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PubMed2000

Long-range order in the src SH3 folding transition state.

One of the outstanding questions in protein folding concerns the degree of heterogeneity in the folding transition state ensemble: does a protein fold via a large multitude of diverse "pathways," or are the elements of native structure assembled in a well defined order? Herein, we build on previous point mutagenesis studies of the src SH3 by directly investigating the association of structural elements and the loss of backbone conformational entropy during folding. Double-mutant analysis of polar residues in the distal beta-hairpin and the diverging turn indicates that the hydrogen bond network between these elements is largely formed in the folding transition state. A 10-glycine insertion in the n-src loop (which connects the distal hairpin and the diverging turn) and a disulfide crosslink at the base of the distal beta-hairpin exclusively affect the folding rate, showing that these structural elements are nearly as ordered in the folding transition state as in the native state. In contrast, crosslinking the base of the RT loop or the N and C termini dramatically slows down the unfolding rate, suggesting that dissociation of the termini and opening of the RT loop precede the rate-limiting step in unfolding. Taken together, these results suggest that essentially all conformations in the folding transition state ensemble have the central three-stranded beta-sheet formed, indicating that, for the src homology 3 domain, there is a discrete order to structure assembly during folding.

Animals↗
PubMed1991

In vitro effects on microtubule dynamics of purified Xenopus M phase-activated MAP kinase.

The protein kinase MAP kinase, also called MAP2 kinase, is a serine/threonine kinase whose activation and phosphorylation are induced by a variety of mitogens, and which is thought to have a critical role in a network of protein kinases in mitogenic signal transduction. A burst in kinase activation and protein phosphorylation may also be important in triggering the dramatic reorganization of the cell during the transition from interphase to mitosis. The interphase-metaphase transition of microtubule arrays is under the control of p34cdc2 kinase, a central control element in the G2-M transition of the cell cycle. Here we show that a Xenopus kinase, closely related to the mitogen-activated mammalian MAP kinase, is phosphorylated and activated during M phase of meiotic and mitotic cell cycles, and that the interphase-metaphase transition of microtubule arrays can be induced by the addition of purified Xenopus M phase-activated MAP kinase or mammalian mitogen-activated MAP kinase to interphase extracts in vitro.

Animals↗
PubMed2003

Silicon, germanium, tin and lead analogues of acetylenes.

Recent experimental results which have described the characterization of the first, stable heavier group 14 element analogues of acetylenes are outlined. It is shown that the use of large terphenyl substituents allows the isolation of transition metal-heavier group 14 element complexes that can achieve essential triple bonding by a three-fold orbital interaction between the transition metal and group 14 moiety. On the other hand the alkyne analogues RMMR (R = Ge, Sn or Pb) display increasing distortions from linearity to trans-bent geometry due to the accumulation of non-bonding electron density at the group 14 element. The non-bonding electron density comes at the expense of electron density in the bonding region between the group 14 elements. Accordingly the bond orders are decreased to values that are near double for the germanium and tin derivatives and single for the lead compound.

Journal Article↗
PubMed1992

Elimination of the yeast RAD6 ubiquitin conjugase enhances base-pair transitions and G.C----T.A transversions as well as transposition of the Ty element: implications for the control of spontaneous mutation.

