Structure of sortase, the transpeptidase that anchors proteins to the cell wall of Staphylococcus aureus

Surface proteins of Gram-positive bacteria play important roles during the pathogenesis of human infections and require sortase for anchoring to the cell-wall envelope. Sortase cleaves surface proteins at the LPXTG motif and catalyzes the formation of an amide bond between the carboxyl group of threonine (T) and the amino group of cell-wall crossbridges. The NMR structure of sortase reveals a unique β-barrel structure, in which the active-site sulfhydryl of cysteine-184 is poised for ionization by histidine-120, presumably enabling the resultant thiolate to attack the LPXTG peptide. Calcium binding near the active site stimulates catalysis, possibly by altering the conformation of a surface loop that recognizes newly translocated polypeptides. The structure suggests a mechanistic relationship to the papain/cathepsin proteases and should facilitate the design of new antiinfective agents.

The crystal structure of the immunity protein of colicin E7 suggests a possible colicin-interacting surface.

The immunity protein of colicin E7 (ImmE7) can bind specifically to the DNase-type colicin E7 and inhibit its bactericidal activity. Here we report the 1.8-angstrom crystal structure of the ImmE7 protein. This is the first x-ray structure determined in the superfamily of colicin immunity proteins. The ImmE7 protein consists of four antiparallel alpha-helices, folded in a topology similar to the architecture of a four-helix bundle structure. A region rich in acidic residues is identified. This negatively charged area has the greatest variability within the family of DNase-type immunity proteins; thus, it seems likely that this area is involved in specific binding to colicin. Based on structural, genetic, and kinetic data, we suggest that all the DNase-type immunity proteins, as well as colicins, share a "homologous-structural framework" and that specific interaction between a colicin and its cognate immunity protein relies upon how well these two proteins' charged residues match on the interaction surface, thus leading to specific immunity of the colicin.

Structure of the N intermediate of bacteriorhodopsin revealed by x-ray diffraction.

X-ray diffraction experiments revealed the structure of the N photointermediate of bacteriorhodopsin. Since the retinal Schiff base is reprotonated from Asp-96 during the M to N transition in the photocycle, and Asp-96 is reprotonated during the lifetime of the N intermediate, or immediately after, N is a key intermediate for understanding the light-driven proton pump. The N intermediate accumulates in large amounts during continuous illumination of the F171C mutant at pH 7 and 5 degrees Celsius. Small but significant changes of the structure were detected in the x-ray diffraction profile under these conditions. The changes were reversible and reproducible. The difference Fourier map indicates that the major change occurs near helix F. The observed diffraction changes between N and the original state were essentially identical to the diffraction changes reported for the M intermediate of the D96N mutant of bacteriorhodopsin. Thus, we find that the protein conformations of the M and N intermediates of the photocycle are essentially the same, in spite of the fact that in M the Schiff base is unprotonated and in N it is protonated. The observed structural change near helix F will increase access of the Schiff base and Asp-96 to the cytoplasmic surface and facilitate the proton transfer events that begin with the decay of the M state.

Three-dimensional tracking of motile bacteria near a solid planar surface.

Knowing how motile bacteria move near and along a solid surface is crucial to understanding such diverse phenomena as the migration of infectious bacteria along a catheter, biofilm growth, and the movement of bacteria through the pore spaces of saturated soil, a critical step in the in situ bioremediation of contaminated aquifers. In this study, a tracking microscope is used to record the three-dimensional motion of Escherichia coli near a planar glass surface. Data from the tracking microscope are analyzed to quantify the effects of bacteria-surface interactions on the swimming behavior of bacteria. The speed of cells approaching the surface is found to decrease in agreement with the mathematical model of Ramia et al. [Ramia, M., Tullock, D. L. & Phan-Tien, N. (1993) Biophys J. 65,755-778], which represents the bacteria as spheres with a single polar flagellum rotating at a constant rate. The tendency of cells to swim adjacent to the surface is shown in computer-generated reproductions of cell traces. The attractive interaction potential between the cells and the solid surface is offered as one of several possible explanations for this tendency.

Tectonic geomorphology assessment of the Ken River catchment near Panna, Madhya Pradesh, India

