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Results for “feature stability”

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At least 343 records · Page 19Linked to original sources

PubMed2003

Effects of random noise on a simple class of growing network models.

We investigate the effects of random noise on network systems. In particular, we consider a simple class of growing network models whose topological structure is determined by the preferred attachment A(k). We introduce a noise-induced attachment A(k) which includes fluctuations in the number of links of individual nodes due to a random noise. We carry out the numerical simulations to show that the topological structure of the networks is determined not only by A(k) but also by the strength of the noise. Analytic and numerical solutions are also presented to support this observation. In addition, we study the stability of networks against attacks under the noisy condition. Similarly, we introduce a noise-induced preferred deletion B(k), and show that noise is an essential feature to determine the stability of networks.

Journal Article↗

PubMed1999

Strategies to achieve coronary arterial plaque stabilization.

Acute coronary syndromes result from fissure, erosion or rupture of a vulnerable atherosclerotic plaque. The characteristics of a vulnerable plaque include a large lipid pool, an abundance of inflammatory cells and mediators, a reduced smooth muscle cell and collagen content and a thin overlying fibrous cap. Potential therapeutic strategies at achieving plaque stabilization have targeted these features. Lipid lowering agents, beta-adrenergic blockers, angiotensin converting enzyme inhibitors and antioxidants have been shown to reduce the incidence of acute coronary syndromes, presumably through plaque stabilization. Matrix metalloproteinase inhibitors as well as macrolide antibiotics and gene therapy approaches show promise in achieving plaque stabilization. The evidence supporting plaque stabilization by these agents and the mechanisms by which these agents stabilize plaques are discussed in detail in this review.

Adrenergic beta-Antagonists↗

PubMed2006

Determining the ratio of the Gaussian curvature and bending elastic moduli of phospholipids from Q(II) phase unit cell dimensions.

A method is presented for measuring M, the ratio of the Gaussian (saddle splay) elastic modulus to the bending elastic modulus of a lipid monolayer. The ratio M is determined from measurements of the equilibrium bicontinuous inverted cubic (Q(II)) phase unit cell size in excess water as a function of temperature. The analysis includes the effect of a curvature elastic term that is second-order in the Gaussian curvature, K. Preliminary results using data on DOPE-Me validate the method. The fitted value of M is within 8% of the value estimated in an earlier treatment. The method can be used to measure changes in M due to addition of exogenous lipids and peptides to a host lipid system. The Gaussian elastic modulus has a substantial effect on the stability of fusion intermediates (stalks, hemifusion diaphragms, and fusion pores). Studying the effects of peptides and different lipids on M via this method may yield insights into how fusion protein moieties stabilize intermediates in membrane fusion in vivo. The contribution of the K2 curvature elastic term to the free energy of Q(II) phase and fusion pores explains some features of fusion pore stability and dynamics, and some peculiar observations concerning the mechanism of L(alpha)/Q(II) phase transitions.

Animals↗

PubMed2006

Structural analysis of the HiPIP from the acidophilic bacteria: Acidithiobacillus ferrooxidans.

Hip is a high-potential iron-sulfur protein (HiPIP) isolated from the acidophilic bacterium, Acidithiobacillus ferrooxidans. In the present work, a structural model of Hip suggests that the role of proline residues is essential to stabilize the protein folding at very low pH. The presence of an unusual disulfide bridge in Hip is demonstrated using mass spectrometry and nuclear magnetic resonance. This disulfide bridge is necessary to anchor the N-terminal extremity of the protein, but is not involved in the acid stability of Hip. The structural parameters correlated with the pH dependence of Hip redox potential are also analysed on the basis of this model. Given that the same structural features can enhance acidic stability and lead to elevated redox potentials, modulation of the redox potentials of electron carriers may be necessary to achieve electron transfer at very low pH.

Acidithiobacillus↗

PubMed2006

Illusory color mixing upon perceptual fading and filling-in does not result in 'forbidden colors'.

