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PubMed2004

The signature molecular descriptor. 3. Inverse-quantitative structure-activity relationship of ICAM-1 inhibitory peptides.

We present a methodology for solving the inverse-quantitative structure-activity relationship (QSAR) problem using the molecular descriptor called signature. This methodology is detailed in four parts. First, we create a QSAR equation that correlates the occurrence of a signature to the activity values using a stepwise multilinear regression technique. Second, we construct constraint equations, specifically the graphicality and consistency equations, which facilitate the reconstruction of the solution compounds directly from the signatures. Third, we solve the set of constraint equations, which are both linear and Diophantine in nature. Last, we reconstruct and enumerate the solution molecules and calculate their activity values from the QSAR equation. We apply this inverse-QSAR method to a small set of LFA-1/ICAM-1 peptide inhibitors to assist in the search and design of more-potent inhibitory compounds. Many novel inhibitors were predicted, a number of which are predicted to be more potent than the strongest inhibitor in the training set. Two of the more potent inhibitors were synthesized and tested in-vivo, confirming them to be the strongest inhibiting peptides to date. Some of these compounds can be recycled to train a new QSAR and develop a more focused library of lead compounds.

Drug Design↗
PubMed1994

Mutations in the K+ channel signature sequence.

Potassium channels share a highly conserved stretch of eight amino acids, a K+ channel signature sequence. The conserved sequence falls within the previously defined P-region of voltage-activated K+ channels. In this study we investigate the effect of mutations in the signature sequence of the Shaker channel on K+ selectivity determined under bi-ionic conditions. Nonconservative substitutions of two threonine residues and the tyrosine residue leave selectivity intact. In contrast, mutations at some positions render the channel nonselective among monovalent cations. These findings are consistent with a proposal that the signature sequence contributes to a selectivity filter. Furthermore, the results illustrate that the hydroxyl groups at the third and fourth positions, and the aromatic group at position seven, are not essential in determining K+ selectivity.

Amino Acid Sequence↗
PubMed1999

Alignment of a sparse protein signature with protein sequences: application to fold prediction for three small globulins.

A novel algorithm has been developed for scoring the match between an imprecise sparse signature and all the protein sequences in a sequence database. The method was applied to a specific problem: signatures were derived from the probable folding nucleus and positions obtained from the determined interactions that occur during the folding of three small globular proteins and points of inter-element contact and sequence comparison of the actual three-dimensional structures of the same three proteins. In the case of two of these, lysozyme and myoglobin, the residues in the folding nucleus corresponded well to the key residues spotted by examination of the structures and in the remaining case, barnase, they did not. The diagnostic performance of the two types of signatures were compared for all three proteins. The significance of this for the application of an understanding of the protein folding mechanisms for structure prediction is discussed. The algorithm is generic and could be applied to other user-defined problems of sequence analysis.

Amino Acid Sequence↗
PubMed1999

Carbon isotopic fractionation in lipids from methanotrophic bacteria II: the effects of physiology and environmental parameters on the biosynthesis and isotopic signatures of biomarkers.

