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PubMed1986

The health of the chronically mentally ill: a review of the literature.

This paper reviews three areas of research on the health of the chronically mentally ill: epidemiological studies on this population, studies exploring the clinical interface of physical and psychiatric disorder, and studies illuminating barriers to adequate health care for this population. Its purpose is to increase our understanding of the unique health problems facing the chronically mentally ill so that appropriate interventions can be developed. The review suggests that greater attention to this area should result in improved physical health as well as improved psychiatric intervention. The implications for policy, practice, and research are discussed.

Chronic Disease↗

PubMed2006

Robot control with biological cells.

At present there exists a large gap in size, performance, adaptability and robustness between natural and artificial information processors for performing coherent perception-action tasks under real-time constraints. Even the simplest organisms have an enviable capability of coping with an unknown dynamic environment. Robots, in contrast, are still clumsy if confronted with such complexity. This paper presents a bio-hybrid architecture developed for exploring an alternate approach to the control of autonomous robots. Circuits prepared from amoeboid plasmodia of the slime mold Physarum polycephalum are interfaced with an omnidirectional hexapod robot. Sensory signals from the macro-physical environment of the robot are transduced to cellular scale and processed using the unique micro-physical features of intracellular information processing. Conversely, the response form the cellular computation is amplified to yield a macroscopic output action in the environment mediated through the robot's actuators.

Animals↗

PubMed2004

The nuclear xenobiotic receptor CAR: structural determinants of constitutive activation and heterodimerization.

Constitutive androstane receptor (CAR) induces xenobiotic, bilirubin, and thyroid hormone metabolism as a heterodimer with the retinoid X receptor (RXR). Unlike ligand-dependent nuclear receptors, CAR is constitutively active. Here, we report the heterodimeric structure of the CAR and RXR ligand binding domains (LBDs), which reveals an unusually large dimerization interface and a small CAR ligand binding pocket. Constitutive CAR activity appears to be mediated by the compact nature of the CAR LBD that displays several unique features including a shortened AF2 helix and helix H10, which are linked by a two-turn helix that normally adopts an extended loop in other receptors, and an extended helix H2 that stabilizes the canonical LBD fold by packing tightly against helix H3. These structural observations provide a molecular framework for understanding the atypical transcriptional activation properties of CAR.

Amino Acid Sequence↗

PubMed1996

Zinc mediated dimer of human interferon-alpha 2b revealed by X-ray crystallography.

BACKGROUND: The human alpha-interferon (huIFN-alpha) family displays broad spectrum antiviral, antiproliferative and immunomodulatory activities on a variety of cell types. The diverse biological activities of the IFN-alpha's are conveyed to cells through specific interactions with cell-surface receptors. Despite considerable effort, no crystal structure of a member of this family has yet been reported, because the quality of the protein crystals have been unsuitable for crystallographic studies. Until now, structural models of the IFN-alpha's have been based on the structure of murine IFN-beta (muIFN-beta). These models are likely to be inaccurate, as the amino acid sequence of muIFN-beta differs significantly from the IFN-alpha's at proposed receptor-binding sites. Structural information on a huIFN-alpha subtype would provide an improved basis for modeling the structures of the entire IFN-alpha family. RESULTS: The crystal structure of recombinant human interferon-alpha 2b (huIFN-alpha 2b) has been determined at 2.9 A resolution. HuIFN-alpha 2b exists in the crystal as a noncovalent dimer, which associates in a novel manner. Unlike other structurally characterized cytokines, extensive interactions in the dimer interface are mediated by a zinc ion (Zn2+). The overall fold of huIFN-alpha 2b is most similar to the structure of muIFN-beta. Unique to huIFN-alpha 2b is a 3(10) helix in the AB loop which is held to the core of the molecule by a disulfide bond. CONCLUSIONS: The structure of huIFN-alpha 2b provides an accurate model for analysis of the > 15 related type 1 interferon molecules. HuIFN-alpha 2b displays considerable structural similarity with muIFN-beta, interleukin-10 and interferon-gamma, which also bind related class 2 cytokine receptors. From these structural comparisons and numerous studies on the effects of mutations on biological activity, we have identified protein surfaces that appear to be important in receptor activation. This study also reveals the potential biological importance of the huIFN-alpha 2b dimer.

