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Xu Z, Cao Q, Manyande A, Xiong S, Du H. Analysis of the binding selectivity and inhibiting mechanism of chlorogenic acid isomers and their interaction with grass carp endogenous lipase using multi-spectroscopic, inhibition kinetics and modeling methods. Food Chem 2022; 382:132106. [PMID: 35240531 DOI: 10.1016/j.foodchem.2022.132106] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 12/10/2021] [Accepted: 01/05/2022] [Indexed: 11/19/2022]
Abstract
Polyphenols are inhibitors for lipase, but the binding selectivity and mechanism of polyphenol isomers and how they interact with lipase are not clear. Here, chlorogenic acid (CGA) isomers, neochlorogenic acid (NCGA) and cryptochlorogenic acid (CCGA) were used to explore the binding selectivity and mechanism of lipase. An inhibition assay indicated that both CGA isomers had dose-dependent inhibitory effects on lipase; however, the inhibitory effect of NCGA was better (IC50: 0.647 mg/mL) than that of CCGA (IC50: 0.677 mg/mL). NCGA and CCGA formed complexes with lipase at a molar ratio of 1:1, and the electrostatic interaction force plays a major role in the lipase-CCGA system. Molecular dynamics studies demonstrated that NCGA had a greater impact on the structure of lipase. The multi-spectroscopic and modeling results explained the effects of micro-structural changes on the binding site, the interaction force and the inhibition rate of the isomers when they combined with lipase.
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Affiliation(s)
- Zeru Xu
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China; National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, Hubei 430070, PR China
| | - Qiongju Cao
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China; National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, Hubei 430070, PR China
| | - Anne Manyande
- School of Human and Social Sciences, University of West London, Middlesex TW8 9GA, UK
| | - Shanbai Xiong
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China; National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, Hubei 430070, PR China
| | - Hongying Du
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, PR China; National R & D Branch Center for Conventional Freshwater Fish Processing, Wuhan, Hubei 430070, PR China.
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2
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Cao Q, Huang Y, Zhu QF, Song M, Xiong S, Manyande A, Du H. The mechanism of chlorogenic acid inhibits lipid oxidation: An investigation using multi-spectroscopic methods and molecular docking. Food Chem 2020; 333:127528. [DOI: 10.1016/j.foodchem.2020.127528] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 06/06/2020] [Accepted: 07/05/2020] [Indexed: 02/06/2023]
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3
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Mondal P. In silico decryption of serotonin-receptor binding: local non-covalent interactions and long-range conformational changes. RSC Adv 2020; 10:37995-38003. [PMID: 35515142 PMCID: PMC9057181 DOI: 10.1039/d0ra05559j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 03/08/2021] [Accepted: 09/15/2020] [Indexed: 01/10/2023] Open
Abstract
Serotonin-receptor binding is the key step in the process behind serotonin functionality, including several psychological and physiological behaviours. This study is focused on identifying the main non-covalent interactions controlling the stability of serotonin-receptor complexes as well as the main conformational changes in the receptor due to serotonin-receptor binding using classical molecular dynamics simulations and quantum chemical calculations. A qualitative analysis based on two order parameters ((i) the centre of mass distance and (ii) the angle between the surface normals of each aromatic residue and serotonin in the binding site) on the serotonin-receptor complex trajectory suggests that the T-type stacking interaction is predominant in the binding site. Quantum chemical calculations of the stacking interaction energy provide the quantitative contributions of important aromatic residues to the stabilization of the complex. Furthermore, a three body stacking interaction (named 'L'-type) was observed and likely contributes to the stability of the complex. Direct and water-mediated hydrogen bonding between the residues in the binding site and serotonin contributes to the complex stability. Principal component analysis of the molecular dynamics simulation trajectory of the serotonin-receptor complex and the apo-receptor in water indicates that the whole receptor is significantly stabilized due to serotonin binding. An analysis based on the dynamic cross correlation function reflects the strong correlation between trans-membrane (TM)3, TM5, TM6 (containing residues responsible for the stacking interaction and hydrogen bonding) and mini-G0 which may participate in signal transduction leading to the functionality of serotonin.
