Background: The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static protein structures to the outside solvent.

We have developed an algorithm, "MOLE," for the rapid, fully automated location and characterization of molecular channels, tunnels, and pores. This algorithm has been made freely available on the Internet (http://mole.chemi.muni.cz/) and overcomes many of the shortcomings and limitations of the recently developed CAVER software. The core of our MOLE algorithm is a Dijkstra's path search algorithm, which is applied to a Voronoi mesh. Tests on a wide variety of biomolecular systems including gramicidine, acetylcholinesterase, cytochromes P450, potassium channels, DNA quadruplexes, ribozymes, and the large ribosomal subunit have demonstrated that the MOLE algorithm performs well. MOLE is thus a powerful tool for exploring large molecular channels, complex networks of channels, and molecular dynamics trajectories in which analysis of a large number of snapshots is required.

Natural polyphenols are known to exhibit a lot of different biological properties, including antioxidant activity. For some polyphenols these activities are attributed to the presence of a guaiacol moiety. In the present paper we focus on the role of this moiety. For this purpose nine different compounds were enzymatically synthesized from guaiacol. To elucidate the structure-activity relationship of these polyphenols, DFT-(PCM)B3P86/6-311+G(2d,3pd)//(PCM)B3P86/6-31+G(d,p) calculations supported the experimental DPPH free radical scavenging activities. The antioxidant activities were correlated to (i) O-H BDEs (bond dissociation enthalpies), (ii) BDE(D) (BDE of a second H atom abstraction from the phenoxyradicals), (iii) spin density, (iv) HOMO (highest occupied molecular orbital) distribution, (v) IPs (ionization potentials), (vi) DeltaG and DeltaG(#) free energies of HAT (H atom transfer), and (vii) HAT rate constants. BDE(D) appeared to be the most important descriptor to understand the free radical scavenging ability of these compounds.

We have carried out an extended reference set of explicit solvent molecular dynamics simulations (63 simulations with 8.4 μs of simulation data) of canonical A-RNA duplexes. Most of the simulations were done using the latest variant of the Cornell et al. AMBER RNA force field bsc0χ(OL3), while several other RNA force fields have been tested. The calculations show that the A-RNA helix compactness, described mainly by geometrical parameters inclination, base pair roll, and helical rise, is sequence-dependent. In the calculated set of structures, the inclination varies from 10° to 24°. On the basis of simulations with modified bases (inosine and 2,6-diaminopurine), we suggest that the sequence-dependence of purely canonical A-RNA double helix is caused by the steric shape of the base pairs, i.e., the van der Waals interactions. The electrostatic part of stacking does not appear to affect the A-RNA shape. Especially visible is the role of the minor groove amino group of purines. This resembles the so-called Dickerson-Calladine mechanical rules suggested three decades ago for the DNA double helices. We did not identify any long-living backbone substate in A-RNA double helices that would resemble, for example, the B-DNA BI/BII dynamics. The variability of the A-RNA compactness is due to mutual movements of the consecutive base pairs coupled with modest change of the glycosidic χ torsion. The simulations further show that the A-RNA compactness is modestly affected by the water model used, while the effect of ionic conditions, investigated in the range from net-neutral condition to ~0.8 M monovalent ion excess salt, is smaller.