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PubMed1979

Studies on protein folding, unfolding and fluctuations by computer simulation. III. Effect of short-range interactions.

The theoretical model of proteins on the two-dimensional square lattice, introduced previously, is extended to include the specific short-range interactions. Attractive long-range interactions with various specificities and non-specific repulsive long-range interactions in the form of self-avoidance of the polymer chain are also operative in the model. Dynamics of the model protein is studied by a Monte Carlo method. The short-range interactions are found to accelerate the folding and unfolding transitions. Non-specific part of the attractive long-range interactions have a competing effect of decelerating the transitions. When the short-range interactions are weighted beyond a certain extent over the attractive long-range interactions are weighted beyond a certain extent over the attractive long-range interactions, the all-or-none character of the folding and unfolding transitions is destroyed. How the destruction proceeds is quantitatively expressed in terms of the S-H curves. The limiting case of dominance of the specific short-range interactions over the attractive long-range interactions is studied in detail. The lattice polymer in this limit does not behave like a globular protein at all. This observation leads to a reexamination of the currently popular notion of the dominance of the short-range interactions. A new concept of consistency is proposed to replace it. Possible mechanisms of the acceleration of the transitions by the specific short-range interactions are discussed.

Computers↗

PubMed1988

The solution conformation of the antibacterial peptide cecropin A: a nuclear magnetic resonance and dynamical simulated annealing study.

The solution conformation of the antibacterial polypeptide cecropin A from the Cecropia moth is investigated by nuclear magnetic resonance (NMR) spectroscopy under conditions where it adopts a fully ordered structure, as judged by previous circular dichroism studies [Steiner, H. (1982) FEBS Lett. 137, 283-287], namely, 15% (v/v) hexafluoroisopropyl alcohol. By use of a combination of two-dimensional NMR techniques the 1H NMR spectrum of cecropin A is completely assigned. A set of 243 approximate interproton distance restraints is derived from nuclear Overhauser enhancement (NOE) measurements. These, together with 32 distance restraints for the 16 intrahelical hydrogen bonds identified on the basis of the pattern of short-range NOEs, form the basis of a three-dimensional structure determination by dynamical simulated annealing [Nilges, M., Clore, G.M., & Gronenborn, A.M. (1988) FEBS Lett. 229, 317-324]. The calculations are carried out starting from three initial structures, an alpha-helix, an extended beta-strand, and a mixed alpha/beta structure. Seven independent structures are computed from each starting structure by using different random number seeds for the assignments of the initial velocities. All 21 calculated structures satisfy the experimental restraints, display very small deviations from idealized covalent geometry, and possess good nonbonded contacts. Analysis of the 21 converged structure indicates that there are two helical regions extending from residues 5 to 21 and from residues 24 to 37 which are very well defined in terms of both atomic root mean square differences and backbone torsion angles. For the two helical regions individually the average backbone rms difference between all pairs of structures is approximately 1 A. The long axes of the two helices lie in two planes, which are at an angle of 70-100 degrees to each other. The orientation of the helices within these planes, however, cannot be determined due to the paucity of NOEs between the two helices.

Anti-Bacterial Agents↗

PubMed2025

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation.

The Klebsiella pneumoniae species complex inhabits a wide variety of hosts and environments, and is a major cause of antimicrobial resistant infections. Genomics has revealed the population comprises multiple species/sub-species and hundreds of distinct co-circulating sub-lineage (SLs) that are associated with distinct gene complements. A substantial fraction of the pan-genome is predicted to be involved in metabolic functions and hence these data are consistent with metabolic differentiation at the SL level. However, this has so far remained unsubstantiated because in the past it was not possible to explore metabolic variation at scale. Here, we used a combination of comparative genomics and high-throughput genome-scale metabolic modeling to systematically explore metabolic diversity across the K. pneumoniae species complex (n = 7,835 genomes). We simulated growth outcomes for each isolate using carbon, nitrogen, phosphorus, and sulfur sources under aerobic and anaerobic conditions (n = 1,278 conditions per isolate). We showed that the distributions of metabolic genes and growth capabilities are structured in the population, and confirmed that SLs exhibit unique metabolic profiles. In vitro co-culture experiments demonstrated reciprocal commensalistic cross-feeding between SLs, effectively extending the range of conditions supporting individual growth. We propose that these substrate specializations may promote the existence and persistence of co-circulating SLs by reducing nutrient competition and facilitating commensal interactions. Our findings have implications for understanding the eco-evolutionary dynamics of K. pneumoniae and for the design of novel strategies to prevent opportunistic infections caused by this World Health Organization priority antimicrobial resistant pathogen.