The RAD6 gene of the yeast Saccharomyces cerevisiae encodes an enzyme that conjugates ubiquitin to other proteins. Defects in RAD6 confer a mutator phenotype due, in part, to an increased rate of transposition of the yeast Ty element. To further delineate the role of protein ubiquitination in the control of spontaneous mutagenesis in yeast, we have characterized 202 mutations that arose spontaneously in the SUP4-o gene carried on a centromere vector in a RAD6 deletion strain. The resulting mutational spectrum was compared to that for 354 spontaneous SUP4-o mutations isolated in the isogenic wild-type parent. This comparison revealed that the rad6 mutator enhanced the rate of single base-pair substitution, as well as Ty insertion, but did not affect the rates of the other mutational classes detected. Relative to the wild-type parent, Ty inserted at considerably more SUP4-o positions in the rad6 strain with a significantly smaller fraction detected at a transposition hotspot. These findings suggest that, in addition to the rate of transposition, protein ubiquitination might influence the target site specificity of Ty insertion. The increase in the substitution rate accounted for approximately 90% of the rad6 mutator effect but only the two transitions and the G. C----T.A transversion were enhanced. Analysis of the distribution of these events within SUP4-o suggested that the site specificity of the substitutions was influenced by DNA sequence context. Transformation of heteroduplex plasmid DNAs into the two strains demonstrated that the rad6 mutator did not reduce the efficiency of correcting mismatches that could give rise to the transitions or transversion nor did it bias restoration of the mismatches to the incorrect base-pairs. These results are discussed in relation to possible mechanisms that might link ubiquitination of proteins to spontaneous mutation rates.

Base Composition↗
PubMed2003

Way-marking behaviour: an aid to spatial navigation in the wood mouse (Apodemus sylvaticus).

BACKGROUND: During their movements in the wild, wood mice (Apodemus sylvaticus) distribute small objects, such as leaves or twigs, which are often visually conspicuous. Our experiments demonstrate that these marks serve as points of reference during exploration. Way-marking, as we call it, may diminish the likelihood of losing an "interesting" location, perhaps following disturbance by, for example, a predator or conspecific. Way-marks, being readily portable, may be a less confusing method of marking ephemeral sites than scent marks. They may also be a safer option for local navigation insofar as scent marks can easily be detected by a predator. RESULTS: In an experiment, conspicuous natural candidate way-marks were removed from a simple arena and wood mice were given white plastic discs instead. The wood mice picked up these discs and re-distributed them about their arena; as the mice moved, they repeatedly re-positioned the discs and usually spent a considerable time near recently repositioned discs. Analysis revealed a statistically significant association between the location of places in which the mice had positioned way-marks and the subsequent pattern of their movements. In a separate analysis, based on the context in which each behaviour occurred, we used the components and sequences of wood mouse behaviour to deduce the motivation behind each activity. One set of behaviour patterns, the elements of which were closely linked by the high transition probabilities amongst them, were interpreted as linked elements of exploration; whenever the mice transported a disc it was in association with these exploratory behaviours. This evidence that transporting discs is set in the motivational context of exploratory behaviour supports the conclusion that way-marking is part of the wood mouse's system of spatial orientation. CONCLUSION: We conclude that way-marking - a behaviour not previously described in mammals other than humans - serves solely as an aid to spatial navigation during exploration.

Animals↗
PubMed2005

Reconstruction of the src-SH3 protein domain transition state ensemble using multiscale molecular dynamics simulations.

We use an integrated computational approach to reconstruct accurately the transition state ensemble (TSE) for folding of the src-SH3 protein domain. We first identify putative TSE conformations from free energy surfaces generated by importance sampling molecular dynamics for a fully atomic, solvated model of the src-SH3 protein domain. These putative TSE conformations are then subjected to a folding analysis using a coarse-grained representation of the protein and rapid discrete molecular dynamics simulations. Those conformations that fold to the native conformation with a probability (P(fold)) of approximately 0.5, constitute the true transition state. Approximately 20% of the putative TSE structures were found to have a P(fold) near 0.5, indicating that, although correct TSE conformations are populated at the free energy barrier, there is a critical need to refine this ensemble. Our simulations indicate that the true TSE conformations are compact, with a well-defined central beta sheet, in good agreement with previous experimental and theoretical studies. A structured central beta sheet was found to be present in a number of pre-TSE conformations, however, indicating that this element, although required in the transition state, does not define it uniquely. An additional tight cluster of contacts between highly conserved residues belonging to the diverging turn and second beta-sheet of the protein emerged as being critical elements of the folding nucleus. A number of commonly used order parameters to identify the transition state for folding were investigated, with the number of native Cbeta contacts displaying the most satisfactory correlation with P(fold) values.

