimer and to the interfacial binding site. Binding of cholesterol is also observed at sites on the extra-membranous luminal domains of Scap, but the properties of these sites suggest that they will be unoccupied in vivo. Comparing the structure of Scap in the dimer with that predicted by AlphaFold for monomeric Scap suggests that dimer formation could result in relocation of TM helix 7 of Scap and of the loop between TM6 and 7, and that this could be the key change on Scap that signals that there is a high concentration of cholesterol in the ER.
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Affiliation(s)
- Anthony G Lee
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
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21
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Das S, Roy S, Bhattacharyya D. Understanding the role of non-Watson-Crick base pairs in DNA-protein recognition: Structural and energetic aspects using crystallographic database analysis and quantum chemical calculation. Biopolymers 2022; 113:e23492. [PMID: 35615897 DOI: 10.1002/bip.23492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/22/2022] [Accepted: 05/03/2022] [Indexed: 11/06/2022]
Abstract
Specific recognition of DNA base sequences by proteins is vital for life-cycles of all organisms. In a large number of crystal structures of protein-DNA complexes, DNA conformation significantly deviates from the canonical B-DNA structure. A key question is whether such alternate conformations exist prior to protein binding and one is selected for complexation or the structure observed is induced by protein binding. Non-canonical base pairs, such as Hoogsteen base pairs, are often observed in crystal structures of protein-DNA complexes. We decided to explore whether the occurrence of such non-canonical base pairs in protein-DNA complexes is induced by the protein or is selected from pre-existing conformations. Detailed quantum chemical calculations with dispersion-corrected density functional theory (DFT-D) indicated that most of the non-canonical base pairs with DNA bases are stable even in the absence of the interacting amino acids. However, the G:G Hoogsteen base pair, which also appears in the telomere structure, appears to be unstable in the absence of other stabilizing agents, such as positively charged amino acids. Thus, the stability of many of the non-canonical base pair containing duplexes may be close to the canonical B-DNA structure and hence energetically accessible in the ground state; suggesting that the selection from pre-existing conformations may be an important mechanism for observed non-canonical base pairs in protein-DNA complexes.
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Affiliation(s)
- Soumi Das
- Department of Biophysics, Bose Institute, Kolkata, India
| | - Siddhartha Roy
- Department of Biophysics, Bose Institute, Kolkata, India
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22
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Van Guyse JFR, Leiske MN, Verjans J, Bernhard Y, Hoogenboom R. Accelerated Post‐Polymerization Amidation of Polymers with Side‐Chain Ester Groups by Intramolecular Activation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202201781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Joachim F. R. Van Guyse
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
- Present address: Innovation Center of NanoMedicine Kawasaki Institute of Industrial Promotion 3-25-14, Tonomachi, Kawasaki-ku Kawasaki 210-0821 Japan
| | - Meike N. Leiske
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Jente Verjans
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
| | - Yann Bernhard
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
- Present address: Université de Lorraine, UMR CNRS 7053 L2CM Faculté des Sciences et Technologies, BP 70239 54506 Vandoeuvre-lès-Nancy Cedex France
| | - Richard Hoogenboom
- Supramolecular Chemistry Group Centre of Macromolecular Chemistry (CMaC) Department of Organic and Macromolecular Chemistry Ghent University Krijgslaan 281 S4 9000 Ghent Belgium
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23
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Hanazono Y, Hirano Y, Takeda K, Kusaka K, Tamada T, Miki K. Revisiting the concept of peptide bond planarity in an iron-sulfur protein by neutron structure analysis. SCIENCE ADVANCES 2022; 8:eabn2276. [PMID: 35594350 PMCID: PMC9122329 DOI: 10.1126/sciadv.abn2276] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
The planarity of the peptide bond is important for the stability and structure formation of proteins. However, substantial distortion of peptide bonds has been reported in several high-resolution structures and computational analyses. To investigate the peptide bond planarity, including hydrogen atoms, we report a 1.2-Å resolution neutron structure of the oxidized form of high-potential iron-sulfur protein. This high-resolution neutron structure shows that the nucleus positions of the amide protons deviate from the peptide plane and shift toward the acceptors. The planarity of the H─N─C═O plane depends strongly on the pyramidalization of the nitrogen atom. Moreover, the orientation of the amide proton of Cys75 is different in the reduced and oxidized states, possibly because of the electron storage capacity of the iron-sulfur cluster.
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Affiliation(s)
- Yuya Hanazono
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Yu Hirano
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki 319-1106, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
| | - Kazuki Takeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Katsuhiro Kusaka
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106 Japan
| | - Taro Tamada
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Tokai, Ibaraki 319-1106, Japan
| | - Kunio Miki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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24
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Barrios A, Estrada M, Moon JH. Carbamoylated Guanidine-Containing Polymers for Non-Covalent Functional Protein Delivery in Serum-Containing Media. Angew Chem Int Ed Engl 2022; 61:e202116722. [PMID: 34995405 DOI: 10.1002/anie.202116722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 11/08/2022]
Abstract
Despite the high potential of controlling cellular processes and treating various diseases by intracellularly delivered proteins, current delivery systems exhibit poor efficiency due to poor serum stability, cellular entry, and cytosolic availability of proteins. Here, we report a novel functional group, phenyl carbamoylated guanidine (Ph-CG), that greatly enhances the delivery efficiency to various types of cells. Owing to the substantially lowered pKa , the hydrophobic Ph-CG offers optimized inter-macromolecular interactions via enhanced hydrogen-bonding and hydrophobic interactions. The coplanarity of Ph-CG also leads to the better intracellular entry of protein complexes. Intracellularly delivered apoptosis-inducing enzymes and antibodies significantly induce cell viability inhibitions in a serum-containing medium. The newly developed Ph-CG can be introduced to various existing carriers, leading to the realization of future therapeutic protein delivery.
