当前位置： SCI文献检索 > JOURNAL OF MOLECULAR MODELING期刊下所有文献 > Importance of amino acids Leu135 and Tyr236 for the interaction between EhCFIm25 and RNA: a molecular dynamics simulation study.

Importance of amino acids Leu135 and Tyr236 for the interaction between EhCFIm25 and RNA: a molecular dynamics simulation study.

Abstract：

:The CFIm25 subunit of the heterotetrameric cleavage factor Im (CFIm) is a critical factor in the formation of the poly(A) tail at mRNA 3' end, regulating the recruitment of polyadenylation factors, poly(A) site selection, and cleavage/polyadenylation reactions. We previously reported the homologous protein (EhCFIm25) in Entamoeba histolytica, the protozoan causing human amoebiasis, and showed the relevance of conserved Leu135 and Tyr236 residues for RNA binding. We also identified the GUUG sequence as the recognition site of EhCFIm25. To understand the interactions network that allows the EhCFIm25 to maintain its three-dimensional structure and function, here we performed molecular dynamics simulations of wild-type (WT) and mutant proteins, alone or interacting with the GUUG molecule. Our results indicated that in the presence of the GUUG sequence, WT converged more quickly to lower RMSD values in comparison with mutant proteins. However, RMSF values showed that movements of amino acids of WT and EhCFIm25*L135 T were almost identical, interacting or not with the GUUG molecule. Interestingly, EhCFIm25*L135 T, which is the only mutant with a slight RNA binding activity experimentally, presents the same stabilization of bend structures and alpha helices as WT, notably in the C-terminus. Moreover, WT and EhCFIm25*L135 T presented almost the same number of contacts that mainly involve lysine residues interacting with the G4 nucleotide. Overall, our data proposed a clear description of the structural and mechanistic data that govern the RNA binding capacity of EhCFIm25.

journal_name

J Mol Model

journal_title

Journal of molecular modeling

authors

Ospina-Villa JD,García-Contreras J,Rosas-Trigueros JL,Ramírez-Moreno E,López-Camarillo C,Zamora-López B,Marchat LA,Zamorano-Carrillo A

doi

10.1007/s00894-018-3729-1

subject

Has Abstract

pub_date

2018-07-12 00:00:00

pages

202

issue

8

eissn

1610-2940

issn

0948-5023

pii

10.1007/s00894-018-3729-1

journal_volume

24

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR MODELING文献大全
  • Theoretical study of the complementarity in halogen-bonded complexes involving nitrogen and halogen as negative sites.

    abstract：:This article analyzes the interplay between X···N and X···X halogen bonds interactions in NCX···NCX···XCH3 complexes, where X=Cl and Br. To better understand the properties of these systems, the corresponding dyads were also studied. These effects are studied theoretically in terms of geometric and energetic features ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2101-3

    authors： Esrafili MD,Vakili M,Solimannejad M

    更新日期：2014-02-01 00:00:00

  • First-principles study of the structural transformation, electronic structure, and optical properties of crystalline 2,6-diamino-3,5-dinitropyrazine-1-oxide under high pressure.

    abstract：:Periodic first-principles calculations have been performed to study the effect of high pressure on the geometric, electronic, and absorption properties of 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105) under hydrostatic pressures of 0-50 GPa. Obvious irregular changes in lattice constants, unit-cell angles, bond le...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1995-5

    authors： Wu Q,Yang C,Pan Y,Xiang F,Liu Z,Zhu W,Xiao H

    更新日期：2013-12-01 00:00:00

  • A theoretical study of substituent effects on tautomerism of 2-hydroxybenzimidazoles.

    abstract：:The geometries, relative stabilities of some 4(7) and 5(6) substituted 2-hydroxybenzimidazole derivatives were calculated with full geometry optimization using AM1 and PM3 in aqueous phase. With the exception of molecules 4, 6 and 7 for all the 4(7) and 5(6) substituted 2-hydroxybenzimidazole derivatives the 3H and ke...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-003-0150-0

    authors： Oğretir C,Yarligan S,Berber H,Arslan T,Topal S

    更新日期：2003-12-01 00:00:00

  • Capture carcinogenic aromatic compounds by the design of new tweezer compounds: a theoretical study.

    abstract：:Both [5]-circulene and [7]-circulene can be selected to design the molecular tweezers theoretically using the DFT method. Leaning on the cyclic polymerization mechanism, we obtain four new tweezer compounds. Theoretical results offer that tweezer compound (I) is additionally stable than other compounds because it has ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-020-04558-3

    authors： Issa AA,Obayes HR

    更新日期：2020-09-29 00:00:00

  • Neighboring group stabilization by sigma-holes.

