Experiment on compaction of air-dried soil under drop shocks

For the requirement in container nursery culture that growing media should be achieved the appropriate degree compaction, this paper presents an experiment on the compaction dynamics of air-dried soil under repetitive drop shocks, as a preliminary step toward the mechanization of this compaction method. The drop height used to adjust the shock intensity included 2 mm, 4 mm, 5 mm and 6 mm. And the overall packing density of soil in a vertically stratified cylinder vessel and the local packing density in each layer were taken as indicators of soil compaction states. The stretched exponential function derived from KWW law than the empirical inverse-logarithmic function has been found to be more suitable for expressing the temporal evolution of soil compaction, according to the results of curve-fitting to test values of the overall and local density. It is inherent in this experimental configuration that the drop shock intensity even at a constant drop height varies with drop times, owing to the interaction between the soil packing itself and drop shocks caused by the combination of the packing and the container. But the function t/τf(t,H) is manifested as a straight line on the drop times t with the line slope related to the drop height H, so the soil compaction dynamics caused by its drop shocks and that under the condition with actively controlled intensity actually share the common relaxation law. In addition, the soil’s one-dimensional distribution of local packing density showed a slight positive gradient as similar as monodisperse particles did.

RABDAM: quantifying specific radiation damage in individual protein crystal structures

Radiation damage remains one of the major limitations to accurate structure determination in protein crystallography (PX). Despite the use of cryo-cooling techniques, it is highly probable that a number of the structures deposited in the Protein Data Bank (PDB) have suffered substantial radiation damage as a result of the high flux densities of third generation synchrotron X-ray sources. Whereas the effects of global damage upon diffraction pattern reflection intensities are readily detectable, traditionally the (earlier onset) site-specific structural changes induced by radiation damage have proven difficult to identify within individual PX structures. More recently, however, development of theBDamagemetric has helped to address this problem.BDamageis a quantitative, per-atom metric identifies potential sites of specific damage by comparing the atomicB-factor values of atoms that occupy a similar local packing density environment in the structure. Building upon this past work, this article presents a program,RABDAM, to calculate theBDamagemetric for all selected atoms within any standard-format PDB or mmCIF file.RABDAMprovides several useful outputs to assess the extent of damage suffered by an input PX structure. This free and open-source software will allow assessment and improvement of the quality of PX structures both previously and newly deposited in the PDB.

Dissecting the roles of local packing density and longer-range effects in protein sequence evolution

What are the structural determinants of protein sequence evolution? A number of site-specific structural characteristics have been proposed, most of which are broadly related to either the density of contacts or the solvent accessibility of individual residues. Most importantly, there has been disagreement in the literature over the relative importance of solvent accessibility and local packing density for explaining site-specific sequence variability in proteins. We show here that this discussion has been confounded by the definition of local packing density. The most commonly used measures of local packing, such as the contact number and the weighted contact number, represent by definition the combined effects of local packing density and longer-range effects. As an alternative, we here propose a truly local measure of packing density around a single residue, based on the Voronoi cell volume. We show that the Voronoi cell volume, when calculated relative to the geometric center of amino-acid side chains, behaves nearly identically to the relative solvent accessibility, and both can explain, on average, approximately 34\% of the site-specific variation in evolutionary rate in a data set of 209 enzymes. An additional 10\% of variation can be explained by non-local effects that are captured in the weighted contact number. Consequently, evolutionary variation at a site is determined by the combined action of the immediate amino-acid neighbors of that site and of effects mediated by more distant amino acids. We conclude that instead of contrasting solvent accessibility and local packing density, future research should emphasize the relative importance of immediate contacts and longer-range effects on evolutionary variation.

Local Packing Density Is the Main Structural Determinant of the Rate of Protein Sequence Evolution at Site Level

Functional and biophysical constraints result in site-dependent patterns of protein sequence variability. It is commonly assumed that the key structural determinant of site-specific rates of evolution is the Relative Solvent Accessibility (RSA). However, a recent study found that amino acid substitution rates correlate better with two Local Packing Density (LPD) measures, the Weighted Contact Number (WCN) and the Contact Number (CN), than with RSA. This work aims at a more thorough assessment. To this end, in addition to substitution rates, we considered four other sequence variability scores, four measures of solvent accessibility (SA), and other CN measures. We compared all properties for each protein of a structurally and functionally diverse representative dataset of monomeric enzymes. We show that the best sequence variability measures take into account phylogenetic tree topology. More importantly, we show that both LPD measures (WCN and CN) correlate better than all of the SA measures, regardless of the sequence variability score used. Moreover, the independent contribution of the best LPD measure is approximately four times larger than that of the best SA measure. This study strongly supports the conclusion that a site’s packing density rather than its solvent accessibility is the main structural determinant of its rate of evolution.