The Fox-1 RNA recognition motif (RRM) domain is an important member of the RRM protein family. We report a 1.8 Å X-ray structure of the free Fox-1 containing six distinct monomers. We use this and the nuclear magnetic resonance (NMR) structure of the Fox-1 protein/RNA complex for molecular dynamics (MD) analyses of the structured hydration. The individual monomers of the X-ray structure show diverse hydration patterns, however, MD excellently reproduces the most occupied hydration sites. Simulations of the protein/RNA complex show hydration consistent with the isolated protein complemented by hydration sites specific to the protein/RNA interface. MD predicts intricate hydration sites with water-binding times extending up to hundreds of nanoseconds. We characterize two of them using NMR spectroscopy, RNA binding with switchSENSE and free-energy calculations of mutant proteins. Both hydration sites are experimentally confirmed and their abolishment reduces the binding free-energy. A quantitative agreement between theory and experiment is achieved for the S155A substitution but not for the S122A mutant. The S155 hydration site is evolutionarily conserved within the RRM domains. In conclusion, MD is an effective tool for predicting and interpreting the hydration patterns of protein/RNA complexes. Hydration is not easily detectable in NMR experiments but can affect stability of protein/RNA complexes.

• MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• motiv rozpoznávající RNA genetika   MeSH
• mutageneze cílená MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• rekombinantní proteiny chemie   genetika   metabolismus   MeSH
• RNA metabolismus   MeSH
• sestřihové faktory chemie   genetika   metabolismus   MeSH
• simulace molekulární dynamiky MeSH
• substituce aminokyselin MeSH
• vazebná místa MeSH
• voda chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• RBFOX1 protein, human MeSH Prohlížeč
• rekombinantní proteiny MeSH
• RNA MeSH
• sestřihové faktory MeSH
• voda MeSH

The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.

• MeSH
• DNA chemie   MeSH
• G-kvadruplexy * MeSH
• guanin chemie   MeSH
• konformace nukleové kyseliny MeSH
• ligandy MeSH
• RNA chemie   MeSH
• rozpouštědla chemie   MeSH
• simulace molekulární dynamiky * MeSH
• telomery chemie   MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• DNA MeSH
• guanin MeSH
• ligandy MeSH
• RNA MeSH
• rozpouštědla MeSH

We describe a novel, fundamental property of nucleobase structure, namely, pyramidilization at the N1/9 sites of purine and pyrimidine bases. Through a combined analyses of ultra-high-resolution X-ray structures of both oligonucleotides extracted from the Nucleic Acid Database and isolated nucleotides and nucleosides from the Cambridge Structural Database, together with a series of quantum chemical calculations, molecular dynamics (MD) simulations, and published solution nuclear magnetic resonance (NMR) data, we show that pyramidilization at the glycosidic nitrogen is an intrinsic property. This property is common to isolated nucleosides and nucleotides as well as oligonucleotides-it is also common to both RNA and DNA. Our analysis suggests that pyramidilization at N1/9 sites depends in a systematic way on the local structure of the nucleoside. Of note, the pyramidilization undergoes stereo-inversion upon reorientation of the glycosidic bond. The extent of the pyramidilization is further modulated by the conformation of the sugar ring. The observed pyramidilization is more pronounced for purine bases, while for pyrimidines it is negligible. We discuss how the assumption of nucleic acid base planarity can lead to systematic errors in determining the conformation of nucleotides from experimental data and from unconstrained MD simulations.

• MeSH
• deoxyadenosiny chemie   MeSH
• deoxycytidin chemie   MeSH
• dusík chemie   MeSH
• krystalografie rentgenová MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• oligonukleotidy chemie   MeSH
• počítačová simulace MeSH
• purinové nukleosidy chemie   MeSH
• purinové nukleotidy chemie   MeSH
• puriny chemie   MeSH
• pyrimidinové nukleosidy chemie   MeSH
• pyrimidinové nukleotidy chemie   MeSH
• pyrimidiny chemie   MeSH
• sacharidy chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 2'-deoxyadenosine MeSH Prohlížeč
• deoxyadenosiny MeSH
• deoxycytidin MeSH
• dusík MeSH
• oligonukleotidy MeSH
• purinové nukleosidy MeSH
• purinové nukleotidy MeSH
• puriny MeSH
• pyrimidinové nukleosidy MeSH
• pyrimidinové nukleotidy MeSH
• pyrimidiny MeSH
• sacharidy MeSH

Hybrid QM/MM methods combine the rigor of quantum mechanical (QM) calculations with the low computational cost of empirical molecular mechanical (MM) treatment allowing to capture dynamic properties to probe critical atomistic details of enzyme reactions. Catalysis by RNA enzymes (ribozymes) has only recently begun to be addressed with QM/MM approaches and is thus still a field under development. This review surveys methodology as well as recent advances in QM/MM applications to RNA mechanisms, including those of the HDV, hairpin, and hammerhead ribozymes, as well as the ribosome. We compare and correlate QM/MM results with those from QM and/or molecular dynamics (MD) simulations, and discuss scope and limitations with a critical eye on current shortcomings in available methodologies and computer resources. We thus hope to foster mutual appreciation and facilitate collaboration between experimentalists and theorists to jointly advance our understanding of RNA catalysis at an atomistic level.

