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Zhang Y, Bux K, Attana F, Wei D, Haider S, Parkinson GN. Structural descriptions of ligand interactions to RNA quadruplexes folded from the non-coding region of pseudorabies virus. Biochimie 2024:S0300-9084(24)00139-1. [PMID: 38876382 DOI: 10.1016/j.biochi.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 05/02/2024] [Accepted: 06/12/2024] [Indexed: 06/16/2024]
Abstract
To rationalise the binding of specific ligands to RNA-quadruplex we investigated several naphthalene diimide ligands that interact with the non-coding region of Pseudorabies virus (PRV). Herein we report on the x-ray structure of the naphthalene diimide ND11 with an RNA G-quadruplex putative forming sequence from rPRV. Consistent with previously observed rPRV sequence it assembles into a bimolecular RNA G-quadruplex consisting of a pair of two tetrads stacked 3' to 5'. We observe that ND11 interacts by binding on both the externally available 5' and 3' quartets. The CUC (loop 1) is structurally altered to enhance the 5' mode of interaction. These loop residues are shifted significantly to generate a new ligand binding pocket whereas the terminal A14 residue is lifted away from the RNA G-quadruplex tetrad plane to be restacked above the bound ND11 ligand NDI core. CD analysis of this family of NDI ligands shows consistency in the spectra between the different ligands in the presence of the rPRV RNA G-quadruplex motif, reflecting a common folded topology and mode of ligand interaction. FRET melt assay confirms the strong stabilising properties of the tetrasubstituted NDI compounds and the contributions length of the substituted groups have on melt temperatures.
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Affiliation(s)
- Yashu Zhang
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK; Key Laboratory of Pesticide Toxicology and Application Technique, College of Plant Protection, Shandong Agricultural University, Taian, China; State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Khair Bux
- Faculty of Life Science, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, 75600, Pakistan
| | - Fedaa Attana
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
| | - Dengguo Wei
- National Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Shozeb Haider
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK
| | - Gary N Parkinson
- Department of Pharmaceutical and Biological Chemistry, University College London School of Pharmacy, London, WC1N 1AX, UK.
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Wang X, Sheng Y, Cui H, Qiao J, Song Y, Li X, Huang H. Corner Engineering: Tailoring Enzymes for Enhanced Resistance and Thermostability in Deep Eutectic Solvents. Angew Chem Int Ed Engl 2024; 63:e202315125. [PMID: 38010210 DOI: 10.1002/anie.202315125] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
Deep eutectic solvents (DESs), heralded for their synthesis simplicity, economic viability, and reduced volatility and flammability, have found increasing application in biocatalysis. However, challenges persist due to a frequent diminution in enzyme activity and stability. Herein, we developed a general protein engineering strategy, termed corner engineering, to acquire DES-resistant and thermostable enzymes via precise tailoring of the transition region in enzyme structure. Employing Bacillus subtilis lipase A (BSLA) as a model, we delineated the engineering process, yielding five multi-DESs resistant variants with highly improved thermostability, such as K88E/N89 K exhibited up to a 10.0-fold catalytic efficiency (kcat /KM ) increase in 30 % (v/v) choline chloride (ChCl): acetamide and 4.1-fold in 95 % (v/v) ChCl: ethylene glycol accompanying 6.7-fold thermal resistance improvement than wild type at ≈50 °C. The generality of the optimized approach was validated by two extra industrial enzymes, endo-β-1,4-glucanase PvCel5A (used for biofuel production) and esterase Bs2Est (used for plastics degradation). The molecular investigations revealed that increased water molecules at substrate binding cleft and finetuned helix formation at the corner region are two dominant determinants governing elevated resistance and thermostability. This study, coupling corner engineering with obtained molecular insights, illuminates enzyme-DES interaction patterns and fosters the rational design of more DES-resistant and thermostable enzymes in biocatalysis and biotransformation.
