The impact of the histidyl residue position on the formation and stability of Cu(ii) complexes and their ability of ROS generation

Cu(ii) complexes with Ac-H1WKGPLR-NH, Ac-EH2KA-NH2, and Ac-KEH3K-NH2 peptides are able to generate reactive oxygen species.

Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin

Substantial increase in the temporal resolution of the stepping of dimeric molec- ular motors is possible by tracking the position of a large gold nanoparticle (GNP) attached to a labeled site on one of the heads. This technique was used to measure the stepping trajectories of conventional kinesin (Kin1) using the time dependent position of the GNP as a proxy. The trajectories revealed that the detached head always passes to the right of the head that is tightly bound to the microtubule (MT) during a step. In interpreting the results of such experiments, it is implicitly assumed that the GNP does not significantly alter the diffusive motion of the detached head. We used coarse-grained simulations of a system consisting of the MT-Kin1 complex with and without attached GNP to investigate how the stepping trajectories are affected. The two significant findings are: (1) The GNP does not faithfully track the position of the stepping head. (2) The rightward bias is typically exaggerated by the GNP. Both these findings depend on the precise residue position to which the GNP is attached. Surprisingly, we predict that the stepping trajectories of kinesin are not significantly affected if, in addition to the GNP, a 1 μm diameter cargo is attached to the coiled coil. Our simulations suggest the effects of the large probe have to be considered when inferring the stepping mechanisms using GNP tracking experiments.

Identification of biochemically neutral positions in liver pyruvate kinase

Understanding how each residue position contributes to protein function has been a long-standing goal in protein science. Substitution studies have historically focused on conserved protein positions. However, substitutions of nonconserved positions can also modify function. Indeed, we recently identified nonconserved positions that have large substitution effects in human liver pyruvate kinase (hLPYK), including altered allosteric coupling. To facilitate a comparison of which characteristics determine when a nonconserved position does vs. does not contribute to function, the goal of the current work was to identify neutral positions in hLPYK. However, existing hLPYK data showed that three features commonly associated with neutral positions – high sequence entropy, high surface exposure, and alanine scanning – lacked the sensitivity needed to guide experimental studies. We used multiple evolutionary patterns identified in a sequence alignment of the PYK family to identify which positions were least patterned, reasoning that these were most likely to be neutral. Nine positions were tested with a total of 117 amino acid substitutions. Although exploring all potential functions is not feasible for any protein, five parameters associated with substrate/effector affinities and allosteric coupling were measured for hLPYK variants. For each position, the aggregate functional outcomes of all variants were used to quantify a “neutrality” score. Three positions showed perfect neutral scores for all five parameters. Furthermore, the nine positions showed larger neutral scores than 17 positions located near allosteric binding sites. Thus, our strategy successfully enriched the dataset for positions with neutral and modest substitutions.

Influence of stubble quality and degree of soil-stubble contact on N2O emission

The organic residue position and C/N ratio regulate decomposition rate and, therefore, nitrogen (N) release to the soil. The N₂O emission from soil is produced by nitrification and denitrification processes. These processes are affected by the mineral N concentration, water filled pore space (WFPS) and soil temperature. The N₂O emission from soils covered by corn and soybean residues has been little studied so far. The aim of the present study was to evaluate the C/N ratio of corn and soybean residues and their contact degree with the soil on soil N₂O emissions. A greenhouse experiment was conducted with a completely randomized design and N₂O emission was determined using closed chambers. The N₂O emissions were affected by the residue position and not by its origin (soybean = corn). Treatments with residue on the surface had the highest N₂O emissions at the beginning of the trial, while residue incorporation showed constant values of N₂O emission during the experiment. Soil N₂O emissions were explained by two controlling variables: the WFPS and the N-NO₃^– soil concentration. The WFPS separated the emission values of N₂O into two groups (threshold value near 77% WFPS). When the WFPS exceeded the threshold value, the emissions of N₂O were partially explained by the concentration of N-NO₃^– soil.