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At least 361 records · Page 20Linked to original sources
PubMed1999

Protein structure prediction by global optimization of a potential energy function.

An approach based exclusively on finding the global minimum of an appropriate potential energy function has been used to predict the unknown structures of five globular proteins with sizes ranging from 89 to 140 amino acid residues. Comparison of the computed lowest-energy structures of two of them (HDEA and MarA) with the crystal structures, released by the Protein Data Bank after the predictions were made, shows that large fragments (61 residues) of both proteins were predicted with rms deviations of 4.2 and 6.0 A for the Calpha atoms, for HDEA and MarA, respectively. This represents 80% and 53% of the observed structures of HDEA and MarA, respectively. Similar rms deviations were obtained for approximately 60-residue fragments of the other three proteins. These results constitute an important step toward the prediction of protein structure based solely on global optimization of a potential energy function for a given amino acid sequence.

Bacterial Proteins↗
PubMed2006

M-score: a knowledge-based potential scoring function accounting for protein atom mobility.

A knowledge-based potential scoring function, named M-Score, has been developed based upon 2331 high-resolution crystal structures of protein-ligand complexes. M-Score considers the mobility of protein atoms, describing the location of each protein atom by a Gaussian distribution instead of a fixed position based upon the isotropic B-factors. This leads to an increase in the number of atom-pairs in the construction of knowledge-based potentials and a smoothing effect on the pairwise distribution functions. M-Score was validated using 896 complexes which were not included in the 2331 data set and whose experimentally determined binding affinities were available. The overall linear correlation coefficient (r) between the calculated scores and experimentally determined binding affinities (pKi or pKd) for these 896 complexes is -0.49. Evaluation of M-Score against 17 protein families showed that we obtained good to excellent correlations for six protein families, modest correlations for four protein families, and poor correlations for the remaining seven protein families.

Algorithms↗
PubMed2000

Potential energy function for continuous state models of globular proteins.

One of the approaches to protein structure prediction is to obtain energy functions which can recognize the native conformation of a given sequence among a zoo of conformations. The discriminations can be done by assigning the lowest energy to the native conformation, with the guarantee that the native is in the zoo. Well-adjusted functions, then, can be used in the search for other (near-) natives. Here the aim is the discrimination at relatively high resolution (RMSD difference between the native and the closest nonnative is around 1 A) by pairwise energy potentials. The potential is trained using the experimentally determined native conformation of only one protein, instead of the usual large survey over many proteins. The novel feature is that the native structure is compared to a vastly wider and more challenging array of nonnative structures found not only by the usual threading procedure, but by wide-ranging local minimization of the potential. Because of this extremely demanding search, the native is very close to the apparent global minimum of the potential function. The global minimum property holds up for one other protein having 60% sequence identity, but its performance on completely dissimilar proteins is of course much weaker.

Computational Biology↗
PubMed1996

The effects of triiodothyronine on hemodynamic status and cardiac function in potential heart donors.

