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At least 901 records · Page 50Linked to original sources
PubMed2003

Multimeric threading-based prediction of protein-protein interactions on a genomic scale: application to the Saccharomyces cerevisiae proteome.

MULTIPROSPECTOR, a multimeric threading algorithm for the prediction of protein-protein interactions, is applied to the genome of Saccharomyces cerevisiae. Each possible pairwise interaction among more than 6000 encoded proteins is evaluated against a dimer database of 768 complex structures by using a confidence estimate of the fold assignment and the magnitude of the statistical interfacial potentials. In total, 7321 interactions between pairs of different proteins are predicted, based on 304 complex structures. Quality estimation based on the coincidence of subcellular localizations and biological functions of the predicted interactors shows that our approach ranks third when compared with all other large-scale methods. Unlike other in silico methods, MULTIPROSPECTOR is able to identify the residues that participate directly in the interaction. Three hundred seventy-four of our predictions can be found by at least one of the other studies, which is compatible with the overlap between two different other methods. From the analysis of the mRNA abundance data, our method does not bias towards proteins with high abundance. Finally, several relevant predictions involved in various functions are presented. In summary, we provide a novel approach to predict protein-protein interactions on a genomic scale that is a useful complement to experimental methods.

DNA, Fungal↗
PubMed1998

Two functional states of the CD11b A-domain: correlations with key features of two Mn2+-complexed crystal structures.

In the presence of bound Mn2+, the three- dimensional structure of the ligand-binding A-domain from the integrin CR3 (CD11b/CD18) is shown to exist in the "open" conformation previously described only for a crystalline Mg2+ complex. The open conformation is distinguished from the "closed" form by the solvent exposure of F302, a direct T209-Mn2+ bond, and the presence of a glutamate side chain in the MIDAS site. Approximately 10% of wild-type CD11b A-domain is present in an "active" state (binds to activation-dependent ligands, e.g., iC3b and the mAb 7E3). In the isolated domain and in the holoreceptor, the percentage of the active form can be quantitatively increased or abolished in F302W and T209A mutants, respectively. The iC3b-binding site is located on the MIDAS face and includes conformationally sensitive residues that undergo significant shifts in the open versus closed structures. We suggest that stabilization of the open structure is independent of the nature of the metal ligand and that the open conformation may represent the physiologically active form.

Amino Acid Substitution↗
PubMed2002

On the number of experiments required to find the causal structure of complex systems.

The need to capture the complexity of biological systems in a simpler formalism is the underlying impetus of biological sciences. Understanding the function of many biological complex systems, such as genetic networks or molecular signalling pathways, requires precise identification of the interactions between their individual components. A number of questions in the study of complex systems are then important-in particular, what can be inferred about the interactions in a complex system from an arbitrary set of experiments, and, what is the minimum number of experiments required to characterize the system? This paper shows that the problem of finding the minimal causal structure of a system based on a set of observations is computationally intractable for even moderately sized systems (it is NP-hard), but a reasonable approximation can be found in a relatively short (polynomial) time. Next, it is shown that the number of experiments required to characterize a complex system grows exponentially with the upper bound on the number of immediate upstream influences of each element, but only logarithmically with the number of elements in the system. This makes it possible to study biological systems with extremely large number of interacting elements and relatively sparse interconnections, such as gene regulatory and cell signalling networks. Finally, the construction of a randomized experimental sequence which achieves this bound is discussed.

Animals↗
PubMed2007

A flexible model for multivariate interval-censored survival times with complex correlation structure.

We focus on the analysis of multivariate survival times with highly structured interdependency and subject to interval censoring. Such data are common in developmental genetics and genetic epidemiology. We propose a flexible mixed probit model that deals naturally with complex but uninformative censoring. The recorded ages of onset are treated as possibly censored ordinal outcomes with the interval censoring mechanism seen as arising from a coarsened measurement of a continuous variable observed as falling between subject-specific thresholds. This bypasses the requirement for the failure times to be observed as falling into non-overlapping intervals. The assumption of a normal age-of-onset distribution of the standard probit model is relaxed by embedding within it a multivariate Box-Cox transformation whose parameters are jointly estimated with the other parameters of the model. Complex decompositions of the underlying multivariate normal covariance matrix of the transformed ages of onset become possible. The new methodology is here applied to a multivariate study of the ages of first use of tobacco and first consumption of alcohol without parental permission in twins. The proposed model allows estimation of the genetic and environmental effects that are shared by both of these risk behaviours as well as those that are specific.

