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PubMed1997

Investigation of group migration in the fragmentation of bis(trimethylsilyl) ethers of diols separated by rigid groups.

Two fragmentations of (CH3)3SiO-CR2-X-CR2-OSi(CH3)3, where X is a rigid group such as a triple bond or an aromatic ring, are losses of a methyl or R group (where R is H or alkyl). The metastable-ion dissociations of [M-R]+ and [M-CH3]+ ions include the rearrangement of a trimethylsilyl (TMS) cation and a (CH3)2Si = O neutral species through an ion-neutral complex. On the basis of tandem mass spectrometry (MS/MS), exact mass measurement and isotopic labeling experiments, it has been established that the two trimethylsilyloxy groups in the TMS ethers interact across a wide range of distances via an ion-neutral complex. The migration of a TMS cation occurs when the group that is bound to carbon is expelled as a radical by an oxygen-directed cleavage to give a trimethylsilylated oxonium ion. If, on the other hand, a methyl radical is lost from the silicon atom, then (CH3)2Si = O migrates. The mobilities of the TMS cation and the neutral (CH3)2Si = O are governed by the capability of the rigid group to delocalize charge.

Ethers↗

PubMed1997

Histologic comparison of tibial articular surfaces against rigid materials and artificial articular cartilage.

After endoprosthetic replacement of the femoral head, marked pathologic changes of the acetabulum, such as penetration and ulceration, often occur. These changes are caused by the rigid material surface properties of the prosthesis and the lack of damping effects. In this study, we compared the time-dependent changes of tibial articular surfaces with three kinds of femoral implant under loading conditions in dogs. Marked pathologic changes of the menisci and tibial articular cartilage were observed from 8 weeks after implantation with hard material implants, whereas the tibial joint surface against an artificial articular cartilage was still intact 24 weeks postoperatively. These results showed clearly that marked pathologic changes of the articular cartilage against rigid materials occurred and were caused by the surface properties of the counterfaces and high friction coefficients of ceramic and metal materials used.

Animals↗

PubMed1998

Near-UV, circular dichroism, and fluorescence spectra of a rigid rodlike helical polysilane bearing trietheral moiety in ethanol/water.

An optically active, rigid rodlike helical polysilane with 6, 9, 12-trioxatetradecyl and (S)-2-methylbutyl substituents (1) was newly obtained as a very high molecular weight polymer of several million. Due to the presence of trietheral substituent, 1 was readily soluble in a polar solvent such as ethanol and a mixture of ethanol and water, but was insoluble in pure water. Polysilane 1 in pure ethanol at room temperature exhibited an intense and narrow ultraviolet (UV) and circular dichroism (CD) absorptions at 323 nm, associated with an almost mirror imaged fluorescence (FL) at 328 nm, that are characteristics of rigid rodlike, single-screw-sense helical polysilanes reported previously. When solution temperature was changed from 60 degrees C to -104 degrees C, a global shape of 1 expanded associated with an increase of segment length, whereas a screw pitch tended to be wound tightly. On the other hand, as a solvent polarity became poor, a global shape of 1 shrunk associated with an decrease of segment length and formed a chiral motif with an M-helicity between two helical segments with a kink. At a ratio of 50% of ethanol/water of 50:50 (v/v), 1 became insoluble and formed aggregates.

Circular Dichroism↗

PubMed2000

Scoring docked conformations generated by rigid-body protein-protein docking.

Rigid-body methods, particularly Fourier correlation techniques, are very efficient for docking bound (co-crystallized) protein conformations using measures of surface complementarity as the target function. However, when docking unbound (separately crystallized) conformations, the method generally yields hundreds of false positive structures with good scores but high root mean square deviations (RMSDs). This paper describes a two-step scoring algorithm that can discriminate near-native conformations (with less than 5 A RMSD) from other structures. The first step includes two rigid-body filters that use the desolvation free energy and the electrostatic energy to select a manageable number of conformations for further processing, but are unable to eliminate all false positives. Complete discrimination is achieved in the second step that minimizes the molecular mechanics energy of the retained structures, and re-ranks them with a combined free-energy function which includes electrostatic, solvation, and van der Waals energy terms. After minimization, the improved fit in near-native complex conformations provides the free-energy gap required for discrimination. The algorithm has been developed and tested using docking decoys, i.e., docked conformations generated by Fourier correlation techniques. The decoy sets are available on the web for testing other discrimination procedures. Proteins 2000;40:525-537.