Klebsiella pneumoniae↗

PubMed1977

Pulmonary mechanics in normal rats.

A versatile, whole-body pressure, or volume plethysmographic system for the study of pulmonary mechanics in anesthetized, tracheotomized rats has been described. Lung volumes and lung compliance values were in good agreement with those previously reported. Pulmonary resistance and chest wall compliance values were lower than those previously reported. Total dynamic compliance remained independent of respiratory frequency between 40 and 320 breaths/min. Flow-limiting behavior was demonstrated from a series of imposed forced expiratory maneuvers of graded effort. With a deflation pressure of 30 cmH2O, the effort-independent range of maximum flow extended to 40-50% of vital capacity. Maximal flow-static recoil pressure relationships were essentially linear over the effort independent portion of the flow-volume curve. Substitution of a low-density gas mixture (80% He-20% O2) for air resulted in increased forced expiratory flow rates but the magnitude of the response was considerably less than that which has been reported in man.

Airway Resistance↗

PubMed1992

Automatic focus correction for spot-scan imaging of tilted specimens.

The variation in defocus within an image of a highly tilted specimen can be a serious source of artifact. Spot-scan imaging can be combined with dynamic focusing to greatly reduce this range of defocus. A protocol is described for determining the parameters required for the automatic focus compensation during the recording of a spot-scan image. Images of a gold test specimen demonstrate the efficacy of this procedure in extending the area of the image that contains high-quality data. In case the tilt angle or resolution is high enough that the height difference of the specimen within each small illuminated area is larger than the depth of field, the image must be treated to compensate for the focus variation. The same principle is used as was developed for compensation of conventional images of tilted specimens.

Artifacts↗

PubMed1976

Force-velocity relations and fiber composition in human knee extensor muscles.

Standardized measurements of dynamic strength of the kneee extensor muscles were performed in 25 healthy male subjects (17-37 yr) by means of isokinetic contractions, i.e., knee extensions with constant angular velocities. Overall variation between double determinations of maximal torque throughout the 90 degrees arc of motion (0 degrees = fully extended leg) averaged 10% for the different constant velocities chosen. At any given angle of the knee the torque produced was higher for isometric than for dynamic contractions. Dynamic torque decreased gradually with increased speed of shortening. Peak dynamic torque was reached at knee angles in the range: 55-66 degrees, with a displacement toward smaller knee angles with higher angular velocities. Correlations were demonstrated between peak torque produced at the highest speed of muscle shortening and percent as well as relative area of fast twitch fibers in the contracting muscle. In addition muscles with a high percentage of fast twitch fibers had the highest maximal contraction speeds. These observations on intact human skeletal muscle are consistent with earlier findings in animal skeletal muscle preparations.

Adolescent↗

PubMed1992

Pantalar and tibiotalocalcaneal arthrodesis for post-traumatic osteoarthrosis of the ankle and hindfoot.

Twenty-one patients had a unilateral extended arthrodesis of the ankle and hindfoot (a tibiotalocalcaneal procedure in thirteen patients and a pantalar procedure in eight) for post-traumatic osteoarthrosis or deformity, or both. The operation was performed through a transfibular extended lateral approach, and autogenous bone graft and rigid internal fixation was used. A final alignment of 0 to 5 degrees of valgus, 0 to 5 degrees of calcaneus, and external rotation equal to that of the contralateral side was sought. Subjective and objective evaluation, including a personal interview, physical examination, and radiographic and dynamic pedobarographic analysis, was performed at a mean interval of thirty-two months (range, twenty-four to fifty-four months) after the operation. A solid fusion was achieved in eighteen (86 per cent) of the twenty-one patients. There were five malunions (24 per cent) and two superficial wound problems (10 per cent). Of the seventeen patients who were not retired from work, eleven returned to work: nine to an occupation that involved standing and two to a sedentary occupation. Although seventeen (81 per cent) of the twenty-one patients reported that they were much improved, twenty (95 per cent) had some pain, and most benefited from modifications in shoe-wear. Patients who had had a tibiotalocalcaneal arthrodesis were more mobile and functioned at a higher level than those who had had a pantalar arthrodesis. Extended arthrodesis of the ankle and hindfoot is a complex, technically demanding procedure, and should be regarded as a salvage operation capable of producing a satisfactory result and usually providing a reasonable alternative to amputation.

