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P P Schmidt

Publications and source records attributed to P P Schmidt.

At least 19 recordsLinked to original sources
PubMed2005

Analysis of local anharmonicity using Gaussian model potentials and cartesian oscillator basis sets: example, HCN.

This paper examines local anharmonic vibrations in molecules using an analysis that starts with an ab initio potential energy surface, fits a model potential constructed of Gaussian basis functions, and proceeds to a quantum mechanical analysis of the anharmonic modes using Cartesian harmonic oscillator basis functions in a variational calculation. The objective of this work is to suggest methods, with origins in nuclear and molecular (electronic) quantum mechanics, that should be useful for the accurate analysis of the local anharmonic motions of hydrogen, and perhaps other atoms or small molecular fragments, residing in molecularly complicated but otherwise harmonic environments.

Journal Article↗
PubMed2001

The effect of substrate, dihydrobiopterin, and dopamine on the EPR spectroscopic properties and the midpoint potential of the catalytic iron in recombinant human phenylalanine hydroxylase.

Phenylalanine hydroxylase (PAH) is a tetrahydrobiopterin (BH(4)) and non-heme iron-dependent enzyme that hydroxylates L-Phe to L-Tyr. The paramagnetic ferric iron at the active site of recombinant human PAH (hPAH) and its midpoint potential at pH 7.25 (E(m)(Fe(III)/Fe(II))) were studied by EPR spectroscopy. Similar EPR spectra were obtained for the tetrameric wild-type (wt-hPAH) and the dimeric truncated hPAH(Gly(103)-Gln(428)) corresponding to the "catalytic domain." A rhombic high spin Fe(III) signal with a g value of 4.3 dominates the EPR spectra at 3.6 K of both enzyme forms. An E(m) = +207 +/- 10 mV was measured for the iron in wt-hPAH, which seems to be adequate for a thermodynamically feasible electron transfer from BH(4) (E(m) (quinonoid-BH(2)/BH(4)) = +174 mV). The broad EPR features from g = 9.7-4.3 in the spectra of the ligand-free enzyme decreased in intensity upon the addition of L-Phe, whereas more axial type signals were observed upon binding of 7,8-dihydrobiopterin (BH(2)), the stable oxidized form of BH(4), and of dopamine. All three ligands induced a decrease in the E(m) value of the iron to +123 +/- 4 mV (L-Phe), +110 +/- 20 mV (BH(2)), and -8 +/- 9 mV (dopamine). On the basis of these data we have calculated that the binding affinities of L-Phe, BH(2), and dopamine decrease by 28-, 47-, and 5040-fold, respectively, for the reduced ferrous form of the enzyme, with respect to the ferric form. Interestingly, an E(m) value comparable with that of the ligand-free, resting form of wt-hPAH, i.e. +191 +/- 11 mV, was measured upon the simultaneous binding of both L-Phe and BH(2), representing an inactive model for the iron environment under turnover conditions. Our findings provide new information on the redox properties of the active site iron relevant for the understanding of the reductive activation of the enzyme and the catalytic mechanism.

Biopterins↗
PubMed2001

Formation of a protonated trihydrobiopterin radical cation in the first reaction cycle of neuronal and endothelial nitric oxide synthase detected by electron paramagnetic resonance spectroscopy.

