Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations

Molecular modeling of nucleic Acid structure: electrostatics and solvation

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand its structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as multiple minima or conformational sampling problems, and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These subjects are discussed in detail in this unit.

Identification of amino acids in the human tetherin transmembrane domain responsible for HIV-1 Vpu interaction and susceptibility

Tetherin, also known as BST-2/CD317/HM1.24, is an antiviral cellular protein that inhibits the release of HIV-1 particles from infected cells. HIV-1 viral protein U (Vpu) is a specific antagonist of human tetherin that might contribute to the high virulence of HIV-1. In this study, we show that three amino acid residues (I34, L37, and L41) in the transmembrane (TM) domain of human tetherin are critical for the interaction with Vpu by using a live cell-based assay. We also found that the conservation of an additional amino acid at position 45 and two residues downstream of position 22, which are absent from monkey tetherins, are required for the antagonism by Vpu. Moreover, computer-assisted structural modeling and mutagenesis studies suggest that an alignment of these four amino acid residues (I34, L37, L41, and T45) on the same helical face in the TM domain is crucial for the Vpu-mediated antagonism of human tetherin. These results contribute to the molecular understanding of human tetherin-specific antagonism by HIV-1 Vpu.

Modelling proteins: conformational sampling and reconstruction of folding kinetics

In the last decades biomolecular simulation has made tremendous inroads to help elucidate biomolecular processes in-silico. Despite enormous advances in molecular dynamics techniques and the available computational power, many problems involve long time scales and large-scale molecular rearrangements that are still difficult to sample adequately. In this review we therefore summarise recent efforts to fundamentally improve this situation by decoupling the sampling of the energy landscape from the description of the kinetics of the process. Recent years have seen the emergence of many advanced sampling techniques, which permit efficient characterisation of the relevant family of molecular conformations by dispensing with the details of the short-term kinetics of the process. Because these methods generate thermodynamic information at best, they must be complemented by techniques to reconstruct the kinetics of the process using the ensemble of relevant conformations. Here we review recent advances for both types of methods and discuss their perspectives to permit efficient and accurate modelling of large-scale conformational changes in biomolecules. This article is part of a Special Issue entitled: Protein Dynamics: Experimental and Computational Approaches.

The unique structure of A-tracts and intrinsic DNA bending

Short runs of adenines are a ubiquitous DNA element in regulatory regions of many organisms. When runs of 4–6 adenine base pairs (‘A-tracts’) are repeated with the helical periodicity, they give rise to global curvature of the DNA double helix, which can be macroscopically characterized by anomalously slow migration on polyacrylamide gels. The molecular structure of these DNA tracts is unusual and distinct from that of canonical B-DNA. We review here our current knowledge about the molecular details of A-tract structure and its interaction with sequences flanking them of either side and with the environment. Various molecular models were proposed to describe A-tract structure and how it causes global deflection of the DNA helical axis. We review old and recent findings that enable us to amalgamate the various findings to one model that conforms to the experimental data. Sequences containing phased repeats of A-tracts have from the very beginning been synonymous with global intrinsic DNA bending. In this review, we show that very often it is the unique structure of A-tracts that is at the basis of their widespread occurrence in regulatory regions of many organisms. Thus, the biological importance of A-tracts may often be residing in their distinct structure rather than in the global curvature that they induce on sequences containing them.

Molecular modeling of nucleic acid structure: electrostatics and solvation

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics.

The A--B transition: temperature and base composition effects on hydration of DNA

Natural DNAs and some polynucleotides organised in fiber present the A--B form transition at a relative humidity (r.h.) which depends on the temperature. A shift of the midpoint of that helix--helix transition to higher r.h. values is observed when the temperature is risen. It is shown that the average number of water molecules associated to a nucleotide pair is the relevant parameter for the A-B transition and that this parameter can be given a precise value by a combination of different r.h. and temperature values. The minimum number of water molecules necessary to get the B form depends on the base composition of the DNA. It is observed that AT base pairs have a higher affinity toward water molecules than GC base pairs. In the B form there are 27 water molecules per GC nucleotide pair and 44 per AT pair. Moreover, we noted that the fraction of nucleotides in the B form as a function of the average number of water molecules associated per base pair does not depend on the temperature. The A helical form is obtained with about 11 water molecules per nucleotide pair and this number is not very sensitive to the base composition of DNA.

