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PubMed2001

Product development: using a 3D computer model to optimize the stability of the Rocket powered wheelchair.

A three-dimensional (3D) lumped-parameter model of a powered wheelchair was created to aid the development of the Rocket prototype wheelchair and to help explore the effect of innovative design features on its stability. The model was developed using simulation software, specifically Working Model 3D. The accuracy of the model was determined by comparing both its static stability angles and dynamic behavior as it passed down a 4.8-cm (1.9") road curb at a heading of 45 degrees with the performance of the actual wheelchair. The model's predictions of the static stability angles in the forward, rearward, and lateral directions were within 9.3, 7.1, and 3.8% of the measured values, respectively. The average absolute error in the predicted position of the wheelchair as it moved down the curb was 2.2 cm/m (0.9" per 3'3") traveled. The accuracy was limited by the inability to model soft bodies, the inherent difficulties in modeling a statically indeterminate system, and the computing time. Nevertheless, it was found to be useful in investigating the effect of eight design alterations on the lateral stability of the wheelchair. Stability was quantified by determining the static lateral stability angles and the maximum height of a road curb over which the wheelchair could successfully drive on a diagonal heading. The model predicted that the stability was more dependent on the configuration of the suspension system than on the dimensions and weight distribution of the wheelchair. Furthermore, for the situations and design alterations studied, predicted improvements in static stability were not correlated with improvements in dynamic stability.

Computer Simulation↗

PubMed2005

Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.

The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a hyperthermostable xylanase, has been solved in its native form and in complex with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into the substrate subsite and the molecular features for thermal stability, we compared TmxB with family 10 xylanase structures from nine microorganisms. As expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common among the glycoside hydrolase family 10. The enzyme active site and the environment surrounding the xylooligosaccharide of TmxB are highly similar to those of family 10 xylanases. However, only two xylose moieties were found in its binding pocket from the TmxB-xylotriose complex structure. This finding suggests that TmxB could be a potential biocatalyst for the large-scale production of xylobiose. The result of structural analyses also indicated that TmxB possesses some additional features that account for its thermostability. In particular, clusters of aromatic residues together with a lack of exposed hydrophobic residues are characteristic of the TmxB structure. TmxB has also a significant number of ion pairs on the protein surface that are not found in other thermophilic family 10 xylanases.

Bacterial Proteins↗

PubMed1987

Importance of conserved residues for the conformation of the T-loop in tRNAs.

The conformation of the T-loop of yeast tRNA(Asp) was studied by structural mapping techniques using chemical and enzymatic probes and by three-dimensional graphics modeling with the known crystallographic structures of tRNAs as references. The structural importance of C61 (conserved in the T-stem of all tRNAs) for the loop conformation was directly checked by ethylnitrosourea phosphate alkylation, either on the 3'-half tRNAAsp molecule or on a variant in which C61 was replaced by U61. The reactivity of P60 against ethylnitrosourea alkylation in the variant emphasizes the role of the hydrogen bond between this phosphate and position N4 of C61 for stabilizing the conformation of the T-loop. Experiments on several tRNA variants, containing C61 but altered in the sequence or in the length of the T-loop, indicate that other structural features help to stabilize the hydrogen bond network around P60. Evidence is presented that the reverse Hoogsteen base pair T54-A58 contributes to this stabilization by maintaining the hydrogen bonding between the 2'OH of ribose 58 and P60. Using graphics modeling and based on the chemical data. T-loops of several variants were constructed. It appears that both the constant length of the T-loop and the presence of psi 55 are crucial for the correct interaction between the T- and D-loops. The conclusion of this study is that the T-loop in tRNA possesses an intrinsic conformation (mainly governed by the constant residues) existing primarily without the structural context of the entire tRNA molecule.

Base Composition↗

PubMed1996

Cuticle cell defects in lamellar ichthyosis hair and anomalous hair shaft syndromes visualized after detergent extraction.