Models, Molecular↗
PubMedDate not supplied

Thermal analysis of whole soils and sediment.

Thermal analysis techniques were utilized to investigate the thermal properties of two soils and a lignite coal obtained from the International Humic Substances Society (IHSS), and sediment obtained from The Netherlands. Differential scanning calorimetry (DSC) revealed glass transition behavior of each sample at temperatures ranging from 52 degrees C for Pahokee peat (euic, hyperthermic Lithic Medisaprists), 55 degrees C for a Netherlands (B8) sediment, 64 degrees C for Elliott loam (fine, illitic, mesic Aquic Arguidolls), to 70 degrees C for Gascoyne leonardite. Temperature-modulated differential scanning calorimetry (TMDSC) revealed glass transition behavior at similar temperatures, and quantified constant-pressure specific heat capacity (Cp) at 0 degrees C from 0.6 J g(-1) degrees C(-1) for Elliott loam and 0.8 J g(-1) degrees C(-1) for the leonardite, to 1.0 J g(-1) degrees C(-1) for the peat and the sediment. Glass transition behavior showed no distinct correlation to elemental composition, although Gascoyne Leonardite and Pahokee peat each demonstrated glass transition behavior similar to that reported for humic acids derived from these materials. Thermomechanical analysis (TMA) revealed a large thermal expansion followed by a matrix collapse for each sample between 20 and 30 degrees C, suggesting the occurrence of transition behavior of unknown origin. Thermal transitions occurring at higher temperatures more representative of glass transition behavior were revealed for the sediment and the peat.

Calorimetry, Differential Scanning↗
PubMed1989

[Malignant mesodermal mixed tumor of the bladder: report of a case].

An 81-year-old woman was admitted to our clinic due to gross hematuria. A large bulky pedunculated mass was found in the bladder by cystoscopic examination. Subtotal cystectomy and bilateral cutaneostomy was performed on January 12, 1987. Histologically the tumor was composed of carcinomatous and sarcomatous elements. The carcinomatous element was composed fundamentally of grade 2, transitional cell carcinoma with numerous foci of squamous metaplasia. The sarcomatous element was composed of myxosarcomatous, chondro-sarcomatous pattern and non-differentiated malignant spindle cell component. Immunohistochemical examination demonstrated the presence of cytokeratin and epithelial membrane antigen in the spindle cell and more obvious carcinomatous regions, using the avidin-biotin conjugated immunoperoxidase technique. The patient died 3 months after operation. Autopsy findings showed multiple organ metastasis which were composed of carcinomatous and sarcomatous elements.

Aged↗
PubMedDate not supplied

Quantitative evaluations in gray crows: generalization of the relative attribute "larger set".

Four gray crows were trained to choose the larger of two sets presented to them within the "1-12" range. The color, form, and size of the stimulus elements on cards, as well as the patterns of their disposition, were varied constantly during training, while at the same time prohibiting the use of extraneous features not relating to the number of elements. In order to exclude choice on the basis of the total area of the elements, series of presentations with variation of the ratio of the number of elements and their total area were carried out: in half of the presentations the larger set consisted of small elements, and the smaller set of large elements; in the second half, the reverse. In this range all of the birds demonstrated a high accuracy of evaluations (75.3 +/- 2.4%), including when there were minimal differences between the sets to be compared. Thus, in the "1-12" range, the crows were found to be capable of accurately comparing sets precisely on the basis of the number of elements in them. When a transition was made to a new "10-20" range, all of the crows demonstrated a successful transfer of the developed reaction (71.5 +/- 2.3%). However, when the ratio of the number of elements and their total area was varied, only two birds were able to cope with this task (71.9 +/- 3.6%). Overall, the results obtained indicate a capacity of crows for the formation of the concept "larger set," and are regarded as a manifestation of a high level of development of reflective activity.