Algorithms↗

PubMed2001

A (13)C NMR study on [3-(13)C]-, [1-(13)C]Ala-, or [1-(13)C]Val-labeled transmembrane peptides of bacteriorhodopsin in lipid bilayers: insertion, rigid-body motions, and local conformational fluctuations at ambient temperature.

We have recorded (13)C NMR spectra of selectively [3-(13)C]Ala-, [1-(13)C]Ala-, or [1-(13)C]Val-labeled synthetic transmembrane peptides of bacteriorhodopsin (bR) and enzymatically cleaved C-2 fragment in the solid and dimyristoylphosphatidylcholine bilayer. It turned out that these transmembrane peptides either in hexafluoroisopropanol or cast from it take an ordinary alpha-helix (alpha(I)-helix) irrespective of their amino acid sequences with reference to the conformation-dependent (13)C chemical shifts of (Ala)(n) taking the alpha-helix form. These transmembrane peptides are not always static in the lipid bilayer as in the solid state but undergo rigid-body motions with various frequencies as estimated from suppressed peaks either by fast isotropic or large-amplitude motions (>10(8) Hz) or intermediate frequencies (10(5) or 10(3) Hz). Further, (13)C chemical shifts of the [3-(13)C]Ala-labeled peptides in the bilayer were displaced downfield by 0.3-1.1 ppm depending upon amino acid sequence with respect to those in the solid state, which were explained in terms of local conformational fluctuation (10(2) Hz) deviated from the torsion angles (alpha(II)-helix) from those of standard alpha-helix, under anisotropic environment in lipid bilayer, in addition to the above-mentioned rigid-body motions. The carbonyl (13)C peaks, on the other hand, are not sensitively displaced by such local anisotropic fluctuations, because they are more sensitive to the manner of hydrogen-bond interactions. The amino acid sequences of these peptides inserted within the bilayer were not always the same as those of intact bR, causing disposition of the transmembrane alpha-helical segment from that of intact bR. Finally, we confirmed that the (13)C NMR peak positions of the random coil form are located at the boundary between the alpha-helix and a turned structure in loop regions.

Alanine↗

PubMed2001

Oligosaccharides display both rigidity and high flexibility in water as determined by 13C NMR relaxation and 1H,1H NOE spectroscopy: evidence of anti-phi and anti-psi torsions in the same glycosidic linkage.

The trisaccharide beta-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe has been investigated by molecular dynamics (MD) simulations and NMR experiments in water. 13C spin-lattice (T1) and spin-spin (T2) relaxation times, together with 1H,13C NOE data were measured at two magnetic field strengths (9.4 and 14.1 T) in a 277 K D2O solution. Relaxation data interpreted by means of the model-free formalism revealed a rigid (S2 approximately 0.9) oligosaccharide tumbling in solution. 1H,1H Cross-relaxation rates were determined at 600 MHz by 1D DPFGSE NOESY and T-ROESY experiments, which provided high quality data and subsequently proton-proton distances within the trisaccharide. The presence of anti conformers at both torsions of a glycosidic linkage is demonstrated for the first time. MD simulations were carried out to facilitate analysis of the NOE data. In total, 15 simulations-starting from five different conformational states--were performed, with production runs of up to 10 ns, resulting in 83 ns of oligosaccharide dynamics in water. anti Conformers were populated to different degrees in the simulations, especially at the phi2 torsion angle. By combining the results from the NOE experiments and the MD simulations, the anti conformers at the (1-->2)-linkage were quantified as 7% anti-phi2 and 2% anti-psi2, revealing a highly flexible trisaccharide in which large conformational changes occur. From the MD simulations, interresidue hydrogen bonding, from HO2" to O2 or O3, was significantly populated (approximately 40%) in both of the anti conformational states. The contentious issue over rigidity versus flexibility in oligosaccharides has thus been thoroughly examined, showing that the dynamics should be taken into account for a relevant description of the molecular system.

Carbohydrate Conformation↗

PubMed2005

Serotonin transporter intron 2 polymorphism associated with rigid-compulsive behaviors in Dutch individuals with pervasive developmental disorder.