Adult↗

PubMed1991

Nuclear magnetic resonance investigations of calcium antagonist drugs. II: Conformational and dynamic features of verapamil in [2H6]DMSO.

Conformational features of verapamil in [2H6]DMSO have been delineated by measuring 13C and 1H NMR parameters. Spin-lattice relaxation rates were interpreted within the frame of an extended alkane chain with segmental motions hampered by the aromatic substituents at both ends. The effective correlation times were all evaluated in the range 0.16-0.22 ns at 293 K. The aromatic rings were found to lie somewhat out-of-plane with the alkane chain. The NMR data were used to construct a Dreiding model of the most probable spatial arrangement and a molecular modeling system was utilized to represent the "preferred" conformation of verapamil in solution.

Calcium Channel Blockers↗

PubMed2026

Engineering the Vero Cell Lineage: Toward a Programmable Vaccine Manufacturing Platform.

Vero cells remain an indispensable continuous substrate for human viral vaccine manufacturing. Despite decades of empirical process optimization, intrinsic genomic instability, including segmental aneuploidy and dynamic chromatin rearrangements, continues to limit the durability of engineered phenotypes under sustained viral burden and bioreactor stress. Here, we review the expanding engineering toolkit for the Vero lineage across a three-layered functional framework: the membrane interface, cytoplasmic foundry, and nuclear blueprint, evaluating translational prospects at each level. Receptor transplantation and morphological reprogramming have broadened viral entry range and enabled suspension-adapted culture formats, while metabolic flux management and temporally controlled apoptosis modulation have addressed intracellular production bottlenecks, albeit often with trade-offs between productivity, biosafety, and long-term population stability. At the genomic level, targeted perturbations of transcriptional regulators and emerging epigenetic interventions offer more durable gains, yet expression drift, clonal heterogeneity, and karyotypic instability during extended passaging highlight the need for locus-level precision rather than constitutive trait installation. Looking forward, infection-responsive dynamic logic circuits and the systematic identification of Vero-specific genomic safe harbors could shift the paradigm toward a conditionally responsive manufacturing architecture. Collectively, these advances suggest a pathway for transitioning the Vero lineage from a passive, empirically optimized biological substrate into a conditionally responsive, genomically stable, and programmable platform for modern vaccine preparedness.

Vero cells↗

PubMed1991

A 1H NMR study of human calcitonin in solution.

Human calcitonin (hCT) has been investigated by NMR at 400 MHz in DMSOd6 and in an 85% DMSOd6-15% 1H2O (v/v) cryoprotective mixture. All backbone and side-chain resonances have been assigned, and the secondary structure has been determined in both solvents. In DMSOd6, the simultaneous presence of d alpha N, dNN, and some specific weak medium-range nuclear Overhauser effects, together with the amide temperature coefficients and the analysis of the NH-alpha CH spin-spin coupling constants, indicates that hCT is highly flexible but with three domains (comprising segments Asn3-Gly10, Gln14-Thr21, and Thr25-Ala31) in extended conformations which dynamically transform into isolated beta turns in the N- and C-terminal regions and into adjacent tight turns, resembling a 3(10) helix structure, in the central part. The DMSO-water mixture rigidifies the polypeptide chain, favoring an ordered, extended conformation. NOESY data indicate the presence of a short double-stranded antiparallel beta sheet in the central region made by residues 16-21 and connected by a two-residue hairpin loop formed by residues 18 and 19. Two tight turns, formed by residues 3-6 and 28-31, were also identified. The central beta sheet does not favor an amphipathic distribution of the residues as found for salmon calcitonin [Motta, A., Castiglione Morelli, M. A., Goud, N., & Temussi, P. A. (1989) Biochemistry 28, 7998-8002]. This is in agreement with the smaller tendency of hCT to form the amphipathic alpha helix, postulated to be responsible for the interaction of hCT with lipids. The possible role of the cis-trans isomerism of Pro is discussed.

Amino Acid Sequence↗

PubMed1992

Intracellular HRP study of nociceptive neurons within the ventrobasal complex of the cat thalamus.

