Cloning and characterization of an alpha-enolase of the oral pathogen Streptococcus mutans that binds human plasminogen

Streptococcus mutans is the etiologic agent of dental caries and is a causative agent of infective endocarditis. While the mechanisms by which S. mutans cells colonize heart tissue is not clear, it is thought that bacterial binding to extracellular matrix and blood conponents is crucial in the development of endocarditis. Previously, we have demonstrated that S. mutans cells have the capacity to bind and activate plasminogen to plasmin. Here we report the first cloning and characterization of an α-enolase of S. mutans that binds plasminogen. The functional identity of the purified recombinant α-enolase protein was confirmed by its ability to catalyze the conversion of 2-phosphoglycerate to phosphoenolpyruvate. The protein exhibited a K_m of 9.5 mM and a V_max of 31.0 mM/min/mg. The α-enolase protein was localized in the cytoplasmic, cell wall and extracellular fractions of S. mutans. Binding studies using an immunoblot analysis revealed that human plasminogen binds to the enolase enzyme of S. mutans. These findings identify S. mutans α-enolase as a binding molecule used by this oral pathogen to interact with the blood component, plasminogen. Further studies of this interaction may be critical to understand the pathogenesis of endocarditis caused by S. mutans.     

Insights into Cu(I) exchange in HAH1 using quantum mechanical and molecular simulations

The human antioxidant protein, HAH1, is an important participant in a Cu(I) transport chain, delivering one Cu(I) ion to the Wilson's (WND) or Menkes disease protein (MNK). Full geometry optimizations and second-derivative calculations were performed on several binding site models using the B3LYP functional to derive parameters for the construction of a novel molecular mechanical (MM) force field for Cu(I) and its ligating residues in HAH1. MM minimization and molecular dynamics (MD) calculations were then performed using the AMBER suite to validate the newly generated force field. The X-ray crystal structure of the protein and the geometry of the Cu(I) binding site within the protein were reproduced by the MD simulations on the protein based on rmsd and visual inspection, validating the new force field parameters. The results from the quantum mechanical (QM) and MD simulations suggest that either a two- or three-coordinate exchange reaction is preferred and that it is unlikely that a four-coordinate Cu(I) species plays a role in copper exchange.     

The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization

Many copies of mammalian mitochondrial DNA contain a short triple-stranded region, or displacement loop (D-loop), in the major noncoding region. In the 35 years since their discovery, no function has been assigned to mitochondrial D-loops. We purified mitochondrial nucleoprotein complexes from rat liver and identified a previously uncharacterized protein, ATAD3p. Localization studies suggested that human ATAD3 is a component of many, but not all, mitochondrial nucleoids. Gene silencing of ATAD3 by RNA interference altered the structure of mitochondrial nucleoids and led to the dissociation of mitochondrial DNA fragments held together by protein, specifically, ones containing the D-loop region. In vitro, a recombinant fragment of ATAD3p bound to supercoiled DNA molecules that contained a synthetic D-loop, with a marked preference over partially relaxed molecules with a D-loop or supercoiled DNA circles. These results suggest that mitochondrial D-loops serve to recruit ATAD3p for the purpose of forming or segregating mitochondrial nucleoids.     

Accuracy and repeatability of an optical motion analysis system for measuring small deformations of biological tissues

Optical motion analysis techniques have been widely used in biomechanics for measuring large-scale motions such as gait, but have not yet been significantly explored for measuring smaller movements such as the tooth displacements under load. In principle, very accurate measurements could be possible and this could provide a valuable tool in many engineering applications. The aim of this study was to evaluate accuracy and repeatability of the Qualisys ProReflex-MCU120 system when measuring small displacements, as a step towards measuring tooth displacements to characterise the properties of the periodontal ligament. Accuracy and repeatability of the system was evaluated using a wedge comparator with a resolution of 0.25 microm to provide measured marker displacements in three orthogonal directions. The marker was moved in ten steps in each direction, for each of seven step sizes (0.5, 1, 2, 3, 5, 10, and 20 microm), repeated five times. Spherical and diamond markers were tested. The system accuracy (i.e. percentage of maximum absolute error in range/measurement range), in the 20-200 microm ranges, was +/-1.17%, +/-1.67% and +/-1.31% for the diamond marker in x, y and z directions, while the system accuracy for the spherical marker was +/-1.81%, +/-2.37% and +/-1.39%. The system repeatability (i.e. maximum standard deviation in the measurement range) measured under the different days, light intensity and temperatures for five times, carried out step up and then step down measurements for the same step size, was +/-1.7, +/-2.3 and +/-1.9 microm for the diamond marker, and +/-2.6, +/-3.9 and +/-1.9 microm for the spherical marker in x, y and z directions, respectively. These results demonstrate that the system suffices accuracy for measuring tooth displacements and could potentially be useful in many other applications.     

