Biomedical subjects

Jirí Sponer

Publications and source records attributed to Jirí Sponer.

At least 19 recordsLinked to original sources

PubMed2007

Molecular dynamics simulations of RNA: an in silico single molecule approach.

RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNA-small molecule and RNA-protein complexes. Increased cooperation between theorists and experimentalists will allow expanded judicious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structure-function relationships in diverse and complex RNA molecules. .

Catalysis↗

PubMed2006

Calculation of structural behavior of indirect NMR spin-spin couplings in the backbone of nucleic acids.

Calculated indirect NMR spin-spin coupling constants (J-couplings) between (31)P, (13)C, and (1)H nuclei were related to the backbone torsion angles of nucleic acids (NAs), and it was shown that J-couplings can facilitate accurate and reliable structural interpretation of NMR measurements and help to discriminate between their distinct conformational classes. A proposed stepwise procedure suggests assignment of the J-couplings to torsion angles from the sugar part to the phosphodiester link. Some J-couplings show multidimensional dependence on torsion angles, the most prominent of which is the effect of the sugar pucker. J-couplings were calculated in 16 distinct nucleic acid conformations, two principal double-helical DNAs, B- and A-, the main RNA form, A-RNA, as well as in 13 other RNA conformations. High-level quantum mechanics calculations used a baseless dinucleoside phosphate as a molecular model, and the effect of solvent was included. The predicted J-couplings correlate reliably with available experimental data from the literature.

Algorithms↗

PubMed2006

Mechanism of action of anticancer titanocene derivatives: an insight from quantum chemical calculations.

Titanocene derivatives exhibit high potential in the treatment of cisplatin-resistant tumor types. Density functional theory calculations were performed on the hydrated form of five drug candidates differing in the pendant arms attached to the aromatic rings. A qualitative correlation has been found between the experimentally measured anticancer activity of alkylammonium-functionalized titanocene derivatives and the computed free energy change of the proton-induced dissociation reaction of these compounds. The results indicate that differences in the cytotoxic activities could be related to the solvation properties of the protolysis products, whereas no correlation was found with gas-phase properties of these molecules. Contrary to the free energy change of the protolysis reaction, other molecular properties, such as the geometrical parameters or the binding energies of the cyclopentadienyl rings in solution, do not correlate with the in vitro cytotoxic activity of these drug candidates.

Antineoplastic Agents↗

PubMed2006

Trapped water molecules are essential to structural dynamics and function of a ribozyme.

Ribozymes are catalytically competent examples of highly structured noncoding RNAs, which are ubiquitous in the processing and regulation of genetic information. Combining explicit-solvent molecular dynamics simulation and single molecule fluorescence spectroscopy approaches, we find that a ribozyme from a subviral plant pathogen exhibits a coupled hydrogen bonding network that communicates dynamic structural rearrangements throughout the catalytic core in response to site-specific chemical modification. Trapped long-residency water molecules are critical for this network and only occasionally exchange with bulk solvent as they pass through a breathing interdomain base stack. These highly structured water molecules line up in a string that may potentially also be involved in specific base catalysis. Our observations suggest important, still underappreciated roles for specifically bound water molecules in the structural dynamics and function of noncoding RNAs.

Base Pairing↗

PubMed2006

Structure, dynamics, and elasticity of free 16s rRNA helix 44 studied by molecular dynamics simulations.

Molecular dynamics (MD) simulations were employed to investigate the structure, dynamics, and local base-pair step deformability of the free 16S ribosomal helix 44 from Thermus thermophilus and of a canonical A-RNA double helix. While helix 44 is bent in the crystal structure of the small ribosomal subunit, the simulated helix 44 is intrinsically straight. It shows, however, substantial instantaneous bends that are isotropic. The spontaneous motions seen in simulations achieve large degrees of bending seen in the X-ray structure and would be entirely sufficient to allow the dynamics of the upper part of helix 44 evidenced by cryo-electron microscopic studies. Analysis of local base-pair step deformability reveals a patch of flexible steps in the upper part of helix 44 and in the area proximal to the bulge bases, suggesting that the upper part of helix 44 has enhanced flexibility. The simulations identify two conformational substates of the second bulge area (bottom part of the helix) with distinct base pairing. In agreement with nuclear magnetic resonance (NMR) and X-ray studies, a flipped out conformational substate of conserved 1492A is seen in the first bulge area. Molecular dynamics (MD) simulations reveal a number of reversible alpha-gamma backbone flips that correspond to transitions between two known A-RNA backbone families. The flipped substates do not cumulate along the trajectory and lead to a modest transient reduction of helical twist with no significant influence on the overall geometry of the duplexes. Despite their considerable flexibility, the simulated structures are very stable with no indication of substantial force field inaccuracies.