Brain death is associated with altered cardiac function and low concentrations of circulating triiodothryronine (T3). However, the effects of T3 administration on hemodynamic status and cardiac function in potential heart donors remain controversial. Thirty-seven brain-dead patients were randomly and blindly allocated to receive an intravenous bolus of either 0.2 microgram/kg T3 (n = 19) or saline placebo (n = 18). Measurements included conventional hemodynamic and echocardiographic variables of cardiac volume conditions and systolic function of the left ventricle (fractional area change [FAC], velocity of myocardial fiber shortening) using a transesophageal probe, arterial and mixed venous blood gas parameters, and serum thyroid hormone concentrations. The mean concentration of T3 was 1.86 +/- 1.55 pmol/L, and only six patients (16%) had normal values of T3 in control conditions. There was no significant correlation between T3 concentration and FAC (R = 0.17, not significant). All patients receiving T3 had normalized serum T3 concentration (7.55 +/- 2.56 pmol/L) in contrast to patients receiving saline (1.48 +/- 1.26 pmol/L). No significant differences in hemodynamic and echocardiographic parameters were observed between the placebo and T3 groups. Indeed, FAC remained unchanged after T3 (44% +/- 17% vs 46% +/- 22%) or placebo (47% +/- 18% vs 50% +/- 14%) administration. In 20 patients with impaired left ventricular function (FAC < 50%), FAC remained unchanged after T3 (n = 10; 34% +/- 12% vs 30% +/- 10%) or placebo (n = 10; 38% +/- 12% vs 35% +/- 13%) administration. In 17 patients in whom organ harvesting was delayed, transesophageal echocardiography was performed 6 h later and no significant changes in FAC were noted in the T3 group (n = 8; 49% +/- 17% vs 44% +/- 17%) and the placebo group (n = 9; 51% +/- 18% vs 47% +/- 18%). In conclusion, T3 administration did not improve hemodynamic status and myocardial function in brain-dead patients, suggesting that the euthyroid sick syndrome is not the main determinant of myocardial dysfunction in these patients.

Adolescent↗
PubMed2000

Multiple-sequence information provides protection against mis-specified potential energy functions in the lattice model of proteins

The neutral nets in the lattice models of proteins are composed of a group of similar sequences that encode for the same native structure. The maximal neutral nets in an HP and an AB lattice model are investigated by exhaustive enumeration in the conformation space. The result demonstrates that the performance of mis-specified potential functions can be improved significantly by averaging over sequences in the neutral nets.

Journal Article↗
PubMed2000

Antigen-specific T helper cell function: differential cytokine expression in primary and memory responses.

Distinguishing between the development of functional potential in antigen-specific T helper (Th) cells and the delivery of these specialized functions in vivo has been difficult to resolve. Here, we quantify the frequency of cytokine-producing cells within the primary and memory B10.BR Th cell response to pigeon cytochrome c (PCC). In vitro analysis of acquired functional potential indicated no Th1/Th2 cytokine polarity at the peak of the primary response with surprisingly little evidence for the selective preservation of interleukin (IL)-2, tumor necrosis factor (TNF)-alpha, IL-4, and interferon (IFN)-gamma potentials into the memory compartment. However, the expression of these functional potentials appears tightly regulated in vivo. The staggered appearance of primary response cytokines directly ex vivo contrasts markedly with their rapid coordinate expression in the memory response. Frequencies of IL-2-, TNF-alpha-, IFN-gamma-, and IL-10-expressing memory responders increased over their primary response counterparts, but were still markedly lower than revealed in vitro. IL-4-, IFN-gamma-, and IL-10-expressing Th cells remained at low but stable frequencies over the first 6 d of the memory response. Analysis of T cell receptor beta chain sequences of IL-4- and TNF-alpha-expressing PCC-specific Th cells provides evidence for early functional commitment among clonal progeny. These data indicate that the development of functional potential is a consequence of initial antigen experience, but delivery of specialized functions is differentially regulated in primary and memory immune responses.

Amino Acid Sequence↗
PubMed2007

Monte Carlo sampling of near-native structures of proteins with applications.

Since a protein's dynamic fluctuation inside cells affects the protein's biological properties, we present a novel method to study the ensemble of near-native structures (NNS) of proteins, namely, the conformations that are very similar to the experimentally determined native structure. We show that this method enables us to (i) quantify the difficulty of predicting a protein's structure, (ii) choose appropriate simplified representations of protein structures, and (iii) assess the effectiveness of knowledge-based potential functions. We found that well-designed simple representations of protein structures are likely as accurate as those more complex ones for certain potential functions. We also found that the widely used contact potential functions stabilize NNS poorly, whereas potential functions incorporating local structure information significantly increase the stability of NNS.

Computer Simulation↗
PubMed1991

Dimensional oscillation. A fast variation of energy embedding gives good results with the AMBER potential energy function.