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Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Yijie Sheng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- RWTH Aachen University, Templergraben 55, 52062, Aachen, Germany
- Current address: Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL 61801, USA
| | - Jie Qiao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Yibo Song
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
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3
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Drici N. The influence of the hydrogen-bond network on the structure and dynamics of the RAPRKKG heptapeptide and its mutants. J Mol Graph Model 2023; 125:108598. [PMID: 37586130 DOI: 10.1016/j.jmgm.2023.108598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 08/02/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023]
Abstract
The structural behaviour of the RAPRKKG heptapeptide after individual or multiple mutations was inspected through molecular dynamics simulation. The nature of the mutations provided information on the flexibility of the heptapeptide and on how water molecules establish hydrogen bonds with it. The structural behaviour of the wild-type and the mutated structures were measured through the analysis of protein‒protein and protein‒solvent hydrogen bonds. The conformational behaviours of the different structures were analysed through free energy landscape analysis. The flexibility characteristics of the mutants seem to depend on the reorganization of water molecules and their static or dynamic behaviour around amino acid side chains.
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Affiliation(s)
- Nedjoua Drici
- University of Mostaganem, Abdelhamid Ibn Badis, Faculty of Exact Sciences and Informatics, Chemin des cretes ex INES, Mostaganem, 27000, Algeria; Laboratoire de Chimie Physique Macromoleculaire LCPM, University of Oran1 Ahmed benbella, Oran, 31000, Algeria.
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Yamamoto Y, Lu F, Nakanishi T, Hayashi S. Liquid Structures and Diffusion Dynamics of Alkyl-Pyrene Liquids Studied by Molecular Dynamics Simulations. J Phys Chem B 2023. [PMID: 37093669 DOI: 10.1021/acs.jpcb.2c08385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Functional molecular liquids (FMLs) based on alkylated π-conjugated molecules have attracted attention as solvent-free and nonvolatile liquid materials with prominent optoelectronic features. Recently, novel FML compounds containing pyrene as the functional core were synthesized, and their rheological and photochemical properties were investigated. Although the molecules differ only in the number of alkyl chain substituents and their substitution positions, their viscosity coefficients are largely different beyond the Stokes-Einstein relation on the assumption of identical microscopic friction, indicating that local microscopic molecular interactions are crucial for the macroscopic rheological properties. Here, we report a theoretical study on the rheological properties of the alkyl-pyrene liquids by means of atomistic molecular dynamics (MD) simulations. We performed long-time MD simulations for tens of microseconds to obtain ample statistical samples of the alkyl-pyrene liquids and analyzed their liquid structures and diffusion dynamics based on spatiotemporal correlation functions. We found the formation of characteristic local liquid structures of π-π stacking of the pyrene moieties and locally anisotropic and anomalous diffusion dynamics, which remarkably vary depending on the alkyl substituent patterns. The present results provide an atomistic insight into the macroscopic rheological properties of alkyl-π FMLs and molecular design strategy for them.
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Affiliation(s)
- Yuki Yamamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8052, Japan
| | - Fengniu Lu
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan
| | - Takashi Nakanishi
- International Center for Materials Nanoarchitectonics (WPI-MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba 305-0044, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake-Cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8052, Japan
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Yin Z, Chen H, Yang L, Peng C, Qin Y, Wang T, Sun W, Wang C. Investigations of CO 2 Capture from Gas Mixtures Using Porous Liquids. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1255-1266. [PMID: 33443439 DOI: 10.1021/acs.langmuir.0c03276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Porous liquids, a new porous material with fluidity, can be applied in numerous fields, such as gas storage and/or separation. In this work, the separation of binary gas mixtures CO2/N2 and CO2/CH4 with porous liquids was examined by molecular dynamics (MD) simulations. The pure gas adsorption capacity was analyzed with different concentrations of porous liquids. The dependence of the separation effect of a gas mixture on the total pressure and temperature was investigated. Meanwhile, for both CO2/N2 and CO2/CH4 systems, the adsorption and separation effects of porous liquids with a cage:solvent ratio of 1:12 are better than those of 1:91 and 1:170. The results of the spatial distribution function and/or trajectories indicated that porous liquids prefer CO2, leading to the location of CO2 in the channels formed in porous liquids. However, N2 and CH4 are hardly adsorbed into the bulk. The diffusion of gas molecules follows the order of CO2 > N2 (for CO2/N2) and CH4 > CO2 (for CO2/CH4) in the bulk and N2 > CO2 (for CO2/N2) and CH4 > CO2 (for CO2/CH4) at the interface of porous liquids. Upon increasing the concentrations of porous liquids, the working capacities of CO2 show small decreases in CO2/N2 and CO2/CH4 systems, but the sorbent selection parameters are higher in pressure- and temperature-swing adsorption processes. The porous liquid with a cage:solvent ratio of 1:12 is more suitable for the separation of CO2/N2 and CO2/CH4 systems than ratios of 1:91 and 1:170.