Nitric oxide synthase (EC 1.14.13.39; NOS) converts L-arginine into NO and L-citrulline in a two-step reaction with Nomega-hydroxy-L-arginine (NOHLA) as an intermediate. The active site iron in NOS has thiolate axial heme-iron ligation as found in the related monooxygenase cytochrome P450. In NOS, tetrahydrobiopterin (BH4) is an essential cofactor for both steps, but its function is controversial. Previous optical studies of the reaction between reduced NOS with O2 at -30 degrees C suggested that BH4 may serve as an one-electron donor in the first cycle, implying formation of a trihydrobiopterin radical. We investigated the same reaction under identical conditions with electron paramagnetic resonance spectroscopy. With BH4-containing full-length neuronal NOS we obtained an organic free radical (g-value 2.0042) in the presence of Arg, and a similar radical was observed with the endothelial NOS oxygenase domain in the presence of Arg and BH4. Without substrate the radical yield was greatly (10x) diminished. Without BH4, or with NOHLA instead of Arg, no radical was observed. With 6-methyltetrahydropterin or 5-methyl-BH4 instead of BH4, radicals with somewhat different spectra were formed. On the basis of simulations we assign the signals to trihydropterin radical cations protonated at N5. This is the first study that demonstrates the formation of a protonated trihydrobiopterin radical with the constitutive isoforms of NOS, and the first time the radical was obtained without exogenous BH4. These results offer strong support for redox cycling of BH4 in the first reaction cycle of NOS catalysis (BH4 <--> BH3.H+).

Animals↗
PubMed2000

The role of tetrahydrobiopterin in the activation of oxygen by nitric-oxide synthase.

We have studied the reaction of reduced nitric-oxide synthase (NOS) with molecular oxygen at -30 degrees C. In the first reaction cycle (from L-Arg to hydroxy-L-Arg), an oxygen adduct complex formed rapidly. Experiments in the absence of the reductase domain demonstrated that this complex was then further reduced by one electron stemming from the cofactor tetrahydrobiopterin (BH4). Spectral evidence suggested an iron(IV) porphyrin pi-cation radical as an intermediate. The nature of the oxidized BH4 was identified by EPR as a BH3* radical. Within the second cycle (from hydroxy-L-Arg to citrulline and NO), an iron(III)-NO complex could be identified clearly by its spectral characteristics. The strict requirement of BH4 for its formation suggests that BH4 plays a redox role, although transient, also in the second reaction cycle.

Biopterins↗
PubMed1998

Kinetic evidence that a radical transfer pathway in protein R2 of mouse ribonucleotide reductase is involved in generation of the tyrosyl free radical.

Class I ribonucleotide reductases consist of two subunits, R1 and R2. The active site is located in R1; active R2 contains a diferric center and a tyrosyl free radical (Tyr.), both essential for enzymatic activity. The proposed mechanism for the enzymatic reaction includes the transport of a reducing equivalent, i.e. electron or hydrogen radical, across a 35-A distance between Tyr. in R2 and the active site in R1, which are connected by a hydrogen-bonded chain of conserved, catalytically essential amino acid residues. Asp266 and Trp103 in mouse R2 are part of this radical transfer pathway. The diferric/Tyr. site in R2 is reconstituted spontaneously by mixing iron-free apoR2 with Fe(II) and O2. The reconstitution reaction requires the delivery of an external reducing equivalent to form the diferric/Tyr. site. Reconstitution kinetics were investigated in mouse apo-wild type R2 and the three mutants D266A, W103Y, and W103F by rapid freeze-quench electron paramagnetic resonance with >/=4 Fe(II)/R2 at various reaction temperatures. The kinetics of Tyr. formation in D266A and W103Y is on average 20 times slower than in wild type R2. More strikingly, Tyr. formation is completely suppressed in W103F. No change in the reconstitution kinetics was found starting from Fe(II)-preloaded proteins, which shows that the mutations do not affect the rate of iron binding. Our results are consistent with a reaction mechanism using Asp266 and Trp103 for delivery of the external reducing equivalent. Further, the results with W103F suggest that an intact hydrogen-bonded chain is crucial for the reaction, indicating that the external reducing equivalent is a H. Finally, the formation of Tyr. is not the slowest step of the reaction as it is in Escherichia coli R2, consistent with a stronger interaction between Tyr. and the iron center in mouse R2. A new electron paramagnetic resonance visible intermediate named mouse X, strikingly similar to species X found in E. coli R2, was detected only in small amounts under certain conditions. We propose that it may be an intermediate in a side reaction leading to a diferric center without forming the neighboring Tyr.

Animals↗
PubMed1998

Relationship between visual skills and performance on saccadic eye movement testing.

