SMART: identification and annotation of domains from signalling and extracellular protein sequences

SMART is a simple modular architecture research tool and database that provides domain identification and annotation on the WWW (http://coot.embl-heidelberg.de/SMART). The tool compares query sequences with its databases of domain sequences and multiple alignments whilst concurrently identifying compositionally biased regions such as signal peptide, transmembrane and coiled coil segments. Annotated and unannotated regions of the sequence can be used as queries in searches of sequence databases. The SMART alignment collection represents more than 250 signalling and extracellular domains. Each alignment is curated to assign appropriate domain boundaries and to ensure its quality. In addition, each domain is annotated extensively with respect to cellular localisation, species distribution, functional class, tertiary structure and functionally important residues.

The effect of anti-diuretic hormone on the endolymphatic sac of the inner ear

The anti-diuretic hormone vasopressin (AVP) regulates water excretion from the kidney by increasing the water permeability of the collecting duct. AVP binds to V2-receptors and induces the translocation of aquaporin-2 water channels (AQP-2) into the apical plasma membrane of principal cells. By this mechanism AVP controls water reabsorption in the kidney. The effects of AVP on the endolymphatic sac (ES) of the inner ear, which is thought to mediate reabsorption of endolymph, were investigated. Both the V2-receptor and the AQP-2 water channel were found to be expressed in the ES epithelium. In the ES AVP binds to receptors most probably of the V2-subtype. Application of AVP to organotypically cultured ES inhibits membrane turnover in ribosomal-rich cells of the ES epithelia, which is thought to mediate translocation of AQP-2 into the surface membrane. This suggests that AVP has contrasting effects in the inner ear and kidney, which may be physiologically useful for maintaining endolymphatic pressure during severe hypovolemia. Animal experiments show that AVP causes endolymphatic hydrops after systemic application to guinea-pigs, which suggests a causal role for the increased AVP levels found in humans suffering from Ménière's disease.

Superantigen-targeted therapy: phase I escalating repeat dose trial of the fusion protein PNU-214565 in patients with advanced gastrointestinal malignancies

Antibody-directed, superantigen-induced cytotoxicity has been shown to have potent in vitro and in vivo antitumor effects in preclinical models. In the present study, PNU-214565, a recombinant fusion protein consisting of the Fab of the monoclonal antibody C242 and staphylococcal enterotoxin A (SEA), was used in an escalating repeat dose Phase I clinical trial in patients with advanced gastrointestinal malignancies. A prior single-dose Phase I clinical trial had demonstrated safety at doses of 1.5 ng/kg with toxicities of fever and hypotension that were not dose related. Twenty-seven patients (age range, 36-75 years; median, 62; 14 males and 13 females; 23 colorectal and 4 pancreatic) were treated in the present study with one cycle of four consecutive daily 3-h infusions of PNU-214565 at doses of 0.15 ng/kg (n = 3); 0.5 ng/kg (n = 3), 1.5 ng/kg (n = 4), 2.75 ng/kg (n = 12), and 3.5 ng/kg (n = 5). All patients had a good performance status [Eastern Cooperative Oncology Group: PS = 0 (n = 15), PS = 1 (n = 12)]. As in the single-dose trial, fever and hypotension were the most common toxicities. Dose-limiting toxicity (DLT), consisting of transient hypotension responsive to dopamine, was experienced by one patient treated at the 2.75 ng/kg dose level. One patient with pancreatic cancer metastatic to the liver experienced a partial response of hepatic metastases with stable pancreatic head abnormalities by computed tomography scan. Further dose escalation was suspended when two patients treated in a companion repeat dose Phase I study experienced DLT at the 4 ng/kg dose level. Multiparameter analyses on all patients treated in the two companion single-dose and two-repeated-dose Phase I trials revealed that the levels of patients' pretreatment anti-SEA antibodies protected against toxicity at a given drug dose. By jointly considering weight and the baseline anti-SEA concentration in a patient, it is possible to assign a PNU-214565 dose that will induce systemic cytokine release (a surrogate test to assess for the presence of uncomplexed drug and its ability to induce systemic cellular activation) without DLT. This pharmacodynamically based dosing scheme will be tested in future repeated-dose clinical trials and will define maximally tolerated doses of this powerful new immunotherapy approach.

