DNA polymerase beta catalysis: are different mechanisms possible?

DNA polymerases are crucial constituents of the complex cellular machinery for replicating and repairing DNA. Discerning mechanistic pathways of DNA polymerase on the atomic level is important for revealing the origin of fidelity discrimination. Mammalian DNA polymerase beta (pol beta), a small (39 kDa) member of the X-family, represents an excellent model system to investigate polymerase mechanisms. Here, we explore several feasible low-energy pathways of the nucleotide transfer reaction of pol beta for correct (according to Watson-Crick hydrogen bonding) G:C basepairing versus the incorrect G:G case within a consistent theoretical framework. We use mixed quantum mechanics/molecular mechanics (QM/MM) techniques in a constrained energy minimization protocol to effectively model not only the reactive core but also the influence of the rest of the enzymatic environment and explicit solvent on the reaction. The postulated pathways involve initial proton abstraction from the terminal DNA primer O3'H group, nucleophilic attack that extends the DNA primer chain, and elimination of pyrophosphate. In particular, we analyze several possible routes for the initial deprotonation step: (i) direct transfer to a phosphate oxygen O(Palpha) of the incoming nucleotide, (ii) direct transfer to an active site Asp group, and (iii) transfer to explicit water molecules. We find that the most probable initial step corresponds to step (iii), involving initial deprotonation to water, which is followed by proton migration to active site Asp residues, and finally to the leaving pyrophosphate group, with an activation energy of about 15 kcal/mol. We argue that initial deprotonation steps (i) and (ii) are less likely as they are at least 7 and 11 kcal/mol, respectively, higher in energy. Overall, the rate-determining step for both the correct and the incorrect nucleotide cases is the initial deprotonation in concert with nucleophilic attack at the phosphate center; however, the activation energy we obtain for the mismatched G:G case is 5 kcal/mol higher than that of the matched G:C complex, due to active site structural distortions. Taken together, our results support other reported mechanisms and help define a framework for interpreting nucleotide specificity differences across polymerase families, in terms of the concept of active site preorganization or the so-called "pre-chemistry avenue".     

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

We develop an "end-transfer configurational bias Monte Carlo" method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin (oligonucleosome) at different salt conditions compared to other Monte Carlo moves. Our method extends traditional configurational bias by deleting a repeating motif (monomer) from one end of the biopolymer and regrowing it at the opposite end using the standard Rosenbluth scheme. The method's sampling efficiency compared to local moves, pivot rotations, and standard configurational bias is assessed by parameters relating to translational, rotational, and internal degrees of freedom of the oligonucleosome. Our results show that the end-transfer method is superior in sampling every degree of freedom of the oligonucleosomes over other methods at high salt concentrations (weak electrostatics) but worse than the pivot rotations in terms of sampling internal and rotational sampling at low-to-moderate salt concentrations (strong electrostatics). Under all conditions investigated, however, the end-transfer method is several orders of magnitude more efficient than the standard configurational bias approach. This is because the characteristic sampling time of the innermost oligonucleosome motif scales quadratically with the length of the oligonucleosomes for the end-transfer method while it scales exponentially for the traditional configurational-bias method. Thus, the method we propose can significantly improve performance for global biomolecular applications, especially in condensed systems with weak nonbonded interactions and may be combined with local enhancements to improve local sampling.     

Kinetic lattice grand canonical Monte Carlo simulation for ion current calculations in a model ion channel system

An algorithm in which kinetic lattice grand canonical Monte Carlo simulations are combined with mean field theory (KLGCMC/MF) is presented to calculate ion currents in a model ion channel system. In this simulation, the relevant region of the system is treated by KLGCMC simulations, while the rest of the system is described by modified Poisson-Boltzmann mean field theory. Calculation of reaction field due to induced charges on the channel/water and membrane/water boundaries is carried out using a basis-set expansion method [Im and Roux, J. Chem. Phys. 115, 4850 (2001)]. Calculation of ion currents, electrostatic potentials, and ion concentrations, as obtained from the KLGCMC/MF simulations, shows good agreement with Poisson-Nernst-Planck (PNP) theory predictions when the channel and membrane have the same dielectric constant as water. If the channel and membrane have a lower dielectric constant than water, however, there is a considerable difference between the KLGCMC/MF and PNP predictions. This difference is attributed to the reaction field, which is missing in PNP theory. It is demonstrated that the reaction field as well as fixed charges in the channel play key roles in selective ion transport. Limitations and further development of the current KLGCMC/MF approach are also discussed.     

Mechanism of reaction of alkyl radicals with (Ni(II)L)2+ complexes in aqueous solutions

The reactions of methyl radicals, CH(3), with the macrocyclic complexes Ni(II)L(1-5) (L(1-5) = cyclam derivatives, vide infra) and Ni(II)edta in aqueous solutions were studied. Methyl radicals react with all these nickel complexes, forming intermediates with Ni(III)-C sigma-bonds. The L(m)Ni(III)-CH(3) complexes are formed in equilibria processes with relatively fast forward rate constants of k(f) > 1 x 10(8) M(-1) s(-1) (except in the case of NiL(2)-trans I cyclam, where the reaction is slower). In all cases the decomposition of the transient complexes occurs via the homolytic cleavage of the metal-carbon sigma-bond. When the homolysis is relatively slow, an isomerisation process of the transient is also observed with the exception of NiL(2), where no isomerisation was observed. The results suggest that the strength of the Ni(III)-CH(3)sigma-bond is mainly affected by steric hindrance.     

