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J Kraut

Publications and source records attributed to J Kraut.

At least 91 records · Page 5Linked to original sources
PubMed1986

Functional role of aspartic acid-27 in dihydrofolate reductase revealed by mutagenesis.

The crystal structures and enzymic properties of two mutant dihydrofolate reductases (Escherichia coli) were studied in order to clarify the functional role of an invariant carboxylic acid (aspartic acid at position 27) at the substrate binding site. One mutation, constructed by oligonucleotide-directed mutagenesis, replaces Asp27 with asparagine; the other is a primary-site revertant to Ser27. The only structural perturbations involve two internally bound water molecules. Both mutants have low but readily measurable activity, which increases rapidly with decreasing pH. The mutant enzymes were also characterized with respect to relative folate: dihydrofolate activities and kinetic deuterium isotope effects. It is concluded that Asp27 participates in protonation of the substrate but not in electrostatic stabilization of a positively charged, protonated transition state.

Aspartic Acid↗
PubMed1985

The 2.6-A crystal structure of Pseudomonas putida cytochrome P-450.

The crystal structure of Pseudomonas putida cytochrome P-450cam in the ferric, camphor bound form has been determined and partially refined to R = 0.23 at 2.6 A. The single 414 amino acid polypeptide chain (Mr = 45,000) approximates a triangular prism with a maximum dimension of approximately 60 A and a minimum of approximately 30 A. Twelve helical segments (A through L) account for approximately 40% of the structure while antiparallel beta pairs account for only approximately 10%. The unexposed iron protoporphyrin IX is sandwiched between two parallel helices designated the proximal and distal helices. The heme iron atom is pentacoordinate with the axial sulfur ligand provided by Cys 357 which extends from the N-terminal end of the proximal (L) helix. A substrate molecule, 2-bornanone (camphor), is buried in an internal pocket just above the heme distal surface adjacent to the oxygen binding site. The substrate molecule is held in place by a hydrogen bond between the side chain hydroxyl group of Tyr 96 and the camphor carbonyl oxygen atom in addition to complementary hydrophobic contacts between the camphor molecule and neighboring aliphatic and aromatic residues. The camphor is oriented such that the exo-surface of C5 would contact an iron bound, "activated" oxygen atom for stereoselective hydroxylation.

Amino Acid Sequence↗
PubMed1985

Refined crystal structures of Escherichia coli and chicken liver dihydrofolate reductase containing bound trimethoprim.

Refined crystal structures are reported for complexes of Escherichia coli and chicken dihydrofolate reductase containing the antibiotic trimethoprim (TMP). Structural comparison of these two complexes reveals major geometrical differences in TMP binding that may be important in understanding the stereo-chemical basis of this inhibitor's selectivity for bacterial dihydrofolate reductases. For TMP bound to chicken dihydrofolate reductase we observe an altered binding geometry in which the 2,4-diaminopyrimidine occupies a position in closer proximity (by approximately 1 A) to helix alpha B compared to the pyrimidine position for TMP or methotrexate bound to E. coli dihydrofolate reductase. One important consequence of this deeper insertion of the pyrimidine into the active site of chicken dihydrofolate reductase is the loss of a potential hydrogen bond that would otherwise form between the carbonyl oxygen of Val-115 and the inhibitor's 4-amino group. In addition, for TMP bound to E. coli dihydrofolate reductase, the inhibitor's benzyl side chain is positioned low in the active-site pocket pointing down toward the nicotinamide-binding site, whereas, in chicken dihydrofolate reductase, the benzyl group is accommodated in a side channel running upward and away from the cofactor. As a result, the torsion angles about the C5-C7 and C7-C1' bonds for TMP bound to the bacterial reductase (177 degrees, 76 degrees) differ significantly from the corresponding angles for TMP bound to chicken dihydrofolate reductase (-85 degrees, 102 degrees). Finally, when TMP binds to the chicken holoenzyme, the Tyr-31 side chain undergoes a large conformational change (average movement is 5.4 A for all atoms beyond C beta), rotating down into a new position where it hydrogen bonds via an intervening water molecule to the backbone carbonyl oxygen of Trp-24.