Amino Acid Sequence↗

PubMed2026

EPIC: multi-objective guided diffusion for epitope design in TCR-pMHC complexes.

MOTIVATION: T cell receptor (TCR) recognition of peptide-major histocompatibility complex (pMHC) complexes is central to adaptive immunity, yet rational design of immunogenic epitopes remains elusive due to complex triplet binding constraints and data scarcity. No existing method can generate epitopes satisfying simultaneous requirements for antigenicity, MHC presentation, and TCR specificity. RESULTS: We present EPIC, a multi-objective diffusion framework that decomposes TCR-pMHC binding into three biologically grounded sub-tasks, enabling training-free gradient guidance without end-to-end retraining. By integrating ESM-based classifiers with a peptide diffusion generator, EPIC leverages heterogeneous immunological interaction datasets to generate diverse, context-aware epitopes. EPIC-designed top-three epitopes achieve lower predicted interface energies compared to ground-truth epitopes in 78.31% of test cases, while maintaining 80.1% sequence novelty and comparable structural confidence. Generated epitopes exhibit 100% uniqueness, high diversity (64.05%), and high antigenicity scores (0.4723). To our knowledge, EPIC is the first computational framework capable of de novo epitope design while explicitly integrating the triplet constraints of TCR-pMHC binding. This paradigm shift from discovery to design unlocks new potential for personalized cancer vaccines, precision adoptive T cell therapy, and rapid response to emerging infectious diseases. AVAILABILITY AND IMPLEMENTATION: The source code of EPIC is available at https://github.com/Octopus125/EPIC and archived on Zenodo (DOI: 10.5281/zenodo.18537646).

Receptors, Antigen, T-Cell↗

PubMedDate not supplied

A pilot program to promote professional growth for neuroscience nurses.

A pilot program was developed as a strategy to increase professional growth on a neuroscience unit. The primary objective of the program was to allow staff nurses to participate in activities that interface with the neuroscience patient population. Nurses could choose an area of interest that related to their unit responsibilities. This experience provided the participants with the unique opportunity to participate in patient care from the perspective of another discipline. The staff were enthusiastic about the experience and shared it eagerly with their peers. Participants' evaluation of the program was overwhelmingly favorable. The data suggest that this program was an effective means of increasing professional growth and staff development.

Education, Nursing, Continuing↗

PubMed2000

DARWIN: a program for docking flexible molecules.

A new program named "DARWIN" has been developed to perform docking calculations with proteins and other biological molecules. The program uses the Genetic Algorithm to optimize the molecule's conformation and orientation under the selective pressure of minimizing the potential energy of the complex. A unique feature of DARWIN is that it communicates with the molecular mechanics program CHARMM to make the energy calculations. A second important feature is its parallel interface, which allows simultaneous use of multiple stand-alone copies of CHARMM to rapidly evaluate large numbers of potential solutions. This permits an "accuracy first" approach to docking, which avoids many of the common assumptions and shortcuts often made to reduce computation time. The method was applied to three protein-carbohydrate complexes: the crystallographically determined structures of Concanavalin A and Fab Se155-4; and a model structure for Fab ME36.1. Conformations close to the crystal structures were obtained with this approach, but some "false positive" solutions were also selected. Many of these could be eliminated by introducing different methods for simulating solvent effects. An effective screening method for docking a database of compounds to a single target enzyme using DARWIN is also presented.

Algorithms↗

PubMed2000

The effect of a silane coupling agent on the bond strength of bone cement and cobalt-chrome alloy.

