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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2913-2930. [PMID: 35412817 DOI: 10.1021/acs.jctc.2c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, MALTA Consolider Team, Oviedo E-33006, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
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2
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2208-2232. [PMID: 35313106 DOI: 10.1021/acs.jctc.1c01128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- MALTA Consolider Team, Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
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Coba‐Jiménez L, Maza J, Guerra M, Deluque‐Gómez J, Cubillán N. Interaction of Ciprofloxacin with Arabinose, Glucosamine, Glucuronic Acid and Rhamnose: Insights from Genetic Algorithm and Quantum Chemistry. ChemistrySelect 2022. [DOI: 10.1002/slct.202103836] [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)
- Ludis Coba‐Jiménez
- Programa de Química Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia
| | - Julio Maza
- Programa de Química Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia
| | - Mayamarú Guerra
- Laboratorio de Óptica y Procesamiento de Imágenes Facultad de Ciencias Básicas Universidad Tecnológica de Bolívar Turbaco Colombia
| | - Julio Deluque‐Gómez
- Programa de Ingeniería Industrial Facultad de Ingenierías Universidad de la Guajira Riohacha Colombia
| | - Néstor Cubillán
- Programa de Química Facultad de Ciencias Básicas Universidad del Atlántico Barranquilla Colombia
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Wang C, Shen S, Li Y, Pan H, Zhou Z, Li J, Wu B, Jing S, Guo C, Fan J, Guo H. The influence of the size of aromatic monomers on the structure and catalytic activity of polymer solid acids. NEW J CHEM 2022. [DOI: 10.1039/d1nj02596a] [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
High activity hyper-crosslinked polymer solid acids (HCPSAs) were prepared from different aromatic monomers, and the structure was regulated by selecting the type and size of aromatic monomers.
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Affiliation(s)
- Cui Wang
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Shuguang Shen
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Yehui Li
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Huajie Pan
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Zijian Zhou
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Jing Li
- College of Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Bin Wu
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Shuaiqi Jing
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Chenyuan Guo
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Jimin Fan
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
| | - Hongsheng Guo
- College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China
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5
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Duan Z, Luo Q, Dai X, Li X, Gu L, Zhu H, Tian X, Zhang H, Gong Q, Gu Z, Luo K. Synergistic Therapy of a Naturally Inspired Glycopolymer-Based Biomimetic Nanomedicine Harnessing Tumor Genomic Instability. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2104594. [PMID: 34554623 DOI: 10.1002/adma.202104594] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 08/03/2021] [Indexed: 02/05/2023]
Abstract
Inspired by natural saccharide-protein complexes, a stimuli-responsive biodegradable and branched glycopolymer-pyropheophorbide-a (Ppa) conjugate (BSP) with saccharide units for cancer therapy is constructed. A linear glycopolymeric conjugate (LSP), a branched glycopolymeric conjugate (BShP) from Ppa with long carbon chains, and a branched conjugate (BHSP) based on poly[N-(2-hydroxypropyl) methacrylamide] (polyHPMA) without saccharide units are prepared as controls. Through structure-activity relationship studies, BSP with a 3D network structure forms stable nanostructures via weak intermolecular interactions, regulating the stacking state of Ppa to improve the singlet oxygen quantum yield and the corresponding photodynamic therapy (PDT) effect. BSP shows high loading of olaparib, and are further coated with tumor cell membranes, resulting in a biomimetic nanomedicine (CM-BSPO). CM-BSPO shows highly efficient tumor targeting and cellular internalization properties. The engulfment of CM-BSPO accompanied with laser irradiation results in a prominent antitumor effect, evidenced by disruption of cell cycles in tumor cells, increased apoptosis and DNA damage, and subsequent inhibition of repair for damaged DNA. The mechanism for the synergistic effect from PDT and olaparib is unveiled at the genetic and protein level through transcriptome analysis. Overall, this biodegradable and branched glycopolymer-drug conjugate could be effectively optimized as a biomimetic nanomedicine for cancer therapy.