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Affiliation(s)
- Alfonso Barrios
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institutes, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - Marilen Estrada
- Department of Natural and Applied Sciences, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - Joong Ho Moon
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institutes, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
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25
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Sasikumar D, Vinod K, Sunny J, Hariharan M. Exciton interactions in helical crystals of a hydrogen-bonded eumelanin monomer. Chem Sci 2022; 13:2331-2338. [PMID: 35310511 PMCID: PMC8864807 DOI: 10.1039/d1sc06755a] [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: 12/03/2021] [Accepted: 01/19/2022] [Indexed: 12/04/2022] Open
Abstract
Eumelanin, a naturally occurring group of heterogeneous polymers/aggregates providing photoprotection to living organisms, consist of 5,6-dihydroxyindole (DHI) and 5,6-dihydroxyindole-2-carboxylic acid (DHICA) building blocks. Despite their prevalence in the animal world, the structure and therefore the mechanism behind the photoprotective broadband absorption and non-radiative decay of eumelanin remain largely unknown. As a small step towards solving the incessant mystery, DHI is crystallized in a non-protic solvent environment to obtain DHI crystals having a helical packing motif. The present approach reflects the solitary directional effect of hydrogen bonds between the DHI chromophores for generating the crystalline assembly and filters out any involvement of the surrounding solvent environment. The DHI single crystals having an atypical chiral packing motif (P212121 Sohncke space group) incorporate enantiomeric zig-zag helical stacks arranged in a herringbone fashion with respect to each other. Each of the zig-zag helical stacks originates from a bifurcated hydrogen bonding interaction between the hydroxyl substituents in adjacent DHI chromophores which act as the backbone structure for the helical assembly. Fragment-based excited state analysis performed on the DHI crystalline assembly demonstrates exciton delocalization along the DHI units that connect each enantiomeric helical stack while, within each stack, the excitons remain localized. Fascinatingly, over the time evolution for generation of single-crystals of the DHI-monomer, mesoscopic double-helical crystals are formed, possibly attributed to the presence of covalently connected DHI trimers in chloroform solution. The oligomeric DHI (in line with the chemical disorder model) along with the characteristic crystalline packing observed for DHI provides insights into the broadband absorption feature exhibited by the chromophore.
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Affiliation(s)
- Devika Sasikumar
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Maruthamala P.O., Vithura Thiruvananthapuram Kerala 695551 India
| | - Kavya Vinod
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Maruthamala P.O., Vithura Thiruvananthapuram Kerala 695551 India
| | - Jeswin Sunny
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Maruthamala P.O., Vithura Thiruvananthapuram Kerala 695551 India
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Maruthamala P.O., Vithura Thiruvananthapuram Kerala 695551 India
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26
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Abstract
The fundamental relationships between the structure and properties of liquids are far from being well understood. For instance, the structural origins of many liquid anomalies still remain unclear, but liquid-liquid transitions (LLT) are believed to hold a key. However, experimental demonstrations of LLTs have been rather challenging. Here, we report experimental and theoretical evidence of a second-order-like LLT in molten tin, one which favors a percolating covalent bond network at high temperatures. The observed structural transition originates from the fluctuating metallic/covalent behavior of atomic bonding, and consequently a new paradigm of liquid structure emerges. The liquid structure, described in the form of a folded network, bridges two well-established structural models for disordered systems, i.e., the random packing of hard-spheres and a continuous random network, offering a large structural midground for liquids and glasses. Our findings provide an unparalleled physical picture of the atomic arrangement for a plethora of liquids, shedding light on the thermodynamic and dynamic anomalies of liquids but also entailing far-reaching implications for studying liquid polyamorphism and dynamical transitions in liquids. Unraveling the structural origin of liquid anomalies remains a challenging topic. Xu et al. propose a folded-network structural model for molten tin and provide insights into the observed second-order-like structural transition.
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27
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Barrios A, Estrada M, Moon JH. Carbamoylated Guanidine‐Containing Polymers for Non‐Covalent Functional Protein Delivery in Serum‐Containing Media. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Alfonso Barrios
- Florida International University chemistry and biochemistry UNITED STATES
| | - Marilen Estrada
- Florida International University Natural and Applied Sciences UNITED STATES
| | - Joong Ho Moon
- Florida International University Chemistry and Biochemistry 11200 SW 8th St.MMC CP311 33199 Miami UNITED STATES
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28
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On cellulose spatial organization and interactions as unraveled by diffraction and spectroscopic methods throughout the 20 th century. PURE APPL CHEM 2021. [DOI: 10.1515/pac-2021-0306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
This contribution attempts to describe the path towards determination of cellulose crystal structure down to atomic coordinates, towards the determination of its molecular conformation, as well as towards the details of the intricate pattern of hydrogen bonds and their dynamics. This path started at the beginning of the 20th century with X-ray diffraction, continued with electron diffraction, infrared and Raman spectroscopy, and significant knowledge was gained by methods of NMR spectroscopy. Towards the end of the 20th century and at the beginning of the 21st century, X-ray diffraction in conjunction with neutron diffraction provided the position of hydrogens, which led to detailed description of the geometry of hydrogen bonding network in cellulose. Quantum chemical and molecular dynamics calculations, polarized infrared spectroscopy and sum frequency generation vibrational spectroscopy were used to identify the origins of the vibrational modes in cellulose and to describe their extensive coupling mediated by hydrogen bonds. The role of amphiphilic character of cellulose macromolecule (and consequent hydrophobic interactions) in cellulose properties and behavior has been gaining more recognition in the 21st century.
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29
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Reynolds DP, Storer MC, Hunter CA. An empirical model for solvation based on surface site interaction points. Chem Sci 2021; 12:13193-13208. [PMID: 34745551 PMCID: PMC8513935 DOI: 10.1039/d1sc03392a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/07/2021] [Indexed: 11/21/2022] Open
Abstract
Surface site interaction points (SSIP) provide a quantitative description of the non-covalent interactions a molecule makes with the environment based on specific intermolecular contacts, such as H-bonds. Summation of the free energy of interaction of each SSIP across the surface of a molecule allows calculation of solvation energies and partition coefficients. A rule-based approach to the assignment of SSIPs based on chemical structure has been developed, and a combination of experimental data on the formation of 1 : 1 H-bonded complexes in non-polar solvents and partition of solutes between different solvents was used to parameterise the method. The resulting model is simple to implement using just a spreadsheet and accurately describes the transfer of a wide range of different solutes from water to a wide range of different organic solvents (overall rmsd is 1.4 kJ mol-1 for 1713 data points). The hydrophobic effect as well as the properties of perfluorocarbon solvents are described well by the model, and new descriptors have been determined for range of organic solvents that were not accessible by direct investigation of H-bond formation in non-polar solvents.