Controls on the carbon isotopic signatures of methanotroph biomarkers have been further explored using cultured organisms. Growth under conditions which select for the membrane-bound particulate form of the methane monooxygenase enzyme (pMMO) leads to a significantly higher isotopic fractionation than does growth based on the soluble isozyme in both RuMP and serine pathway methanotrophs; in an RuMP type the delta delta 13Cbiomass equaled -23.9% for pMMO and -12.6% for sMMO. The distribution of biomarker lipids does not appear to be significantly affected by the dominance of one or the other MMO type and their isotopic compositions generally track those of the parent biomass. The 13C fractionation behaviour of serine pathway methanotrophs is very complex, reflecting the assimilation of both methane and carbon dioxide and concomitant dissimilation of methane-derived carbon. A limitation in CH4 availability leads to the production of biomass which is 13C-enriched with respect to both carbon substrates and this occurs irrespective of MMO type. This startling result indicates that there must be an additional fractionation step downstream from the MMO reaction which leads to incorporation of 13C-enriched carbon at the expense of dissimilation of 13C-depleted CO2. In these organisms, polyisoprenoid lipids are 13C-enriched compared to polymethylenic lipid which is the reverse of that found in the RuMP types. Serine cycle hopanoids, for example, can vary anywhere from 12% depleted to 10% enriched with respect to the CH4 substrate depending on its concentration. Decrease in growth temperature caused an overall increase in isotopic fractionation. In the total biomass, this effect tended to be masked by physiological factors associated with the type of organism and variation in the bulk composition. The effect was, however, clearly evident when monitoring the 13C signature of total lipid and individual biomarkers. Our results demonstrate that extreme carbon isotopic depletion in field samples and fossil biomarker lipids can be indicative of methanotrophy but the converse is not always true. For example, the hopanoids of a serine cycle methanotroph may be isotopically enriched by more than 10% compared to the substrate methane when the latter is limiting. In other words, hopanoids from some methanotrophs such as M. trichosporium would be indistinguishable from those of cyanobacteria or heterotrophic bacteria on the basis of either chemical structure or carbon isotopic signature.

Biomarkers↗
PubMed2000

Signature-peptide approach to detecting proteins in complex mixtures.

The objective of the work presented in this paper was to test the concept that tryptic peptides may be used as analytical surrogates of the protein from which they were derived. Proteins in complex mixtures were digested with trypsin and classes of peptide fragments selected by affinity chromatography, lectin columns were used in this case. Affinity selected peptide mixtures were directly transferred to a high-resolution reversed-phase chromatography column and further resolved into fractions that were collected and subjected to matrix-assisted laser desorption ionization (MALDI) mass spectrometry. The presence of specific proteins was determined by identification of signature peptides in the mass spectra. Data are also presented that suggest proteins may be quantified as their signature peptides by using isotopically labeled internal standards. Isotope ratios of peptides were determined by MALDI mass spectrometry and used to determine the concentration of a peptide relative to that of the labeled internal standard. Peptides in tryptic digests were labeled by acetylation with acetyl N-hydroxysuccinimide while internal standard peptides were labeled with the trideuteroacetylated analogue. Advantages of this approach are that (i) it is easier to separate peptides than proteins, (ii) native structure of the protein does not have to be maintained during the analysis, (iii) structural variants do not interfere and (iv) putative proteins suggested from DNA databases can be recognized by using a signature peptide probe.

Amino Acid Sequence↗
PubMed1998

Preliminary clinical-radiological assessment of a MR tissue signature model in human stroke.

We evaluated the ability of an MR signature model (SM) of cerebral ischemic injury to stage the evolution of cellular damage in human stroke. In 19 patients with ischemic stroke of presumed embolic or non-embolic cause we carried out diffusion-weighted and T2-weighted MR imaging within 48 h of onset, and obtained apparent diffusion coefficient of water (ADCw), and T2 weighted images. We used the signatures obtained from these ADCw/T2 maps to formulate two patterns of damage signifying accelerated or non-accelerated progression of cellular death after stroke onset. Those patients with the accelerated pattern corresponded to those with the neuroradiological (NRC) and clinical diagnosis (TOAST.1 and TOAST.2) of presumed embolic stroke, with clinical diagnosis performed blinded both to NRC and to SM. Agreement between the SM and NRC was substantial (kappa=0.62), moderate (0.60<kappa<0.40) between the SM or NRC and TOAST.2, and fair (0.40<kappa<0.20) among the SM or NRC and TOAST.1. We believe these results constitute a preliminary validation of the MR tissue signature modeling in clinical stroke assessment.

Adult↗
PubMed2003

Stable carbon and nitrogen isotope signatures indicate recovery of marine biota from sewage pollution at Moa Point, New Zealand.