The structure of the AMBER potential energy surface of the cyclic tetrapeptide cyclotetrasarcosyl is analyzed as a function of the dimensionality of coordinate space. It is found that the number of local energy minima decreases as the dimensionality of the space increases until some limit at which point equipotential subspaces appear. The applicability of energy embedding methods to finding global energy minima in this type of energy-conformation space is explored. Dimensional oscillation, a computationally fast variant of energy embedding is introduced and found to sample conformation space widely and to do a good job of finding global and near-global energy minima.

Computer Simulation↗
PubMed1993

An appearance-function shift in children's object naming.

The relative importance of appearance and potential function in children's object naming was examined. Potential function is an object capability that may not be currently realized (e.g. an empty mug has the potential to hold coffee). In Study 1, sixteen children from each of three age groups (3;8, 4;8, and 6;1) were taught novel names for unfamiliar objects; they then had to decide whether these applied to items that resembled the training objects in either appearance or potential function. The youngsters were also shown deceptive objects (e.g., an eraser that looked like a pencil) and had to choose between familiar appearance and function names for them (e.g., pencil or eraser). The frequency of function-based responding in both tasks increased with age. In Study 2, the name training procedure was revised so that equal emphasis was given to both apparent and functional features. The main results of the first study were replicated. Neither study obtained evidence of a strong relation between the appearance-function shift and increased understanding of the appearance-reality distinction.

Child Language↗
PubMed1975

A new approach to empirical intermolecular and conformational potential energy functions. II. Applications to crystal packing, rotational barriers, and conformational analysis.

An empirical potential energy function based on the interactions of electrons and nuclei (EPEN) has been tested on molecules other than those used for its parameterization. The results indicate that this energy function is able to predict reliably the lowest energy conformations, the potential energy differences between conformations, rotational barrier heights, and dipole moments for a series of alkanes, amines, alcohols, and carbohydrates. Crystal packing studies on n-hexane, n-octane, methylamine, methanol, and alpha-d-glucose, using this same potential, indicate that it is also reliable for calculating intermolecular interaction energies and low-energy orientations.

1-Propanol↗
PubMed2004

Synaptic strengthening mediated by bone morphogenetic protein-dependent retrograde signaling in the Drosophila CNS.

Retrograde signaling is an essential component of synaptic development and physiology. Previous studies show that bone morphogenetic protein (BMP)-dependent retrograde signaling is required for the proper development of the neuromuscular junction (NMJ) in Drosophila. These studies, moreover, raised the significant possibility that the development of central motor circuitry might similarly be reliant on such signaling. To test this hypothesis, retrograde signaling between postsynaptic motoneurons and their presynaptic interneurons is examined. Postsynaptic expression of an adenylate cyclase encoded by rutabaga (rut), is sufficient to strengthen synaptic transmission at these identified central synapses. Results are presented to show that the underlying mechanism is dependent on BMP retrograde signaling. Thus, presynaptic expression of an activated TGF-beta receptor, thickvien (tkv), or postsynaptic expression of a TGF-beta ligand, glass-bottom boat (gbb), is sufficient to phenocopy strengthening of synaptic transmission. In the absence of gbb, endogenous synaptic transmission is significantly weakened and, moreover, postsynaptic overexpression of rut is unable to potentiate synaptic function. Potentiation of presynaptic neurotransmitter release, mediated by increased postsynaptic expression of gbb, is dependent on normal cholinergic activity, indicative that either the secretion of this retrograde signal, or its transduction, is activity dependent. Thus, in addition to the development of the NMJ and expression of myoactive FMRFamide-like peptides in specific central neurons, the results of the present study indicate that this retrograde signaling cascade also integrates the development and function of central motor circuitry that controls movement in Drosophila larvae.

Adenylyl Cyclases↗
PubMed2001

Hemodynamic and electroencephalographic responses to illusory figures: recording of the evoked potentials during functional MRI.

