Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition

Sequence dependence of DNA conformation plays a crucial role in its recognition by proteins and ligands. To clarify the relationship between sequence and conformation, it is necessary to quantify the conformational energy and specificity of DNA. Here, we make a systematic analysis of dodecamer DNA structures including all the 136 unique tetranucleotide sequences at the center by molecular dynamics simulations. Using a simplified conformational model with six parameters to describe the geometry of adjacent base pairs and harmonic potentials along these coordinates, we estimated the equilibrium conformational parameters and the harmonic potentials of mean force for the central base-pair steps from many trajectories of the simulations. This enabled us to estimate the conformational energy and the specificity for any given DNA sequence and structure. We tested our method by using sequence-structure threading to estimate the conformational energy and the Z-score as a measure of specificity for many B-DNA and A-DNA crystal structures. The average Z-scores were negative for both kinds of structures, indicating that the potential of mean force from the simulation is capable of predicting sequence specificity for the crystal structures and that it may be used to study the sequence specificity of both types of DNA. We also estimated the positional distribution of conformational energy and Z-score within DNA and showed that they are strongly position dependent. This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands.     

Stress-induced nonlinear structural transition in DNA

DNA undergoes structural transition between right-handed B form and left-handed Z form upon twisting. We describe this phenomenon as a stress-induced nonlinear excitation, and show that the twisting of a circular DNA leads to a domain wall type excitation, in which a certain length of Z domain appears with a pair of domain walls. Detailed examination of the nonlinear stress-strain relationship shows that there is an attractive interaction between the domain walls with exponential distance dependence.     

Properties of phosphorothioate DNA analogs. An ab initio study of prototype model linkages derived from dimethyl-phosphate anion

Ab initio HF and MP2 calculations on prototype model linkages of phosphorothioate DNA backbones illuminate the effects of phosphorothioation on electronic and structural properties of DNA backbone. The replacement of a bridging oxygen atom by sulfur in the phosphodiester linkage is energetically favored over that of replacement of a non-bridging oxygen atom. In phosphorothioate derivatives containing the P(OS)_nb moiety, the non-bridging oxygen atom always bears a higher negative charge than the non-bridging sulfur. Additional calculations on protonated (neutral) adducts suggest that phosphorothioation of the phosphodiester linkage lowers its proton affinity. Moreover, protonation of the non-bridging oxygen atom at phosphorous is favored over the protonation of the non-bridging sulfur atom for linkages containing the P(OS)_nb moiety. The ab initio calculated structural parameters are compared to the available crystallographic data of small phosphorothioate molecules and phosphorothioate oligodeoxynucleotides. These results have implications upon the biological activity of phosphorothioate DNA analogs.     

Direct,Enantioselective, and Nickel(II) Catalyzed Reactions of N-Azidoacetyl Thioimides with Trimethyl Orthoformate: A New Combined Methodology for the Rapid Synthesis of Lacosamide and Derivatives

A direct and highly enantioselective reaction of N-azidoacetyl-1,3-thiazolidine-2-thione with trimethyl orthoformate catalyzed by Tol-BINAPNiCl₂ in the presence of TESOTf and 2,6-lutidine is reported. The heterocyclic scaffold can be easily removed by addition of a wide array of amines to give the corresponding enantiomerically pure 2-azido-3,3-dimethoxypropanamides in high yields. Appropriate manipulation of the N-benzyl amide derivative provides an efficient access to the antiepileptic agent lacosamide through a new enantioselective C−C bond-forming process. DFT computational studies uncover clues for the understanding of the remarkable stereocontrol of the addition of a nickel(II) enolate to a putative oxocarbenium intermediate from trimethyl orthoformate.     

Spectroscopic and electronic structure studies of copper(II) binding to His111 in the human prion protein fragment 106-115: evaluating the role of protons and methionine residues

The prion protein (PrP(C)) is implicated in the spongiform encephalopathies in mammals, and it is known to bind Cu(II) at the N-terminal region. The region around His111 has been proposed to be key for the conversion of normal PrP(C) to its infectious isoform PrP(Sc). The principal aim of this study is to understand the role of protons and methionine residues 109 and 112 in the coordination of Cu(II) to the peptide fragment 106-115 of human PrP, using different spectroscopic techniques (UV-vis absorption, circular dichroism, and electron paramagnetic resonance) in combination with detailed electronic structure calculations. Our study has identified a proton equilibrium with a pK(a) of 7.5 associated with the Cu(II)-PrP(106-115) complex, which is ascribed to the deprotonation of the Met109 amide group, and it converts the site from a 3NO to a 4N equatorial coordination mode. These findings have important implications as they imply that the coordination environment of this Cu binding site at physiological pH is a mixture of two species. This study also establishes that Met109 and Met112 do not participate as equatorial ligands for Cu, and that Met112 is not an essential ligand, while Met109 plays a more important role as a weak axial ligand, particularly for the 3NO coordination mode. A role for Met109 as a highly conserved residue that is important to regulate the protonation state and redox activity of this Cu binding site, which in turn would be important for the aggregation and amyloidogenic properties of the protein, is proposed.     

Radiationless transitions of molecules with large nuclear rearrangement

Radiationless transitions of molecules accompanied by a large nuclear rearrangement were investigated. A general formula which includes interference effects among promoting modes was used. Numerical analysis for the model system revealed that the energy-gap dependence of the transition probability exhibits quite different behavior from the usual gaussian-type dependence.     

PROTON TRANSFER IN THE PRIMARY PROCESS OF VISION

Abstract— Proton transfer was theoretically examined as a possible primary process of vision. The motion of protons in the adiabatic potential of the Schiff base hydrogen bond was investigated in terms of quantum mechanics. The probability of proton transfer from the Schiff base nitrogen (i.e. the unprotonation of Schiff base) was found to increase as the retinal rotated around 11–12. double bond by 90°. The results also suggested that the proton transfer can take place before or during the transition from the excited to ground state (excited state proton transfer). We proposed that such excited state proton transfer is one of the elementary processes in primary visual photochemistry, and this process leads to the unprotonated visual pigment, hyposorhodopsin, which has been experimentally verified as one of the primary photoproducts of rhodopsin. The probability of this process could be comparable to the conventional process leading to the protonated intermediate, bathorhodopsin. The relation of these results with the recent experimental data is discussed.     

SIMULATION ANALYSIS OF THE PHOTOCONVERSION PROCESS OF SQUID RHODOPSIN AT LIQUID HELIUM TEMPERATURE

The photoconversion process among squid rhodopsin, bathorhodopsin isorhodopsin and hypsorhodopsin was studied at liquid helium temperature. We evaluated the relative quantum yields of the photoconversion among four pigments by analysing the time-dependent change of absorption spectra. The result suggests that hypsorhodopsin is the common intermediate of rhodopsin and isorhodopsin, and there is no direct conversion between rhodopsin and isorhodopsin. Furthermore, rhodopsin converts to hypsorhodopsin or bathorhodopsin much more efficiently than does isorhodopsin, and bathorhodopsin does not convert directly to hypsorhodopsin. It was also found that rhodopsin and isorhodopsin convert to bathorhodopsin more efficiently than to hypsorhodopsin. In particular, the quantum yield of conversion from rhodopsin to bathorhodopsin was found to be about twice as large as that from rhodopsin to hypsorhodopsin. This result is somewhat in disagreement with the result obtained from the laser flash experiments at room and liquid nitrogen temperatures. The reason for the difference between the two experimental results is discussed.