Animals↗
PubMed1985

Dihydrofolate reductase. The stereochemistry of inhibitor selectivity.

X-ray structural results are reported for 10 triazine and pyrimidine inhibitors of dihydrofolate reductase, each one studied as a ternary complex with NADPH and chicken dihydrofolate reductase. Analysis of these data and comparison with structural results from the preceding paper (Matthews, D.A., Bolin, J.T., Burridge, J.M., Filman, D.J., Volz, K.W., Kaufman, B. T., Beddell, C.R., Champness, J.N., Stammers, D.K., and Kraut, J. (1985) J. Biol. Chem. 260, 381-391) in which we contrasted binding of the antibiotic trimethoprim (TMP) to chicken dihydrofolate reductase on the one hand with its binding to Escherichia coli dihydrofolate reductase on the other, permit identification of differences that are important in accounting for TMP's selectivity. The crystallographic evidence strongly suggests that loss of a potential hydrogen bond between the 4-amino group of TMP and the backbone carbonyl of Val-115 when TMP binds to chicken dihydrofolate reductase but not when it binds to the E. coli reductase is the major factor responsible for this drug's more potent inhibition of bacterial dihydrofolate reductase. A key finding of the current study which is important in understanding why TMP binds differently to chicken and E. coli dihydrofolate reductases is that residues on opposite sides of the active-site cleft in chicken dihydrofolate reductase are about 1.5-2.0 A further apart than are structurally equivalent residues in the E. coli enzyme.

Animals↗
PubMed1984

The crystal structure of fluoride-inhibited cytochrome c peroxidase.

The three-dimensional crystal structure of yeast cytochrome c peroxidase complexed with fluoride (F- or HF) has been determined by difference Fourier techniques and partially refined at 2.5-A resolution. Fluoride binding induces significant perturbations of the enzyme structure of the distal side of the heme. The major effect occurs at the active-site arginine residue (Arg-48) which moves about 2 A in order to optimize hydrogen-bonded interactions with the fluorine atom. A small readjustment of the distal histidine (His-52), about 0.5 A, is also seen upon fluoride binding. Additionally, a hydrogen-bonded network of 4 water molecules at the active site is reorganized. No significant movements are detectable in either the heme itself or in the proximal histidine ligand. These observations imply that movement of the Arg-48 side chain may play a key role in the enzymic mechanism of cytochrome c peroxidase. Although we cannot unequivocally determine whether fluoride is bound as HF or F-, the hydrogen-bonding pattern around the ligand points to the protonated form. Structural comparison suggests that there is a difference between the tautomeric state of the imidazole side chain of the distal histidine in cytochrome c peroxidase and of the similarly positioned distal histidine in the globins. This difference accounts for the observation that cytochrome c peroxidase preferentially binds the protonated form of ligands, whereas the globins bind the anionic form. The tautomer indicated by the peroxidase structure is the one required for acid base catalysis (Poulos, T.L., and Finzel, B. C. (1984) in Peptide and Protein Reviews (Decker, M., ed) in press).

Cytochrome-c Peroxidase↗
PubMed1984

Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution.

The crystal structure of cytochrome c peroxidase (EC 1.11.1.5) has been refined to an R factor of 0.20 computed for all reflections to 1.7 A. The refined molecular model includes 263 bound water molecules and allows for x-ray scattering by amorphous solvent. The mean positional error in atomic coordinates is estimated to lie between 0.12 and 0.21 A. Two factors are identified which may account for the ability of the enzyme to stabilize high-oxidation states of the heme iron during catalysis: 1) the proximal histidine forms a hydrogen bond with a buried aspartic acid side chain, Asp-235; and 2) the heme environment is more polar than in the cytochromes c or globins, owing to the presence of the partially buried side-chain of Arg-48 and five water molecules bound in close proximity to the heme. Two of these occupy the presumed peroxide-binding site. Two candidates are likely for the side chain that is oxidized to a free radical during formation of Compound I: 1) Trp-51, which rests 3.3 A above the heme plane in close proximity (2.7 A) to the sixth coordination position; and 2) Met-172, which is 3.7 A from the heme. Nucleophilic stabilization of the methionyl cation radical may be possible via Asp-235. His-181 is found to lie coplanar with the heme in a niche between the two propionates near the suspected cytochrome c-binding site. A network of hydrogen bonds involving this histidine may provide a preferred pathway for electron transfer between hemes.