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Affiliation(s)
- Zhenyu Duan
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
- West China Medical School Sichuan University Chengdu 610041 China
| | - Qiang Luo
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
- West China Medical School Sichuan University Chengdu 610041 China
| | - Xinghang Dai
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
- West China Medical School Sichuan University Chengdu 610041 China
| | - Xiaoling Li
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
- West China Medical School Sichuan University Chengdu 610041 China
| | - Lei Gu
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
- West China Medical School Sichuan University Chengdu 610041 China
| | - Hongyan Zhu
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
| | - Xiaohe Tian
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology Chinese Academy of Medical Sciences Chengdu 610041 China
| | - Hu Zhang
- Amgen Bioprocessing Centre Keck Graduate Institute Claremont CA 91711 USA
| | - Qiyong Gong
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
- West China Medical School Sichuan University Chengdu 610041 China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology Chinese Academy of Medical Sciences Chengdu 610041 China
| | - Zhongwei Gu
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
| | - Kui Luo
- Huaxi MR Research Center (HMRRC) Department of Radiology National Clinical Research Center for Geriatrics Frontiers Science Center for Disease‐Related Molecular Network State Key Laboratory of Biotherapy West China Hospital Sichuan University Chengdu 610041 China
- West China Medical School Sichuan University Chengdu 610041 China
- Functional and Molecular Imaging Key Laboratory of Sichuan Province, and Research Unit of Psychoradiology Chinese Academy of Medical Sciences Chengdu 610041 China
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6
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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7
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Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations. Int J Biol Macromol 2020; 157:1-9. [DOI: 10.1016/j.ijbiomac.2020.03.251] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/12/2020] [Accepted: 03/30/2020] [Indexed: 02/03/2023]
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8
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Lansky S, Salama R, Shulami S, Lavid N, Sen S, Schapiro I, Shoham Y, Shoham G. Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein. J Mol Biol 2020; 432:2099-2120. [PMID: 32067952 DOI: 10.1016/j.jmb.2020.01.041] [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: 10/10/2019] [Revised: 01/19/2020] [Accepted: 01/30/2020] [Indexed: 11/27/2022]
Abstract
ABC importers are membrane proteins responsible for the transport of nutrients into the cells of prokaryotes. Although the structures of ABC importers vary, all contain four conserved domains: two nucleotide-binding domains (NBDs), which bind and hydrolyze ATP, and two transmembrane domains (TMDs), which help translocate the substrate. ABC importers are also dependent on an additional protein component, a high-affinity substrate-binding protein (SBP) that specifically binds the target ligand for delivery to the appropriate ABC transporter. AbnE is a SBP belonging to the ABC importer for arabino-oligosaccharides in the Gram-positive thermophilic bacterium Geobacillus stearothermophilus. Using isothermal titration calorimetry (ITC), purified AbnE was shown to bind medium-sized arabino-oligosaccharides, in the range of arabino-triose (A3) to arabino-octaose (A8), all with Kd values in the nanomolar range. We describe herein the 3D structure of AbnE in its closed conformation in complex with a wide range of arabino-oligosaccharide substrates (A2-A8). These structures provide the basis for the detailed structural analysis of the AbnE-sugar complexes, and together with complementary quantum chemical calculations, site-specific mutagenesis, and isothermal titration calorimetry (ITC) experiments, provide detailed insights into the AbnE-substrate interactions involved. Small-angle X-ray scattering (SAXS) experiments and normal mode analysis (NMA) are used to study the conformational changes of AbnE, and these data, taken together, suggest clues regarding its binding mode to the full ABC importer.
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Affiliation(s)
- Shifra Lansky
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Rachel Salama
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Smadar Shulami
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Noa Lavid
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel
| | - Saumik Sen
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel; Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Igor Schapiro
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel; Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel
| | - Yuval Shoham
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa, 32000, Israel.
| | - Gil Shoham
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 91904, Israel.
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9
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Yang H, Liu YL, Tao YY, Yang W, Yang CP, Zhang J, Qian LZ, Liu H, Wang ZY. Bioinformatic and biochemical analysis of the key binding sites of the pheromone binding protein of Cyrtotrachelus buqueti Guerin-Meneville (Coleoptera: Curculionidea). PeerJ 2019; 7:e7818. [PMID: 31632851 PMCID: PMC6796961 DOI: 10.7717/peerj.7818] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/03/2019] [Indexed: 12/19/2022] Open
Abstract
The bamboo snout beetle Cyrtotrachelus buqueti is a widely distributed wood-boring pest found in China, and its larvae cause significant economic losses because this beetle targets a wide range of host plants. A potential pest management measure of this beetle involves regulating olfactory chemoreceptors. In the process of olfactory recognition, pheromone-binding proteins (PBPs) play an important role. Homology modeling and molecular docking were conducted in this study for the interaction between CbuqPBP1 and dibutyl phthalate to better understand the relationship between PBP structures and their ligands. Site-directed mutagenesis and binding experiments were combined to identify the binding sites of CbuqPBP1 and to explore its ligand-binding mechanism. The 3D structural model of CbuqPBP1 has six a-helices. Five of these a-helices adopt an antiparallel arrangement to form an internal ligand-binding pocket. When docking dibutyl phthalate within the active site of CbuqPBP1, a CH-π interaction between the benzene ring of dibutyl phthalate and Phe69 was observed, and a weak hydrogen bond formed between the ester carbonyl oxygen and His53. Thus, Phe69 and His53 are predicted to be important residues of CbuqPBP1 involved in ligand recognition. Site-directed mutagenesis and fluorescence assays with a His53Ala CbuqPBP1 mutant showed no affinity toward ligands. Mutation of Phe69 only affected binding of CbuqPBP1 to cedar camphor. Thus, His53 (Between α2 and α3) of CbuqPBP1 appears to be a key binding site residue, and Phe69 (Located at α3) is a very important binding site for particular ligand interactions.