BACKGROUND: The biochemical bases for fragility in most of the rare brittle hair shaft syndromes are unknown. The hypothesis being investigated in several syndromes is that the hair cuticle cells show defects in cross-linked protein features. Since transglutaminases stabilize protein structures by cross-linking them, hair from autosomal recessive lamellar ichthyosis patients lacking keratinocyte transglutaminase was examined to find whether this enzyme participates in hair shaft stabilization. METHODS: Hair shaft samples from patients afflicted with lamellar ichthyosis or several brittle hair syndromes were examined ultrastructurally by transmission electron microscopy after vigorous extraction with detergent and reducing agent to reveal cross-linked protein features. RESULTS: In hair cuticle cells from three patients with lamellar ichthyosis the marginal band (A layer) was present but nonuniform and subject to breakage, while in a fourth sample it was missing altogether. The exocuticle appeared less dense than in normal hair, consistent with extensive protein loss during detergent extraction. In cuticle cells from trichothiodystrophy hair, the exocuticle layer was essentially fully extractable in one sample, while in two others (from siblings) the exocuticle appeared less dense and the A layer was absent or greatly reduced in thickness. A sample of proximal trichorrhexis nodosa also displayed defects in cuticle cells, in which the endocuticle layer appeared subject to rupture. The outer cuticle cells in monilethrix hair displayed a thinning of the A layer and less dense exocuticle, while the cortex exhibited regions lacking remnant cell borders. Pili annulati hair displayed large gaps in the cortex, presumably reflecting the air-filled cavities characteristic of this syndrome, and wavy borders of some cuticle cells. CONCLUSIONS: Observations with autosomal recessive lamellar ichthyosis hair indicate that keratinocyte transglutaminase has a major role in maturation of the cuticle but appears unnecessary for stabilization of cell borders in the cortex. Defective cross-linking was also evident in cuticle cells of trichothiodystrophy and monilethrix.

Cross-Linking Reagents↗

PubMed2005

Prediction of collagen stability from amino acid sequence.

An algorithm was derived to relate the amino acid sequence of a collagen triple helix to its thermal stability. This calculation is based on the triple helical stabilization propensities of individual residues and their intermolecular and intramolecular interactions, as quantitated by melting temperature values of host-guest peptides. Experimental melting temperature values of a number of triple helical peptides of varying length and sequence were successfully predicted by this algorithm. However, predicted T(m) values are significantly higher than experimental values when there are strings of oppositely charged residues or concentrations of like charges near the terminus. Application of the algorithm to collagen sequences highlights regions of unusually high or low stability, and these regions often correlate with biologically significant features. The prediction of stability from sequence indicates an understanding of the major forces maintaining this protein motif. The use of highly favorable KGE and KGD sequences is seen to complement the stabilizing effects of imino acids in modulating stability and may become dominant in the collagenous domains of bacterial proteins that lack hydroxyproline. The effect of single amino acid mutations in the X and Y positions can be evaluated with this algorithm. An interactive collagen stability calculator based on this algorithm is available online.

Algorithms↗

PubMedDate not supplied

Assessment and visualization of the curvature of the left ventricle from 3D medical images.

We address the problem of using curvature features to assess the three-dimensional (3D) motion of the left ventricle. The adequacy of this approach depends on the actual characteristics of the curvature of the left ventricle and particularly on the spatial and temporal stability of these features. From experimental data, we compute the distribution of the Gaussian curvature over the surface of the left ventricle by using an iterative procedure. The results are visualized in 3D through a voxel-based surface rendering technique. We show that the Gaussian curvature remains stable along the cardiac cycle. This curvature feature could thus provide a reliable basis for further 3D motion analysis of the left ventricle.

Algorithms↗

PubMed1996

[Clinical usefulness of stored electrograms in implantable defibrillators].