• MeSH
• biofyzika metody   MeSH
• fosfáty chemie   MeSH
• fosforylace MeSH
• hořčík chemie   MeSH
• katalýza MeSH
• konformace nukleové kyseliny MeSH
• kvantová teorie MeSH
• lidé MeSH
• molekulární modely MeSH
• počítačová simulace MeSH
• ribozomy chemie   MeSH
• RNA katalytická chemie   MeSH
• RNA virová chemie   MeSH
• RNA chemie   MeSH
• software MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• fosfáty MeSH
• hammerhead ribozyme MeSH Prohlížeč
• hořčík MeSH
• RNA katalytická MeSH
• RNA virová MeSH
• RNA MeSH

This review provides a critical assessment of the advantages and limitations of modeling methods available for guanine quadruplex (G-DNA) molecules. We characterize the relations of simulations to the experimental techniques and explain the actual meaning and significance of the results. The following aspects are discussed: pair-additive approximation of the empirical force fields, sampling limitations stemming from the simulation time and accuracy of description of base stacking, H-bonding, sugar-phosphate backbone and ions by force fields. Several methodological approaches complementing the classical explicit solvent molecular dynamics simulations are commented on, including enhanced sampling methods, continuum solvent methods, free energy calculations and gas phase simulations. The successes and pitfalls of recent simulation studies of G-DNA are demonstrated on selected results, including studies of cation interactions and dynamics of G-DNA stems, studies of base substitutions (inosine, thioguanine and mixed tetrads), analysis of possible kinetic intermediates in folding pathway of a G-DNA stem and analysis of loop regions of G-DNA molecules.

• MeSH
• DNA chemie   MeSH
• G-kvadruplexy * MeSH
• guanin chemie   MeSH
• ligandy MeSH
• molekulární modely MeSH
• počítačová simulace MeSH
• termodynamika MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• guanin MeSH
• ligandy MeSH

The formation of a cation-stabilized guanine quadruplex (G-DNA) stem is an exceptionally slow process involving complex kinetics that has not yet been characterized at atomic resolution. Here, we investigate the formation of a parallel stranded G-DNA stem consisting of four strands of d(GGGG) using molecular dynamics simulations with explicit inclusion of counterions and solvent. Due to the limitations imposed by the nanosecond timescale of the simulations, rather than watching for the spontaneous formation of G-DNA, our approach probes the stability of possible supramolecular intermediates (including two-, three-, and four-stranded assemblies with out-of-register base pairing between guanines) on the formation pathway. The simulations suggest that "cross-like" two-stranded assemblies may serve as nucleation centers in the initial formation of parallel stranded G-DNA quadruplexes, proceeding through a series of rearrangements involving trapping of cations, association of additional strands, and progressive slippage of strands toward the full stem. To supplement the analysis, approximate free energies of the models are obtained with explicit consideration of the integral cations. The approach applied here serves as a prototype for qualitatively investigating other G-DNA molecules using molecular dynamics simulation and free-energy analysis.

• MeSH
• časové faktory MeSH
• DNA chemie   MeSH
• G-kvadruplexy MeSH
• guanin chemie   MeSH
• ionty MeSH
• kationty MeSH
• kinetika MeSH
• konformace nukleové kyseliny MeSH
• molekulární konformace MeSH
• molekulární modely MeSH
• oligonukleotidy chemie   MeSH
• sodík chemie   MeSH
• software MeSH
• teplota MeSH
• termodynamika MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• DNA MeSH
• guanin MeSH
• ionty MeSH
• kationty MeSH
• oligonukleotidy MeSH
• sodík MeSH

Explicit solvent and counterion molecular dynamics simulations have been carried out for a total of >80 ns on the bacterial and spinach chloroplast 5S rRNA Loop E motifs. The Loop E sequences form unique duplex architectures composed of seven consecutive non-Watson-Crick basepairs. The starting structure of spinach chloroplast Loop E was modeled using isostericity principles, and the simulations refined the geometries of the three non-Watson-Crick basepairs that differ from the consensus bacterial sequence. The deep groove of Loop E motifs provides unique sites for cation binding. Binding of Mg(2+) rigidifies Loop E and stabilizes its major groove at an intermediate width. In the absence of Mg(2+), the Loop E motifs show an unprecedented degree of inner-shell binding of monovalent cations that, in contrast to Mg(2+), penetrate into the most negative regions inside the deep groove. The spinach chloroplast Loop E shows a marked tendency to compress its deep groove compared with the bacterial consensus. Structures with a narrow deep groove essentially collapse around a string of Na(+) cations with long coordination times. The Loop E non-Watson-Crick basepairing is complemented by highly specific hydration sites ranging from water bridges to hydration pockets hosting 2 to 3 long-residing waters. The ordered hydration is intimately connected with RNA local conformational variations.