A retinally stabilized object readily undergoes perceptual fading. It is commonly believed that the color of the apparently vanished object is filled in with the color of the background because the features of the filled-in area are determined by features located outside the stabilized boundary. Crane, H. D., & Piantanida, T. P. (1983) (On seeing reddish green and yellowish blue. Science, 221, 1078-1080) reported that the colors that are perceived upon full or partial perceptual fading can be 'forbidden' in the sense that they violate color opponency theory. For example, they claimed that their subjects could perceive "reddish greens" and "yellowish blues." Here we use visual stimuli composed of spatially alternating stripes of two different colors to investigate the characteristics of color mixing during perceptual filling-in, and to determine whether 'forbidden colors' really occur. Our results show that (1) the filled-in color is not solely determined by the background color, but can be the mixture of the background and the foreground color; (2) apparent color mixing can occur even when the two colors are presented to different eyes, implying that color mixing during filling-in is in part a cortical phenomenon; and (3) perceived colors are not 'forbidden colors' at all, but rather intermediate colors.

Adult↗

PubMed2003

Production of fertile somatic hybrid plants between Oriental hybrid lily and Liliumxformolongi.

Somatic hybridizations via electrofusion were performed in combinations of Oriental hybrid lilies (cvs. Acapulco and Shirotae) and Liliumxformolongi hort. (cv. Hakucho). Electrofusion-treated protoplasts divided only under nurse culture. The divided protoplasts grew into calli on the culture medium containing picloram, and the calli were then transferred to the hormone-free culture medium for induction of plant regeneration. The regenerants were transferred to a greenhouse, and were grown until the flower stage. In the fusion combinations of Acapulco + Hakucho and Shirotae + Hakucho, four regenerants apparently showed different morphological features compared with their parents. The results of molecular analyses by means of cleaved amplified polymorphic sequences markers and flow cytometry confirmed that these regenerants were somatic hybrid plants. Furthermore, we examined the stability of the morphological features of the hybrids in the next generations. This is the first report to describe the successful realization of Lilium somatic hybridization via protoplast fusion.

Cell Division↗

PubMed2003

Protein stability and plasticity of the hydrophobic cavity in wheat ns-LTP.

Plant ns-LTPs display an original structure with four helices and a flexible C-terminus, maintained together by four disulphide bridges and delineating an elongated central hydrophobic cavity. In order to relate these structural features to the protein stability and plasticity, combined molecular mechanics and simulated annealing calculations were undertaken on a wheat ns-LTP "mutant" with Cys-Ala replacement and with the application of core inter-residue restraints up to 2 A, reducing the cross-section size of the hydrophobic cavity. Analysis of the energy-minimized structures shows that removal of the disulphide bridges results in structures with a lower total energy and a smaller cavity volume. A 1-ns MD simulation at 300K in water, underlines that, despite the absence of a well-packed hydrophobic core, the native structure is extremely stable at room temperature and the cavity is not hydrated. This confirms that the disulphide bridges are essential for the existence of the cavity, whereas its plasticity depends both on the hydrophobic chain lining the cavity and on the C-terminal flexibility. A high temperature (500K) MD simulation confirms the stability of the secondary structure elements and the flexibility of the loops and of the C-terminal segment. Two important structural transitions during this simulation are discussed and possible routes for the insertion and release of hydrophobic ligands are suggested.

Alanine↗

PubMed2005

Molecular properties of food allergens.

Plant food allergens belong to a rather limited number of protein families and are also characterized by a number of biochemical and physicochemical properties, many of which are also shared by food allergens of animal origin. These include thermal stability and resistance to proteolysis, which are enhanced by an ability to bind ligands, such as metal ions, lipids, or steroids. Other types of lipid interaction, including membranes or other lipid structures, represent another feature that might promote the allergenic properties of certain food proteins. A structural feature clearly related to stability is intramolecular disulfide bonds alongside posttranslational modifications, such as N-glycosylation. Some plant food allergens, such as the cereal seed storage prolamins, are rheomorphic proteins with polypeptide chains that adopt an ensemble of secondary structures resembling unfolded or partially folded proteins. Other plant food allergens are characterized by the presence of repetitive structures, the ability to form oligomers, and the tendency to aggregate. A summary of our current knowledge regarding the molecular properties of food allergens is presented. Although we cannot as yet predict the allergenicity of a given food protein, understanding of the molecular properties that might predispose them to becoming allergens is an important first step and will undoubtedly contribute to the integrative allergenic risk assessment process being adopted by regulators.

Allergens↗

PubMed1999

Protein stabilization: a common consequence of mutations in independently derived v-Myc alleles.

