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At least 307 records · Page 17Linked to original sources

PubMed2002

Free-thiol Cys331 exposed during activation process is critical for native tetramer structure of cathepsin C (dipeptidyl peptidase I).

The mature bovine cathepsin C (CC) molecule is composed of four identical monomers, each proteolytically processed into three chains. Five intrachain disulfides and three nonpaired cysteine residues per monomer were identified. Beside catalytic Cys234 in the active site, free-thiol Cys331 and Cys424 were characterized. Cys424 can be classified as inaccessible buried residue. Selective modification of Cys331 results in dissociation of native CC tetramer into dimers. The 3D homology-based model of the CC catalytic core suggests that Cys331 becomes exposed as the activation peptide is removed during procathepsin C activation. The model further shows that exposed Cys331 is surrounded by a surface hydrophobic cluster, unique to CC, forming a dimer-dimer interaction interface. Substrate/inhibitor recognition of the active site in the CC dimer differs significantly from that in the native tetramer. Taken together, a mechanism is proposed that assumes that the CC tetramer formation results in a site-specific occlusion of endopeptidase-like active site cleft of each CC monomeric unit. Thus, tetramerization provides for the structural basis of the dipeptidyl peptidase activity of CC through a substrate access-limiting mechanism different from those found in homologous monomeric exopeptidases cathepsin H and B. In conclusion, the mechanism of tetramer formation as well as specific posttranslational processing segregates CC in the family of papain proteases.

Amino Acid Sequence↗

PubMed2006

Fine structure of neuronal and glial processes in neuropathology.

The cells of the nervous system are characterized by their well-formed cell processes and by cell-to-cell relationships that they form. The neuron reveals essentially cylindrical processes, which form synaptic junctions. On the other hand, the peripheral parts of the glial cells are mainly sheet-like in nature. Thus, the oligodendroglial cell elaborates many sheet-like processes, each of which forms a segment of the myelin sheath. Unique cell junction, transverse bands are present at the interface of oligodendroglial processes and the axon. Finally, the astrocytes also form elaborate sheet-like processes, which separate most of the CNS from the mesodermal tissue as well as surrounding certain neuronal surfaces, including synapses. Punctate adhesions, gap junctions and other adhesive devices are present between astrocytic processes. Defects or anomalies in the neuronal and glial cell processes characterize numerous pathological conditions.

Animals↗

PubMed2006

The signaling helix: a common functional theme in diverse signaling proteins.

BACKGROUND: The mechanism by which the signals are transmitted between receptor and effector domains in multi-domain signaling proteins is poorly understood. RESULTS: Using sensitive sequence analysis methods we identify a conserved helical segment of around 40 residues in a wide range of signaling proteins, including numerous sensor histidine kinases such as Sln1p, and receptor guanylyl cyclases such as the atrial natriuretic peptide receptor and nitric oxide receptors. We term this helical segment the signaling (S)-helix and present evidence that it forms a novel parallel coiled-coil element, distinct from previously known helical segments in signaling proteins, such as the Dimerization-Histidine phosphotransfer module of histidine kinases, the intra-cellular domains of the chemotaxis receptors, inter-GAF domain helical linkers and the alpha-helical HAMP module. Analysis of domain architectures allowed us to reconstruct the domain-neighborhood graph for the S-helix, which showed that the S-helix almost always occurs between two signaling domains. Several striking patterns in the domain neighborhood of the S-helix also became evident from the graph. It most often separates diverse N-terminal sensory domains from various C-terminal catalytic signaling domains such as histidine kinases, cNMP cyclase, PP2C phosphatases, NtrC-like AAA+ ATPases and diguanylate cyclases. It might also occur between two sensory domains such as PAS domains and occasionally between a DNA-binding HTH domain and a sensory domain. The sequence conservation pattern of the S-helix revealed the presence of a unique constellation of polar residues in the dimer-interface positions within the central heptad of the coiled-coil formed by the S-helix. CONCLUSION: Combining these observations with previously reported mutagenesis studies on different S-helix-containing proteins we suggest that it functions as a switch that prevents constitutive activation of linked downstream signaling domains. However, upon occurrence of specific conformational changes due to binding of ligand or other sensory inputs in a linked upstream domain it transmits the signal to the downstream domain. Thus, the S-helix represents one of the most prevalent functional themes involved in the flow of signals between modules in diverse prokaryote-type multi-domain signaling proteins. REVIEWERS: This article was reviewed by Frank Eisenhaber, Arcady Mushegian and Sandor Pongor.