Adolescent↗
PubMed1977

Structural ambiguity and limits to coping.

How well a person can cope with any situation is determined, among other factors, by his ability to resolve the ambiguity of that situation, which in turn depends on its structural complexity. We attempted to analyze a whole range of situations in terms of three dimesions: differentiations, the number of alternatives perceived; articulation, the differentiation and rankability of these alternatives; and loading, the emotional loading (positive or negative) associated with the situation. The efficiency of mapping with these dimensions was investigated by analyzing the effects of 75 situations on coping, as reported in the literature. These were divided into three groups, 25 situations in each, associated with good coping, reduced coping, and failure to come (in terms of performance relative to a baseline or to the population's norm). The interaction between the demands imposed by the complexity of the situation and the success of coping was analyzed by the Multidimensional Scalogram Analysis (MSA). Results show effectiveness of coping to be inversely related to the structural complexity of a situation, mapped in terms of articulation, loading and differentiation. The relative importance of these dimensions is as ordered above; this offers a possible way to construct an "ambiguity score" which may be the primary factor determining the coping limit set by any situation.

Adaptation, Psychological↗
PubMed2000

Structure and complex twinning of dysprosium disilicate (Dy2Si2O7), type B

Dysprosium disilicate (Dy(2)Si(2)O(7)) is triclinic with a = 6.6158 (2), b = 6.6604 (2), c = 12.0551 (4) A, alpha = 94.373 (2), beta = 90.836 (2), gamma = 91.512 (2) degrees, V = 529.4 (1) A(3), space group P1;, Z = 4 and D(x) = 6.156 g cm(-3). The structure (single-crystal X-ray, R = 0.033, wR = 0.041) is built from a linear triple tetrahedral group [Si(3)O(10)] and isolated [SiO(4)] tetrahedron cross-linked by Dy(3+) in one sixfold and three eightfold coordinated positions, and corresponds to the presently revised type B structure of Ho(2)Si(2)O(7). The formation of the unusual linear triple tetrahedral group in the type B structure allows for a more continuous transition in the mean size of REE(3+)O(n) (REE = rare earth element) polyhedra in REE disilicates through the 4f transition metal series. The crystal of Dy(2)Si(2)O(7) investigated was complexly twinned such that the diffraction pattern was also consistent with a larger dimensionally monoclinic unit cell (a = 22.5354, b = 14.2102, c = 6.6158 A, beta = 91.788 degrees ), which resulted in an apparent superstructure of the type B structure in space group C1;. Lattice coincidence with the type B unit cell appears to have been maintained during crystal synthesis and quenching by the complex sector-zoned growth twin.

Journal Article↗
PubMed1999

The bacterial flagella motor.

The bacterial flagellum is probably the most complex organelle found in bacteria. Although the ribosome may be made of slightly more subunits, the bacterial flagellum is a more organized and complex structure. The limited number of flagella must be targeted to the correct place on the cell membrane and a structure with cytoplasmic, cytoplasmic membrane, outer membrane and extracellular components must be assembled. The process of controlled transcription and assembly is still not fully understood. Once assembled, the motor complex in the cytoplasmic membrane rotates, driven by the transmembrane ion gradient, at speeds that can reach many 100 Hz, driving the bacterial cell at several body lengths a second. This coupling of an electrochemical gradient to mechanical rotational work is another fascinating feature of the bacterial motor. A significant percentage of a bacterium's energy may be used in synthesizing the complex structure of the flagellum and driving its rotation. Although patterns of swimming may be random in uniform environments, in the natural environment, where cells are confronted with gradients of metabolites and toxins, motility is used to move bacteria towards their optimum environment for growth and survival. A sensory system therefore controls the switching frequency of the rotating flagellum. This review deals primarily with the structure and operation of the bacterial flagellum. There has been a great deal of research in this area over the past 20 years and only some of this has been included. We apologize in advance if certain areas are covered rather thinly, but hope that interested readers will look at the excellent detailed reviews on those areas cited at those points.

