Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 7 de 7
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
Phys Chem Chem Phys ; 13(3): 1222-9, 2011 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-21082116

RESUMO

Hfq is a bacterial protein involved in RNA metabolism. Besides this, Hfq's role in DNA restructuring has also been suggested. Since this mechanism remains unclear, we examined the DNA conformation upon Hfq binding by combining vibrational spectroscopy and neutron scattering. Our analysis reveals that Hfq, which preferentially interacts with deoxyadenosine rich sequences, induces partial opening of dA-dT sequences accompanied by sugar repuckering of the dA strand and hence results in a heteronomous A/B duplex. Sugar repuckering is probably correlated with a global dehydration of the complex. By taking into account Hfq's preferential binding to A-tracts, which are commonly found in promoters, potential biological implications of Hfq binding to DNA are discussed.


Assuntos
DNA/química , Proteínas de Escherichia coli/química , Fator Proteico 1 do Hospedeiro/química , Difração de Nêutrons , Conformação de Ácido Nucleico , Ligação Proteica , Estrutura Terciária de Proteína , Espectroscopia de Infravermelho com Transformada de Fourier
2.
Spectrochim Acta A Mol Biomol Spectrosc ; 73(5): 805-14, 2009 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-19442575

RESUMO

The effect of hexahydrated monovalent and divalent cations on the geometrical and vibrational features of dimethyl phosphate, dimethyl phosphorothioate and dimethyl phosphorodithioate anions (simple suitable model compounds representing the anionic moieties of natural and some modified nucleic acids) was studied. For this purpose, density functional theory (DFT) calculations were carried out at the B3LYP/6-31++G* level. Our results indicate that only K(+) and Mg(2+) prefer to be located in the bisector plane of the PO(2)(-) angle, whereas Li(+) and Na(+) deviate from this plane. Monovalent and divalent cations are slightly deviated from the OPS(-) bisector plane and are found closer to the free oxygen atom. Moreover, the present calculations have shown that in contrast to the general belief, the g(-)g(-) conformer (with respect to the torsion angles defined around the P-O ester bonds) is not always the energetically most favorable. For instance, the g(-)t conformer presents the lowest energy in the case of dimethyl phosphorothioate. The calculated vibrational wavenumbers obtained for dimethyl phosphate and dimethyl phosphorothioate interacting with hydrated sodium counterion, were compared with those previously recorded by Raman scattering and infrared absorption (IR) in aqueous solutions. It has been evidenced that the use of explicit solvent versus dielectric continuum, considerably improves the agreement between the theoretical and observed characteristic wavenumbers.


Assuntos
Cátions/química , Compostos Organofosforados/química , Compostos Organotiofosforados/química , Fosfatos/química , Simulação por Computador , Modelos Moleculares , Conformação Molecular , Teoria Quântica , Espectrofotometria Infravermelho , Análise Espectral Raman , Água/química
3.
Biophys Chem ; 138(3): 107-14, 2008 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-18814946

RESUMO

The X-ray structure for the type IIE EcoRII restriction endonuclease has been resolved [X.E. Zhou, Y. Wang, M. Reuter, M. Mucke, D.H. Kruger, E.J. Meehan and L. Chen. Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. J. Mol. Biol. 335 (2004) 307-319.], but the structure of the R.EcoRII-DNA complex is still unknown. The aim of this article was to examine the structure of the pre-reactive R.EcoRII-DNA complex in solution by fluorescence spectroscopy. The structure for the R.EcoRII-DNA complex was resolved by determining the fluorescence resonance energy transfer (FRET) between two fluorescent dyes, covalently attached near the EcoRII recognition sites, that were located at opposite ends of a lengthy two-site DNA molecule. Analysis of the FRET data from the two-site DNA revealed a likely model for the arrangement of the two EcoRII recognition sites relative to each other in the R.EcoRII-DNA complex in the presence of Ca(2+) ions. According to this model, the R.EcoRII binds the two-site DNA and forms a DNA loop in which the EcoRII recognition sites are 20+/-10 A distant to each other and situated at an angle of 70+/-10 degrees.


Assuntos
DNA/química , Desoxirribonucleases de Sítio Específico do Tipo II/química , Sequência de Bases , Sítios de Ligação , Cristalografia por Raios X , Transferência Ressonante de Energia de Fluorescência , Modelos Teóricos , Dados de Sequência Molecular , Conformação de Ácido Nucleico , Ligação Proteica , Conformação Proteica , Soluções
4.
J Am Chem Soc ; 130(12): 4187-95, 2008 Mar 26.
Artigo em Inglês | MEDLINE | ID: mdl-18311975

RESUMO

Structural information on acetylcholine and its two agonists, nicotine, and muscarine has been obtained from the interpretation of infrared spectra recorded in the gas-phase or in low pH aqueous solutions. Simulated IR spectra have been obtained using explicit water molecules or a polarization continuum model. The conformational space of the very flexible acetylcholine ions is modified by the presence of the solvent. Distances between its pharmacophoric groups cover a lower range in hydrated species than in isolated species. A clear signature of the shift of protonation site in nicotine ions is provided by the striking change of their infrared spectrum induced by hydration. On the contrary, structures of muscarine ions are only slightly influenced by the presence of water.


