STING Millennium Suite: integrated software for extensive analyses of 3d structures of proteins and their complexes

Background  

The integration of many aspects of protein/DNA structure analysis is an important requirement for software products in general area of structural bioinformatics. In fact, there are too few software packages on the internet which can be described as successful in this respect. We might say that what is still missing is publicly available, web based software for interactive analysis of the sequence/structure/function of proteins and their complexes with DNA and ligands. Some of existing software packages do have certain level of integration and do offer analysis of several structure related parameters, however not to the extent generally demanded by a user.     

Single channel measurements demonstrate the voltage dependence of permeation through N-type and L-type CaV channels

The delivery of Ca²⁺ into cells by Ca_V channels provides the trigger for many cellular actions, such as cardiac muscle contraction and neurotransmitter release. Thus, a full understanding of Ca²⁺ permeation through these channels is critical. Using whole-cell voltage-clamp recordings, we recently demonstrated that voltage modulates the apparent affinity of N-type (Ca_V2.2) channels for permeating Ca²⁺ and Ba²⁺ ions. While we took many steps to ensure the high fidelity of our recordings, problems can occur when Ca_V currents become large and fast, or when currents run down. Thus, we use here single channel recordings to further test the hypothesis that permeating ions interact with N-type channels in a voltage-dependent manner. We also examined L-type (Ca_V1.2) channels to determine if these channels also exhibit voltage-dependent permeation. Like our whole-cell data, we find that voltage modulates N-channel affinity for Ba²⁺ at voltages > 0 mV, but has little or no effect at voltages < 0 mV. Furthermore, we demonstrate that permeation through L-channel is also modulated by voltage. Thus, voltage-dependence may be a common feature of divalent cation permeation through Ca_V1 and Ca_V2 channels (i.e. high-voltage activated Ca_V channels). The voltage dependence of Ca_V1 channel permeation is likely a mechanism mediating sustained Ca²⁺ influx during the plateau phase of the cardiac action potential.     

Genome-scale metabolic reconstruction and <Emphasis Type="Italic">in silico</Emphasis> analysis of methylotrophic yeast <Emphasis Type="Italic">Pichia pastoris</Emphasis> for strain improvement

Background  

Pichia pastoris has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive in silico model of P. pastoris can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism.     

Evaluation of liposomal clodronate for treatment of malignant histiocytosis in dogs

Malignant histiocytosis (MH) is an aggressive cancer derived from myeloid lineage cells in both dogs and humans. In dogs, the tumor is characterized by the rapid development of metastatic tumors in multiple sites, including especially the lungs and lymph nodes. Humans develop an analogous disease known as Langerhans cell histiocytosis, which primarily affects children and young adults. Because these tumors are often resistant to conventional chemotherapy, there is a need for newer therapeutic approaches. Systemic administration of liposomal clodronate (LC) has been shown to effectively deplete phagocytic cells (e.g., macrophages and dendritic cells) in mice. We investigated therefore whether LC could also be used to treat naturally occurring MH in dogs. First, the susceptibility of canine MH cells to LC-mediated killing was assessed in vitro. Then the clinical safety and effectiveness of LC as a treatment for MH was assessed in a pilot study in five pet dogs with spontaneous MH. We found that canine MH cells were very susceptible to LC-induced apoptotic cell death, whereas other tumor cell lines were resistant to killing by LC. Studies using labeled liposomes demonstrated that susceptibility to LC killing was directly related to the efficiency of liposome uptake. In pet dogs with spontaneous MH, we found that a short course of LC treatment elicited significant tumor regression in two of five treated animals. These findings suggest that liposomal delivery of clodronate and possibly other bisphosphonates may offer an effective new approach to treatment of histiocytic neoplasms in dogs and humans.     

A Single Amino Acid Change in CaV1.2 Channels Eliminates the Permeation and Gating Differences Between Ca2+ and Ba2+

Glutamate scanning mutagenesis was used to assess the role of the calcicludine binding segment in regulating channel permeation and gating using both Ca²⁺ and Ba²⁺ as charge carriers. As expected, wild-type Ca_V1.2 channels had a Ba²⁺ conductance ~2× that in Ca²⁺ (G_Ba/G_Ca = 2) and activation was ~10 mV more positive in Ca²⁺ vs. Ba²⁺. Of the 11 mutants tested, F1126E was the only one that showed unique permeation and gating properties compared to the wild type. F1126E equalized the Ca_V1.2 channel conductance (G_Ba/G_Ca = 1) and activation voltage dependence between Ca²⁺ and Ba²⁺. Ba²⁺ permeation was reduced because the interactions among multiple Ba²⁺ ions and the pore were specifically altered for F1126E, which resulted in Ca²⁺-like ionic conductance and unitary current. However, the high-affinity block of monovalent cation flux was not altered for either Ca²⁺ or Ba²⁺. The half-activation voltage of F1126E in Ba²⁺ was depolarized to match that in Ca²⁺, which was unchanged from that in the wild type. As a result, the voltages for half-activation and half-inactivation of F1126E in Ba²⁺ and Ca²⁺ were similar to those of wild-type in Ca²⁺. This effect was specific to F1126E since F1126A did not affect the half-activation voltage in either Ca²⁺ or Ba²⁺. These results indicate that residues in the outer vestibule of the Ca_V1.2 channel pore are major determinants of channel gating, selectivity, and permeation.     