Locations and morphological characteristics of nociceptive specific (NS) and wide dynamic range (WDR) neurons of the ventrobasal (VB) thalamic complex were studied using an intracellular HRP injection technique in cats anesthetized with urethane and chloralose. Both NS and WDR neurons were found within the marginal zone of the VB complex. Their somata were confined to the VB complex, but dendrites were extended into the structures of the thalamus surrounding the VB complex. NS neurons were found in the caudal part of the VB complex, whereas WDR neurons were found more rostrally. Examinations of their locations within the marginal zone of the VB complex confirmed the somatotopic organization, as found previously. We also confirmed the previous reports that there are 3 different types of low-threshold mechanoreceptive (LTM) neurons within the VB complex. They are type I, type II and type III neurons. Both NS and WDR neurons were either type I or type II neurons. Obvious morphological differences were not found between LTM neurons and two classes of nociceptive VB neurons investigated.

Animals↗

PubMedDate not supplied

Controlled deposition of tantalum powder in a cast of the human airways: applications for aerosol bronchography.

A hollow latex cast of the human larynx and tracheobronchial tree extending to 2 mm diameter airways "inhaled" tantalum powder (mass median aero-dynamic diameter equals 9.2 mum, omicron-g equals 1.41) at 8 liters/min. Tantalum deposited within the cast as predicted by preliminary deposition calculations. These calculations predicted deposition surface densities among greater than 2 mm diam. airways to have a range of similar to 2:1, and also predicted less than 5% alveolar deposition. A deposition surface density of 8 mg/cm-2 provided good bronchographic visualization. Single rice grains located within some airways were distinctly outlined. The small amount of tantalum needed to outline the airways be a simulated voluntary inhalation indicates that tantalum may be suitable for use as a bronchographic contrast medium when administered under strictly controlled exposure conditions.

Aerosols↗

PubMed1991

Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane.

Computer simulations of phospholipid membranes have been carried out by using a combined approach of molecular and stochastic dynamics and a mean field based on the Marcelja model. First, the single-chain mean field simulations of Pastor et al. [(1988) J. Chem. Phys. 89, 1112-1127] were extended to a complete dipalmitoylphosphatidylcholine molecule; a 102-ns Langevin dynamics simulation is presented and compared with experiment. Subsequently, a hexagonally packed seven-lipid array was simulated with Langevin dynamics and a mean field at the boundary and with molecular dynamics (and no mean field) in the center. This hybrid method, mean field stochastic boundary molecular dynamics, reduces bias introduced by the mean field and eliminates the need for periodic boundary conditions. As a result, simulations extending to tens of nanoseconds may be carried out by using a relatively small number of molecules to model the membrane environment. Preliminary results of a 20-ns simulation are reported here. A wide range of motions, including overall reorientation with a nanosecond decay time, is observed in both simulations, and good agreement with NMR, IR, and neutron diffraction data is found.

Computer Simulation↗

PubMed1986

Extension of a binaural cross-correlation model by contralateral inhibition. I. Simulation of lateralization for stationary signals.

Running interaural cross correlation is a basic assumption to model the performance of the binaural auditory system. Although this concept is particularly suited to simulate psychoacoustic localization phenomena, there exist some localization effects which cannot be explained by pure cross correlation. In this paper a model of interaural cross correlation is extended by a "contralateral-inhibition mechanism" and by "monaural detectors" in order to simulate a wide range of psychoacoustic lateralization data. The extended model explains lateralization of pure tones with interaural time differences as well as with interaural level differences. Multiple images are predicted for tones with characteristic combinations of interaural signal parameters and for noise signals with different degrees of interaural cross correlation. The model is also capable of simulating dynamic lateralization phenomena, such as the "law of the first wave front" which is dealt with in a companion paper [Lindemann, J. Acoust. Soc. Am. 80, 1623-1630 (1986)]. The present paper is restricted to a comparison of the model predictions for stationary signals with the results of dichotic listening experiments.

Auditory Perception↗

PubMed1986

Variability of evolutionary rates of DNA.

