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L N Johnson

Publications and source records attributed to L N Johnson.

At least 91 records · Page 5Linked to original sources
PubMed1994

Analysis of the structure of Pseudomonas glumae lipase.

The lipase produced by Pseudomonas glumae is monomeric in the crystalline state and has a serine protease-like catalytic triad; Ser87-His285-Asp263. The largest domain of the protein resembles closely a subset of the frequently observed alpha/beta-hydrolase fold and contains a well-defined calcium site. This paper describes structural analysis of this protein, focusing on (i) structural comparison with the lipase from Geotrichum candidum, (ii) the probable nature of the conformational change involved in substrate binding and (iii) structural variations amongst the family of Pseudomonas lipases. This analysis reveals similarities between P. glumae lipase and G. candidum lipase involving secondary structural elements of the hydrolase core and the loops carrying the catalytic serine and histidine residues. A possible functional equivalence has also been identified between parts of the two molecules thought to be involved in a conformational change. In addition, determination of the structure of P. glumae lipase has allowed rationalization of previously reported protein engineering experiments, which succeeded in improving the stability of the enzyme with respect to proteolysis.

Amino Acid Sequence↗
PubMed1994

Incidence of nonarteritic and arteritic anterior ischemic optic neuropathy. Population-based study in the state of Missouri and Los Angeles County, California.

This population-based study was undertaken to obtain information on age-, sex-, and race-specific incidence of nonarteritic and arteritic anterior ischemic optic neuropathy for the State of Missouri and for Los Angeles County, California. Among subjects who were 50 or older the estimated mean annual incidence rates per 100,000 population were 2.30 for nonarteritic anterior ischemic optic neuropathy and 0.36 for arteritic anterior ischemic optic neuropathy. White individuals appear to be at significantly higher risk of developing nonarteritic anterior ischemic optic neuropathy than black or Hispanic individuals, suggesting possible genetic predisposition.

Acute Disease↗
PubMed1994

Working time of synthetic elastomeric impression material.

This study will introduce a new method for measuring the working time of elastomeric impression materials, taking into account the perceived shortcomings of existing systems for evaluating these times. The working times of various commercially available polysulfide, addition reaction silicones and polyethers were determined at room temperature (20 degrees C), following storage in a refrigerator (6 degrees C), and at mouth temperature (35 degrees C). At room temperature, the polysulfides demonstrated the longest working times and the silicones the shortest. Both the polysulfides and the silicones had longer working times following storage at 6 degrees C for 24 hours. However, the polyethers were found to be unusable at this temperature. All the impression materials had shorter working times when placed into the testing apparatus, which had been heated to mouth temperature.

Dental Impression Materials↗
PubMed1993

The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate.

The family of lipases (triacylglycerol-acyl-hydrolases EC 3.1.1.3) constitutes an interesting class of enzymes because of their ability to interact with lipid-water interfaces, their wide range of substrate specificities, and their potential industrial applications. Here we report the first crystal structure of a bacterial lipase, from Pseudomonas glumae. The structure is formed from three domains, the largest of which contains a subset of the alpha/beta hydrolase fold and a calcium site. Asp263, the acidic residue in the catalytic triad, has previously been mutated into an alanine with only a modest reduction in activity.

Amino Acid Sequence↗
PubMed1993

Crystallographic binding studies on the allosteric inhibitor glucose-6-phosphate to T state glycogen phosphorylase b.

Glucose-6-phosphate is an important allosteric inhibitor of glycogen phosphorylase b that restrains the enzyme in the inactive state in resting muscle. A crystallographic binding study by diffusion of glucose-6-phosphate into performed crystals of T state phosphorylase b has been carried out at 2.3 A resolution and the structure refined by restrained crystallographic least-squares and simulated annealing to give a crystallographic R-value of 0.203. The inhibitor binds at the AMP allosteric effector site at the subunit-subunit interface of the dimer. The phosphate groups of the glucose-6-phosphate and AMP occupy partially overlapping sites and make similar contacts to two arginine residues (Arg309 and Arg310) but in glucose-6-phosphate there is a contact to a third arginine (Arg242). The glucopyranose of glucose-6-phosphate and the adenine ribose of AMP occupy different positions. Including the contacts to the three arginine residues by the phosphate group, the glucose-6-phosphate makes a total of 11 hydrogen-bonds to the enzyme and all but one of these are to charged groups. The O-2 hydroxyl hydrogen-bonds to the main-chain carbonyl oxygen of Val40' from the other subunit and this interaction appears important for the allosteric response. There are substantial conformational changes both in the vicinity of the glucose-6-phosphate (involving for example Phe196 and Arg309) and at the subunit interface (involving residues 42' to 51' and 192 to 196). These shifts tighten the binding of the inhibitor and the interface. Comparison of the glucose-6-phosphate complex with the T state native phosphorylase b and the R state phosphorylase a structures shows that there is a graded response from T state glucose-6-phosphate complex through T state phosphorylase b to R state phosphorylase a that suggests that glucose-6-phosphate promotes a tight structure that is more "tensed" than native T state phosphorylase b. The results show how the same allosteric effector site can exhibit a tight binding site for the activator AMP in the R state structure and a tight binding site for glucose-6-phosphate in the modified T state structure.