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Affiliation(s)
- Zhijian Yin
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Houyang Chen
- Department of Chemical and Biological Engineering, University at Buffalo, The State University of New York, Buffalo, New York 14260-4200, United States
| | - Li Yang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Changjun Peng
- School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuanhang Qin
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Tielin Wang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Wei Sun
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
| | - Cunwen Wang
- Key Laboratory of Green Chemical Process of Ministry of Education, Key Laboratory of Novel Reactor and Green Chemical Technology of Hubei Province, School of Chemical Engineering and Pharmacy, Wuhan Institute of Technology, Wuhan 430205, China
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6
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Leherte L, Haufroid M, Mirgaux M, Wouters J. Investigation of bound and unbound phosphoserine phosphatase conformations through elastic network models and molecular dynamics simulations. J Biomol Struct Dyn 2020; 39:3958-3974. [PMID: 32448044 DOI: 10.1080/07391102.2020.1772883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The human phosphoserine phosphatase (hPSP) catalyses the last step in the biosynthesis of L-serine. It involves conformational changes of the enzyme lid once the substrate, phosphoserine (PSer), is bound in the active site. Here, Elastic Network Model (ENM) is applied to the crystal structure of hPSP to probe the transition between open and closed conformations of hPSP. Molecular Dynamics (MD) simulations are carried out on several PSer-hPSP systems to characterise the intermolecular interactions and their effect on the dynamics of the enzyme lid. Systems involving either Ca++ or Mg++ are considered. The first ENM normal mode shows that an open-closed transition can be explained from a simple description of the enzyme in terms of harmonic potentials. Principal Component Analyses applied to the MD trajectories also highlight a trend for a closing/opening motion. Different PSer orientations inside the enzyme cavity are identified, i.e. either the carboxylate, the phosphate group of PSer, or both, are oriented towards the cation. The interaction patterns are analysed in terms of hydrogen bonds, electrostatics, and bond critical points of the electron density distributions. The latter approach yields a global description of the bonding intermolecular interactions. The PSer orientation determines the content of the cation coordination shell and the mobility of the substrate, while Lys158 and Thr182, involved in the reaction mechanism, are always in interaction with the substrate. Closed enzyme conformations involve Met52-Gln204, Arg49-Glu29, and Arg50-Glu29 interactions. Met52, as well as Arg49 and Arg50, also stabilize PSer inside the cavity. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Laurence Leherte
- Laboratoire de Chimie Biologique Structurale, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), NAmur MEdicine & Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Marie Haufroid
- Laboratoire de Chimie Biologique Structurale, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), NAmur MEdicine & Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Manon Mirgaux
- Laboratoire de Chimie Biologique Structurale, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), NAmur MEdicine & Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
| | - Johan Wouters
- Laboratoire de Chimie Biologique Structurale, Unité de Chimie Physique Théorique et Structurale, Department of Chemistry, NAmur Research Institute for LIfe Sciences (NARILIS), NAmur MEdicine & Drug Innovation Center (NAMEDIC), Namur Institute of Structured Matter (NISM), University of Namur, Namur, Belgium
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7
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Silanteva IA, Komolkin AV, Morozova EA, Vorontsov-Velyaminov PN, Kasyanenko NA. Role of Mono- and Divalent Ions in Peptide Glu-Asp-Arg-DNA Interaction. J Phys Chem B 2019; 123:1896-1902. [PMID: 30762356 DOI: 10.1021/acs.jpcb.8b10359] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of the regulatory biologically active peptide Glu-Asp-Arg (EDR) with DNA is considered by spectral, NMR, viscosimetry, and molecular dynamics methods. It was shown that EDR can partly penetrate into the major groove of DNA and affect the base atoms, mainly the N7 and O6 of guanine. It was observed that Mg2+ ions can promote DNA-EDR interaction due to their effective screening of the negatively charged phosphate groups of DNA. This action of Mg2+ remains in salted solution as well.
