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PubMed2003

Structural classification of zinc fingers: survey and summary.

Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation and apoptosis. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins and small molecules. Here we present a comprehensive classification of zinc finger spatial structures. We find that each available zinc finger structure can be placed into one of eight fold groups that we define based on the structural properties in the vicinity of the zinc-binding site. Three of these fold groups comprise the majority of zinc fingers, namely, C2H2-like finger, treble clef finger and the zinc ribbon. Evolutionary relatedness of proteins within fold groups is not implied, but each group is divided into families of potential homologs. We compare our classification to existing groupings of zinc fingers and find that we define more encompassing fold groups, which bring together proteins whose similarities have previously remained unappreciated. We analyze functional properties of different zinc fingers and overlay them onto our classification. The classification helps in understanding the relationship between the structure, function and evolutionary history of these domains. The results are available as an online database of zinc finger structures.

Algorithms↗

PubMedDate not supplied

[NMR study of complex formation of aromatic ligands with heptadeoxynucleotide 5'-d(GCGAAGC) forming stable hairpin structure in aqueous solution].

Complex formation of hairpin-producing heptadeoxynucleotide 5'-d(GCGAAGC) with aromatic molecules: acridine dye proflavine and anthracycline antibiotic daunomycin was studied by one-dimensional 1H NMR and two-dimensional correlation 1H-1H (2M-TOCSY, 2M-NOESY), 1H-31P (2M-HMBC) NMR spectroscopy (500 and 600 MHz) in aqueous solution. Concentration and temperature dependences for the chemical shifts of ligand protons were measured, molecular models of equilibrium in solution were developed, and equilibrium thermodynamic parameters for the formation of intercalation complexes were calculated. Spatial structures of dye and antibiotic complexes with the heptamer hairpin were constructed on the basis of 2M-NOE data and the calculated values of limiting chemical shifts of ligand protons.

Daunorubicin↗

PubMed1992

Amino acid sequencing of a trypsin inhibitor by refined 1.6 A X-ray crystal structure of its complex with porcine beta-trypsin.

The stoichiometric complex formed between porcine beta-trypsin and the Momordica charantia, Linn. Cucurbitaceae trypsin inhibitor-A (MCTI-A) was crystallized and its X-ray crystal structure determined using molecular replacement method. The primary sequence and topology of the inhibitor was determined by recognizing the electron density and refined to a final R value of 0.167 (7.0-1.6 A) with RMS deviation of bond lengths from standard values 0.012 A. The sequence was compared with those obtained by other groups and was found to be similar to the squash proteinase inhibitor. Its spatial structure and the conformation of its primary binding segment from Cys-3I (P3) to Glu-7I (P3') which contains the reactive scissile bond Arg-5I C-Ile-6I N were also very similar with other squash family proteinase inhibitors.

Amino Acid Sequence↗

PubMed1990

The changes of circular dichroism and fluorescence spectra, and the comparison with inactivation rates of angiotensin converting enzyme in guanidine solutions.

The circular dichroism (CD) spectrum of angiotensin converting enzyme (peptidyl-dipeptide hydrolase, EC 3.4.15.1) in the ultraviolet region was shown to have down negative peaks at 208 and 222 nm, indicating its peptide chain has an alpha-helical structure. The conformational changes of the enzyme during denaturation in guanidine solutions of increasing concentration, for 24 h at 4 degrees C, were associated with the disappearance of the two negative peaks of the CD spectra, less alpha-helical structure to various extents, a decrease in intensity of the intrinsic protein fluorescence, a red shift in the emission maximum at 340 nm and an increase in the band-width of the spectrum delta lambda. Together these findings demonstrate unfolding of the folded peptide chain of angiotensin converting enzyme and consequent exposure of its aromatic amino acid residues during denaturation. The rates of ellipticity (theta 220) changes of the enzyme during denaturation were less than those of the decrease in fluorescence intensity, demonstrating that the rate of degradation of its secondary structure was slower than that of its tertiary structure. Both the rates of inactivation and conformational change of the enzyme increased with increasing guanidine concentrations, within the range of 1.0-3.0 M. The enzyme inactivation had separate fast and slow processes. Both the rates and the extents of inactivation were much faster and larger than those of conformational changes. Compared with other enzymes, therefore, the angiotensin converting enzyme molecule appears to have a stable spatial structure, but its active site conformation is relatively unstable during denaturation.

Animals↗

PubMed2004

Analysis of tryptophan surface accessibility in proteins by MALDI-TOF mass spectrometry.