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Affiliation(s)
- Hua Yang
- Sichuan Agricultural University, Key Laboratory of Ecological Forestry Engineering of Sichuan Province/ College of Forestry, Chengdu, Sichuan, China
| | - Yan-Lin Liu
- Sichuan Agricultural University, Key Laboratory of Ecological Forestry Engineering of Sichuan Province/ College of Forestry, Chengdu, Sichuan, China
| | - Yuan-Yuan Tao
- Sichuan Agricultural University, Key Laboratory of Ecological Forestry Engineering of Sichuan Province/ College of Forestry, Chengdu, Sichuan, China
| | - Wei Yang
- Sichuan Agricultural University, Key Laboratory of Ecological Forestry Engineering of Sichuan Province/ College of Forestry, Chengdu, Sichuan, China
| | - Chun-Ping Yang
- Sichuan Agricultural University, Key Laboratory of Ecological Forestry Engineering of Sichuan Province/ College of Forestry, Chengdu, Sichuan, China
| | - Jing Zhang
- Provincial Key Laboratory of Agricultural Environmental Engineering, Sichuan Agricultural University, Chengdu, China
| | - Li-Zhi Qian
- Sichuan Agricultural University, Key Laboratory of Ecological Forestry Engineering of Sichuan Province/ College of Forestry, Chengdu, Sichuan, China
| | - Hao Liu
- Sichuan Agricultural University, Key Laboratory of Ecological Forestry Engineering of Sichuan Province/ College of Forestry, Chengdu, Sichuan, China
| | - Zhi-Yong Wang
- Key Laboratory of Control and Resource Development of Bamboo Pest of Sichuan Province, Leshan, China
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10
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Single-walled carbon nanotubes in tetrahydrofuran solution: microsolvation from first-principles calculations. J Mol Model 2019; 25:206. [PMID: 31256236 DOI: 10.1007/s00894-019-4050-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 04/24/2019] [Indexed: 10/26/2022]
Abstract
The molecular interactions between the commonly used solvent tetrahydrofuran (THF) and single-walled carbon nanotubes (SWCNT) are studied using density functional theory calculations and Car-Parrinello molecular dynamics simulations. The competitive interplay between THF-THF and THF-SWCNT interactions via C-H⋯O and C-H⋯π hydrogen bonds is analyzed in detail. The binding energies for different global and local energy minima configurations of THF monomers, dimers, trimers, and tetramers on SWCNT(10,0) were determined. The adsorbed species are analyzed in terms of their coordination to the surface via weak hydrogen bonds of the C-H⋯π type and in terms of their ability to form intermolecular C-H⋯O hydrogen bonds, which are responsible for the self-aggregation of THF molecules and a possible dimerization or tetramerization process. A special focus is put on the pseudorotation of the THF molecules at finite temperatures and on the formation of blue-shifting hydrogen bonds.
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11
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Lee KH, Schnupf U, Sumpter BG, Irle S. Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution. ACS OMEGA 2018; 3:16899-16915. [PMID: 31458314 PMCID: PMC6643604 DOI: 10.1021/acsomega.8b02213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/07/2018] [Indexed: 05/12/2023]
Abstract
Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowest-energy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span less than 10 kcal/mol. Both second- as well as third-order DFTB methods are exhibiting similar deviations from B3LYP. Even after the inclusion of empirical dispersion corrections in vacuum, these deviations remain for a large majority of isomer energies and geometries when compared to dispersion-corrected B3LYP.