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Affiliation(s)
- Irina A Silanteva
- Faculty of Physics , Saint Petersburg State University , 7-9 Universitetskaya embankment , Saint Petersburg 199034 , Russia
| | - Andrei V Komolkin
- Faculty of Physics , Saint Petersburg State University , 7-9 Universitetskaya embankment , Saint Petersburg 199034 , Russia
| | - Ekaterina A Morozova
- Faculty of Physics , Saint Petersburg State University , 7-9 Universitetskaya embankment , Saint Petersburg 199034 , Russia
| | - Pavel N Vorontsov-Velyaminov
- Faculty of Physics , Saint Petersburg State University , 7-9 Universitetskaya embankment , Saint Petersburg 199034 , Russia
| | - Nina A Kasyanenko
- Faculty of Physics , Saint Petersburg State University , 7-9 Universitetskaya embankment , Saint Petersburg 199034 , Russia
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8
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Silanteva I, Komolkin AV. Representation of DNA environment: Spiral staircase distribution function. J Comput Chem 2018; 39:2300-2306. [PMID: 30299550 DOI: 10.1002/jcc.25549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 12/17/2022]
Abstract
In the present study, we investigated the local structure of DNA and its environment using a new visualization technique. The spiral staircase distribution function (SSDF) is determined as two-dimensional density distribution of atoms of water and ligands in local reference frames linked with each base pair of poly-DNA molecule, either GC or AT. This property of SSDF provides opportunity to study sequence-specific binding of ions, peptides, and other agents derived from a molecular dynamics computer simulation. The spatial structure of double-stranded DNA environment in water solution containing either Mg2+ or Na+ ions was investigated using of SSDF. The distributions of ions around GC and AT base pairs are shown separately. It is observed that Mg2+ ions interact with DNA atoms by means of the layer of water molecules and penetrate into the major groove only. Na+ ions have a direct contact with DNA atoms and penetrate both into the major and minor grooves of DNA. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Irina Silanteva
- Faculty of Physics, Saint Petersburg State University, Universitetsaya emb., 7-9, Saint Petersburg, 199034, Russian Federation
| | - Andrei V Komolkin
- Faculty of Physics, Saint Petersburg State University, Universitetsaya emb., 7-9, Saint Petersburg, 199034, Russian Federation
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10
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Cang X, Du Y, Mao Y, Wang Y, Yang H, Jiang H. Mapping the Functional Binding Sites of Cholesterol in β2-Adrenergic Receptor by Long-Time Molecular Dynamics Simulations. J Phys Chem B 2013; 117:1085-94. [DOI: 10.1021/jp3118192] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaohui Cang
- Drug Discovery and
Design Center, State Key Laboratory of Drug Research, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yun Du
- Drug Discovery and
Design Center, State Key Laboratory of Drug Research, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yanyan Mao
- Drug Discovery and
Design Center, State Key Laboratory of Drug Research, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yuanyuan Wang
- Drug Discovery and
Design Center, State Key Laboratory of Drug Research, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Huaiyu Yang
- Drug Discovery and
Design Center, State Key Laboratory of Drug Research, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- Drug Discovery and
Design Center, State Key Laboratory of Drug Research, Shanghai Institute
of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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11
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Cabana J, Holleran B, Beaulieu MÈ, Leduc R, Escher E, Guillemette G, Lavigne P. Critical hydrogen bond formation for activation of the angiotensin II type 1 receptor. J Biol Chem 2012; 288:2593-604. [PMID: 23223579 DOI: 10.1074/jbc.m112.395939] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
G protein-coupled receptors contain selectively important residues that play central roles in the conformational changes that occur during receptor activation. Asparagine 111 (N111(3.35)) is such a residue within the angiotensin II type 1 (AT(1)) receptor. Substitution of N111(3.35) for glycine leads to a constitutively active receptor, whereas substitution for tryptophan leads to an inactivable receptor. Here, we analyzed the AT(1) receptor and two mutants (N111G and N111W) by molecular dynamics simulations, which revealed a novel molecular switch involving the strictly conserved residue D74(2.50). Indeed, D74(2.50) forms a stable hydrogen bond (H-bond) with the residue in position 111(3.35) in the wild-type and the inactivable receptor. However, in the