Bacteria↗
PubMed2005

Multicolor spectral karyotyping in multiple myeloma.

Multiple myeloma is a plasma cell disorder characterized at the cytogenetic level by aneuploid karyotypes with numerous complex structural aberrations. Unfortunately, conventional chromosome-banding techniques are unable to resolve many of these aberrations. Multicolor Spectral Karyotyping (SKY) is a molecular cytogenetic technique that utilizes chromosome-painting probes for characterizing complex structural chromosome aberrations. This innovative technology allows the simultaneous display of each of the 24 different chromosomes in a different color. Chromosomal sites of rearrangement or translocation between different chromosomes are visualized by a change in the color at the point of the aberration. The SKY technique makes possible the identification of chromosomal bands of unknown origin, including trans locations, insertions, complex rearrangements, and marker chromosomes, which, in many cases, go unresolved by traditional banding methods.

Bone Marrow Cells↗
PubMed2004

Multichannel mould processing of 3D structures from microporous coralline hydroxyapatite granules and chitosan support materials for guided tissue regeneration/engineering.

A three-dimensional composite material was produced from microporous coralline origin hydroxyapatite (HA) microgranules, chitosan fibers and chitosan membrane. Cylindrical HA microgranules were oriented along channel direction within multichannel mould space and aligned particles were supported with fibers and a chitosan membrane. The positive replica of mould channels was clasp fixed to produce thicker scaffolds. Light microphotographs of the developed complex structure showed good adhesion between the HA particles, the fibers and the supporting membrane. The composite material showed 88% (w/w) swelling in one hour and preserved the complex structure of the original material upon long-term incubation in physiological medium. MEM extract test of HA chitosan complex showed no cell growth inhibition and cell viability assay (MTS) indicated over 90% cell viability.

Animals↗
PubMed2005

Complex genetic structure of the rabies virus in Bangkok and its surrounding provinces, Thailand: implications for canine rabies control.

Dog vaccination and population management have been suggested as priorities in attempts at disease control in canine rabies-endemic countries. Budget limitations and the complexity of social, cultural and religious variables have complicated progress in the developing world. In Bangkok, Thailand, an intensive canine vaccination and sterilization programme has been in place since November 2002. Our objective was to determine if the rabies virus could be mapped according to its genetic variations and geographical location on the small localized scale of Bangkok and its surrounding provinces. Phylogenetic characterization of 69 samples from Bangkok and five neighbouring and two remote provinces, by limited sequence analysis of the rabies virus nucleoprotein gene, distinguished six different clades. Rabies viruses of four clades were intermixed in Bangkok and in the surrounding highly populated regions whereas the other two clades were confined to rural and less populated provinces. Such a complex pattern of gene flow, particularly in Bangkok, may affect the outcome of canine control programmes.

Animals↗
PubMed2004

Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1.

Acylpeptide hydrolases (APH; also known as acylamino acid releasing enzyme) catalyze the removal of an N-acylated amino acid from blocked peptides. The crystal structure of an APH from the thermophilic archaeon Aeropyrum pernix K1 to 2.1 A resolution confirms it to be a member of the prolyl oligopeptidase family of serine proteases. The structure of apAPH is a symmetric homodimer with each subunit comprised of two domains. The N-terminal domain is a regular seven-bladed beta-propeller, while the C-terminal domain has a canonical alpha/beta hydrolase fold and includes the active site and a conserved Ser445-Asp524-His556 catalytic triad. The complex structure of apAPH with an organophosphorus substrate, p-nitrophenyl phosphate, has also been determined. The complex structure unambiguously maps out the substrate binding pocket and provides a basis for substrate recognition by apAPH. A conserved mechanism for protein degradation from archaea to mammals is suggested by the structural features of apAPH.

