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PubMed1994

Force system developed from closed coil springs.

The present paper provides data on load-deflection rate and maximal force generated for 19 coil springs. The force level at activation and deactivation was registered at intervals of 5 mm between 0 and 100 per cent extension. Ten springs of each type were analysed. The following questions were answered. How many of the springs exhibited the behaviour of a superelastic spring and how many types of springs differed significantly from each other with respect to force deflection rate and maximal force level at 100 per cent extension? Of the products tested only the springs from GAC exhibited the behaviour characteristic of the superelastic wire. The 19 products could, from a clinical point of view, be classified into four different groups with regard to force deflection rate and five groups with regard to maximal force. The variation within each product also differed between the products with the lowest intra-product variation seen in the TP springs. In light of the present findings it is obvious that manufacturers' information was not satisfactory. The need for more thorough user information is stressed.

Elasticity↗
PubMed2003

The load/deflection characteristics of thermally activated orthodontic archwires.

The objective of the study was to investigate the load/deflection characteristics of three commercially available thermally active nickel-titanium orthodontic archwires using a standard nickel-titanium archwire as a control. The thermally active wires were Regency Thermal, Orthoform, and Eurotherm and the control was Memory. Round 0.4 mm and rectangular 0.4 x 0.56 mm wires were subjected to 2 and 4 mm of deflection in a water bath at temperatures of 20, 30, and 40 degrees C and forces were measured in three-point bend and phantom head situations. Analysis of variance revealed that, irrespective of the test set up and wire type, wire size had a significant effect (P < 0.001) on the forces produced. An increase in size from 0.4 mm round to 0.4 x 0.56 mm rectangular wire approximately doubled the force values for a given deflection. The effect of wire deflection on the force values varied according to the test system, forces being much higher in the phantom head tests than in the beam tests. In the beam tests, an increase in wire deflection from 2 to 4 mm had no significant effect on the forces exerted, but in the phantom head tests the forces produced by each wire at 4 mm deflection were four to five times greater than those at 2 mm deflection. Each of the thermally active wires produced less force that the non-thermally active wire. However, there was a large variation between the three types of thermally active wire. In the beam tests each 10 degrees C rise in temperature from 20 to 40 degrees C had a highly significant effect on the force produced by each thermoelastic wire (P < 0.001). In the phantom head tests there were significant force increases between 20 and 30 degrees C (P < 0.001), but between 30 and 40 degrees C the forces did not change significantly.

Analysis of Variance↗
PubMed2005

Influence of autoclave sterilization on the surface parameters and mechanical properties of six orthodontic wires.

Orthodontic wires are frequently packaged in individual sealed bags in order to avoid cross-contamination. The instructions on the wrapper generally advise autoclave sterilization of the package and its contents if additional protection is desired. However, sterilization can modify the surface parameters and the mechanical properties of many types of material. The aim of this research was to determine the influence of one of the most widely used sterilization processes, autoclaving (18 minutes at 134 degrees C, as recommended by the French Ministry of Health), on the surface parameters and mechanical properties of six wires currently used in orthodontics (one stainless steel alloy: Tru-Chrome RMO; two nickel-titanium shape memory alloys: Neo Sentalloy and Neo Sentalloy with Ionguard GAC; and three titanium-molybdenum alloys: TMA(R) and Low Friction TMA Ormco and Resolve GAC). The alloys were analysed on receipt and after sterilization, using surface structure observation techniques, including optical, scanning electron and atomic force microscopy and profilometry. The mechanical properties were assessed by three-point bending tests. The results showed that autoclave sterilization had no adverse effects on the surface parameters or on the selected mechanical properties. This supports the possibility for practitioners to systematically sterilize wires before placing them in the oral environment.

Chromium Alloys↗
PubMed2005

Evolution of flexural rigidity according to the cross-sectional dimension of a superelastic nickel titanium orthodontic wire.

