Movement patterns of Antillean manatees in Chetumal Bay (Mexico) and coastal Belize: A challenge for regional conservation

Information from 15 satellite‐tracked Antillean manatees (Trichechus manatus manatus) was analyzed in order to assess individual movements, home ranges, and high‐use areas for conservation decisions. Manatees were captured in Chetumal Bay, Mexico, and tagged with Argos‐monitored satellite transmitters. Location of the manatees and physical characteristics were assessed to describe habitat properties. Most manatees traveled to freshwater sources. The Maximum Area Size (MAS) for each manatee was determined using the observation‐area method. Additional kernel densities of 95% home range and 50% Center of Activity (COA) were also calculated, with manatees having 1–3 COAs. Manatees exhibited two different movement patterns: remaining in Chetumal Bay, and long‐distance (up to 240 km in 89 d). The residence time in Chetumal Bay was higher for females (89.6% of time) than for males (72.0%), but the daily travel rate (0.4–0.5 km/d) was similar for both sexes. Most of the COAs fell within Natural Protected Areas (NPA). However, manatees also travel for long distances into unprotected areas, where they face uncontrolled boat traffic, fishing activities, and habitat loss. Conservation of movement corridors may promote long‐distance movements and facilitate genetic exchange.     

Crystal structure of human cytosolic aspartyl‐tRNA synthetase,a component of multi‐tRNA synthetase complex

Human cytosolic aspartyl‐tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi‐tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways. Here, we report the crystal structure of DRS at a resolution of 2.25 Å. DRS is a homodimer with a dimer interface of 3750.5 Ų which comprises 16.6% of the monomeric surface area. Our structure reveals the C‐terminal end of the N‐helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N‐helix for the transfer of tRNA^Asp to elongation factor 1α. From our analyses of the crystal structure and post‐translational modification of DRS, we suggest that the phosphorylation of Ser146 provokes the separation of DRS from the MSC and provides the binding site for an interaction partner with unforeseen functions.Proteins 2013; 81:1840–1846. © 2013 Wiley Periodicals, Inc.     

Evolutionary patterns of Clavatoraceae (Charophyta) in the mesogean basins analysed according to environmental change during Malm and lower cretaceous

Evolutionary patterns of Clavatoraceae during the Malm and the Lower Cretaceous can be understood by considering how palaeoecological constraints of these charophytes were affected by palaeoenvironmental change. Speciation of Clavatoraceae reached maxima in the Tithonian and especially in the Lower Barremian, coinciding with an important areal extension and environmental diversification of freshwater swamps. Extinction reached a peak in the Upper Barremian, coinciding with the marine flooding of freshwater environments in Mesogea, and continued through the Aptian and Albian due to substitution of carbonatic freshwater swamps by terrigenous deltaic environments and probably by development of highly competitive aquatic flora of angiosperms. Anagenetic change within species attained maxima during the Berriasian and Lower Barremian, when freshwater environments became extensively developed. Absence of change (stasis) was marked during the Valanginian and Hauterivian, in a geological context of environmental stability and areal reduction of the freshwater environments.     

Late Wenlock (Middle Silurian) global Bioevent: Possible chemical cause for mass graptolite mortalities

Graptolites nearly became extinct in the latest Wenlock in all preserved stratigraphic sequences of this age. Graptolite mortalities occurred along the western coast of Laurentia and at sites that surrounded the Proto‐Tethys. Graptolite mass mortalities took place among deep‐water, open ocean dwelling organisms. After the mass mortalities, only the Pristiograptus dubius group and retiolids surface or near‐surface dwellers, survived. For a period of time, little speciation or diversification occurred. The base of the Ludlow is marked by diversification, with appearances of S. colonus, M. nilssoni and other groups which occur in near surface waters. None of the extensive plate movements postulated for the Silurian readily explain the mass extinctions that occurred. During the Silurian, global temperatures were warmer than present and atmospheric oxygen concentrations were lower, creating extensive oceanic anoxia. Below the oxygenated surface layers of the ocean, was an anoxic, non‐sulfidic zone (i.e. nitrate‐reducing) above a sulfidic zone. Graptolites lived over a range of depth from the oxygenated zone to either near or in the nitrate‐reducing zones. As the oxygen concentration declined through the Silurian, the depth of the oxic zone would have become shoaler with expanding anoxia. Late Wenlock graptolites that were unable to migrate to shallower depths, living in borderline oxygen conditions, could have been killed, resulting in the mortalities of the late Wenlock. Only those graptolites that were surface dwellers survived, adapted and reradiated.     