The effect of visual skills, such as binocularity, on saccadic eye movement test performance is currently unknown. Therefore, the relationship between performance on commonly used clinical saccadic eye movement tests and visual skill was studied in a masked investigation of 181 kindergartners and first graders (mean age 6.25 years) from a middle class, suburban, elementary school near Cleveland, Ohio. The New York State Optometric Association King-Devick saccade test (NYSOA K-D) and the Developmental Eye Movement test (DEM) were employed because they are two commonly used clinical saccadic eye movement tests. A Modified Clinical Technique (MCT) vision screening and Randot stereoacuity test were performed to evaluate other visual skills. Analysis revealed that for the whole study population, total errors on the NYSOA K-D were significantly related to referral on the MCT screening (p = 0.015) and stereoacuity worse than 100 sec arc (p = 0.011). A trend toward significance was also found between DEM ratio and stereoacuity worse than 50 sec arc for the whole study population. However, in the children who passed the MCT, stereoacuity was not found to be significantly related to performance on NYSOA K-D or DEM. Thus, our findings indicate that visual difficulties may affect performance on the NYSOA K-D in this population.

Child↗
PubMed1998

Vision screening of preschool children: evaluating the past, looking toward the future.

Vision problems of preschool children are detectable with a comprehensive eye examination; however, it is estimated that only 14% of children below the age of 6 years receive an eye examination. Screening is advocated as a cost-effective alternative to identify children in need of further vision care. Thirty-four states recommend or require vision screening of preschool children. Although laws and guidelines exist, only 21% of preschool children are actually screened for vision problems. There is little agreement concerning the best screening methods, and no validated, highly effective model for screening vision of preschool children. Newer screening tests have been designed specifically for preschool populations, and can be administered by lay screeners. Many have not been validated. Several are recommended by states or organizations without convincing scientific evidence of their effectiveness. This paper summarizes current laws and guidelines for preschool vision screening in the United States, reviews advantages and disadvantages of several test procedures, and provides recommendations for developing future preschool vision screening programs.

Child, Preschool↗
PubMed1997

Activation of the anaerobic ribonucleotide reductase from Escherichia coli. The essential role of the iron-sulfur center for S-adenosylmethionine reduction.

The anaerobic ribonucleotide reductase of Escherichia coli catalyzes the synthesis of the deoxyribonucleotides required for anaerobic DNA synthesis. The enzyme is an alpha2beta2 heterotetramer. In its active form, the large alpha2 subunit contains an oxygen-sensitive glycyl radical, whereas the beta2 small protein harbors a [4Fe-4S] cluster that joins its two polypeptide chains. Formation of the glycyl radical in the inactive enzyme requires S-adenosylmethionine (AdoMet), dithiothreitol, K+, and either an enzymatic (reduced flavodoxin) or chemical (dithionite or 5-deazaflavin plus light) reducing system. Here, we demonstrate that AdoMet is directly reduced by the Fe-S center of beta2 during the activation of the enzyme, resulting in methionine and glycyl radical formation. Direct binding experiments showed that AdoMet binds to beta2 with a Kd of 10 microM and a 1:1 stoichiometry. Binding was confirmed by EPR spectroscopy that demonstrated the formation of a complex between AdoMet and the [4Fe-4S] center of beta2. Dithiothreitol triggered the cleavage of AdoMet, leading to an EPR-silent form of beta2 and, in the case of alpha2beta2, to glycyl radical formation. In both instances, 3 methionines were formed per mol of protein. Our results indicate that the Fe-S center of beta2 is directly involved in the reductive cleavage of AdoMet and suggest a new biological function for an iron-sulfur center, i.e redox catalysis, as recently proposed by others (Staples, R. C., Ameyibor, E., Fu, W., Gardet-Salvi, L., Stritt-Etter, A. L., Schürmann, P., Knaff, D. B., and Johnson, M. K. (1996) Biochemistry 35, 11425-11434).

Catalysis↗
PubMed1997

Cloning and characterization of the R1 and R2 subunits of ribonucleotide reductase from Trypanosoma brucei.