Debonding of the cement-implant interface has been hypothesized to be the leading initial indicator of failed total hip prostheses. Many attempts have been made to increase the bond strength of this interface by precoating the implant, increasing the implant's surface roughness, and creating macro-grooves or channels on the implant. However, each of these approaches introduces new complications. This study introduces a unique silane coupling agent used to chemically bond the bone cement to the implant. Cylindrical cobalt-chrome samples were treated with the silane coupling agent, bonded to polymethylmethacrylate, and pushed out to failure. The mean shear strengths were compared to the failure strengths of untreated samples. Half of the specimens were tested immediately following cement curing, and the other half were tested after immersion in saline solution for 60 days. The mean shear strength of the silane-coated samples ranged from 18.2 to 24.1 MPa, and the mean shear strength of the uncoated samples ranged from 7.6 to 15.0 MPa. The increase in strength following silane coating noted in this study may increase the longevity of the implant by decreasing debonding at the interface and, therefore, subsequent failure due to loosening.

Bone Cements↗

PubMed2005

Crystal structure of a nicotinate phosphoribosyltransferase from Thermoplasma acidophilum.

We have determined the crystal structure of nicotinate phosphoribosyltransferase from Themoplasma acidophilum (TaNAPRTase). The TaNAPRTase has three domains, an N-terminal domain, a central functional domain, and a unique C-terminal domain. The crystal structure revealed that the functional domain has a type II phosphoribosyltransferase fold that may be a common architecture for both nicotinic acid and quinolinic acid (QA) phosphoribosyltransferases (PRTase) despite low sequence similarity between them. Unlike QAPRTase, TaNAPRTase has a unique extra C-terminal domain containing a zinc knuckle-like motif containing 4 cysteines. The TaNAPRTase forms a trimer of dimers in the crystal. The active site pocket is formed at dimer interfaces. The complex structures with phosphoribosylpyrophosphate (PRPP) and nicotinate mononucleotide (NAMN) showed, surprisingly, that functional residues lining on the active site of TaNAPRTase are quite different from those of QAPRTase, although their substrates are quite similar to each other. The phosphate moiety of PRPP and NAMN is anchored to the phosphate-binding loops formed by backbone amides, as found in many alpha/beta barrel enzymes. The pyrophosphate moiety of PRPP is located at the entrance of the active site pocket, whereas the nicotinate moiety of NAMN is located deep inside. Interestingly, the nicotinate moiety of NAMN is intercalated between highly conserved aromatic residues Tyr(21) and Phe(138). Careful structural analyses combined with other NAPRTase sequence subfamilies reveal that TaNAPRTase represents a unique sequence subfamily of NAPRTase. The structures of TaNAPRTase also provide valuable insight for other sequence subfamilies such as pre-B cell colony-enhancing factor, known to have nicotinamide phosphoribosyltransferase activity.

Amino Acid Sequence↗

PubMed1984

The biomaterial-tissue interface: a morphological study utilizing conventional and alternative ultrastructural modalities.

The interface between oral tissues and ceramic endosteal dental implants was investigated in 36 experimental cases in dog jaws. Conventional electron microscopic modalities showed those tissues adjacent to the implants to be viable with no adverse cellular response to the biomaterial. A procedure to retrieve additional ultrastructural data from previously processed biological material was developed to expand upon these data. This included surface-etching with oxygen plasma of routinely processed electron microscopy specimens and formalin fixed histological specimens for scanning electron microscopy (SEM) study; and, cryofracturing of similar histological specimens for additional transmission electron microscopic (TEM) analysis. Results from these alternative protocols supported our observations from conventional studies of the direct association of bone and epithelia to the implant. In addition, they demonstrated a unique portrayal of the epithelial maturation patterns. Further, this alternative TEM method showed excellent retention of cellular integrity and demonstrated a hemidesmosomal-external basal lamina attachment apparatus at the junctional epithelial-implant interface. This latter composite attachment structure was not retained in our previous conventional microdissection procedures. Thus, the interface between oral tissues and the single crystal sapphire endosteal dental implant could be elucidated by these protocols.

Animals↗

PubMed2005

Crystal structure of a novel FAD-, FMN-, and ATP-containing L-proline dehydrogenase complex from Pyrococcus horikoshii.