Aeropyrum↗
PubMed2004

Complex haplotype structure of the human GNAS gene identifies a recombination hotspot centred on a single nucleotide polymorphism widely used in association studies.

The alpha subunit of the heterotrimeric G protein Gs (Gsalpha) is involved in numerous physiological processes and is a primary determinant of cellular responses to extracellular signals. Genetic variations in the Gsalpha gene may play an important role in complex diseases and drug responses. To characterize the genetic diversity in this locus, we resequenced exons and flanking introns of the gene in 44 genomic samples and analysed the haplotype structure of the gene in an additional 50 African-Americans and 50 Caucasians. Significant differences in allele frequency for nearly all the genotyped single nucleotide polymorphism (SNPs) were detected between the two ethnic groups. Linkage disequilibrium (LD) analysis of this locus revealed two haplotype blocks characterized by strong LD and reduced haplotype diversity, especially in Caucasians. Between the two blocks is a narrow (approximately 3 kb) recombination hotspot centred on exons 4 and 5, and a widely used genetic marker in association studies in this region (rs7121) was in linkage equilibrium with the rest of the gene. The haplotype structure of the GNAS locus warrants reevaluation of previous association studies that used marker rs7121 and affects choice of SNP markers to be used in future studies of this locus.

Black or African American↗
PubMed2003

A phosphorus supported multisite coordinating tris hydrazone P(S)[N(Me)N=CH-C6H4-o-OH]3 as an efficient ligand for the assembly of trinuclear metal complexes: synthesis, structure, and magnetism.

A phosphorus supported multisite coordinating ligand P(S)[N(Me)N=CH-C(6)H(4)-o-OH](3) (2) was prepared by the condensation of the phosphorus tris hydrazide P(S)[N(Me)NH(2)](3) (1) with o-hydroxybenzaldehyde. The reaction of 2 with M(OAc)(2).xH(2)O (M = Mn, Co, Ni, x = 4; M = Zn, x = 2) afforded neutral trinuclear complexes [P(S)[N(Me)N=CH-C(6)H(4)-o-O](3)](2)M(3) [M = Mn (3), Co (4), Ni (5), and Zn (6)]. The X-ray crystal structures of compounds 2-6 have been determined. The structures of 3-6 reveal that the trinculear metal assemblies are nearly linear. The two terminal metal ions in a given assembly have an N(3)O(3) ligand environment in a distorted octahedral geometry while the central metal ion has an O(6) ligand environment also in a slightly distorted octahedral geometry. In all the complexes, ligand 2 coordinates to the metal ions through three imino nitrogens and three phenolate oxygens; the latter act as bridging ligands to connect the terminal and central metal ions. The compounds 2-6 also show intermolecular C-H...S=P contacts in the solid-state which lead to the formation of polymeric supramolecular architectures. The observed magnetic data for the (s = 5/2)3 L(2)(Mn(II))(3) derivative, 3, show an antiferromagnetic nearest- and next-nearest-neighbor exchange (J = -4.0 K and J' = -0.15 K; using the spin Hamiltonian H(HDvV) = -2J(S(1)S(2) + S(2)S(3)) - 2J'S(1)S(3)). In contrast, the (s = 1)(3) L(2)(Ni(II))(3) derivative, 5, displays ferromagnetic nearest-neighbor and antiferromagnetic next-nearest-neighbor exchange interactions (J = 4.43 K and J' = -0.28 K; H = H(HDvV)+ S(1)DS(1) + S(2)DS(2)+ S(3)DS(3)). The magnetic behavior of the L(2)(Co(II))(3) derivative, 4, reveals only antiferromagnetic exchange analogous to 3 (J = -4.5, J' = -1.4; same Hamiltonian as for 3).

Journal Article↗
PubMed2003

Ferrocenyl-functionalised terpyridines and their transition-metal complexes: syntheses, structures and spectroscopic and electrochemical properties.

