Two-dimensional 1H and 31P NMR spectra and restrained molecular dynamics structure of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex

Assignment of the 1H and 31P NMR spectra of an extrahelical adenosine tridecamer oligodeoxyribonucleotide duplex, d(CGCAGAATTCGCG)2, has been made by two-dimensional 1H-1H and heteronuclear 31P-1H correlated spectroscopy. The downfield 31P resonance previously noted by Patel et al. (1982) has been assigned by both 17O labeling of the phosphate as well as a pure absorption phase constant-time heteronuclear 31P-1H correlated spectrum and has been associated with the phosphate on the 3' side of the extrahelical adenosine. JH3'-P coupling constants for each of the phosphates of the tridecamer were obtained from the 1H-31P J-resolved selective proton-flip 2D spectrum. By use of a modified Karplus relationship the C4-C3'-O3-P torsional angles (epsilon) were obtained. There exists a good linear correlation between 31P chemical shifts and the epsilon torsional angle. The 31P chemical shifts and epsilon torsional angles follow the general observation that the more internal the phosphate is located within the oligonucleotide sequence, the more upfield the 31P resonance occurs. Because the extrahelical adenosine significantly distorts the deoxyribose phosphate backbone conformation even several bases distant from the extrahelical adenosine, 31P chemical shifts show complex site- and sequence-specific variations. Modeling and NOESY distance-restrained energy minimization and restrained molecular dynamics suggest that the extrahelical adenosine stacks into the duplex. However, a minor conformation is also observed in the 1H NMR, which could be associated with a structure in which the extrahelical adenosine loops out into solution.     

Characterization of proline-containing right-handed alpha-helix by molecular dynamics studies

Proline residues play a special role in shaping the secondary and tertiary structures of proteins. Many of these aspects have been studied in great detail. Current interest lies in elucidating the structure of right-handed alpha-helical fragments which contain proline in the middle of the helix. Such structures play an important role in membrane proteins and in the tight packing of globular proteins. Analysis of several crystal structures and energy minimization using flexible geometry have elucidated the nature of the bend produced by proline in the right-handed alpha-helical structure. Molecular dynamics (MD) simulation studies are ideally suited to characterize rigidity or flexibility in different parts of the molecule and can also give an idea of various conformations of the molecule which can exist at a given temperature. Hence, MD studies on Ace-(Ala)6-Pro-(Ala)3-NHMe have been carried out for 100 ps after equilibration and the resulting trajectories have been analyzed. Information regarding the average values, r.m.s. fluctuations of internal parameters and the time spent in different conformations are discussed. Energy minimization has been carried out on selected MD simulated points in order to analyze the characteristics of different conformations.     

NMR and molecular modeling characterization of RGD containing peptides.

The tripeptide sequence arginine-glycine-aspartic acid (RGD) has been shown to be the key recognition segment in numerous cell adhesion proteins. The solution conformation and dynamics in DMSO-d6 of the cyclic pentapeptides, [formula: see text], a potent fibrinogen receptor antagonist, and [formula: see text], a weak fibrinogen receptor antagonist, have been characterized by nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. 1H-1H distance constraints derived from two-dimensional NOE spectroscopy and torsional angle constraints obtained from 3JNH-H alpha coupling constants, combined with computer-assisted modeling using conformational searching algorithms and energy minimization have allowed several low energy conformations of the peptides to be determined. Low temperature studies in combination with molecular dynamics simulations suggest that each peptide does not exist in a single, well-defined conformation, but as an equilibrating mixture of conformers in fast exchange on the NMR timescale. The experimental results can be fit by considering pairs of low energy conformers. Despite this inherent flexibility, distinct conformational preferences were found which may be related to the biological activity of the peptides.     