    abstract：:We have used density-functional theory to investigate the neighboring-group stabilization of iodine, arsenic, and phosphorus-centered oxyanion moieties in species such as deprotonated 2-iodoxybenzoic acid (IBX) and its analogs. The magnitudes of different stabilizing effects and further candidates for analogous stabil...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-009-0567-1

    authors： O'Hair RA,Williams CM,Clark T

    更新日期：2010-03-01 00:00:00

  • Benchmarking and optimization of molecular simulation models of zinc dialkyldithiophosphate and calcium sulfonate oil additives.

    abstract：:We present an ab initio based molecular mechanics model for prominent additives used in lubricants to moderate oil-steel interfaces. The force field is created for zinc dialkyldithiophosphate and calcium sulfonate charge neutral ligand-ion-ligand complexes and benchmarked to the widely spread generalized amber force f...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-3980-0

    authors： Ectors P,Zahn D

    更新日期：2019-03-25 00:00:00

  • Reaction mechanisms of DNT with hydroxyl radicals for advanced oxidation processes-a DFT study.

    abstract：:In advanced oxidation processes (AOPs), the detailed degradation mechanisms of a typical explosive of 2,4-dinitrotoluene (DNT) can be investigated by the density function theory (DFT) method at the SMD/M062X/6-311+G(d) level. Several possible degradation routes for DNT were explored in the current study. The results s...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3277-0

    authors： Zhou Y,Yang Z,Yang H,Zhang C,Liu X

    更新日期：2017-04-01 00:00:00

  • Stereochemistry and spectroscopic analysis of bis-Betti base derivatives of 2,3-dihydroxynaphthalene.

    abstract：:Density functional theory (DFT) was used to study the stereochemistry, thermodynamic stability, and spectra of recently synthesized bis-Betti base derivatives of 2,3-dihydroxynaphthalene obtained through multicomponent reactions of 2,3-dihydroxynaphthalene with aminoisoxazole and benzaldehyde derivatives. The stereoch...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-2936-x

    authors： Zamani M,Shafiee M,Keshavarz MH

    更新日期：2016-04-01 00:00:00

  • Exploring 3D structure of human gonadotropin hormone receptor at antagonist state using homology modeling, molecular dynamic simulation, and cross-docking studies.

    abstract：:Human gonadotropin hormone receptor, a G-protein coupled receptor, is the target of many medications used in fertility disorders. Obtaining more structural information about the receptor could be useful in many studies related to drug design. In this study, the structure of human gonadotropin receptor was subjected to...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-3091-0

    authors： Sakhteman A,Khoddami M,Negahdaripour M,Mehdizadeh A,Tatar M,Ghasemi Y

    更新日期：2016-09-01 00:00:00

  • DFT modeling, UV-Vis and IR spectroscopic study of acetylacetone-modified zirconia sol-gel materials.

    abstract：:Theoretical and spectroscopic studies of a series of monomeric and dimeric complexes formed through the modification of a zirconium butoxide precursor with acetylacetone and subsequent hydrolysis and/or condensation have been performed by applying DFT/B3LYP/6-31++G(d) and highly accurate RI-ADC(2) methods as well as I...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1257-3

    authors： Georgieva I,Danchova N,Gutzov S,Trendafilova N

    更新日期：2012-06-01 00:00:00

  • An analysis of hydrophobic interactions of thymidylate synthase with methotrexate: free energy calculations involving mutant and native structures bound to methotrexate.

    abstract：:Since the human body for many reasons can adapt and become resistant to drugs, it is important to develop and validate computer aided drug design (CADD) methods that could help predict binding affinity changes that can result from these resistant enzymes. The free energy perturbation (FEP) methodology is the most accu...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-009-0535-9

    authors： Reddy RN,Mutyala RR,Aparoy P,Reddanna P,Reddy MR

    更新日期：2010-02-01 00:00:00

  • Modeling the adsorption of aromatic compounds on the TiO2/SiO2 catalyst.

    abstract：:The Grand Canonical Monte Carlo method was used to analyse the phenomenon of adsorption of aromatic compounds (i.e. phenol, toluene, benzoic acid and salicylic acid) on the surface of the titania-silica (TiO2/SiO2) catalyst. We found that different types of interactions play important roles in the adsorption of molecu...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-007-0189-4

    authors： Szyja B,Brodzik K

    更新日期：2007-07-01 00:00:00

  • APUAMA: a software tool for reaction rate calculations.