Terpyridine ligands of the type Fc'-X-tpy (Fc'=ferrocenyl or octamethylferrocenyl, X=rigid spacer, tpy'=4'-substituted 2,2':6',2''-terpyridine) were prepared, crystallographically characterised and used for the synthesis of di- and trinuclear bis(terpyridine) complexes of RuII, FeII and ZnII. Donor-sensitiser dyads and triads based on RuII were thoroughly investigated by (spectro)electrochemistry, UV/Vis, transient absorption and luminescence spectroscopy, and an energy level scheme was derived on the basis of the data collected. Intramolecular quenching of the photoexcited RuII complexes by the redox-active Fc' groups can occur reductively and by energy transfer. Both the redox potential of the donor Fc' and the nature of the spacer X have a decisive influence on excited-state lifetimes and emission properties of the complexes. Some of the compounds show room-temperature luminescence, which is unprecedented for ferrocenyl-functionalised compounds of this kind.

Journal Article↗
PubMed2002

Crystal structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization.

PDZ domains bind to short segments within target proteins in a sequence-specific fashion. Glutamate receptor-interacting protein (GRIP)/ABP family proteins contain six to seven PDZ domains and interact via the sixth PDZ domain (class II) with the C termini of various proteins including liprin-alpha. In addition the PDZ456 domain mediates the formation of homo- and heteromultimers of GRIP proteins. To better understand the structural basis of peptide recognition by a class II PDZ domain and PDZ-mediated multimerization, we determined the crystal structures of the GRIP1 PDZ6 domain alone and in complex with a synthetic C-terminal octapeptide of human liprin-alpha at resolutions of 1.5 and 1.8 A, respectively. Remarkably, unlike other class II PDZ domains, Ile-736 at alphaB5 rather than conserved Leu-732 at alphaB1 makes a direct hydrophobic contact with the side chain of the Tyr at the -2 position of the ligand. Moreover, the peptide-bound structure of PDZ6 shows a slight reorientation of helix alphaB, indicating that the second hydrophobic pocket undergoes a conformational adaptation to accommodate the bulkiness of the Tyr side chain, and forms an antiparallel dimer through an interface located at a site distal to the peptide-binding groove. This configuration may enable formation of GRIP multimers and efficient clustering of GRIP-binding proteins.

Adaptor Proteins, Signal Transducing↗
PubMed1987

Isolation of functional alpha beta heterodimers from the purified human placental alpha 2 beta 2 heterotetrameric insulin receptor complex. A structural basis for insulin binding heterogeneity.

To investigate the role of subunit communication in the insulin binding and tyrosine-specific protein kinase activities of the purified human placental insulin receptor, we have developed the methodology to isolate a functional alpha beta heterodimeric insulin receptor complex from the native alpha 2 beta 2 heterotetrameric disulfide-linked state. The dissociation of the alpha 2 beta 2 heterotetrameric insulin receptor into an alpha beta heterodimer was found to be approximately 50% efficient by treatment with alkaline pH (8.75) and dithiothreitol (2 mM). Removal of the dithiothreitol and pH neutralization (pH 7.60) by rapid Sephadex G-50 gel filtration resulted in the preservation of tracer insulin binding activity. The nondissociated alpha 2 beta 2 heterotetrameric and alpha beta heterodimeric insulin receptor complexes could then be effectively separated by Bio-Gel A-1.5m gel filtration. Scatchard analyses of insulin binding to the alpha 2 beta 2 heterotetrameric control or dithiothreitol-treated but nondissociated alpha 2 beta 2 heterotetrameric insulin receptor complexes demonstrated a curvilinear binding isotherm with a maximum of 1 mol of insulin bound/mol of alpha 2 beta 2 heterotetrameric complex. However, binding analyses performed on the isolated alpha beta heterodimeric complex yielded a nearly linear binding curve also, with 1 mol of insulin bound/mol of alpha beta heterodimeric complex at saturation. These data demonstrate that the insulin half-site binding reactivity observed in the alpha 2 beta 2 heterotetrameric insulin receptor complex results from either an asymmetric assembly of identical alpha beta heterodimers or from absolute negative cooperativity.

Chromatography, Gel↗