Myc is overexpressed in many cancers as a result of gene rearrangement or amplification, but coding sequence changes which cluster in the N-terminal transactivation domain also appear to play a role in tumour progression. The prototypic v-Myc gene of MC29 virus differs from avian c-Myc by a series of mutations, including a change at a regulatory phosphorylation site within the mutational hotspot (thr-61) which is known to potentiate transformation in vitro. We now show that the mutation at thr-61 stabilizes the v-Myc protein (turnover difference) and that this single mutation is both necessary and sufficient for the phenotype. A major involvement of the proteasome in Myc degradation was confirmed, but surprisingly, a dilysine motif adjacent to thr-61 proved not to be the ubiquitin target. Two other v-Myc genes which carry a mutation at thr-61 (avian MH2) or a large deletion encompassing this domain (feline T17) were found to be stabilized to a similar extent as MC29, showing that stabilization is a common feature of independently derived Myc oncogenes. These results suggest a common selective process in the genesis of these three viral oncoproteins and a mechanistic link with Jun, Fos and Myb oncoproteins which are also stabilized relative to their cellular counterparts.

Alleles↗

PubMed2005

Structural determinants of protein stabilization by solutes. The important of the hairpin loop in rubredoxins.

Despite their high sequence homology, rubredoxins from Desulfovibrio gigas and D. desulfuricans are stabilized to very different extents by compatible solutes such as diglycerol phosphate, the major osmolyte in the hyperthermophilic archaeon Archaeoglobus fulgidus[Lamosa P, Burke A, Peist R, Huber R, Liu M Y, Silva G, Rodrigues-Pousada C, LeGall J, Maycock C and Santos H (2000) Appl Environ Microbiol66, 1974-1979]. The principal structural difference between these two proteins is the absence of the hairpin loop in the rubredoxin from D. desulfuricans. Therefore, mutants of D. gigas rubredoxin bearing deletions in the loop region were constructed to investigate the importance of this structural feature on protein intrinsic stability, as well as on its capacity to undergo stabilization by compatible solutes. The three-dimensional structure of the mutant bearing the largest deletion, Delta17/29, was determined by 1H-NMR, demonstrating that, despite the drastic deletion, the main structural features were preserved. The dependence of the NH chemical shifts on temperature and solute concentration (diglycerol phosphate or mannosylglycerate) provide evidence of subtle conformational changes induced by the solute. The kinetic stability (as assessed from the absorption decay at 494 nm) of six mutant rubredoxins was determined at 90 degrees C and the stabilizing effect exerted by both solutes was assessed. The extent of protection conferred by each solute was highly dependent on the specific mutant examined: while the half-life for iron release in the wild-type D. gigas rubredoxin increased threefold in the presence of 0.1 M diglycerol phosphate, mutant Delta23/29 was destabilized. This study provides evidence for solute-induced compaction of the protein structure and occurrence of weak, specific interactions with the protein surface. The relevance of these findings to our understanding of the molecular basis for protein stabilization is discussed.

Desulfovibrio gigas↗

PubMed1996

Axial muscle function during lizard locomotion

It was recently reported that the epaxial muscles of a lizard, Varanus salvator, function to stabilize the trunk during locomotion, and it was suggested that this stabilizing role may be a shared derived feature of amniotes. This result was unexpected because it had previously been assumed that the epaxial muscles of lizards function to produce lateral bending during locomotion and that only in mammals and birds were the epaxial muscles active in stabilizing the trunk. These results and the inferences made from them lead to two questions. (1) Is the pattern of epaxial muscle activity observed in V. salvator representative of a basal lizard condition or is it a derived condition that evolved within lizards? (2) If the epaxial muscles do not produce lateral bending, which muscles do carry out this function? These questions were addressed by collecting synchronous electromyographic (EMG) and kinematic data from two lizard species during walking and running. EMG data were collected from the epaxial muscles of a lizard species from a basal clade, Iguana iguana, in order to address the first question. EMG data were collected from the hypaxial muscles of both Iguana iguana and Varanus salvator to address the second question. The timing of epaxial muscle activity in Iguana iguana relative to the kinematics of limb support and lateral trunk bending is similar to that observed in Varanus salvator, a finding that supports the hypothesis that the epaxial muscles stabilize the trunk during locomotion in lizards and that this stabilizing role is a basal feature of lizards. Therefore, a stabilizing function of the epaxial muscles is most parsimoniously interpreted as a basal amniote feature. In both Iguana iguana and Varanus salvator, the activity of two of the hypaxial muscles, the external oblique and rectus abdominis, is appropriately timed for the production of lateral bending. This indicates that elements of the hypaxial musculature, not the epaxial musculature, are the primary lateral bending muscles of lizards.