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Affiliation(s)
- Padmabati Mondal
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences and Technologies, Indian Institute of Science Education and Research (IISER) Tirupati Tirupati 517507 Andhra Pradesh India +91 877 2500 926
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4
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Evaluating role of the x–π (x = π and/or CH) stacking interactions in adsorption of the (4E,4E)-4-(4-hydroxyphenyldiazenyl)-N-((furan-2-Yl)methylene)benzenamine antibacterial in armchair boron nitride nanotube. CHEMICAL PAPERS 2020. [DOI: 10.1007/s11696-020-01137-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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5
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Pascual-Colino J, Beobide G, Castillo O, Lodewyckx P, Luque A, Pérez-Yáñez S, Román P, Velasco LF. Adenine nucleobase directed supramolecular architectures based on ferrimagnetic heptanuclear copper(II) entities and benzenecarboxylate anions. J Inorg Biochem 2019; 202:110865. [PMID: 31669692 DOI: 10.1016/j.jinorgbio.2019.110865] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/27/2019] [Accepted: 09/15/2019] [Indexed: 11/17/2022]
Abstract
Two planar organic anions, benzoate and benzene-1,4-dicarboxylate (terephthalate), have been selected as potential π-stacking intercalators among ferrimagnetic [Cu7(μ-adeninato)6(μ3-OH)6(μ-H2O)6]2+ heptameric discrete entities. The resulting supramolecular architecture is highly dependent on the negative charge density distribution, mainly located in the carboxylate groups of the organic anions. In this sense, the benzoate anion, with just one carboxylate group, does not allow its intercalation between the adeninato ligands as it would imply a high steric hindrance among the heptameric entities. As a consequence, these benzoate anions are located inside the voids of the crystal structure reducing the accessible volume of compound [Cu7(μ-adeninato)6(μ3-OH)6(μ-H2O)6](benzoate)2·~17H2O (1). On the contrary, the terephthalate anion, containing two carboxylate groups at opposite sites, adopts a π-stacking sandwich arrangement between two adeninato ligands that affords the porous open structure of formula [Cu7(μ-adeninato)6(μ3-OH)6(μ-H2O)6](terephthalate)·nH2O (2a, 2b; n: 12 and 24, respectively). In addition to that, the less directional nature of the π-stacking interactions in comparison to the complementary hydrogen bonding based supramolecular metal-organic frameworks (SMOFs), suits them with a flexible architecture able to reversibly adsorb/desorb water (up to a 25-30% at 20 °C) altogether with the expansion/shrinkage of the crystal structure. The bridging adeninato and hydroxido ligands are effective magnetic exchange mediators to provide a ST = 5/2 ferrimagnetic state for the heptanuclear entity.
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Affiliation(s)
- Jon Pascual-Colino
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, UPV/EHU, Apartado 644, 48080 Bilbao, Spain
| | - Garikoitz Beobide
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, UPV/EHU, Apartado 644, 48080 Bilbao, Spain
| | - Oscar Castillo
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, UPV/EHU, Apartado 644, 48080 Bilbao, Spain.
| | - Peter Lodewyckx
- Departament of Chemistry, Royal Military Academy, Renaissancelaan 30, 1000 Brussels, Belgium
| | - Antonio Luque
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, UPV/EHU, Apartado 644, 48080 Bilbao, Spain
| | - Sonia Pérez-Yáñez
- Departamento de Química Inorgánica, Facultad de Farmacia, Universidad del País Vasco, UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Pascual Román
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, UPV/EHU, Apartado 644, 48080 Bilbao, Spain
| | - Leticia F Velasco
- Departament of Chemistry, Royal Military Academy, Renaissancelaan 30, 1000 Brussels, Belgium
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6
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DL-3-Aminoisobutyric acid: vibrational, NBO and AIM analysis of N-H⋯O bonded-zwitterionic dimer model. Heliyon 2019; 5:e01933. [PMID: 31286081 PMCID: PMC6587070 DOI: 10.1016/j.heliyon.2019.e01933] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/03/2019] [Accepted: 06/06/2019] [Indexed: 01/18/2023] Open
Abstract
A zwitterionic dimer model constructed of inter-molecular -N-H⋯O bonding has been proposed for the solid sample of DL-3-Aminoisobutyric acid consistent with IR absorption and Raman spectral features measured in the 3500-400/50 cm-1. This zwitterionic dimer model in water as solvent has been computed at B3LYP/6-311++G(d,p) and B3LYP-D3/6-311++G(d,p) levels including Grimme's dispersion correction associated with the -N-H⋯O interaction and SCRF-SMD method. Of the several possible monomer and dimer conformational structures, the most stable dimer constructed of two zwitterion monomer units has produced vibrational modes due to the -NH3 + cation and -CO2‾ anion involved in the -N-H⋯O bonding in fair agreement with the observed broad but composite IR modal features near the 3500-2000 cm-1. Except for the frequency of asymmetric stretching mode of the -NH3 + cation, its symmetric and bending modes agree with the observed values. As for the -CO2‾ anion, the frequencies of all of its modes are in good agreement with the experiment. Natural bond orbital (NBO), molecular electrostatic potential (MEP), atoms-in-molecules (AIM) and non-covalent interaction (NCI) analyses have been used to understand electronic characterization of the -N-H⋯O bonding.