BACKGROUND AND PURPOSE: The storage of intracavitary electrograms by the automatic implantable defibrillators is one of the latest advantages. The objective of this study was to determine the clinical utility and limitations of electrograms stored by the new generation of defibrillators. MATERIAL AND METHODS: We have implanted at our institution 43 generators with the facility of storing electrograms; 8 Ventak P2, 17 PRxII, and 1 PRxIII from CPI, 14 Jewel, from Medtronic and 3 Guardian ATP 4215, from Telectronics. All were implanted with an endocavitary system lead, an only one patient needed a subcutaneous patch. Mean age was 57 +/- 16 years, 36 were males and 7 women. The mean left ventricular ejection fraction was 44 +/- 23%. The mean follow up was 6 +/- 8 months (limits 1-20 months). RESULTS: We registered and analyzed a total of 268 episodes in 20 patients. Fourteen (82%) received what was considered appropriate therapy. Three patients (from 17 with any treatment delivered by the defibrillator) presented an inappropriate therapy. The parameters, "onset" and "stability", were differentiated in each arrhythmia, the "onset" is useful to differentiate sinus tachycardia, but not atrial fibrillation, from ventricular tachycardia. Programming a stability value between 30-40 mseg eliminates 88% of inappropriate therapies due to atrial fibrillation. In all patients, the identification of the event, facilitated by the stored electrograms, allowed us to resolve the problem. CONCLUSIONS: The programmable features "onset" and "stability" allowed us to eliminate a significant number of inappropriate therapies. The stored electrograms facilitate the identification of the events, leading to treatment by the generator, and were very useful in guiding the clinical management of the patient.

Adult↗

PubMed2026

Isolation, identification, and genomic characterization of Staphylococcus aureus phage vB_SauL_202595 and its bacteriostatic application in dairy products.

Staphylococcus aureus is an important pathogen associated with bovine mastitis and dairy product contamination, posing economic and public health risks through the food chain. In this study, a temperate phage, vB_SauL_202595, was isolated from a dairy farm environmental sample using S. aureus SHZ-0127 as the host, and its biological characteristics, genomic features, and antibacterial activity in dairy matrices were evaluated. vB_SauL_202595 lysed 18 of 66 tested S. aureus strains, with a lysis susceptibility rate of 27.3%, including 5 highly susceptible strains, indicating a relatively limited host range. The optimal multiplicity of infection was 0.01, the latent period was approximately 30 min, and the burst size was approximately 316 PFU/cell. The phage remained stable at 4°C-37°C and pH 6-10. Genome analysis showed that vB_SauL_202595 belongs to the class Caudoviricetes, has a genome of 44,503 bp with 33.59% GC content, and encodes 63 predicted proteins. No typical antibiotic resistance genes or major virulence factors were detected; however, integrase and repressor genes were identified, supporting its temperate nature. vB_SauL_202595 inhibited S. aureus SHZ-0127 growth, reduced mature biofilm biomass, and decreased viable bacterial counts in milk and yogurt, with reductions of 1.23 and 1.42 log10 CFU/mL under representative conditions, respectively. From a One Health perspective, these findings provide foundational evidence for reducing S. aureus contamination and related antimicrobial resistance risks along the dairy chain. Overall, vB_SauL_202595 represents a candidate phage resource for dairy-associated S. aureus biocontrol research, but its limited host range and lysogeny-related genes require further safety assessment before food-related applications.IMPORTANCEStaphylococcus aureus is a major pathogen associated with bovine mastitis and a common contaminant in dairy products, causing economic losses and public health risks through the food chain. Although phage-based biocontrol has emerged as a promising strategy for controlling S. aureus contamination in dairy products, systematic evidence regarding phage activity in actual dairy matrices remains limited. In this study, we isolated and characterized a dairy farm environment-derived temperate phage, vB_SauL_202595, and evaluated its biological characteristics, genomic features, host range, stability, biofilm removal ability, and antibacterial performance in milk and yogurt. These findings provide foundational experimental evidence for phage-based dairy biocontrol against S. aureus. However, due to its limited host range and lysogeny-related genomic features, vB_SauL_202595 should be considered a candidate phage resource for further study. Broader validation, including phage-cocktail testing, long-term storage assays, product quality assessment, and regulatory safety evaluation, is needed before practical application.