Vision screening of preschool children: evaluating the past, looking toward the future

Vision problems of preschool children are detectable with a comprehensive eye examination; however, it is estimated that only 14% of children below the age of 6 years receive an eye examination. Screening is advocated as a cost-effective alternative to identify children in need of further vision care. Thirty-four states recommend or require vision screening of preschool children. Although laws and guidelines exist, only 21% of preschool children are actually screened for vision problems. There is little agreement concerning the best screening methods, and no validated, highly effective model for screening vision of preschool children. Newer screening tests have been designed specifically for preschool populations, and can be administered by lay screeners. Many have not been validated. Several are recommended by states or organizations without convincing scientific evidence of their effectiveness. This paper summarizes current laws and guidelines for preschool vision screening in the United States, reviews advantages and disadvantages of several test procedures, and provides recommendations for developing future preschool vision screening programs.

Prediction of 10 repetition maximum for short-arc quadriceps exercise from hand-held dynamometer and anthropometric measurements

Short-arc quadriceps exercise are commonly prescribed in physical therapy for strengthening knee extensor musculature. Determining the appropriate starting resistance has traditionally been a trial-and-error procedure. Therefore, developing an expedient method of estimating the correct starting resistance may lead to a more accurate exercise prescription. The primary purpose of this study was to establish a technique for predicting an individual's 10 repetition maximum (10 RM) based on hand-held dynamometer (HHD) strength recording and additional anthropometric predictor variables. Fifty healthy subjects (31 males and 19 females), aged 22-53 years, participated in the study. A prediction equation for determining 10 RM using HHD strength recording, weight, gender, and age was developed. By implementing this equation, clinicians can predict a normal, healthy, young to middle-aged adult's 10 RM within +/- 4.17 kg with a 95% confidence level (SEE = 2.13 kg).

SMART, a simple modular architecture research tool: identification of signaling domains

Accurate multiple alignments of 86 domains that occur in signaling proteins have been constructed and used to provide a Web-based tool (SMART: simple modular architecture research tool) that allows rapid identification and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable variety of domain combinations known. Comparison with established databases showed that 25% of our domain set could not be deduced from SwissProt and 41% could not be annotated by Pfam. SMART is able to determine the modular architectures of single sequences or genomes; application to the entire yeast genome revealed that at least 6.7% of its genes contain one or more signaling domains, approximately 350 greater than previously annotated. The process of constructing SMART predicted (i) novel domain homologues in unexpected locations such as band 4.1-homologous domains in focal adhesion kinases; (ii) previously unknown domain families, including a citron-homology domain; (iii) putative functions of domain families after identification of additional family members, for example, a ubiquitin-binding role for ubiquitin-associated domains (UBA); (iv) cellular roles for proteins, such predicted DEATH domains in netrin receptors further implicating these molecules in axonal guidance; (v) signaling domains in known disease genes such as SPRY domains in both marenostrin/pyrin and Midline 1; (vi) domains in unexpected phylogenetic contexts such as diacylglycerol kinase homologues in yeast and bacteria; and (vii) likely protein misclassifications exemplified by a predicted pleckstrin homology domain in a Candida albicans protein, previously described as an integrin.

Specific interactions between the syntrophin PDZ domain and voltage-gated sodium channels

Syntrophins are modular proteins belonging to the dystrophin associated glycoprotein complex and are thought to be involved in the regulation of the muscular system. Screening of peptide libraries revealed selectivity of the synotrophin PDZ domain toward the motif R/K/Q-E-S/T-X-V-COO- found to be highly conserved in the alpha-subunit C-terminus of vertebrate voltage gated sodium channels (VGSCs). The solution structure of the domain in complex with the peptide G-V-K-E-S-L-V shows specific interactions between the conserved residues in the peptide and syntrophin-characteristic residues in the domain. We propose that syntrophins localize VGSCs to the dystrophin network through its PDZ domain.

Regulation of the human IgE receptor (Fc epsilonRII/CD23) by Epstein-Barr virus (EBV): Ku autoantigen binds specifically to an EBV-responsive enhancer of CD23

