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C Lim

Publications and source records attributed to C Lim.

At least 55 records · Page 3Linked to original sources
PubMed1999

Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI.

The multiconformer nature of solution nuclear magnetic resonance (NMR) structures of proteins results from the effects of intramolecular dynamics, spin diffusion and an uneven distribution of structural restraints throughout the molecule. A delineation of the former from the latter two contributions is attempted in this work for an ensemble of 15 NMR structures of the protein Escherichia coli ribonuclease HI (RNase HI). Exploration of the dynamic information content of the NMR ensemble is carried out through correlation with data from two crystal structures and a 1.7-ns molecular dynamics (MD) trajectory of RNase HI in explicit solvent. Assessment of the consistency of the crystal and mean MD structures with nuclear Overhauser effect (NOE) data showed that the NMR ensemble is overall more compatible with the high-resolution (1.48 A) crystal structure than with either the lower-resolution (2.05 A) crystal structure or the MD simulation. Furthermore, the NMR ensemble is found to span more conformational space than the MD simulation for both the backbone and the sidechains of RNase HI. Nonetheless, the backbone conformational variability of both the NMR ensemble and the simulation is especially consistent with NMR relaxation measurements of two loop regions that are putative sites of substrate recognition. Plausible side-chain dynamic information is extracted from the NMR ensemble on the basis of (i) rotamericity and syn-pentane character of variable torsion angles, (ii) comparison of the magnitude of atomic mean-square fluctuations (msf) with those deduced from crystallographic thermal factors, and (iii) comparison of torsion angle conformational behavior in the NMR ensemble and the simulation. Several heterogeneous torsion angles, while adopting non-rotameric/syn-pentane conformations in the NMR ensemble, exist in a unique conformation in the simulation and display low X-ray thermal factors. These torsions are identified as sites whose variability is likely to be an artifact of the NMR structure determination procedure. A number of other torsions show a close correspondence between the conformations sampled in the NMR and MD ensembles, as well as significant correlations among crystallographic thermal factors and atomic msf calculated from the NMR ensemble and the simulation. These results indicate that a significant amount of dynamic information is contained in the NMR ensemble. The relevance of the present findings for the biological function of RNase HI, protein recognition studies, and previous investigations of the motional content of protein NMR structures are discussed.

Cluster Analysis↗
PubMed1999

Ribavirin polarizes human T cell responses towards a Type 1 cytokine profile.

BACKGROUND/AIMS: The therapeutic benefit of ribavirin, a nucleoside analog, in the treatment of chronic HCV infection is seen even in the absence of any apparent direct antiviral effect. We surmised that ribavirin may act by eliciting altered virus-specific immune responses. Because antiviral immunity is predominantly mediated by cytotoxic T cells and antiviral cytokines, we sought to determine whether ribavirin could promote antiviral (Type 1) cytokine expression in human T cells. METHODS: Isolated human T cells were activated in vitro with enterotoxin B or with phorbol ester plus ionomycin. Cytokine ELISAs were performed on culture supernatants, cytokine mRNA was detected following RT-polymerase chain reaction of T cell RNA, and T cell proliferation measured using MTT assay. RESULTS: Ribavirin enhanced a Type 1 (IL-2, IFNgamma, TNFalpha) while suppressing a Type 2 cytokine response (IL-4, IL-5 and IL-10), at the level of both protein and mRNA expression. Ribavirin mediated comparable effects on cytokine expression both following activation of specific T cell subpopulations with superantigen and following activation of a larger percentage of T cells via pharmacologic means. The in vitro effect on cytokine expression following ribavirin treatment was comparable in both CD4+ or CD8+ T cell subsets and was observed in a dose range that promoted T cell proliferation. CONCLUSIONS: These data support the view that ribavirin promotes a Type 1 cytokine-mediated immune response, a property which may account in part for its ability to enhance the antiviral activity of interferon-alpha in the treatment of chronic HCV infection.

