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PubMed2004

Atom-bond electronegativity equalization method fused into molecular mechanics. I. A seven-site fluctuating charge and flexible body water potential function for water clusters.

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces "the hydrogen bond interaction region" in which a new parameter k(lp,H)(R(lp,H)) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom-atom interaction, i.e., oxygen-oxygen, hydrogen-hydrogen, oxygen-hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H(2)O)(n) (n=2-6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems.

Journal Article↗
PubMed2004

Improving the accuracy of interpolated potential energy surfaces by using an analytical zeroth-order potential function.

We present a method for improving the accuracy and efficiency of interpolation methods, in which an analytical zeroth-order potential-energy surface is employed as a reference surface. To investigate and test the method, we apply it to hydrogen peroxide where there exists an accurate analytical surface which we take as the "exact" surface for obtaining the energies and derivatives for fitting and assessing the accuracy. Examples are given for four-dimensional and six-dimensional surfaces interpolated by using either the modified Shepard or second-degree interpolating moving least-squares approach, with comparisons for cases with and without using the zeroth-order potential.

Journal Article↗
PubMedDate not supplied

[Large subunit of translation initiation factor--3 p170 contains potentially functional nuclear localization signals].

Eukaryotic translation factors and their subunits can have independent cellular functions, including regulation of nuclear events. We analyzed primary structure of p170 large subunit of human translation initiation factor eIF3 and found four potential bipartite nuclear localization signals (NLS). Then we studied whether these NLS were functional, that is were able to direct protein to cell nucleus. Complementary DNA of p170 fragments were expressed in cultured CV-1 and Cos-1 green monkey cells, and localization of fused with GFP proteins was determined by fluorescent microscopy. We established that p170 molecule possessed at least two functional NLS which determined nuclear localization of p170 fragments. At the same time more long p170 fragments containing the same functional NLS could be retained in cytoplasm. We speculate that either using specific factors or after limited proteolysis p170 can enter cell nucleus and participate in genome expression regulation. Also we do not exclude the possibility that functioning of p170 in cytoplasm can be regulated by reversible binding of importins to its NLS.

Animals↗
PubMed1996

The contribution of alpha 2-noradrenergic mechanisms of prefrontal cortical cognitive function. Potential significance for attention-deficit hyperactivity disorder.

This article aims to review research in nonhuman primates demonstrating that norepinephrine can enhance the cognitive functioning of the prefrontal cortex through actions at alpha 2 A-adrenergic receptors postjunctional to noradrenergic terminals. As prefrontal cortex cognitive deficits are prominent in several psychiatric disorders, including attention-deficit hyperactivity disorder, these basic findings may have relevance for the development of novel pharmacotherapies.

Adrenergic alpha-Agonists↗
PubMed1998

Proline brackets and identification of potential functional sites in proteins: toxins to therapeutics.

Protein toxins induce their specific pharmacological effects through protein protein interaction. Identification of these protein-protein interaction sites could lead to prototypes of highly specific therapeutic agents. However, deciphering the structure function relationships of protein toxins and locating the functional sites is a difficult, tedious and cumbersome task. We recently developed a novel predictive method to identify potential protein protein interaction sites directly from the amino acid sequence of a protein (R. M. Kini and H. J. Evans (1996) FEBS Lett. 385, 81-86) based on the presence of proline residues, a common residue found predominantly in the flanking segments of protein-protein interaction sites (R. M. Kini and H. J. Evans (1996) Biochem. Biophys. Res. Commun. 212, 1115-1124). It is a simple and straight-forward method. This review describes the new method and its application to solve structure function relationships of protein toxins. The method is useful in identifying functional sites in toxins, despite the subtle and complex nature of their structure function relationships and saves significant amounts of time and money.

Amino Acid Sequence↗
PubMed2005

T-screen to quantify functional potentiating, antagonistic and thyroid hormone-like activities of poly halogenated aromatic hydrocarbons (PHAHs).

The present study investigates chemical thyroid hormone disruption at the level of thyroid hormone receptor (TR) functioning. To this end the (ant)agonistic action of a series of xenobiotics was tested in the newly developed T-screen. This assay makes use of a GH3 rat pituitary cell line, that specifically proliferates when exposed to 3,3',5-triiodo-L-thyronine (T3). The growth stimulatory effect is mediated via T3-receptors. (Ant)agonistic and potentiating action of compounds was studied in absence and presence of T3 at its EC50 level (0.25 nM). The compounds tested included the specific TR-antagonist amiodarone, as well as a series of brominated diphenyl ethers (BDEs), including specifically synthesized BDEs with a structural resemblance to 3,5-diiodo-L-thyronine (T2), T3 and T4 (3,3',5,5'-tetraiodo-L-thyronine). The results obtained reveal that only BDE206 and amiodarone are specific antagonists. Interestingly some compounds which did not respond in the T-screen in absence of T3, potentiated effects when tested in combination with T3. This points at possibilities for disruption at the TR in vivo, where exposure generally occurs in presence of T3. Altogether the results of the present study show that the newly developed T-screen can be used as a valuable tool for identification and quantification of compounds active in disturbing thyroid hormone homeostasis at the level of TR-functioning.