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Affiliation(s)
- Ka Hung Lee
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Bredesen
Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Udo Schnupf
- Department
of Chemistry and Biochemistry, Bradley University, Peoria, Illinois 61625, United States
- E-mail: (U.S.)
| | - Bobby G. Sumpter
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Stephan Irle
- Department
of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
- Computational Sciences and Engineering Division &
Chemical Sciences
Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- E-mail: (S.I.)
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12
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Shen C, Gong Z, Gao L, Gu M, Huan L, Wang S, Xie J. Theoretical study on host-guest interaction between pillar[4]arene and molecules or ions. J Mol Model 2018; 24:199. [PMID: 29987452 DOI: 10.1007/s00894-018-3736-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 06/25/2018] [Indexed: 10/28/2022]
Abstract
In order to systematically explore the general rule of the host-guest chemistry for pillararenes, this work investigates the weak interactions between pillar[4]arene and some typical guests (anions, cations, and dumbbell-shaped molecules) by using density functional theory (DFT) calculations at the ωB97XD/6-311G(d,p) level. The strong molecular recognition ability of pillar[4]arene has been discussed based on the geometry structure, electronic structure, and thermodynamic properties of the host-guest complexes. The results show that the equivalent lower and upper rims of the pillar[4]arene can be combined with both anion and cation, and its cavity can accommodate the alkyl part of the dumbbell-shaped molecule. The main host-guest interactions between pillar[4]arene and guests are hydrogen bond, cation-π, anion-π, and hydrophobic interaction by visualization of weak interactions using the Multiwfn program. Pillar[4]arene will form a more stable host-guest complex with the guest, which possesses conjugate structure and weak steric repulsion. This work intends to provide a theoretical basis for enriching the host-guest chemistry, understanding the supramolecular morphology, and expanding the applications of the pillararenes.
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Affiliation(s)
- Chao Shen
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, Jiangsu, China
| | - Zhenyu Gong
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, Jiangsu, China
| | - Lei Gao
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, Jiangsu, China
| | - Minglong Gu
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, Jiangsu, China
| | - Long Huan
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, Jiangsu, China
| | - Sicong Wang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Nankai University, Tianjin, 300071, China
| | - Ju Xie
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, 225002, Jiangsu, China.
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), Nankai University, Tianjin, 300071, China.
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13
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Houser J, Kozmon S, Mishra D, Mishra SK, Romano PR, Wimmerová M, Koča J. Influence of Trp flipping on carbohydrate binding in lectins. An example on Aleuria aurantia lectin AAL. PLoS One 2017; 12:e0189375. [PMID: 29232414 PMCID: PMC5726637 DOI: 10.1371/journal.pone.0189375] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 11/20/2017] [Indexed: 11/19/2022] Open
Abstract
Protein-carbohydrate interactions are very often mediated by the stacking CH-π interactions involving the side chains of aromatic amino acids such as tryptophan (Trp), tyrosine (Tyr) or phenylalanine (Phe). Especially suitable for stacking is the Trp residue. Analysis of the PDB database shows Trp stacking for 265 carbohydrate or carbohydrate like ligands in 5 208 Trp containing motives. An appropriate model system to study such an interaction is the AAL lectin family where the stacking interactions play a crucial role and are thought to be a driving force for carbohydrate binding. In this study we present data showing a novel finding in the stacking interaction of the AAL Trp side chain with the carbohydrate. High resolution X-ray structure of the AAL lectin from Aleuria aurantia with α-methyl-l-fucoside ligand shows two possible Trp side chain conformations with the same occupation in electron density. The in silico data shows that the conformation of the Trp side chain does not influence the interaction energy despite the fact that each conformation creates interactions with different carbohydrate CH groups. Moreover, the PDB data search shows that the conformations are almost equally distributed across all Trp-carbohydrate complexes, which would suggest no substantial preference for one conformation over another.
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Affiliation(s)
- Josef Houser
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Stanislav Kozmon
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Deepti Mishra
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sushil K. Mishra
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Structural Glycobiology Team, Systems Glycobiology Research Group, RIKEN Global Research Cluster, Wako, Saitama, Japan
| | - Patrick R. Romano
- Baruch S. Blumberg Institute, Doylestown, Pennsylvania, United States of America
| | - Michaela Wimmerová
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail: (JK); (MW)
| | - Jaroslav Koča
- CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
- * E-mail: (JK); (MW)
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14
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Abstract
Many carbohydrate-binding proteins contain aromatic amino acid residues in their binding sites. These residues interact with carbohydrates in a stacking geometry via CH/π interactions. These interactions can be found in carbohydrate-binding proteins, including lectins, enzymes and carbohydrate transporters. Besides this, many non-protein aromatic molecules (natural as well as artificial) can bind saccharides using these interactions. Recent computational and experimental studies have shown that carbohydrate–aromatic CH/π interactions are dispersion interactions, tuned by electrostatics and partially stabilized by a hydrophobic effect in solvated systems.