Surface accessible amino acids can play an important role in proteins. They can participate in enzyme's active center structure or in specific intermolecular interactions. Thus, the information about selected amino acids' surface accessibility can contribute to the understanding of protein structure and function. In this paper, we present a simple method for surface accessibility mapping of tryptophan side chains by their chemical modification and identification by MALDI-TOF mass spectrometry. The reaction with 2-hydroxy-5-nitrobenzyl bromide, a common and highly specific covalent modification of tryptophan, seems to be very useful for this purpose. The method was tested on four model proteins with known spatial structure. In the native proteins (1) only surface accessible tryptophan side chains were found to react with the modification agent and (2) no buried one was found to react at lower reagent concentrations. These results indicate that the described method can be a potent tool for identification of surface-located tryptophan side chain in a protein of unknown conformation.

2-Hydroxy-5-nitrobenzyl Bromide↗

PubMed1981

Spontaneous reference systems in individuals.

In a series of five experiments the referencing function of spatial structures was investigated. The problem was (a) to determine whether subjects' effective frames of reference and their object figures could be experimentally identified, (b) to determine whether the analyses developed for this purpose were adequate, and (c) to determine some conditions of frames of reference. Graduate and undergraduate students were asked to reconstruct and to recall multiply-embedded figures viewed earlier. In these figures the spatial orientation of the figure elements was manipulated. Both reconstruction and recall errors were analyzed to identify subjects' effective frames of reference and their object figures. A single-subject design was used throughout. Frames of reference and their objects could be identified in Exp. 1. This experiment also showed the appropriateness of the analyses. Exp. 2 indicated that embedding figures provide one condition for identifying frames of reference. Exps. 3 to 5 demonstrated that changes in element figures, measurement, and reduction of trials and number of elements did not eliminate frames of reference. Differences in types of frames of reference were found. These differences were interpreted to indicate that some subjects use content, others formal schema (referents) to evaluate spatial orientation.

Adult↗

PubMed2026

SIVA: diagonal integration of spatial multi-omics data via spatially informed variational autoencoders and anchor guidance.

MOTIVATION: Understanding cellular states and regulatory programs requires integrative analysis of multiple omics layers. Although recent spatial sequencing technologies allow molecular profiling of cells within their tissue context, paired spatial multi-omics assays are still limited by technical complexity and cost. This creates a pressing need for diagonal integration methods that enable joint analysis of unpaired spatial omics datasets. RESULTS: We propose SIVA, a deep generative framework based on Spatially-Informed Variational Autoencoders with Anchor Guidance, for diagonal integration of spatial multi-modal data. SIVA employs modality-specific variational autoencoders (VAEs) with a hybrid latent embedding that integrates Gaussian process and standard Gaussian priors, enabling joint modeling of spatially structured variation and dominant underlying data distributions across modalities. To facilitate cross-modal alignment in the absence of one-to-one cell correspondence, SIVA adopts a dual integration strategy combining global distribution alignment via Maximum Mean Discrepancy and local correspondence guidance using mutual nearest neighbor anchors. Extensive experiments across multiple cross-slice integration scenarios demonstrate that SIVA achieves robust and accurate integration of unpaired spatial omics datasets, consistently outperforming existing methods. AVAILABILITY AND IMPLEMENTATION: The source codes are available at https://github.com/PelenJiang/SIVA.

Autoencoder↗

PubMed2006

Reconciling empirical ecology with neutral community models.

Neutral community models embody the idea that individuals are ecologically equivalent, having equal fitness over all environmental conditions, and describe how the spatial dynamics and speciation of such individuals can produce a wide range of patterns of distribution, diversity, and abundance. Neutral models have been controversial, provoking a rush of tests and comments. The debate has been spurred by the suggestion that we should test mechanisms. However, the mechanisms and the spatial scales of interest have never clearly been described, and consequently, the tests have often been only peripherally relevant. At least two mechanisms are present in spatially structured neutral models. Dispersal limitation causes clumping of a species, which increases the strength of intraspecific competition and reduces the strength of interspecific competition. This may prolong coexistence and enhance local and regional diversity. Speciation is present in some neutral models and gives a donor-controlled input of new species, many of which remain rare or are short lived, but which directly add to species diversity. Spatial scale is an important consideration in neutral models. Ecological equivalence and equal fitness have implicit spatial scales because dispersal limitation and its emergent effects operate at population levels, and populations and communities are defined at a chosen spatial scale in recent neutral models; equality is measured relative to a metacommunity, and this necessitates defining the spatial scale of that metacommunity. Furthermore, dispersal has its own scales. Thorough empirical tests of neutral models will require both tests of mechanisms and pattern-producing ability, and will involve coupling theoretical models and experiments.