Unrestrained stochastic dynamics simulations of the UUCG tetraloop using an implicit solvation model

Three unrestrained stochastic dynamics simulations have been carried out on the RNA hairpin GGAC[UUCG] GUCC, using the AMBER94 force field (Cornell et al., 1995. J. Am. Chem. Soc. 117:5179-5197) in MacroModel 5.5 (Mohamadi et al., 1990. J. Comp. Chem. 11:440-467) and either the GB/SA continuum solvation model (Still et al., 1990. J. Am. Chem. Soc. 112:6127-6129) or a linear distance-dependent dielectric (1/R) treatment. The linear distance-dependent treatment results in severe distortion of the nucleic acid structure, restriction of all hydroxyl dihedrals, and collapse of the counterion atmosphere over the course of a 5-ns simulation. An additional vacuum simulation without counterions shows somewhat improved behavior. In contrast, the two GB/SA simulations (1.149 and 3.060 ns in length) give average structures within 1.2 A of the initial NMR structure and in excellent agreement with results of an earlier explicit solvent simulation (Miller and Kollman, 1997. J. Mol. Biol. 270:436-450). In a 3-ns GB/SA simulation starting with the incorrect UUCG tetraloop structure (Cheong et al., 1990. Nature. 346:680-682), this loop conformation converts to the correct loop geometry (Allain and Varani, 1995. J. Mol. Biol. 250:333-353), suggesting enhanced sampling relative to the previous explicit solvent simulation. Thermodynamic effects of 2'-deoxyribose substitutions of loop nucleotides were experimentally determined and are found to correlate with the fraction of time the ribose 2'-OH is hydrogen bonded and the distribution of the hydroxyl dihedral is observed in the GB/SA simulations. The GB/SA simulations thus appear to faithfully represent structural features of the RNA without the computational expense of explicit solvent.

Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation

Hydration around the DNA fragment d(C5T5).(A5G5) is presented from two molecular dynamics simulations of 10 and 12 ns total simulation time. The DNA has been simulated as a flexible molecule with both the CHARMM and AMBER force fields in explicit solvent including counterions and 0.8 M additional NaCl salt. From the previous analysis of the DNA structure B-DNA conformations were found with the AMBER force-field and A-DNA conformations with CHARMM parameters. High-resolution hydration patterns are compared between the two conformations and between C.G and T.A base-pairs from the homopolymeric parts of the simulated sequence. Crystallographic results from a statistical analysis of hydration sites around DNA crystal structures compare very well with the simulation results. Differences between the crystal sites and our data are explained by variations in conformation, sequence, and limitations in the resolution of water sites by crystal diffraction. Hydration layers are defined from radial distribution functions and compared with experimental results. Excellent agreement is found when the measured experimental quantities are compared with the equivalent distribution of water molecules in the first hydration shell. The number of water molecules bound to DNA was found smaller around T.A base-pairs and around A-DNA as compared to B-DNA. This is partially offset by a larger number of water molecules in hydrophobic contact with DNA around T.A base-pairs and around A-DNA. The numbers of water molecules in minor and major grooves have been correlated with helical roll, twist, and inclination angles. The data more fully explain the observed B-->A transition at low humidity.

Importance of explicit salt ions for protein stability in molecular dynamics simulation

The accurate and efficient treatment of electrostatic interactions is one of the challenging problems of molecular dynamics simulation. Truncation procedures such as switching or shifting energies or forces lead to artifacts and significantly reduced accuracy. The particle mesh Ewald (PME) method is one approach to overcome these problems by providing a computationally efficient means of calculating all long-range electrostatic interactions in a periodic simulation box by use of fast Fourier transformation techniques. For the application of the PME method to the simulation of a protein with a net charge in aqueous solution, counterions are added to neutralize the system. The usual procedure is to add charge-balancing counterions close to charged residues to neutralize the protein surface. In the present article, we show that for MD simulation of a small protein of marginal stability, the YAP-WW domain, explicit modeling of 0.2 M ionic strength (in addition to the charge-balancing counterions) is necessary to maintain a stable protein structure. Without explicit ions throughout the periodic simulation box, the charge-balancing counterions on the protein surface diffuse away from the protein, resulting in destruction of the beta-sheet secondary structure of the WW domain.