Antiviral Agents↗
PubMed1999

Increased potency of an aptameric G-rich oligonucleotide is associated with novel functional properties of phosphorothioate linkages.

We previously showed that inhibition of the expression of CD28 (an essential immune receptor on T cells) mediated by a phosphorothioate (PS)-modified aptameric oligodeoxynucleotide (ODN) sequence, GR1, resulted in reduced T cell responses in vitro and in vivo. Using GR1 sequences differing only in the amount of terminal PS linkages (chimeric SO-ODN), the present study demonstrated that even after a substantial reduction in PS linkages, this 18-mer ODN sequence could still confer functionality in the ODN-mediated inhibition of CD28 expression. We showed that secondary structure and full retention of the ability to form a specific protein-ODN complex and to increase cellular uptake in activated Jurkat T cells were critical parameters in the determination of the magnitude of bioactivity of chimeric SO-ODN. We report that a chimeric SO-ODN with terminal PS linkages that total 9 (ICN 17221) or 12 (ICN 17263) was sufficient to inhibit CD28 expression and suppress in vivo inflammatory ear responses to contact allergen in mice with similar potency to the 17-thioate S-ODN (ICN 16064). Interestingly, all chimeric SO-ODN showed similar in vitro nuclease resistance. These data suggest alternate functional properties for PS linkages, unrelated to nuclease resistance, in enhancing the bioactivity of a G-rich aptamer.

Animals↗
PubMed1999

Effect of eradication of Helicobacter pylori on the benign gastric ulcer recurrence--a 24 month follow-up study.

OBJECTIVES: To evaluate the effect of eradication of Helicobacter pylori (H. pylori) on the recurrence of benign gastric ulcer (BGU) in the patients with BGU. METHODS: This study was performed for 40 H. pylori-positive BGU patients cured of BGU and H. pylori eradicated, and for 25 H. pylori-positive patients (non-eradicated group) who were not treated with H. pylori eradication regimen or H. pylori was not eradicated. Four different methods--CLOtest, microscopy of Gram stained mucosal smear, culture and histology of modified Giemsa staining--were taken for identifying colonization of H. pylori before treatment, and 4 weeks after completion of triple therapy. For the control group in which triple therapy was not tried, follow-up gastroscopy was done to confirm the healing of the ulcer. To detect BGU recurrence, the gastroscopy was performed at 6, 12, 18, and 24 months after therapy. RESULTS: In the non-eradicated group, the BGU recurrence rate was 16% within 6 months, 40% within 1 year, 56% within 18 months and 60% within 2 years. The respective recurrence rates in the 40 patients in whom the bacteria had been eradicated were 0%, 7.5%, 10% and 10% (4 patients), respectively. Among the four BGU-recurred patients in whom H. pylori had been eradicated, one patient was found to have BGU recurring with H. pylori positive again in one year, and another two patients had NSAIDs ingestion history. CONCLUSION: The eradication of H. pylori in patients with BGU reduces the recurrence of BGU. In addition, the major causes of BGU recurrence look like NSAIDs ingestion and reinfection of H. pylori.

Adult↗
PubMed1998

Undescended testes: incidence in 1,002 consecutive male infants and outcome at 1 year of age.

In a study of 1,002 consecutive Malaysian male newborns, 48 (4.8%) were found to have undescended testes (UDT). The rate and laterality of the UDT were associated with lower birth weight (P < 0.001) and prematurity (P < 0.001). Boys with UDT were also more likely to have other congenital abnormalities of the external genitalia, the commonest being hydrocele. No correlation between UDT and maternal age, birth order, social class, or mode of delivery was demonstrated in this study. Although 26/34 (76.5%) of UDT achieved full spontaneous descent by 1 year of age, 1.1% of all infants whose testes remained undescended required regular long-term follow-up with surgical referral and correction at an appropriate time. A premature infant with UDT is more likely to achieve full testicular descent at 1 year of age than a term infant.

Birth Rate↗
PubMed1998

Prediction of an anti-IgE binding site on IgE.