Base Pairing↗

PubMed2006

Indirect NMR spin-spin coupling constants 3J(P,C) and 2J(P,H) across the P-O...H-C link can be used for structure determination of nucleic acids.

Calculated indirect NMR spin-spin coupling constants (3)J(P,C) and (2)J(P,H) were correlated with the local structure of the P-O...H-C linkage between the nucleic acid (NA) backbone phosphate and the H-C group(s) of a nucleic acid base. The calculations were carried out for selected nucleotides from the large ribosomal subunit (Ban et al. Science 2000, 289, 905) with the aim of identifying NMR parameters suitable for detection of certain noncanonical RNA structures. As calculations in the model system, dimethyl-phosphate-guanine, suggest, the calculated indirect spin-spin couplings across the linkage are sensitive to the mutual orientation and distance between the phosphate and nucleic acid base. A short distance between the nucleic acid base and phosphate group and the angles C...P-O and P...C-H smaller than 50 degrees are prerequisites for a measurable spin-spin interaction of either coupling (|J| > 1 Hz). A less favorable arrangement of the P-O...H-C motif, e.g., in nucleotides of the canonical A-RNA, results in an effective dumping of both spin-spin interactions and insignificant values of the NMR coupling constants. The present work indicates that quantum chemical calculations of the indirect spin-spin couplings across the P-O...H-C motif can help detect some rare but important backbone topologies, as seen for example in the reverse kink-turn. Measuring of (3)J(P,C) and (2)J(P,H) couplings can therefore provide critical constraints on the NA base and phosphate geometry and help to determine the structure of NAs.

Carbon↗

PubMed2006

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme.

The hepatitis delta virus (HDV) ribozyme is an RNA enzyme from the human pathogenic HDV. Cations play a crucial role in self-cleavage of the HDV ribozyme, by promoting both folding and chemistry. Experimental studies have revealed limited but intriguing details on the location and structural and catalytic functions of metal ions. Here, we analyze a total of approximately 200 ns of explicit-solvent molecular dynamics simulations to provide a complementary atomistic view of the binding of monovalent and divalent cations as well as water molecules to reaction precursor and product forms of the HDV ribozyme. Our simulations find that an Mg2+ cation binds stably, by both inner- and outer-sphere contacts, to the electronegative catalytic pocket of the reaction precursor, in a position to potentially support chemistry. In contrast, protonation of the catalytically involved C75 in the precursor or artificial placement of this Mg2+ into the product structure result in its swift expulsion from the active site. These findings are consistent with a concerted reaction mechanism in which C75 and hydrated Mg2+ act as general base and acid, respectively. Monovalent cations bind to the active site and elsewhere assisted by structurally bridging long-residency water molecules, but are generally delocalized.

Base Sequence↗

PubMed2006

Copper cation interactions with biologically essential types of ligands: a computational DFT study.

This work presents a systematic theoretical study on Cu(I) and Cu(II) cations in variable hydrogen sulfide-aqua-ammine ligand fields. These ligands model the biologically most common environment for Cu ions. Molecular structures of the complexes were optimized at the density functional theory (DFT) level. Subsequent thorough energy analyses revealed the following trends: (i) The ammine complexes are the most stable, followed by those containing the aqua and hydrogen sulfide ligands, which are characterized by similar stabilization energies. (ii) The most preferred Cu(I) coordination number is 2 in ammine or aqua ligand fields. A qualitatively different binding picture was obtained for complexes with H(2)S ligands where the 4-coordination is favored. (iii) The 4- and 5-coordinated structures belong to the most stable complexes for Cu(II), regardless of the ligand types. Vertical and adiabatic ionization potentials of Cu(I) complexes were calculated. Charge distribution (using the natural population analysis (NPA) method) and molecular orbital analyses were performed to elucidate the nature of bonding in the examined systems. The results provide in-depth insight into the Cu-binding properties and can be, among others, used for the calibration of bioinorganic force fields.

Algorithms↗

PubMed2006

Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps.