Two novel types of dye-linked L-proline dehydrogenase complex (PDH1 and PDH2) were found in a hyperthermophilic archaeon, Pyrococcus horikoshii OT3. Here we report the first crystal structure of PDH1, which is a heterooctameric complex (alphabeta)4 containing three different cofactors: FAD, FMN, and ATP. The structure was determined by x-ray crystallography to a resolution of 2.86 angstroms. The structure of the beta subunit, which is an L-proline dehydrogenase catalytic component containing FAD as a cofactor, was similar to that of monomeric sarcosine oxidase. On the other hand, the alpha subunit possessed a unique structure composed of a classical dinucleotide fold domain with ATP, a central domain, an N-terminal domain, and a Cys-clustered domain. Serving as a third cofactor, FMN was located at the interface between the alpha and beta subunits in a novel configuration. The observed structure suggests that FAD and FMN are incorporated into an electron transfer system, with electrons passing from the former to the latter. The function of ATP is unknown, but it may play a regulatory role. Although the structure of the alpha subunit differs from that of the beta subunit, except for the presence of an analogous dinucleotide domain with a different cofactor, the structural characteristics of PDH1 suggest that each represents a divergent enzyme that arose from a common ancestral flavoenzyme and that they eventually formed a complex to gain a new function. The structural characteristics described here reveal the PDH1 complex to be a unique diflavin dehydrogenase containing a novel electron transfer system.

Adenosine Triphosphate↗

PubMed2005

Probing binding-mode diversity in guanidinium-oxoanion host-guest systems.

An attempt to experimentally estimate the role of binding-mode diversity (structural fuzziness) on the molecular recognition seen in the prominent guanidinium-oxoanion host-guest pair is described. The global heat response as measured by isothermal titration calorimetry in acetonitrile, which was obtained from the interaction of five different but structurally closely related guanidinium hosts with three rigid phosphinate guests of decreasing accessibility of their binding sites, is correlated to provide a trend analysis. All host-guest associations of 1:1 stoichiometry in this series are strongly enthalpy-driven. The change in complexation entropy can be related to the tightness of the mutual fit of the host-guest partners, which approaches a minimum limit and is interpreted as the unique lock-and-key binding mode. The ordinary host-guest complexation in this ensemble features substantial positive entropy changes that correlate inversely with the binding interface area. This finding excludes desolvation effects as the major cause of entropy production, and provides evidence for the existence of a broad variety of complex configurations rather than a single binding mode to represent the associated host-guest pair. This result bears on the molecular design of systems that vitally depend on structural fidelity, such as nanoassemblies or homogeneous catalysis.

Anions↗

PubMed1998

Probing RegA/RNA interactions using electrospray ionization-fourier transform ion cyclotron resonance-mass spectrometry.

The interactions of bacteriophage T4 regA protein, a unique translational regulator, with RNAs of various size and sequence were studied using electrospray ionization-Fourier transform ion cyclotron resonance-mass spectrometry. Using very gentle interface conditions, regA/RNA complexes with a 1:1 binding stoichiometry were observed for all four target RNAs studied, consistent with solution binding studies. Competitive binding of target RNAs and their degradation products with regA demonstrated that the loss of a single nucleotide resulted in a dramatic change in binding affinity in some cases. Competitive binding of regA with four target RNAs revealed similar relative binding affinity order to that suggested by previous in vitro repression experiments. The use of sustained off-resonance irradiation for collisionally induced dissociation of a regA/RNA complex suggested the potential for directly obtaining information regarding the regA binding domain.

Bacterial Proteins↗

PubMed1988

Photochemical reactions of dyes and olefins in monolayer films and supported multilayers.

The studies cited in this paper demonstrate that the unique environment provided by L. B. films and supported multilayers can produce a variety of molecular effects on photochemical reactivity that can, in turn, result in films, interfaces or surfaces having macroscopic properties which can be modulated by light. Although these investigations have been focused on molecular reactivity in films and how it can be modified (or persist unchanged), the results suggest several possible technological applications which might result from investigations directed more closely to them.

Alkenes↗

PubMed2005

Existence of lipid microdomains in bilayer of dipalmitoyl phosphatidylcholine (DPPC) and 1-stearoyl-2-docosahexenoyl phosphatidylserine (SDPS) and their perturbation by chlorpromazine: a 13C and 31P solid-state NMR study.