Binding Sites↗
PubMed1984

A comparison of prazosin versus nadolol in combination with a diuretic.

The comparative efficacy and effects on total body potassium of prazosin and polythiazide vs nadolol and polythiazide in the treatment of patients with mild to moderate essential hypertension unresponsive to diuretic alone were compared in an open, crossover trial involving 20 male patients. Both prazosin and nadolol reduced blood pressure to goal values in both study phases. Side effects were minor, and only 1 patient dropped out of treatment for reasons unrelated to the study drugs. Neither prazosin nor nadolol in combination with thiazide had significant additional adverse effects on total body potassium. These findings confirm that the efficacy of prazosin is equivalent to that of nadolol in the long-term management of patients with essential hypertension.

Adrenergic beta-Antagonists↗
PubMed1983

Directed mutagenesis of dihydrofolate reductase.

Three mutations of the enzyme dihydrofolate reductase were constructed by oligonucleotide-directed mutagenesis of the cloned Escherichia coli gene. The mutations--at residue 27, aspartic acid replaced with asparagine; at residue 39, proline replaced with cysteine; and at residue 95, glycine replaced with alanine--were designed to answer questions about the relations between molecular structure and function that were raised by the x-ray crystal structures. Properties of the mutant proteins show that Asp-27 is important for catalysis and that perturbation of the local structure at a conserved cis peptide bond following Gly-95 abolishes activity. Substitution of cysteine for proline at residue 39 results in the appearance of new forms of the enzyme that correspond to various oxidation states of the cysteine. One of these forms probably represents a species cross-linked by an intrachain disulfide bridge between the cysteine at position 85 and the new cysteine at position 39.

Amino Acid Sequence↗
PubMed1983

Visual evoked potentials and long latency event-related potentials in chronic renal failure.

We studied auditory event-related potentials elicited in a target detection paradigm (P300) and pattern shift visual evoked potentials (PVEPs) in 22 patients with chronic renal failure and no clinical evidence of cognitive or visual impairment. Thirteen patients were maintained on chronic hemodialysis, and 9 patients were receiving a low-protein diet. Thirty-three percent of patients receiving the low-protein diet and 58% of the dialysis patients had abnormal P300 latencies. Most patients tested had abnormal PVEP. Four hemodialysis patients had elevated serum parathyroid hormone (PTH) levels, and 9 had normal or slightly elevated values. P300 and PVEP latencies were abnormal in both groups. These observations indicate that elevated PTH levels are not solely responsible for the abnormalities in all patients. P300 and PVEP may be valuable in evaluating neuronal dysfunction in the patient with chronic renal failure.

Adult↗
PubMed1982

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.

X-ray data have been extended to 1.7 A for a binary complex of Escherichia coli dihydrofolate reductase with methotrexate and a ternary complex of Lactobacillus casei dihydrofolate reductase with methotrexate and NADPH. Models for both structures have been refined to R factors of 0.15 and include parameters for fixed and liquid solvent. The two species of dihydrofolate reductase resemble one another even more closely than was thought to be the case prior to refinement. Several new structural features have also been discovered. Among them are a cis peptide linking Gly-97 and Gly-98 (L. Casei numbering) in both species, an alpha helix involving residues 43 through 50 in the E. coli enzyme, and the existence of what may be a specific hydration site on exposed alpha helices. Refinement has led to a revised description of the details of methotrexate binding. We now see that a fixed water molecule mediates the interaction between methotrexate's 2-amino group and Thr-116 (L. casei numbering) and that the inhibitor's 4-amino group makes two hydrogen bonds with the enzyme (instead of one). Other revisions are also discussed. A hypothetical model for substrate binding is proposed in which the pteridine ring is turned upside down while all protein and solvent atoms remain fixed. Asp-26 in this model is hydrogen bonded to the substrate's 2-amino group and to N3.

Binding Sites↗
PubMed1982

Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. II. Environment of bound NADPH and implications for catalysis.