Staphylococcus aureus↗

PubMed2003

Interaction and flocculation of spherical colloids wetted by a surface-induced corona of paranematic order.

Particles dispersed in a liquid crystal above the nematic-isotropic phase transition are wetted by a surface-induced corona of paranematic order. Such coronas give rise to pronounced two-particle interactions. In this paper, we report details on the analytical and numerical study of these interactions published recently [Phys. Rev. Lett. 86, 3915 (2001)]. We especially demonstrate how for large particle separations the asymptotic form of a Yukawa potential arises. We show that the Yukawa potential is a surprisingly good description for the two-particle interactions down to distances of the order of the nematic coherence length. Based on this fact, we extend earlier studies on a temperature induced flocculation transition in electrostatically stabilized colloidal dispersions [Phys. Rev. E 61, 2831 (2000)]. We employ the Yukawa potential to establish a flocculation diagram for a much larger range of the electrostatic parameters, namely, the surface charge density and the Debye screening length. As a distinguished feature, a kinetically stabilized dispersion close to the nematic-isotropic phase transition is found.

Journal Article↗

PubMed1999

Characterization of structural features important for T7 RNAP elongation complex stability reveals competing complex conformations and a role for the non-template strand in RNA displacement.

We have characterized the roles of the phage T7 RNA polymerase (RNAP) thumb subdomain and the RNA binding activity of the N-terminal domain in elongation complex (EC) stability by evaluating how disrupting these structures affects the dissociation rates of halted ECs. Our results reveal distinct roles for these elements in EC stabilization. On supercoiled or partially single-stranded templates the enzyme with a deletion of the thumb subdomain is exceptionally unstable. However, on linear duplex templates the polymerase which has been proteolytically cleaved within the N-terminal domain is the most unstable. The differences in the effects of these RNAP modifications on the stability of ECs on the different templates appear to be due to differences in EC structure: on the linear duplex templates the RNA is properly displaced from the DNA, but on the supercoiled or partially single-stranded templates an extended RNA:DNA hybrid makes a larger contribution to the conformational state of the EC. The halted EC can therefore exist either in a conformation in which the RNA is displaced from the DNA and forms an interaction with the RNAP, or in a conformation in which a more extended RNA:DNA hybrid is present and the RNA:RNAP interaction is less extensive. The partitioning between these competing conformations appears to be a function of the energetics of template reannealing and the relative strengths of the RNA:RNAP interaction and the RNA:DNA hybrid.

Bacteriophage T7↗

PubMed2005

Impaired genomic stability and increased oxidative stress exacerbate different features of Ataxia-telangiectasia.

Ataxia-telangiectasia (A-T) is a multisystem, cancer-predisposing genetic disorder caused by deficiency of the ATM protein. To dissect the A-T phenotype, we augmented specific features of the human disease by generating mouse strains that combine Atm deficiency with dysfunction of other proteins. Increasing oxidative stress by combining deficiencies in Atm and superoxide dismutase 1 (Sod1) exacerbated growth retardation and markedly reduced the mean survival time following ionizing radiation. In contrast, increasing genomic instability by combining deficiencies of Atm and the mismatch repair protein Mlh1 caused a moderate increase in radiation sensitivity and dramatic increase in aggressive lymphomas, compared with thes Atm-/- single knockout. Remarkably, Atm, Mlh1 or Mlh1/Atm single or double heterozygosity did not significantly affect the life span of the various genotypes. Mlh1/Atm double null tumors were polyclonal, whereas the tumors in other genotypes were mono- or oligoclonal, demonstrating the high predisposition of thymocytes with this genotype to become malignant. Chromosomal aberrations in the tumors were localized mainly in chromosomes 12 and 15. The genomic region on chromosome 15, which contains the gene for the c-Myc oncoprotein, was commonly amplified, and elevated levels of the c-Myc protein were subsequently observed in the tumors. Our data suggest that impaired genomic instability is an important contributing factor to cancer predisposition in A-T, whereas oxidative stress is more important in the radiation sensitivity and growth retardation facets of this disease.