A combination of computation techniques have been used to determine the binding site and amino acid residues on IgE that are critical for binding to a therapeutic anti-IgE. Homology modeling was used to model parts of IgE and of an antibody that binds to IgE. Docking simulations using shape descriptions were then carried out using the models to determine which residues in the IgE are involved in the binding interaction. The anti-IgE has been determined to bind close to some of the residues that are believed to be in the Fc(epsilon)RI receptor site on IgE, therefore preventing IgE from binding to Fc(epsilon)RI on mast cells and basophils and causing the release of pharmacologic mediators from these cells. Experiments have been suggested to verify the binding site and the residues involved in binding to anti-IgE.

Amino Acid Sequence↗
PubMed1997

Connections of the hippocampal formation in humans: I. The mossy fiber pathway.

The hippocampal formation has been one of the most extensively studied cortical regions in rats, yet little is known about the anatomical connections of the hippocampus in primates, especially humans. With the use of an antibody against the calcium-binding protein, calbindin-D28K, in normal autopsy tissue and the neuronal tracers biocytin or biotinylated dextrans in in vitro slice preparations from tissue removed during surgery for intractable epilepsy, we examined the human hippocampal mossy fiber pathway. The injections of biocytin into the dentate granule cell layer labeled neurons in a Golgi-like manner, revealing the presence of basal dendrites on about 30% of the granule cells. The granule cell axons, the mossy fibers, initially formed a diffuse plexus of fibers in the polymorphic layer before organizing into fiber fascicles in the hilar pyramidal region. These fiber fascicles were much more prominent rostrally than caudally. Within the hilus and proximal portions of the extrahilar CA3 field, the mossy fibers ran through the pyramidal cell layer, and while near the transition to field CA2, the fibers turned superficially and crossed the pyramidal layer to run in the stratum lucidum. All of these features, seen following injections of tracer into hippocampal slices from the brains of epileptics, were confirmed by calbindin-staining of mossy fibers in normal brains. Biocytin-labeled mossy fiber axons revealed two characteristic types of enlargements: small varicosities and larger expansions. The expansions were found throughout the neuropil and were highly irregular, diaminobenzidine-dense profiles that had pleiomorphic modes of attachment to the parent axon. Electron microscopic images of these biocytin labeled expansions revealed that they were large synaptic boutons bearing asymmetric synapses. This study indicates that the human mossy fiber pathway shows some minor deviations from the rodent brain but little difference from monkeys. We argue that these changes mirror a phylogenetic growth of the CA3 pyramidal neurons (subfield CA3c) into the hilus rather than an evolutionary change of the mossy fiber pathway. This growth of subfield CA3c and the increase in mossy fibers running through the pyramidal layer (and a presumed accompanying increase in proximal basal dendritic contacts) may reflect a growing role of the projection from the dentate granule cells to subfield CA3c and from there to field CA1 in the primate hippocampus.

Adult↗
PubMed1997

Connections of the hippocampal formation in humans: II. The endfolial fiber pathway.

We investigated the anatomical connections of the pyramidal neurons located within the hilar region of the dentate gyrus of the human hippocampus, neurons which do not have a rodent equivalent. The myeloarchitectural patterns of the human hippocampus indicated the presence of a distinct fiber pathway, the endfolial fiber pathway, in the stratum oriens of the hilus and field CA3. By using the fluorescent lipophilic dye DiI in formalin-fixed human hippocampal tissue, we demonstrated that this is a continuous fiber pathway between the deep hilar region and CA2. This fiber pathway did not enter the fimbria or alveus along the entire distance of the traced pathway and ran exclusively in the stratum oriens of the hilus and CA3. Tracing studies with biocytin in in vitro human hippocampal slices indicated that the hilar and CA3 pyramidal neurons contributed to this pathway. Out distally in field CA3, the long transverse fibers became short and choppy, suggesting that they were beginning to move out of the plane of the tissue slice. Numerous fibers from this pathway were seen crossing the pyramidal layer. Based on comparative studies, we propose that the endfolial fiber system is a component of the hilar Schaffer collateral system in humans. The presence of a significant Schaffer collateral system from the pyramidal neurons in the hilar region would indicate that these neurons are anatomically related to the CA3 pyramidal neurons. Therefore, we suggest the inclusion of the human hilar pyramidal neurons within Lorente de No's field CA3 and, in particular, within subfield CA3c.