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7
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Zhu M, Wang L, Wang Y, Zhou J, Ding J, Li W, Xin Y, Fan S, Wang Z, Wang Y. Biointeractions of Herbicide Atrazine with Human Serum Albumin: UV-Vis, Fluorescence and Circular Dichroism Approaches. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15010116. [PMID: 29324720 PMCID: PMC5800215 DOI: 10.3390/ijerph15010116] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 12/17/2022]
Abstract
The herbicide atrazine is widely used across the globe, which is a great concern. To investigate its potential toxicity in the human body, human serum albumin (HSA) was selected as a model protein. The interaction between atrazine and HSA was investigated using steady-state fluorescence spectroscopy, synchronous fluorescence spectroscopy, UV-Vis spectroscopy, three-dimensional (3D) fluorescence spectroscopy and circular dichroism (CD) spectroscopy. The intrinsic fluorescence of HSA was quenched by the atrazine through a static quenching mechanism. Fluorescence spectra at two excitation wavelengths (280 and 295 nm) showed that the fluorescence quenched in HSA was mainly contributed to by tryptophan residues. In addition, the atrazine bound to HSA, which induced changes in the conformation and secondary structure of HSA and caused an energy transfer. Thermodynamic parameters revealed that this binding is spontaneous. Moreover, electrostatic interactions play a major role in the combination of atrazine and HSA. One atrazine molecule can only bind to one HSA molecule to form a complex, and the atrazine molecule is bound at site II (subdomain IIIA) of HSA. This study furthers the understanding of the potential effects posed by atrazine on humans at the molecular level.
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Affiliation(s)
- Meiqing Zhu
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Lijun Wang
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Yu Wang
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Jie Zhou
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Jie Ding
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Wei Li
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Yue Xin
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Shisuo Fan
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Zhen Wang
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
| | - Yi Wang
- Key Laboratory of Agri-Food Safety of Anhui Province, School of Resources and Environment, Anhui Agricultural University, Hefei 230036, China.
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8
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Gholipour A, Farhadi S, Neyband RS. Theoretical investigation of the nature and strength of simultaneous interactions of π–π stacking and halogen bond including NMR, SAPT, AIM and NBO analysis. Struct Chem 2016. [DOI: 10.1007/s11224-016-0784-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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The influence of substituents on cooperativity between CH···π and N···H hydrogen bonds in a T-shaped configuration: X-benzene⊥(FH···pyrazine···HF) complexes as a working model. Struct Chem 2016. [DOI: 10.1007/s11224-016-0777-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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Nakarada Đ, Etinski M, Petković M. Using Density Functional Theory To Study Neutral and Ionized Stacked Thymine Dimers. J Phys Chem A 2016; 120:7704-7713. [PMID: 27626138 DOI: 10.1021/acs.jpca.6b06493] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stacking interactions in thymine dimers are studied with density functional theory. According to our calculations, six dimers of comparable stability can be prepared at low temperature, but dimerization is impossible at room temperature due to the large entropy contribution that accompanies it. Analysis of vibrational anharmonic coupling terms shows that each of the dimers exhibits distinct vibrational dynamics. Properties of electron density in the intermolecular region are used to analyze neutral stacked species and their ionized forms. Bond paths and critical points in the intermolecular region are identified, but a simple relationship between binding energy and total electron density in the intermolecular critical points could not be found due to an uneven electron distribution in the binding region. The reduced density gradient was confirmed to be a useful tool for analysis of weak stacking interactions. Those interactions also affect vertical and adiabatic ionization energies, which are computed to be slightly lower for the dimers compared to the monomer.