The choice of the most suitable orthodontic wire for each stage of treatment requires estimation of the forces generated. In theory, the selection of wire sequences should initially utilize a lower flexural rigidity; thus clinicians use smaller round cross-sectional dimension wires to generate lighter forces during the preliminary alignment stage. This assessment is true for conventional alloys, but not necessarily for superelastic nickel titanium (NiTi). In this case, the flexural rigidity dependence on cross-sectional dimension differs from the linear elasticity prediction because of the martensitic transformation process. It decreases with increasing deflection and this phenomenon is accentuated in the unloading process. This behaviour should lead us to consider differently the biomechanical approach to orthodontic treatment. The present study compared bending in 10 archwires made from NiTi orthodontics alloy of two cross-sectional dimensions. The results were based on microstructural and mechanical investigations. With conventional alloys, the flexural rigidity was constant for each wire and increased largely with the cross-sectional dimension for the same strain. With NiTi alloys, the flexural rigidity is not constant and the influence of size was not as important as it should be. This result can be explained by the non-constant elastic modulus during the martensite transformation process. Thus, in some cases, treatment can begin with full-size (rectangular) wires that nearly fill the bracket slot with a force application deemed to be physiologically desirable for tooth movement and compatible with patient comfort.

Dental Alloys↗
PubMed1998

Importance of a flexible hinge near the motor domain in kinesin-driven motility.

Conventional kinesin is a molecular motor consisting of an N-terminal catalytic motor domain, an extended stalk and a small globular C-terminus. Whereas the structure and function of the catalytic motor domain has been investigated, little is known about the function of domains outside the globular head. A short coiled-coil region adjacent to the motor domain, termed the neck, is known to be important for dimerization and may be required for kinesin processivity. We now provide evidence that a helix-disrupting hinge region (hinge 1) that separates the neck from the first extended coiled-coil of the stalk plays an essential role in basic motor activity. A fast fungal kinesin from Syncephalastrum racemosum was used for these studies. Deletion, substitution by a coiled-coil and truncation of the hinge 1 region all reduce motor speed and uncouple ATP turnover from gliding velocity. Insertion of hinge 1 regions from two conventional kinesins, Nkin and DmKHC, fully restores motor activity, whereas insertion of putative flexible linkers of other proteins does not, suggesting that hinge 1 regions of conventional kinesins can functionally replace each other. We suggest that this region is essential for kinesin movement in its promotion of chemo-mechanical coupling of the two heads and therefore the functional motor domain should be redefined to include not only the catalytic head but also the adjacent neck and hinge 1 domains.

Adenosine Triphosphatases↗
PubMed2000

A dynamically tuned double-stranded RNA binding mechanism for the activation of antiviral kinase PKR.

A key step in the activation of interferon-inducible antiviral kinase PKR involves differential binding of viral double-stranded RNA (dsRNA) to its two structurally similar N-terminal dsRNA binding motifs, dsRBM1 and dsRBM2. We show here, using NMR spectroscopy, that dsRBM1 with higher RNA binding activity exhibits significant motional flexibility on a millisecond timescale as compared with dsRBM2 with lower RNA binding activity. We further show that dsRBM2, but not dsRBM1, specifically interacts with the C-terminal kinase domain. These results suggest a dynamically tuned dsRNA binding mechanism for PKR activation, where motionally more flexible dsRBM1 anchors to dsRNA, thereby inducing a cooperative RNA binding for dsRBM2 to expose the kinase domain.

Amino Acid Sequence↗
PubMed2002

Differential increases in average isokinetic power by specific muscle groups of older women due to variations in training and testing.

BACKGROUND: As a person ages, leg speed and power decrease. These changes are associated with increased falls and reduced gait speed. It has been shown that upper leg training in younger persons results in increased strength and power at the specific speed at which resistance training is applied, although there are only limited data concerning speed-specific training effects on lower leg activity. However, because both upper and lower leg speed and power influence gait and balance, it is important to determine the training speeds that selectively improve these variables in older persons. METHODS: No studies have examined selective speed-specific changes in performance for the upper and lower leg muscles in older individuals. Therefore, we compared shifts in the power-velocity relationship after high-speed (HS) and low-speed (LS) isokinetic training of knee extensors (KE) and flexors (KF), dorsiflexors (DF), and plantar flexors (PF) in community-dwelling women (ages 61 to 75). Subjects were randomly assigned to a HS training, LS training, or control (C) group. Training occurred three times a week for 12 weeks. HS training occurred at 4.73 rad.s(-1) (knee) and 3.14 rad.s(-1) (ankle); LS training for both joint actions was at 1.05 rad.s(-1). RESULTS: HS training improved KE power at intermediate (3.14 rad.s(-1); p =.0007) and high (5.24 rad.s(-1); p =.0004) testing speeds. Neither the HS nor LS group showed any change in KF as a result of the training. Both LS and HS training improved DF power at all testing speeds; however, PF power improved only with LS training and only at 1.05 rad.s(-1) (p =.0132) and 3.14 rad.s(-1) (p =.0310). CONCLUSIONS: Our results suggest that, in older women, lower leg training should occur at lower training speeds than upper leg training. Additionally, attention to differential speed-specific training of knee and ankle actions could improve power production, mobility, balance, and other functional measures in older persons.