Simulation of conformational possibilities of DNA via calculation of nonbonded interactions of complementary dinucleoside phosphate complexes

Using classical potential functions, we carried out potential-energy calculations on the complementary deoxydinucleoside phosphate complexes dApdA:dUpdU, dUpdA:dUpdA, and dApdU:dApdU. All dihedral and bond angles, except those of the nitrogen bases, were varied. The resulting minimum-energy conformations of the complexes are close to DNA A- and B-family conformations, with a typical arrangement of the nitrogen bases. The dihedral and bond angles of one of the molecules forming the complex can thereby differ by several degrees from those of the other molecule. For different base sequences, some dihedral and bond angles may vary over a range of several degrees without appreciably changing the total energy of the complex. Some low-energy conformations of the complexes corresponding to other regions of the conformational space are also found. The biological consequences of possible changes in dihedral and bond angles, occurring on interaction with other molecules, are discussed.     

Stereochemistry of nucleic acids and polynucleotides. VI. Minimum energy conformations of dimethyl phosphate

As part of a study on the conformation of polynucleotides and nucleic acids the preferred conformations of the model conpound dimethyl phosphate are worked out using potential energy functions. In calculating the total potential energy associated with the conformation, nonbonded, torsional, and electrostatic terms have been considered. The variation of the total conformational energy is represented as a function of two torsion angles ? and ψ which are the rotations about the two phosphoester bonds. The most stable conformations are found to be the gauche–gauche conformations about these bonds. The conformations observed for phosphodiesters in the solid state and in the proposed structures of polynucleotides and nucleic acids cluster around the minimum. Also, regions of minimum energy correspond well with the typical allowed regions of a representative dinucleotide.     

UV photoelectron spectroscopy and ab initio characterization of valence orbital structures and conformations of neutral phosphate esters

The HeI UV photoelectron spectrum of trimethyl phosphate (TMP) has been measured and interpreted with the aid of SCF molecular orbital calculations carried out with STO-3G, STO-3G* and 4-31G basis functions. The photoelectron spectrum of TMP is more accurately reproduced by results from 4-31G calculations than by results from STO-3G or STO-3G* calculations. However, all three basis sets yield results which predict the same assignment of the photoelectron spectrum. Results at the 4-31G level indicate that whether calculations are based on crystallographic bond angles and bond lengths or on STO-3G optimized geometries has little effect on the energetic ordering of the upper occupied orbitals. The energetic ordering of orbitals is also found to be only weakly dependent upon the torsional angle phi, describing rotation of ester groups about P-O bonds and upon the torsional angle psi, describing rotation of methyl groups about C-O bonds. For trimethyl phosphate, with C3 symmetry, the vertical ionization potentials of the upper occupied orbitals are 10.81 eV (8e), 11.4 eV (9a), 11.93 eV (7e), 12.6-12.9 eV (8a and 6e), 14.4 eV (7a) and 15.0-16.0 eV (5e and 6a). Calculations at the 4-31G level indicate that many of the highest occupied orbitals in neutral dimethyl phosphate and methyl phosphate have energies and electron distributions similar to orbitals in TMP. For TMP, a search for optimized values of phi and psi has been carried out at the STO-3G*level. In agreement with previous NMR studies and with classical potential calculations, the STO-3G* results indicate that both the gauche (phi = 53.1 degrees) and anticlinal (phi = 141.9 degrees) conformations are thermally accessible. Also in agreement with the classical potential calculations, the STO-3G* results predict that in the all gauche conformation energy is minimized when the methyl groups assume a staggered geometry (psi = 60 degrees to 80 degrees) and that an energy maximum occurs for an eclipsed geometry (phi = 0 degrees to 20 degrees). A study of the dependence of optimized values of O-P-O ester bond angles on the torsional angles, phi, was carried out at the STO-3G, STO-3G* and 4-31G levels. The results demonstrate that for C3 symmetry, the coupling of O-P-O angles to phi is influence by repulsive steric interactions.     

Structural basis of hierarchical multiple substates of a protein. III: Side chain and main chain local conformations

An analysis is carried out of differences in the minimum energy conformations obtained in the previous paper by energy minimization starting from conformations sampled by a Monte Carlo simulation of conformational fluctuations in the native state of a globular protein, bovine pancreatic trypsin inhibitor. Main conformational differences in each pair of energy minima are found usually localized in several side chains and in a few local main chain segments. Such side chains and local main chain segments are found to take a few distinct local conformations in the minimum energy conformations. Energy minimum conformations can thus be described in terms of combinations of these multiple local conformations.     

