Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations.

A method is described for identifying collective motions in proteins from molecular dynamics trajectories or normal mode simulations. The method makes use of the covariances of atomic positional fluctuations. It is illustrated by an analysis of the bovine pancreatic trypsin inhibitor. Comparison of the covariance and cross-correlation matrices shows that the relative motions have many similar features in the different simulations. Many regions of the protein, especially regions of secondary structure, move in a correlated manner. Anharmonic effects, which are included in the molecular dynamics simulations but not in the normal analysis, are of some importance in determining the larger scale collective motions, but not the more local fluctuations. Comparisons of molecular dynamics simulations in the present and absence of solvent indicate that the environment is of significance for the long-range motions.     

Gap-phase dynamics and coexistence of a long-lived pioneer and shade-tolerant tree species in the canopy of an old-growth coastal temperate rain forest of Chiloé Island, Chile

Aim A major question with regard to the ecology of temperate rain forests in south‐central Chile is how pioneer and shade‐tolerant tree species coexist in old‐growth forests. We explored the correspondence between tree regeneration dynamics and life‐history traits to explain the coexistence of these two functional types in stands apparently representing a non‐equilibrium mixture. Location This study was conducted in northern Chiloé Island, Chile (41.6° S, 73.9° W) in a temperate coastal rain forest with no evidence of stand disruption by human impact. Methods We assessed stand structure by sampling all stems within two 50 × 20 m and four 5 × 100 m plots. A 600‐m long transect, with 20 uniformly spaced sampling points, was used to quantify seedling and sapling densities, obtain increment cores, and randomly select 10 tree‐fall gaps. We used tree‐ring analysis to assess establishment periods and to relate the influences of disturbances to the regeneration dynamics of the main canopy species. Results Canopy emergent tree species were the long‐lived pioneer Eucryphia cordifolia and the shade‐tolerant Aextoxicon punctatum. Shade‐tolerant species such as Laureliopsis philippiana and several species of Myrtaceae occupied the main canopy. The stem diameter distribution for E. cordifolia was distinctly unimodal, while for A. punctatum it was multi‐modal, with all age classes represented. Myrtaceae accounted for most of the small trees. Most tree seedlings and saplings occurred beneath canopy gaps. Based on tree‐ring counts, the largest individuals of A. punctatum and E. cordifolia had minimum ages estimated to be > 350 years and > 286 years, respectively. Shade‐tolerant Myrtaceae species and L. philippiana had shorter life spans (< 200 years). Most growth releases, regardless of tree species, were moderate and have occurred continuously since 1750. Main conclusions We suggest that this coastal forest has remained largely free of stand‐disrupting disturbances for at least 450 years, without substantial changes in canopy composition. Release patterns are consistent with this hypothesis and suggest that the disturbance regime is dominated by individual tree‐fall gaps, with sporadic multiple tree falls. Long life spans, maximum height and differences in shade tolerance provide a basis for understanding the long‐term coexistence of pioneer and shade‐tolerant tree species in this coastal, old‐growth rain forest, despite the rarity of major disturbances.     

Interactions of mono spermine porphyrin derivative with DNAs

In this work, we have characterized the interactions of monospermine porphyrin derivative with calf thymus DNA (ct-DNA) and poly (dG-dC)₂ in both B and Z conformation. By several spectroscopic techniques (UV–vis, electronic circular dichroism and resonance light scattering), the binding modes of monospermine porphyrin derivative with different DNA sequences have been elucidated. In the presence of ct-DNA, the porphyrin binds along the external double helix as well as in the presence of B conformation of poly (dG-dC)₂. Whilst when the Z form of the poly (dG-dC)₂ is induced, a slight intercalation of the porphyrin between the basis has been detected.     