The feasibility of recording event-related potentials (ERP) during functional MRI (fMRI) scanning using higher level cognitive stimuli was studied. Using responses to illusory figures in a visual oddball task, evoked potentials were obtained with their expected configurations and latencies. A rapid stimulation scheme using randomly varied trial lengths was employed, and class-wise characteristics of the hemodynamic response were obtained by a nonlinear analysis of the fMRI time series. Implications and limitations of conducting combined ERP-fMRI experiments using higher level cognitive stimuli are discussed. EEG/fMRI results revealed a sequential activation of striate and extrastriate occipital cortex along the ventral path of object processing for Kanizsa figures. Interestingly, Kanizsa figures activated the human motion area MT. Targets resulted in activations of frontal and parietal cortex which were not activated for standard stimuli.

Adult↗
PubMed2005

Changes in AMPA subunit expression in the mouse brain after chronic treatment with the antidepressant maprotiline: a link between noradrenergic and glutamatergic function?

Potentiation of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor function has been proposed as being useful in the treatment of depression, but thus far, little is known about the possible changes in AMPA receptor expression in the brain, after antidepressant treatment. The present study was carried out to study the expression of AMPA receptor subunits in different brain regions of mice that had been chronically injected with maprotiline. The latter is a modified tricyclic antidepressant that functions as a noradrenaline uptake inhibitor. Daily intraperitoneal injection with 10 mg/kg maprotiline for 30 days resulted in significantly increased GluR1 and GluR2/3 subunit expression in the nucleus accumbens and dorsal striatum as detected by immunohistochemistry; and significantly increased GluR1 and GluR2/3 expression in the hippocampus, as demonstrated by Western blot analysis. No change, or a decrease in GluR2 expression was detected in all the brain regions by both immunohistochemistry and Western blots. The increase in GluR1 and GluR2/3, but no increase in GluR2 subunits suggests that there could be an increase in calcium permeability of AMPA receptors in limbic/striatal brain regions after maprotiline treatment. This could lead to increased synaptic activity or plasticity in the hippocampus and striatum, and may underlie the therapeutic effect of maprotline, and possibly, other antidepressant drugs.

Animals↗
PubMed2006

Genetic variation in IGF1, IGF-1R, IGFALS, and IGFBP3 in breast cancer survival among Chinese women: a report from the Shanghai Breast Cancer Study.

Disruption of the balance of IGF (Insulin like growth factor) pathway constituents has been implicated in the etiology and progression of breast and other cancers. We hypothesized that genetic polymorphisms in IGF system members may be associated with breast cancer survival and evaluated this hypothesis in a cohort of 1,455 women diagnosed with breast cancer between 1996 and 1998 in Shanghai, China. Nineteen functional or potentially functional polymorphisms were evaluated in the IGF-1, IGF-1R, IGFALS, and IGFBP3 genes. Disease recurrence and vital status were obtained with a median follow-up time of 7.1 years. Cox proportional hazards models were used to estimate hazard ratios (HR) and 95% confidence intervals (CI). Overall, no significant association was noted between any of the 19 polymorphisms and survival. However, subgroup analyses demonstrated apparent interactions between menopausal status and survival for several (Single nucleotide polymorphism) SNPs in the IGF-1R and IGFBP3 genes. Carriers of the A/G or G/G genotypes (rs951715) in the IGF-1R gene had an increased risk of death among post-menopausal women (HR = 1.7, 95% CI = 1.1-2.7). Significant associations with breast cancer survival in pre-menopausal women were found for two IGFBP3 polymorphisms (rs2854744 and rs3110697), with an additional polymorphism (rs6413441) reaching borderline significance (P = 0.05). Hazard ratios for overall survival among pre-menopausal women were 1.5 (95% CI = 1.1-2.0) for the C/T-T/T genotypes (rs3110697), 1.4 (95% CI = 1.0-1.9) for the A/C-C/C genotypes (rs2854744), and 1.4 (95% CI = 1.0-1.9) for the N/A-A/A genotypes (rs6413441). Taken together, these data suggest that polymorphisms in the IGF-1R and IGFBP3 genes may be associated with altered survival among subgroups of breast cancer patients defined by menopausal status.