Molecular dynamics simulation of PNPLA3 I148M polymorphism reveals reduced substrate access to the catalytic cavity

A missense mutation I148M in PNPLA3 (patatin‐like phospholipase domain‐containing 3 protein) is significantly correlated with nonalcoholic fatty liver disease (NAFLD). To glean insights into mutation's effect on enzymatic activity, we performed molecular dynamics simulation and flexible docking studies. Our data show that the size of the substrate‐access entry site is significantly reduced in mutants, which limits the access of palmitic acid to the catalytic dyad. Besides, the binding free energy calculations suggest low affinity for substrate to mutant enzyme. The substrate‐bound system simulations reveal that the spatial arrangement of palmitic acid is distinct in wild‐type from that in mutant. The substrate recognition specificity is lost due to the loop where the I148M mutation was located. Our results provide strong evidence for the mechanism by which I148M affects the enzyme activity and suggest that mediating the dynamics may offer a potential avenue for NAFLD. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

π–π Stacking mediated drug–drug interactions in human CYP2E1

Because of having many low molecular mass substrates, CYP2E1 is of particular interests to the pharmaceutical industry. Many evidences showed that this enzyme can adopt multiple substrates to significantly reduce the oxidation rate of the substrates. The detailed mechanism for this observation is still unclear. In the current study, we employed GPU‐accelerated molecular dynamics simulations to study the multiple‐binding mode of human CYP2E1, with an aim of offering a mechanistic explanation for the unexplained multiple‐substrate binding. Our results showed that Thr303 and Phe478 were key factors for the substrate recognition and multiple‐substrate binding. The former can form a significant hydrogen bond to recognize and position the substrate in the productive binding orientation in the active site. The latter acted as a mediator for the substrate communications via π–π stacking interactions. In the multiple‐binding mode, the aforementioned π–π stacking interactions formed by the aromatic rings of both substrates and Phe478 drove the first substrate far away from the catalytic center, orienting in an additional binding position and going against the substrate metabolism. All these findings could give atomic insights into the detailed mechanism for the multiple‐substrate binding in human CYP2E1, providing useful information for the drug metabolism mechanism and personalized use of clinical drugs. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

Temperature‐dependent conformational change affecting Tyr11 and sweetness loops of brazzein

The sweet protein brazzein, a member of the Csβα fold family, contains four disulfide bonds that lend a high degree of thermal and pH stability to its structure. Nevertheless, a variable temperature study has revealed that the protein undergoes a local, reversible conformational change between 37 and 3°C with a midpoint about 27°C that changes the orientations and side‐chain hydrogen bond partners of Tyr8 and Tyr11. To test the functional significance of this effect, we used NMR saturation transfer to investigate the interaction between brazzein and the amino terminal domain of the sweet receptor subunit T1R2; the results showed a stronger interaction at 7°C than at 37°C. Thus the low temperature conformation, which alters the orientations of two loops known to be critical for the sweetness of brazzein, may represent the bound state of brazzein in the complex with the human sweet receptor. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

ACA‐specific RNA sequence recognition is acquired via the loop 2 region of MazF mRNA interferase

MazF is an mRNA interferase that cleaves mRNAs at a specific RNA sequence. MazF from E. coli (MazF‐ec) cleaves RNA at A and CA. To date, a large number of MazF homologs that cleave RNA at specific three‐ to seven‐base sequences have been identified from bacteria to archaea. MazF‐ec forms a dimer, in which the interface between the two subunits is known to be the RNA substrate‐binding site. Here, we investigated the role of the two loops in MazF‐ec, which are closely associated with the interface of the MazF‐ec dimer. We examined whether exchanging the loop regions of MazF‐ec with those from other MazF homologs, such as MazF from Myxococcus xanthus (MazF‐mx) and MazF from Mycobacterium tuberculosis (MazF‐mt3), affects RNA cleavage specificity. We found that exchanging loop 2 of MazF‐ec with loop 2 regions from either MazF‐mx or MazF‐mt3 created a new cleavage sequence at (A/U)(A/U)AA and C in addition to the original cleavage site, A and CA, whereas exchanging loop 1 did not alter cleavage specificity. Intriguingly, exchange of loop 2 with 8 or 12 consecutive Gly residues also resulted in a new RNA cleavage site at (A/U)(A/U)AA and C. The present study suggests a method for expanding the RNA cleavage repertoire of mRNA interferases, which is crucial for potential use in the regulation of specific gene expression and for biotechnological applications. Proteins 2013. © 2012 Wiley Periodicals, Inc.     

The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from Methanobrevibacter ruminantium

Methenyltetrahydromethanopterin cyclohydrolase (Mch) is involved in the methanogenesis pathway of archaea as a C₁ unit carrier where N⁵‐formyl‐tetrahydromethanopterin is converted to methenyl‐tetrahydromethanopterin. Mch from Methanobrevibacter ruminantium was cloned, purified, crystallized and its crystal structure solved at 1.37 Å resolution. A biologically active trimer, the enzyme is composed of two domains including an N‐terminal domain of six α‐helices encompassing a series of four β‐sheets and a predominantly anti‐parallel β–sheet at the C‐terminus flanked on one side by α‐helices. Sequence and structural alignments have helped identify residues involved in substrate binding and trimer formation. Proteins 2013; 81:2064–2070. © 2013 Wiley Periodicals, Inc.