Testing the vibrational exciton and the local mode models on the instructive cases of dicarvone,dipinocarvone, and dimenthol vibrational circular dichroism spectra

The vibrational circular dichroism (VCD) spectra of dicarvone ( 1 ), dipinocarvone ( 2 ), and dimenthol ( 3 ) have been recorded in the range 900–3200 cm⁻¹, encompassing the mid-infrared (mid-IR), the CO stretching, and the CH-stretching regions. For compound 3 also, the fundamental and the first overtone OH stretching regions have been investigated by IR/NIR absorption and VCD. Density functional theory (DFT) calculations allow one to interpret the IR and VCD spectra and to confirm the configuration/conformational studies previously conducted by X-ray diffraction. The most intense VCD signals are associated with the vibrational normal modes involving symmetry-related groups close to the CC bond connecting covalently the two molecular units. The vibrational exciton (VCDEC) model is fruitfully tested on the VCD data of compounds 1 and 2 for the spectroscopic regions at ~1700 cm⁻¹, and the local mode model is tested on compound 3 at ~3500 and ~6500 cm⁻¹. For compounds 1 and 2 also, ECD spectra are reported, and the exciton mechanism is tested also there, and connections to the VCDEC model are examined.     

Ruthenium mediated C-H activation of benzaldehyde thiosemicarbazones: Synthesis, structure and, spectral and electrochemical properties of the resulting complexes

Reaction of five 4R-benzaldehyde thiosemicarbazones (R = OCH₃, CH₃, H, Cl and NO₂) with [Ru(PPh₃)₃(CO)(H)Cl] in refluxing methanol in the presence of a base (NEt₃) affords complexes of two different types, viz. 1-R and 2-R. In the 1-R complexes the thiosemicarbazone is coordinated to ruthenium as a dianionic tridentate C,N,S-donor via C-H bond activation. Two triphenylphosphines and a carbonyl are also coordinated to ruthenium. The tricoordinated thiosemicarbazone ligand is sharing the same equatorial plane with ruthenium and the carbonyl, and the PPh₃ ligands are mutually trans. In the 2-R complexes the thiosemicarbazone ligand is coordinated to ruthenium as a monoanionic bidentate N,S-donor forming a four-membered chelate ring with a bite angle of 63.91(11)°. Two triphenylphosphines, a carbonyl and a hydride are also coordinated to ruthenium. The coordinated thiosemicarbazone ligand, carbonyl and hydride constitute one equatorial plane with the metal at the center, where the carbonyl is trans to the coordinated nitrogen of the thiosemicarbazone and the hydride is trans to the sulfur. The two triphenylphosphines are trans. Structures of the 1-CH₃ and 2-CH₃ complexes have been determined by X-ray crystallography. All the complexes show intense transitions in the visible region, which are assigned, based on DFT calculations, to transitions within orbitals of the thiosemicarbazone ligand. Cyclic voltammetry on the complexes shows two oxidations of the coordinated thiosemicarbazone on the positive side of SCE and a reduction of the same ligand on the negative side.     

Enhancing the separation of phosphorylated proteins in gel electrophoresis with dinuclear bispyridylmethylamine-tyrosine-acrylamide complexes

Bispyridylmethylamine-tyrosine-acrylamide ligands were prepared from protected tyrosine and dipyridylmethylamine by a twofold Mannich reaction and converted into acryl amides. Their manganese complexes were used as gel additives to increase the specific phosphate affinity in SDS-PAGE protein separations. The modified gel showed a distinct mobility shift of phosphorylated α-casein in comparison to the dephosphorylated protein.     

Soft bottom species richness and diversity as a function of depth and iceberg scour in Arctic glacial Kongsfjorden (Svalbard)

Macrozoobenthic soft-sediment communities of central Arctic Kongsfjorden inhabiting six depth zones between 5 and 30 m were sampled using SCUBA-diving during June–August 2003 and analysed comparatively. About 63 taxa were found, nine of which had not been reported for Kongsfjorden and four for Svalbard. Suspension feeding or surface and sub-surface detritivorous polychaetes and deposit-feeding amphipods were dominant. Only 11 of the 63 taxa (45 species and additional 18 families not further identified) inhabited the complete depth range. Biomass ranged from 3.5 to 25.0 g ash free dry mass m⁻² and mean Shannon diversity (Log e) was 2.06. Similarity clustering from abundance and biomass data showed a significant difference between the shallow station (5 m) and the rest. The latter formed two sub-groups (10–20 and 25–30 m). Depth is irrevocably correlated with ice-scouring. Thus the differences in diversity together with the predicted iceberg scour intensity support the ‘intermediate disturbance hypothesis’ indicating that habitats impacted by moderate iceberg scouring enable higher diversity. In contrast, biotopes frequently affected only host pioneer communities, while mature, less diverse assemblages dominate depths of low impact.