Biomedical subjects

A Svendsen

Publications and source records attributed to A Svendsen.

At least 37 records · Page 2Linked to original sources

PubMed1998

Active serine involved in the stabilization of the active site loop in the Humicola lanuginosa lipase.

We have investigated the binding properties of and dynamics in Humicola lanuginosa lipase (Hll) and the inactive mutant S146A (active Ser146 substituted with Ala) using fluorescence spectroscopy and molecular dynamics simulations, respectively. Hll and S146A show significantly different binding behavior for phosphatidylcholine (PC) and phosphatidylglycerol (PG) liposomes. Generally, higher binding affinity is observed for Hll than the S146A mutant. Furthermore, depending on the matrix, the addition of the transition state analogue benzene boronic acid increases the binding affinity of S146A, whereas only small changes are observed for Hll suggesting that the active site lid in the latter opens more easily and hence more lipase molecules are bound to the liposomes. These observations are in agreement with molecular dynamics simulations and subsequent essential dynamics analyses. The results reveal that the hinges of the active site lid are more flexible in the wild-type Hll than in S146A. In contrast, larger fluctuations are observed in the middle region of the active site loop in S146A than in Hll. These findings reveal that the single mutation (S146A) of the active site serine leads to substantial conformational alterations in the H. lanuginosa lipase and different binding affinities.

Alanine↗

PubMed1998

Scoring functions for computational algorithms applicable to the design of spiked oligonucleotides.

Protein engineering by inserting stretches of random DNA sequences into target genes in combination with adequate screening or selection methods is a versatile technique to elucidate and improve protein functions. Established compounds for generating semi-random DNA sequences are spiked oligonucleotides which are synthesised by interspersing wild type (wt) nucleotides of the target sequence with certain amounts of other nucleotides. Directed spiking strategies reduce the complexity of a library to a manageable format compared with completely random libraries. Computational algorithms render feasible the calculation of appropriate nucleotide mixtures to encode specified amino acid subpopulations. The crucial element in the ranking of spiked codons generated during an iterative algorithm is the scoring function. In this report three scoring functions are analysed: the sum-of-square-differences function s, a modified cubic function c, and a scoring function m derived from maximum likelihood considerations. The impact of these scoring functions on calculated amino acid distributions is demonstrated by an example of mutagenising a domain surrounding the active site serine of subtilisin-like proteases. At default weight settings of one for each amino acid, the new scoring function m is superior to functions s and c in finding matches to a given amino acid population.

Algorithms↗

PubMed1998

Effect of mutations in Candida antarctica B lipase.

Three variants of the Candida antarctica B lipase have been constructed and characterized. The variant containing the T103G mutation, which introduces the consensus sequence G-X-S-X-G found in most other known lipases, shows an increased thermostability but retains only half the specific activity of the native enzyme. Also in ester synthesis the activity is lowered but the specificity and enantioselectivity remains unchanged. The W104H mutant, in which more space is introduced into the active site, has more dramatically changed properties. Both the thermostability and the specific activity are slightly reduced but the activity and specificity in ester synthesis is highly different from the native enzyme. In general, the activity is very low and the enantioselectivity is, furthermore, highly reduced. Finally, the mutation M72L was introduced to increase the oxidation stability of the enzyme. This variant did exhibit an increased resistance towards oxidation but the thermostability was, unfortunately, also reduced.

Candida↗

PubMed1998

Bacteremia in nursing home patients. Prevalence among patients presenting to an emergency department.