Adult↗
PubMed1997

Oligonucleotide-mediated inhibition of CD28 expression induces human T cell hyporesponsiveness and manifests impaired contact hypersensitivity in mice.

Ligation of CD28 provides a costimulatory signal essential for Ag-mediated T cell activation via the TCR. Blocking CD28 ligation can inhibit cytokine expression and elicits a state of T cell hyporesponsiveness. In this study, we examined the effect of inhibiting CD28 expression on in vitro and in vivo T cell responses. To address this, we have synthesized a series of G-rich phosphorothioate oligonucleotides that inhibited activation-induced transcription and cell surface expression of CD28 on human T cells. CD28 blockade was selective, as expression of other activation-induced receptors was unaffected by oligonucleotide treatment. Using strategic changes to base composition, we identified a minimal 12-mer sequence, containing two sets of four contiguous guanosines separated by 3 to 5 bases, which conferred activity in vitro. Furthermore, inhibition of CD28 expression mediated by one representative active oligonucleotide, GR1, resulted in a concomitant dose-dependent diminution of anti-CD3/PMA-induced cytokine (IL-2, IFN-gamma, IL-8) production. Inhibition of IL-2 synthesis was dependent on CD28 expression, as GR1 failed to abrogate activated IL-2 production in a CD28-deficient T cell line, HUT 78. The inhibitory activity of GR1 reduced T cell proliferative responses in MLR and induced Ag-specific T cell hyporesponsiveness to alloantigens. Finally, s.c. administration of GR1 impaired in vivo contact hypersensitivity responses in mice and was associated with substantially decreased CD28 and IFN-gamma mRNA expression in lymph node cells. Collectively, our studies show the tolerogenic potential of oligonucleotide-mediated CD28 inhibition on T cell activation, in vitro and in vivo.

Animals↗
PubMed1997

Grit blasting and the marginal accuracy of two ceramic veneer systems--a pilot study.

STATEMENT OF PROBLEM: Margins of ceramic restorations can be damaged during removal of investment materials with grit blasting and result in relatively large marginal discrepancies and excessive marginal discrepancies with greater exposure of cement to the oral environment. Subsequent dissolution of cement can encourage plaque retention, dental caries, and periodontal problems. PURPOSE: This study compared marginal adaptation of ceramic veneers created by the refractory die technique (R), Dicor glass ceramic technique (D), and effects of grit blasting on their margins. MATERIAL AND METHODS: Two groups of ceramic veneers were constructed for each system, one without grit blasting (R g and D g) and one with grit blasting (R+g and D+g). RESULTS: Statistical analyses revealed that grit blasting had a greater effect in reducing marginal accuracy for Dicor ceramic veneers compared with refractory die ceramic veneers.

Air↗
PubMed1997

Accuracy and precision of NMR relaxation experiments and MD simulations for characterizing protein dynamics.