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Affiliation(s)
- Đura Nakarada
- Faculty of Physical Chemistry, University of Belgrade , Studentski trg 12-16, 11 158 Belgrade, Serbia
| | - Mihajlo Etinski
- Faculty of Physical Chemistry, University of Belgrade , Studentski trg 12-16, 11 158 Belgrade, Serbia
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade , Studentski trg 12-16, 11 158 Belgrade, Serbia
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11
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Marchione D, McCoustra MRS. Non-covalent interaction of benzene with methanol and diethyl ether solid surfaces. Phys Chem Chem Phys 2016; 18:20790-801. [DOI: 10.1039/c6cp01787h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We have investigated the interactions involved at the interface of binary, layered ices (benzene on methanol and on diethyl ether) by means of laboratory experiments and ab initio calculations on model clusters.
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12
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Delarami HS, Ebrahimi A. Theoretical investigation of the backbone···π and π···π stacking interactions in substituted-benzene||3-methyl-2′-deoxyadenosine: a perspective to the DNA repair. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1118569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hojat Samareh Delarami
- Computational Quantum Chemistry Laboratory, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ali Ebrahimi
- Computational Quantum Chemistry Laboratory, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
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13
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McDermott SM, Guo X, Carnes J, Stuart K. Differential Editosome Protein Function between Life Cycle Stages of Trypanosoma brucei. J Biol Chem 2015; 290:24914-31. [PMID: 26304125 DOI: 10.1074/jbc.m115.669432] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 11/06/2022] Open
Abstract
Uridine insertion and deletion RNA editing generates functional mitochondrial mRNAs in Trypanosoma brucei. The mRNAs are differentially edited in bloodstream form (BF) and procyclic form (PF) life cycle stages, and this correlates with the differential utilization of glycolysis and oxidative phosphorylation between the stages. The mechanism that controls this differential editing is unknown. Editing is catalyzed by multiprotein ∼20S editosomes that contain endonuclease, 3'-terminal uridylyltransferase, exonuclease, and ligase activities. These editosomes also contain KREPB5 and KREPA3 proteins, which have no functional catalytic motifs, but they are essential for parasite viability, editing, and editosome integrity in BF cells. We show here that repression of KREPB5 or KREPA3 is also lethal in PF, but the effects on editosome structure differ from those in BF. In addition, we found that point mutations in KREPB5 or KREPA3 differentially affect cell growth, editosome integrity, and RNA editing between BF and PF stages. These results indicate that the functions of KREPB5 and KREPA3 editosome proteins are adjusted between the life cycle stages. This implies that these proteins are involved in the processes that control differential editing and that the 20S editosomes differ between the life cycle stages.
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Affiliation(s)
- Suzanne M McDermott
- From the Center for Infectious Disease Research, formerly known as Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Xuemin Guo
- From the Center for Infectious Disease Research, formerly known as Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Jason Carnes
- From the Center for Infectious Disease Research, formerly known as Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Kenneth Stuart
- From the Center for Infectious Disease Research, formerly known as Seattle Biomedical Research Institute, Seattle, Washington 98109
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14
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Cysewski P, Oliński R. Structural, electronic and energetic consequences of epigenetic cytosine modifications. Phys Chem Chem Phys 2015; 17:19616-24. [PMID: 26151626 DOI: 10.1039/c5cp02188j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen bonding patterns of cytosine and its seven C5-modifed analogues paired with canonical guanine were studied using the first principle approach. Both global minima and biologically relevant conformations were studied. The former resulted from full gradient geometry optimizations of hydrogen bonded pairs, while the latter were obtained based on 125 d(GpC) dinucleotides found in the PDB database. The obtained energetic, electronic and structural data lead to the conclusion that the epigenetically relevant modification of cytosine may have serious consequences on hydrogen bonding with guanine. First of all, the significant substituent effects were observed for such trends as charges on sites involved in hydrogen bonding, the total intermolecular interaction energy or electron densities at bond critical points. Moreover, the molecular orbital polarization contribution resulting from energy decomposition expressed in terms of absolutely localized molecular orbitals exhibited an inverse linear correlation with frozen density contributions. A substituent effect on the amount of charge transfer from pyrimidine toward guanine was also observed. The increase of intermolecular interactions of guanine with modified cytosine is associated with the increase of the electro-donating character of the C5-substituent. However, only pairs involving 5-methylcytosine are more stable than those formed by canonical cytosine. Furthermore, the energy differences observed for global minima also remain important for a broad range of displacement and angular parameters defining pair conformations in model d(GpC) dinucleotides. Due to the sensitivities of intermolecular interactions to mutual arrangements of monomers the modification of cytosine at the C5 site can significantly alter the actual energy profiles. Consequently, it may be anticipated that the modified dinucleotides will adopt different conformations than a standard G-C pair in a B-DNA double helix.