OBJECTIVE: To measure the prevalence of bacteremia and any correlation between signs and symptoms, risk factors, and laboratory data in elderly patients. DESIGN: Prospective analysis. All patients were contacted by the study nurse at 48 hours and 7 days after study entry. SETTING: Adult tertiary care hospital with an emergency department managing 48,000 visits yearly in a metropolitan area of 250,000. PARTICIPANTS: Members of the study population referred to the emergency department for medical or surgical problems. Of 113 nursing home patients, blood culture results were available for 111. MAIN OUTCOME MEASURES: Blood cultures were obtained by standard protocol. Demographic and medical information was collected from the medical record. Three groups of patients were compared with respect to symptoms, risk factors, laboratory data, and outcome. RESULTS: Group 1 (n = 86) had two sets of negative blood cultures. Group 2 (n = 10) had true-positive cultures. Group 3 (n = 15) had false-positive cultures of Staphylococcus epidermidis. The prevalence of bacteremia was 9.8% in the study population. No risk factors were predictive of bacteremia. Great variation in signs and symptoms were noted in all three groups, none correlating with bacteremia. Although seven of the 10 patients with positive cultures were febrile, this association did not reach statistical significance. All groups had high admission (> 50%) and mortality (20% to 37%) rates. CONCLUSIONS: The prevalence of bacteremia in the nursing home population presenting to the emergency department was 9.8%. The symptoms and signs of bacteremia in this population were variable and nonspecific. The high rate of false-positive cultures in this setting is of concern.

Adult↗

PubMed1997

An enzyme linked immunosorption assay for tissue factor pathway inhibitor.

An assay for the quantification of full-length and carboxy-terminus truncated tissue factor pathway inhibitor (TFPI) has been developed. The assay is a classical two-antibody sandwich assay with a monoclonal capture antibody directed against the third Kunitz-type domain of human TFPI and a polyclonal rabbit peroxidase-labelled anti-human TFPI detecting antibody. The assay is sensitive to full-length and carboxy-terminus truncated TFPI with intact third Kunitz-type domain, but not to two-domain TFPI. TFPI associated with lipoproteins is not or only sparsely detected and TFPI in complex with factor Xa only partially measured. The assays gives linear reference curves in the dose range of 5 to 100 ng/ml in a double logarithmic plot. The normal range assessed from analyses on citrated plasma from 81 normal human donors is 7.8 to 26.0 ng/ml (average +/- 2 SD, log-normal distribution). There is no statistically significant difference between TFPI levels measured in 10 fasting and 10 non-fasting individuals. The reproducibility of the assay is about 5.6-5.9% (relative standard error) and the within-days and between-day reproducibilities are 4.7-5.1% and 5.9-8.5%, respectively. The assay is in very good agreement with a commercial ELISA assay recently marketed. A robust, reproducible and convenient ELISA assay for the determination of full-length and three-domain TFPI has been developed.

Animals↗

PubMed1997

Computational studies of the activation of lipases and the effect of a hydrophobic environment.

We have investigated the activation pathway of three wild type lipases and three mutants using molecular dynamics techniques combined with a constrained mechanical protocol. The activation of these lipases involves a rigid body hinge-type motion of a single helix, which is displaced during activation to expose the active site and give access to the substrate. Our results suggest that the activation of lipases is enhanced in a hydrophobic environment as is generally observed in experiments. The energy gain upon activation varies between the different lipases and depends strongly on the distribution of the charged residues in the activating loop region. In a low dielectric constant medium (such as a lipid environment), the electrostatic interactions between the residues located in the vicinity of the activating loop (lipid contact zone) are dominant and determine the activation of the lipases. Calculations of the pKas qualitatively indicate that some titratable residues experience significant pK shifts upon activation. These calculations may provide sufficient details for an understanding of the origin and magnitude of a given electrostatic effect and may provide an avenue for exploring the activation pathway of lipases.

Binding Sites↗

PubMed1997

Essential dynamics of lipase binding sites: the effect of inhibitors of different chain length.