    abstract：:APUAMA is a free software designed to determine the reaction rate and thermodynamic properties of chemical species of a reagent system. With data from electronic structure calculations, the APUAMA determine the rate constant with tunneling correction, such as Wigner, Eckart and small curvature, and also, include the r...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3337-5

    authors： Euclides HO,P Barreto PR

    更新日期：2017-06-01 00:00:00

  • Simulations on the possibility of formation of complexes between fluorouracil drug and cucurbit[n]urils: ab initio van der Waals DFT study.

    abstract：:The binding geometry of fluorouracil/cucurbit[n]urils (CB[n]s) complexes with n = 5-8 is investigated using the first-principles van der Waals density functional (vdW-DF) method, involving full geometry optimization. Such host-guest complexes are typically calculated using conventional DFT method, which significantly ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1936-3

    authors： Sabet M,Ganji MD

    更新日期：2013-09-01 00:00:00

  • The first intermediates in the bromination of bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane, combination of experiments and theoretical results.

    abstract：:Bicyclo[3.3.1]nonylidenebicyclo[3.3.1]nonane (1) and adamantylideneadamantane (Ad=Ad) are two caged olefins with closely related structures at the double bond. Both compounds react instantaneously with Br2 in chlorinated hydrocarbon solvents to give mixtures of olefin-Br2 aggregates identified as the 1:1 pi-complex an...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0038-2

    authors： Chiappe C,Pomelli CS,Lenoir D,Wattenbach C

    更新日期：2006-07-01 00:00:00

  • QM/MM investigation of substrate binding of subclass B3 metallo-β-lactamase SMB-1 from Serratia marcescents: insights into catalytic mechanism.

    abstract：:Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-020-4330-y

    authors： Mu X,Xu D

    更新日期：2020-03-07 00:00:00

  • Theoretical 49Ti NMR chemical shifts.

    abstract：:49Ti chemical shifts for a total of 20 titanium complexes are reported, and several levels of theory are evaluated in order to identify a reliable approach for the calculation of titanium NMR data. The popular B3LYP/6-31G(d)//B3LYP/6-31G(d) proves to give very good agreement with experimental data over a range from 1,...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0081-z

    authors： Koch R,Bruhn T

    更新日期：2006-07-01 00:00:00

  • Insights into amprenavir resistance in E35D HIV-1 protease mutation from molecular dynamics and binding free-energy calculations.

    abstract：:Drug resistance is a very important factor contributing to the failure of current HIV therapies. The ability to understand the resistance mechanism of HIV-protease mutants may be useful in developing more effective and longer lasting treatment regimens. In this paper, we report the first computational study of the cli...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-006-0121-3

    authors： Meiselbach H,Horn AH,Harrer T,Sticht H

    更新日期：2007-02-01 00:00:00

  • A comparative interplay between small heterorings and hypofluorous acids.

    abstract：:Through the B3LYP/6-311++G(d,p) calculations, theoretical studies of structural parameters, electronic properties, infrared vibration modes, and charge density topologies on the C2H4O∙∙∙HX and C2H5N∙∙∙HX (X = F or O-F) heterocylic hydrogen complexes are presented. The H-bond distances and high energies point out stron...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2829-4

    authors： Oliveira BG

    更新日期：2015-11-01 00:00:00

  • A mechanistic investigation on the formation and rearrangement of silaspiropentane: A theoretical study.

    abstract：:The formation of silaspiropentane from addition of singlet silacyclopropylidene 1 and silacyclopropylidenoid 8 to ethylene has been investigated separately at the B3LYP, X3LYP, WB97XD, and M05-2X theories using the 6-31+G(d,p) basis set. The silacycloproylidenoid addition follows a stepwise route. In contrast, a conce...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-3016-y

    authors： Yildiz CB,Azizoglu A

    更新日期：2016-07-01 00:00:00

  • Trends in σ-hole strengths and interactions of F3MX molecules (M = C, Si, Ge and X = F, Cl, Br, I).

    abstract：:It is well-established that many covalently-bonded atoms of Groups IV-VII have directionally-specific regions of positive electrostatic potential (σ-holes) through which they can interact with negative sites. In the case of Group VII, this is called "halogen bonding." We have studied two series of molecules: the F3MX ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1571-4

    authors： Bundhun A,Ramasami P,Murray JS,Politzer P

    更新日期：2013-07-01 00:00:00

  • Structure and localisation of drug binding sites on neurotransmitter transporters.