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Affiliation(s)
- P Cysewski
- Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Physical Chemistry Department, Kurpińskiego 5, Bydgoszcz, Poland.
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15
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Momeni Z, Ebrahimi A. Investigation of the effect of π–π stacking interaction on the properties of –CONH2 functional group of benzamide. Struct Chem 2015. [DOI: 10.1007/s11224-015-0615-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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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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17
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Masoodi HR, Zakarianezhad M, Bagheri S, Makiabadi B, Shool M. Substituent effects on some calculated NMR data in T-shaped configuration of benzene dimer. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Cuesta IG, Sánchez de Merás AMJ. Energy interactions in amyloid-like fibrils from NNQQNY. Phys Chem Chem Phys 2014; 16:4369-77. [PMID: 24458317 DOI: 10.1039/c3cp53551g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We use large-scale MP2 calculations to analyze the interactions appearing in amyloid fibers, which are difficult to determine experimentally. To this end, dimers and trimers of the hexapeptide NNQQNY from the yeast prion-like protein Sup35 were considered as model systems. We studied the energy interactions present in the three levels of organization in which the formation of amyloid fibrils is structured. The structural changes in the hydrogen bonds were studied too. It was found that the most energetic process is the formation of the β-sheet, which is equally due to both hydrogen bonds and van der Waals interactions. The aromatic rings help stabilize these aggregates through stacking of the aromatic rings of tyrosine, the stability produced by the aromatics residues increasing with their aromaticity. The formation of the basic unit of the assembled proto-fiber, the steric zipper, is less energetic and is associated to both dispersion forces and hydrogen bonds. The interactions between pair of β-sheets across the peptide-to-peptide contact through the tyrosine rings are cooperative and due to dispersion effects. Moreover, the strength of this interaction can rationalize the variation of mobility of the aromatic ring in the tyrosine units found in solid NMR experiments.
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Affiliation(s)
- Inmaculada García Cuesta
- Instituto de Ciencia Molecular, Universidad de Valencia, P.O. Box 22085, E-46071 Valencia, Spain.
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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: 110] [Impact Index Per Article: 10.0] [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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21
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Hęclik K, Dębska B, Dobrowolski JC. On the non-additivity of the substituent effect in ortho-, meta- and para-homo-disubstituted benzenes. RSC Adv 2014. [DOI: 10.1039/c4ra02294g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The non-additivity of the substituent effect in para-, meta-, and ortho- homo-disubstituted benzenes on π-valence orbitals is smaller than that on σ-ones. The former increases while the latter decreases with π-electron-donating character of the substituent which demonstrates the role of hyperconjugation in the substituent effect.
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Affiliation(s)
- K. Hęclik
- Rzeszow University of Technology
- 35-959 Rzeszow, Poland
- National Medicines Institute
- 00-723 Warsaw, Poland
| | - B. Dębska
- Rzeszow University of Technology
- 35-959 Rzeszow, Poland
| | - J. Cz. Dobrowolski
- National Medicines Institute
- 00-723 Warsaw, Poland
- Institute of Chemistry and Nuclear Technology
- 03-195 Warsaw, Poland
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22
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Copeland KL, Pellock SJ, Cox JR, Cafiero ML, Tschumper GS. Examination of tyrosine/adenine stacking interactions in protein complexes. J Phys Chem B 2013; 117:14001-8. [PMID: 24171662 DOI: 10.1021/jp408027j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The π-stacking interactions between tyrosine amino acid side chains and adenine-bearing ligands are examined. Crystalline protein structures from the protein data bank (PDB) exhibiting face-to-face tyrosine/adenine arrangements were used to construct 20 unique 4-methylphenol/N9-methyladenine (p-cresol/9MeA) model systems. Full geometry optimization of the 20 crystal structures with the M06-2X density functional theory method identified 11 unique low-energy conformations. CCSD(T) complete basis set (CBS) limit interaction energies were estimated for all of the structures to determine the magnitude of the interaction between the two ring systems. CCSD(T) computations with double-ζ basis sets (e.g., 6-31G*(0.25) and aug-cc-pVDZ) indicate that the MP2 method overbinds by as much as 3.07 kcal mol(-1) for the crystal structures and 3.90 kcal mol(-1) for the optimized structures. In the 20 crystal structures, the estimated CCSD(T) CBS limit interaction energy ranges from -4.00 to -6.83 kcal mol(-1), with an average interaction energy of -5.47 kcal mol(-1), values remarkably similar to the corresponding data for phenylalanine/adenine stacking interactions. Geometry optimization significantly increases the interaction energies of the p-cresol/9MeA model systems. The average estimated CCSD(T) CBS limit interaction energy of the 11 optimized structures is 3.23 kcal mol(-1) larger than that for the 20 crystal structures.