Biodiversity↗

PubMed2026

Structural Features of DNA in TATA-Containing and TATA-Less Core Promoters of RNA Polymerase II Differ.

Nucleotide motifs in the core promoters of eukaryotic protein-coding genes transcribed by RNA polymerase II (Pol II) play an important role in the transcription process. We analyzed the role of an octanucleotide located in the TATA box position. Depending on whether this octanucleotide can form a complex with the TATA-binding protein (TBP), the promoter is classified as either TATA-containing or TATA-less. We analyzed the differences in the primary and spatial structures, as well as their dynamics, in TATA-containing and TATA-less promoters of mammals and plants. We divided the complete promoter sets of six organisms (H. sapiens, M. musculus, C. familiaris, A. thaliana, Z. mays, and H. vulgare) from the EPDnew database into TATA-containing and TATA-less fractions. The sizes of the TATA-containing promoter fractions are significantly smaller than those of the TATA-less fractions in all studied organisms, except in A. thaliana, where the sizes of both fractions are approximately equal. We characterized promoter architecture using variation profiles of various base-pair step parameters, minor-groove width, and the conformational dynamics of native DNA. The architectures of TATA-containing and TATA-less promoters differ significantly. The possible mechanistic influence of DNA structural features on the formation of the pre-initiation complex (PIC) in both types of promoters is discussed.

Promoter Regions, Genetic↗

PubMed2006

A GCUA tetranucleotide loop found in the poliovirus oriL by in vivo SELEX (un)expectedly forms a YNMG-like structure: Extending the YNMG family with GYYA.

The cloverleaf structure in the 5'-untranslated region of enterovirus RNA that regulates viral RNA replication contains an evolutionarily conserved YNMG tetraloop closed by a Y-G base pair. This loop is believed to interact specifically with the viral protease 3C. To further characterize the specificity of this interaction, the tetraloop and two flanking base pairs of the poliovirus RNA were randomized, and viable viral clones were obtained using in vivo SELEX. Among many different mutants with the canonical YNMG sequences to be described elsewhere, a large-plaque-forming clone contained a deviating uGCUAg sequence. The NMR structure of a small hairpin capped with uGCUAg that we present here shows that the GCUA tetraloop adopts a novel fold, which is highly similar to that of the YNMG tetraloop with common stacking properties and hydrogen-bond interactions including an unusual syn conformation of the adenosine. Thermodynamic studies show moderate stabilities of hairpins with canonical YNMG and the novel GCUA loops, which, together with the similarity of spatial structures, illustrates that the tetraloop structure itself is crucial for the RNA-protein interaction required for the viral replication. A re-evaluation of the ribosomal secondary structure database reveals a hairpin containing a GCUA loop, which covaries with YNMG and is involved in a tertiary interaction, and in the 50S ribosomal subunit from Haloarcula marismortui the structurally comparable apex of stem-loop 35a is a recognition site for protein L2. These observations show a more general occurrence and importance of the so-far unrecognized GYYA hairpin loops.

Base Pairing↗

PubMed2005

[Spatial-temporal dynamics of landscape fragmentation in North Shannxi Loess Plateau].

The study of landscape fragmentation is an important means to reveal regional ecological processes. By using the remote sensing data of 1987, 1997 and 2002, and the GIS tools, some representative quantitative indices of the landscape spatial structure and landscape fragmentation in North Shannxi Loess Plateau were calculated, aimed to investigate the relationships between landscape ecological structure and landscape pattern in this area. The results showed that cropland contributed most to the extent of landscape fragmentation, but unused land lacked obvious relationship with it. To get large-area images accurately and promptly is very important for monitoring ecological process in regional scale. Moderate-Resolution Imaging Spectroradiometer (MODIS) images in 2003 were used to derive monthly landscape fragmentation information calculated with Local Index of Spatial Associations (LISA) based on Spatial Statistical Analysis (SSA). The analysis of the fragmented landscape types showed that human disturbance had a main contribution to the seasonal landscape fragmentation. Furthermore, with the increasing percentages of cropland and unused land, landscape became more fragmented, while forestland coverage had inverse effects on the fragmentation.

China↗

PubMed2003

Conservation genetics of the wood ant, Formica lugubris, in a fragmented landscape.