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Affiliation(s)
- Derek P Reynolds
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Maria Chiara Storer
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Christopher A Hunter
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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30
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Su M, Pang Z, Li L, Ren J, Yuan F, Lv F, Han J, Wei Y, Gao Y, Zhang J, Qian S. Charge-assisted bond and molecular self-assembly drive the gelation of lenvatinib mesylate. Int J Pharm 2021; 607:121019. [PMID: 34416330 DOI: 10.1016/j.ijpharm.2021.121019] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/26/2021] [Accepted: 08/15/2021] [Indexed: 10/20/2022]
Abstract
Lenvatinib mesylate (LM) is a first-line anticancer agent for the treatment of unresectable hepatocellular carcinoma, while it formed viscoelastic hydrogel when contacting with aqueous medium, which would significantly hinder its in vitro dissolution. The aim of this study was to systematicly explore the gelation mechanism and gel properties via thermal analysis, rheology, morphology and spectroscopy studies. The formed hydrogel was found to be composed of a new polymorph of crystalline LM, and its mechanical strength depended on the cross-linking degree of the fibrillar network structure. Spectroscopy analyses revealed that the intermolecular hydrogen bonds (the bifurcated hydrogen bond between the adjacent urea groups and the NH⋯OC hydrogen bond between the primary amide groups) as well as π-π stacking interactions (between the benzene ring and the quinoline ring) were suggested to be the driving forces for the self-assembly of LM during gelation process. Additionally, no gelation phenomenon was observed when suspending the base form lenvatinib in water, while it could form gel in various acidic solutions (e.g. hydrochloric acid, phosphoric acid and methanesulfonic acid) because the regenerated N+-H group increased the solubility of lenvatinib and promoted the balance between the dissolution or aggregation of LX (X: acid radical ion) molecules in solutions. In conclusion, the charge-assisted bond N+-H in LM molecule and intermolecular non-covalent interactions drived the hydrogel formation of LM in aqueous media. This study elucidates the gelation mechanism and gel properties of LM hydrogel, which would be helpful to figure out strategy to eliminate its gelation fundamentally and pave the way for its further formulation development in future.
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Affiliation(s)
- Meiling Su
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Zunting Pang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Luyuan Li
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Junjie Ren
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Fang Yuan
- Nanjing F&S Pharmatech Co., Ltd., Nanjing 211805, PR China
| | - Fusheng Lv
- Nanjing F&S Pharmatech Co., Ltd., Nanjing 211805, PR China
| | - Jiawei Han
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Yuanfeng Wei
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China
| | - Yuan Gao
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China.
| | - Jianjun Zhang
- School of Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China.
| | - Shuai Qian
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, PR China.
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31
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Hao Y, Zhang F, Mo S, Zhao J, Wang X, Zhao Y, Zhang L. Biomedical Applications of Supramolecular Materials in the Controllable Delivery of Steroids. Front Mol Biosci 2021; 8:700712. [PMID: 34368229 PMCID: PMC8343020 DOI: 10.3389/fmolb.2021.700712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/13/2021] [Indexed: 01/19/2023] Open
Abstract
Glucocorticoids are a class of steroid hormones secreted from the adrenal glands. The strong anti-inflammatory effects make it be one of the most popular and versatile drugs available to treat chronic inflammatory diseases. Additionally, supramolecular materials have been widely exploited in drug delivery, due to their biocompatibility, tunability, and predictability. Thus, steroid-based supramolecular materials and the release of steroids have been applied in the treatment of inflammatory diseases. This mini-review summarized recent advances in supramolecular materials loaded with glucocorticoid drugs in terms of hydrophobic interactions, electrostatic interactions, hydrogen bonding, and π-π stackings. We also discussed and prospected the application of the glucocorticoid drugs-based supramolecular system on chronic rhinosinusitis, multifactorial inflammatory disease of the nasal and paranasal sinuses mucosal membranes. Overall, supramolecular materials can provide an alternative to traditional materials as a novel delivery platform in clinical practice.
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Affiliation(s)
- Yun Hao
- Department of Otolaryngology Head and Neck Surgery, Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Feiyi Zhang
- Institute for Advanced Materials, Jiangsu University, Zhenjiang, China.,State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Shanshan Mo
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jinming Zhao
- Department of Otolaryngology Head and Neck Surgery, Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Xiangdong Wang
- Department of Otolaryngology Head and Neck Surgery, Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Yan Zhao
- Department of Otolaryngology Head and Neck Surgery, Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China
| | - Luo Zhang
- Department of Otolaryngology Head and Neck Surgery, Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, Beijing, China.,Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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32
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Timmer BJJ, Kooijman A, Schaapkens X, Mooibroek TJ. A Synthetic Galectin Mimic. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brian J. J. Timmer
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Arjaan Kooijman
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Xander Schaapkens
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Tiddo J. Mooibroek
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
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33
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Timmer BJJ, Kooijman A, Schaapkens X, Mooibroek TJ. A Synthetic Galectin Mimic. Angew Chem Int Ed Engl 2021; 60:16178-16183. [PMID: 33964110 PMCID: PMC8361779 DOI: 10.1002/anie.202104924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/30/2021] [Indexed: 12/30/2022]
Abstract
Galectins are a galactoside specific subclass of carbohydrate binding proteins (lectins) involved in various cellular activities, certain cancers, infections, inflammations, and many other biological processes. The molecular basis for the selectivity of galectins is well-documented and revolves around appropriate interaction complementarity: an aromatic residue for C-H⋅⋅⋅π interactions and polar residues for (charge assisted) hydrogen bonds with the axial hydroxyl group of a galactoside. However, no synthetic mimics are currently available. We now report on the design and synthesis of the first galectin mimic (6), and show that it has a higher than 65-fold preference for n-octyl-β-galactoside (8) over n-octyl-β-glucoside (7) in CD2 Cl2 containing 5 % [D6 ]DMSO (with Ka ≥4500 M-1 for 6:8). Molecular modeling informed by nOe studies reveal a high degree of interaction complementarity between 6 and galactoside 8, which is very similar to the interaction complementarity found in natural galectins.