The contrasting relationships between betaine and homocysteine in two clinical cohorts are associated with plasma lipids and drug treatments

Background

Urinary betaine excretion positively correlated with plasma homocysteine in outpatients attending a lipid disorders clinic (lipid clinic study). We aimed to confirm this in subjects with established vascular disease.

Methods

The correlation between betaine excretion and homocysteine was compared in samples collected from subjects 4 months after hospitalization for an acute coronary episode (ACS study, 415 urine samples) and from 158 sequential patients visiting a lipid disorders clinic.

Principal findings

In contrast to the lipid clinic study, betaine excretion and plasma homocysteine did not correlate in the total ACS cohort. Differences between the patient groups included age, non-HDL cholesterol and medication. In ACS subjects with below median betaine excretion, excretion correlated (using log transformed data) negatively with plasma homocysteine (r = −0.17, p = 0.019, n = 199), with no correlation in the corresponding subset of the lipid clinic subjects. In ACS subjects with above median betaine excretion a positive trend (r = +0.10) between betaine excretion and homocysteine was not significant; the corresponding correlation in lipid clinic subjects was r = +0.42 (p = 0.0001). In ACS subjects, correlations were stronger when plasma non-HDL cholesterol and betaine excretion were above the median, r = +0.20 (p = 0.045); in subjects above median non-HDL cholesterol and below median betaine excretion, r = −0.26 (p = 0.012). ACS subjects taking diuretics or proton pump inhibitors had stronger correlations, negative with lower betaine excretion and positive with higher betaine excretion.

Conclusions

Betaine excretion correlates with homocysteine in subjects with elevated blood lipids.     

The effect of calcium ions on the hydrolysis of benzoylarginine ethyl ester by porcine enteropeptidase.

Calcium ions are shown to have a marked pH-dependent effect on the kinetics of benzoyllarginine ethyl ester hydrolysis by porcine enteropeptidase (EC 3.4.21.9). Below pH 6.0, calcium ions stimulate benzoylarginine ethyl ester hydrolysis but inhibit this activity above pH 6.0. This effect is mainly on the Km for benzoylarginine ethyl ester. At pH 5.3, 2mM calcium ions reduce the Km for benzoylarginine ethyl ester from 0.31 mM to 0.26 mM while at pH 6.5 the Km increases four-fold from 0.035 mM to 0.12 mM in the presence of calcium ions. Enteropeptidase activity is not inhibited by ethylenediaminetetra-acetate indicating that calcium ions are a non-essential cofactor for benzoylarginine ethyl ester hydrolysis.     

Hormone replacement therapy: a survey of Ontario physicians' prescribing practices

BACKGROUND: Although much has been written about hormone replacement therapy (HRT), there are few clearcut recommendations on its use. The purpose of this study was to determine Ontario physicians'' patterns of and reasons for prescribing HRT, their use of pretreatment investigations and their surveillance of HRT users, and to determine whether physicians'' reported practice is consistent with existing recommendations. METHODS: A self-administered questionnaire was mailed to a nonproportional stratified sample of 327 Ontario physicians (23.9% gynecologists, 76.1% general practitioners/family physicians [GP/FPs]). Outcome measures were ranking of reasons for prescribing HRT, nature of preliminary testing, regimens prescribed, duration of HRT and frequency of follow-up. RESULTS: The response rate was 60.9% overall (70.9% of the gynecologists, 58.3% of the GP/FPs). Prevention of osteoporosis was reported by 97.4% as an important or very important reason for prescribing HRT; prevention of coronary artery disease was important or very important for 89.3%. When considering whether or not to prescribe HRT, 97.3% stated that breast cancer was an important or very important factor. When presented with hypothetical cases, 97.0% stated that they would prescribe combined estrogen-progestin for a symptomatic woman with an intact uterus; 13.6% stated that they would do so for a woman with no uterus. Most reported that they would prescribe HRT for 12 or more years (73.3%) and would follow up patients every 1 to 2 years (70.6%). INTERPRETATION: Despite controversy about HRT in the published literature, the Ontario physicians surveyed reported similar reasons and patterns of prescribing, pretreatment investigations, and surveillance of postmenopausal women using HRT. These results suggest that Ontario physicians'' knowledge about HRT is consistent with recommendations in the published literature.