Animals↗

PubMed1991

Structural features that give rise to the unusual stability of RNA hairpins containing GNRA loops.

The most frequently occurring RNA hairpins in 16S and 23S ribosomal RNA contain a tetranucleotide loop that has a GNRA consensus sequence. The solution structures of the GCAA and GAAA hairpins have been determined by nuclear magnetic resonance spectroscopy. Both loops contain an unusual G-A base pair between the first and last residue in the loop, a hydrogen bond between a G base and a phosphate, extensive base stacking, and a hydrogen bond between a sugar 2'-end OH and a base. These interactions explain the high stability of these hairpins and the sequence requirements for the variant and invariant nucleotides in the GNRA tetranucleotide loop family.

Base Sequence↗

PubMed2003

Some general features of limited coalescence in solid-stabilized emulsions.

We produce direct and inverse emulsions stabilized by solid mineral particles. If the total amount of particles is initially insufficient to fully cover the oil-water interfaces, the emulsion droplets coalesce such that the total interfacial area between oil and water is progressively reduced. Since it is likely that the particles are irreversibly adsorbed, the degree of surface coverage by them increases until coalescence is halted. We follow the rate of droplet coalescence from the initial fragmented state to the saturated situation. Unlike surfactant-stabilized emulsions, the coalescence frequency depends on time and particle concentration. Both the transient and final droplet size distributions are relatively narrow and we obtain a linear relation between the inverse average droplet diameter and the total amount of solid particles, with a slope that depends on the mixing intensity. The phenomenology is independent of the mixing type and of the droplet volume fraction allowing the fabrication of both direct and inverse emulsion with average droplet sizes ranging from micron to millimetre.

Adsorption↗

PubMed2005

Specificity versus stability in computational protein design.

Protein-protein interactions can be designed computationally by using positive strategies that maximize the stability of the desired structure and/or by negative strategies that seek to destabilize competing states. Here, we compare the efficacy of these methods in reengineering a protein homodimer into a heterodimer. The stability-design protein (positive design only) was experimentally more stable than the specificity-design heterodimer (positive and negative design). By contrast, only the specificity-design protein assembled as a homogenous heterodimer in solution, whereas the stability-design protein formed a mixture of homodimer and heterodimer species. The experimental stabilities of the engineered proteins correlated roughly with their calculated stabilities, and the crystal structure of the specificity-design heterodimer showed most of the predicted side-chain packing interactions and a main-chain conformation indistinguishable from the wild-type structure. These results indicate that the design simulations capture important features of both stability and structure and demonstrate that negative design can be critical for attaining specificity when competing states are close in structure space.

Bacterial Proteins↗

PubMed2006

Attributes of glycosylation in the establishment of the unfolding pathway of soybean agglutinin.

Soybean agglutinin (gSBA) is a tetrameric legume lectin, each of whose subunits are glycosylated. Earlier studies have shown that this protein shows exceptionally high stability in terms of free energy of unfolding when compared to other proteins from the same family. This article deals with the unfolding reactions of the nonglycosylated recombinant form of the protein rSBA and its comparison with the glycosylated counterpart gSBA. The nonglycosylated form features a lower stability when compared to the glycosylated form. Further, the unfolding pathways in the two are widely different. Although the glycosylated form undergoes a simple two-state unfolding, the nonglycosylated species unfolds via a compact monomeric intermediate that is not a molten globule. Representative isothermal and thermal denaturation profiles show that glycosylation accounts for a stabilization of approximately 9 kcal/mol of the tetramer, whereas the difference in T(m) between the two forms is 26 degrees C. Computational studies on the glycan-protein interactions at the noncanonical interface of the protein show that quite a number of hydrogen bond and hydrophobic interactions stabilize the glycoprotein tetramer.

Agglutinins↗

PubMed1996

Relationship between thermal stability and 3-D structure in a homology model of 3-isopropylmalate dehydrogenase from Escherichia coli.