Allosteric Regulation↗
PubMed1993

Solid state 31P cross-polarization/magic angle sample spinning nuclear magnetic resonance of crystalline glycogen phosphorylase b.

(31)P cross-polarization/magic angle sample spinning nuclear magnetic resonance spectra have been obtained for pyridoxal 5'-phosphate (PLP) bound to glycogen phosphorylase b (GPb) in two different crystalline forms, monoclinic and tetragonal. Analysis of the intensities of the spinning sidebands in the nuclear magnetic resonance spectra has enabled estimates of the principal values of the (31)P chemical shift tensors to be obtained. Differences between the two sets of values suggest differences in the environment of the phosphate moiety of the pyridoxal phosphate in the two crystalline forms. The tensor for the tetragonal crystalline form, T state GPb, is fully consistent with those found for dianionic phosphate groups in model compounds. The spectrum for the monoclinic crystalline form, R state GPb, although closer to that of dianionic than monoanionic model phosphate compounds, deviates significantly from that expected for a simple dianion or monoanion. This is likely to result from specific interactions between the PLP phosphate group and residues in its binding site in the protein. A possible explanation for the spectrum of the monoclinic crystals is that the shift tensor is averaged by a proton exchange process between different ionization states of the PLP associated with the presence of a sulfate ion bound in the vicinity of the PLP.

Allosteric Site↗
PubMed1993

Effect of intermittent versus continuous patient monitoring on reliability indices during automated perimetry.

PURPOSE: This prospective, randomized study was undertaken to determine the effect of intermittent versus continuous patient monitoring on reliability indices (fixation losses, false-positive errors, and false-negative errors) during automated static perimetry. METHODS: A practice Humphrey Program C30-2 visual field was administered to 169 subjects (mean age +/- standard deviation, 56 +/- 18 years) for 1.5 minutes, during which time trained technicians continuously monitored all subjects and assessed patient fixation as noted on the eye monitor. The computer-generated reliability indices during the 1.5 minute practice test were recorded. After completion of the practice test, the 169 eyes were randomized to either intermittent or continuous monitor for the permanent C30-2 test. During intermittent monitoring, the technician returned periodically to the examination room to assess the subject's performance. For continuous monitoring, the technician continually assessed the subject's performance while remaining in the examination room throughout the test duration. RESULTS: The mean number of visits per visual field test during intermittent monitoring was 4.0, and mean test duration was 15.8 minutes. There was no difference in the mean deviation, pattern standard deviation, and short-term fluctuation (P = 0.85, 0.98, and 0.41, respectively) of the visual fields for intermittent and continuous monitoring, suggesting similar diffuse depression and localized defects in the visual fields for each group. The mean fixation losses (6.9%), false-positive errors (1.8%), and false-negative errors (5.8%) for the intermittently monitored group were not different from the mean fixation losses (7.8%), false-positive errors, (3.1%) and false-negative errors (5.0%) for the continuously monitored group (P = 0.40, 0.24, and 0.36, respectively). CONCLUSION: Although recommended, continuous monitoring does not appear necessary for all patients undergoing automated perimetry. Error-free reliability indices combined with the technician's judgment of patient reliability during the first 1.5 minutes of C30-2 testing may be a guideline for choosing intermittent monitoring.

Adult↗
PubMed1993

Ocular myasthenia gravis.

Ocular dysfunction accounts for nearly 70% of the initial manifestations of myasthenia gravis. Since the prevalence rate of myasthenia gravis is two to 10 cases per 100,000 population, it is important for clinicians to be cognizant of this disorder and its varied ocular presentations. The clinical manifestations, diagnosis, treatment, and prognosis of ocular myasthenia gravis are reviewed.

Eye Diseases↗
PubMed1993

Composite resin restoratives revisited.

To choose the most suitable composite for the clinical challenge, the clinician must consider a number of issues. This paper examines those issues, as well as how the selected material can best be manipulated to obtain optimum results. It is intended to help the clinician select this material, and to provide information on the clinical relevance of the different compositions and filler sizes of composite materials, proper techniques for light curing--including the effects of light to resin distance and light angulation--and methods that can be used to evaluate the effectiveness of the light-curing unit. The effect of surface finish on wear is also discussed, along with suggestions on proper finishing techniques.