Age Factors↗
PubMed2006

Foot and ankle risk factors for falls in older people: a prospective study.

BACKGROUND: Foot problems are common in older people and are associated with impaired balance and functional ability. Few prospective studies, however, have been undertaken to determine whether foot problems are a risk factor for falls. METHODS: One hundred seventy-six people (56 men and 120 women, mean age 80.1, standard deviation 6.4 years) residing in a retirement village underwent tests of foot and ankle characteristics (including foot posture, range of motion, strength, and deformity) and physiological falls risk factors (including vision, sensation, strength, reaction time, and balance) and were followed for 12 months to determine the incidence of falls. RESULTS: Seventy-one participants (41%) reported falling during the follow-up period. Compared to those who did not fall, fallers exhibited decreased ankle flexibility, more severe hallux valgus deformity, decreased plantar tactile sensitivity, and decreased toe plantarflexor strength; they were also more likely to have disabling foot pain. Discriminant function analysis revealed that decreased toe plantarflexor strength and disabling foot pain were significantly and independently associated with falls after accounting for physiological falls risk factors and age. CONCLUSIONS: Foot and ankle problems increase the risk of falls in older people. Interventions to address these factors may hold some promise as a falls prevention strategy.

Accidental Falls↗
PubMed1997

Is structural flexibility of antigen-binding loops involved in the affinity maturation of anti-DNA antibodies?

Effects of somatic mutations in Ig variable region genes on the affinity maturation of autoantibodies were investigated using single precursor B cell-derived anti-double-stranded DNA mAb generated from an autoimmune disease-prone (NZB x NZW)F1 mouse. Analyses of DNA sequences, homology modeling on a graphic computer and molecular dynamics simulation of antigen-binding sites showed that any single site of mutation and changes in the electrostatic or hydrogen-bonding potential of the residues and in the three-dimensional structure could not solely explain the difference in DNA-binding activities. However, a significant increase in the flexibility of antigen-binding Fv loops, particularly VL CDR1 and VH CDR3, was associated with affinity-maturated anti-DNA antibodies. Such high flexibility of the FV loops may provide the environment where the antibodies could effectively interact with antigen DNA, a model consistent with the 'induced-fit' hypothesis of antigen-antibody interactions.

Amino Acid Sequence↗
PubMed2004

Flexibility exists in the region of [A6-A11, A7-B7] disulfide bonds during insulin precursor folding.

To investigate the possible similarity of the proinsulin folding process with insulin-like growth factor I, two swap-like human proinsulin mutant proteins [A7,A11Ser]-HPI and [A11Ser,A12Cys]-HPI were prepared. Their in vitro refolding yields, oxidation of free thiol groups, circular dichroism spectra, antibody and receptor binding activities and sensitivity to trypsin digestion were studied and compared with both native HPI and [A6,A11Ser]-HPI. The results indicate that the shift mutation in the disulfide bond caused more conformational change and a greater decrease in biological activity than the deletion mutation on the proinsulin molecule. However, the shift of the intra-A chain disulfide bond had little effect on the refolding rate of the molecule. In vitro refolding yields of HPI analogues with shift or deletion mutations in the region of the [A6-A11,A7-B7] disulfide bonds were almost as high as that of wild type HPI suggesting that the region of the [A6-A11,A7-B7] disulfide bonds possesses some flexibility as is found in the corresponding region of insulin-like growth factor I.

Disulfides↗
PubMed2004

Instability of the apo form of aromatic L-amino acid decarboxylase in vivo and in vitro: implications for the involvement of the flexible loop that covers the active site.