Journal Article↗

PubMed2002

Melatonin synthesis enzymes in Macaca mulatta: focus on arylalkylamine N-acetyltransferase (EC 2.3.1.87).

Arylalkylamine N-acetyltransferase (AANAT; serotonin N-acetyltransferase, EC 2.3.1.87) plays a unique transduction role in vertebrate physiology as the key interface between melatonin production and regulatory mechanisms. Circulating melatonin is elevated at night in all vertebrates, because AANAT activity increases in the pineal gland in response to signals from the circadian clock. Circadian regulation of melatonin synthesis is implicated in a variety of human problems, including jet lag, shift work, insomnia, and abnormal activity rhythms in blind persons. In this report AANAT was studied in the rhesus macaque to better understand human melatonin regulation. AANAT mRNA is abundant in the pineal gland and retina, but not elsewhere; AANAT mRNA is uniformly distributed in the pineal gland, but is limited primarily to the photoreceptor outer segments in the retina. Day and night levels of pineal and retinal AANAT mRNA are similar. In contrast, AANAT activity and protein increase more than 4-fold at night in both tissues. The activity of hydroxyindole-O-methyltransferase, the last enzyme in melatonin synthesis, is tonically high in the pineal gland, but is nearly undetectable in the retina; hydroxyindole O-methyltransferase mRNA levels exhibited a similar pattern. This supports the view that the source of circulating melatonin in primates is the pineal gland. The discovery in this study that rhesus pineal AANAT mRNA is high at all times is of special importance because it shows that posttranscriptional control of this enzyme plays a dominant role in regulating melatonin synthesis.

Acetylserotonin O-Methyltransferase↗

PubMed2006

The transcription factor ZBP-89 controls generation of the hematopoietic lineage in zebrafish and mouse embryonic stem cells.

Hematopoietic development is closely linked to that of blood vessels and the two processes are regulated in large part by transcription factors that control cell fate decisions and cellular differentiation. Both blood and blood vessels derive from a common progenitor, termed the hemangioblast, but the factor(s) specifying the development and differentiation of this stem cell population into the hematopoietic and vascular lineages remain ill defined. Here, we report that knockdown of the Krüppel-like transcription factor ZBP-89 in zebrafish embryos results in a bloodless phenotype, caused by disruption of both primitive and definitive hematopoiesis, while leaving primary blood vessel formation intact. Injection of ZBP-89 mRNA into cloche zebrafish embryos, which lack both the hematopoietic and endothelial lineages, rescues hematopoiesis but not vasculogenesis. Injection of mRNA for Stem Cell Leukemia (SCL), a transcription factor that directs hemangioblast development into blood cell precursors, rescues the bloodless phenotype in ZBP-89 zebrafish morphants. Forced expression of ZBP-89 induces the expansion of hematopoietic progenitors in wild-type zebrafish and in mouse embryonic stem cell cultures but inhibits angiogenesis in vivo and in vitro. These findings establish a unique regulatory role for ZBP-89, positioned at the interface between early blood and blood vessel development.

Animals↗

PubMed1996

Osteopontin: an interfacial extracellular matrix protein in mineralized tissues.

Among the noncollagenous matrix proteins found in mineralized tissues (MTs), colloidal-gold immunocytochemistry has demonstrated that the ultrastructural distribution of osteopontin (OPN) is unique in that this protein preferentially accumulates at MT interfaces. In bone, OPN is present as a major component of cell- and matrix-matrix interfacial structures termed laminae limitantes and cement lines, respectively. Here, we review the implications of this distinct, interfacial tissue distribution as it relates to the properties and functional motifs of OPN (e.g. RGD, polyAsp, phosphorylation) in different MTs, and more specifically, how it pertains to current theory on the cellular and extracellular matrix (ECM) events associated with bone remodeling. The production of OPN as one of the earliest, and latest, secretory activities of the osteoblast lineage is discussed, together with a consideration of the role of OPN in cement lines and laminae limitantes in bone and in other normal, pathological and healing MTs such as teeth, kidney stones, bone wound healing and implant osseointegration. Further to its ability to influence cell dynamics, calcification and possibly tissue cohesion in MTs, it is proposed that OPN in cement lines may also promote adhesion between apposing substrata. With regard to this latter function, it is suggested that the molecular interactions within, and biomechanical properties of, such an OPN-rich interfacial zone may be important in minimizing strain-induced fatigue damage and microcrack propagation in bone and across other MT interfaces.