Ribonucleotide reductase (RNR) catalyzes the rate limiting step in the de novo synthesis of deoxyribonucleotides by directly reducing ribonucleotides to the corresponding deoxyribonucleotides. To keep balanced pools of deoxyribonucleotides, all nonviral RNRs studied so far are allosterically regulated. Most eukaryotes contain a class I RNR, which is a heterodimer of two nonidentical subunits called proteins R1 and R2. We have isolated cDNAs encoding the R1 and R2 proteins from Trypanosoma brucei. The amino acid sequence identities with the mouse R1 and R2 subunits are 58% and 63%, respectively. Recombinant active trypanosome R1 and R2 proteins were expressed in Escherichia coli and purified. The R2 protein contains an iron-tyrosyl free radical center verified by EPR spectroscopy and iron analyses. Measurement of cytidine 5'-diphosphate reduction by the trypanosome RNR in the presence of various allosteric effectors showed that the activity is highest with dTTP, dGTP, or dATP and considerably lower with ATP. The effect of dGTP is either activating (alone) or inhibitory (in the presence of ATP). Filter binding studies indicated that there are two classes of allosteric effector binding sites that bind ATP or dATP (low-affinity dATP site) and ATP, dATP, dGTP, or dTTP (high-affinity dATP site), respectively. Therefore, the structural organization of the allosteric sites is very similar to the mammalian RNRs, whereas the allosteric regulation of cytidine 5'-diphosphate reduction is unique. Hopefully, this difference can be used to target the trypanosome RNR for therapeutic purposes.

Amino Acid Sequence↗
PubMed1997

Cryoenzymic studies on yeast 3-phosphoglycerate kinase. Attempt to obtain the kinetics of the hinge-bending motion.

This is a continuation of a study on the 3-phosphoglycerate kinase (PGK) reaction in the direction of 1,3-bisphosphoglycerate (bPG) formation: ATP + 3-phosphoglycerate (PG) <==> ADP + bPG [Schmidt, P. P., Travers, F., & Barman, T. (1995) Biochemistry 34, 824-832]. We showed that species containing bPG accumulate in the steady state, but their low concentrations and rapid kinetics of formation precluded a full study, even under cryoenzymic conditions in 40% ethylene glycol. Here we studied the PGK reaction in 30% methanol. The transient kinetics of bPG formation were obtained by chemical sampling: PGK was mixed with PG and [gamma-32P]ATP in a rapid flow quench apparatus, the mixture aged 4 ms up and quenched in acid, and the [1-(32)P]bPG was determined. The time course consisted of a rapid rise of bPG (kinetics k(obs)) and a steady state phase. In methanol, the amplitude of the rise was large (>50% of the PGK in the steady state), and k(obs) was measurable. Fluorescence stopped flow was used to study the formation of the binary E x PG and E x ATP. The affinities of PGK for ATP and PG were high in methanol (Kd = 102 and 1.5 microM, respectively), but the kinetics of the formation of E x PG and E x ATP were too rapid to be measured. From these and the chemical sampling experiments, we propose a reaction scheme for PGK: a rapid formation of the collision complex E x PG x ATP (K1), a slow isomerisation to E* x PG x ATP (k2,k(-2)), a rapid phosphorylation transfer step to E x bPG x ADP (K3), and a slow release of the products (k4). In our scheme, k(obs) is the reflection mainly of k2 and k(-2) and the steady state of k4. Using a computer simulation procedure, k2/K1 = 0.37 microM(-1) s(-1), k(-2) = 33 s(-1), K3 = 4, and k4 = 7.1 s(-1). We propose that k(obs) measures the kinetics of the putative hinge-bending motion of PGK, i.e., the conformational change that is necessary for the substrates to line up for phosphoryl transfer.

Adenosine Triphosphate↗
PubMed1997

Kinetics of transient radicals in Escherichia coli ribonucleotide reductase. Formation of a new tyrosyl radical in mutant protein R2.