Base-stacking energies in ten unique B-DNA base-pair steps and some other arrangements were evaluated by the second-order Møller-Plesset (MP2) method, complete basis set (CBS) extrapolation, and correction for triple (T) electron-correlation contributions. The CBS(T) calculations were compared with decade-old MP2/6-31G*(0.25) reference data and AMBER force field. The new calculations show modest increases in stacking stabilization compared to the MP2/6-31G*(0.25) data and surprisingly large sequence-dependent variation of stacking energies. The absolute force-field values are in better agreement with the new reference data, while relative discrepancies between quantum-chemical (QM) and force-field values increase modestly. Nevertheless, the force field provides good qualitative description of stacking, and there is no need to introduce additional pair-additive electrostatic terms, such as distributed multipoles or out-of-plane charges. There is a rather surprising difference of about 0.1 A between the vertical separation of base pairs predicted by quantum chemistry and derived from crystal structures. Evaluations of different local arrangements of the 5'-CG-3' step indicate a sensitivity of the relative stacking energies to the level of calculation. Thus, describing quantitative relations between local DNA geometrical variations and stacking may be more complicated than usually assumed. The reference calculations are complemented by continuum-solvent assessment of solvent-screening effects.

Base Pairing↗

PubMed2006

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs.

MP2 and CCSD(T) complete basis set (CBS) limit interaction energies and geometries for more than 100 DNA base pairs, amino acid pairs and model complexes are for the first time presented together. Extrapolation to the CBS limit is done by using two-point extrapolation methods and different basis sets (aug-cc-pVDZ - aug-cc-pVTZ, aug-cc-pVTZ - aug-cc-pVQZ, cc-pVTZ - cc-pVQZ) are utilized. The CCSD(T) correction term, determined as a difference between CCSD(T) and MP2 interaction energies, is evaluated with smaller basis sets (6-31G** and cc-pVDZ). Two sets of complex geometries were used, optimized or experimental ones. The JSCH-2005 benchmark set, which is now available to the chemical community, can be used for testing lower-level computational methods. For the first screening the smaller training set (S22) containing 22 model complexes can be recommended. In this case larger basis sets were used for extrapolation to the CBS limit and also CCSD(T) and counterpoise-corrected MP2 optimized geometries were sometimes adopted.

Amino Acids↗

PubMed2006

Molecular dynamics simulations of sarcin-ricin rRNA motif.

Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, hydration, cation binding and other SRD features is presented. The SRD is surprisingly static in multiple 25 ns long simulations and lacks any non-local motions, with root mean square deviation (r.m.s.d.) values between averaged MD and high-resolution X-ray structures of 1-1.4 A. Modest dynamics is observed in the tetraloop, namely, rotation of adenine in its apex and subtle reversible shift of the tetraloop with respect to the adjacent base pair. The deformed flexible region in low-resolution rat X-ray structure is repaired by simulations. The simulations reveal few backbone flips, which do not affect positions of bases and do not indicate a force field imbalance. Non-Watson-Crick base pairs are rigid and mediated by long-residency water molecules while there are several modest cation-binding sites around SRD. In summary, SRD is an unusually stiff rRNA building block. Its intrinsic structural and dynamical signatures seen in simulations are strikingly distinct from other rRNA motifs such as Loop E and Kink-turns.

Animals↗

PubMed2006

RNA kink-turns as molecular elbows: hydration, cation binding, and large-scale dynamics.

The presence of Kink-turns (Kt) at key functional sites in the ribosome (e.g., A-site finger and L7/L12 stalk) suggests that some Kink-turns can confer flexibility on RNA protuberances that regulate the traversal of tRNAs during translocation. Explicit solvent molecular dynamics demonstrates that Kink-turns can act as flexible molecular elbows. Kink-turns are associated with a unique network of long-residency static and dynamical hydration sites that is intimately involved in modulating their conformational dynamics. An implicit solvent conformational search confirms the flexibility of Kink-turns around their X-ray geometries and identifies a second low-energy region with open structures that could correspond to Kink-turn geometries seen in solution experiments. An extended simulation of Kt-42 with the factor binding site (helices 43 and 44) shows that the local Kt-42 elbow-like motion fully propagates beyond the Kink-turn, and that there is no other comparably flexible site in this rRNA region. Kink-turns could mediate large-scale adjustments of distant RNA segments.

Binding Sites↗

PubMed2005

Sugar pucker modulates the cross-correlated relaxation rates across the glycosidic bond in DNA.

