Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins

Zinc is indispensable to all forms of life as it is an essential component of many different proteins involved in a wide range of biological processes. Not differently from other metals, zinc in proteins can play different roles that depend on the features of the metal-binding site. In this work, we describe zinc sites in proteins with known structure by means of three-dimensional templates that can be automatically extracted from PDB files and consist of the protein structure around the metal, including the zinc ligands and the residues in close spatial proximity to the ligands. This definition is devised to intrinsically capture the features of the local protein environment that can affect metal function, and corresponds to what we call a minimal functional site (MFS). We used MFSs to classify all zinc sites whose structures are available in the PDB and combined this classification with functional annotation as available in the literature. We classified 77% of zinc sites into ten clusters, each grouping zinc sites with structures that are highly similar, and an additional 16% into seven pseudo-clusters, each grouping zinc sites with structures that are only broadly similar. Sites where zinc plays a structural role are predominant in eight clusters and in two pseudo-clusters, while sites where zinc plays a catalytic role are predominant in two clusters and in five pseudo-clusters. We also analyzed the amino acid composition of the coordination sphere of zinc as a function of its role in the protein, highlighting trends and exceptions. In a period when the number of known zinc proteins is expected to grow further with the increasing awareness of the cellular mechanisms of zinc homeostasis, this classification represents a valuable basis for structure-function studies of zinc proteins, with broad applications in biochemistry, molecular pharmacology and de novo protein design

Elucidation of the ATP7B N-Domain Mg2+-ATP Coordination Site and Its Allosteric Regulation

The diagnostic of orphan genetic disease is often a puzzling task as less attention is paid to the elucidation of the pathophysiology of these rare disorders at the molecular level. We present here a multidisciplinary approach using molecular modeling tools and surface plasmonic resonance to study the function of the ATP7B protein, which is impaired in the Wilson disease. Experimentally validated in silico models allow the elucidation in the Nucleotide binding domain (N-domain) of the Mg2+-ATP coordination site and answer to the controversial role of the Mg2+ ion in the nucleotide binding process. The analysis of protein motions revealed a substantial effect on a long flexible loop branched to the N-domain protein core. We demonstrated the capacity of the loop to disrupt the interaction between Mg2+-ATP complex and the N-domain and propose a role for this loop in the allosteric regulation of the nucleotide binding process

Processes and patterns of oceanic nutrient limitation

Microbial activity is a fundamental component of oceanic nutrient cycles. Photosynthetic microbes, collectively termed phytoplankton, are responsible for the vast majority of primary production in marine waters. The availability of nutrients in the upper ocean frequently limits the activity and abundance of these organisms. Experimental data have revealed two broad regimes of phytoplankton nutrient limitation in the modern upper ocean. Nitrogen availability tends to limit productivity throughout much of the surface low-latitude ocean, where the supply of nutrients from the subsurface is relatively slow. In contrast, iron often limits productivity where subsurface nutrient supply is enhanced, including within the main oceanic upwelling regions of the Southern Ocean and the eastern equatorial Pacific. Phosphorus, vitamins and micronutrients other than iron may also (co-)limit marine phytoplankton. The spatial patterns and importance of co-limitation, however, remain unclear. Variability in the stoichiometries of nutrient supply and biological demand are key determinants of oceanic nutrient limitation. Deciphering the mechanisms that underpin this variability, and the consequences for marine microbes, will be a challenge. But such knowledge will be crucial for accurately predicting the consequences of ongoing anthropogenic perturbations to oceanic nutrient biogeochemistry. © 2013 Macmillan Publishers Limited. All rights reserved

Harmful Elements in Estuarine and Coastal Systems

Estuaries and coastal zones are dynamic transitional systems which provide many economic and ecological benefits to humans, but also are an ideal habitat for other organisms as well. These areas are becoming contaminated by various anthropogenic activities due to a quick economic growth and urbanization. This chapter explores the sources, chemical speciation, sediment accumulation and removal mechanisms of the harmful elements in estuarine and coastal seawaters. It also describes the effects of toxic elements on aquatic flora and fauna. Finally, the toxic element pollution of the Venice Lagoon, a transitional water body located in the northeastern part of Italy, is discussed as a case study, by presenting the procedures adopted to measure the extent of the pollution, the impacts on organisms and the restoration activities

Transition Metal Abundances in Microbial Carbonate: A Pilot Study Based on In Situ LA-ICP-MS Analysis

The ability to recognize the former existence of microbes as well as the biological origin of marine precipitates, such as putative microbialites, is crucial for understanding the development and history of early life on Earth. Increasingly, such rocks hold keys to understanding the geochemical evolution of the oceans and linked Earth systems. Vital trace elements previously have received relatively little attention as clues to the origin of carbonate rocks, and low abundance transition elements in particular, have been difficult to analyse in carbonate matrices for technical reasons. We have used laser ablation-inductively coupled plasma-mass spectroscopy for the in situ measurement of a broad suite of vital transition metals in Late Devonian reefal limestones that contain coeval microbialite (the calcimicrobe Renalcis), stromatoporoid sponge skeleton, early marine cement, and later diagenetic cement. Comparative experiments conducted in two different ion extraction modes determined theoretical detection limits for transition elements on NIST reference material SRM 612. Analyses of NIST glasses SRM 614 and 616 demonstrate accuracy relative to previously published data. On that basis we have identified significant enrichment of the vital elements V, Sn, Cu and Zn within the Renalcis. The stromatoporoid skeleton by contrast is enriched only in V. Earliest cements, which also may have been mediated to some degree by microbial biofilms on the basis of their morphology, show a much smaller degree of enrichment, and later cements show no enrichment, with the exception of Zn, which is concentrated in the latest cement. Fine particulate carbonate sediments (micrite) show variable metal enrichments that are attributable to varying contributions from detrital siliciclastic contamination. Renalcis was also enriched above the sponge and cements in regards to Mn, Cd, Co, and possibly Cr, but at less robust levels. Molybdenum and Sb were found not to be enriched in the Renalcis, and Ni, although clearly very low in concentration, could not be evaluated owing to its high detection limit. We additionally were able to identify specific zones of contamination in Renalcis encountered as the laser drilled deeper into the carbonate. Time resolved analysis allows exclusion of such contaminants from integration into the results. Successful application of the new technique will now allow us to assess metal uptake in ancient carbonates with implications for interpreting the biogenicity of putative microbialites