The polyunsaturated fatty acid docosahexaenoic acid (DHA, 22:6, n-3) is found at a level of about 50% in the phospholipids of neuronal tissue membranes and appears to be crucial to human health. Dipalmitoyl phosphatidylcholine (DPPC, 16:0/16:0 PC) and the DHA containing 1-stearoyl-2-docosahexenoyl phosphatidylserine (SDPS) were used to make DPPC (60%)/SDPS (40%) bilayers with and without 10 mol% chlorpromazine (CPZ), a cationic, amphiphilic phenothiazine. Resonances that are present in 13C NMR spectrum of the DPPC (60%)/SDPS (40%) sample and that disappear in presence of 10% CPZ most probably are due to the special interface environment, e.g. the hydrophobic mismatch, at the interface of DPPC and SDPS microdomains in the DPPC/SDPS bilayer. In itself the appearance of resonances at novel chemical shift values is a clear demonstration of a unique chemical environment in the DPPC (60%)/SDPS (40%) bilayer. The findings of the study presented here suggest CPZ bound to the phosphate of SDPS will slow down and partially inhibit such a DHA acyl chain movement in the DPPC/SDPS bilayer. This would affect the area occupied by a SDPS molecule (in the bilayer) and probably the thickness of the bilayer where SDPS molecules reside as well. It is quite likely that such CPZ caused changes can affect the function of proteins embedded in the bilayer.

1,2-Dipalmitoylphosphatidylcholine↗

PubMed2005

Biotechnology, the brain and the future.

Several new approaches to illness, inspired by recent advances in molecular biology, informatics and nanoscience, are readily applicable to diseases of the central nervous system. Novel classes of drugs will widen the scope of therapeutic action beyond merely modifying transmitter function and stem cell and gene therapies could offer an even more selective mode of targeting. Further into the future, nanotechnology has the potential to allow development of new medicines and novel access routes via miniaturized monitoring and screening devices: these systems, together with increasing use of carbon-silicon interfacing, will challenge traditional neuropharmacology. As the 21(st) century unfolds, the structure and function of the brain, which is incomparable with any other organ, will present unique technological and ethical questions.

Animals↗

PubMed1997

Studies on the regulation of the mitochondrial alpha-ketoacid dehydrogenase complexes and their kinases.

Five mitochondrial protein kinases, all members of a new family of protein kinases, have now been identified, cloned, expressed as recombinant proteins, and partially characterized with respect to catalytic and regulatory properties. Four members of this unique family of eukaryotic protein kinases correspond to pyruvate dehydrogenase kinase isozymes which regulate the activity of the pyruvate dehydrogenase complex, an important regulatory enzyme at the interface between glycolysis and the citric acid cycle. The fifth member of this family corresponds to the branched-chain alpha-ketoacid dehydrogenase kinase, an enzyme responsible for phosphorylation and inactivation of the branched-chain alpha-ketoacid dehydrogenase complex, the most important regulatory enzyme in the pathway for the disposal of branched-chain amino acids. At least three long-term control mechanisms have evolved to conserve branched chain amino acids for protein synthesis during periods of dietary protein insufficiency. Increased expression of the branched-chain alpha-ketoacid dehydrogenase kinase is perhaps the most important because this leads to phosphorylation and nearly complete inactivation of the liver branched-chain alpha-ketoacid dehydrogenase complex. Decreased amounts of the liver branched-chain alpha-ketoacid dehydrogenase complex secondary to a decrease in liver mitochondria also decrease the liver's capacity for branched-chain keto acid oxidation. Finally, the number of E1 subunits of the branched-chain alpha-ketoacid dehydrogenase complex is reduced to less than a full complement of 12 heterotetramers per complex in the liver of protein-starved rats. Since the E1 component is rate-limiting for activity and also the component of the complex inhibited by phosphorylation, this decrease in number further limits overall enzyme activity and makes the complex more sensitive to regulation by phosphorylation in this nutritional state. The branched-chain alpha-ketoacid dehydrogenase kinase phosphorylates serine 293 of the E1 alpha subunit of the branched-chain alpha-ketoacid dehydrogenase complex. Site-directed mutagenesis of amino acid residues surrounding serine 293 reveals that arginine 288, histidine 292 and aspartate 296 are critical to dehydrogenase activity, that histidine 292 is critical to binding the coenzyme thiamine pyrophosphate, and that serine 293 exists at or in close proximity to the active site of the dehydrogenase. Alanine scanning mutagenesis of residues in the immediate vicinity of the phosphorylation site (serine 293) indicates that only arginine 288 is required for recognition of serine 293 as a phosphorylation site by the branched-chain alpha-ketoacid dehydrogenase kinase. Phosphorylation appears to inhibit dehydrogenase activity by introducing a negative charge directly into the active site pocket of the E1 dehydrogenase component of the branched-chain alpha-ketoacid dehydrogenase complex. A model based on the X-ray crystal structure of transketolase is being used to predict residues involved in thiamine pyrophosphate binding and to help visualize how phosphorylation within the channel leading to the reactive carbon of thiamine pyrophosphate inhibits catalytic activity. The isoenzymes of pyruvate dehydrogenase kinase differ greatly in terms of their specific activities, kinetic parameters and regulatory properties. Chemically-induced diabetes in the rat induces significant changes in the pyruvate dehydrogenase kinase isoenzyme 2 in liver. Preliminary findings suggest hormonal control of the activity state of the pyruvate dehydrogenase complex may involves tissue specific induced changes in expression of the pyruvate dehydrogenase kinase isoenzymes.