Theoretical studies of an exceptionally stable RNA tetraloop: observation of convergence from an incorrect NMR structure to the correct one using unrestrained molecular dynamics

We report on the results of five independent and unrestrained molecular dynamics simulations of an RNA tetraloop, r(GGACUUCGGUCC), and its related structures with the loop UUCG sugars changed to deoxyribose. Two separate NMR structures have been reported for the loop portion of this molecule, with the second refinement resulting in a slightly different and more accurate conformation for the loop. The root-mean-square deviation (RMSd) between the two NMR structures, for the loop portions only, is 2.5 A. Our simulations, starting from the two NMR structures, demonstrate that this tetraloop is a very stable and rigid structure with both nanosecond length simulations staying very close to the initial structures. Additionally, both simulations preserved most, if not all, of the NMR-derived interactions and violated very few of the nuclear Overhauser effect (NOE)-derived distances used in the structure refinements. However, when the two NMR structures were simulated with deoxyriboses in the loops instead of the native riboses, the flexibility of the systems increased and we observed a conversion from the incorrect to the correct loop conformation in the simulation which started in the incorrect loop conformation. When the riboses were subsequently re-introduced back into the structure which underwent the conversion, the agreement between this simulation and the one starting from the correct NMR structure was a remarkably low 0.5 A, demonstrating an almost complete convergence from the incorrect to the correct structure using unrestrained molecular dynamics.

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin

The hydration of the tRNA(Asp) anticodon hairpin was investigated through the analysis of six 500 ps multiple molecular dynamics (MMD) trajectories generated by using the particle mesh Ewald method for the treatment of the long-range electrostatic interactions. Although similar in their dynamical characteristics, these six trajectories display different local hydration patterns reflecting the landscape of the "theoretical" conformational space being explored. The statistical view gained through the MMD strategy allowed us to characterize the hydration patterns around important RNA structural motifs such as a G-U base-pair, the anticodon U-turn, and two modified bases: pseudouridine and 1-methylguanine. The binding of ammonium counterions to the hairpin has also been investigated. No long-lived hydrogen bond between water and a 2'-hydroxyl has been observed. Water molecules with long-residence times are found bridging adjacent pro-Rp phosphate atoms. The conformation of the pseudouridine is stiffened by a water-mediated base-backbone interaction and the 1-methylguanine is additionally stabilized by long-lived hydration patterns. Such long-lived hydration patterns are essential to ensure the structural integrity of this hairpin motif. Consequently, our simulations confirm the conclusion reached from an analysis of X-ray crystal structures according to which water molecules form an integral part of nucleic acid structure. The fact that the same conclusion is reached from a static and a dynamic point of view suggests that RNA and water together constitute the biologically relevant functional entity.

Hydration effects on the duplex stability of phosphoramidate DNA-RNA oligomers

Recent studies on uniformly modified oligonucleotides containing 3'-NHP(O)(O-)O-5'internucleoside linkages (3'amidate) and alternatively modified oligonucleotides containing 3'-O(O-)(O)PNH-5'internucleoside linkages (5'amidate) have shown that 3'amidate duplexes, formed with DNA or RNA complementary strands, are more stable in water than those of the corresponding phosphodiesters. In contrast, 5'amidates do not form duplexes at all. There is no steric reason that the 5'amidate duplex should not form. We demonstrate that these differences arise from differential solvation of the sugar-phosphate backbones. By molecular dynamics calculations on models of 10mer single-stranded DNA and double-stranded DNA-RNA molecules, both with and without the phosphoramidate backbone modifications, we show that the single-stranded 3'amidate and 5'amidate backbones are equally well solvated, but the 5'amidate backbone is not adequately solvated in an A-form duplex. These results are supported by quantum chemical free energy of solvation calculations which show that the 3'amidate backbone is favored relative to the 5'amidate backbone.

DNA structural forms

In the years that have passed since the publication of Wolfram Saenger's classic book on nucleic acid structure (Saenger, 1984), a considerable amount of new data has been accumulated on the range of conformations which can be adopted by DNA. Many unusual species have joined the DNA zoo, including new varieties of two, three and four stranded helices. Much has been learnt about intrinsic DNA curvature, dynamics and conformational transitions and many types of damaged or deformed DNA have been investigated. In this article, we will try to summarise this progress, pointing out the scope of the various experimental techniques used to study DNA structure, and, where possible, trying to discern the rules which govern the behaviour of this subtle macromolecule. The article is divided into six major sections which begin with a general discussion of DNA structure and then present successively, B-DNA, DNA deformations, A-DNA, Z-DNA and DNARNA hybrids. An extensive set of references is included and should serve the reader who wishes to delve into greater detai.