Pyridoxine deficiency caused a decrease in the amount of aromatic L-amino acid decarboxylase (AADC) in PC12 cells to less than 5% of the control. The degree of the enzyme saturation with the coenzyme pyridoxal 5'-phosphate (PLP) was around 90% for both the control and the pyridoxine-deficient cells, contrary to earlier reports by others. Mathematical analysis of the result indicated that the AADC apoenzyme is degraded at least 20-fold faster than the holoenzyme in the cells. To determine the mechanism of the preferential degradation of the apoenzyme, in vitro model studies were carried out. AADC has a flexible loop that covers the active site. This loop was easily leaved by proteases at similar rates for both the holoenzyme and the apoenzyme. However, in the presence of the substrate analog, dopa methyl ester, the holoenzyme was not cleaved by proteases, while the apoenzyme was cleaved similarly. These results indicated that the ligand that forms a Schiff base (aldimine) with PLP is fixed to the active site and stabilizes the flexible loop. The structure of the rat AADC-dopa complex modeled on the crystal structure of pig AADC showed that the flexible loop can fit in the concave surface at the entrance of the active site, its aliphatic and aromatic residues forming hydrophobic interactions with the substrate catechol ring. It was postulated that the flexible loop of the holoenzyme is stabilized in vivo by taking a closed structure that holds the PLP-substrate aldimine, while the apoenzyme cannot bind the substrate and its flexible loop is easily cleaved, leading to the preferential degradation of the apoenzyme.

Animals↗
PubMed1999

Damage increases the flexibility of duplex DNA.

It is proposed that much of the recognition of specific types of damaged DNAs is based on accessible structural features, while much of the recognition of damaged DNAs, as a class, is based on flexibility. The more flexible a DNA the faster its diffusion rate. The diffusion rates of each member of a series of damaged duplex DNAs has been found to be significantly faster than that of the corresponding undamaged duplex DNA. The damaged sites studied include apurinic and apyrimidinic a basic sites, thymine glycol and urea. The presence of mismatched sites also increases the diffusion. Thus, damaged DNAs appear to have sufficient flexibility for recognition and the flexibility may allow damaged sites to act as a universal joint or hinge that allows distant sites on the DNA to come together.

DNA↗
PubMed2000

Theoretical design of antisense genes with statistically increased efficacy.

Endogenous expression of antisense RNA represents one major way of applying antisense nucleic acids. To express antisense RNA intracellularly, recombinant antisense genes have to be designed and introduced into cells where the target RNA is encountered. Efficient annealing between the antisense RNA and the target RNA is crucial for efficacy and is strongly influenced by RNA structure. Here we extend structural rules for the design of in vitro transcribed antisense RNAs to the design of recombinant antisense genes. Intracellularly expressed antisense RNA transcripts contain a central antisense portion and additional flanking vector-derived sequences. A computer algorithm was generated to compose large sets of antisense genes, to calculate secondary structures of the transcribed sequences and to select for favorable structures of antisense RNA in terms of annealing and efficacy. The biological test system to measure efficiency of antisense genes was human immunodeficiency virus type 1 (HIV-1) replication in 293T cells. When considering the lower intracellular steady-state levels of favorably structured endogenous transcripts, an antisense effect against HIV-1 replication was observed that was up to 60-fold stronger than that measured for predicted unfavorable species. The computational selection was successful for antisense portions of 300 nt but not 100 nt in length. This theoretical design of antisense genes supports their improved application under time- and labor-saving conditions.

Algorithms↗
PubMed2000

Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo.

Poly(dA.dT) sequences (T-tracts) are abundant genomic DNA elements with unusual properties in vitro and an established role in transcriptional regulation of yeast genes. In vitro T-tracts are rigid, contribute to DNA bending, affect assembly in nucleosomes and generate a characteristic pattern of CPDs (cyclobutane pyrimidine dimers) upon irradiation with UV light (UV photofootprint). In eukaryotic cells, where DNA is packaged in chromatin, the DNA structure of T-tracts is unknown. Here we have used in vivo UV photofootprinting and DNA repair by photolyase to investigate the structure and accessibility of T-tracts in yeast promoters (HIS3, URA3 and ILV1). The same characteristic photofootprints were obtained in yeast and in naked DNA, demonstrating that the unusual T-tract structure exists in living cells. Rapid repair of CPDs in the T-tracts demonstrates that these T-tracts were not folded in nucleosomes. Moreover, neither datin, a T-tract binding protein, nor Gcn5p, a histone acetyltransferase involved in nucleosome remodelling, showed an influence on the structure and accessibility of T-tracts. The data support a contribution of this unusual DNA structure to transcriptional regulation.