• MeSH
• bakteriální RNA chemie   MeSH
• chybné párování bází MeSH
• denaturace nukleových kyselin MeSH
• druhová specificita MeSH
• Escherichia coli chemie   MeSH
• hořčík chemie   MeSH
• konformace nukleové kyseliny MeSH
• makromolekulární látky MeSH
• molekulární modely * MeSH
• párování bází * MeSH
• počítačová simulace MeSH
• pohyb těles MeSH
• RNA ribozomální 5S chemie   MeSH
• RNA rostlin chemie   MeSH
• rozpouštědla chemie   MeSH
• sodík chemie   MeSH
• Spinacia oleracea chemie   MeSH
• vazebná místa MeSH
• voda chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH
• srovnávací studie MeSH
• validační studie MeSH
• Názvy látek
• bakteriální RNA MeSH
• hořčík MeSH
• makromolekulární látky MeSH
• RNA ribozomální 5S MeSH
• RNA rostlin MeSH
• rozpouštědla MeSH
• sodík MeSH
• voda MeSH

A two-dimensional, quantitative J-correlation NMR experiment for precise measurements of the proton-carbon vicinal coupling constants 3J(C2)/4-H1' and 3J(C6)/8-H1' in uniformly 13C-labeled nucleic acids is presented. To reduce loss of signal due to 1H-13C dipole-dipole relaxation, a multiple-quantum constant time experiment with appropriately incorporated band selective 1H and 13C pulses was applied. The experiment is used to obtain the 3J(C2)/4-H1' and 3J(C6)/8-H1' coupling constants in a uniformly 13C, 15N-labeled [d(G4T4G4)]2 quadruplex. The measured values and glycosidic torsion angles in the G-quadruplex, obtained by restrained molecular dynamics with explicit solvent using the previously published restraints, along with selected data from the literature are used to check and modify existing parameters of the Karplus equations. The parameterizations obtained using glycosidic torsion angles derived from the original solution and recently determined X-ray structures are also compared.

• MeSH
• DNA chemie   MeSH
• matematika MeSH
• molekulární modely MeSH
• nukleární magnetická rezonance biomolekulární * MeSH
• oligodeoxyribonukleotidy chemie   MeSH
• radioizotopy uhlíku MeSH
• rozpouštědla MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH
• Názvy látek
• DNA MeSH
• oligodeoxyribonukleotidy MeSH
• radioizotopy uhlíku MeSH
• rozpouštědla MeSH

Unrestrained 5-20-ns explicit-solvent molecular dynamics simulations using the Cornell et al. force field have been carried out for d[GCG(N)11GCG]2 (N, purine base) considering guanine*cytosine (G*C), adenine*thymine (A*T), inosine*5-methyl-cytosine (I*mC), and 2-amino-adenine*thymine (D*T) basepairs. The simulations unambiguously show that the structure and elasticity of N-tracts is primarily determined by the presence of the amino group in the minor groove. Simulated A-, I-, and AI-tracts show almost identical structures, with high propeller twist and minor groove narrowing. G- and D-tracts have small propeller twisting and are partly shifted toward the A-form. The elastic properties also differ between the two groups. The sequence-dependent electrostatic component of base stacking seems to play a minor role. Our conclusions are entirely consistent with available experimental data. Nevertheless, the propeller twist and helical twist in the simulated A-tract appear to be underestimated compared to crystallographic studies. To obtain further insight into the possible force field deficiencies, additional multiple simulations have been made for d(A)10, systematically comparing four major force fields currently used in DNA simulations and utilizing B and A-DNA forms as the starting structure. This comparison shows that the conclusions of the present work are not influenced by the force field choice.

• MeSH
• DNA chemie   MeSH
• konformace nukleové kyseliny MeSH
• molekulární modely MeSH
• párování bází MeSH
• polydeoxyribonukleotidy chemie   MeSH
• pružnost MeSH
• puriny chemie   MeSH
• vodíková vazba MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• polydeoxyribonukleotidy MeSH
• puriny MeSH