The dependence of N1/9 and C1' chemical shielding (CS) tensors on the glycosidic bond orientation (chi) and sugar pucker (P) in the DNA nucleosides 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine was studied using the calculation methods of quantum chemistry. The results indicate that these CS-tensors exhibit a significant degree of conformational dependence on chi and P structural parameters. The presented data test underlying assumptions of currently established methods for interpretation of cross-correlated relaxation rates between the N1/9 chemical shielding tensor and C1'-H1' dipole-dipole (Ravindranathan et al. J. Biomol. NMR 2003, 27, 365-75. Duchardt et al. J. Am. Chem. Soc. 2004, 126, 1962-70) and highlight possible limitations of these methods when applied to DNA.

Computer Simulation↗

PubMed2005

Sugar edge/sugar edge base pairs in RNA: stabilities and structures from quantum chemical calculations.

Cis and trans sugar edge/sugar edge (SE/SE) binding patterns are essential building units of RNAs. For example, SE/SE interactions form the A-minor motifs, the most important tertiary interaction type in functional RNAs. This study provides an in-depth structure and stability analysis for these two base pair families. Gas-phase-optimized geometries are reported for 12 cis and 7 trans SE/SE base pairs and contrasted to their X-ray counterparts. Interaction energies are computed at the RIMP2 level of theory using the density-functional-theory-optimized geometries. There is a good overall agreement between the optimized and X-ray geometries of the cis SE/SE base pairs. In contrast, only three of the seven trans SE/SE binding patterns could be optimized without a significant distortion of the X-ray geometry. Note, however, that many SE/SE base pairs participate in broader networks of interactions; thus it is not surprising to see some of them to deviate from the X-ray geometry in a complete isolation. Computed interaction energies reveal that all 12 known cis SE/SE binding patterns are very stable. Among the trans SE/SE binding patterns, only the rG/rG, rG/rC, and rA/rG base pairs are sufficiently stable in the crystal geometry. Prediction has been made for some structures not yet detected by crystallography, namely, cis rC/rC, rG/rC, rG/rU, and rU/rU and trans rG/rA base pairs. Interestingly, the new cis SE/SE binding patterns are not necessarily isosteric with the remaining 12 members of this family. The trans rG/rA base pair represents a viable option for base pairing in RNA to be identified by future X-ray studies. In a complete lack of structural information, prediction of other unknown members of the trans SE/SE family was not attempted. Analysis of the interaction energies shows a very large electron correlation component of the interaction energy, pointing at the elevated role of dispersion energy as compared to other types of base pairs. This likely is profitable for stabilization of SE/SE binding patterns in polar environments and could be one of the reasons why the A-minor motif is the leading type of tertiary interactions in RNAs.

Base Pairing↗

PubMed2005

Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations.

The hepatitis delta virus (HDV) ribozyme is a self-cleaving RNA enzyme involved in the replication of a human pathogen, the hepatitis delta virus. Recent crystal structures of the precursor and product of self-cleavage, together with detailed kinetic analyses, have led to hypotheses on the catalytic strategies employed by the HDV ribozyme. We report molecular dynamics (MD) simulations (approximately 120 ns total simulation time) to test the plausibility that specific conformational rearrangements are involved in catalysis. Site-specific self-cleavage requires cytidine in position 75 (C75). A precursor simulation with unprotonated C75 reveals a rather weak dynamic binding of C75 in the catalytic pocket with spontaneous, transient formation of a H-bond between U-1(O2') and C75(N3). This H-bond would be required for C75 to act as the general base. Upon protonation in the precursor, C75H+ has a tendency to move towards its product location and establish a firm H-bonding network within the catalytic pocket. However, a C75H+(N3)-G1(O5') H-bond, which would be expected if C75 acted as a general acid catalyst, is not observed on the present simulation timescale. The adjacent loop L3 is relatively dynamic and may serve as a flexible structural element, possibly gated by the closing U20.G25 base-pair, to facilitate a conformational switch induced by a protonated C75H+. L3 also controls the electrostatic environment of the catalytic core, which in turn may modulate C75 base strength and metal ion binding. We find that a distant RNA tertiary interaction involving a protonated cytidine (C41) becomes unstable when left unprotonated, leading to disruptive conformational rearrangements adjacent to the catalytic core. A Na ion temporarily compensates for the loss of the protonated hydrogen bond, which is strikingly consistent with the experimentally observed synergy between low pH and high Na+ concentrations in mediating residual self-cleavage of the HDV ribozyme in the absence of divalents.