Model-free parameters obtained from nuclear magnetic resonance (NMR) relaxation experiments and molecular dynamics (MD) simulations commonly are used to describe the intramolecular dynamical properties of proteins. To assess the relative accuracy and precision of experimental and simulated model-free parameters, three independent data sets derived from backbone 15N NMR relaxation experiments and two independent data sets derived from MD simulations of Escherichia-coli ribonuclease HI are compared. The widths of the distributions of the differences between the order parameters for pairs of NMR data sets are congruent with the uncertainties derived from statistical analyses of individual data sets; thus, current protocols for analyzing NMR data encapsulate random uncertainties appropriately. Large differences in order parameters for certain residues are attributed to systematic differences between samples for intralaboratory comparisons and unknown, possibly magnetic field-dependent, experimental effects for interlaboratory comparisons. The widths of distributions of the differences between the order parameters for two NMR sets are similar to widths of distributions for an NMR and an MD set or for two MD sets. The linear correlations between the order parameters for an MD set and an NMR set are within the range of correlations observed between pairs of NMR sets. These comparisons suggest that the NMR and MD generalized order parameters for the backbone amide N-H bond vectors are of comparable accuracy for residues exhibiting motions on a fast time scale (< 100 ps). Large discrepancies between NMR and MD order parameters for certain residues are attributed to the occurrence of "rare" motional events over the simulation trajectories, the disruption of an element of secondary structure in one of the simulations, and lack of consensus among the experimental data sets. Consequently, (easily detectable) severe distortions of local protein structure and infrequent motional events in MD simulations appear to be the most serious artifacts affecting the accuracy and precision, respectively, of MD order parameters relative to NMR values. In addition, MD order parameters for motions on a fast (< 100 ps) timescale are more precisely determined than their NMR counterparts, thereby permitting more detailed dynamic characterization of biologically important residues by MD simulation than is sometimes possible by experimental methods. Proteins 28:481-493, 1997.

Computer Simulation↗
PubMed1996

Positive charge at position 549 is essential for phosphatidylinositol 4,5-bisphosphate-hydrolyzing but not phosphatidylinositol-hydrolyzing activities of human phospholipase C delta1.

Point mutagenesis, phosphatidylinositol (PI), and phosphatidylinositol 4,5-bisphosphate (PIP2) hydrolysis assays and equilibrium centrifugation PIP2 assays were used to study the functional roles of four highly conserved arginine residues in the Y region of human phospholipase C delta1 (PLCdelta1) (Arg-527, -549, -556, -701). Most of the mutant enzymes were either partially defective or fully active in their abilities to catalyze the hydrolysis of PI or PIP2. However, upon substitution of Arg-549 by glycine or histidine, the mutant enzyme was defective in its ability to catalyze the hydrolysis of PIP2, but it is still able to hydrolyze PI. Replacing Arg-549 with lysine had little effect on the level of PI and PIP2 hydrolytic activities of the mutant enzyme. The residual PIP2 hydrolyzing activity of R549H is highly dependent on pH. R549H showed 5-10% of the PIP2-hydrolyzing activity of the native enzyme between pH 5 and 7 and nondetectable PIP2-hydrolyzing activity at pH 8. The PIP2-hydrolyzing activity of R549G was not detectable at all pH values. Kinetic analysis of PLCdelta1-catalyzed PIP2 hydrolysis revealed that the micellar dissociation constant Ks and interfacial Michaelis constant Km were similar in the native, R549K, and R549H enzymes; but the specific activity at the saturated substrate mole fraction and infinite level of substrate (Vmax) of the R549H mutant were reduced by a factor of 15. PIP2 competitively inhibits the native enzyme to hydrolyze PI at both pH 7 and 8. However, PIP2 inhibits R549H only at pH 7.0 and does not inhibit R549G at either pH. Taken together, these results suggest that positive charge at position 549 of PLCdelta1 protein is essential for the enzyme to recognize and catalyze the hydrolysis of PIP2 but not PI.

Calcium↗
PubMed1996

Significance of intermittency in men with lower urinary tract symptoms.