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Affiliation(s)
- Kari L Copeland
- Department of Chemistry and Biochemistry, University of Mississippi , University, Mississippi 38677, United States
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23
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Ebrahimi A, Karimi P, Akher FB, Behazin R, Mostafavi N. Investigation of the π–π stacking interactions without direct electrostatic effects of substituents: the aromatic∥aromatic and aromatic∥anti-aromatic complexes. Mol Phys 2013. [DOI: 10.1080/00268976.2013.830784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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24
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Wells RA, Kellie JL, Wetmore SD. Significant strength of charged DNA-protein π-π interactions: a preliminary study of cytosine. J Phys Chem B 2013; 117:10462-74. [PMID: 23991905 DOI: 10.1021/jp406829d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The present work characterized the preferred gas-phase structure and optimum interaction energy of both parallel stacked and perpendicular T-shaped dimers between cytosine (C), as a representative nucleobase, and aspartic/glutamic acid (DE), aspartate/glutamate (DE(-)) or arginine (R(+)), using detailed M06-2X/6-31+G(d,p) potential energy surface scans as a function of the relative monomer orientation. Through comparison to previous literature on the π-π interactions between the DNA nucleobases and the aromatic amino acid residues, this work will allow for comparisons between DNA-protein interactions involving aromatic and acyclic R-side chains, as well as comparisons of the relative geometric dependence and magnitude of π-π (C:DE), πcation-π (C:R(+)), and πanion-π (C:DE(-)) interactions. Our results show that the preferred relative monomer orientation is highly dependent on the monomer composition and charge, and is dictated by electrostatic-driven interactions. More importantly, for the first time, we report that the π-π interactions between cytosine and (neutral) aspartic/glutamic acid are up to approximately -40 kJ mol(-1), while the πcation-π or πanion-π interactions between cytosine and arginine or aspartate/glutamate are up to approximately -90 and -99 kJ mol(-1), respectively. An extensive investigation of the effects of the computational methodology implemented, including comparisons to detailed CCSD(T)/CBS potential energy surfaces and interaction energies, supports the use of M06-2X, as well as ωB97X-D, to study DNA-protein π-π interactions of varying composition and charge. Most importantly, the CCSD(T)/CBS results verify the strong nature of these DNA-protein π-π interactions, as well as the unique nature of the πcation-π and πanion-π counterparts. Therefore, our results emphasize that a wide variety of different types of noncovalent interactions between both cyclic and acyclic π-containing components can significantly contribute to the stability of DNA-protein complexes and likely play a larger role in biology than currently accepted.
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Affiliation(s)
- Rachael A Wells
- Department of Chemistry and Biochemistry, University of Lethbridge , 4401 University Drive West, Lethbridge, Alberta, Canada T1K 3M4
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25
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Gholipour AR, Saydi H, Neiband MS, Neyband RS. Simultaneous interactions of pyridine with substituted benzene ring and H–F in X-ben⊥pyr···H–F complexes: a cooperative study. Struct Chem 2011. [DOI: 10.1007/s11224-011-9882-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Leavens FMV, Churchill CDM, Wang S, Wetmore SD. Evaluating how discrete water molecules affect protein-DNA π-π and π(+)-π stacking and T-shaped interactions: the case of histidine-adenine dimers. J Phys Chem B 2011; 115:10990-1003. [PMID: 21809837 DOI: 10.1021/jp205424z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Changes in the magnitude of (M06-2X/6-31+G(d,p)) π-π stacking and T-shaped (nucleobase-edge and amino acid-edge) interactions between (neutral or protonated) histidine (His) and adenine (A) dimers upon microsolvation with up to four discrete water molecules were determined. A variety of histidine-water interactions were considered including conventional (N-H···O, N···H-O, C-H···O) hydrogen bonding and nonconventional (X-H···π (neutral His) or lone-pair···π (protonated His)) contacts. Overall, the effects of discrete His-H(2)O interactions on the neutral histidine-adenine π-π contacts are negligible (<3 kJ mol(-1) or 15%) regardless of the type of water binding, the number of water molecules bound, or the His-A dimer (stacked or (amino acid- or nucleobase-edge) T-shaped) configuration. This suggests that previously reported gas-phase binding strengths for a variety of neutral amino acid-nucleobase dimers are likely relevant for a wide variety of (microsolvated) environments. In contrast, the presence of water decreases the histidine-adenine π(+)-π interaction by up to 15 kJ mol(-1) (or 30%) for all water binding modes and orientations, as well as different stacked and T-shaped His(+)-A dimers. Regardless of the larger effect of discrete histidine-water interactions on the magnitude of the π(+)-π compared with π-π interactions, the π(+)-π binding strengths remain substantially larger than the corresponding π-π contacts. These findings emphasize the distinct nature of π(+)-π and π-π interactions and suggest that π(+)-π contacts can provide significant stabilization in biological systems relative to π-π contacts under many different environmental conditions.