Animals↗

PubMed2005

Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.

MOTIVATION: Elucidation of the full network of protein-protein interactions is crucial for understanding of the principles of biological systems and processes. Thus, there is a need for in silico methods for predicting interactions. We present a novel algorithm for automated prediction of protein-protein interactions that employs a unique bottom-up approach combining structure and sequence conservation in protein interfaces. RESULTS: Running the algorithm on a template dataset of 67 interfaces and a sequentially non-redundant dataset of 6170 protein structures, 62 616 potential interactions are predicted. These interactions are compared with the ones in two publicly available interaction databases (Database of Interacting Proteins and Biomolecular Interaction Network Database) and also the Protein Data Bank. A significant number of predictions are verified in these databases. The unverified ones may correspond to (1) interactions that are not covered in these databases but known in literature, (2) unknown interactions that actually occur in nature and (3) interactions that do not occur naturally but may possibly be realized synthetically in laboratory conditions. Some unverified interactions, supported significantly with studies found in the literature, are discussed. AVAILABILITY: http://gordion.hpc.eng.ku.edu.tr/prism CONTACT: agursoy@ku.edu.tr; okeskin@ku.edu.tr.

Algorithms↗

PubMed2005

Structure of the Fab fragment of F105, a broadly reactive anti-human immunodeficiency virus (HIV) antibody that recognizes the CD4 binding site of HIV type 1 gp120.

We have determined the crystal structure of the Fab fragment from F105, a broadly reactive human antibody with limited potency that recognizes the CD4 binding site of gp120. The structure reveals an extended CDR H3 loop with a phenylalanine residue at the apex and shows a striking pattern of serine and tyrosine residues. Modeling the interaction between gp120 and F105 suggests that the phenylalanine may recognize the binding pocket of gp120 used by Phe(43) of CD4 and that numerous tyrosine and serine residues form hydrogen bonds with the main chain atoms of gp120. A comparison of the F105 structure to that of immunoglobulin G1 b12, a much more potent and broadly neutralizing antibody with an overlapping epitope, suggests similarities that contribute to the broad recognition of human immunodeficiency virus by both antibodies. While the putative epitope for F105 shows significant overlap with that predicted for b12, it appears to differ from the b12 epitope in extending across the interface between the inner and outer domains of gp120. In contrast, the CDR loops of b12 appear to interact predominantly with the outer domain of gp120. The difference between the predicted epitopes for b12 and F105 suggests that the unique potency of b12 may arise from its ability to avoid the interface between the inner and outer domains of gp120.

Amino Acid Sequence↗

PubMed1998

DICOM versus HL7 for modality interfacing.

Digital modalities such as CT, MRI, Ultrasound and Computerized Radiography systems, generating softcopy images to be used by a Picture Archiving and Communication System (PACS), need to identify the images properly in order to retrieve and manage them. In many cases, a technologist re-enters patient demographic and study related information at the modality, even although it is usually already present somewhere in the hospital information system (IS). In order to achieve a higher level of efficiency and uniquely identify the created image objects, it is obvious that an interface between the IS and modality to exchange this information is highly desired. There are two options for a modality vendor to implement an IS interface, either using the Health Level (HL7) or Digital Imaging Communication in Medicine (DICOM) communication standard. This paper will explain characteristics of both protocols, and demonstrate that it is preferred to use DICOM versus HL7. In addition, it will show that DICOM is supported by most modality vendors, based on the result of a poll of their Modality Worklist versus HL7 support.