Journal Article↗

PubMed1985

Seventeen base pairs of region I encode a novel tripartite binding signal for SV40 T antigen.

Three sequence components direct high affinity binding of dimeric SV40 T antigen to SV40 origin region I. Two signals are encoded by two directly repeated 5'-GAGGC-3' pentanucleotides. Approximately equal contributions to binding stability are made by each pentanucleotide, and both spacing and orientation of the pentanucleotides are important for binding affinity. The third vital component is contained in a 5'-TTTTTTG-3' spacer sequence that separates the pentanucleotides. Sequence-specific features of the spacer stabilize binding to the adjacent pentanucleotides. The asymmetry of the spacer suggests that a novel binding mechanism is involved. Because the alignment of T antigen on mutant and wild-type DNAs is similar, we propose that any two of the three sequence signals are sufficient to determine the unique arrangement of a bound protein dimer.

Antigens, Polyomavirus Transforming↗

PubMed2005

Influence of stem geometry on the stability of polished tapered cemented femoral stems.

Polished, tapered stems are now widely used for cemented total hip replacement and many such designs have been introduced. However, a change in stem geometry may have a profound influence on stability. Stems with a wide, rectangular proximal section may be more stable than those which are narrower proximally. We examined the influence of proximal geometry on stability by comparing the two-year migration of the Exeter stem with a more recent design, the CPS-Plus, which has a wider shoulder and a more rectangular cross-section. The hypothesis was that these design features would increase rotational stability. Both stems subsided approximately 1 mm relative to the femur during the first two years after implantation. The Exeter stem was found to rotate into valgus (mean 0.2 degrees , sd 0.42 degrees ) and internally rotate (mean 1.28 degrees , sd 0.99 degrees ). The CPS-Plus showed no significant valgus rotation (mean 0.07 [correction] degrees, sd 0.29 [correction] degrees ) or internal rotation (mean -0.03 degrees , sd 0.75 degrees ). A wider, more rectangular cross-section improves rotational stability and may have a better long-term outcome.

Aged↗

PubMed1996

Multiple wavelength anomalous diffraction (MAD) crystal structure of rusticyanin: a highly oxidizing cupredoxin with extreme acid stability.

The X-ray crystal structure of the oxidized form of the extremely stable and highly oxidizing cupredoxin rusticyanin from Thiobacillus ferrooxidans has been determined by the method of multiwavelength anomalous diffraction (MAD) and refined to 1.9 A resolution. Like other cupredoxins, rusticyanin is a copper-containing metalloprotein, which is composed of a core beta-sandwich fold. In rusticyanin the beta-sandwich is composed of a six- and a seven-stranded beta-sheet. Also like other cupredoxins, the copper ion is coordinated by a cluster of four conserved residues (His85, Cys138, His143, Met148) arranged in a distorted tetrahedron. Rusticyanin has a redox potential of 680 mV, roughly twice that of any other cupredoxin, and it is optimally active at pH values < or = 2. By comparison with other cupredoxins, the three-dimensional structure of rusticyanin reveals several possible sources of the chemical differences, including more ordered secondary structure and more intersheet connectivity than other cupredoxins. The acid stability and redox potential of rusticyanin may also be enhanced over other cupredoxins by a more extensive internal hydrogen bonding network and by more extensive hydrophobic interactions surrounding the copper binding site. Finally, reduction in the number of charged residues surrounding the active site may also make a major contribution to acid stability. We propose that the resulting rigid copper binding site, which is constrained by the surrounding hydrophobic environment, structurally and electronically favours Cu(I). We propose that the two extreme chemical properties of rusticyanin are interrelated; the same unique structural features that enhance acid stability also lead to elevated redox potential.

Azurin↗

PubMed2004

Local factors determine the stabilization of monocular ambiguous and binocular rivalry stimuli.

Perceptual alternation in viewing bistable stimuli can be slowed or halted if the stimuli are presented intermittently. Memory of the recent perceptual experience has been proposed to explain this stabilization effect. But the nature of this "perceptual memory" remains unclear. By using a bistable rotating cylinder and two dichoptically presented orthogonal gratings, we explored the features that are important for the stabilization by changing a particular feature of the stimuli between alternate presentations. For the rotating cylinder, changing its color, rotating speed, size, or its stereo depth had no or minimal effect on the stabilization of its perceived rotation direction. For binocular rivalry, when the two gratings were matched in strength and then swapped between the two eyes synchronously with the intermittent presentation, the percepts were usually stabilized to one eye. In both cases, perceptual stabilization occurred only if the stimuli were presented to the same retinal location. These results suggest that the stabilization of monocular bistable stimuli is likely due to the removal of local adaptation, insensitive to the features that define the object identity. For binocular rivalry, preservation of the direction of interocular suppression rather than memory of the stimulus identity accounts for the stabilization effect.