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Affiliation(s)
- Brian J. J. Timmer
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Arjaan Kooijman
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Xander Schaapkens
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Tiddo J. Mooibroek
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
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34
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Lee AG. Interfacial binding sites for cholesterol on GABA A receptors and competition with neurosteroids. Biophys J 2021; 120:2710-2722. [PMID: 34022235 DOI: 10.1016/j.bpj.2021.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/06/2021] [Accepted: 05/13/2021] [Indexed: 01/17/2023] Open
Abstract
γ-Aminobutyric acid type A (GABAA) receptors in the brain are located in the outer membranes of brain cells where the concentration of cholesterol is high. Of the 25 available high-resolution structures available for GABAA receptors, none were determined in the presence of cholesterol, but four include resolved molecules of cholesterol hemisuccinate (CHS). Here, a molecular docking procedure is used to sweep the transmembrane (TM) surfaces of the receptors for cholesterol binding sites. Cholesterol docking poses determined in this way match 89% of the resolved CHS when CHS molecules deemed unlikely to represent typical bound cholesterols are excluded. The receptors are pentameric, and their TM surfaces consist of a set of five facets, each including pairs of TM helices from two adjacent subunits. Each facet contains hydrophobic hollows running from one side of the membrane to the other, within which are six potential binding sites for cholesterol, three on each side of the membrane. High-resolution structures of GABAA receptors with bound neurosteroids show that neurosteroids bind in these cholesterol binding sites, so the binding of neurosteroids and cholesterol will be competitive.
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Affiliation(s)
- Anthony G Lee
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom.
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35
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Bojarska J, New R, Borowiecki P, Remko M, Breza M, Madura ID, Fruziński A, Pietrzak A, Wolf WM. The First Insight Into the Supramolecular System of D,L-α-Difluoromethylornithine: A New Antiviral Perspective. Front Chem 2021; 9:679776. [PMID: 34055746 PMCID: PMC8155678 DOI: 10.3389/fchem.2021.679776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/26/2021] [Indexed: 12/28/2022] Open
Abstract
Targeting the polyamine biosynthetic pathway by inhibiting ornithine decarboxylase (ODC) is a powerful approach in the fight against diverse viruses, including SARS-CoV-2. Difluoromethylornithine (DFMO, eflornithine) is the best-known inhibitor of ODC and a broad-spectrum, unique therapeutical agent. Nevertheless, its pharmacokinetic profile is not perfect, especially when large doses are required in antiviral treatment. This article presents a holistic study focusing on the molecular and supramolecular structure of DFMO and the design of its analogues toward the development of safer and more effective formulations. In this context, we provide the first deep insight into the supramolecular system of DFMO supplemented by a comprehensive, qualitative and quantitative survey of non-covalent interactions via Hirshfeld surface, molecular electrostatic potential, enrichment ratio and energy frameworks analysis visualizing 3-D topology of interactions in order to understand the differences in the cooperativity of interactions involved in the formation of either basic or large synthons (Long-range Synthon Aufbau Modules, LSAM) at the subsequent levels of well-organized supramolecular self-assembly, in comparison with the ornithine structure. In the light of the drug discovery, supramolecular studies of amino acids, essential constituents of proteins, are of prime importance. In brief, the same amino-carboxy synthons are observed in the bio-system containing DFMO. DFT calculations revealed that the biological environment changes the molecular structure of DFMO only slightly. The ADMET profile of structural modifications of DFMO and optimization of its analogue as a new promising drug via molecular docking are discussed in detail.
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Affiliation(s)
- Joanna Bojarska
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Roger New
- Faculty of Science & Technology, Middlesex University, London, United Kingdom
| | - Paweł Borowiecki
- Faculty of Chemistry, Department of Drugs Technology and Biotechnology, Laboratory of Biocatalysis and Biotransformation, Warsaw University of Technology, Warsaw, Poland
| | | | - Martin Breza
- Department of Physical Chemistry, Slovak Technical University, Bratislava, Slovakia
| | - Izabela D. Madura
- Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland
| | - Andrzej Fruziński
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Anna Pietrzak
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
| | - Wojciech M. Wolf
- Chemistry Department, Institute of Ecological and Inorganic Chemistry, Technical University of Lodz, Lodz, Poland
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36
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Port VC, Zeoly LA, Coelho F, Cormanich RA. Through space JFH spin-spin coupling constant transmission pathways in 2-(trifluoromethyl)thiophenol: formation of unusual stabilizing bifurcated CFHS and CFSH interactions. Phys Chem Chem Phys 2021; 23:9080-9088. [PMID: 33646206 DOI: 10.1039/d0cp05887d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Given its importance and the possibility of organic F to participate in hydrogen bonds (H-bonds), the understanding of its behavior as a H-bond acceptor with different donors is crucial. The interest in organofluorine compounds and the works related to the study of the participation of this atom in non-covalent interactions is constantly growing. Following recent studies in this subject, we evaluated the existence of two bifurcated intramolecular interactions, a bifurcated CFHS H-bond in the cis conformer of 2-trifluoromethylthiophenol and an unusual, bifurcated CFSH interaction in the trans conformer. The JFH spin-spin coupling constant (SSCC) was evaluated for 2-trifluoromethylthiophenol both experimentally by 1H and 19F NMR and theoretically using the natural bond orbitals (NBO), the quantum theory of atoms in molecules (QTAIM) and the non-covalent interactions (NCI) framework. Although both interactions are crucial for the stabilization of the conformer geometries, the observed positive JFH spin-spin coupling constant (SSCC) is mainly resultant from the trans conformer, which has a large calculated positive SSCC, and is transmitted through steric interactions involving the F lone pairs and the σSH bonding orbital.
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Affiliation(s)
- Vinícius C Port
- University of Campinas, Chemistry Institute, Monteiro Lobato Street, Campinas, São Paulo 13083-862, Brazil.
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37
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Tiwari S, Arya N, Mishra SK, Suryaprakash N. Competing HB acceptors: an extensive NMR investigations corroborated by single crystal XRD and DFT calculations. RSC Adv 2021; 11:15195-15202. [PMID: 35424030 PMCID: PMC8698242 DOI: 10.1039/d1ra02538d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/11/2021] [Indexed: 11/21/2022] Open
Abstract
A series of N-benzoylanthranilamide derivatives have been synthesized with the substitution of competitive HB acceptors and investigated by NMR spectroscopy and single crystal XRD. The interesting rivalry for HB acceptance between [double bond splayed left]C[double bond, length as m-dash]O and X (F or OMe) is observed in the investigated molecules which leads to an unusual increase in the electron density at the site of one of the NH protons, reflecting in the high field resonance in the 1H NMR spectrum. The NMR experimental findings and single crystal XRD are further reinforced by the DFT studies.