Bisphenol A-Glycidyl Methacrylate↗
PubMed1992

The molecular mechanism for the tetrameric association of glycogen phosphorylase promoted by protein phosphorylation.

The allosteric transition of glycogen phosphorylase promoted by protein phosphorylation is accompanied by the association of a pair of functional dimers to form a tetramer. The conformational changes within the dimer that lead to the creation of a protein recognition surface have been analyzed from a comparison of the crystal structures of T-state dimeric phosphorylase b and R-state tetrameric phosphorylase a. Regions of the structure that participate in the tetramer interface are situated within structural subdomains. These include the glycogen storage subdomain, the C-terminal subdomain and the tower helix. The subdomains undergo concerted conformational transitions on conversion from the T to the R state (overall r.m.s. shifts between 1 and 1.7 A) and, together with the quaternary conformational change within the functional dimer, create the tetramer interface. The glycogen storage subdomain and the C-terminal subdomain are distinct from those regions that contribute to the dimer interface, but shifts in the subdomains are correlated with the allosteric transitions that are mediated by the dimer interface. The structural properties of the tetramer interface are atypical of an oligomeric protein interface and are more similar to protein recognition surfaces observed in protease inhibitors and antibody-protein antigen complexes. There is a preponderance of polar and charged residues at the tetramer interface and a high number of H-bonds per surface area (one H-bond per 130 A2). In addition, the surface area made inaccessible at the interface is relatively small (1,142 A2 per subunit on dimer to tetramer association compared with 2,217 A2 per subunit on monomer-to-dimer association).

Allosteric Regulation↗
PubMed1992

Control of phosphorylase b conformation by a modified cofactor: crystallographic studies on R-state glycogen phosphorylase reconstituted with pyridoxal 5'-diphosphate.

Previous crystallographic studies on glycogen phosphorylase have described the different conformational states of the protein (T and R) that represent the allosteric transition and have shown how the properties of the 5'-phosphate group of the cofactor pyridoxal phosphate are influenced by these conformational states. The present work reports a study on glycogen phosphorylase b (GPb) complexed with a modified cofactor, pyridoxal 5'-diphosphate (PLPP), in place of the natural cofactor. Solution studies (Withers, S.G., Madsen, N.B., & Sykes, B.D., 1982, Biochemistry 21, 6716-6722) have shown that PLPP promotes R-state properties of the enzyme indicating that the cofactor can influence the conformational state of the protein. GPb complexed with pyridoxal 5'-diphosphate (PLPP) has been crystallized in the presence of IMP and ammonium sulfate in the monoclinic R-state crystal form and the structure refined from X-ray data to 2.8 A resolution to a crystallographic R value of 0.21. The global tertiary and quaternary structure in the vicinity of the Ser 14 and the IMP sites are nearly identical to those observed for the R-state GPb-AMP complex. At the catalytic site the second phosphate of PLPP is accommodated with essentially no change in structure from the R-state structure and is involved in interactions with the side chains of two lysine residues (Lys 568 and Lys 574) and the main chain nitrogen of Arg 569. Superposition of the T-state structure shows that were the PLPP to be incorporated into the T-state structure there would be a close contact with the 280s loop (residues 282-285) that would encourage the T to R allosteric transition. The second phosphate of the PLPP occupies a site that is distinct from other dianionic binding sites that have been observed for glucose-1-phosphate and sulfate (in the R state) and for heptulose-2-phosphate (in the T state). The results indicate mobility in the dianion recognition site, and the precise position is dependent on other linkages to the dianion. In the modified cofactor the second phosphate site is constrained by the covalent link to the first phosphate of PLPP. The observed position in the crystal suggests that it is too far from the substrate site to represent a site for catalysis.

Amino Acid Sequence↗
PubMed1992

Time-resolved protein crystallography.

Advances in synchrotron radiation technology have allowed exposure times from protein crystals of the order of milliseconds to be used routinely, and in exceptional circumstances exposure times of 100 ps have been obtained. However, many data sets take seconds to record because of the slow time scale of film change or crystal reorientation or translation when more than one exposure is required. This problem has been addressed by Amemiya et al. (1989). There has been considerable progress in methods to initiate reactions in protein crystals, especially the development of photolabile caged compounds but also temperature jump, pH jump, and diffusion. Although flash lamps deliver pulses of 100 mJ/ms, often several pulses are required to release sufficient product, and reaction initiation can take several seconds. Laser illumination can provide more powerful input, but the laser must be accommodated within the restricted space at the synchrotron station. The requirement to maintain synchrony among the molecules in the crystal lattice as the reaction proceeds and to ensure that the lifetime of intermediates is longer than data collection rates emphasizes the need for chemical characterization of the reaction under study. As Ringe advocated in the studies with chymotrypsin, it may be more profitable to devise conditions under which certain intermediates along the reaction pathway accumulate in the crystal and to record these in a series of discrete steps rather than continuous monitoring of the reaction. The Laue method is limited to those proteins that give well-ordered crystals and problems of transient disorder on initiation of reaction and problems of radiation damage need to be overcome or avoided by suitable experimental protocols.(ABSTRACT TRUNCATED AT 250 WORDS)

Proteins↗
PubMed1992

Catalytic mechanism of glycogen phosphorylase.