Interdependence of conformational variables in double-helical DNA

DNA exhibits conformational polymorphism, with the details depending on the sequence and its environment. To understand the mechanisms of conformational polymorphism and these transitions, we examine the interrelationships among the various conformational variables of DNA. In particular, we examine the stress-strain relation among conformational variables, describing base-pair morphology and their effects on the backbone conformation. For the calculation of base pairs, we use the method previously developed to calculate averages over conformational variables of DNA. Here we apply this method to calculate the Boltzmann averages of conformational variables for fixed values of one particular conformational variable, which reflects the strain in the structure responding to a particular driving stress. This averaging over all but one driving variable smooths the usual rough energy surface to permit observation of the effects of one conformational variable at a time. The stress-strain analyses of conformational variables of base pair slide, twist, and roll, which exhibit characteristic changes during the conformational transition of DNA, have shown that the conformational changes of base pairs are strongly correlated with one another. Furthermore, the stress-strain relations are not symmetrical with respect to these variables, i.e., the response of one coordinate to another is different from the reverse direction. We also examine the effect of conformational changes in base-pair variables on the sugar-backbone conformation by using the minimization method we developed. The conformational changes of base pairs affect the sugar pucker and other dihedral angles of the backbone of DNA, but each variable affects the sugar-backbone differently. In particular, twist is found to have the most influence in affecting the sugar pucker and backbone conformation. These calculated conformational changes in base pairs and backbone segments are consistent with experimental observations and serve to validate the calculation method.

Large-amplitude picosecond anisotropy decay of the intrinsic fluorescence of double-stranded DNA

The conformational flexibility of the DNA double helix is of great interest because of its potential role in protein recognition, packaging into chromosomes, formation of photodefects, and interaction with drugs. Theory finds that DNA is very flexible; however, there is a scarcity of experimental results that examine intrinsic properties of the DNA bases for the inherent flexibility in solution. We have studied the dynamics of poly(dA).poly(dT) and (dA)20.(dT)20 in a 50 mM cacodylate, 0.1 M NaCl, pH 7 buffer by using the time-correlated picosecond fluorescence anisotropy of thymine selectively excited at 293 nm. For both nucleic acids, a large-amplitude biphasic decrease in the anisotropy is observed that has a very fast, large-amplitude component on the picosecond time scale and a slower, smaller-amplitude component on the nanosecond time scale. These modes are sensitive to sucrose concentration, and are greatly attenuated at 77% sucrose by volume. This observation suggests that motions of the bases make a significant contribution to the observed fluorescence depolarization (in the absence of sucrose). Measurements on the single-stranded systems poly(dT) and (dT)20 reveal a much smaller amplitude of the very fast depolarization mode. These observations are consistent with a mechanism that involves concerted motions in the interior of the double-stranded systems.

A structural basis for a phosphoramide mustard-induced DNA interstrand cross-link at 5'-d(GAC)

Phosphoramide mustard-induced DNA interstrand cross-links were studied both in vitro and by computer simulation. The local determinants for the formation of phosphoramide mustard-induced DNA interstrand cross-links were defined by using different pairs of synthetic oligonucleotide duplexes, each of which contained a single potentially cross-linkable site. Phosphoramide mustard was found to cross-link dG to dG at a 5'-d(GAC)-3'. The structural basis for the formation of this 1,3 cross-link was studied by molecular dynamics and quantum chemistry. Molecular dynamics indicated that the geometrical proximity of the binding sites also favored a 1,3 dG-to-dG linkage over a 1,2 dG-to-dG linkage in a 5'-d(GCC)-3' sequence. While the enthalpies of 1,2 and 1,3 mustard cross-linked DNA were found to be very close, a 1,3 structure was more flexible and may therefore be in a considerably higher entropic state.