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Affiliation(s)
- Surbhi Tiwari
- NMR Research Centre and Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore 560012 India +91 80 23601550 +91 80 23607344 +91 80 22933300 +91 98 45124802
| | - Neeru Arya
- NMR Research Centre and Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore 560012 India +91 80 23601550 +91 80 23607344 +91 80 22933300 +91 98 45124802
| | - Sandeep Kumar Mishra
- Department of Physics and NMR Research Centre, Indian Institute of Science Education and Research Pune 411008 India
| | - N Suryaprakash
- NMR Research Centre and Solid State and Structural Chemistry Unit, Indian Institute of Science Bangalore 560012 India +91 80 23601550 +91 80 23607344 +91 80 22933300 +91 98 45124802
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38
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Verma N, Tao Y, Kraka E. Systematic Detection and Characterization of Hydrogen Bonding in Proteins via Local Vibrational Modes. J Phys Chem B 2021; 125:2551-2565. [DOI: 10.1021/acs.jpcb.0c11392] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Niraj Verma
- Department of Chemistry, Southern Methodist University, Dallas Texas United States
| | - Yunwen Tao
- Department of Chemistry, Southern Methodist University, Dallas Texas United States
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, Dallas Texas United States
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39
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Mao S, Haruehanroengra P, Ranganathan SV, Shen F, Begley TJ, Sheng J. Base Pairing and Functional Insights into N3-Methylcytidine (m 3C) in RNA. ACS Chem Biol 2021; 16:76-85. [PMID: 33332971 DOI: 10.1021/acschembio.0c00735] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
N3-methylcytidine (m3C) is present in both eukaryotic tRNA and mRNA and plays critical roles in many biological processes. We report the synthesis of the m3C phosphoramidite building block and its containing RNA oligonucleotides. The base-pairing stability and specificity studies show that the m3C modification significantly disrupts the stability of the Watson-Crick C:G pair. Further m3C decreases the base pairing discrimination between C:G and the other mismatched C:A, C:U, and C:C pairs. Our molecular dynamic simulation study further reveals the detailed structural insights into the m3C:G base pairing pattern in an RNA duplex. More importantly, the biochemical investigation of m3C using reverse transcription in vitro shows that N3-methylation specifies the C:A pair and induces a G to A change using HIV-1-RT, MMLV-RT, and MutiScribe-RT enzymes, all with relatively low replication fidelity. For other reverse transcriptases with higher fidelity like AMV-RT, the methylation could completely shut down DNA synthesis. Our work provides detailed insights into the thermostability of m3C in RNA and a foundation for developing new molecular tools for mapping m3C in different RNA contexts and exploring the biochemical and biomedical potentials of m3C in the design and development of RNA based therapeutics.
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40
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Lendvay G, Majzik E, Bereczki L, Domján A, Trif L, Sajó IE, Franguelli FP, Farkas A, Klébert S, Bombicz P, Németh C, Szilágyi IM, Kótai L. (Me 2NH 2) 10[H 2-Dodecatungstate] polymorphs: dodecatungstate cages embedded in a variable dimethylammonium cation + water of crystallization matrix. RSC Adv 2021; 11:3713-3724. [PMID: 35424281 PMCID: PMC8694218 DOI: 10.1039/d0ra09997j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 12/26/2020] [Indexed: 11/21/2022] Open
Abstract
Two polymorphs and a solvatomorph of a new dimethylammonium polytungstate-decakis(dimethylammonium) dihydrogendodecatungstate, (Me2NH2)10(W12O42)·nH2O (n = 10 or 11)-have been synthesized. Their structures were characterized by single-crystal X-ray diffraction and solid-phase NMR methods. The shape of the dodecatungstate anions is essentially the same in all three structures, their interaction with the cations and water of crystallization, however, is remarkably variable, because the latter forms different hydrogen-bonded networks, and provides a highly versatile matrix. Accordingly, the N-H⋯O and C-H⋯O hydrogen bonds are positioned in each crystal lattice in a variety of environments, characteristic to the structure, which can be distinguished by solid-state 1H-CRAMPS, 13C, 15N CP MAS and 1H-13C heteronuclear correlation NMR. Thermogravimetry of the solvatomorphs also reflect the difference and multiformity of the environment of the water molecules in the different crystal lattices. The major factors behind the variability of the matrix are the ability of ammonium cations to form two hydrogen bonds and the rigidity of the polyoxometalate anion cage. The positions of the oxygen atoms in the latter are favourable for the formation of bifurcated and trifurcated cation-anion hydrogen bonds, some which are so durable that they persist after the crystals are dissolved in water, forming ion associates even in dilute solutions. The H atom involved in furcated hydrogen bonds cannot be exchanged by deuterium when the compound is dissolved in D2O. An obvious consequence of the versatility of the matrix is the propensity of these compounds to form multiple polymorphs.