An early and critical event in immortalization of human B cells by Epstein-Barr virus (EBV) is induction of CD23 expression. CD23 is constitutively expressed in all EBV-immortalized B cells and its expression is tightly linked with immortalization. We have previously shown that activation of CD23 by EBV occurs at the transcriptional level and is mediated, in part, by EBV-responsive enhancer elements in the region of the type a promoter. We have localized one EBV-responsive enhancer (designated EBVRE) to a 37 bp sequence in intron 1 of type a CD23 that contains a GC-rich sequence that binds nuclear protein(s) from EBV-positive but not EBV-negative cells with sequence specificity. This EBVRE-binding activity was enhanced by protein phosphorylation and did not react with antibodies to the ubiquitous GC box transcription factor, Sp1. We have now shown by protein purification with peptide sequencing and immunological reactivity that p70/p80 Ku autoantigen [the DNA-binding component of DNA-dependent protein kinase (DNA-PK)] binds to this EBVRE with high affinity and sequence specificity. Although Ku autoantigen is ubiquitously expressed, an EBV-specific DNA-protein complex that contains Ku was elicited from EBV-positive but not EBV-negative nuclear extracts. Furthermore, the formation of this EBV-specific DNA-Ku complex was dramatically enhanced by protein phosphorylation. Thus, we have identified EBVRE-binding activity that contains the Ku autoantigen, is DNA sequence specific and is present in EBV-positive but not EBV-negative nuclear extracts. The possible functional significance of the Ku autoantigen-EBVRE interaction is discussed in light of the role of DNA-PK in phosphorylation and activation of several transcription factors. We suggest that phosphorylation of the EBV-specific EBVRE-binding activity by DNA-PK may modulate its activity as a transcription factor.

Cytoplasmic signalling domains: the next generation

Since the late 1980s, when Src-homology SH2 and SH3 domains were identified, the repertoire of non-catalytic signalling domains has increased to number over 30. As it is expected that further regulatory domains shall be found, unravelling the complex network of their interactions remains an on-going challenge.

Standards and practice guidelines as the foundation for clinical practice

The structure and organization of health care delivery are in the midst of rapid change. Health care providers from a variety of disciplines are being challenged to define their practice and the expected patient outcomes resulting from their processes of care delivery. Standards and clinical practice guidelines are important tools for enhancing the quality of health care delivery and for documenting care. The article describes a process for developing standards and clinical practice guidelines and presents an organizational scheme for them. Based on recommendations from diverse national groups, a format for practice guidelines is presented, and a system for implementation and ongoing evaluation is recommended.

Superantigen-based immunotherapy: a phase I trial of PNU-214565, a monoclonal antibody-staphylococcal enterotoxin A recombinant fusion protein, in advanced pancreatic and colorectal cancer

PURPOSE

To establish the maximum-tolerated dose (MTD) and define the toxicities of a single-dose infusion of PNU-214565, a recombinant Escherichia coli-derived fusion protein of Staphylococcal enterotoxin A (SEA) and the Fab-fragment of the C242 monoclonal antibody in patients with advanced colorectal and pancreatic carcinomas. To investigate the capability of PNU-214565 to induce a superantigen (SAg) response resulting in cytokine production and tumor regression.

PATIENTS AND METHODS

Twenty-one patients (age range, 39 to 76 years; median, 64; 12 men, nine women; 18 colorectal, three pancreatic cancers) were treated with a single 3-hour infusion of PNU-214565, with doses ranging from 0.01 to 1.5 ng/kg. All patients had prior chemotherapy and a good performance status Eastern Cooperative Oncology Group [ECOG] performance status [PS] = 0 [n = 10]; PS = 1 [n = 11]), 10 had prior radiation, and 18 had prior surgery.

RESULTS

Fever and hypotension were the most common toxicities. Fever of any grade occurred in 16 of 21 patients (76%): four of 21 (19%) with grade 2 and two of 21 (9.5%) with grade 3. Hypotension of any grade occurred in 13 of 21 (62%): four of 21 with grade 2 and one of 21 (5%) with grade 3. Interleukin-2 (IL-2) and tumor necrosis factor alpha (TNF alpha) induction correlated with toxicity. In the two patients with grade 3 fever, peak IL-2 and TNF alpha levels were 2.9 IU/mL and 165 pg/mL, and 8.3 IU/mL and 245 pg/mL, respectively. Transient, > or = 50% decreases in circulating monocytes were observed in 17 of 21 patients as early as 0.5 hours (median time, 2 hours) from the start of infusion. Decreases (mean 33%) in circulating lymphocytes were observed in seven of 21 patients. All three patients with grade 3 toxicity were treated at the 0.5-ng/kg dose. The significance of baseline anti-SEA, human antimouse antibody (HAMA), CA242-soluble antigen levels, and T-cell receptor variable beta region (TCR V beta) subsets and histocompatibility leukocyte antigen-DR (HLA-DR) genotypes was assessed as possible predictors of toxicity. All toxicities were transient and easily managed. No grade 3 toxicity occurred at the higher dose levels.

CONCLUSION

PNU-214565, a SAg-based tumor targeted therapy, is safe when given as a single 3-hour infusion at doses up to 1.5 ng/kg. The MTD for a single dose was not determined. The safety of a repeated dose schedule is currently under investigation, beginning with doses determined to be safe in this trial.