OBJECTIVES: To determine the relationship between the symptom of intermittency, objective evidence of intermittency on uroflow traces, benign prostatic enlargement, and bladder outlet obstruction (BOO) in men with lower urinary tract symptoms (LUTS). METHODS: The prevalence of the symptom of intermittency was determined from a symptom questionnaire in 165 men presenting with LUTS. Objective evidence of intermittency during voiding was assessed from uroflow traces, and prostate volume was measured by transrectal ultrasound. Combined pressure-flow studies were performed to determine the presence or absence of BOO. RESULTS: There was relatively poor agreement between the symptom of intermittency and objective evidence of its presence. Of the 35 patients who reported intermittency most or all of the time, 21 showed no objective evidence of intermittency on uroflowmetry. The symptom of intermittency was not significantly related to the presence of BOO (P = 0.42) and the group-specific urethral resistance factor (URA) did not differ significantly (P = 0.87) between those men who complained of intermittency and those who did not (median URA, 35 versus 32 cm H2O). However, objective evidence of intermittency on uroflow traces was significantly related to BOO (P = 0.016), and those patients with objective evidence of intermittency had higher URA values (median, 43 versus 32 cm H2O). Objective evidence of intermittency had a specificity of 98% and positive predictive value of 92% for the presence of BOO. Neither the symptom of intermittency nor objective evidence of its presence was significantly related to prostate size. CONCLUSIONS: Although the symptom of intermittency does not seem to be related to BOO or prostate size, objective evidence of intermittency on flow curve traces is specific for outflow obstruction, and as such its presence could potentially be of value in the assessment of men with lower urinary tract symptoms.

Aged↗
PubMed1996

The value of multiple free-flow studies in men with lower urinary tract symptoms.

OBJECTIVE: To assess the variability of free-flow studies in men presenting with lower urinary tract symptoms (LUTS) suggestive of benign prostatic obstruction (BPO) and to determine the sensitivity, specificity and predictive values of consecutive measurements of maximum flow rate for the presence of bladder outlet obstruction (BOO) at several threshold values. PATIENTS AND METHODS: The value of multiple free-flow studies was assessed in 165 men presenting with LUTS suggestive of BPO. Each patient was requested to void four times into a uroflowmeter and the voided volume and post-void residual urine volume (PVR) were also measured. The variability of the maximum flow rate (Qmax), voided volume and PVR between consecutive voids was assessed. In addition, the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of various thresholds of Qmax for the presence of BOO were calculated for each consecutive void. RESULTS: The mean Qmax on void 1 was 10.2 mL/s and the mean maximum value for Qmax between voids 1 and 2 was 12.5 mL/s. For voids 1, 2 and 3, the mean maximum Qmax was 13.9 mL/s and for voids 1 to 4 it was 15.2 mL/s. There were no significant changes in PVR among any of these voids. There was a statistically significant, although small, decrease in voided volume between voids 1 to 3 and voids 1 to 4. The specificity and PPV of Qmax for BOO increased with each subsequent void, such that using a threshold value for Qmax of 10 mL/s on the fourth void, the specificity and PPV for BOO were 96% and 93%, respectively. CONCLUSIONS: There was a significant increase in Qmax with each successive void when men with LUTS suggestive of BPO performed multiple free-flow measurements and consequently, single free-flow measurements substantially underestimated the maximum Qmax that these patients achieved. The specificity and PPV of Qmax for BOO can be improved considerably by performing multiple free-flow studies and by carefully selecting an appropriate threshold value (although whether pressure-flow studies are unnecessary will depend on what level of specificity and PPV is deemed acceptable in clinical practice). These findings should be considered if free-flow studies are to be used as the basis for deciding the clinical management of men with LUTS and may be particularly useful for urologists with limited facilities for pressure-flow studies.

Aged↗
PubMed1996

The significance of terminal dribbling in men with lower urinary tract symptoms.

