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Biomedical subjects

R Brem

Publications and source records attributed to R Brem.

10 recordsLinked to original sources
PubMed2003

Inhibition of proliferation by 1-8U in interferon-alpha-responsive and non-responsive cell lines.

Interferon (IFN)-inducible proteins of the 1-8 gene family mediate homotypic adhesion and transduction of antiproliferative signals. Their induction correlates with inhibition of cell growth while they are often repressed in the course of malignant transformation and tumor development. Ras-mediated transformation of mouse mast cells is associated with downregulation of 1-8U expression and interferon-alpha (IFN-alpha) treatment reverts the proliferation rate to normal levels together with induction of 1-8U. Conversely, the antiproliferative responses of IFN-alpha in sensitive human melanoma cells are accompanied by 1-8U induction. Here we provide direct evidence that recombinant expression of 1-8U in human cell lines is sufficient to block cell proliferation. Based on the abundant expression and subcellular localization to the plasma membrane and exosome-like structures, we propose a model capable of explaining the pleiotropic functions of 1-8 family proteins in tumor cells and during normal development.

Animals↗
PubMed2001

Global analysis of differential gene expression after transformation with the v-H-ras oncogene in a murine tumor model.

Mouse PB-3c mast cells stably transfected with the v-H-ras oncogene induce tumor formation in vivo when implanted into mice. Such tumor cells are characterized by an autocrine IL-3 loop. DNA microarrays allow simultaneous transcript imaging of several thousand genes and the technique was applied in this tumor model to analyse gene expression following malignant transformation. Using three independent tumor lines derived from the same precursor the expression of about 400 out of 11 000 genes was modulated in each tumor. A subset of only 75 genes (0.68%) is shared and up- or downregulated in all three lines. A significant portion of this gene pool possesses functions related to tumorigenesis such as cell adhesion, signaling or transcriptional regulation. Apart from a number of expressed sequence tags (EST's) we find downregulation of four interferon-inducible genes in the tumor lines. Finally, when we extrapolate our data to the complete mouse genome, we estimate that about 500 genes are differentially expressed in tumor cells compared to the precursor cell PB-3c.

Animals↗
PubMed1999

The effect of multiple binding modes on empirical modeling of ligand docking to proteins.

A popular approach to the computational modeling of ligand/receptor interactions is to use an empirical free energy like model with adjustable parameters. Parameters are learned from one set of complexes, then used to predict another set. To improve these empirical methods requires an independent way to study their inherent errors. We introduce a toy model of ligand/receptor binding as a workbench for testing such errors. We study the errors incurred from the two state binding assumption--the assumption that a ligand is either bound in one orientation, or unbound. We find that the two state assumption can cause large errors in free energy predictions, but it does not affect rank order predictions significantly. We show that fitting parameters using data from high affinity ligands can reduce two state errors; so can using more physical models that do not use the two state assumption. We also find that when using two state models to predict free energies, errors are more severe on high affinity ligands than low affinity ligands. And we show that two state errors can be diagnosed by systematically adding new binding modes when predicting free energies: if predictions worsen as the modes are added, then the two state assumption in the fitting step may be at fault.

Computer Simulation↗
PubMed1998

Contributions of orientation and hydrogen bonding to catalysis in Asn229 mutants of thymidylate synthase.

We have determined structures of binary and ternary complexes of five Asn229 variants of thymidylate synthase (TS) and related their structures to the kinetic constants measured previously. Asn229 forms two hydrogen bonds to the pyrimidine ring of the substrate 2'-deoxyuridine-5'-monophosphate (dUMP). These hydrogen bonds constrain the orientation of dUMP in binary complexes with dUMP, and in ternary complexes with dUMP and the TS cofactor, 5,10-methylene-5,6,7,8-tetrahydrofolate. In N229 mutants, where these hydrogen bonds cannot be made, dUMP binds in a misoriented or more disordered fashion. Most N229 mutants exhibit no activity for the dehalogenation of 5-bromo-dUMP, which requires correct orientation of dUMP against Cys198. Since bound dUMP forms the binding surface against which the pterin ring of cofactor binds, misorientation of dUMP results in higher Km values for cofactor. At the same time, binding of the cofactor aids in ordering and positioning dUMP for catalysis. Hydrophobic mutants, such as N229I, favor an arrangement of solvent molecules and side-chains around the ligands similar to that in a proposed transition state for ternary complex formation in wild-type TS, and kcat values are similar to the wild-type value. Smaller, more hydrophilic mutants favor arrangements of the solvent and side-chains surrounding the ligands that do not resemble the proposed transition state. These changes correspond to decreases in kcat of up to 2000-fold, with only modest increases in Km or Kd. These results are consistent with the proposal that the hydrogen-bonding network between water, dUMP and side-chains in the active-site cavity contributes to catalysis in TS. Asn229 has the unique ability to maintain this critical network, without sterically interfering with dUMP binding.