Capillary Rise for Thermodynamic Characterization of Solid Particle Surface

Surface properties in terms of surface free energy of solid particles were investigated using capillary rise experimental methods based on Washburn's equation. Two different approaches related to height and weight gain measurements were validated by silica flour and calcium carbonate surface studies. Dispersive components of the surface free energy and nondispersive components of solid-liquid energy of interaction were computed. Some differences observed are related to experimental data acquisitions. Many experimental difficulties, which led in the past to inaccurate wettability characteristics, have been controlled. A new link to the so-called geometrical factor of Washburn's equation has also been established after comparison of theoretical and experimental static and hydrodynamic radii. The high precision of the weight gain approach was achieved by strict control of experimental parameters such as temperature, powder packing, and sintered glass porosity.

SAM as a protein interaction domain involved in developmental regulation

More than 60 previously undetected SAM domain-containing proteins have been identified using profile searching methods. Among these are over 40 EPH-related receptor tyrosine kinases (RPTK), Drosophila bicaudal-C, a p53 from Loligo forbesi, and diacyglycerol-kinase isoform delta. This extended dataset suggests that SAM is an evolutionary conserved protein binding domain that is involved in the regulation of numerous developmental processes among diverse eukaryotes. A conserved tyrosine in the SAM sequences of the EPH related RPTKs is likely to mediate cell-cell initiated signal transduction via the binding of SH2 containing proteins to phosphotyrosine.

Mechanism and specificity of human alpha-1,3-fucosyltransferase V

Human alpha-1,3-fucosyltransferase catalyzes the transfer of the L-fucose moiety from guanosine diphosphate-beta-L-fucose (GDP-Fuc) to acceptor sugars to form biologically important fucoglycoconjugates, including sialyl Lewis x (SLex). Evidence for a general base mechanism is supported by a pH-rate profile that revealed a catalytic residue with a pKa of 4.1. The characterized solvent kinetic isotope effect (Dv = 2.9, Dv/k = 2.1) in a proton inventory study indicates that only one-proton transfer is involved in the catalytic step leading to the formation of the transition state. Evidence for Mn2+ as an electrophilic catalyst was supported by the observation that the nonenzymatic transfer of L-fucose from GDP-Fuc to the hydroxyl group of water in the presence of 10 mM MnCl2 at 20 degrees C was accelerated from K(obs)= 3.5 x 10(-6) to 3.8 x 10(-5) min-1. Using the GDP-Fuc hydrolysis as the nonenzymatic rate, the enzymatic proficiency of FucT V, (Kcat/Ki,GDP-fuc. K(m),1.acNAc)/K(non), was estimated to be 1.2 x 10(10) M-1 with a transition-state affinity of 8.6 x 10(-11) M. The Km for Mn2+ was determined to be 6.1 mM, and alternative divalent metal cofactors were identified as Ca2+, Co2+, and Mg2+. Detailed kinetic characterization of the acceptor sugar specificity indicated that incorporation of hydrophobic functionality [e.g. -O-(CH2)5CO2CH3] to the reducing end of the acceptor sugar substantially decreased the K(m),acceptor by over 100-fold. The role of the nucleotide was investigated by studying the inhibition of nucleotides, including the guanosine series. The inhibitory potency trend (GTP approximately GDP > GMP > > guanosine) is consistent with bidentate chelation of Mn2+ by GDP-Fuc. The role of charge and distance in the synergistic inhibitory effect by the combination of GDP, an aza sugar, and the acceptor sugar was probed. A mechanism for fucosyl transfer incorporating these findings is proposed and discussed.

Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide

The WW domain is a new protein module with two highly conserved tryptophans that binds proline-rich peptide motifs in vitro. It is present in a number of signalling and regulatory proteins, often in several copies. Here we investigate the solution structure of the WW domain of human YAP65 (for Yes kinase-associated protein) in complex with proline-rich peptides containing the core motif PPxY. The structure of the domain with the bound peptide GTPPPPYTVG is a slightly curved, three-stranded, antiparallel beta-sheet. Two prolines pack against the first tryptophan, forming a hydrophobic buckle on the convex side of the sheet. The concave side has three exposed hydrophobic residues (tyrosine, tryptophan and leucine) which form the binding site for the ligand. A non-conserved isoleucine in the amino-terminal flanking region covers a hydrophobic patch and stabilizes the WW domain of human YAP65 in vitro. The structure of the WW domain differs from that of the SH3 domain and reveals a new design for a protein module that uses stacked aromatic surface residues to arrange a binding site for proline-rich peptides.