Stable carbon and nitrogen isotopes have been used to assess sewage contamination of a sewage outfall, discharging milli-screened effluent into Moa Point Bay, New Zealand, and monitor the recovery of flora and fauna after the outfall's closure. An initial study characterising the extent of the discharge and the effects on seaweed (Ulva lactuca L.), blue mussels (Mytilus galloprovincialis) and limpets (Cellana denticulata) from the area, showed effects of the sewage discharge on flora and fauna were localised within in the bay. The immediate area surrounding the discharge area was found to contain limited biodiversity, with an abundance of Ulva lactuca, a bright green lettuce-like seaweed, typically found in areas with high nutrient input, limpets and small blue mussels. The nitrogen isotopic signature (delta15N) is shown to be a good tracer of sewage pollution in seaweed and associated grazers (i.e. limpets) as a result of the increased contribution of urea and ammonia to seawater nitrogen derived from the effluent. The carbon isotopic signature (delta13C) is suggested as a more appropriate sewage tracer for mussels, which filter feed the effluent's particulate organic matter from the water. Lower carbon:nitrogen ratios were found in Ulva lactuca sampled from around the outfall region compared to uncontaminated control sites. However carbon:nitrogen ratios do not vary significantly amongst shellfish species. After closure, monitoring continued for 9 months and showed that the carbon and nitrogen isotopic signatures of algae (Ulva lactuca L.) returned to similar control site levels within 3 months. Limpet and blue mussels (Cellana denticulata and Mytilus galloprovincialis) showed slower recovery times than the Ulva lactuca, with detectable levels of the sewage-derived carbon and nitrogen remaining in the animal's tissue for up to 9 months.

Animals↗
PubMed1998

Object recognition using spatiotemporal signatures.

The sequence of images generated by motion between observer and object specifies a spatiotemporal signature for that object. Evidence is presented that such spatiotemporal signatures are used in object recognition. Subjects learned novel, three-dimensional, rotating objects from image sequences in a continuous recognition task. During learning, the temporal order of images of a given object was constant. During testing, the order of images in each sequence was reversed, relative to its order during learning. This image sequence reversal produced significant reaction time increases and recognition rate decreases. Results are interpreted in terms of object-specific spatiotemporal signatures.

Form Perception↗
PubMed1996

Probing the chemical basis of binding activity in an SH3 domain by protein signature analysis.

BACKGROUND: Modifying the covalent structure of a protein is an effective empirical route to probing three-dimensional structure and biological function. Here we describe a combinatorial protein chemistry strategy for studying structure-activity relationships in proteins. Our approach (termed 'protein signature analysis') involves functional selection from an array of self-encoded protein analogs prepared by total synthesis, coupled to a simple chemical readout that unambiguously identifies the modified proteins in the resulting active and inactive populations. RESULTS: Protein signature analysis was used to study the interaction of the amino-terminal SH3 domain from the cellular adaptor protein c-Crk with its cognate proline-rich peptide, C3G. Using a functional selection assay, the qualitative effects of scanning a series of synthetic analog units through the amino-acid sequence of the SH3 domain were evaluated. The analog units were designed to alter both amino-acid sidechains and the polypeptide backbone within the protein. These chemical studies revealed that the sidechain of Asp 150 in the SH3 domain is essential for ligand binding and that changes in the structure of the polypeptide backbone can also result in loss of binding activity. CONCLUSIONS: These chemical studies have provided new insight into how ligand binding is related to the covalent structure of the SH3 domain. Protein signature analysis is a powerful and conceptually novel way of studying the molecular and chemical basis of protein function; it combines the advantages of systematic modification of a protein's chemical structure with the practical convenience of combinatorial synthesis.

Amino Acid Sequence↗
PubMed2002

Developing a methodology for an inverse quantitative structure-activity relationship using the signature molecular descriptor.