Asparagine↗
PubMed1997

Diffusion imaging of human breast.

It is shown that diffusion-weighted imaging is possible in the human breast. Diffusion constants were measured in the breast parenchyma of four volunteers with no known breast lesions. The apparent diffusion constant of water measured in regions of interest chosen in normal human breast fibroglandular tissue was 1.64 +/- 0.19 x 10(-5) cm2/S and that measured in the area of fatty breast tissue was 0.32 +/- 0.18 x 10(-5) cm2/S. The resulting images indicate that fibroglandular tissue and fat can be clearly distinguished in diffusion-weighted as well as in absolute diffusion images of the breast. Potential future applications of this technology for the study of breast pathologies are suggested.

Adipose Tissue↗
PubMed1995

Designing amino acid sequences to fold with good hydrophobic cores.

We present two methods for designing amino acid sequences of proteins that will fold to have good hydrophobic cores. Given the coordinates of the desired target protein or polymer structure, the methods generate sequences of hydrophobic (H) and polar (P) monomers that are intended to fold to these structures. One method designs hydrophobic inside, polar outside; the other minimizes an energy function in a sequence evolution process. The sequences generated by these methods agree at the level of 60-80% of the sequence positions in 20 proteins in the Protein Data Bank. A major challenge in protein design is to create sequences that can fold uniquely, i.e. to a single conformation rather than to many. While an earlier lattice-based sequence evolution method was shown not to design unique folders, our method generates unique folders in lattice model tests. These methods may also be useful in designing other types of foldable polymer not based on amino acids.

Amino Acid Sequence↗
PubMed1985

Time course of alpha-1-acid glycoprotein and its relation to myocardial enzymes after acute myocardial infarction.

The acute phase reactant, alpha-1-acid glycoprotein, binds to a number of basic antiarrhythmic drugs, including lidocaine, quinidine, propranolol, imipramine and disopyramide. Binding to alpha-1-acid glycoprotein accounts for a decrease in free drug fraction and may alter the expected concentration: response relation of drugs particularly when there are unpredictably large or rapid changes in alpha-1-acid glycoprotein. To determine the time course and magnitude of alpha-1-acid glycoprotein for 1 month after acute myocardial infarction (AMI), blood samples were collected from 27 patients, 14 with AMI and 13 with a chest pain syndrome but no AMI. Patients with AMI had a significant increase in alpha-1-acid glycoprotein after 72 hours (mean 153 +/- 35 mg/dl) (p less than 0.05), and the maximum was observed on day 7 (mean 165 +/- 53 mg/dl) (p less than 0.05), returning to baseline by 28 days. There was no significant change in alpha-1-acid glycoprotein in patients with chest pain but no AMI. Regression analysis showed a significant relation between creatine kinase (p less than 0.005) and lactic dehydrogenase (p less than 0.001) vs alpha-1-acid glycoprotein indicating alpha-1-acid glycoprotein concentration is high in patients with large AMI. Changes in binding resulting from alpha-1-acid glycoprotein during AMI could account for misinterpretation of total drug concentration and response to antiarrhythmic drugs acutely, during convalescence and at discharge.

Adult↗
PubMed1983

Antiarrhythmic plasma-concentration range of imipramine against ventricular premature depolarizations.

The antiarrhythmic plasma-concentration range of imipramine with desmethylimipramine was determined in 15 cardiac patients with ventricular arrhythmias. When more than 80% efficacy was reached, subjects' plasma concentrations of imipramine and desmethylimipramine were determined by gas chromatography. The imipramine dose required for suppression of ventricular premature depolarizations (VPDs) ranged from 50 to 400 mg a day (1.6 to 3.9 mg/kg/day). Peak plasma imipramine concentration was reached at 2.5 +/- 0.92 hr and peak plasma desmethylimipramine concentration at 4.1 +/- 2.8 hr after imipramine. At 80%, VPD suppression, mean steady-state plasma concentration of imipramine with desmethylimipramine ranged from 74 to 385 ng/ml. The ratio of plasma imipramine to desmethylimipramine ranged from 0.5 to 5.5 (median = 1.3). The elimination t1/2 for the parent compound, imipramine, ranged from 4 to 14.4 hr. Imipramine is an effective antiarrhythmic drug with sustained duration of action, although its elimination t1/2 is relatively short.

Adult↗
PubMedDate not supplied

Identification of metastasis-associated genes by transcriptional profiling of a metastasizing versus a non-metastasizing human melanoma cell line.

In order to identify genes associated with the metastatic phenotype we have compared the expression pattern of 6800 genes in a metastatic (NMCL-1) versus a non-metastatic (530) human melanoma cell line making use of DNA microarrays. The differentially expressed genes identified are involved in control of transcription, regulation of the cell-cycle, proteolysis, cell adhesion, immune response and signaling. A remarkable feature of the system under investigation is the consistent down-regulation of MHC-related and cell adhesion mediating genes in the metastatic cell line.

Animals↗