Structure and Dynamics of Double Helical DNA in Torsion Angle Hyperspace: A Molecular Mechanics Approach

Abstract

Analysis of the conformational space populated by the torsion angles and the correlation between the conformational energy and the sequence of DNA are important for fully understanding DNA structure and function. Presence of seven variable torsion angles about single covalent bonds in DNA main chain puts a big challenge for such analysis. We have carried out restrained energy minimization studies for four representative dinucleosides, namely d(ApA):d(TpT), d(CpG):d(CpG), d(GpC):d(GpC) and d(CpA):d(TpG) to determine the energy hyperspace of DNA in context to the values of the torsion angles and the structural properties of the DNA conformations populating the favorable regions of this energy hyperspace. The torsion angles were manipulated by constraining their values at the reference points and then performing energy minimization. The energy minima obtained on the potential energy contour plots mostly correspond to the conformations populated in crystal structures of DNA. Some novel favorable conformations that are not present in crystal structure data are also found. The plots also suggest few low energy routes for conformational transitions or the associated energy barrier heights. Analyses of base pairing and stacking possibility reveal structural changes accompanying these transitions as well as the flexibility of different base steps towards variations in different torsion angles.     

Determination of the conformation of d(GGAAATTTCC)2 in solution by use of 1H NMR and restrained molecular dynamics

The conformation of the putative bent DNA d(GGAAATTTCC)2 in solution was studied by use of 1H NMR and restrained molecular dynamics. Most of the resonances were assigned sequentially. A total of 182 interproton distance restraints were determined from two-dimensional nuclear Overhauser effect spectra with short mixing times. Torsion angle restraints for each sugar moiety were determined by qualitative analysis of a two-dimensional correlated spectrum. Restrained molecular dynamics was carried out with the interproton distances and torsion angles incorporated into the total energy function of the system in the form of effective potential terms. As initial conformations for restrained molecular dynamics, classical A-DNA and B-DNA were adopted. The root mean square deviation (rmsd) between these two conformations is 5.5 A. The conformations obtained by use of restrained molecular dynamics are very similar to each other, the rmsd being 0.8 A. On the other hand, the conformations obtained by use of molecular dynamics without experimental restraints or restrained energy minimization depended heavily on the initial conformations, and convergence to a similar conformation was not attained. The conformation obtained by use of restrained molecular dynamics exhibits a few remarkable features. The second G residue takes on the BII conformation [Fratini, A. V., Kopka, M. L., Drew, H. R., & Dickerson, R. E. (1982) J. Biol. Chem. 257, 14686-14707] rather than the standard BI conformation. There is discontinuity of the sugar puckering between the eighth T and ninth C. The minor groove of the oligo(dA) tract is rather compressed. As a result, d(GGAAATTTCC)2 is bent.     

Stereochemistry of nucleic acids and their constituents. IV. Allowed and preferred conformations of nucleosides,nucleoside mono-, di-, tri-, tetraphosphates,nucleic acids and polynucleotides

A uniform notation and convention is suggested to describe the torsional angles in nucleic acids and their derivatives. The torsional angle χ, relating the stereochemistry of the base with respect to the sugar, shows more variation for the β-purine glycosides than for the β-pyrimidine glycosides. This variation is attributed to the fact that the β-purine derivatives may form intramolecular O(5′)-H…N(3) hydrogen bonding. The χ values for the α-purine and α-pyrimidine glycosides show preference for the –syn-clinal (or anti) conformation. The mode of puckering of the sugar also influences the χ value. The various possible conformations for the furanose ring are described by the torsional angles τ₀ τ₁, τ₂, τ₃, τ₄, about the five ring bonds. From an analysis of the torsional angles (ω, ?, ψ, ψ′, ?′, ω′) about the sugar phosphate bonds in the x-ray structures of the known nucleosides, nucleotides, phosphodiesters, nucleic acids, and related compounds, and from a consideration of molecular models, it is found that the possible conformations for the backbone of helical nucleic acids is strikingly limited. Most importantly, the preferred conformation of the nucleotide unit in poly nucleotides and nucleic acids turns out to be the same as that found for the nucleotide in the crystal structure. It is observed that base “stacking” is a consequence of the restricted backbone conformation. The torsional angles are illustrated in the form of conformational “wheels”. Interrelation between the torsion angles about successive pairs of sugar-phosphate bonds are presented in the form of conformational maps: ω,?; ?,ψ; ψ.ψ′; ψ′,?′; ?′,ω′; ω′,ω. The ω′,ω map shows the perferred conformations about the inter-nucleotide bonds of right- and left-handed helices and the possible conformations of phosphodiesters. The preferred conformation of the pyrophosphate and triphosphate is that in which the phosphate oxygens display a staggered arrangement when viewed along the P–P axis. A plausible structure and conformation for the ATPM^2? backbound complex is presented. This structure differs from that proposed by SzentGyorgi in that the metal (only transition metals are considered here) is not bound to the NH₂ nitrogen of adenine, but rather is simultaneously bound to N(7) of the ring and three phosphates (α, β, γ), or N(7) of the ring and two phosphates (β, γ). The remaining metal coordination may be satisfied by solvent–metal or enzyme–metal bonds.     