The concept of signature as a molecular descriptor is introduced and various topological indices used in quantitative structure-activity relationships (QSARs) are expressed as functions of the new descriptor. The effectiveness of signature versus commonly used descriptors in QSAR analysis is demonstrated by correlating the activities of 121 HIV-1 protease inhibitors. Our approach to the inverse-QSAR problem consists of first finding the optimum sets of descriptor values best matching a target activity and then generating a focused library of candidate structures from the solution set of descriptor values. Both steps are facilitated by the use of signature.

Algorithms↗
PubMed2002

Use of signature-tagged mutagenesis in pathogenesis studies.

From 2000-2001, over 10 studies have been completed, using signature-tagged mutagenesis, on a variety of bacterial pathogens. Investigators are examining the attenuated strains in additional in vivo, cell culture or in vitro assays to further characterize and catalog the mutants. Notable advances included screening of the attenuated mutants en masse in other assays, verification that mutant strains are defective for growth in specific host tissues, and identification of potential live-attenuated vaccine candidates. In addition, researchers are using signature-tagged strains to characterize the infection process, which is providing snapshots of bottlenecks and quantitative measurements of bacterial spread from tissue to tissue. This review focuses on themes emerging from signature-tagged mutagenesis studies completed on bacterial pathogens since mid-2000.

Animals↗
PubMed2002

Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia.

Human T cell leukemias can arise from oncogenes activated by specific chromosomal translocations involving the T cell receptor genes. Here we show that five different T cell oncogenes (HOX11, TAL1, LYL1, LMO1, and LMO2) are often aberrantly expressed in the absence of chromosomal abnormalities. Using oligonucleotide microarrays, we identified several gene expression signatures that were indicative of leukemic arrest at specific stages of normal thymocyte development: LYL1+ signature (pro-T), HOX11+ (early cortical thymocyte), and TAL1+ (late cortical thymocyte). Hierarchical clustering analysis of gene expression signatures grouped samples according to their shared oncogenic pathways and identified HOX11L2 activation as a novel event in T cell leukemogenesis. These findings have clinical importance, since HOX11 activation is significantly associated with a favorable prognosis, while expression of TAL1, LYL1, or, surprisingly, HOX11L2 confers a much worse response to treatment. Our results illustrate the power of gene expression profiles to elucidate transformation pathways relevant to human leukemia.

Adaptor Proteins, Signal Transducing↗
PubMedDate not supplied

Neurochemical signatures revealed by glutamine labeling in the chicken retina.

Postembedding immunocytochemistry was used to determine the retinal distribution of the amino acid glutamine, and characterize amino acid signatures in the avian retinal ganglion cell layer. Glutamine is a potential precursor of glutamate and some glutamatergic neurons may use this amino acid to sustain production of glutamate for neurotransmission. Ganglion cells, cells in the inner nuclear layer, and some photoreceptors exhibited glutamine immunoreactivity of varying intensity. Ganglion cells demonstrated the highest level of immunoreactivity which indicates either slow glutamine turnover or active maintenance of a large standing glutamine pool relative to other glutamatergic neurons. Müller's cells in the avian retina are involved in glutamate uptake and carbon recycling by the rapid conversion of glutamate to glutamine, thus explaining the low glutamate and high glutamine immunoreactivity found throughout Müller's cells. Most chicken retinal ganglion cells are glutamate (E) and glutamine (Q) immunoreactive but display diverse signatures with presumed functional subsets of cells displaying admixtures of E and Q with GABA (gamma) and/or glycine (G). The four major ganglion cell signatures are (1) EQ; (2) EQ gamma; (3) EQG; and (4) EQ gamma G.

Animals↗
PubMed2004

PCB loading from sediment in the Hudson River: congener signature analysis of pathways.