Acetyltransferases↗
PubMed2000

Misincorporation of 2'-deoxyoxanosine into DNA: a molecular basis for NO-induced mutagenesis derived from theoretical calculations.

A wide range of theoretical methods, including high level ab initio, density functional, self-consistent reaction field, molecular dynamics and thermodynamic integration calculations, have been used to analyze the mutagenic properties of oxanosine. The major tautomeric forms in the gas phase and aqueous solution have been determined. The ability of oxanosine to recognize thymine and cytosine in the gas phase and in the DNA environment has been compared with that of guanine. A physicochemical explanation for the mutagenic properties of oxanosine is suggested.

Base Pairing↗
PubMed2000

Local conformational variations observed in B-DNA crystals do not improve base stacking: computational analysis of base stacking in a d(CATGGGCCCATG)(2) B<-->A intermediate crystal structure.

The crystal structure of d(CATGGGCCCATG)(2) shows unique stacking patterns of a stable B<-->A-DNA intermediate. We evaluated intrinsic base stacking energies in this crystal structure using an ab initio quantum mechanical method. We found that all crystal base pair steps have stacking energies close to their values in the standard and crystal B-DNA geometries. Thus, naturally occurring stacking geometries were essentially isoenergetic while individual base pair steps differed substantially in the balance of intra-strand and inter-strand stacking terms. Also, relative dispersion, electrostatic and polarization contributions to the stability of different base pair steps were very sensitive to base composition and sequence context. A large stacking flexibility is most apparent for the CpA step, while the GpG step is characterized by weak intra-strand stacking. Hydration effects were estimated using the Langevin dipoles solvation model. These calculations showed that an aqueous environment efficiently compensates for electrostatic stacking contributions. Finally, we have carried out explicit solvent molecular dynamics simulation of the d(CATGGGCCCATG)(2) duplex in water. Here the DNA conformation did not retain the initial crystal geometry, but moved from the B<-->A intermediate towards the B-DNA structure. The base stacking energy improved in the course of this simulation. Our findings indicate that intrinsic base stacking interactions are not sufficient to stabilize the local conformational variations in crystals.

Base Composition↗
PubMed2000

Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide.

The dynamic behavior of HIV-1 TAR and its complex with argininamide is investigated by means of molecular dynamics simulations starting from NMR structures, with explicit inclusion of water and periodic boundary conditions particle mesh Ewald representation of the electrostatic energy. During simulations of free and argininamide-bound TAR, local structural patterns, as determined by NMR experiments, were reproduced. An interdomain motion was observed in the simulations of free TAR, which is absent in the case of bound TAR, leading to the conclusion that the free conformation of TAR is intrinsically more flexible than the bound conformation. In particular, in the bound conformation the TAR-argininamide interface is very well ordered, as a result of the formation of a U.A.U base triple, which imposes structural constraints on the global conformation of the molecule. Free energy analysis, which includes solvation contributions, was used to evaluate the influence of van der Waals and electrostatic terms on formation of the complex and on the conformational rearrangement from free to bound TAR.

Adenine↗
PubMed2001

Novel display of knotted DNA molecules by two-dimensional gel electrophoresis.

We describe a two-dimensional agarose gel electrophoresis procedure that improves the resolution of knotted DNA molecules. The first gel dimension is run at low voltage, and DNA knots migrate according to their compactness. The second gel dimension is run at high voltage, and DNA knots migrate according to other physical parameters such as shape and flexibility. In comparison with one-dimensional gel electrophoresis, this procedure segregates the knotted DNA molecules from other unknotted forms of DNA, and partially resolves populations of knots that have the same number of crossings. The two-dimensional display may allow quantitative and qualitative characterization of different types of DNA knots simply by gel velocity.

Coliphages↗