Various intrinsic factors connected to the special features of sociality influence the persistence of social insect populations, including low effective population size, reduced amount of genetic variation easily leading to inbreeding depression, and spatially structured populations. In this work, we studied an isolated, small and fragmented population system of the red wood ant Formica lugubris, and evaluated the impact of social and genetic population structure on the persistence and conservation of the populations. The effective population size was large in our study population because all nests were polygynous. As a result, and despite the apparent isolation, the amount of nuclear genetic variability was similar to that in a nonisolated population system. Lack of inbreeding, as well as a high level of variability, indirectly suggests that this population does not suffer from inbreeding depression. The spatial distribution of genetic variation between local populations suggests intensive, but strongly male-biased, nuclear gene flow. Thus, the persistence of this population system does not seem to be threatened by any immediate social or genetic factor, but colonization of new habitat patches may be difficult because of restricted female dispersal.

Animals↗

PubMed1994

A model for the development of simple cell receptive fields and the ordered arrangement of orientation columns through activity-dependent competition between ON- and OFF-center inputs.

Neurons in the primary visual cortex of higher mammals respond selectively to light/dark borders of a particular orientation. The receptive fields of simple cells, a type of orientation-selective cell, consist of adjacent, oriented regions alternately receiving ON-center and OFF-center excitatory input. I show that this segregation of inputs within receptive fields can occur through an activity-dependent competition between ON-center and OFF-center inputs, just as segregation of inputs between different postsynaptic cells into ocular dominance columns appears to occur through activity-dependent competition between left-eye and right-eye inputs. These different outcomes are proposed to result, not from different mechanisms, but from different spatial structures of the correlations in neural activity among the competing inputs in each case. Simple cells result if ON-center inputs are best correlated with other ON-center inputs, and OFF with OFF, at small retinotopic separations, but ON-center inputs are best correlated with OFF-center inputs at larger separations. This hypothesis leads robustly to development of simple cell receptive fields selective for orientation and spatial frequency, and to the continuous and periodic arrangement of preferred orientation across the cortex. Input correlations determine the mean preferred spatial frequency and degree of orientation selectivity. Estimates of these correlations based on measurements in adult cat retina (Mastronarde, 1983a,b) produce quantitative predictions for the mean preferred spatial frequencies of cat simple cells across eccentricities that agree with experiments (Movshon et al., 1978b). Intracortical interactions are the primary determinant of cortical organization. Simple cell spatial phases can play a key role in this organization, so arrangements of spatial phases and preferred orientations may need to be studied together to understand either alone. Possible origins for other cortical features including spatial frequency clusters, afferent ON/OFF segregation, blobs, pinwheels, and opponent inhibition within simple cell receptive fields are suggested. A number of strong experimental tests of the hypothesis are proposed.

Algorithms↗

PubMedDate not supplied

Mammalian metallothionein.

Chemical, spectroscopic, and structural studies have established the metallothioneins (MTs) to be a widely occurring family of polypeptidic bioinorganic structures. They are distinguished by an extremely high metal (Zn, Cd, Cu) and Cys content and by the arrangement of these components in metal-thiolate clusters. By structural criteria the MTs have recently been subdivided into three classes (Fowler et al., Experientia Suppl. 52, 19-22, 1987). Class I MTs include mammalian MTs and related forms. Class II MTs display no such relationships, and Class III MTs are atypical polypeptides made up of repetitive gamma-glutamylcysteinyl units. Amino acid sequences of over 50 MTs are now known. In mammals, over 55% of the residues, including the 20 Cys, are conserved. Mammalian MTs are genetically polymorphous. Thus, in human tissues and cell lines closely related structures of ten functional isoMTs have been determined either by amino acid or nucleotide sequencing. A comparable degree of polymorphism also exists in the rabbit. Mammalian MTs have been inferred to bind a total of seven bivalent metal ions (Me) through thiolate coordination in two separate clusters, i.e., Me(II)3(Cys)9 and Me(II)4(Cys)11. This two-cluster model has now fully been confirmed by the spatial structures of rat MT-2 and rabbit MT-2a determined by 2D NMR spectroscopy in aqueous solution.

Amino Acid Sequence↗

PubMed2004

Effects of neighbourhood size and connectivity on the spatial Continuous Prisoner's Dilemma.

The Prisoner's Dilemma, a two-person game in which the players can either cooperate or defect, is a common paradigm for studying the evolution of cooperation. In real situations cooperation is almost never all or nothing. This observation is the motivation for the Continuous Prisoner's Dilemma, in which individuals exhibit variable degrees of cooperation. It is known that in the presence of spatial structure, when individuals "play against" (i.e. interact with) their neighbours, and "compare to" ("learn from") them, cooperative investments can evolve to considerable levels. Here, we examine the effect of increasing the neighbourhood size: we find that the mean-field limit of no cooperation is reached for a critical neighbourhood size of about five neighbours on each side in a Moore neighbourhood, which does not depend on the size of the spatial lattice. We also find the related result that in a network of players, the critical average degree (number of neighbours) of nodes for which defection is the final state does not depend on network size, but only on the network topology. This critical average degree is considerably (about 10 times) higher for clustered (social) networks, than for distributed random networks. This result strengthens the argument that clustering is the mechanism which makes the development and maintenance of the cooperation possible. In the lattice topology, it is observed that when the neighbourhood sizes for "interacting" and "learning" differ by more than 0.5, cooperation is not sustainable, even for neighbourhood sizes that are below the mean-field limit of defection. We also study the evolution of neighbourhood sizes, as well as investment level. Here, we observe that the series of the interaction and learning neighbourhoods converge, and a final cooperative state with considerable levels of average investment is achieved.