    abstract：:The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in eac...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-009-0478-1

    authors： Ravna AW,Sylte I,Dahl SG

    更新日期：2009-10-01 00:00:00

  • Druggability and drug-likeness concepts in drug design: are biomodelling and predictive tools having their say?

    abstract：:The drug discovery process typically involves target identification and design of suitable drug molecules against these targets. Despite decades of experimental investigations in the drug discovery domain, about 96% overall failure rate has been recorded in drug development due to the "undruggability" of various ident...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章,评审

    doi：10.1007/s00894-020-04385-6

    authors： Agoni C,Olotu FA,Ramharack P,Soliman ME

    更新日期：2020-05-08 00:00:00

  • Characterization of adenosine receptor in its native environment: insights from molecular dynamics simulations of palmitoylated/glycosylated, membrane-integrated human A(2B) adenosine receptor.

    abstract：:Selective A(2B) receptor antagonists and agonists may play a role in important pathologies such as gastrointestinal, neurological (i.e., Alzheimer disease and dementia) and hypersensitive disorders (i.e., asthma), diabetes, atherosclerosis, restenosis and cancer. Hence, it is regarded as a good target for the developm...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1427-y

    authors： Mansourian M,Madadkar-Sobhani A,Mahnam K,Fassihi A,Saghaie L

    更新日期：2012-09-01 00:00:00

  • Understanding the recognition mechanisms of Zα domain of human editing enzyme ADAR1 (hZα(ADAR1)) and various Z-DNAs from molecular dynamics simulation.

    abstract：:The Z-DNA-binding domain of human double-stranded RNA adenosine deaminase I (hZαADAR1) can specifically recognize the left-handed Z-DNA which preferentially occurs at alternating purine-pyrimidine repeats, especially the CG-repeats. The interactions of hZαADAR1 and Z-DNAs in different sequence contexts can affect many...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-014-2500-5

    authors： Wang Q,Li L,Wang X,Liu H,Yao X

    更新日期：2014-11-01 00:00:00

  • Impacts of the charged residues mutation S48E/N62H on the thermostability and unfolding behavior of cold shock protein: insights from molecular dynamics simulation with Gō model.

    abstract：:The cold shock protein from the hyperthermophile Thermotoga maritima (Tm-Csp) exhibits significantly higher thermostability than its homologue from the thermophile Bacillus caldolyticus (Bc-Csp). Experimental studies have shown that the electrostatic interactions unique to Tm-Csp are responsible for improving its ther...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-2958-4

    authors： Su JG,Han XM,Zhao SX,Hou YX,Li XY,Qi LS,Wang JH

    更新日期：2016-04-01 00:00:00

  • Insight into the dynamic interaction between different flavonoids and bovine serum albumin using molecular dynamics simulations and free energy calculations.

    abstract：:In this study, the binding of Bovine serum albumin (BSA) with three flavonoids, kaempferol-3-O-a-L-rhamnopyranosyl-(1-3)-a-L-rhamnopyranosyl-(1-6)-b-D-galacto- pyranoside (drug 1),kaempfol-7-O-rhamnosyl-3-O-rutinoside (drug 2)andkaempferide-7-O-(4"-O-acetylrhamnosyl)-3-O-ruti- noside (drug 3) is investigated by molecu...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1649-z

    authors： Niu X,Gao X,Wang H,Wang X,Wang S

    更新日期：2013-03-01 00:00:00

  • G2, G3, and complete basis set calculations of the thermodynamic properties of cis- and trans-triazene.

    abstract：:Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane's unsaturated analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies of combustion, specific enthalpies of combustion, and proton affiniti...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-007-0248-x

    authors： Richard RM,Ball DW

    更新日期：2008-01-01 00:00:00

  • Mixtures of amino-acid based ionic liquids and water.

    abstract：:New ionic liquids (ILs) involving increasing numbers of organic and inorganic ions are continuously being reported. We recently developed a new force field; in the present work, we applied that force field to investigate the structural properties of a few novel imidazolium-based ILs in aqueous mixtures via molecular d...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2783-1

    authors： Chaban VV,Fileti EE

    更新日期：2015-09-01 00:00:00

  • A quantum-chemical study of the binding ability of βXaaHisGlyHis towards copper(II) ion.

    abstract：:The present study analyzed binding of Cu(2+) to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches in...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1162-9

    authors： Czyżnikowska Z,Brasuń J

    更新日期：2012-04-01 00:00:00