UV Photoelectron Spectroscopy and Ab Initio Characterization of Valence Orbital Structures and Conformations of Neutral Phosphate Esters

Abstract

The Hel UV photoelectron spectrum of trimethyl phosphate (TMP) has been measured and interpreted with the aid of SCF molecular orbital calculations carried out with STO-3G, STO-3G* and 4–31G basis functions. The photoelectron spectrum of TMP is more accurately reproduced by results from 4–31G calculations than by results from STO-3G or STO-3G* calculations. However, all three basis sets yield results which predict the same assignment of the photoelectron spectrum. Results at the 4–31G level indicate that whether calculations are based on crystallographic bond angles and bond lengths or on STO-3G optimized geometries has little effect on the energetic ordering of the upper occupied orbitals. The energetic ordering of orbitals is also found to be only weakly dependent upon the torsional angle φ, describing rotation of ester groups about P-O bonds and upon the torsional angle ψ, describing rotation of methyl groups about C-O bonds. For trimethyl phosphate, with C₃ symmetry, the vertical ionization potentials of the upper occupied orbitals are 10.81 eV (8e), 11.4 eV (9a), 11.93 eV (7e), 12.6–12.9 eV (8a and 6e), 14.4 eV (7a) and 15.0–16.0 eV(5e and 6a). Calculations at the 4–31G level indicate that many of the highest occupied orbitals in neutral dimethyl phosphate and methyl phosphate have energies and electron distributions similar to orbitals in TMP.

For TMP, a search for optimized values of φ and ψ has been carried out at the STO-3G* level. In agreement with previous NMR studies and with classical potential calculations, the STO- 3G* results indicate that both the gauche φ= 53.1 °) and anticlinal (φ = 141.9°) conformations are thermally accessible. Also in agreement with the classical potential calculations, the STO-3G* results predict that in the all gauche conformation energy is minimized when the methyl groups assume a staggered geometry (ψ= 60° to 80°) and that an energy maximum occurs for an eclipsed geometry (ψ = 0° to 20°). A study of the dependence of optimized values of O-P-O ester bond angles on the torsional angles, φ, was carried out at the STO-3G, STO-3G* and 4–31G levels. The results demonstrate that for C₃ symmetry, the coupling of O-P-O angles to φ is influenced by repulsive steric interactions.     

A comparison of the CHARMM, AMBER and ECEPP potentials for peptides. I. Conformational predictions for the tandemly repeated peptide (Asn-Ala-Asn-Pro)9