Animals↗

PubMed2006

Hyperbranched poly(amino ester)s with different terminal amine groups for DNA delivery.

Hyperbranched poly(amino ester)s containing tertiary amines in the core and primary, secondary, and tertiary amines in the periphery, respectively, were evaluated for DNA delivery in vitro. The same core structure facilitated the investigation on the effects of the terminal amine type on the properties of hyperbranched poly(amino ester)s for DNA delivery. The hydrolysis of the poly(amino ester)s was monitored using (1)H NMR. The results reflected that the terminal amine type had negligible effects on the hydrolysis rate but was much slower than that of linear poly(amino ester)s, probably due to the compact hyperbranched spatial structure preventing the accessibility of water. In comparison with PEI 25 K, the hyperbranched poly(amino ester)s showed much lower cytotoxicity in Cos7, HEK293, and HepG2 cells. Gel electrophoresis indicated that poly(amino ester)s could condense DNA efficiently, and the zeta potentials and sizes of the complexes formed with different weight ratios of hyperbranched poly(amino ester)s and DNA were measured. Remarkably, all the hyperbranched poly(amino ester)s showed DNA transfection efficiency comparable to PEI 25 K in Cos7, HEK293, and HepG2 cells regardless of the terminal amine type. Therefore, the terminal amine type had insignificant effects on the hydrolysis rate, cytotoxicity, DNA condensation capability, and in vitro DNA transfection efficiency of the hyperbranched poly(amino ester)s.

Animals↗

PubMed1978

The 1H nuclear-magnetic-resonance spectra of Neurotoxin I and cardiotoxin Vii4 from Naja mossambica mossambica.

Two toxins from the venom of Naja mossambica mossambica, neurotoxin I and cardiotoxin VII4, were investigated in aqueous solution by high-resolution 1H nuclear magnetic resonance (NMR) techniques at 360 MHz. The spectral characterization of the proteins included determination of the number of slowly exchanging amide protons which can be observed in 2H2O solution, measurement of the amide proton chemical shifts and exchange rates, characterization of the aromatic spin systems and the internal mobilities of aromatic rings, and studies of the pH dependence of the NMR spectra. For numerous resonances of labile and non-labile protons quite outstanding pH titration shifts were observed. It is suggested that these NMR parameters provide a useful basis for comparative structural studies of different proteins in the large group of homologous snake toxins. As a first application the NMR data presently available in the literature on neurotoxin II from Naja naja oxiana, toxin alpha from Naja nigricollis and erabutoxin a and b from Laticauda semifasciata have been used to compare these three proteins with neurotoxin I from Naja mossambica mossambica. This preliminary comparative study provides evidence that the same type of spatial structure prevails for these four homologous neurotoxins and that the folding of the backbone corresponds quite closely to that observed in the crystal structure of erabutoxin b. A second application is the comparison of cardiotoxin VII4 from Naja mossambica mossambica with the neurotoxins. The experimental data indicate that the folding of the polypeptide backbone is closely similar, but that the cardiotoxin molecule is markedly more flexible than the neurotoxins.

Amino Acid Sequence↗

PubMed2005

Mixed messengers, unified message: spatial grouping from temporal structure.

In dynamic visual environments, objects can differ from their backgrounds in terms of their associated temporal structure--the time course of changes in some stimulus property defining object and background. In a series of experiments, we investigated whether different "messengers" of temporal structure group into coherent spatial forms. Observers viewed arrays of Gabor patches in which different temporal structures designated figure and ground regions; extracting the figure required grouping across synchronized orientation, spatial frequency, phase, and/or contrast changes. Observers were able to extract spatial form from temporal structure even when information had to be combined across different messengers. Further, mixing messengers of temporal structure proved cost-free: task performance when grouping across messengers approximated performance when all information resided within a single messenger. Thus, the visual system can abstract temporal structure regardless of the messenger of the dynamic event; a coherent spatial structure emerges from this abstracted temporal structure.

Artifacts↗