Projection structure of the membrane domain of Escherichia coli respiratory complex I at 8 A resolution

Respiratory complex I (NADH:ubiquinone oxidoreductase) is an L-shaped multisubunit protein assembly consisting of a hydrophobic membrane arm and a hydrophilic peripheral arm. It catalyses the transfer of two electrons from NADH to quinone coupled to the translocation of four protons across the membrane. Although we have solved recently the crystal structure of the peripheral arm, the structure of the complete enzyme and the coupling mechanism are not yet known. The membrane domain of Escherichia coli complex I consists of seven different subunits with total molecular mass of 258 kDa. It is significantly more stable than the whole enzyme, which allowed us to obtain well-ordered two-dimensional crystals of the domain, belonging to the space group p22(1)2(1). Comparison of the projection map of negatively stained crystals with previously published low-resolution structures indicated that the characteristic curved shape of the membrane domain is remarkably well conserved between bacterial and mitochondrial enzymes, helping us to interpret projection maps in the context of the intact complex. Two pronounced stain-excluding densities at the distal end of the membrane domain are likely to represent the two large antiporter-like subunits NuoL and NuoM. Cryo-electron microscopy on frozen-hydrated crystals allowed us to calculate a projection map at 8 A resolution. About 60 transmembrane alpha-helices, both perpendicular to the membrane plane and tilted, are present within one membrane domain, which is consistent with secondary structure predictions. A possible binding site and access channel for quinone are found at the interface with the peripheral arm. Tentative assignment of individual subunits to the features of the map has been made. The location of subunits NuoL and NuoM at substantial distance from the peripheral arm, which contains all the redox centres of the complex, indicates that conformational changes are likely to play a role in the mechanism of coupling between electron transfer and proton pumping.     

Cryopreservation of kangaroo spermatozoa using alternative approaches that reduce cytotoxic exposure to glycerol

Alternative techniques for the cryopreservation of kangaroo spermatozoa that reduced or eliminated the need for glycerol were investigated including; (1) freezing spermatozoa with 20% glycerol in pre-packaged 0.25 mL Cassou straws to enable rapid dilution of the glycerol post-thaw, (2) investigating the efficacy of 20% (v/v) dimethyl sulphoxide (DMSO) and dimethylacetamide (DMA—10%, 15% and 20% v/v) as cryoprotectants and (3) vitrification of spermatozoa with or without cryoprotectant (20% v/v glycerol, 20% v/v DMSO and 20% v/v DMA). Immediate in-straw post-thaw dilution of 20% glycerol and cryopreservation of spermatozoa in 20% DMSO produced no significant improvement in post-thaw viability of kangaroo spermatozoa. Spermatozoa frozen in 20% DMA showed post-thaw motility and plasma membrane integrity of 12.7 ± 1.9% and 22.7 ± 5.4%, respectively, while kangaroo spermatozoa frozen by ultra-rapid freezing techniques showed no evidence of post-thaw viability. The use of 10–20% DMA represents a modest but significant improvement in the development of a sperm cryopreservation procedure for kangaroos.     

The effect of cryoprotectant on kangaroo sperm ultrastructure and mitochondrial function

This study examined the effect of cryoprotectants (20% DMSO, a 10% DMSO/10% glycerol mixture, 20% glycerol and 1 M sucrose solution) on kangaroo sperm structure and function, along with the effect of varying concentrations of glycerol on sperm mitochondrial function. Eastern grey kangaroo cauda epididymidal spermatozoa were incubated for 10 min at 35 °C in each cryoprotectant and the plasma membrane integrity (PMI) and motility assessed using light microscopy. The same samples were fixed for TEM and the ultrastructural integrity of the spermatozoa examined. To investigate the effect of glycerol on the kangaroo sperm mitochondrial function, epididymidal spermatozoa were incubated with JC-1 in Tris–citrate media at 35 °C for 20 min in a range of glycerol concentrations (0%, 5%, 10%, 15% and 20%) and the mitochondrial membrane potential (MMP) and plasma membrane integrity determined. As expected, incubation of spermatozoa in 20% glycerol for 10 min resulted in a significant reduction in motility, PMI and ultrastructural integrity. Interestingly, incubation in 20% DMSO resulted in no significant reduction in motility or PMI but a significant loss of structural integrity when compared to the control spermatozoa (0% cryoprotectant). However, 20% DMSO was overall less damaging to sperm ultrastructure than glycerol, a combination of 10% glycerol and 10% DMSO, and sucrose. While all glycerol concentrations had an adverse effect on mitochondrial function, the statistical models presented for the relationship between MMP and glycerol predicted that spermatozoa, when added to 20% glycerol, would lose half of their initial MMP immediately at 35 °C and MMP would halve after 19.4 min at 4 °C. Models for the relationship between PMI and glycerol predicted that spermatozoa would lose half of their initial PMI after 1.8 min at 35 °C and PMI would halve after 21.1 min at 4 °C. These results suggest that if glycerol is to be used as a cryoprotectant for kangaroo spermatozoa then it is best administered at 4 °C and that mitochondrial function is more sensitive to glycerol than PMI. Future research should be directed at investigating strategies that reduce exposure of spermatozoa to glycerol during processing and that test the cryoprotective properties of 20% DMSO for kangaroo spermatozoa.     

Reduction, classification and ranking of motion analysis data: an application to osteoarthritic and normal knee function data

There are certain major obstacles to using motion analysis as an aid to clinical decision making. These include: the difficulty in comprehending large amounts of both corroborating and conflicting information; the subjectivity of data interpretation; the need for visualization; and the quantitative comparison of temporal waveform data. This paper seeks to overcome these obstacles by applying a hybrid approach to the analysis of motion analysis data using principal component analysis (PCA), the Dempster-Shafer (DS) theory of evidence and simplex plots. Specifically, the approach is used to characterise the differences between osteoarthritic (OA) and normal (NL) knee function data and to produce a hierarchy of those variables that are most discriminatory in the classification process. Comparisons of the results obtained with the hybrid approach are made with results from artificial neural network analyses.