A search for low-energy helical and near-helical conformations of the tandemly repeated peptide (Asn-Ala-Asn-Pro)9 was undertaken by minimization of the CHARMM potential energy function from eight starting conformations; the latter were obtained from the two low-energy conformations of this repeated peptide found by Gibson & Scheraga, Proc. Natl. Acad. Sci. USA 83, 5649-5653 (1986), and the single conformation found by Brooks et al., Proc. Natl. Acad. Sci. USA 84, 4470-4474 (1987), and from modifications of these three conformations. The same eight starting conformations, as determined by dihedral angles, were used for minimizations of the AMBER and ECEPP potentials. Comparison of the final conformations by least-squares superposition of their C alpha atoms, and by inspection of the parameters of the ideal helix or coiled coil that most closely matched the coordinates of their C alpha atoms in a least-squares sense, showed that: (1) energy minimization, starting from the same conformation but using any two different potentials, could lead to final conformations whose resemblance to each other varied from acceptable to highly unsatisfactory; (2) the ordering of the final energy-minimized conformations, and the energy differences between them, were quite different for all three potentials; (3) the extent of agreement or disagreement between pairs of conformations generated using CHARMM and AMBER, CHARMM and ECEPP, or AMBER and ECEPP, respectively, was not significantly different. The lowest-energy conformation generated using each of the potentials was a left-handed helix, whose pitch and number of residues per turn were similar to those of the left-handed helix found by Gibson & Scheraga. Although the starting conformation which led to the lowest-energy conformation was different for all three potentials, pairwise superposition of the C alpha atoms in the final conformations showed root-mean-square deviations of only 1.0-1.3 A. It is concluded that energy minimizations starting from a large enough sample of initial conformations might on occasion lead to essentially the same conformational prediction whichever potential is used; however, if the sample of starting points is small, predictions based on the three potentials will usually diverge.     

Nuclear magnetic resonance and molecular modeling studies on O-beta-D-galactopyranosyl-(1----4)-O-beta-D-xylopyranosyl-(1----0)-L-se rine, a carbohydrate-protein linkage region fragment from connective tissue proteoglycans

The solution conformation of O-beta-D-galactopyranosyl-(1----4)-O-beta-D-xylopyranosyl-(1----0)-L-ser ine (GXS), a carbohydrate-protein linkage region fragment from connective tissue proteoglycans, was investigated by two-dimensional NMR spectroscopy and molecular modeling calculations. Specifically, the 1H and 13C resonances were assigned by 2D-COSY and by 1H-13C heteronuclear correlation spectroscopy methods. 2D-NOESY was used to generate distance constraints between the galactose and xylose and between the xylose and serine residues. The 1H vicinal coupling constants for the sugars and the serine were also determined. A general molecular modeling methodology suitable for complex carbohydrates was developed. This methodology employed molecular dynamics and energy minimization procedures together with the application of inter-residue spatial constraints across the linkages derived from 2D-NOESY. The first step in this methodology is the generation of a wide variety of starting conformations that span the (phi, psi) space for each linkage. In the present study, nine such conformations were constructed for each linkage using the torsion angles phi and psi corresponding to the gauche+, gauche-, and trans configurations across each of the two bonds constituting the linkage. These conformations were subjected to a combined molecular dynamics/energy minimization refinement using the NOESY derived constraints as pseudoenergy functions. Families of conformations for the whole molecule were then constructed from the structures derived for each linkage. Characterization of GXS using this methodology identified a single family of conformations that are consistent with the solution phase NMR data on this molecule.     

Can local energy minimization refine the PDB structures of different resolution universally?

Local energy minimization was statistically tested as the refinement strategy for PDB structure pairs of different resolution. The 13 pairs of structures with the only difference being the resolution were extracted from PDB and represented structures of 11 identical proteins obtained with different x-ray diffraction techniques. The rmsd distribution was calculated for these pairs before and after local energy minimization of each structure. MMFF94 was used for energy calculations and the quasi-Newtonian method was used for local energy minimization. By comparison of these two rmsd distributions, the local energy minimization was proved to statistically increase the structural differences in pairs, so it cannot be used for refinement purposes. To explore the prospects of complex refinement strategies based on energy minimization, randomized structures were obtained by moving the initial PDB structures as far as the minimized structures had been moved in the multidimensional space of atomic coordinates. For these randomized structures the rmsd distribution was calculated and compared with the one for minimized structures. The significant differences in their mean values proved the energy surface of the protein to have only few minima near the conformations of different resolution obtained by x-ray analysis for PDB. Some other results we obtained exploring the energy surface near these conformations are also presented. These results are expected to be useful for the development of new protein refinement strategies based on energy minimization.     