Amiodarone↗
PubMed1999

Analysis of a Zebrafish semaphorin reveals potential functions in vivo.

The semaphorin/collapsin gene family is a large and diverse family encoding both secreted and transmembrane proteins, some of which are thought to act as repulsive axon guidance molecules. However, the function of most semaphorins is still unknown. We have cloned and characterized several semaphorins in the zebrafish in order to assess their in vivo function. Zebrafish semaZ2 is expressed in a dynamic and restricted pattern during the period of axon outgrowth that indicates potential roles in the guidance of several axon pathways. Analysis of mutant zebrafish with reduced semaZ2 expression reveals axon pathfinding errors that implicate SemaZ2 in normal guidance.

Amino Acid Sequence↗
PubMed1993

Antibiotics and neutrophil function--potential immunomodulating activities.

The advent of cytokines as possible therapeutic agents has stimulated investigation of old and new antibiotics for their potential activity as immunomodulators over and above their primary bactericidal or bacteristatic activity. Such investigations have focused largely on in-vitro functions of peripheral blood cells such as polymorphonuclear leucocytes and monocytes. Graded doses of various antibiotics have been tested for their ability to affect functions such as chemotaxis, phagocytic ingestion and killing, as well as particular biochemical mechanisms, such as a generation of superoxide. These drugs have been shown to have no effect on host defences (beta-lactams), or depress immune function (tetracyclines and teicoplanin), or display synergy with the immune system (macrolides and quinolones), or enhance immune function (certain cephalosporins). In several instances, biological activity has been demonstrated at drug concentrations outside the therapeutic range. In addition, it has been recognized that a number of drugs can be concentrated within the phagocytic cells and, by so doing, are transported to the site of infection with consequent increased efficacy. It has also been demonstrated that subinhibitory concentrations of certain drugs can influence bacterial expression of structural and soluble virulence factors. Alterations of this kind have been shown to potentiate bacterial susceptibility to phagocytosis. Notwithstanding these in-vitro examples of immunomodulation, definite proof of clinical benefit is still lacking.

Adjuvants, Immunologic↗
PubMed2004

A potentially functional mariner transposable element in the protist Trichomonas vaginalis.

Mariner transposable elements encoding a D,D34D motif-bearing transposase are characterized by their pervasiveness among, and exclusivity to, animal phyla. To date, several hundred sequences have been obtained from taxa ranging from cnidarians to humans, only two of which are known to be functional. Related transposons have been identified in plants and fungi, but their absence among protists is noticeable. Here, we identify and characterize Tvmar1, the first representative of the mariner family to be found in a species of protist, the human parasite Trichomonas vaginalis. This is the first D,D34D element to be found outside the animal kingdom, and its inclusion in the mariner family is supported by both structural and phylogenetic analyses. Remarkably, Tvmar1 has all the hallmarks of a functional element and has recently expanded to several hundred copies in the genome of T. vaginalis. Our results show that a new potentially active mariner has been found that belongs to a distinct mariner lineage and has successfully invaded a nonanimal, single-celled organism. The considerable genetic distance between Tvmar1 and other mariners may have valuable implications for the design of new, high-efficiency vectors to be used in transfection studies in protists.

Amino Acid Sequence↗
PubMed1985

[Functional potentials of the microcirculatory system in patients with thrombo-obliterative arterial diseases of the lower extremities].

Photoangiotensiotonography in the microcirculation system was used in order to study hemodynamic indices and its functional potencies in patients with thrombo-obliterating diseases of the lower extremity arteries. The progress of the disease was established to be followed by a considerable decrease of the main indices of hemodynamics in microvessels and the functional capacity of the microcirculation system.

Adult↗
PubMed1992

Oct-1 and Oct-2 potentiate functional interactions of a transcription factor with the proximal sequence element of small nuclear RNA genes.

The promoters of both RNA polymerase II- and RNA polymerase III-transcribed small nuclear RNA (snRNA) genes contain an essential and highly conserved proximal sequence element (PSE) approximately 55 bp upstream from the transcription start site. In addition, the upstream enhancers of all snRNA genes contain binding sites for octamer-binding transcription factors (Octs), and functional studies have indicated that the PSE and octamer elements work cooperatively. The present study has identified and characterized a novel transcription factor (designated PTF) which specifically binds to the PSE sequence of both RNA polymerase II- and RNA polymerase III-transcribed snRNA genes. PTF binding is markedly potentiated by Oct binding to an adjacent octamer site. This potentiation is effected by Oct-1, Oct-2, or the conserved POU domain of these factors. In agreement with these results and despite the independent binding of Octs to the promoter, PTF and Oct-1 enhance transcription from the 7SK promoter in an interdependent manner. Moreover, the POU domain of Oct-1 is sufficient for significant in vitro activity in the presence of PTF. These results suggest that essential activation domains reside in PTF and that the potentiation of PTF binding by Octs plays a key role in the function of octamer-containing snRNA gene enhancers.