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Affiliation(s)
- György Lendvay
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary
| | - Eszter Majzik
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary .,University of Technology and Economics, Department of Inorganic and Analytical Chemistry Budapest H-1111 Hungary
| | - Laura Bereczki
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary
| | - Attila Domján
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary
| | - László Trif
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary
| | - István E Sajó
- University of Pécs, János Szentágothai Research Centre Pécs H-7624 Hungary
| | - Fernanda Paiva Franguelli
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary .,University of Technology and Economics, Department of Inorganic and Analytical Chemistry Budapest H-1111 Hungary
| | - Attila Farkas
- University of Technology and Economics, Department of Organic Chemistry Budapest H-1111 Hungary
| | - Szilvia Klébert
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary
| | - Petra Bombicz
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary
| | - Csaba Németh
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary
| | - Imre Miklós Szilágyi
- University of Technology and Economics, Department of Inorganic and Analytical Chemistry Budapest H-1111 Hungary
| | - László Kótai
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences Budapest H-1117 Hungary .,Deuton-X Ltd. Selmeci u. 89 Érd H-2030 Hungary
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41
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Fighting cancer with translation inhibitors: a quantum mechanics view on the complex between the antitumor marine alkaloid agelastatin A and the yeast 80S ribosome. Struct Chem 2021. [DOI: 10.1007/s11224-020-01706-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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42
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Kondrashov OV, Galimzyanov TR, Molotkovsky RJ, Batishchev OV, Akimov SA. Membrane-Mediated Lateral Interactions Regulate the Lifetime of Gramicidin Channels. MEMBRANES 2020; 10:membranes10120368. [PMID: 33255806 PMCID: PMC7760706 DOI: 10.3390/membranes10120368] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/22/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022]
Abstract
The lipid matrix of cellular membranes is an elastic liquid crystalline medium. Its deformations regulate the functionality and interactions of membrane proteins,f membrane-bound peptides, lipid and protein-lipid domains. Gramicidin A (gA) is a peptide, which incorporates into membrane leaflets as a monomer and may form a transmembrane dimer. In both configurations, gA deforms the membrane. The transmembrane dimer of gA is a cation-selective ion channel. Its electrical response strongly depends on the elastic properties of the membrane. The gA monomer and dimer deform the membrane differently; therefore, the elastic energy contributes to the activation barriers of the dimerization and dissociation of the conducting state. It is shown experimentally that channel characteristics alter if gA molecules have been located in the vicinity of the conducting dimer. Here, based on the theory of elasticity of lipid membranes, we developed a quantitative theoretical model which allows explaining experimentally observed phenomena under conditions of high surface density of gA or its analogues, i.e., in the regime of strong lateral interactions of gA molecules, mediated by elastic deformations of the membrane. The model would be useful for the analysis and prediction of the gA electrical response in various experimental conditions. This potentially widens the possible applications of gA as a convenient molecular sensor of membrane elasticity.
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Affiliation(s)
- Oleg V. Kondrashov
- Correspondence: (O.V.K.); (S.A.A.); Tel.: +7-495-955-4776 (O.V.K.); +7-495-955-4776 (S.A.A.)
| | | | | | | | - Sergey A. Akimov
- Correspondence: (O.V.K.); (S.A.A.); Tel.: +7-495-955-4776 (O.V.K.); +7-495-955-4776 (S.A.A.)
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Blanco S, Macario A, García‐Calvo J, Revilla‐Cuesta A, Torroba T, López JC. Microwave Detection of Wet Triacetone Triperoxide (TATP): Non‐Covalent Forces and Water Dynamics. Chemistry 2020; 27:1680-1687. [DOI: 10.1002/chem.202003499] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/16/2020] [Indexed: 11/07/2022]
Affiliation(s)
- Susana Blanco
- Departamento de Química Física y Química Inorgánica Facultad de Ciencias, IU CINQUIMA Universidad de Valladolid 47011 Valladolid Spain
| | - Alberto Macario
- Departamento de Química Física y Química Inorgánica Facultad de Ciencias, IU CINQUIMA Universidad de Valladolid 47011 Valladolid Spain
| | - José García‐Calvo
- Departamento de Química Facultad de Ciencias Universidad de Burgos 09001 Burgos Spain
| | - Andrea Revilla‐Cuesta
- Departamento de Química Facultad de Ciencias Universidad de Burgos 09001 Burgos Spain
| | - Tomas Torroba
- Departamento de Química Facultad de Ciencias Universidad de Burgos 09001 Burgos Spain
| | - Juan Carlos López
- Departamento de Química Física y Química Inorgánica Facultad de Ciencias, IU CINQUIMA Universidad de Valladolid 47011 Valladolid Spain
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Xavier BM, Zein AA, Venes A, Wang J, Lee JY. Transmembrane Polar Relay Drives the Allosteric Regulation for ABCG5/G8 Sterol Transporter. Int J Mol Sci 2020; 21:ijms21228747. [PMID: 33228147 PMCID: PMC7699580 DOI: 10.3390/ijms21228747] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022] Open
Abstract
The heterodimeric ATP-binding cassette (ABC) sterol transporter, ABCG5/G8, is responsible for the biliary and transintestinal secretion of cholesterol and dietary plant sterols. Missense mutations of ABCG5/G8 can cause sitosterolemia, a loss-of-function disorder characterized by plant sterol accumulation and premature atherosclerosis. A new molecular framework was recently established by a crystal structure of human ABCG5/G8 and reveals a network of polar and charged amino acids in the core of the transmembrane domains, namely, a polar relay. In this study, we utilize genetic variants to dissect the mechanistic role of this transmembrane polar relay in controlling ABCG5/G8 function. We demonstrated a sterol-coupled ATPase activity of ABCG5/G8 by cholesteryl hemisuccinate (CHS), a relatively water-soluble cholesterol memetic, and characterized CHS-coupled ATPase activity of three loss-of-function missense variants, R543S, E146Q, and A540F, which are respectively within, in contact with, and distant from the polar relay. The results established an in vitro phenotype of the loss-of-function and missense mutations of ABCG5/G8, showing significantly impaired ATPase activity and loss of energy sufficient to weaken the signal transmission from the transmembrane domains. Our data provide a biochemical evidence underlying the importance of the polar relay and its network in regulating the catalytic activity of ABCG5/G8 sterol transporter.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily G, Member 5/chemistry
- ATP Binding Cassette Transporter, Subfamily G, Member 5/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 5/metabolism
- ATP Binding Cassette Transporter, Subfamily G, Member 8/chemistry
- ATP Binding Cassette Transporter, Subfamily G, Member 8/genetics
- ATP Binding Cassette Transporter, Subfamily G, Member 8/metabolism
- Adenosine Triphosphatases/chemistry
- Adenosine Triphosphatases/genetics
- Adenosine Triphosphatases/metabolism
- Adenosine Triphosphate/chemistry
- Adenosine Triphosphate/metabolism
- Allosteric Regulation
- Binding Sites
- Biological Transport
- Cholesterol/chemistry
- Cholesterol/metabolism
- Cholesterol Esters/chemistry
- Cholesterol Esters/metabolism
- Cholic Acid/chemistry
- Cholic Acid/metabolism
- Gene Expression
- Humans
- Hypercholesterolemia/genetics
- Hypercholesterolemia/metabolism
- Hypercholesterolemia/pathology
- Intestinal Diseases/genetics
- Intestinal Diseases/metabolism
- Intestinal Diseases/pathology
- Kinetics
- Lipid Metabolism, Inborn Errors/genetics
- Lipid Metabolism, Inborn Errors/metabolism
- Lipid Metabolism, Inborn Errors/pathology
- Lipoproteins/chemistry
- Lipoproteins/genetics
- Lipoproteins/metabolism
- Models, Molecular
- Mutation
- Phytosterols/adverse effects
- Phytosterols/genetics
- Phytosterols/metabolism
- Pichia/chemistry
- Pichia/genetics
- Pichia/metabolism
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Thermodynamics
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Affiliation(s)
- Bala M. Xavier
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (B.M.X.); (A.A.Z.); (A.V.)
| | - Aiman A. Zein
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (B.M.X.); (A.A.Z.); (A.V.)
| | - Angelica Venes
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (B.M.X.); (A.A.Z.); (A.V.)