New details of NADPH binding to Lactobacillus casei dihydrofolate reductase have become visible as a result of crystallographic refinement to an R factor of 0.152 at 1.7 A resolution. Conformational torsion angles for bound NADPH have been extensively revised and specific interatomic contacts responsible for cofactor binding have been identified. In addition, several structurally conserved water molecules are seen to mediate the protein-ligand interaction. In the nicotinamide binding site three oxygen atoms of the enzyme lie in the plane of the pyridine ring and close to ring carbons 2, 4, and 6. The placement of these polar groups suggests that the enzyme stabilizes a C4-carbonium electronic isomer of oxidized nicotinamide in the transition state. Pyramidalization of ring nitrogen N1 in the transition state might be promoted by a fixed water molecule positioned to donate a hydrogen bond to the N1 lone pair orbital. Pyramidalization could also relieve an unfavorable steric contact due to the observed rotation of the nicotinamide's carboxamide group by 180 degrees from its most stable conformation.

Binding Sites↗
PubMed1981

Prevention of hypoxemia during dialysis by the use of sequential isolated ultrafiltration-diffusion dialysis with bicarbonate dialyzate.

Previous studies have demonstrated that hypoxemia does not occur during isolated ultrafiltration, but does occur during diffusion dialysis with acetate, whether it is performed alone or following a period of isolated ultrafiltration. To determine if the substitution of bicarbonate for acetate in dialyzate could prevent hypoxemia, we studied the effect of sequential isolated ultrafiltration-diffusion dialysis with bicarbonate on arterial oxygen concentration. There was no significant change in pO2 during isolated ultrafiltration or the subsequent period of diffusion dialysis. In addition, excess body fluid could be removed and effective dialysis achieved without marked tachycardia or fluctuation in blood pressure. We conclude that sequential isolated ultrafiltration diffusion dialysis with bicarbonate is a safe and effective way of dialyzing patients without producing hypoxemia or cardiovascular instability.

Bicarbonates↗
PubMed1980

A hypothetical model of the cytochrome c peroxidase . cytochrome c electron transfer complex.

A hypothetical three-dimensional model of the cytochrome c peroxidase . tuna cytochrome c complex is presented. The model is based on known x-ray structures and supported by chemical modification and kinetic data. Cytochrome c peroxidase contains a ring of aspartate residues with a spatial distribution on the molecular surface that is complementary to the distribution of highly conserved lysines surrounding the exposed edge of the cytochrome c heme crevice, namely lysines 13, 27, 72, 86, and 87. These lysines are known to play a functional role in the reaction with cytochrome c peroxidase, cytochrome oxidase, cytochrome c1, and cytochrome b5. A hypothetical model of the complex was constructed with the aid of a computer-graphics display system by visually optimizing hydrogen bonding interactions between complementary charged groups. The two hemes in the resulting model are parallel with an edge separation of 16.5 A. In addition, a system of inter- and intramolecular pi-pi and hydrogen bonding interactions forms a bridge between the hemes and suggests a mechanism of electron transfer.

Amino Acids↗
PubMed1979

Dihydrofolate reductase from Lactobacillus casei. Stereochemistry of NADPH binding.

The NADPH molecule binds to dihydrofolate reductase in an extended conformation. Several of the individual dihedral angles, especially in the adenine mononucleotide portion of the coenzyme, differ from their minimum energy conformations. The ribose phosphate portions of the coenzyme are involved in numerous specific hydrogen-bonded and charge-charge interactions. The adenine ring resides in an apparently nonspecific hydrophobic cleft and the nicotinamide ring is bound within an intricately constructed cavity, one wall of which includes the pyrazine ring of bound methotrexate. Two rather extended loops (residues 10 to 24 and 117 to 135) connecting beta A to alpha B and beta F to beta G, respectively, move 2 to 3 A when NADPH binds to dihydrofolate reductase. No overall structural homology is evident between the dinucleotide binding domains of dihydrofolate reductase on the one hand and the four NAD+-dependent dehydrogenases of known structure on the other. However, binding does occur in both cases at the carboxyl edge of a region of parallel beta sheet flanked by a pair of alpha helices.

Binding Sites↗