constitutively active mutant N111G-AT(1) receptor, residue D74 is reoriented to form a new H-bond with another strictly conserved residue, N46(1.50). When expressed in HEK293 cells, the mutant N46G-AT(1) receptor was poorly activable, although it retained a high binding affinity. Interestingly, the mutant N46G/N111G-AT(1) receptor was also inactivable. Molecular dynamics simulations also revealed the presence of a cluster of hydrophobic residues from transmembrane domains 2, 3, and 7 that appears to stabilize the inactive form of the receptor. Whereas this hydrophobic cluster and the H-bond between D74(2.50) and W111(3.35) are more stable in the inactivable N111W-AT(1) receptor, the mutant N111W/F77A-AT(1) receptor, designed to weaken the hydrophobic core, showed significant agonist-induced signaling. These results support the potential for the formation of an H-bond between residues D74(2.50) and N46(1.50) in the activation of the AT(1) receptor.
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Affiliation(s)
- Jérôme Cabana
- Department of Pharmacology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, Sherbrooke, Quecec J1H 5N4, Canada
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Conformational study of bovine lactoferricin in membrane-micking conditions by molecular dynamics simulation and circular dichroism. Biometals 2010; 24:259-68. [PMID: 21088870 DOI: 10.1007/s10534-010-9390-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2010] [Accepted: 11/07/2010] [Indexed: 10/18/2022]
Abstract
Lactoferricins are potent antimicrobial peptides released by pepsin cleavage of Lactoferrins. Bovine Lactoferricin (LfcinB) has higher activity than the intact bovine Lactoferrin, and is the most active among the other Lactoferricins of human, murine and caprine origin. In the intact protein the fragment corresponding to LfcinB is in an helical conformation, while in water LfcinB adopts an amphipathic β-hairpin structure. However, whether any of these structural motifs is the antibacterial active conformation, i.e., the one interacting with bacterial membrane components, remains to be seen. Here we present Circular Dichroism (CD) spectra and Molecular Dynamics (MD) simulations indicating that in membrane-mimicking solvents the LfcinB adopts an amphipathic β-hairpin structure similar to that observed in water, but differing in the dynamic behavior of the side-chains of the two tryptophan residues. In the membrane-mimicking solvent these side-chains show a high propensity to point towards the hydrophobic environment, rather than being in the hydrophobic core as seen in water, while the backbone preserves the hairpin conformation as found in water. These results suggest that the tryptophans might act as anchors pulling the stable, solvent-invariant hairpin structure into the membrane.
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14
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Khelashvili G, Grossfield A, Feller SE, Pitman MC, Weinstein H. Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. Proteins 2009; 76:403-17. [PMID: 19173312 PMCID: PMC4101808 DOI: 10.1002/prot.22355] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An unresolved question about GPCR function is the role of membrane components in receptor stability and activation. In particular, cholesterol is known to affect the function of membrane proteins, but the details of its effect on GPCRs are still elusive. Here, we describe how cholesterol modulates the behavior of the TM1-TM2-TM7-helix 8(H8) functional network that comprises the highly conserved NPxxY(x)(5,6)F motif, through specific interactions with the receptor. The inferences are based on the analysis of microsecond length molecular dynamics (MD) simulations of rhodopsin in an explicit membrane environment. Three regions on the rhodopsin exhibit the highest cholesterol density throughout the trajectory: the extracellular end of TM7, a location resembling the high-density sterol area from the electron microscopy data; the intracellular parts of TM1, TM2, and TM4, a region suggested as the cholesterol binding site in the recent X-ray crystallography data on beta(2)-adrenergic GPCR; and the intracellular ends of TM2-TM3, a location that was categorized as the high cholesterol density area in multiple independent 100 ns MD simulations of the same system. We found that cholesterol primarily affects specific local perturbations of the helical TM domains such as the kinks in TM1, TM2, and TM7. These local distortions, in turn, relate to rigid-body motions of the TMs in the TM1-TM2-TM7-H8 bundle. The specificity of the effects stems from the nonuniform distribution of cholesterol around the protein. Through correlation analysis we connect local effects of cholesterol on structural perturbations with a regulatory role of cholesterol in the structural rearrangements involved in GPCR function.