Two putatively functional polymorphisms of the serotonin transporter gene (HTT, SLC6A4) were examined for associations with risk for pervasive developmental disorders (PDDs) and specific autism phenotypes. Dutch patients diagnosed with PDD (N = 125, age range 5-20 years, DSM-IV-TR based criteria, ADI-R and ADOS behavioral assessments) and their parents (N = 230) were genotyped for promoter ins/del (5-HTTLPR) and intron 2 variable number of tandem repeats (VNTR) alleles. Using the transmission disequilibrium test (TDT), no disorder-specific preferential transmission of promoter (long and short) or intron 2 (10- and 12-repeat) alleles was observed. However, multivariate analysis of continuous autism-related behavioral measures revealed that subjects with intron 2 12/12 genotype were significantly more impaired in the rigid-compulsive domain (P = 0.008). Quantitative TDT (QTDT) analysis also showed significant association of the intron 2 VNTR 12-repeat allele with rigid-compulsive behavior (P = 0.015). These results suggest that intron 2 VNTR alleles or nearby polymorphisms in linkage disequilibrium may play a role in specific aspects of the behavioral phenotype of autism.

Adolescent↗

PubMed1992

Influence of teeth, alveoli, and periodontal ligaments on torsional rigidity in human mandibles.

We investigated the influence of teeth, periodontal ligaments, and alveoli on the structural integrity of human mandibles loaded in torsion. Surface bone strain was recorded from the mandibular corpus below the first molar on each of four specimens. These specimens were loaded by an external force that caused primarily torsion about the long axis of the corpus, and bone strain was recorded under the following conditions: 1) all supporting structures intact, 2) all supporting structures intact and the M1 loaded by a simulated bite force, 3) M1 removed and 4) alveolar bone of the M1 removed. For comparative purposes, experiments were also designed to investigate the effects of intermittent holes on the torsional rigidity of a baboon femur. This permitted comparison of the mechanical behavior of the mandibles with that of a more homogeneous bony member. These experiments suggest that the presence of teeth within alveoli has a measurable role in the maintenance of torsional rigidity. The condition of the periodontal ligament also appears to influence these stress-bearing capabilities. Moreover, the alveolar bone supporting the teeth also provides structural support for countering torsional loads. For the specific case of corpus twisting, the mandible does not behave as a member with open or closed sections as predicted by theoretical models. The observed magnitudes of bone strain, however, conform more closely to the predictions generated by a closed-section model.

Adult↗

PubMed1990

[Hypertensive acting 5-(beta-aminoethyl)aminoisoxazoles: synthesis and screening of derivatives with with partially rigid C-5 side chains and omega-position heterocyclics].

Isoxazoles with a 1,2-diaminoethane side chain at C-5 are synthesized by nucleophilic substitution of 5-chloro derivatives. Using piperazine, imidazolidine and 1,2-diaminocyclohexane, resp., isoxazoles with partially rigid chains at C-5 are formed. The same procedure succeeds in the synthesis of isoxazoles having a heterocycle at the omega-position of the side chain. The hypertensive activity of all new compounds is shown for the pithed and the anaesthetized rat, resp. According to structure activity relationships the hypertensive activity of compounds 7 and 8, resp., is mainly determined by the heterocycle at the omega-position (piperazine greater than piperidine approximately pyrrolidine greater than morpholine). Derivatives 2-5 with partially rigid 5-(beta-aminoethyl)amino side chains show less hypertensive activity than the corresponding compounds without restrictions.

Anesthesia↗

PubMed2004

Understanding the alpha-helix to coil transition in polypeptides using network rigidity: predicting heat and cold denaturation in mixed solvent conditions.

Thermodynamic stability in polypeptides is described using a novel Distance Constraint Model (DCM). Here, microscopic interactions are represented as constraints. A topological arrangement of constraints define a mechanical framework. Each constraint in the framework is associated with an enthalpic and entropic contribution. All accessible topological arrangements of distance constraints form an ensemble of mechanical frameworks, each representing a microstate of the polypeptide. A partition function is calculated exactly using a transfer matrix approach, where in many respects the DCM is similar to the Lifson-Roig model. The crucial difference is that the effect of network rigidity is explicitly calculated for each mechanical framework in the ensemble. Network rigidity is a mechanical interaction that provides a mechanism for long-range molecular cooperativity and enables a proper treatment of the nonadditivity of a microscopic free energy decomposition. Accounting for (1) helix <--> coil conformation changes along the backbone similar to the Lifson-Roig model, (2) i to i + 4 hydrogen-bond formation <--> breaking similar to the Zimm-Bragg model, and (3) structured <--> unstructured solvent interaction (hydration effects), a six-parameter DCM describes normal and inverted helix-coil transitions in polypeptides. Under suitable mixed solvent conditions heat and cold denaturation is predicted. Model parameters are fitted to experimental data showing different degrees of cold denaturation in monomeric polypeptides in aqueous hexafluoroisopropanol (HFIP) solution at various HFIP concentrations. By assuming a linear HFIP concentration dependence (up to 6% by mole fraction) on model parameters, all essential experimentally observed features are captured.