Diagnostic Imaging↗

PubMed2006

Expression of SWAP-70 in the uterus and feto-maternal interface during embryonic implantation and pregnancy in the rhesus monkey (Macaca mulatta).

SWAP-70 is a unique signaling protein involved in multiple processes including lymphatic cell activation, migration, adhesion, and cytoskeleton organization. Its role in reproductive system remains to be unclear. In the present study, the spatial and temporal expression of SWAP-70 in the uterus during normal menstrual cycle as well as on the feto-maternal interface during pregnancy was investigated in the rhesus monkey by in situ hybridization and immunohistochemistry. It was shown that SWAP-70 was mainly expressed in glandular epithelial cells of uterine endometrium, and the level peaked at the mid-secretory stage. At the beginning of embryonic implantation, SWAP-70 was intensely expressed at the implantation site, mainly localized in glandular and luminal epithelial cells, as well as in primary trophoblasts and epithelial plaque. High level of SWAP-70 was observed in villous cytotrophoblast (VCT), syncytiotrophoblast (ST), column cytotrophoblast, trophoblast shell, interstitial trophoblast, and endovascular trophoblast during gestational days 15-25. From gestational day 50 to term, expression of SWAP-70 decreased evidently and was restricted in VCT cells. What's more, SWAP-70 co-localized with F-actin on the feto-maternal interface, especially in highly motive extravillous trophoblasts. The data indicate that SWAP-70 may be involved in regulating motility of trophoblast cells during embryonic implantation and placentation.

Animals↗

PubMed2005

Macroscopic optical mapping of excitation in cardiac cell networks with ultra-high spatiotemporal resolution.

Optical mapping of cardiac excitation using voltage- and calcium-sensitive dyes has allowed a unique view into excitation wave dynamics, and facilitated scientific discovery in the cardiovascular field. At the same time, the structural complexity of the native heart has prompted the design of simplified experimental models of cardiac tissue using cultured cell networks. Such reduced experimental models form a natural bridge between single cells and tissue/organ level experimental systems to validate and advance theoretical concepts of cardiac propagation and arrhythmias. Macroscopic mapping (over >1cm(2) areas) of transmembrane potentials and intracellular calcium in these cultured cardiomyocyte networks is a relatively new development and lags behind whole heart imaging due to technical challenges. In this paper, we review the state-of-the-art technology in the field, examine specific aspects of such measurements and outline a rational system design approach. Particular attention is given to recent developments of sensitive detectors allowing mapping with ultra-high spatiotemporal resolution (>5 megapixels/s). Their interfacing with computer platforms to match the high data throughput, unique for this new generation of detectors, is discussed here. This critical review is intended to guide basic science researchers in assembling optical mapping systems for optimized macroscopic imaging with high resolution in a cultured cell setting. The tools and analysis are not limited to cardiac preparations, but are applicable for dynamic fluorescence imaging in networks of any excitable media.

Action Potentials↗

PubMed2003

Stabilizing the open conformation of the integrin headpiece with a glycan wedge increases affinity for ligand.

The affinity of the extracellular domain of integrins for ligand is regulated by conformational changes signaled from the cytoplasm. Alternative types of conformational movement in the ligand-binding headpiece have been proposed. In one study, electron micrograph image averages of the headpiece of integrin aV beta 3 show two different conformations. The open conformation of the headpiece is present when a ligand mimetic peptide is bound and differs from the closed conformation in the presence of an obtuse angle between the beta 3 subunit hybrid and I-like domains. We tested the hypothesis that opening of the hybrid-I-like domain interface increases ligand-binding affinity by mutationally introducing an N-glycosylation site into it. Both beta 3 and beta1 integrin glycan wedge mutants exhibit constitutively high affinity for physiological ligands. The data uniquely support one model of integrin activation and suggest that movement at the interface with the hybrid domain pulls down the C-terminal helix of the I-like domain and activates its metal ion-dependent adhesion site, analogously to activation of the integrin I domain.

Animals↗

PubMed1995

The registration function as a critical dependency in a lifetime clinical record (LCR).