The biochemical activity of enzymes, such as lipases, is often associated with structural changes in the enzyme resulting in selective and stereospecific reactions with the substrate. To investigate the effect of a substrate and its chain length on the dynamics of the enzyme, we have performed molecular dynamics simulations of the native Rhizomucor miehei lipase (Rml) and lipase-dialkylphosophate complexes, where the length of the alkyl chain ranges from two to 10 carbon atoms. Simulations were performed in water and trajectories of 400 ps were used to analyse the essential motions in these systems. Our results indicate that the internal motions of the Rml and Rml complexes occur in a subspace of only a few degrees of freedom. A high flexibility is observed in solvent-exposed segments, which connect beta-sheets and helices. In particular, loop regions Gly35-Lys50 and Thr57-Asn63 fluctuate extensively in the native enzyme. Upon activation and binding of the inhibitor, involving the displacement of the active site loop, these motions are considerably suppressed. With increasing chain length of the inhibitor, the fluctuations in the essential subspace increase, levelling off at a chain length of 10, which corresponds to the size of the active-site groove.

Amino Acid Sequence↗

PubMed1996

Theoretical investigation of the dynamics of the active site lid in Rhizomucor miehei lipase.

Interfacial activation of Rhizomucor miehei lipase is accompanied by a hinge-type motion of a single helix (residues 83-94) that acts as a lid over the active site. Activation of the enzyme involves the displacement of the lid to expose the active site, suggesting that the dynamics of the lid could be of mechanistic and kinetic importance. To investigate possible activation pathways and to elucidate the effect of a hydrophobic environment (as would be provided by a lipid membrane) on the lid opening, we have applied molecular dynamics and Brownian dynamics techniques. Our results indicate that the lipase activation is enhanced in a hydrophobic environment. In nonpolar low-dielectric surroundings, the lid opens in approximately 100 ns in the BD simulations. In polar high-dielectric (aqueous) surroundings, the lid does not always open up in simulations of up to 900 ns duration, but it does exhibit some gating motion, suggesting that the enzyme molecule may exist in a partially active form before the catalytic reaction. The activation is controlled by the charged residues ARG86 and ASP91. In the inactive conformation, ASP91 experiences repulsive forces and pushes the lid toward the open conformation. Upon activation ARG86 approaches ASP61, and in the active conformation, these residues form a salt bridge that stabilizes the open conformation.

Binding Sites↗

PubMed1996

The role of Glu87 and Trp89 in the lid of Humicola lanuginosa lipase.

The importance of Glu87 and Trp89 in the lid of Humicola lanuginosa lipase for the hydrolytic activity at the water/lipid interface was investigated by site-directed mutagenesis. It was found that the effect on the hydrolytic activity upon the replacement of Trp89 with Phe, Leu, Gly or Glu was substrate dependent. The Trp89 mutants displayed an altered chain length specificity towards triglycerides, with a higher relative activity towards triacetin and trioctanoin compared with tributyrin. Trp89 was shown to be less important in the hydrolysis of vinyl esters compared with ethyl esters and triglycerides. An exclusive effect on the acylation reaction rate by the mutation of Trp89 was consistent with the data. It is suggested that Trp89 is important in the process of binding the acyl chain of the substrate into the active site for optimal acylation reaction rate. The Trp89Phe mutation resulted in an increased hydrolytic activity towards 2-alkylalkanoic acid esters. This is suggested to be due to reduction of unfavourable van der Waals contacts between Trp89 and the 2-substituent of the substrate. Thus, in contrast to natural substrates, Trp89 has a negative impact on the catalytic efficiency when substrates with bulky acyl chains are used. In contrast to the Trp89 mutations, the effect on the hydrolytic activity of the Glu87Ala mutation was almost substrate independent, 35-70% activity of wild-type lipase. A reduction of both the acylation and deacylation reaction was consistent with the data.

Acylation↗

PubMed1996

Randomized, placebo controlled trial of withdrawal of slow-acting antirheumatic drugs and of observer bias in rheumatoid arthritis.