Molecular mechanics and dynamics studies on two structurally related amide-modified DNA backbones for antisense technology

The effect of the replacement of the natural phosphodiester linkage -C3'-O-PO2-O-CH2-C4'- in the DNA strand of RNA.DNA hybrid duplexes by either of the two amide linkages -C3'-CH2-CO-NH-CH2-C4'- or -C3'-CH2-NH-CO-CH2-C4' has been investigated by molecular mechanics (MM) and molecular dynamics (MD) simulations. Conformational analysis has been used to assess various low-energy conformers of the amide-modified backbones. MD simulations have been carried out to study the dynamic behavior of the modified duplexes. The modified RNA.DNA hybrid double helices kept a conservative base pairing scheme during the MD simulations. Although the general behavior has been found to be similar to that of the corresponding wild-type hybrid duplexes, some notable differences, especially regarding the sugar puckering in the amide-modified DNA strands, have been observed. The behavior of the RNA strands in the hybrid duplexes has not been affected by the modified DNA strands and is similar to that in wild-type RNA.DNA duplexes.

Grand canonical Monte Carlo molecular and thermodynamic predictions of ion effects on binding of an oligocation (L8+) to the center of DNA oligomers

Grand canonical Monte Carlo (GCMC) simulations are reported for aqueous solutions containing excess univalent salt (activities a +/- = 1.76-12.3 mM) and one of the following species: an octacationic rod-like ligand, L8+; a B-DNA oligomer with N phosphate charges (8 < or = N < or = 100); or a complex resulting from the binding of L8+ at the center of an N-mer (24 < or = N < or = 250). Simplified models of these multiply charged species are used in the GCMC simulations to predict the fundamental coulombic contributions to the following experimentally relevant properties: 1) the axial distance over which ligand binding affects local counterion concentrations at the surface of the N-mer; 2) the dependence on N of GCMC preferential interaction coefficients, gamma 32MC identical to delta C3/delta C2l a +/-, T, where C3 and C2 are, respectively, the molar concentrations of salt and the multiply charged species (ligand, N-mer or complex); and 3) the dependence on N of SaKobs identical to d in Kobs/d in a +/- = delta (magnitude of ZJ + 2 gamma 32J), where Kobs is the equilibrium concentration quotient for the binding of L8+ to the center of an N-mer and delta denotes the stoichiometric combination of terms, each of which pertains to a reactant or product J having magnitude of ZJ charges. The participation of electrolyte ions in the ligand binding interaction is quantified by the magnitude of SaKobs, which reflects the net (stoichiometrically weighted) difference in the extent of thermodynamic binding of salt ions to the products and reactants. Results obtained here from GCMC simulations yield a picture of the salient molecular consequences of binding a cationic ligand, as well as thermodynamic predictions whose applicability can be tested experimentally. Formation of the central complex is predicted to cause a dramatic reduction in the surface counterion (e.g., Na+) concentration over a region including but extending well beyond the location of the ligand binding site. For binding a cationic ligand, SaKobs is predicted to be negative, indicating net electrolyte ion release in the binding process. At small enough N, -SaKobs is predicted to decrease strongly toward zero with decreasing N. At intermediate N, -SaKobs appears to exceed its limiting value as N-->infinity.

Molecular dynamics simulations of a r(GA12G).d(CT12C) hybrid duplex

RNA.DNA hybrid duplexes are relevant in various biological mechanisms like transcription and replication. Enzymes like RNase H cleave specifically the RNA strand in RNA.DNA duplexes. In antisense technology the complexation of mRNA with "modified" oligo(deoxy)-nucleotides leads to new hybrid duplexes. The knowledge about structure and dynamical behavior on an atomic level is fundamental for the understanding of any process involving hybrid duplexes. Therefore, molecular dynamics studies (200 picoseconds of trajectory) on a hybrid duplex structure r(GA12G).d(CT12C) were performed. During the stimulations, the deoxyribose residues assumed a puckering state between C2'-endo and C3'-endo, with an average mode around O4'-endo-C1'-exo, whereas the riboses of the RNA strand remained in the C3'-endo puckering domain. The results are compared to those obtained for the DNA.DNA duplex d(GA12G).d(CT12C) under identical simulation conditions. The DNA strand in the hybrid duplex behaves similar to that in a standard B-type DNA duplex. The helical parameters of the hybrid duplex however are closer to A- than to B-type. These observations suggest that RNA.DNA hybrid double helices are neither clearly A-form nor B-form. The furanoses in both strands can assume different puckering modes without the appearance of major geometrical constraints. The simulation results are in excellent agreement with recent experimental data.