Proposals for the catalytic mechanism of glycogen phosphorylase based on crystallographic studies with the T-state form of the enzyme are reviewed in the light of new structural data from studies with the R-state enzyme. The observed position for a sulfate ion at the catalytic site and the crystallographic binding studies of glucose-1-P to the R-state enzyme support the previous proposals in which the 5'-phosphate group of the essential cofactor pyridoxal phosphate functions as an acid-base to promote attack by the substrate phosphate on the polysaccharide substrate. The sulfate (phosphate) recognition site, which is fully formed only in the R state, comprises interactions from the side chains of Arg-569 and Lys-574 and the main chain nitrogen of Gly-135 at the start of an alpha-helix. The interactions of the cofactor 5'-phosphate do not change between the T and the R state. Other groups on the protein play important roles in binding the substrate but are not involved in the catalytic reaction. The presumed reactive conformation of bound substrate has been observed with heptulose-2-P in the T state and in this conformation stereoelectronic arguments suggest the C(1)-O(1) bond is weakened. For the natural substrate glucose-1-P it is proposed that the reactive conformation is achieved only in the presence of the oligosaccharide component in the reactive ternary enzyme-substrate complex. The phosphate recognition sites are discussed.

Binding Sites↗
PubMed1992

Expression of the phosphorylase kinase gamma subunit catalytic domain in Escherichia coli.

The catalytic subunit of phosphorylase b kinase (gamma) and an engineered truncated form (gamma-trc, residues 1-297) have been expressed in Escherichia coli. The truncated protein included the entire catalytic domain as defined by sequence alignment with other protein kinases but lacked the putative calmodulin binding domain. Full-length protein was produced in insoluble aggregates. Some activity was regenerated by solubilization in urea and dilution into renaturating buffer but the activity was found to be associated with a smaller molecular weight component. Full-length protein could not be refolded successfully. The truncated gamma subunit was produced in the soluble fraction of the cell as well as in inclusion bodies. The insoluble protein was refolded by dilution from urea and purified to homogeneity, in a one step separation on DEAE-Sepharose to give a protein mol. wt 32,000 +/- 2000 with a high sp. act. of 5.3 mumol 32P incorporated into phosphorylase b(PPB)/min/nmol. Kinetic parameters gave Km for ATP 46 +/- 3 microM and Km for PPb 27 +/- 1 microM. The sp. act. and the Km values are comparable to those observed for the activated holoenzyme and indicate that the gamma-trc retains the substrate recognition and catalytic properties. The ratio of activities at pH 6.8/8.2 was 0.84. gamma-trc was inhibited by ADP with a Ki of 52 microM and was sensitive to activation by Mg2+ and inhibition by Mn2+, properties that are characteristic of the holoenzyme and the isolated gamma subunit. Calmodulin which confers calcium sensitivity on the isolated gamma subunit had no effect on the enzymic properties of gamma-trc.(ABSTRACT TRUNCATED AT 250 WORDS)

Adenosine Diphosphate↗
PubMed1992

Glycogen phosphorylase: control by phosphorylation and allosteric effectors.

Structural studies of muscle glycogen phosphorylase during the last two decades have provided a detailed mechanism for the molecular basis of the control by phosphorylation and by allosteric effectors and the catalytic mechanism. Control by phosphorylation is effected by a disorder to order transition of the NH2-terminal residues that promotes localized changes in the structure of the protein at the region of subunit-subunit contacts and larger changes in the quaternary structure. The covalently attached phosphate group acts like an allosteric effector but the full manifestation of the response is also dependent on the NH2-terminal tail residues. The noncovalently bound allosteric effectors produce similar shifts in the structural states although these are bound at sites that are remote from the serine-phosphate site. The communication from these sites to the catalytic site is through long-range interactions that result in activation of the enzyme through opening access to the buried catalytic site and through creation of the substrate phosphate recognition site by an interchange of an acidic group with a basic group. Recent advances in expression systems have opened the way to a study of properties both for the muscle and other isozymes and other species that should illuminate the different regulatory roles of the enzyme in different tissues and organisms. The allosteric mechanism of activation of phosphorylase by phosphorylation may be relevant to other enzymes although it is now known that other mechanisms such as electrostatic steric blocking mechanisms also exist.

Allosteric Regulation↗