Empirical solvation models in the context of conformational energy searches: application to bovine pancreatic trypsin inhibitor.

Continuum solvation models that estimate free energies of solvation as a function of solvent accessible surface area are computationally simple enough to be useful for predicting protein conformation. The behavior of three such solvation models has been examined by applying them to the minimization of the conformational energy of bovine pancreatic trypsin inhibitor. The models differ only with regard to how the constants of proportionality between free energy and surface area were derived. Each model was derived by fitting to experimentally measured equilibrium solution properties. For two models, the solution property was free energy of hydration. For the third, the property was NMR coupling constants. The purpose of this study is to determine the effect of applying these solvation models to the nonequilibrium conformations of a protein arising in the course of global searches for conformational energy minima. Two approaches were used: (1) local energy minimization of an ensemble of conformations similar to the equilibrium conformation and (2) global search trajectories using Monte Carlo plus minimization starting from a single conformation similar to the equilibrium conformation. For the two models derived from free energy measurements, it was found that both the global searches and local minimizations yielded conformations more similar to the X-ray crystallographic structures than did searches or local minimizations carried out in the absence of a solvation component of the conformational energy. The model derived from NMR coupling constants behaved similarly to the other models in the context of a global search trajectory. For one of the models derived from measured free energies of hydration, it was found that minimization of an ensemble of near-equilibrium conformations yielded a new ensemble in which the conformation most similar to the X-ray determined structure PTI4 had the lowest total free energy. Despite the simplicity of the continuum solvation models, the final conformation generated in the trajectories for each of the models exhibited some of the characteristics that have been reported for conformations obtained from molecular dynamics simulations in the presence of a bath of explicit water molecules. They have smaller root mean square (rms) deviations from the experimentally determined conformation, fewer incorrect hydrogen bonds, and slightly larger radii of gyration than do conformations derived from search trajectories carried out in the absence of solvent.     

Synthesis, X-ray crystallographic structures of thio substituted N-acetyl N'-methylamide alanine and evaluation of sp sulfur parameters of the CFF91 force field.

Acetyl thioalanine N-methyl (Ac-Alat-NHMe) and thioacetyl alanine N-methyl (Act-Ala-NHMe) were synthesized, crystallized and their X-ray diffraction structures determined for the first time. Both molecules adopted beta-sheet conformations and showed similar hydrogen bonding patterns with one molecular surface forming two oxo hydrogen bonds and the other forming two thio hydrogen bonds. The crystal structure data for the two thioamides provided a validation of the thioamide parameters for the newly derived CFF91 force field because the observed crystal (phi, psi) angles were situated in the global minimum regions of the theoretical (phi, psi) map predicted using the parameters. In addition, the parameters were further validated because conformational energy minimization of the crystal structure produced low deviations in unit cell dimensions, bond lengths, bond angles and torsional angles, and a 120-ps molecular dynamics simulation also gave a low deviation for the most probable N-H...S=C bond distance.     

Conformational analysis of the 3'-5'-cyclic dinucleotide d less than pApA greater than by means of molecular mechanics

The conformational properties of the cyclic dinucleotide d less than pApA greater than were studied by means of molecular mechanics calculations in which a multiconformation analysis was combined with minimum energy calculations. In this approach models of possible conformers are built by varying the torsion angles of the molecule systematically. These models are then subjected to energy minimization; in the present investigation use was made of the AMBER Force field. It followed that the lowest energy conformer has a pseudo-two-fold axis of symmetry. In this conformer the deoxyribose sugars adopt a N-type conformation. The conformation of the sugar-phosphate backbone is determined by the following torsion angles: alpha +, beta t, gamma +, epsilon t and zeta +. The conformation of this ringsystem corresponds to the structure derived earlier by means of NMR spectroscopy and X-ray diffraction. The observation of a preference for N-type sugar conformations in this molecule can be explained by the steric hindrance induced between opposite H3' atoms when one sugar is switched from N- to S-type puckers. The sugars can in principle switch from N- to S-type conformations, but this requires at least the transition of gamma + to gamma -. In this process the molecule obtains an extended shape in which the bases switch from a pseudo-axial to a pseudo-equatorial position. The calculations demonstrate that, apart from the results obtained for the lowest energy conformation, the 180 degrees change in the propagation direction of the phosphate backbone can be achieved by several different combinations of the backbone torsion angles. It appeared that in the low energy conformers five higher order correlations are found. The combination of torsion angles which are involved in changes in the propagation direction of the sugar-phosphate backbone in DNA-hairpin loops and in tRNA, are found in the dataset obtained for cyclic d less than pApA greater than. It turns out, that in the available examples, 180 degrees changes in the backbone direction are localized between two adjacent nucleotides.     