- Biomedical Sciences Program, Department of Biology, Faculty of Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Junmei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15206, USA
- Correspondence: (J.W.); (J.-Y.L.); Tel.: +1-412-383-3268 (J.W.); +1-613-562-5800 (ext. 8308) (J.-Y.L.)
| | - Jyh-Yeuan Lee
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON K1H 8M5, Canada; (B.M.X.); (A.A.Z.); (A.V.)
- Correspondence: (J.W.); (J.-Y.L.); Tel.: +1-412-383-3268 (J.W.); +1-613-562-5800 (ext. 8308) (J.-Y.L.)
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Pantelopulos GA, Panahi A, Straub JE. Impact of Cholesterol Concentration and Lipid Phase on Structure and Fluctuation of Amyloid Precursor Protein. J Phys Chem B 2020; 124:10173-10185. [PMID: 33135883 PMCID: PMC7958706 DOI: 10.1021/acs.jpcb.0c07615] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Elevated levels of cellular cholesterol have been identified as one factor contributing to the onset of Alzheimer's disease (AD). Specific interaction between cholesterol and the amyloid precursor protein (APP), investigated via NMR experiments and computational studies, has been proposed to play a critical role in the processing of APP by secretases and the biogenesis of amyloid-β (Aβ) protein. We present all-atom molecular dynamics simulations of the 40-residue congener of the C-terminal domain of APP, C9916-55 (C99), in cholesterol-enriched DMPC lipid bilayers. We investigated the effect of cholesterol concentration on the conformational ensemble of wild-type C99 and C99-cholesterol associations at the low pH of endosomal environments, at which residues E22 and D23 are neutral. C99 was also characterized in liquid ordered domains for Dutch (E22Q) and Iowa (D23N) Familial AD mutants at low pH and for the wild-type sequence using protonation states characteristic of neutral pH. Our results reproduce the equilibrium constant of past NMR characterizations of the C99-cholesterol interaction but are not consistent with the C99-cholesterol binding hypothesis. We find that the lifetimes of both DMPC and cholesterol complexed with C99 display a power-law distribution of residence lifetimes. Longer-lived C99-DMPC and C99-cholesterol complexes are primarily stabilized by salt bridges and hydrogen bonds of lysine amines to phosphate and hydroxyl groups. Nevertheless, specific interfaces for C99-cholesterol association which are not present for DMPC can be identified. Changes to C99-cholesterol interfaces are found to depend on C99 tilt angle and orientation of the juxtamembrane domain of C99 containing residues E22 and D23. These observations support a more nuanced view of the C99-cholesterol interaction than has previously been suggested. We propose that cholesterol modulates the conformation and activity of C99 and other small transmembrane proteins indirectly through induction of the liquid ordered phase and directly through hydrogen bonding. This suggests a critical role for membrane heterogeneity introduced by cholesterol in modulating the structural ensemble of C99 and the production of Aβ.
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Affiliation(s)
- George A Pantelopulos
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Afra Panahi
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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Stylianakis I, Shalev A, Scheiner S, Sigalas MP, Arkin IT, Glykos N, Kolocouris A. The balance between side-chain and backbone-driven association in folding of the α-helical influenza A transmembrane peptide. J Comput Chem 2020; 41:2177-2188. [PMID: 32735736 DOI: 10.1002/jcc.26381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
The correct balance between attractive, repulsive and peptide hydrogen bonding interactions must be attained for proteins to fold correctly. To investigate these important contributors, we sought a comparison of the folding between two 25-residues peptides, the influenza A M2 protein transmembrane domain (M2TM) and the 25-Ala (Ala25 ). M2TM forms a stable α-helix as is shown by circular dichroism (CD) experiments. Molecular dynamics (MD) simulations with adaptive tempering show that M2TM monomer is more dynamic in nature and quickly interconverts between an ensemble of various α-helical structures, and less frequently turns and coils, compared to one α-helix for Ala25 . DFT calculations suggest that folding from the extended structure to the α-helical structure is favored for M2TM compared with Ala25 . This is due to CH⋯O attractive interactions which favor folding to the M2TM α-helix, and cannot be described accurately with a force field. Using natural bond orbital (NBO) analysis and quantum theory atoms in molecules (QTAIM) calculations, 26 CH⋯O interactions and 22 NH⋯O hydrogen bonds are calculated for M2TM. The calculations show that CH⋯O hydrogen bonds, although individually weaker, have a cumulative effect that cannot be ignored and may contribute as much as half of the total hydrogen bonding energy, when compared to NH⋯O, to the stabilization of the α-helix in M2TM. Further, a strengthening of NH⋯O hydrogen bonding interactions is calculated for M2TM compared to Ala25 . Additionally, these weak CH⋯O interactions can dissociate and associate easily leading to the ensemble of folded structures for M2TM observed in folding MD simulations.