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Affiliation(s)
- Fern M V Leavens
- Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4
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27
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Kruszynski R. A structural and theoretical study of the intermolecular interactions in 8-hydroxyquinolinium-7-carboxylate monohydrate. Acta Crystallogr C 2011; 67:o230-4. [DOI: 10.1107/s0108270111021585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 06/04/2011] [Indexed: 11/10/2022] Open
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28
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Rutledge LR, Navarro-Whyte L, Peterson TL, Wetmore SD. Effects of Extending the Computational Model on DNA–Protein T-shaped Interactions: The Case of Adenine–Histidine Dimers. J Phys Chem A 2011; 115:12646-58. [DOI: 10.1021/jp203248j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Lex Navarro-Whyte
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Terri L. Peterson
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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29
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Churchill CDM, Rutledge LR, Wetmore SD. Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components. Phys Chem Chem Phys 2010; 12:14515-26. [PMID: 20927465 DOI: 10.1039/c0cp00550a] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and the aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) monomers containing the biological backbone (either the protein backbone or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that the protein backbone strengthens, while the deoxyribose sugar either strengthens or weakens, the interaction calculated using truncated models, the reasons for these effects were unknown. The present work explains these observations by dissecting the interaction energy of the extended complexes into individual backbone···π and π···π components. Our calculations reveal that the total interaction energy of the extended complex can be predicted as a sum of the backbone···π and π···π components, which indicates that the biological backbone does not significantly affect the ring system through π-polarization. Instead, we find that the backbone can indirectly affect the magnitude of the π···π contribution by changing the relative ring orientations in extended dimers compared with truncated dimers. Furthermore, the strengths of the individual backbone···π contributions are determined to be significant (up to 18 kJ mol(-1)). Therefore, the origin of the energetic change upon model extension is found to result from a balance between an additional (attractive) backbone···π component and differences in the strength of the π···π interaction. In addition, to understand the effects of the biological backbone on the stacking interactions at DNA-protein interfaces in nature, we analyzed the stacking interactions found in select DNA-protein crystal structures, and verified that an additive approach can be used to examine the strength of these interactions in biological complexes. Interestingly, although the presence of attractive backbone···π contacts is qualitatively confirmed using the quantum theory of atoms in molecules (QTAIM), QTAIM electron density analysis is unable to quantitatively predict the additive relationship of these interactions. Most importantly, this work reveals that both the backbone···π and π···π components must be carefully considered to accurately determine the overall stability of DNA-protein assemblies.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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30
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Rutledge LR, Churchill CDM, Wetmore SD. A preliminary investigation of the additivity of pi-pi or pi+-pi stacking and T-shaped interactions between natural or damaged DNA nucleobases and histidine. J Phys Chem B 2010; 114:3355-67. [PMID: 20151654 DOI: 10.1021/jp911990g] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Previous computational studies have examined pi-pi and pi(+)-pi stacking and T-shaped interactions in nucleobase-amino acid dimers, yet it is important to investigate how additional amino acids affect these interactions since simultaneous contacts often appear in nature. Therefore, this paper investigates the geometries and binding strengths of amino acid-nucleobase-amino acid trimers, which are compared to the corresponding nucleobase-amino acid dimer interactions. We concentrate on systems containing the natural nucleobase adenine or its (cationic) damaged counterpart, 3-methyladenine, and the aromatic amino acid histidine, in both the neutral and protonated forms. This choice of molecules provides information about pi-pi and pi(+)-pi stacking and T-shaped interactions in asymmetric, biologically relevant systems. We determined that both stacked and T-shaped interactions, as well as both pi-pi and pi(+)-pi interactions, exhibit geometric additivity. To investigate the energetic additivity in our