This thesis focuses on tectonic geomorphology and the response of the Ken River catchment to postulated tectonic forcing along a NE-striking monocline fold in the Panna region, Madhya Pradesh, India. Peninsular India is underlain by three northeast-trending paleotopographic ridges of Precambrian Indian basement, bounded by crustal-scale faults. Of particular interest is the Pokhara lineament, a crustal scale fault that defines the eastern edge of the Faizabad ridge, a paleotopographic high cored by the Archean Bundelkhand craton. The Pokhara lineament coincides with the monocline structure developed in the Proterozoic Vindhyan Supergroup rocks along the Bundelkhand cratonic margin. A peculiar, deeply incised meander-like feature, preserved along the Ken River where it flows through the monocline, may be intimately related to the tectonic regime of this system. This thesis examines 41 longitudinal stream profiles across the length of the monocline structure to identify any tectonic signals generated from recent surface uplift above the Pokhara lineament. It also investigates the evolution of the Ken River catchment in response to the generation of the monocline fold. Digital Elevation Models (DEM) from Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) were used to delineate a series of tributary watersheds and extract individual stream profiles which were imported into MATLAB for analysis. Regression limits were chosen to define distinct channel segments, and knickpoints were defined at breaks between channel segments where there was a discrete change in the steepness of the channel profile. The longitudinal channel profiles exhibit the characteristics of a fluvial system in transient state. There is a significant downstream increase in normalized steepness index in the channel profiles, as well as a general increase in concavity downstream, with some channels exhibiting convex, over-steepened segments. Normalized steepness indices and uppermost knickpoint elevations are on average much higher in streams along the southwest segment of the monocline compared to streams along the northeast segment. Most channel profiles have two to three knickpoints, predominantly exhibiting slope-break morphology. These data have important implications for recent surface uplift above the Pokhara lineament. Furthermore, geomorphic features preserved along the Ken River suggest that it is an antecedent river. The incised meander-like feature appears to be the abandoned river valley of a former Ken River course that was captured during the evolution of the landscape by what is the present day Ken River.

Chemical composition of the chalcophanite rich surface of an encrusted rock ashore Lake Macquarie, Australia

Mineralogical interest in the nature of manganese oxide particulates in natural marine water (Suess, 1979), natural lake water (Klaveness, 1977), and simulated lake water (Giovanoli, 1980), prompted a search for such particulates in a large New South Wales coastal lake. The investigated waters did show the existence of manganese oxide replacement phenomena in fragmentary sedimentary rocks near the south margin of Lake Macquarie. The black crusts of manganese oxide discovered on rocks close to the waterline have revealed a three layers structure. Layer A (0-35 micron), adjacent to the rock, is composed essentially of kaolinite of weathering origin, together with low levels of manganese oxide without detectable Zn. Layer B (35-80 micron) follows as a manganese oxide layer containing admixed kaolinite and low amounts of Zn. Layer C (80-130 micron) is the closest to the surface and is made of Chalcophanite containing 10-15% of ZnO.

Near-shore wave power characterized with a remotely controlled surface vehicle in Admiralty Inlet, Puget Sound, WA

Senior thesis written for Oceanography 445

Molecular dynamics characterization of n-octyl-beta-D-glucopyranoside micelle structure in aqueous solution

n-Octyl-beta-D-glueopyranoside (OG) is a non-ionic glycolipid, which is used widely in biotechnical and biochemical applications. All-atom molecular dynamics simulations from two different initial coordinates and velocities in explicit solvent have been performed to characterize the structural behaviour of an OG aggregate at equilibrium conditions. Geometric packing properties determined from the simulations and small angle neutron scattering experiment state that OG micelles are more likely to exist in a non-spherical shape, even at the concentration range near to the critical micelle concentration (0.025 M). Despite few large deviations in the principal moment of inertia ratios, the average micelle shape calculated from both simulations is a prolate ellipsoid. The deviations at these time scales are presumably the temporary shape change of a micelle. However, the size of the micelle and the accessible surface areas were constant during the simulations with the micelle surface being rough and partially elongated. Radial distribution functions computed for the hydroxyl oxygen atoms of an OG show sharper peaks at a minimum van der Waals contact distance than the acetal oxygen, ring oxygen, and anomeric carbon atoms. This result indicates that these atoms are pointed outwards at the hydrophilic/hydrophobic interface, form hydrogen bonds with the water molecules, and thus hydrate the micelle surface effectively. (c) 2005 Elsevier Inc. All rights reserved.

Solution structure and characterization of the LGR8 receptor binding surface of insulin-like peptide 3

Insulin-like peptide 3 (INSL3), a member of the relaxin peptide family, is produced in testicular Leydig cells and ovarian thecal cells. Gene knock-out experiments have identified a key biological role in initiating testes descent during fetal development. Additionally, INSL3 has an important function in mediating male and female germ cell function. These actions are elicited via its recently identified receptor, LGR8, a member of the leucine-rich repeat-containing G-protein- coupled receptor family. To identify the structural features that are responsible for the interaction of INSL3 with its receptor, its solution structure was determined by NMR spectroscopy together with in vitro assays of a series of B-chain alanine-substituted analogs. Synthetic human INSL3 was found to adopt a characteristic relaxin/ insulin-like fold in solution but is a highly dynamic molecule. The four termini of this two-chain peptide are disordered, and additional conformational exchange is evident in the molecular core. Alanine-substituted analogs were used to identify the key residues of INSL3 that are responsible for the interaction with the ectodomain of LGR8. These include Arg(B16) and Val(B19), with His(B12) and Arg(B20) playing a secondary role, as evident from the synergistic effect on the activity in double and triple mutants involving these residues. Together, these amino acids combine with the previously identified critical residue, Trp(B27), to form the receptor binding surface. The current results provide clear direction for the design of novel specific agonists and antagonists of this receptor.