The upper Hudson River (NY) was subjected to massive PCB contamination over a period of three decades. A large inventory of PCBs remains in contaminated sediments of the river, most notably in the Thompson Island Pool. During the summer, flow crossing the Thompson Island Pool exhibits a large and consistent PCB load gain. This load gain is not associated with scouring flows and is not accompanied by an increase in suspended solids. A variety of hypotheses have been proposed to explain this load gain, including flux of contaminated porewater and dissolution of unverified reservoirs of pure PCBs. A wealth of congener-specific PCB data is available for the site throughout the 1990s. Interpretation of the Thompson Island Pool load gain is facilitated by examination of the PCB congener signature of the gain and comparison to the signature of potential sources. This examination suggests that neither the flux of porewater nor the dissolution of unaltered Aroclors are the predominant source of the load gain. Instead, the congener signature is consistent with a mixed source consisting of porewater flux and non-scour flux of contaminated sediments. The non-scour sediment flux, which reaches a maximum in the beginning of the summer growing season, is likely driven by a variety of biological and anthropogenic processes, including bioturbation by benthic organisms, bioturbation by demersal fish, scour by propwash, mechanical scour by boats and floating debris in nearshore areas, and uprooting of macrophytes.

Animals↗
PubMed2006

Particle number emissions and source signatures of an industrial facility.

The work presented was conducted within the scope of a larger study investigating impacts of the Stuart Oil Shale project, a facility operating to the north of the industrial city of Gladstone, Australia. The aims of the investigations were threefold: (a) the identification of the plant signatures in terms of particle size distributions in the submicrometer range (13-830 nm) through stack measurements, (b) exploring the applicability of these signatures in tracing the source contributions at locations of interest, at a distance from the plant, and (c) assessing the contribution of the plant to the total particle number concentration at locations of interest. The stack measurements conducted for three different conditions of plant operation showed that the particle size distributions were bimodal with average modal count median diameters (CMDs) of 24 (SD 4) and 52 (SD 9) nm. The average of all the particle size distributions recorded within the plant sector at a site located 4.5 km from the plant, over the sampling period when the plant was operating, also showed a bimodal distribution. The modal CMDs in this case were 27 and 50 nm, similar to those at the stack. This bimodal size distribution is distinct from the size distribution of the most common ambient anthropogenic emission source, which is vehicle emissions, and can be considered as a signature of this source. The average contribution of the plant (for plant sector winds) was estimated to be (10.0 +/- 3.8) x 10(2) particles cm(-3) and constituted approximately a 50% increase overthe local particle ambient concentration for plant sector winds. This increase in particle number concentration compared to the local background concentration, while high compared to the clean environment concentration, is not significant when compared to concentrations generally encountered in the urban environment of Brisbane.

Air Pollutants↗
PubMed2005

Determination of single particle mass spectral signatures from light-duty vehicle emissions.