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15
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Hayashi S, Sugibayashi Y, Nakanishi W. Behavior of interactions between hydrogen chalcogenides and an anthracene π-system elucidated by QTAIM dual functional analysis with QC calculations. RSC Adv 2017. [DOI: 10.1039/c7ra04224h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The nature of the interactions between chalcogenides and the anthracene p-system, EH2-*-p(C14H10), is predicted to be close to that of EH2-*-p(C10H8), although the partial structures around the central rings can be found in EH2-*-p(C6H6).
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Affiliation(s)
- Satoko Hayashi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama
- 640-8510 Japan
| | - Yuji Sugibayashi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama
- 640-8510 Japan
| | - Waro Nakanishi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama
- 640-8510 Japan
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16
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Chu TS, Liu BT. Establishing new mechanisms with triplet and singlet excited-state hydrogen bonding roles in photoinduced liquid dynamics. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1148450] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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17
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Hayashi S, Sugibayashi Y, Nakanishi W. Quantum chemical calculations with the AIM approach applied to the π-interactions between hydrogen chalcogenides and naphthalene. RSC Adv 2016. [DOI: 10.1039/c6ra04738f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The nature of π-interactions in (EH2)n–*–π(C10H8) (n = 1 and 2: E = O, S, Se and Te) is elucidated with QTAIM-DFA. They have the character of the vdW-nature of the pure-CS interactions, except for HHTe–*–π(C10H8), which seems stronger than others.
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Affiliation(s)
- Satoko Hayashi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama
- 640-8510 Japan
| | - Yuji Sugibayashi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama
- 640-8510 Japan
| | - Waro Nakanishi
- Department of Material Science and Chemistry
- Faculty of Systems Engineering
- Wakayama University
- Wakayama
- 640-8510 Japan
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18
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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19
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Ring- and side-group conformational properties of di-O-acylated xylopyranosides: A computational study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Wilson KA, Wetmore SD. A Survey of DNA–Protein π–Interactions: A Comparison of Natural Occurrences and Structures, and Computationally Predicted Structures and Strengths. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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21
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Wilson KA, Kellie JL, Wetmore SD. DNA-protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar. Nucleic Acids Res 2014; 42:6726-41. [PMID: 24744240 PMCID: PMC4041443 DOI: 10.1093/nar/gku269] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π-π stacking, π-π T-shaped or sugar-π contacts. Three hundred forty-four nucleobase-amino acid π-π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA-protein sugar-π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C-H···π and/or lone-pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π-π and sugar-π interactions display a range of relative monomer orientations and therefore interaction energies (up to -50 (-70) kJ mol(-1) for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA-protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.
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Affiliation(s)
- Katie A Wilson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, AB, T1K 3M4, Canada
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22
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Lucas R, Peñalver P, Gómez-Pinto I, Vengut-Climent E, Mtashobya L, Cousin J, Maldonado OS, Perez V, Reynes V, Aviñó A, Eritja R, González C, Linclau B, Morales JC. Effects of sugar functional groups, hydrophobicity, and fluorination on carbohydrate-DNA stacking interactions in water. J Org Chem 2014; 79:2419-29. [PMID: 24552250 DOI: 10.1021/jo402700y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Carbohydrate-aromatic interactions are highly relevant for many biological processes. Nevertheless, experimental data in aqueous solution relating structure and energetics for sugar-arene stacking interactions are very scarce. Here, we evaluate how structural variations in a monosaccharide including carboxyl, N-acetyl, fluorine, and methyl groups affect stacking interactions with aromatic DNA bases. We find small differences on stacking interaction among the natural carbohydrates examined. The presence of fluorine atoms within the pyranose ring slightly increases the interaction with the C-G DNA base pair. Carbohydrate hydrophobicity is the most determinant factor. However, gradual increase in hydrophobicity of the carbohydrate does not translate directly into a steady growth in stacking interaction. The energetics correlates better with the amount of apolar surface buried upon sugar stacking on top of the aromatic DNA base pair.