Animals↗
PubMed1994

Remote sensing as a landscape epidemiologic tool to identify villages at high risk for malaria transmission.

A landscape approach using remote sensing and geographic information system (GIS) technologies was developed to discriminate between villages at high and low risk for malaria transmission, as defined by adult Anopheles albimanus abundance. Satellite data for an area in southern Chiapas, Mexico were digitally processed to generate a map of landscape elements. The GIS processes were used to determine the proportion of mapped landscape elements surrounding 40 villages where An. albimanus abundance data had been collected. The relationships between vector abundance and landscape element proportions were investigated using stepwise discriminant analysis and stepwise linear regression. Both analyses indicated that the most important landscape elements in terms of explaining vector abundance were transitional swamp and unmanaged pasture. Discriminant functions generated for these two elements were able to correctly distinguish between villages with high and low vector abundance, with an overall accuracy of 90%. Regression results found both transitional swamp and unmanaged pasture proportions to be predictive of vector abundance during the mid-to-late wet season. This approach, which integrates remotely sensed data and GIS capabilities to identify villages with high vector-human contact risk, provides a promising tool for malaria surveillance programs that depend on labor-intensive field techniques. This is particularly relevant in areas where the lack of accurate surveillance capabilities may result in no malaria control action when, in fact, directed action is necessary. In general, this landscape approach could be applied to other vector-borne diseases in areas where 1) the landscape elements critical to vector survival are known and 2) these elements can be detected at remote sensing scales.

Animals↗
PubMed2001

Polymerized lipid vesicles as colorimetric biosensors for biotechnological applications.

Supramolecular chemical assemblies composed of polydiacetylene (PDA) exhibit rapid colorimetric transitions upon specific interactions with a variety of biological analytes in aqueous solutions. Among the analytes that give rise to the unique blue-red color changes are lipophilic enzymes, antibacterial peptides, ions, antibodies, and membrane penetration enhancers. The chemical assemblies include conjugated PDA, responsible for the chromatic transitions, and the molecular recognition elements, which are either chemically or physically associated with the PDA. Thus, by incorporation of specific recognition elements, the system can be designed in ways allowing for highly selective identification of analytes. In particular, receptors and epitopes can be incorporated within the sensor assembly, which then determine the specificity of the colorimetric transitions. The PDA-based molecular assemblies are robust and can be readily applied to diagnosis of physiological molecules and for rapid screening of chemical and biological libraries, for example, in 96 well-plate platforms.

Journal Article↗
PubMed1999

A pseudoautosomal boundary-like element adjacent to the SSAV1 locus at 18q21.

Pseudoautosomal boundary-like (PABL) elements have been found at transition sites between genomic regions with different GC-contents. A new PAB related sequence was found immediately adjacent to the S71 provirus on human chromosome 18q21.1-2 (officially designated the SSAV1 locus). The S71 PABL element was full-length as defined by comparison with elements identified at the pseudoautosomal boundaries of the sex chromosomes and in the MHC region. The 3'-ends of all PABL elements showed significant homology to functional CpG-islands, indicating that this similarity is a new common feature of PABL elements.

Base Sequence↗
PubMed2005

Mixed ligand complexes of bis(phenylimine) Schiff base ligands incorporating pyridinium moiety Synthesis, characterization and antibacterial activity.