Reconstitution of the tyrosyl radical in ribonucleotide reductase protein R2 requires oxidation of a diferrous site by oxygen. The reaction involves one externally supplied electron in addition to the three electrons provided by oxidation of the Tyr-122 side chain and formation of the mu-oxo-bridged diferric site. Reconstitution of R2 protein Y122F, lacking the internal pathway involving Tyr-122, earlier identified two radical intermediates at Trp-107 and Trp-111 in the vicinity of the di-iron site, suggesting a novel internal transfer pathway (Sahlin, M., Lassmann, G., Pötsch, S., Sjöberg, B. -M., and Gräslund, A. (1995) J. Biol. Chem. 270, 12361-12372). Here, we report the construction of the double mutant W107Y/Y122F and its three-dimensional structure and demonstrate that the tyrosine Tyr-107 can harbor a transient, neutral radical (Tyr-107(.)). The Tyr-107(.) signal exhibits the hyperfine structure of a quintet with coupling constants of 1.3 mT for one beta-methylene proton and 0.75 mT for each of the 3 and 5 hydrogens of the phenyl ring. Rapid freeze quench kinetics of EPR-visible intermediates reveal a preferred radical transfer pathway via Trp-111, Glu-204, and Fe-2, followed by a proton coupled electron transfer through the pi-interaction of the aromatic rings of Trp-(Tyr-)107 and Trp-111. The kinetic pattern observed in W107Y/Y122F is considerably changed as compared with Y122F: the Trp-111(.) EPR signal has vanished, and the Tyr-107(.) has the same formation rate as does Trp-111(.) in Y122F. According to the proposed consecutive reaction, Trp-111(.) becomes very short lived and is no longer detectable because of the faster formation of Tyr-107(.). We conclude that the phenyl rings of Trp-111 and Tyr-107 form a better stacking complex so that the proton-coupled electron transfer is facilitated compared with the single mutant. Comparison with the formation kinetics of the stable tyrosyl radical in wild type R2 suggests that these protein-linked radicals are substitutes for the missing Tyr-122. However, in contrast to Tyr-122(.) these radicals lack a direct connection to the radical transfer pathway utilized during catalysis.

Crystallography, X-Ray↗
PubMed1997

The relation of clinical saccadic eye movement testing to reading in kindergartners and first graders.

Although a substantial body of research has demonstrated an association between reading and eye movements, this association has not been examined in kindergartners. Therefore, the relation between psychometric eye movement scores and reading skill was studied in a masked investigation with 181 kindergartners and first graders (mean age 6.25 years) from a middle class, suburban, elementary school near Cleveland, Ohio. Eye movements were evaluated with the New York State Optometric Association King-Devick (NYSOA K-D; Bernell Corporation, South Bend, IN) and the Developmental Eye Movement tests (DEM; Bernell Corporation, South Bend, IN). Digit knowledge was assessed with Reversals Frequency Test Execution subtest (Gardner). Reading performance was measured with Metropolitan Achievement Test 6 (MAT6) Reading Test and teachers' assessments. The number of unknown or reversed numbers on Gardner was significantly related to test times on the NYSOA K-D and DEM, but not the DEM ratio. Outcome on NYSOA K-D, determined by errors in conjunction with test time, was significantly related to reading ability in 5-year-olds (p = 0.0129), 6-year-olds (p = 0.0167), and the entire subject group when controlling for age (p = 0.0008). Our findings suggest that: (1) DEM factors out automaticity of number knowledge; (2) the NYSOA K-D can be completed by kindergartners; (3) the DEM is too difficult for many kindergarteners; and (4) performance on the NYSOA K-D is related to reading performance in 5- and 6-year-olds in kindergarten.

Child↗
PubMed1997

Reliability of the NYSOA King-Devick saccadic eye movement test in kindergartners and first graders.