Base Sequence↗

PubMed2005

Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs.

Due to the presence of the 2'-OH hydroxyl group of ribose, RNA molecules utilize an astonishing variability of base pairing patterns to build up their structures and perform the biological functions. Many of the key RNA base pairing families have no counterparts in DNA. In this study, the trans Watson-Crick/sugar edge (trans WC/SE) RNA base pair family has been characterized using quantum chemical and molecular mechanics calculations. Gas-phase optimized geometries from density functional theory (DFT) calculations and RIMP2 interaction energies are reported for the 10 crystallographically identified trans WC/SE base pairing patterns. Further, stable structures are predicted for all of the remaining six possible members of this family not seen in RNAs so far. Among these novel six base pairs, the computations substantially refine two structures suggested earlier based on simple isosteric considerations. For two additional trans WC/SE base pairs predicted in this study, no arrangement was suggested before. Thus, our study brings a complete set of trans WC/SE base pairing patterns. The present results are also contrasted with calculations reported recently for the cis WC/SE base pair family. The computed base pair sizes are in sound correlation with the X-ray data for all WC/SE pairing patterns including both their cis and trans isomers. This confirms that the isostericity of RNA base pairs, which is one of the key factors determining the RNA sequence conservation patterns, originates in the properties of the isolated base pairs. In contrast to the cis structures, however, the isosteric subgroups of the trans WC/SE family differ not only in their H-bonding patterns and steric dimensions but also in the intrinsic strength of the intermolecular interactions. The distribution of the total interaction energy over the sugar-base and base-base contributions is controlled by the cis-trans isomerism.

Base Pairing↗

PubMed2005

Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.

Large RNA molecules exhibit an astonishing variability of base-pairing patterns, while many of the RNA base-pairing families have no counterparts in DNA. The cis Watson-Crick/sugar edge (cis WC/SE) RNA base pairing is investigated by ab initio quantum chemical calculations. A detailed structural and energetic characterization of all 13 crystallographically detected members of this family is provided by means of B3LYP/6-31G and RIMP2/aug-cc-pVDZ calculations. Further, a prediction is made for the remaining 3 cis WC/SE base pairs which are yet to be seen in the experiments. The interaction energy calculations point at the key role of the 2'-OH group in stabilizing the sugar-base contact and predict all 16 cis WC/SE base-pairing patterns to be nearly isoenergetic. The perfect correlation of the main geometrical parameters in the gas-phase optimized and X-ray structures shows that the principle of isosteric substitutions in RNA is rooted from the intrinsic structural similarity of the isolated base pairs. The present quantum chemical calculations for the first time analyze base pairs involving the ribose 2'-OH group and unambiguously correlate the structural information known from experiments with the energetics of interactions. The calculations further show that the relative importance and absolute value of the dispersion energy in the cis WC/SE base pairs are enhanced compared to the standard base pairs. This may by an important factor contributing to the strength of such interactions when RNA folds in its polar environment. The calculations further demonstrate that the Cornell et al. force field commonly used in molecular modeling and simulations provides satisfactory performance for this type of RNA interactions.

Base Pairing↗

PubMed2005

Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases.

Kink-turn (K-turn) motifs are asymmetric internal loops found at conserved positions in diverse RNAs, with sharp bends in phosphodiester backbones producing V-shaped structures. Explicit-solvent molecular dynamics simulations were carried out for three K-turns from 23S rRNA, i.e., Kt-38 located at the base of the A-site finger, Kt-42 located at the base of the L7/L12 stalk, and Kt-58 located in domain III, and for the K-turn of human U4 snRNA. The simulations reveal hinge-like K-turn motions on the nanosecond timescale. The first conserved A-minor interaction between the K-turn stems is entirely stable in all simulations. The angle between the helical arms of Kt-38 and Kt-42 is regulated by local variations of the second A-minor (type I) interaction between the stems. Its variability ranges from closed geometries to open ones stabilized by insertion of long-residency waters between adenine and cytosine. The simulated A-minor geometries fully agree with x-ray data. Kt-58 and Kt-U4 exhibit similar elbow-like motions caused by conformational change of the adenosine from the nominally unpaired region. Despite the observed substantial dynamics of K-turns, key tertiary interactions are stable and no sign of unfolding is seen. We suggest that some K-turns are flexible elements mediating large-scale ribosomal motions during the protein synthesis cycle.

Adenine↗