The effect of rock surface aspect on growth, size structure and competition in the lichen Rhizocarpon geographicum

Rhizocarpon geographicum is a crustose lichen found frequently on rock surfaces of southern aspect and less frequently on rock surfaces of northern aspect in Gwynedd, North Wales. This study tested the hypothesis that the radial growth of R. geographicum thalli predicts aspect distribution. Thalli of all sizes, however, exhibited significantly greater radial growth over 18 months on northwest compared with southeast facing surfaces. The hypothesis that a more intense competitive environment on northwest facing surfaces may explain the aspect distribution of R. geographicum was then tested. The size frequency distributions of thalli revealed a higher proportion of thalli in the smallest size class and a more restricted thallus size range on the northwest facing surfaces. In addition, thallus mortality appeared to be greater on northwest facing surfaces. Significantly more associated lichen species were present on rock surfaces of northern aspect at sites where R. geographicum was present. The mean frequency of the associated lichen species, however, was significantly lower on surfaces of northern aspect where R. geographicum was present. In addition, two common foliose species at these sites were demonstrated experimentally to overgrow thalli of R. geographicum. It is concluded that the growth of R. geographicum over the study period did not predict aspect distribution and that differences in the competitive environments on northwest and southeast surfaces may be an important factor determining aspect distribution. © 2002 Elsevier Science B.V. All rights reserved.

Pore structure and diffusional properties of hardened cement pastes

This study has investigated the inclusion of pulverised fuel ash (PFA) and blast furnace slag (BFS) into hardened cement pastes (HCP) in retarding the ingress of chloride ions and oxygen molecules from the external environment. The influence of environmental factors such as drying and carbonation on the pore structure and diffusional properties of OPC, OPC/30%PFA and OPC/65%BFS hardened pastes was investigated. Specimens were desorbed from a saturated surface dry condition to a near constant weight at 65% relative humidity (RH) while others were simultaneously exposed to a 65% RH atmosphere and a carbon dioxide atmosphere of up to 5% by volume until there were fully carbonated. The presence of the interfacial zone at the cement paste-aggregate interface was critically reviewed and identified. The influence of the interfacial zone on porosity and chloride ingress in assumed periodic composites of glass bead mortars was also studied. The investigations have demonstrated the following: (a) The use of fly ash and slag in blended cement pastes has resulted in a marked reduction in capillary porosity and rate of chloride ingress. (b) The ratio of oxygen to chloride diffusion coefficients increased from values close to 1 in permeable pastes, to values of around 15 in low-permeability blended fly ash and slag pastes. This supports the view that the diffusion of chloride ions is retarded by the surface charge of the hydrated cement gel in low-permeability pastes. (c) Compared with plain OPC pastes, the carbonation of blended fly ash and slag pastes resulted in a marked increase in the coarse capillary porosity and a corresponding increase in the oxygen and chloride diffusion rates.

A near real-time water surface detection method based on HSV transformation of MODIS multi-Spectral time series data

In the face of global population growth and the uneven distribution of water supply, a better knowledge of the spatial and temporal distribution of surface water resources is critical. Remote sensing provides a synoptic view of ongoing processes, which addresses the intricate nature of water surfaces and allows an assessment of the pressures placed on aquatic ecosystems. However, the main challenge in identifying water surfaces from remotely sensed data is the high variability of spectral signatures, both in space and time. In the last 10 years only a few operational methods have been proposed to map or monitor surface water at continental or global scale, and each of them show limitations. The objective of this study is to develop and demonstrate the adequacy of a generic multi-temporal and multi-spectral image analysis method to detect water surfaces automatically, and to monitor them in near-real-time. The proposed approach, based on a transformation of the RGB color space into HSV, provides dynamic information at the continental scale. The validation of the algorithm showed very few omission errors and no commission errors. It demonstrates the ability of the proposed algorithm to perform as effectively as human interpretation of the images. The validation of the permanent water surface product with an independent dataset derived from high resolution imagery, showed an accuracy of 91.5% and few commission errors. Potential applications of the proposed method have been identified and discussed. The methodology that has been developed 27 is generic: it can be applied to sensors with similar bands with good reliability, and minimal effort. Moreover, this experiment at continental scale showed that the methodology is efficient for a large range of environmental conditions. Additional preliminary tests over other continents indicate that the proposed methodology could also be applied at the global scale without too many difficulties