Patients with rheumatoid arthritis, in stable treatment with methotrexate, penicillamine, or sulfasalazine, were randomized in a double-blind fashion either to continuation of their usual treatment or to placebo. 112 patients were included; 52 patients who refused participation had no more severe disease than the others. The patients felt worse on placebo than on active drug (p = 0.002). The mean differences in number of tender, painful and swollen joints after one month were 2.4 (p = 0.08), 3.0 (p = 0.12) and 2.2 (p = 0.03), respectively. Treatment failure occurred for 42 patients of whom 33 received placebo (p = 0.000,001). There was no difference in the severity of side effects (p = 0.91). The patients guessed their treatment correctly more often than expected (p = 0.02) because of the perceived effect. None of the two observers guessed better than chance, and there were no differences between the observers' evaluations of the joints. The effect of slow-acting antirheumatic drugs was unequivocal and no observer bias occurred.

Aged↗

PubMed1995

Biochemical properties of cloned lipases from the Pseudomonas family.

Three Pseudomonas lipases, representing three subfamilies, were analysed for pH optima, destabilization by EGTA and surfactants, phospholipase and cholesterolesterase side activities. All the Pseudomonas lipases tested showed alkaline pH optima. The Pseudomonas cepacia and the P. pseudoalcaligenes lipases were totally inhibited by EGTA at pH 9, and the latter was also fully inhibited at pH 7. The lipase from P. mendocina was not inhibited by EGTA at any of the pH values tested. These findings indicate that a calcium binding site exists in some of the Pseudomonas lipases. The P. pseudoalcaligenes, P. cepacia and P. mendocina lipases were inhibited by the anionic surfactant SDS at concentrations between 0.01-0.5 mg/ml. The P. pseudoalcaligenes and P. cepacia lipases were not inhibited by the nonionic surfactant Brij35 in concentration up to 1 mg/ml, whereas the lipase from P. mendocina was inhibited at 0.1 mg/ml. The P. pseudoalcaligenes and P. cepacia lipases were found to possess high cholesterol esterase activity. P. pseudoalcaligenes lipase was further found to have high phospholipase activity. Ten Pseudomonas lipase sequences were compared by automatic sequence alignment. On the basis of sequence identity we have classified Pseudomonas lipases into five subfamilies.

Amino Acid Sequence↗

PubMed1995

Difference and ratio plots: simple tools for improved presentation and interpretation of scientific data. Unexpected possibilities for the use of the conglutinin binding assay in inflammatory rheumatic diseases.

11111onglutinin-binding assay (KgBa) has gained widespread use for the detection of circulating immune complexes. A recent paper questioned the interpretation of the results obtained by this method and the validity of the assay (Holmskov et al. (1992) J. Immunol. Methods 148, 225). We now present hitherto unnoted differences between controls and patients with either rheumatoid arthritis or systemic lupus erythematosus. For this we use simple, but unconventional, graphic representations of the data, based on difference plots and ratio plots. Differences between patients with Burkitt's lymphoma and systemic lupus erythematosus from another previously published study (Macanovic, M. and Lachmann, P.J. (1979) Clin. Exp. Immunol. 38, 274) are also represented using ratio plots. Our observations indicate that analysis by regression analysis may often be misleading.

Arthritis, Rheumatoid↗

PubMed1995

Probing a functional role of Glu87 and Trp89 in the lid of Humicola lanuginosa lipase through transesterification reactions in organic solvent.

To reveal the functional role of Glu87 and Trp89 in the lid of Humicola lanuginosa lipase, site-directed mutagenesis at Glu87 and Trp89 was carried out. The catalytic performance of wild-type and mutated lipases was studied in transesterification reactions in cyclohexane at a controlled water activity. Two different acyl donors were used in the investigation: tributyrin, a natural substrate for a lipase, and vinyl butyrate, an activated ester suitable for fast and efficient lipase-catalyzed transformations in preparative organic synthesis. As acyl acceptor 1-heptanol was used. The Glu87Ala mutation decreased the Vmax,app value with tributyrin and vinyl butyrate by a factor of 1.5 and 2, respectively. The Km,app for tributyrin was not affected by the Glu87Ala mutation, but the Km,app for vinyl butyrate increased twofold compared to the wild-type lipase. Changing Trp89 into a Phe residue afforded an enzyme with a 2.7- and 2-fold decreased Vmax,app with the substrates tributyrin and vinyl butyrate, respectively, compared to the wild-type lipase. No significant effects on the Km,app values for tributyrin or vinyl butyrate were seen as a result of the Trp89Phe mutation. However, the introduction of a Glu residue at position 89 in the lid increased the Km,app for tributyrin and vinyl butyrate by a factor of > 5 and 2, respectively. The Trp89Glu mutated lipase could not be saturated with tributyrin within the experimental conditions (0-680 mM) studied here. With vinyl butyrate as a substrate the Vmax,app was only 6% of that obtained with wild-type enzyme.