A statistical analysis of DNA sequences from four nuclear loci and five mitochondrial loci from different orders of mammals is described. A major aim of the study is to describe the variation in the rate of molecular evolution of proteins and DNA. A measure of rate variability is the statistic R, the ratio of the variance in the number of substitutions to the mean number. For proteins, R is found to be in the range 0.16 less than R less than 35.55, thus extending in both directions the values seen in previous studies. An analysis of codons shows that there is a highly significant excess of double substitutions in the first and second positions, but not in the second and third or first and third positions. The analysis of the dynamics of nucleotide evolution showed that the ergodic Markov chain models that are the basis of most published formulas for correcting for multiple substitutions are incompatible with the data. A bootstrap procedure was used to show that the evolution of the individual nucleotides, even the third positions, show the same variation in rates as seen in the proteins. It is argued that protein and silent DNA evolution are uncoupled, with the evolution at both levels showing patterns that are better explained by the action of natural selection than by neutrality. This conclusion is based primarily on a comparison of the nuclear and mitochondrial results.

Animals↗

PubMed1992

Glutamate-immunoreactive terminals synapse on primate spinothalamic tract cells.

Glutamate has been shown to excite spinothalamic tract (STT) neurons and has been localized to primary afferent neurons, spinal cord projection neurons, and interneurons in the spinal cord dorsal horn. The likelihood that glutamate-immunoreactive (GLU-IR) terminals directly innervate STT neurons was investigated. For these studies three lamina IV or V STT cells in the lumbar spinal cords of three monkeys (Macaca fascicularis) were identified electrophysiologically and characterized. Two were identified as high threshold neurons and one as a wide dynamic range neuron. Following intracellular injection of the cells with HRP and reaction to give the cells a Golgi-like appearance, the tissues were processed for electron microscopy. Postembedding immunogold methods with antibodies specific for glutamate were used to identify GLU-IR terminals apposing the somata and dendrites of the STT neurons, including dendrites that extended into laminae IV and III. The GLU-IR terminals were numerous and constituted a mean of 46% of the population counted that appose the STT soma and 50% of the profiles apposing the dendrites. Fifty-four percent of the somatic and 50% of the dendritic surface length was contacted by GLU-IR terminals. Most terminals contained round clear vesicles and some contained a variable number of large dense core vesicles. For one of the three cells examined it was determined that 45% of the terminals apposing the soma were GLU-IR and 30% of the terminals were gamma aminobutyric acid-immunoreactive (GABA-IR). In an additional monkey, a lamina I cell retrogradely labeled from the ventral posterolateral nucleus of the thalamus was found to be ensheathed in glial processes.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

PubMed1985

Characterization of synthetic carrier ampholytes by repetitive scanning of the electric field during focusing.

This paper reports the utilization of a potential gradient array detector for monitoring the dynamics of the electric field during isoelectric focusing. Transient and steady state electric field profiles are presented for synthetic carrier ampholyte mixtures with a wide (approximately 3-10) pH range. Two available commercial products (Ampholine and Pharmalyte) and a laboratory synthesized mixture (PEHA ampholytes) are compared. The formation of conductivity gaps and their migration toward the cathode in extended experiments (cathodic drift) can be visualized with this system.

Ampholyte Mixtures↗

PubMed1990

Temperature dependence of the low frequency dynamics of myoglobin. Measurement of the vibrational frequency distribution by inelastic neutron scattering.

Inelastic neutron scattering spectra of myoglobin hydrated to 0.33 g water (D2O)/g protein have been measured in the low frequency range (1-150 cm-1) at various temperatures between 100 and 350 K. The spectra at low temperatures show a well-resolved maximum in the incoherent dynamic structure factor Sinc(q, omega) at approximately 25 cm-1 and no elastic broadening. This maximum becomes gradually less distinct above 180 K due to the increasing amplitude of quasielastic scattering which extends out to 30 cm-1. The vibrational frequency distribution derived independently at 100 and 180 K are very similar, suggesting harmonic behavior at these temperatures. This result has been used to separate the vibrational motion from the quasielastic motion at temperatures above 180 K. The form of the density of states of myoglobin is discussed in relation to that of other amorphous systems, to theoretical calculations of low frequency modes in proteins, and to previous observations by electron-spin relaxation of fractal-like spectral properties of proteins. The onset of quasielastic scattering above 180 K is indicative of a dynamic transition of the system and correlates with an anomalous increase in the atomic mean-squared displacements observed by Mössbauer spectroscopy (Parak, F., E. W. Knapp, and D. Kucheida. 1982. J. Mol. Biol. 161: 177-194.) and inelastic neutron scattering (Doster, W., S. Cusack, and W. Petry, 1989. Nature [Lond.]. 337: 754-756.) Similar behavior is observed for a hydrated powder of lysozyme suggesting that the low frequency dynamics of globular proteins have common features.

Deuterium↗