Over the past two years, we have successfully migrated the Regenstrief Clinical Information System into our hospital. Integral to this process was the need to develop interfaces and processes supporting movements of patient identification data between the existing clinical management system (Unity, SMS) and Carebase (RCIS). Critical to the implementation of Carebase was the development of an interface between Carebase and the registration system based upon a unique medical record number. Even more critical was the development of stable processes that supported the accurate patient identification and assignment of medical record numbers. The medical record number at our institution is assigned or verified at the time of registration. Major problems occurred when patients presented during system down-times and existing medical record numbers could not be accessed, resulting in multiple registrations and medical record numbers for the same patient. This resulted in data fragmentation and required merging at a later date. Other more serious problems resulted from the assignment of the same medical record number to separate patients and with the mixing of data from multiple patients into one patient record. This was largely due to the failure of clerical personnel to appropriately identify patients at the time of registration, or multiple patients sharing identification documents, a common problem in our geographic area. Given that clinical data was to be maintained and added to the repository for several decades, errors such as these in registration would prove catastrophic. The interfaces between the various clinical systems that pass data to Carebase are all HL-standard and largely prevent data passage if registration data is inaccurate. During the early stages of implementation, approximately 300 exceptions per day were generated from clinical systems attempting to pass data to the repository. Following re¿engineering of the registration process, education of clerical personnel, and analysis of exception type, the number of exceptions due to faulty registration data fell to less than one per week. To achieve improvement in exception volume, several innovative measures were undertaken. Firstly, down-time procedures were changed to require query of the LCR for existing registration data. The LCR was maintained on a separate platform that experienced essentially no down-time and was available for this purpose. This largely eliminated the need for the use of "down-time numbers" or medical record numbers that could be temporarily assigned to patients registered when the registration system was unavailable (data would subsequently be merged into existing patient records if the patient was found to be currently in the system). If the patient was not in the LCR, then a permanent number was assigned in sequence. A registration dataset was developed and encoded onto a magnetic card (Carecard, Eltrax) and carried by patients. This enabled the rapid verification of registration data on subsequent visits to the parent institution or affiliated clinical sites. The issue of fraudulent use of the card and encoded registration dataset, however, remained problematic. Currently, a new imaging system is being installed that will soon enable the inclusion of a photograph of the patient as a component of the registration dataset. Perhaps the most significant change in the registration process involved the education of central registration and admitting personnel. An educational program was developed that reinforced the need for accuracy in collecting registration data, identifying patients, and assigning medical record numbers; more importantly, it stressed the linkage of the registration function and patient care. Lastly, an aggressive approach to monitoring exceptions resulting from errors in registration was developed. A near real-time process for identifying errors in registrations allowed for rapid intervention and feedback to involved de

Medical Records Systems, Computerized↗

PubMedDate not supplied

A water phantom controller for automated acquisition of linac beam parameters.

Three-dimensional water phantoms are routinely used when acquiring the data necessary to commission medical linear accelerators. A new water phantom controller has been developed at our institution that is unique in several aspects. The water phantom controller is based on an IBM XT compatible computer. This has been interfaced to an Artronix three-dimensional water phantom and a commercially available linac setup controller. Some of the unique features of the new controller are (i) its ability to perform three-dimensional coordinate transformations on the fly (this removes the need to level and align the water tank with the beam axes and greatly reduces setup time). (ii) Its ability to communicate with a device which can control the linac operating parameters (this allows the water phantom controller to adjust, for example, the jaw size of the accelerator as it acquires data). (iii) Its ability to output the acquired data in a number of modes, including screen display, hardcopy plot, or disk file that may be transferred to a central treatment planning computer). (iv) Its ability to digitally process the acquired data. This water phantom controller may be used to gather machine data in a highly automated manner, greatly reducing the time required to gather the desired data.

Computers↗

PubMed2004

Facilitated sulfate transfer across the nitrobenzene-water interface as mediated by hydrogen-bonding ionophores.