BACKGROUND: Studies have shown a learning effect frequently occurs on administration of the New York State Optometric Association King-Devick (NYSOA K-D) in 7- to 12-year-old children. However, the reliability of the NYSOA K-D has not been studied in younger children. Further, the effect of visual anomalies on reliability has not been investigated previously. METHODS: The reliability of the NYSOA K-D saccadic eye movement test was assessed in a masked investigation of 52 children in kindergarten and first grade (25 kindergartners [mean age, 5.76 years] and 27 first graders [mean age, 6.78 years]) from a middle-class, suburban, elementary school near Cleveland, Ohio. The MCT was administered to all the children. The NYSOA K-D test was administered to the children and then retested 1 week and 3 weeks later. RESULTS: An evaluation of the NYSOA K-D test/retest results revealed a significant trend toward improved test times in first graders (p = 0.0001). In addition, a high number of children were classified differently from one test administration to the next. CONCLUSION: These findings suggest that the NYSOA K-D is not reliable in kindergarten and first grade children.

Child↗
PubMed1996

High field EPR studies of mouse ribonucleotide reductase indicate hydrogen bonding of the tyrosyl radical.

Ribonucleotide reductase catalyzes by free radical chemistry the reduction of ribonucleotides to deoxyribonucleotides. The R2 protein of a class 1 ribonucleotide reductase contains a stable tyrosyl radical of neutral phenoxy character, which is necessary for normal enzymatic activity. Here we present the EPR spectra from the tyrosyl free radical in the R2 protein from mouse at 9.62, 115, and 245 GHz. We show that the g-value anisotropy of the mouse R2 radical, when precisely determined from high field EPR spectra, is similar to that of the hydrogen bonded dark stable YD middle dot tyrosyl radical of photosystem II and different from that of the Escherichia coli R2 radical. Because the g-value anisotropy is an important indicator of the hydrogen bonding status of the tyrosyl radical, this result suggests that the mouse R2 radical has its tyrosylate oxygen hydrogen bonded with a D2O exchangeable proton, whereas this hydrogen bond is absent in the E. coli enzyme. It is suggested that the observed proton may be derived from the tyrosine that will become a tyrosyl radical.

Animals↗
PubMed1996

The free radical of the anaerobic ribonucleotide reductase from Escherichia coli is at glycine 681.

The anaerobic ribonucleoside triphosphate reductase of Escherichia coli is an iron-sulfur protein carrying an oxygen-sensitive organic radical, which is essential for catalysis. The radical was tentatively proposed to be on glycine 681, based on a comparison with the glycyl radical-containing enzyme pyruvate formate-lyase. By EPR spectroscopy of selectively 2H- and 13C-labeled anaerobic ribonucleotide reductase, the radical was now unambiguously assigned to carbon-2 of a glycine residue. The large 1H hyperfine splitting (1.4 millitesla) was assigned to the alpha-proton. Site-directed mutagenesis was used to change glycine 681 into an alanine residue. In separate experiments, the two adjacent residues, cysteine 680 and tyrosine 682, were changed into serine and phenylalanine, respectively. All mutated proteins were retained on dATP-Sepharose, indicating that the mutant proteins had intact allosteric sites. They also contained amounts of iron comparable with the wild type reductase and showed the same iron-sulfur-related spectrum, suggesting that the mutant proteins were properly folded. Of the three mutant proteins only the G681A protein completely lacked the detectable glycyl radical as well as enzyme activity. Our results identify glycine 681 as the stable free radical site in E. coli anaerobic ribonucleotide reductase.

Base Sequence↗
PubMed1996

Reversible red-ox reactions of the diiron site in the mouse ribonucleotide reductase R2 protein.

The red-ox reactions of the dinuclear iron center of mouse R2 protein upon interaction with different reductants (dithionite alone and with mediators) and oxidants (PES, methylene blue, hydrogen peroxide and para-benzoquinone) have been studied by EPR and optical spectroscopy. The obtained results indicate that the transitions between Fe(III)Fe(III), Fe(II)Fe(III) and Fe(II)Fe(II) states of the dinuclear iron center are reversible and the mu-oxo-bridge may be formed upon oxidation by non-oxygen oxidants. In contrast to the case for the E. coli R2 protein, dithionite alone reduces the tyrosyl radical and diiron center in mouse R2 protein.

Animals↗