In this study, 28 light-duty gasoline vehicles (LDV) were operated on a chassis dynamometer at the California Air Resources Board Haagen-Smit Facility in El Monte, CA. The mass spectra of individual particles emitted from these vehicles were measured using aerosol time-of-flight mass spectrometry (ATOFMS). A primary goal of this study involves determining representative size-resolved single particle mass spectral signatures that can be used in future ambient particulate matter source apportionment studies. Different cycles were used to simulate urban driving conditions including the federal testing procedure (FTP), unified cycle (UC), and the correction cycle (CC). The vehicles were selected to span a range of catalytic converter (three-way, oxidation, and no catalysts) and engine technologies (vehicles models from 1953 to 2003). Exhaust particles were sampled directly from a dilution and residence chamber system using particle sizing instruments and an ATOFMS equipped with an aerodynamic lens (UF-ATOFMS) analyzing particles between 50 and 300 nm. On the basis of chemical composition, 10 unique chemical types describe the majority of the particles with distinct size and temporal characteristics. In the ultrafine size range (between 50 and 100 nm), three elemental carbon (EC) particle types dominated, all showing distinct EC signatures combined with Ca, phosphate, sulfate, and a lower abundance of organic carbon (OC). The relative fraction of EC particle types decreased as particle size increased with OC particles becoming more prevalent above 100 nm. Depending on the vehicle and cycle, several distinct OC particle types produced distinct ion patterns, including substituted aromatic compounds and polycyclic aromatic hydrocarbons (PAH), coupled with other chemical species including ammonium, EC, nitrate, sulfate, phosphate, V, and Ca. The most likely source of the Ca and phosphate in the particles is attributed to the lubricating oil. Significant variability was observed in the chemical composition of particles emitted within the different car categories as well as for the same car operating under different driving conditions. Two-minute temporal resolution measurements provide information on the chemical classes as they evolved during the FTP cycle. The first two minutes of the cold start produced more than 5 times the number of particles than any other portion of the cycle, with one class of ultrafine particles (EC coupled with Ca, OC, and phosphate) preferentially produced. By number, the three EC with Ca classes (which also contained OC, phosphate, and sulfate) were the most abundant classes produced by the nonsmoking vehicles. The smoker category produced the highest number of particles, with the dominant classes being OC comprised of substituted monoaromatic compounds and PAHs, coupled with Ca and phosphate, thus suggesting used lubricating oil was associated with many of these particles. These studies show, by number, EC particles dominate gasoline emissions in the ultrafine size range particularlyforthe lowest emitting newer vehicles, suggesting the EC signature alone cannot be used as a unique tracer for diesels. This represents the first report of high time- and size-resolved chemical composition data showing the mixing state of nonrefractory elements in particles such as EC for vehicle emissions during dynamometer source testing.

Automobiles↗
PubMed1997

Protein phylogenies and signature sequences: evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes.

The evolutionary relationships within prokaryotes and between prokaryotes and eukaryotes is examined based on protein sequence data. Phylogenies and common signature sequences in some of the most conserved proteins point to a close evolutionary relationship between Archaebacteria and Gram-positive bacteria. The monophyletic nature and distinctness of the Archaebacterial domain is not supported by many of the phylogenies. Within Gram-negative bacteria, cyanobacteria are indicated as the deepest branching lineage, and a clade consisting of Archaebacteria, Gram-positive bacteria and cyanobacteria is supported by signature sequences in many proteins. However, the division within the prokaryotic species, viz. Archaebacteria<-->Gram-positive bacteria-->Cyanobacteria-->other groups of Gram-negative bacteria, is indicated to be not very rigid but, instead is an evolutionary continuum. It is expected that certain species will be found which represent intermediates in the above transitions. By contrast to the evolutionary relationships within prokaryotes, the eukaryotic species, which are structurally very different, appear to have originated by a very different mechanism. Protein phylogenies and signature sequences provide evidence that the eukaryotic nuclear genome is a chimera which has received major contributions from both an Archaebacterium and a Gram-negative bacterium. To explain these observations, it is suggested that the ancestral eukaryotic cell arose by a symbiotic fusion event between the above parents and that this fusion event led to the origin of both nucleus and endoplasmic reticulum. The monophyletic nature of all extant eukaryotic species further suggests that a 'successful primary fusion' between the prokaryotic species that gave rise to the ancestral eukaryotic cell took place only once in the history of this planet.

Amino Acid Sequence↗
PubMed2003

Cyanobacterial signature genes.

A comparison of 8 cyanobacterial genomes reveals that there are 181 shared genes that do not have obvious orthologs in other bacteria. These signature genes define aspects of the genotype that are uniquely cyanobacterial. Approximately 25% of these genes have been associated with some function. These signature genes may or may not be involved in photosynthesis but likely they will be in many cases. In addition, several examples of widely conserved gene order involving two or more signature genes were observed. This suggests there may be regulatory processes that have been preserved throughout the long history of the cyanobacterial phenotype. The results presented here will be especially useful because they identify which of the many genes of unassigned function are likely to be of the greatest interest.

Journal Article↗