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Affiliation(s)
- Ricardo Lucas
- Department of Bioorganic Chemistry, Instituto de Investigaciones Químicas, CSIC-Universidad de Sevilla , 49 Américo Vespucio, 41092, Sevilla, Spain
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23
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Moreira da Costa L, Stoyanov SR, Gusarov S, Seidl PR, Walkimar de M. Carneiro J, Kovalenko A. Computational Study of the Effect of Dispersion Interactions on the Thermochemistry of Aggregation of Fused Polycyclic Aromatic Hydrocarbons as Model Asphaltene Compounds in Solution. J Phys Chem A 2014; 118:896-908. [DOI: 10.1021/jp408005h] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Leonardo Moreira da Costa
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Organic Processes, School of Chemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
- Institute
of Chemistry, Universidade Federal Fluminense, Niteroi, RJ 24220-900, Brazil
- Centro Universitário da Zona Oeste, Avenida Manuel Caldeira de Alvarenga 1203, Campo Grande, RJ 23070-200, Brazil
| | - Stanislav R. Stoyanov
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 2V4, Canada
| | - Sergey Gusarov
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
| | - Peter R. Seidl
- Department
of Organic Processes, School of Chemistry, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-901, Brazil
| | | | - Andriy Kovalenko
- National
Institute for Nanotechnology, National Research Council of Canada, 11421
Saskatchewan Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2G8, Canada
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25
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Asensio JL, Ardá A, Cañada FJ, Jiménez-Barbero J. Carbohydrate-aromatic interactions. Acc Chem Res 2013; 46:946-54. [PMID: 22704792 DOI: 10.1021/ar300024d] [Citation(s) in RCA: 359] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recognition of saccharides by proteins has far reaching implications in biology, technology, and drug design. Within the past two decades, researchers have directed considerable effort toward a detailed understanding of these processes. Early crystallographic studies revealed, not surprisingly, that hydrogen-bonding interactions are usually involved in carbohydrate recognition. But less expectedly, researchers observed that despite the highly hydrophilic character of most sugars, aromatic rings of the receptor often play an important role in carbohydrate recognition. With further research, scientists now accept that noncovalent interactions mediated by aromatic rings are pivotal to sugar binding. For example, aromatic residues often stack against the faces of sugar pyranose rings in complexes between proteins and carbohydrates. Such contacts typically involve two or three CH groups of the pyranoses and the π electron density of the aromatic ring (called CH/π bonds), and these interactions can exhibit a variety of geometries, with either parallel or nonparallel arrangements of the aromatic and sugar units. In this Account, we provide an overview of the structural and thermodynamic features of protein-carbohydrate interactions, theoretical and experimental efforts to understand stacking in these complexes, and the implications of this understanding for chemical biology. The interaction energy between different aromatic rings and simple monosaccharides based on quantum mechanical calculations in the gas phase ranges from 3 to 6 kcal/mol range. Experimental values measured in water are somewhat smaller, approximately 1.5 kcal/mol for each interaction between a monosaccharide and an aromatic ring. This difference illustrates the dependence of these intermolecular interactions on their context and shows that this stacking can be modulated by entropic and solvent effects. Despite their relatively modest influence on the stability of carbohydrate/protein complexes, the aromatic platforms play a major role in determining the specificity of the molecular recognition process. The recognition of carbohydrate/aromatic interactions has prompted further analysis of the properties that influence them. Using a variety of experimental and theoretical methods, researchers have worked to quantify carbohydrate/aromatic stacking and identify the features that stabilize these complexes. Researchers have used site-directed mutagenesis, organic synthesis, or both to incorporate modifications in the receptor or ligand and then quantitatively analyzed the structural and thermodynamic features of these interactions. Researchers have also synthesized and characterized artificial receptors and simple model systems, employing a reductionistic chemistry-based strategy. Finally, using quantum mechanics calculations, researchers have examined the magnitude of each property's contribution to the interaction energy.
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Affiliation(s)
- Juan Luis Asensio
- Chemical & Physical Biology, Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid
| | - Ana Ardá
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Jesús Jiménez-Barbero
- Instituto de Química Orgánica General, CSIC, Juan de la Cierva 3, 28006 Madrid, Spain
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26
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Bloom JWG, Raju RK, Wheeler SE. Physical Nature of Substituent Effects in XH/π Interactions. J Chem Theory Comput 2012; 8:3167-74. [DOI: 10.1021/ct300520n] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacob W. G. Bloom
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Rajesh K. Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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