Binding Sites↗

PubMed1995

Complement receptor expression and activation of the complement cascade on B lymphocytes from patients with systemic lupus erythematosus (SLE).

It has previously been reported that the expression of the complement receptors, CR1 on erythrocytes and blood leucocytes and CR2 on B cells, is reduced in patients with SLE, and that the reduced expression of CR1 on erythrocytes is related to disease activity. We have earlier demonstrated that normal B cells are capable of activating the alternative pathway (AP) of complement in a CR2-dependent fashion. In this study we have investigated whether disturbances in this activity may be related to the altered phenotype of SLE B cells. Flow cytometry was used to measure expression of complement receptors and regulatory proteins on B cells from SLE patients, as well as the deposition of C3 fragments occurring in vivo or after in vitro AP activation. We have confirmed, for a proportion of the patients studied, reduced expression of CR1 and CR2 on B cells, and shown a consistency between low CR2 expression and reduced in vitro AP activation in the presence of homologous, normal serum. In addition, the B cells, like erythrocytes, bear raised levels of in vivo-deposited C3dg, but not C3b fragments, compared with normal B cells. The erythrocytes from SLE patients were unable to inhibit in vitro AP activation by B cells in homologous serum. Finally, we demonstrated an inverse relationship between SLE disease activity index (SLEDAI) and the expression of complement receptor 2 (CR2) on SLE B cells. Thus, determination of CR2 on B cells may emerge as an additional laboratory tool in the assessment of SLE activity.

Adult↗

PubMed1994

Trp89 in the lid of Humicola lanuginosa lipase is important for efficient hydrolysis of tributyrin.

To determine whether Trp89 located in the lid of the lipase (EC 3.1.1.3) from Humicola lanuginosa is important for the catalytic property of the enzyme, site-directed mutagenesis at Trp89 was carried out. The kinetic properties of wild type and mutated enzymes were studied with tributyrin as substrate. Lipase variants in which Trp89 was changed to Phe, Leu, Gly or Glu all showed less than 14% of the activity compared to that of the wild type lipase. The Trp89Glu mutant was the least active with only 1% of the activity seen with the wild type enzyme. All Trp mutants had the same binding affinity to the tributyrin substrate interface as did the wild type enzyme. Wild type lipase showed saturation kinetics against tributyrin when activities were measured with mixed emulsions containing different proportions of tributyrin and the nonionic alkyl polyoxyethylene ether surfactant, Triton DF-16. Wild type enzyme showed a Vmax = 6000 +/- 300 mmol.min-1.g-1 and an apparent Km = 16 +/- 2% (vol/vol) for tributyrin in Triton DF-16, while the mutants did not show saturation kinetics in an identical assay. The apparent Km for tributyrin in Triton DF-16 was increased as the result of replacing Trp89 with other residues (Phe, Leu, Gly or Glu). The activities of all mutants were more sensitive to the presence of Triton DF-16 in the tributyrin substrate than was wild type lipase. The activity of the Trp89Glu mutant was decreased to 50% in the presence of 2 vol% Triton DF-16 compared to the activity seen with pure tributyrin as substrate.(ABSTRACT TRUNCATED AT 250 WORDS)

Detergents↗

PubMed1994

Suicides in men with IDDM.