The synthesis and structural characterization of mixed ligand complexes derived from 2,6-pyridinedicarboxaldehydebis(o-hydroxyphenylimine), 2,6-pyridinedicarboxaldehydebis(p-hydroxyphenylimine) (1(ry) ligands) and 2-aminopyridne (2(ry) ligand) are reported. The ligands and their transition metal complexes were characterized on the bases of their elemental analyses, IR, solid reflectance, magnetic moment, molar conductance and thermal analysis (TGA). The mixed ligand complexes are formed in the 1:1:1 (M:L(1) or L(2):L') ratio as found from the elemental analyses and found to have the formulae [MX(2)(L(1) or L(2))(L')].nH(2)O where M = Co(II), Ni(II), Cu(II) and Zn(II), L(1) = 2,6-pyridinedicarboxaldehydebis(p-hydroxyphenylimine), L(2) = 2,6-pyridine dicarboxaldehydebis(o-hydroxyphenylimine), L' = 2-aminopyridine, X = Cl(-) in case of Cu(II) complex and Br(-) in case of Co(II), Ni(II) and Zn(II) complexes and y = 0-3. The molar conductance data reveal that the chelates are non-electrolytes. IR spectra show that the Schiff bases are coordinated to the metal ions in a terdentate manner with NNN donor sites of the pyridine-N and two azomethine-N. While 2-aminopyridine coordinated to the metal ions via its pyridine-N. Magnetic and solid reflectance spectra are used to infer the coordinating capacity of the ligand and the geometrical structure of these complexes are found to be octahedral. The thermal behaviour of these chelates shows that the hydrated water molecules and the anions are removed in a successive two steps followed immediately by decomposition of the ligands (L(1), L(2) and L') in the subsequent steps. The activation thermodynamic parameters, such as, E*, DeltaH*, DeltaS* and DeltaG* are calculated from the TG curves and discussed. The ligands and their metal chelates have been screened for their antimicrobial activities and the findings have been reported, explained and compared with some known antibiotics.

Anti-Bacterial Agents↗
PubMed2001

Canonical binding arrays as molecular recognition elements in the immune system: tetrahedral anions and the ester hydrolysis transition state.

The structures, obtained by X-ray crystallography, of the binding sites of catalytic antibodies raised to bind different phosphonates are compared. Although the amino acid sequences differ, all exhibit a tetrahedral array of hydrogen bond donors (a 'canonical binding array') complementary to the tetrahedral anion, which represents a 'transition state epitope' for the basic hydrolysis of esters and amides. Antibodies for phosphates, arsonates, and sulfonates are found also to possess the tetrahedral anion canonical binding array.

Animals↗
PubMed1991

cDNA sequence and deduced amino acid sequence of the precursor of the 37-kDa inner envelope membrane polypeptide from spinach chloroplasts. Its transit peptide contains an amphiphilic alpha-helix as the only detectable structural element.

We present the nucleotide sequence and the deduced amino acid sequence of a cDNA clone that encodes the entire precursor of the 37-kDa inner envelope membrane protein from spinach chloroplasts. The precursor protein consists of 344 amino acids (Mr 38,976). In vitro processing followed by radiosequence analysis of the in vitro transcribed and translated precursor protein revealed that its transit peptide consists of only 21 amino acid residues. The transit peptide has the potential to form an amphiphilic alpha-helix with a strong hydrophobic moment. It is speculated that this structural element represents an ancestral envelope-targeting domain. The in vitro synthesized precursor protein is directed to the chloroplasts and it is inserted into the envelope membrane in an ATP-dependent manner. The mature protein (323 amino acid residues, Mr 36,830) has a moderate hydrophobicity and contains only one membrane-spanning segment which is located at the C-terminus and possibly anchors the protein within the envelope membrane.

Amino Acid Sequence↗
PubMed2003

Development of new pseudopotential methods: improved model core potentials for the first-row transition metals.

We have recently developed new nonrelativistic and scalar-relativistic pseudopotentials for the first-row transition metal and several main-group elements. These improved Model Core Potentials were tested on a variety of transition metal complexes to determine their accuracy in reproducing electronic structures, bond lengths, and harmonic vibrational frequencies with respect to both all-electron reference data as well as experimental data. The new potentials are also compared with the previous model core potentials available for the first-row transition metals. The new potentials do a superior job at reproducing atomic data, reproduce molecular data as well as the previous version, and in conjunction with new main-group pseudopotentials that have L-shell structure of the valence basis set, they are slightly faster.

Journal Article↗