Adult↗
PubMed1996

Tendon transfers and functional electrical stimulation for restoration of hand function in spinal cord injury.

Spinal cord injury at the C5 and C6 level results in loss of hand function. Electrical stimulation of paralyzed muscles is one approach that has demonstrated significant capacity for restoring grasp and release function. One potential limitation of this approach is that key muscles for stimulation may have lower motor neuron damage, rendering the muscles unexcitable. We have used surgical modification of the biomechanics of the hand to overcome this limitation. Tendon transfer of paralyzed but lower motor neuron intact muscles can compensate for potential function lost owing to muscles with lower motor neuron damage. Such procedures have been performed to provide finger extension, thumb extension, finger flexion, and wrist extension. Additional surgical procedures have been performed to enhance the function provided with electrical stimulation. These are side-to-side synchronization of the finger flexor and extensor tendons, the flexor digitorium superficialis Zancolli-lasso procedure, and thumb interphalangeal joint arthrodesis. These procedures have been performed in 11 patients with C5 and C6 level spinal injuries and functional electrical stimulation neuroprostheses. In these patients, 41 different functional electrical stimulation-related procedures were performed and 38 gave the desired result after surgery. One procedure resulted in no increase or decrease in function or muscle output, and two procedures resulted in a decrease in muscle force or joint range of motion. The issues that must be considered in performing functional electrical stimulation-related tendon transfers are discussed.

Electric Stimulation Therapy↗
PubMed2006

Characteristics of biofilm community formed in the chlorinated biodegradable organic matter-limited tap water.

The aim of this study was to characterize the influence of free chlorine residual on biofilm formation in a chlorinated system in which the biodegradable organic matter (BOM) was limited. The biofilm community was characterized through a community-level physiological profile (CLPP) that was generated using the Biolog GN microplate-based community-level assay. The chlorinated system was run at chlorine residual concentrations of 0.3, 0.5, and 1.0 mg l(-1) with the provision of BOM-limited tap water (0.01 mg l(-1) as assimilable organic carbon and 0.06 mg l(-1) as biodegradable dissolved organic carbon). For comparison, an unchlorinated system was operated in parallel under the same condition. The number of viable heterotrophic bacteria in the biofilm that formed in the chlorinated system over the 3 months of operation averaged 7.2 x 10(3), 4.8 x 10, and 1.6 x 10 CFU cm(-2) for the chlorine residual concentrations of 0.3, 0.5, and 1.0 mg l(-1), respectively. In the unchlorinated system, the average bacterial content was 1.1 x 10(6) CFU cm(-2). Using measures of substrate utilization rate, substrate utilization diversity, and metabolic potential index (MPI), the CLPP patterns demonstrated that the metabolic potentials of the biofilm communities decreased markedly as the chlorine residual levels increased. In particular, the community level of the biofilm that formed in the system with chlorine residual concentration of 1.0 mg l(-1) was the lowest of any biofilm under the tested conditions. The results implied that chlorine residual had a positive biocidal effect on the metabolic potential and/or functional potential of the biofilm community, especially when the BOM level was low. In addition, BOM limitation by itself was not sufficient to control biofilm formation.

Biodegradation, Environmental↗
PubMedDate not supplied

Nosocomial infection control: role of the hospital administrator.

The role of the hospital administrator regarding the implementation and maintenance of programs for the prevention and control of nosocomial infections in U.S. hospitals is discussed. Data obtained in the Study on the Efficacy of Nosocomial Infection Control provide the basis for describing the backgrounds, demographic characteristics, functions, and potential functions of this official as s/he interacts with members of the infection control committee and other hospital staff. The infection control program of a hospital must have the support of the hospital administrator to be effective.

Cross Infection↗