3-Methyl-2-Oxobutanoate Dehydrogenase (Lipoamide)↗

PubMed1996

Induction of nonbilayer structures in diacylphosphatidylcholine model membranes by transmembrane alpha-helical peptides: importance of hydrophobic mismatch and proposed role of tryptophans.

We have investigated the effect of several hydrophobic polypeptides on the phase behavior of diacylphosphatidylcholines with different acyl chain length. The polypeptides are uncharged and consist of a sequence with variable length of alternating leucine and alanine, flanked on both sides by two tryptophans, and with the N- and C-termini blocked. First it was demonstrated by circular dichroism measurements that these peptides adopt an alpha-helical conformation with a transmembrane orientation in bilayers of dimyristoylphosphatidylcholine. Subsequent 31P NMR measurements showed that the peptides can affect lipid organization depending on the difference in hydrophobic length between the peptide and the lipid bilayer in the liquid-crystalline phase. When a 17 amino acid residue long peptide (WALP17) was incorporated in a 1/10 molar ratio of peptide to lipid, a bilayer was maintained in saturated phospholipids containing acyl chains of 12 and 14 C atoms, an isotropic phase was formed at 16 C atoms, and an inverted hexagonal (HII) phase at 18 and 20 C atoms. For a 19 amino acid residue long peptide (WALP19) similar changes in lipid phase behavior were observed, but at acyl chain lengths of 2 C-atoms longer. Also in several cis-unsaturated phosphatidylcholine model membranes it was found that these peptides and a shorter analog (WALP16) induce the formation of nonbilayer structures as a consequence of hydrophobic mismatch. It is proposed that this unique ability of the peptides to induce nonbilayer structures in phosphatidylcholine model membranes is due to the presence of two tryptophans at both sides of the membrane/water interface, which prevent the peptide from aggregating when the mismatch is increased. Comparison of the hydrophobic length of the bilayers with the length of the different peptides showed that it is the precise extent of mismatch that determines whether the preferred lipid organization is a bilayer, isotropic phase, or HII phase. The peptide-containing bilayer and HII phase were further characterized after sucrose density gradient centrifugation of mixtures of WALP16 and dioleoylphosphatidylcholine. 31P NMR measurements of the isolated fractions showed that a complete separation of both components was obtained. Chemical analysis of these fractions in samples with varying peptide concentration indicated that the HII phase is highly enriched in peptide (peptide/lipid molar ratio of 1/6), while the maximum solubility of the peptide in the lipid bilayer is about 1/24 (peptide/lipid, molar). A molecular model of the peptide-induced HII phase is presented that is consistent with the results obtained thus far.

Amino Acid Sequence↗