OBJECTIVE: To determine the relationship between the symptom of terminal dribbling, objective evidence of terminal dribbling on recordings of uroflow, benign prostatic enlargement (BPE) and bladder outlet obstruction (BOO) in men with lower urinary tract symptoms (LUTS). PATIENTS AND METHODS: The prevalence of the symptom of terminal dribbling was determined from a symptom questionnaire completed by 165 men presenting with LUTS. Objective evidence of terminal dribbling during voiding was assessed from uroflow recordings and prostate volume was measured by transrectal ultrasonography. Combined pressure-flow studies were performed to determine the presence or absence of BOO. RESULTS: There was relatively poor agreement between the symptom of terminal dribbling and objective evidence of its presence; 48% of the patients who reported terminal dribbling most or all of the time showed no objective evidence of terminal dribbling on uroflowmetry. The symptom of terminal dribbling was not significantly related to the presence of BOO (P = 0.74) and the group-specific urethral resistance factor (URA) did not differ significantly (P = 0.79) between those men who complained of terminal dribbling and those who did not (median URA 33 and 31 cmH2O, respectively). However, objective evidence of terminal dribbling on uroflow traces was significantly related to BOO (P < 0.001) and those patients with objective evidence of terminal dribbling had higher values of URA (median 39 compared with 28 cmH2O). Objective terminal dribbling had a specificity of 92% and positive predictive value of 88% for the presence of BOO. Neither the symptom of terminal dribbling nor objective evidence of its presence were significantly related to prostatic enlargement. CONCLUSION: While the symptom of terminal dribbling is probably not related to BOO or prostatic enlargement, objective evidence of terminal dribbling on flow curve recording is specific for BOO and as such, its presence could potentially be of value in the assessment of men with LUTS.

Aged↗
PubMed1996

The binding mode of an E-64 analog to the active site of cathepsin B.

Two binding modes of the isobutyl-NH-Eps-Leu-Pro inhibitor to cathepsin B have been proposed. Molecular docking using an empirical force field was carried out to distinguish between the two modes. The search began with manual docking, followed by random perturbations of the docking conformation and cycles of Monte Carlo minimization. Finally, molecular dynamics was carried out for the most favorable docking conformations. The present calculations predict that the isobutyl-NH-Eps-Leu-Pro inhibitor preferentially binds to the S' rather than the S subsites of cathepsin B. The S' binding mode prediction is supported by the X-ray crystal structure of cathepsin B bound to a closely related ethyl-O-Eps-Ile-Pro inhibitor, which was found to bind in the S'subsite with the C-terminal epoxy ring carbon making a covalent bond to the sulfur atom of Cys29. This agreement, in turn, validates our docking strategy. Furthermore, the calculations provide evidence that the dominant contribution to the total stabilization energy of the enzyme-inhibitor complex stems from the strong electrostatic interaction between the negatively charged C-terminal carboxylate group of the ligand and the positively charged imidazolium rings of His110 and His111. The latter are stabilized and held in an optimal orientation for interactions with the C-terminal end of the ligand through a salt bridge between the side chains of His110 and Asp22. By comparison with the crystal structure, some insight into the specificity of the epoxyldipeptide family towards cathepsin B inhibition has been extracted. Both the characteristics of the enzyme (e.g. subsite size and hydrophobicity) as well as the nature of the inhibitor influence the selectivity of an inhibitor towards an enzyme.

Binding Sites↗
PubMed1996

The obstructive effect of a urethral catheter.

PURPOSE: The effect of a urethral catheter on pressure-flow relationships of the urethra has important implications for the practice to this question in the past in men with benign prostatic hyperplasia. We assessed the obstructive effect of an 8 Ch. urethral catheter in men who presented with lower urinary tract symptoms due to benign prostatic hyperplasia. MATERIALS AND METHODS: During combined pressure-flow studies 59 men completed 2 voids of similar volume with and without a urethral catheter in situ. Maximum flow rate, detrusor pressure at maximum flow and the group of specific urethral resistance factor were measured and compared between these 2 voids. RESULTS: There was no significant difference in maximum flow rate between voids (with catheter 9.1 ml. per second versus without catheter 8.6 ml. per second). Although detrusor pressure was significantly greater with the urethral catheter in situ (80 versus 67 cm. water), voids (with catheter 42.1 cm, water versus without catheter 36.6 cm water). CONCLUSIONS: A 8 Ch. catheter does not appear to have a significant obstructive effect in the urethra. This finding has important implications for the practice and interpretation of pressure-flow studies.

Aged↗