Formation of amphiphile self-assembly phases in protic ionic liquids

A range of protic ionic liquids (PILs) have been identified as being capable of supporting the self-assembly of the nonionic surfactants myverol 18-99 K (predominantly monoolein) and phytantriol. PIL-surfactant penetration scans have provided a high throughput technique to determine which lyotropic liquid crystalline phases were formed in the 40 PIL-surfactant systems investigated. Lamellar, inverse hexagonal, and bicontinuous cubic phases that are stable in excess PIL have been observed in surfactant-PIL systems. The studied PILs possess a wide range of solvent properties, including surface tension and viscosity. The nature of the formed amphiphile self-assembly phases is discussed in terms of the PIL structure and solvent properties.     

Inelastic insights for molecular tunneling pathways: bypassing the terminal groups

As an example of the use of inelastic transport to deduce structure in molecular transport junctions, we compute the orientation dependence of the Inelastic Electron Tunneling (IET) spectrum of the 1-pentane monothiolate. We find that upon increasing the tilting angle of the molecule with respect to the normal to the electrode the spectrum changes as the intensity of some vibrations is enhanced. These differences occur because for higher tilting angles the tunneling path that bypasses the terminal group grows in importance. IETS can therefore be used to establish the molecular orientation in junctions terminating with alkyl chains and to investigate experimentally the relative importance of the available tunneling paths.     

Effect of chamber pressure on spreading and splashing of liquid drops upon impact on a dry smooth stationary surface

Liquid drop impacts on a smooth surface were studied at elevated chamber pressures to characterize the effect of gas pressure on drop spreading and splashing. Five common liquids were tested at impact speeds between 1.0 and 3.5 m/s and pressure up to 12 bars. Based on experiments at atmospheric pressure, a modification to the “free spreading” model (Scheller and Bousfield in AIChE Paper 41(6):1357–1367, 1995) has been proposed that improves the prediction accuracy of maximum spread factors from an error of 15–5%. At high chamber pressures, drop spreading and maximum spread factor were found to be independent of pressure. The splash ratio (Xu et al. in Phys Rev Lett 94:184505, 2005) showed a non-constant behavior, and a power-law model was demonstrated to predict the increase in splash ratio with decreasing impact speed in the low impact speed regime. Also, drop shape was found to affect splash promotion or suppression for an asymmetry greater than 7–8% of the equivalent drop diameter. The observations of the current work could be especially useful for the study of formation of deposits and wall combustion in engine cylinders.     

Effect of protic ionic liquids (PILs) on the formation of non-ionic dodecyl poly(ethylene oxide) surfactant self-assembly structures and the effect of these surfactants on the nanostructure of PILs

The ability of a series of non-ionic dodecyl poly(ethylene oxide) surfactants to form micelles in a variety of protic ionic liquids (PILs) was investigated using small and wide angle X-ray scattering (SAXS/WAXS). The C(12)E(n) surfactants with n = 3-8 were examined in PILs which contained either an ethyl, diethyl, triethyl, butyl, pentyl, ethanol or pentanol-ammonium cation in conjunction with either a nitrate or formate anion. The ability of the PILs to support micelles of these surfactants was highly dependent on their liquid nanostructure. The PILs containing hydroxyl groups on the cations were not nanostructured and had very low surfactant solubility (<1 wt%). The highly nanostructured PILs with butylammonium or pentylammonium cations contain large non-polar domains, and had excellent surfactant solubility, but due to the greater hydrocarbon solubility they had insufficient drive from the "solvophobic effect" to enable micelle formation. The PILs of ethylammonium nitrate (EAN), propylammonium nitrate (PAN), diethylammonium formate (DEAF) and triethylammonium formate (TEAF) had smaller non-polar domains, and all supported micelle formation below 20 wt% surfactant. The critical micelle concentration (CMC) of surfactants in EAN were two orders of magnitude greater than in water. The minimum molecular areas of the poly(ethylene oxide) head groups at the air/ionic liquid interface, A(min), were significantly larger in EAN than in water. The SAXS patterns from the micelles present in EAN fitted well to ellipsoids, whereas the micelles present in PAN fitted well to spheres. The nanostructure of select PILs was also influenced by the presence of surfactants.     

DNA-based optomechanical molecular motor

An azobenzene-capped DNA hairpin coupled to an AFM is presented as an optically triggered single-molecule motor. The photoinduced trans to cis isomerization of azobenzene affects both the overall length of the molecule and the ability of the DNA bases to hybridize. Using a combination of molecular dynamics simulations and free energy calculations the unfolding of both isomers along the O5'-O3' extension coordinate is monitored. The potentials of mean force (PMFs) along this coordinate indicate that there are two major differences induced by photoisomerization. The first is that the interbase hydrogen bond and stacking interactions are stable for a greater range of extensions in the trans system than in the cis system. The second difference is due to a decreased chain length of the cis isomer with respect to the trans isomer. These differences are exploited to extract work in optomechanical cycles. The disruption of the hairpin structure gives a maximum of 3.4 kcal mol(-1) of extractable work per cycle with an estimated maximum efficiency of 2.4%. Structure-function insights into the operation of this motor are provided, and the effect of the cantilever stiffness on the extractable work is characterized.     

Incomplete Relative Semi-Abelian Categories

We propose relative (to a distinguished class E of epimorphisms) versions of the so-called old and new style axioms for semi-abelian categories, and prove the equivalence of these two sets of axioms. The same results were obtained before under much stronger completeness/cocompleteness assumptions. One of obvious purposes of such a generalization is to include the trivial case of E being the class of all isomorphisms when the ground category is an arbitrary pointed category.