OBJECTIVE: To investigate the occurrence of suicide in men with insulin-dependent diabetes mellitus (IDDM). RESEARCH DESIGN AND METHODS: A cohort of all Danish men born between 1949 and 1964 (including 1964) who were diagnosed with IDDM before age 20 (n = 1,682) was ascertained earlier. Follow-up from diagnosis to death or 1 January 1991 was based on record linkage with the Danish Civil Registration System and was supplemented with information from death certificates obtained from the Danish National Registry of Deaths. From published vital statistics, cause-specific standardized mortality ratios (SMRs), adjusted for age and calendar time, were calculated. RESULTS: Among the 168 deaths recorded during follow-up, 15 took place in connection with the onset of IDDM and have been excluded. Of the remaining 153 deaths, 12 were officially classified as suicides (SMR 12/7.48 = 1.6, 0.05 < P < 0.1); as for the age-group of 20-24 years, SMR was 2.98, P < 0.05. Furthermore, all deaths officially classified as attributable to unknown causes (n = 28) and accidents (n = 22) were reviewed with respect to unrecognized suicides; as for deaths of unknown causes, three could be reclassified as probable suicides and two as possible suicides, whereas one of the deaths caused by accident could be reclassified as possible suicide. CONCLUSIONS: Young men with IDDM may confer a higher risk of suicide than expected. Furthermore, suicide may represent an underestimated cause of death among patients with IDDM.

Adolescent↗

PubMed1993

Lipases from Rhizomucor miehei and Humicola lanuginosa: modification of the lid covering the active site alters enantioselectivity.

The homologous lipases from Rhizomucor miehei and Humicola lanuginosa showed approximately the same enantioselectivity when 2-methyldecanoic acid esters were used as substrates. Both lipases preferentially hydrolyzed the S-enantiomer of 1-heptyl 2-methyldecanoate (R. miehei: ES = 8.5; H. lanuginosa: ES = 10.5), but the R-enantiomer of phenyl 2-methyldecanoate (ER = 2.9). Chemical arginine specific modification of the R. miehei lipase with 1,2-cyclohexanedione resulted in a decreased enantioselectivity (ER = 2.0), only when the phenyl ester was used as a substrate. In contrast, treatment with phenylglyoxal showed a decreased enantioselectivity (ES = 2.5) only when the heptyl ester was used as a substrate. The presence of guanidine, an arginine side chain analog, decreased the enantioselectivity with the heptyl ester (ES = 1.9) and increased the enantioselectivity with the aromatic ester (ER = 4.4) as substrates. The mutation, Glu 87 Ala, in the lid of the H. lanuginosa lipase, which might decrease the electrostatic stabilization of the open-lid conformation of the lipase, resulted in 47% activity compared to the native lipase, in a tributyrin assay. The Glu 87 Ala mutant showed an increased enantioselectivity with the heptyl ester (ES = 17.4) and a decreased enantioselectivity with the phenyl ester (ER = 2.5) as substrates, compared to native lipase. The enantioselectivities of both lipases in the esterification of 2-methyldecanoic acid with 1-heptanol were unaffected by the lid modifications.

Arginine↗

PubMed1993

Theoretical studies of Rhizomucor miehei lipase activation.

Computational methods have been used to study the extensive conformational change of Rhizomucor miehei lipase upon activation. The present study considers the possible activation route, the energies involved and molecular interactions during the conformational change of the lipase in a hydrophobic environment. The conformational change was studied by conventional molecular dynamics methods and with a combined molecular dynamics and mechanics protocol, in which the conformational change was simulated by restraining C alpha pseudotorsional angles in small steps between the two crystallographically observed positions of the lid. In the closed conformer of the enzyme the active site is completely buried under a short helical loop, 'the lid'. The activation of the lipase consists of a movement of the lid, which results in an open conformer with an exposed active site. From the results of the simulations in the present work we suggest that the lipase in a hydrophobic environment is stabilized in the open form by electrostatic interactions.

Computer Simulation↗