Hydrogen Bonding↗

PubMed1991

Dynamic light scattering from weakly bending rods: estimation of the dynamic bending rigidity of the M13 virus.

A theory is presented for the dynamic structure factor [S(K,t]) of weakly bending rods. This treatment is based on a discrete bead model for the Brownian dynamics in which all bead motions associated with bending are constrained to occur in a plane perpendicular to the end-to-end vector, thus prohibiting extension or contraction along that axis. Preset hydrodynamic interactions are incorporated in a numerically exact manner. The predicted normalized dynamic structure factor S(K,t)/S(K,0) should be valid for short times t such that the rms rotation of the end-to-end vector around any transverse axis is much less than 1.0 radian. With geometrical parameters appropriate for the M13 virus, the intensity autocorrelation function G(2) (K,t) = 1 + magnitude of S(K,t)/S(K,0)2 is calculated over a range of times and scattering vectors K for selected values of the persistence length P. The calculated G(2) (K,t) are fitted to a single exponential with unit baseline over the same range of times as the experimental photon correlation functions, and the apparent diffusion coefficients Dapp (K) are obtained from the best-fit relaxation times. For the sake of completeness, an exact expression is derived for the apparent diffusion coefficient obtained from the initial slope of the dynamic structure factor. However, this does not reduce to the known correct result in the rigid rod limit. To obtain the correct result, the limit of infinite bending rigidity must be taken before the limit of zero time. For this and other reasons, the initial slope value of Dapp (K) is not useful for weakly bending rods. Photon correlation functions are measured for the M13 virus, which is virtually identical to the often-studied fd virus. The experimental photon correlation functions are fitted over 8 relaxation times to a single-exponential plus baseline, and the Dapp (K) are calculated from the best-fit relaxation times. Theoretical curves of Dapp (K) vs K2 for selected values of P are compared with the experimental data, which are satisfactorily reproduced when P = 22000 +/- 2000 A. This dynamic value is close to the static value, P = 20000 +/- 2000 A, reported for the very similar fd virus. The most recent theories of Maeda and Fujime and their dynamic light scattering studies of fd virus are compared with the present results in some detail. Their optimum value of P is in surprisingly good agreement with the present value.

Bacteriophages↗

PubMed1980

Operative choledochoscopy: experience with a rigid choledochoscope.

The use of a choledochoscope after exploration of the common bile ducts should minimize the occurrence of retained common bile duct stones. Experience gained at 50 endoscopies with a rigid choledochoscope is reviewed. In 7 cases stones or debris were found remaining in the bile duct. In one case an unsuspected neoplasm was demonstrated and in another a suspected neoplastic stricture was confirmed. In the remaining 41 cases choledochoscopy showed the ducts to be free of stones. Postoperative cholangiography demonstrated a retained stone in 2 cases. There were 2 deaths in the series. The experience of other authors with rigid and flexible scopes is reviewed.

Adult↗

PubMed1989

Rigid endoscopy under general anaesthesia is safe for chronic injection sclerotherapy.

Injection sclerotherapy for acutely bleeding oesophageal varices has been used in Belfast since 1958. However, a chronic injection sclerotherapy programme with rigid oesophagoscopy under general anaesthesia commenced only in 1979. So far, 82 patients have entered the programme; 57 patients had already received 73 acute injections before commencing chronic sclerotherapy. Subsequently, the 82 patients received 221 chronic injections plus a further 29 acute injections for rebleeding episodes which occurred during the programme. There were 24 Child's grade A patients, 23 B and 35 C; 48 per cent had alcoholic cirrhosis. Forty-eight patients achieved variceal obliteration with a mean of four injections. During the programme 24 patients experienced 42 acute bleeds. There were only two bleeding episodes within 1 week of a chronic injection and eight within 4 weeks. In the 8-year period there have been four early deaths. One occurred 17 days after a chronic injection and three followed acute injections required for rebleeding during the programme. There were 21 late deaths, mostly due to progressive liver failure, and none from rebleeding. We conclude that chronic injection sclerotherapy using rigid oesophagoscopy under general anaesthesia is both safe and effective.

Adolescent↗

PubMed2005

On the rigidity of polynorbornenes with dipolar pendant groups.