Base Sequence↗
PubMed2026

Genome-Resolved Metagenomics Revealed the Functional Potential of Core Novel and Known Genera Key to Processes in Full-Scale Aerobic Granular Sludge Plants.

Microbial communities are critical for nutrient removal in aerobic granular sludge (AGS) wastewater treatment plants (WWTPs). Despite the stable long-term operation of full-scale AGS WWTPs, the microbial populations and functional traits sustaining stable long-term performance remain poorly resolved. To address this gap, the recovered MAG catalog from nine full-scale AGS WWTPs across five countries was analyzed. From this catalog, 74 high-quality core MAGs were identified and used for downstream taxonomic characterization and functional analyses. These high-quality core MAGs spanned 48 established and 7 novel genera, representing 31 known and 43 novel species. Functional analysis linked core MAGs to key WWTP processes: polyphosphate accumulation (9), glycogen accumulation (12), denitrification (62), and nitrification (1). These included four novel MAGs with glycogen-accumulating (3) and polyphosphate-accumulating (1) potential and 11 capable of nitrous oxide reduction, critical for mitigating greenhouse gas emissions. Ca. Phosphoribacter was the most abundant genus, highlighting its underestimated role caused by misclassification as Tetrasphaera in 16S rRNA surveys. Specifically, Ca. P. hodrii was the dominant species, exhibiting enhanced sugar uptake and amino acid synthesis as likely drivers of its enrichment in the AGS WWTPs. Overall, this study resolves for the first time the taxa and functional traits consistently enriched in full-scale AGS systems, enabling a shift from an empirical performance assessment toward biologically informed process interpretation.

Sewage↗
PubMed2003

Two serine residues distinctly regulate the rescue function of Humanin, an inhibiting factor of Alzheimer's disease-related neurotoxicity: functional potentiation by isomerization and dimerization.

The 24-residue peptide Humanin (HN), containing two Ser residues at positions 7 and 14, protects neuronal cells from insults of various Alzheimer's disease (AD) genes and A beta. It was not known why the rescue function of (S14G)HN is more potent than HN by two to three orders of magnitude. Investigating the possibility that the post-translational modification of Ser14 might play a role, we found that HN with D-Ser at position 14 exerts neuroprotection more potently than HN by two to three orders of magnitude, whereas D-Ser7 substitution does not affect the rescue function of HN. On the other hand, S7A substitution nullified the HN function. Multiple series of experiments indicated that Ser7 is necessary for self-dimerization of HN, which is essential for neuroprotection by this factor. These findings indicate that the rescue function of HN is quantitatively modulated by d-isomerization of Ser14 and Ser7-relevant dimerization, allowing for the construction of a very potent HN derivative that was fully neuroprotective at 10 pM against 25 microM A beta1-43. This study provides important clues to the understanding of the neuroprotective mechanism of HN, as well as to the development of novel AD therapeutics.

Alzheimer Disease↗
PubMed1996

New methods for maintaining human renal epithelial cells and analyzing their ion transport functions: potential analysis of genetic disease.

OBJECTIVES: New methods are available to immortalize parenchymal cells from exocrine glands and kidney with retention of differentiation. Adaptation of this technology to small, single-donor biopsy material or surgical specimens could provide genetically homogeneous cells for functional analyses and correlation with genetic background and underlying biochemistry. To develop a methodology useful for renal sodium metabolism, epithelial cell line generation was tested in a hypertensive rat model with features similar to salt-sensitive hypertension in humans. This form of hypertension has a large genetic component and is prevalent in African Americans. DESIGN: Protocols were designed to immortalize primary cultures of microdissected proximal tubule epithelial cells from spontaneously hypertensive (SHR) and control, normotensive Wistar-Kyoto (WKY) rats. Immortalization was based on a replication-defective retrovirus coding for SV40 large T-antigen as positive cell cycle regulator. Transport competent cells that grow on porous filters to form confluent monolayers were selected. RESULTS: Several proximal tubule cell lines have been developed from SHR and WKY rats. The cells retain important differentiated features, such as epithelial polarity, low monolayer conductance, and sodium-succinate cotransport. They are suitable for analyses of electrolyte transport by electrophysiology or imaging of intracellular fluorescent indicator dyes, such as sodium-binding benzofuran isophthalate. CONCLUSION: Feasibility of generating epithelial cell lines from defined renal segments was demonstrated. The cells retain important transport function so that analyses of sodium metabolism and the influence of genetic background on it are possible. The methodology is applicable to human specimens.

Animals↗