trimers, the synergy (E(syn)) and the additivity (E(add)) energy were examined. E(add) reveals that it is important to consider the interaction between the two amino acids when examining the additivity of nucleobase-amino acid interactions. Additionally, E(syn) and E(add) indicate that pi(+)-pi interactions are quite different from pi-pi interactions. The magnitude of E(add) is generally less than 2 kJ mol(-1), which suggests that these interactions are additive. However, the interaction energy analysis does not provide information about the individual interactions in the trimers. Therefore, the quantum theory of atoms in molecules (QTAIM) was implemented. We find inconsistent conclusions from our QTAIM analysis and interaction energy evaluation. However, the magnitudes of the differences between the dimer and trimer critical point properties are extremely small and therefore may not be able to yield conclusive descriptions of differences (if any) between the dimer and trimer interactions. We hypothesize that, due to the limited number of investigations of this type, it is currently unclear how QTAIM can improve our understanding of pi-pi and pi(+)-pi dimers and trimers. Therefore, future work must systematically alter the pi-pi or pi(+)-pi system to definitively determine how the geometry, symmetry, and system size alter the QTAIM analysis, which can then be used to understand biologically relevant complexes.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta T1K 3M4, Canada
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31
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Churchill CDM, Navarro-Whyte L, Rutledge LR, Wetmore SD. Effects of the biological backbone on DNA-protein stacking interactions. Phys Chem Chem Phys 2009; 11:10657-70. [PMID: 20145810 DOI: 10.1039/b910747a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The pi-pi stacking (face-to-face) interactions between the five natural DNA or RNA nucleobases and the four aromatic amino acids were compared using three different types of dimers: (1) a truncated nucleoside (nucleobase) stacked with a truncated amino acid; (2) a truncated nucleoside (nucleobase) stacked with an extended amino acid; and (3) a nucleoside (extended nucleobase) stacked with a truncated amino acid. Systematic (MP2/6-31G*(0.25)) potential energy surface scans reveal important information about the effects of the deoxyribose sugar and protein backbone on the structure and binding energy between truncated nucleobase and amino acid models that are typically implemented in the literature. Most notably, electrostatic and steric interactions arising from the bulkiness of the biological backbones can change the preferred relative orientations of DNA and protein pi-systems. More importantly, the protein backbone can strengthen the stacking energy (by up to 10 kJ mol(-1)), while the deoxyribose moiety can strengthen or weaken the stacking interaction depending on the positioning of the amino acid relative to the sugar residue. These effects are likely due to additional interactions between the amino acid or nucleobase ring and the backbone in the extended monomer rather than significant changes in the properties of the biological pi-systems upon model extension. Since the present work reveals that all calculated DNA-protein stacking interactions are significant and approach the strength of other noncovalent interactions between biomolecules, both pi-pi and backbone-pi interactions must be considered when attempting to gain a complete picture of DNA-protein binding.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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32
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Ebrahimi A, Habibi-Khorassani M, Gholipour AR, Masoodi HR. Interaction between uracil nucleobase and phenylalanine amino acid: the role of sodium cation in stacking. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0588-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Rutledge LR, Durst HF, Wetmore SD. Evidence for Stabilization of DNA/RNA−Protein Complexes Arising from Nucleobase−Amino Acid Stacking and T-Shaped Interactions. J Chem Theory Comput 2009; 5:1400-10. [DOI: 10.1021/ct800567q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Holly F. Durst
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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Ebrahimi A, Habibi M, Sadat Neyband R, Reza Gholipour A. Cooperativity of π-stacking and hydrogen bonding interactions and substituent effects on X-ben‖pyr⋯H–F complexes. Phys Chem Chem Phys 2009; 11:11424-31. [DOI: 10.1039/b912419e] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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35
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Rutledge LR, Wetmore SD. Remarkably Strong T-Shaped Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking. J Chem Theory Comput 2008; 4:1768-80. [DOI: 10.1021/ct8002332] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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