Alteration of the DNA double helix conformation upon incorporation of mispairs as revealed by energy computations and pathways of point mutations.

To explain biochemical and genetic data on spontaneous nucleotide replacements in nucleic acid biosynthesis all the 8 mispairs in normal tautomeric forms have been considered. Possible B-conformations of DNA fragments containing each of such mispairs incorporated between Watson-Crick pairs have been found using computations of the energy of non-bonded interactions via classical potential functions. These conformations have no reduced interatomic contacts. The values of each dihedral angle of the sugar-phosphate backbone fall within the limits of those of double-helical fragments of B-DNA in crystals. These values differ from those of the corresponding angles for the low-energy polynucleotide conformations consisting of canonical pairs by no more than 30 degrees (except for the fragment with the U:U pair for which the C4'-C3'-O-P angle differs by about 50 degrees). The difference in experimentally observed frequencies of various nucleotide replacements in DNA biosynthesis correlates with the difference in the energy of non-bonded interactions and with the extent of the sugar-phosphate backbone distortion for the fragments containing the mispairs which serve as intermediates for the replacements.     

Study of conformations of the adenosine phosphates. II: Adenosine tri- and diphosphate (ATP,ADP)

Using extended Hückel theory (EHT), a theoretical study of the preferred conformations of ATP and ADP are compared with the experimentally observed structures, as the second of a set of studies on the molecular conformations of AMP, ATP and ADP. Results show that EHT yields a minimum energy ATP configuration that corresponds to the observed structure when atoms from the crystal are included in the calculations. Eight torsional angles were examined for ATP and six for ADP with all atoms included in the calculations. Results indicate that torsional rotations involving the adenosine part of the molecule show well-defined local minima. The predominant feature of the pyrophosphate section, however, is a low energy profile enabling the molecule to adapt its conformation to the environmental conditions.     

Assignments of 31P NMR resonances in oligodeoxyribonucleotides: origin of sequence-specific variations in the deoxyribose phosphate backbone conformation and the 31P chemical shifts of double-helical nucleic acids

It is now possible to unambiguously assign all 31P resonances in the 31P NMR spectra of oligonucleotides by either two-dimensional NMR techniques or site-specific 17O labeling of the phosphoryl groups. Assignment of 31P signals in tetradecamer duplexes, (dTGTGAGCGCTCACA)2, (dTAT-GAGCGCTCATA)2, (dTCTGAGCGCTCAGA)2, and (dTGTGTGCGCACACA)2, and the dodecamer duplex d(CGTGAATTCGCG)2 containing one base-pair mismatch, combined with additional assignments in the literature, has allowed an analysis of the origin of the sequence-specific variation in 31P chemical shifts of DNA. The 31P chemical shifts of duplex B-DNA phosphates correlate reasonably well with some aspects of the Dickerson/Calladine sum function for variation in the helical twist of the oligonucleotides. Correlations between experimentally measured P-O and C-O torsional angles and results from molecular mechanics energy minimization calculations show that these results are consistent with the hypothesis that sequence-specific variations in 31P chemical shifts are attributable to sequence-specific changes in the deoxyribose phosphate backbone. The major structural variation responsible for these 31P shift perturbations appears to be P-O and C-O backbone torsional angles which respond to changes in the local helical structure. Furthermore, 31P chemical shifts and JH3'-P coupling constants both indicate that these backbone torsional angle variations are more permissive at the ends of the double helix than in the middle. Thus 31P NMR spectroscopy and molecular mechanics energy minimization calculations appear to be able to support sequence-specific structural variations along the backbone of the DNA in solution.