Facilitated SO4(2-) transfers by hydrogen bond-forming ionophores are investigated across the nitrobenzene (NB)-water interface by using polarography with a dropping electrolyte electrode. Bis-thiourea 1, alpha,alpha'-bis(N'-p-nitrophenylthioureylene)-m-xylene, is found to significantly facilitate the transfer of the highly hydrophilic SO4(2-) whereas its counterpart, N-(p-nitrophenyl)-N'-propylthiourea (ionophore 2), cannot. In contrast to the predominant formation of a 1:1 complex with SO4(2-) in the bulk NB phase, the SO4(2-) transfer assisted by 1 is indeed based on the formation of a 1:2 complex between SO4(2-) and ionophore, even under the condition of [SO4(2-)]aq >> [1]org. Such an exclusive formation of the 1:2 (SO4(2-) to ionophore) complex at the NB-water interface is not observed with structurally similar bis-thiourea 3, alpha,alpha'-bis(N'-phenylthioureylene)-m-xylene, where p-nitrophenyl moietes of bis-thiourea 1 are simply replaced by phenyl groups. The facilitated transfer of SO4(2-) with bis-thiourea 1 is further compared to that of HPO4(2-) and H2PO4- across the NB-water interface, which was previously shown to be assisted by 1 through the formation of the 1:1 and 2:1 (anion to ionophore) complexes, respectively. On the basis of these examinations, unique binding behaviors of hydrogen bond-forming ionophores at the NB-water interface are discussed, with a view towards development of ionophore-based anion-selective chemical sensors.

Journal Article↗

PubMed2004

Unique rodlike surface morphologies in trisilanolcyclohexyl polyhedral oligomeric silsesquioxane films.

A trisilanol derivative of polyhedral oligomeric silsesquioxane (POSS), trisilanolisobutyl-POSS, has recently been reported to form stable monolayers at the air/water interface. This paper explores the mono- and multilayer properties of another POSS derivative, trisilanolcyclohexyl-POSS, with pi-A isotherm and Brewster angle microscopy measurements. Results show that with continuously increasing surface concentration via symmetrical compression, trisilanolcyclohexyl-POSS amphiphiles at the air/water interface undergo a series of phase transitions from traditional Langmuir monolayers (one-POSS-molecule thick) to unique rodlike hydrophobic aggregates in multilayer films (approximately eight-POSS-molecules thick) that are dramatically different from "collapsed" morphologies seen in other systems. Stable and hydrophobic rodlike structure formation on water is presumably due to trisilanolcyclohexyl-POSS' unique molecular structure and strong tendency to form intermolecular hydrogen bonds in the solid state. This result is consistent with existing POSS/polymer composite research, which shows that POSS molecules tend to aggregate and crystallize into lamellar nanocrystals.

Models, Molecular↗

PubMed2002

Orientation and conformation of a lipase at an interface studied by molecular dynamics simulations.

Electron density profiles calculated from molecular dynamics trajectories are used to deduce the orientation and conformation of Thermomyces lanuginosa lipase and a mutant adsorbed at an air-water interface. It is demonstrated that the profiles display distinct fine structures, which uniquely characterize enzyme orientation and conformation. The density profiles are, on the nanosecond timescale, determined by the average enzyme conformation. We outline a computational scheme that from a single molecular dynamics trajectory allows for extraction of electron density profiles referring to different orientations of the lipase relative to an implicit interface. Profiles calculated for the inactive and active conformations of the lipase are compared with experimental electron density profiles measured by x-ray reflectivity for the lipase adsorbed at an air-water interface. The experimental profiles contain less fine structural information than the calculated profiles because the resolution of the experiment is limited by the intrinsic surface roughness of water. Least squares fits of the calculated profiles to the experimental profiles provide areas per adsorbed enzyme and suggest that Thermomyces lanuginosa lipase adsorbs to the air-water interface in a semiopen conformation with the lid oriented away from the interface.

Ascomycota↗

PubMedDate not supplied

Drawtex: a unique dressing that can be tailor-made to fit wounds.

Drawtex is a new and innovative dressing using dispersion technology which works on capillary action. This promotes moist wound healing and provides the optimum environment at the wound interface. This dressing has the ability to absorb exudate 30 times it own weight. The unique capillary action draws the exudate away from the wound bed and into the core of the dressing from where it disperses into a second layer of Drawtex. The practitioner tailors the Drawtex to conform to the wound bed. Drawtex's non-adherence reduces the frequency of dressing change after the first week. This is not the only benefit as it is also very cost-effective at half the price of other modern dressing products.

Absorption↗