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Affiliation(s)
- George Khelashvili
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, New York 10021, USA.
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15
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Wahab HA, Yam WK, Samian MR, Najimudin N. Refinement of a Low-resolution Crystal Structure to Better Understand Erythromycin Interactions on Large Ribosomal Subunit. J Biomol Struct Dyn 2008; 26:131-46. [DOI: 10.1080/07391102.2008.10507230] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Abstract
With the availability of accurate methods to treat the electrostatic long-range interactions, molecular dynamics simulations have resulted in refined dynamical models of the structure of the hydration shell around RNA motifs. The models reviewed here range from basic Watson-Crick to more specific noncanonical base pairs, from "simple" double helices to RNA molecules displaying more complex tertiary folds, and from DNA/RNA hybrid double helices to RNA hybrids formed with a chemically modified strand.
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Affiliation(s)
- P Auffinger
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Modélisations et Simulations des Acides Nucléiques, UPR 9002, 15 rue René Descartes, 67084 Strasbourg Cedex, France
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17
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Affiliation(s)
- Pascal Auffinger
- Institut de Biologie Moléculaire et Cellulaire du CNRS Modélisations et Simulations des Acides Nucléiques, UPR 9002 15 rue René Descartes 67084 Strasbourg Cedex (France)
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Adamiak DA, Rypniewski WR, Milecki J, Adamiak RW. The 1.19 A X-ray structure of 2'-O-Me(CGCGCG)(2) duplex shows dehydrated RNA with 2-methyl-2,4-pentanediol in the minor groove. Nucleic Acids Res 2001; 29:4144-53. [PMID: 11600703 PMCID: PMC60216 DOI: 10.1093/nar/29.20.4144] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The crystal and molecular structure of 2'-O-Me(CGCGCG)(2) has been determined at 1.19 A resolution, at 100 K, using synchrotron radiation. The structure in space group P3(2)12 is a half-turn right-handed helix that includes two 2-methyl-2,4-pentanediol (MPD) molecules bound in the minor groove. The structure deviates from A-form RNA. The duplex is overwound with an average value of 9.7 bp per turn, characterised as having a C3'-endo sugar pucker, very low base pair rise and high helical twist and inclination angles. The structure includes 65 ordered water molecules. Only a single row of water molecules is observed in the minor groove due to the presence of hydrophobic 2'-O-methyl groups. As many as five magnesium ions are located in the structure. Two are in the major groove and interact with O(6) and N(7) of guanosine and N(4) of cytidine residues through their hydration spheres. This work provides the first example of molecular interactions of nucleic acids with MPD, which was used as a precipitant, cryo-solvent and resolution enhancing agent. The two MPD molecules intrude into the hydration network in the minor groove, each forming hydrogen bonds between their secondary hydroxyl group and exo-amino functions of guanosine residues. Comparison of the 2'-O-Me(CGCGCG)(2) structure in the P3(2)12 and P6(1)22 crystals delineates stability of the water network within the minor groove to dehydration by MPD and is of interest for evaluating factors governing small molecule binding to RNA. Intrusion of MPD into the minor groove of 2'-O-Me(CGCGCG)(2) is discussed with respect to RNA dehydration, a prerequisite of Z-RNA formation.
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Affiliation(s)
- D A Adamiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12-14, 61-704 Poznañ, Poland.
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