Assuntos
Acetilcolina/química , Muscarina/química , Nicotina/química , Gases/química , Concentração de Íons de Hidrogênio , Íons/química , Modelos Moleculares , Transição de Fase , Soluções/química , Espectroscopia de Infravermelho com Transformada de Fourier/métodos , Fatores de Tempo , Água/química
5.
J Phys Chem B ; 111(6): 1470-7, 2007 Feb 15.
Artigo em Inglês | MEDLINE | ID: mdl-17243664

RESUMO

Raman scattering and Fourier-transform infrared (FT-IR) attenuated transmission reflectance (ATR) spectra of two alpha-amino acids (alpha-AAs), i.e., glycine and leucine, were measured in H2O and D2O (at neutral pH and pD). This series of observed vibrational data gave us the opportunity to analyze vibrational features of both AAs in hydrated media by density functional theory (DFT) calculations at the B3LYP/6-31++G* level. Harmonic vibrational modes calculated after geometry optimization on the clusters containing each AA and 12 surrounding water molecules, which represent primary models for hydration scheme of amino acids, allowed us to assign the main observed peaks.


Assuntos
Glicina/química , Leucina/química , Peptídeos/química , Espectroscopia de Infravermelho com Transformada de Fourier , Água/química , Óxido de Deutério/química , Ligação de Hidrogênio , Concentração de Íons de Hidrogênio , Estrutura Molecular
6.
Langmuir ; 22(14): 6068-77, 2006 Jul 04.
Artigo em Inglês | MEDLINE | ID: mdl-16800661

RESUMO

Dipalmitoylphosphatidylcholine (DPPC)/water/pyridine reverse micelles have been found to transform from a clear liquid into a glass when the DPPC-to-water volume fraction is in the 0.78-0.89 range at 28 or 26 degrees C depending on whether water is H2O or D2O. Their study by SANS, FT-IR, and 1H NMR for this composition has shown remarkable effects of the isotopic nature of water on their structural and dynamic properties. By SANS, between 38 and 43.5 degrees C, micelles appear as either flexible polymer-like cylinders or short rods depending on whether water is H2O or D2O. On the basis of this dual aspect, micelles have been visualized as branched cylinders whose quasi-spherical branching points would be prone to assemble into short rods. In addition, when water contains more than 40% of D2O, a Bragg reflection emerges at 0.12 A(-1) on SANS spectra, evidencing an organization of micelles. In addition, FT-IR spectra show that DPPC phosphate groups are D bonded only when water is D2O. Consequently, we assumed that forces prone to organize the D2O-containing micelles are D-bonded water bridges between neighboring micelles at the level of their branching points. In fact, ab initio calculations have shown that water dimers are more stable when the bridging atom is D rather than H. These water bridges could be formed due to the fact that branching points, able to slide along micelles, keep close for a longer time when water is D2O than when it is H2O. Indeed, it has been shown experimentally that the lateral diffusion of phospholipid molecules in any layer is slower in the first case. Formation of such bridges triggers a deuteron migration between micelles evidenced by the 1/T1 relaxation rate of deuterons of water in D2O-containing micelles measured at 43 degrees C by 1H NMR.

7.
J Mol Biol ; 356(1): 86-96, 2006 Feb 10.
Artigo em Inglês | MEDLINE | ID: mdl-16337963

RESUMO

Hfq is a nucleic acid-binding protein that functions as a global regulator of gene expression by virtue of its interactions with several small, non-coding RNA species. Originally identified as an Escherichia coli host factor required for RNA phage Qbeta replication, Hfq is now known to post-transcriptionally regulate bacterial gene expression by modulating both mRNA stability and translational activity. Recently shown to be a member of the diverse Sm protein family, Hfq adopts the OB-like fold typical of other Sm and Sm-like (Lsm) proteins, and also assembles into toroidal homo-oligomers that bind single-stranded RNA. Similarities between the structures, functions, and evolution of Sm/Lsm proteins and Hfq are continually being discovered, and we now report an additional, unexpected biophysical property that is shared by Hfq and other Sm proteins: E.coli Hfq polymerizes into well-ordered fibres whose morphologies closely resemble those found for Sm-like archaeal proteins (SmAPs). However, the hierarchical assembly of these fibres is dissimilar: whereas SmAPs polymerize into polar tubes (and striated bundles of such tubes) by head-to-tail stacking of individual homo-heptamers, helical Hfq fibres are formed by cylindrical slab-like layers that consist of 36 subunits arranged as a hexamer of Hfq homo-hexamers (i.e. protofilaments in a 6 x 6 arrangement). The different fibrillar ultrastructures formed by Hfq and SmAP are presented and examined herein, with the overall goal of elucidating another similarity amongst the diverse members of the Sm protein family.


Assuntos
Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Fator Proteico 1 do Hospedeiro/química , Fator Proteico 1 do Hospedeiro/metabolismo , Proteínas Arqueais/genética , Escherichia coli/química , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/ultraestrutura , Fator Proteico 1 do Hospedeiro/genética , Fator Proteico 1 do Hospedeiro/ultraestrutura , Imageamento Tridimensional , Methanobacterium/química , Methanobacterium/genética , Methanobacterium/metabolismo , Microscopia Eletrônica de Transmissão , Modelos Moleculares , Estrutura Quaternária de Proteína , Estrutura Secundária de Proteína , Estrutura Terciária de Proteína , Espectroscopia de Infravermelho com Transformada de Fourier
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...