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Affiliation(s)
- Ioannis Stylianakis
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
| | - Ariella Shalev
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, USA
| | - Michael P Sigalas
- Department of Chemistry, Laboratory of Applied Quantum Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Isaiah T Arkin
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus Givat-Ram, Jerusalem, Israel
| | - Nikolas Glykos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
| | - Antonios Kolocouris
- Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Athens, Greece
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Su CTT, Sinha S, Eisenhaber B, Eisenhaber F. Structural modelling of the lumenal domain of human GPAA1, the metallo-peptide synthetase subunit of the transamidase complex, reveals zinc-binding mode and two flaps surrounding the active site. Biol Direct 2020; 15:14. [PMID: 32993792 PMCID: PMC7522609 DOI: 10.1186/s13062-020-00266-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/30/2020] [Indexed: 02/01/2023] Open
Abstract
Background The transamidase complex is a molecular machine in the endoplasmic reticulum of eukaryotes that attaches a glycosylphosphatidylinositol (GPI) lipid anchor to substrate proteins after cleaving a C-terminal propeptide with a defined sequence signal. Its five subunits are very hydrophobic; thus, solubility, heterologous expression and complex reconstruction are difficult. Therefore, theoretical approaches are currently the main source of insight into details of 3D structure and of the catalytic process. Results In this work, we generated model 3D structures of the lumenal domain of human GPAA1, the M28-type metallo-peptide-synthetase subunit of the transamidase, including zinc ion and model substrate positions. In comparative molecular dynamics (MD) simulations of M28-type structures and our GPAA1 models, we estimated the metal ion binding energies with evolutionary conserved amino acid residues in the catalytic cleft. We find that canonical zinc binding sites 2 and 3 are strongest binders for Zn1 and, where a second zinc is available, sites 2 and 4 for Zn2. Zinc interaction of site 5 with Zn1 enhances upon substrate binding in structures with only one zinc. Whereas a previously studied glutaminyl cyclase structure, the best known homologue to GPAA1, binds only one zinc ion at the catalytic site, GPAA1 can sterically accommodate two. The M28-type metallopeptidases segregate into two independent branches with regard to one/two zinc ion binding modality in a phylogenetic tree where the GPAA1 family is closer to the joint origin of both groups. For GPAA1 models, MD studies revealed two large loops (flaps) surrounding the active site being involved in an anti-correlated, breathing-like dynamics. Conclusions In the light of combined sequence-analytic and phylogenetic arguments as well as 3D structural modelling results, GPAA1 is most likely a single zinc ion metallopeptidase. Two large flaps environ the catalytic site restricting access to large substrates. Reviewers This article was reviewed by Thomas Dandekar (MD) and Michael Gromiha.
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Affiliation(s)
- Chinh Tran-To Su
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Swati Sinha
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore
| | - Birgit Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore.
| | - Frank Eisenhaber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, # 07-01, Matrix, Singapore, 138671, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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48
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Nekvasilová P, Kulik N, Rychlá N, Pelantová H, Petrásková L, Bosáková Z, Cvačka J, Slámová K, Křen V, Bojarová P. How Site‐Directed Mutagenesis Boosted Selectivity of a Promiscuous Enzyme. Adv Synth Catal 2020. [DOI: 10.1002/adsc.202000604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Pavlína Nekvasilová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
- Department of Genetics and Microbiology Faculty of Science Charles University Viničná 5 CZ-12843 Praha 2 Czech Republic
- Department of Analytical Chemistry Faculty of Science Charles University Hlavova 2030/8. CZ-12843 Praha 2 Czech Republic
| | - Natalia Kulik
- Center for Nanobiology and Structural Biology Institute of Microbiology Czech Academy of Sciences Zámek 136 CZ-37333 Nové Hrady Czech Republic
| | - Nikola Rychlá
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
- Department of Health Care Disciplines and Population Protection Faculty of Biomedical Engineering Czech Technical University in Prague Nám. Sítná 3105 CZ-27201 Kladno Czech Republic
| | - Helena Pelantová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Lucie Petrásková
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Zuzana Bosáková
- Department of Analytical Chemistry Faculty of Science Charles University Hlavova 2030/8. CZ-12843 Praha 2 Czech Republic
| | - Josef Cvačka
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nám. 2 CZ-16610 Praha 6 Czech Republic
| | - Kristýna Slámová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Vladimír Křen
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
| | - Pavla Bojarová
- Institute of Microbiology Czech Academy of Sciences Vídeňská 1083 CZ-14220 Praha 4 Czech Republic
- Department of Health Care Disciplines and Population Protection Faculty of Biomedical Engineering Czech Technical University in Prague Nám. Sítná 3105 CZ-27201 Kladno Czech Republic
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Abstract
H-bonding is the predominant geometrical determinant of biomolecular structure and interactions. As such, considerable analyses have been undertaken to study its detailed energetics. The focus, however, has been mostly reserved for H-bonds comprising a single donor and a single acceptor. Herein, we measure the prevalence and energetics of multiplex H-bonds that are formed between three or more groups. We show that 92% of all transmembrane helices have at least one non-canonical H-bond formed by a serine or threonine residue whose hydroxyl side chain H-bonds to an over-coordinated carbonyl oxygen at position i-4, i-3, or i in the sequence. Isotope-edited FTIR spectroscopy, coupled with DFT calculations, enables us to determine the bond enthalpies, pointing to values that are up to 127% higher than that of a single canonical H-bond. We propose that these strong H-bonds serve to stabilize serine and threonine residues in hydrophobic environments while concomitantly providing them flexibility between different configurations, which may be necessary for function.
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Affiliation(s)
- Esther S Brielle
- The Alexander Grass Center for Bioengineering, Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190400, Israel
| | - Isaiah T Arkin
- The Alexander Silberman Institute of Life Sciences. Department of Biological Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem 9190400, Israel
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50
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Rojas-Valencia N, Gómez S, Guerra D, Restrepo A. A detailed look at the bonding interactions in the microsolvation of monoatomic cations. Phys Chem Chem Phys 2020; 22:13049-13061. [PMID: 32478372 DOI: 10.1039/d0cp00428f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Global and local descriptors of the properties of intermolecular bonding, formally derived from independent methodologies (QTAIM, NCI, NBO, density differences) afford a highly complex picture of the bonding interactions responsible for microsolvation of monoatomic cations. In all cases, the dominant factor dictating geometries and interaction strengths is the electrophilic power of the metal cation. The formal charge disrupts the hydrogen bonding network otherwise present in pristine water clusters, making the hydrogen bonds considerably stronger, even inducing some degree of covalency. All MO interactions are highly ionic, with strengths than in some cases approach that of the reference LiCl bond. Accumulation of electron density in the region connecting MO is observed, thus, ionic bonding in the microsolvation of monoatomic cations is not as simple as an electrostatic interaction between opposing charges.
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Affiliation(s)
- Natalia Rojas-Valencia
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia. and Escuela de Ciencias y Humanidades, Departamento de Ciencias Básicas, Universidad Eafit, AA 3300, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, Pisa, 56126, Italy
| | - Doris Guerra
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia.
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