A range of polynorbornenes (PNBs) with fused dipolar pendant groups at C-5,6 positions was synthesized by ring-opening metathesis polymerization catalyzed by a ruthenium carbene complex (Grubbs I). Photophysical studies, EFISH measurements, and atomic force microscopy images have been used to investigate the structures and morphology of these polymers. These results suggest that the polymers may adopt rigid rod-like structures. The presence of the double bonds in PNBs appeared to be indispensable for the rigidity of the polymers. Interaction between unsaturated pendant groups may result in coherent alignment leading to a rod-like structure.

Journal Article↗

PubMed2003

Rigid-body dynamics in the isothermal-isobaric ensemble: a test on the accuracy and computational efficiency.

We have developed a time-reversible rigid-body (rRB) molecular dynamics algorithm in the isothermal-isobaric (NPT) ensemble. The algorithm is an extension of rigid-body dynamics [Matubayasi and Nakahara, J Chem Phys 1999, 110, 3291] to the NPT ensemble on the basis of non-Hamiltonian statistical mechanics [Martyna, G. J. et al., J Chem Phys 1994, 101, 4177]. A series of MD simulations of water as well as fully hydrated lipid bilayer systems have been undertaken to investigate the accuracy and efficiency of the algorithm. The rRB algorithm was shown to be superior to the state-of-the-art constraint-dynamics algorithm SHAKE/RATTLE/ROLL, with respect to computational efficiency. However, it was revealed that both algorithms produced accurate trajectories of molecules in the NPT as well as NVT ensembles, as long as a reasonably short time step was used. A couple of multiple time-step (MTS) integration schemes were also examined. The advantage of the rRB algorithm for computational efficiency increased when the MD simulation was carried out using MTS on parallel processing computer systems; total computer time for MTS-MD of a lipid bilayer using 64 processors was reduced by about 40% using rRB instead of SHAKE/RATTLE/ROLL.

Journal Article↗

PubMed1986

Vascular reorganization and return of rigidity in fracture healing.

The present study addresses the relationship between vascular reorganization and the biomechanical changes occurring during canine long bone fracture healing. A middiaphyseal osteotomy of the radius was performed, and angiographic studies were carried out using India ink injections from 2 to 12 weeks postosteotomy. The radii were harvested, subjected to nondestructive four-point bend testing on an Instron, and then sectioned and cleared according to the Spaltholtz technique. The observed microangiographic patterns were correlated with the calculated rigidity values. Quantitative bone blood flow measurements around the osteotomy were performed on a different group of animals, using the radiotracer microsphere technique, at 3, 6, and 9 weeks postosteotomy to correlate with our qualitative microangiographic results. We demonstrated a direct and predictable relationship between the phase of vascular reorganization and the rigidity. This correlation was present even in our delayed union specimens.

Angiography↗

PubMed1989

The mechanical and morphological properties of bone beneath internal fixation plates of differing rigidity.

The internal fixation of diaphyseal fractures by bone plates is a well recognized treatment. The normal physiological stress of bone is reduced by plates that cause a negative balance of bone-remodeling processes. Many investigators have shown that the degree of stress protection is dependent on the rigidity of the plates. It was the aim of this study to quantify mechanical and morphological changes at different locations in a plated diaphyseal bone as a function of differing plate rigidity. Two types of plates with the same size but different materials were used. The stainless steel plates had a modulus of elasticity and bending stiffness 3.2 times higher than the carbon fiber reinforced carbon plates. Both types of plates were applied to the intact right and left femora of six foxhounds for 6 months. The stiffer stainless steel plates led to a significantly higher bone loss and correspondingly greater loss of mechanical properties. These effects were greatest directly beneath the plate and less with increasing distance from the plate.

Animals↗

PubMed1977

Biological disposition of rigid analogs of amphetamine.

Tissue levels of amphetamine and of amphetamine analogs with a rigid conformation (2-aminoindan, 2-aminotetralin, and 2-aminobenzocycloheptene) were measured in rats by a spectrofluorometric method involving the reaction of the primary amine group with fluorescamine. All drugs were concentrated in tissues, the order of distribution being lungs greater than kidneys greater than liver=spleen=brain greater than muscle greater than fat=heart greater than blood. In brain, amphetamine and 2-aminoindan were present mostly in the supernatant fraction after high speed centrifugation onbrain homogenates; the two higher molecular weight drugs were present at slightly greater concentrations in the particulate fraction. All four drugs disappeared from rat brain with half-lives of 1-2 hr. Iprindole pretreatment increased drug levels in brain and prolonged the half-lives by two- to threefold. The data suggest that the biological disposition of the rigid analogs resembles generally that of amphetamine and that all of the drugs are probably metabolized by ring hydroxilation in the rat.

Amphetamines↗