To reveal the structural basis of the increased thermal stability of 3-isopropylmalate dehydrogenase (IPMDH) from Thermus thermophilus, an extreme thermophile, the homology-based structural model of one mesophilic (Escherichia coli) counterpart, was constructed. Both IPMDHs are homodimeric proteins. We built a model of one subunit using the 3-D structures of the Th. thermophilus IPMDH and the homologous E.coli isocitrate dehydrogenase. Energy minimization and molecular dynamics simulated annealing were performed on the dimer, including a surrounding solvation shell. No serious errors were detected in the refined model using the 3-D profile method. The resulting structure was scrutinized and compared with the structure of the Th.thermophilus IPMDH. Significant differences were found in the non-specific interactions including the hydrophobic effect. The model predicts a higher number of ion pairs in the Th.thermophilus than in the E.coli enzyme. An increase was observed in the stabilities of alpha-helical regions in the thermophilic protein. The preliminary X-ray coordinates of the E.coli IPMDH were received after the completion of this work, allowing an assessment of the model in terms of the X-ray structure. The comparison proved that most of the structural features underlying the stability differences between the two enzymes were predicted correctly.

3-Isopropylmalate Dehydrogenase↗

PubMed2001

Active-site residues are critical for the folding and stability of methylamine dehydrogenase.

Site-directed mutagenesis was used to alter active-site residues of methylamine dehydrogenase (MADH) from Paracoccus denitrificans. Four residues of the beta subunit of MADH which are in close proximity to the tryptophan tryptophylquinone (TTQ) prosthetic group were modified. The crystal structure of MADH reveals that each of these residues participates in hydrogen bonding interactions with other active-site residues, TTQ or water. Relatively conservative mutations which removed the potentially reactive oxygens on the side chains of Thr122, Tyr119, Asp76 and Asp32 each resulted in greatly reduced or undetectable levels of MADH production. The reduction of MADH levels was determined by assays of activity and Western blots of crude extracts with antisera specific for the MADH beta subunit. No activity or cross-reactive protein was detected in extracts of cells expressing D76N, T122A and T122C MADH mutants. Very low levels of active MADH were produced by cells expressing D32N, Y119F, Y119E and Y119K MADH mutants. The Y119F and D32N mutants were purified from cell extracts and found to be significantly less stable than wild-type MADH. Only the T122S MADH mutant was produced at near wild-type levels. Possible roles for these amino acid residues in stabilizing unusual structural features of the MADH beta subunit, protein folding and TTQ biosynthesis are discussed.

Amino Acid Sequence↗

PubMed1976

Chemistry, biological activity, and uses of formamidine pesticides.

The formamidines, a relatively new group of acaricide-insecticides, are novel both in their range of biological activities and in their mode of action, which is presently unknown. This paper is a review of the historical development, properties, structures, uses, and chemistry of this group of pesticides, with particular emphasis on chlordimeform (Galecron or Fundal), N'-4-chloro-o-tolyl-N,N-dimethylformamidine, and amitraz, 1,3=di-(2,4-dimethylphenylimino)-2-methyl-2-azapropane. Their biological activity and uses are defined by their toxicity to spider mites, ticks, and certain insects, and they are particularly effective against juvenile and resistant forms of these organisms. A significant, but poorly understood feature of their field effectiveness is their breadth of toxic action which includes direct lethality, excitant-repellant behavioral effects, and chemosterilization. They are generally of low hazard for nontarget species with the significant exception of predaceous mites. Several aspects of the chemistry of these compounds are considered, including structure--activity relations, synthetic pathways, isomerism and configuration, and their chemical and environmental stability. A significant feature of the metabolism and toxicity of these agents is the possible activation of chlordimeform by N-demethylation in vivo. Strong evidence for this has been presented with the cattle tick, but recent results discussed here suggest that in other species, i.e., mice, German cockroaches or black cutworm eggs, N-demethylation is neither a strong activation nor a detoxication reaction.

Amidines↗