Adult↗

PubMed2002

Design of non-cysteine-containing antimicrobial beta-hairpins: structure-activity relationship studies with linear protegrin-1 analogues.

Protegrins are short, cationic peptides that display potent, broad-spectrum antimicrobial activity. PG-1, the first of the five natural analogues discovered, forms a rigid antiparallel two-stranded beta-sheet that is stabilized by two disulfide bonds. The two strands of the sheet are linked by a short two-residue loop segment. Removal of the disulfide bridges (e.g., in Cys --> Ala analogues) is known to cause marked loss of antimicrobial activity. We have used basic principles of beta-hairpin design to develop linear analogues of PG-1 that lack cysteine but nevertheless display PG-1-like activity. Our most potent reengineered molecules contain three essential design features: (i) the four cysteine residues of PG-1 are replaced by residues that have high propensity for beta-strand conformation, (ii) D-proline is placed at the i + 1 position of the reverse turn to promote a type II' beta-turn, and (iii) amino functionality is incorporated at the gamma-carbon of the D-proline residue to mimic the charge distribution of the natural beta-hairpin. Structural studies revealed that the antimicrobial potency of the non-disulfide-bonded peptides can be correlated to the stability of the beta-hairpin conformations they adopt in aqueous solution. The presence of 150 mM NaCl was found to have little effect on the antimicrobial activity of PG-1, but one of our linear analogues loses some potency under these high salt conditions. Despite this discrepancy in salt sensitivity, NMR and CD data indicate that neither PG-1 nor our linear analogue experiences a significant decrease in beta-hairpin conformational stability in the presence of 150 mM NaCl. Thus, salt inactivation is not due to destabilization of the beta-hairpin conformation. Furthermore, our results show that beta-sheet design principles can be used to replace conformation-stabilizing disulfide bridges with noncovalent conformation-stabilizing features.

Amino Acid Sequence↗

PubMed1976

Computer characterization of sinus rhythm.

Sinus rhythm tracings, including sinus tachycardia and bradycardia, are characterized quantitatively by means of an ECG measurement program which has been subjected to rigorous evaluation. The analysis is performed on tracings of short duration (10 sec). The features of regularity and stability are considered for the R wavetrain. Regularity is evaluated from the normalized differences between sucessive RR intervals. Stability is determined by the ratio of maximum and minimum RR interval durations. Due to the difficulities of automatic beat-to-beat detection and measurement of P waves, an estimate of the PR interval is obtained from a pseudo-PR interval determined from certain features of the P and R wavetrains. The constancy of this pseudo-PR interval is evaluated, and its absolute value is uded as a characteristic of the type of sinus rhythm.

Adult↗

PubMed1994

Geometries, charges, dipole moments and interaction energies of normal, tautomeric and novel bases.

Ab initio molecular orbital calculations with the STO-3G and 4-31G basis sets are performed to study the geometries and interactions of natural and "novel" Watson-Crick base pairs, as well as some non-Watson-Crick base pairs. First the optimized geometries of bases are determined using the STO-3G basis set, and then for the base pairs with the STO-3G and 4-31G basis sets. Interaction energies of these base pairs are evaluated, and their relative stabilities are discussed. Hydrogen bond features, partial charges and dipole moments of the base pairs are described. The calculated stabilities are in reasonable agreement with the limited available experimental data from thermal melting studies. Hydrogen bond geometries at the 4-31G level are in good agreement with the crystal structure data. The order of relative stabilities is found to be: iG:iC > G:C > G:T* > rG:rC > A*:C > Am:U > tau:kappa > chi:kappa > G*:T > A:C* > A:U = A:T where, A*, T*, G* and C* are tautomers, iG and iC are iso-G and iso-C, Am is 2-amino adenine, chi is xanthosine, kappa is 2,4-diaminopyrimidine, tau is 7-methyl oxoformycin B, rG is modified guanine with substitutions at positions 5 and 7, and rC is modified cytosine with a substitution at position 6. Pairing strengths with modified bases may affect the efficiency of protein production.

Adenine↗