Active human cytomegalovirus protease is a dimer

The quaternary state of the human cytomegalovirus (hCMV) protease has been analyzed in relation to its catalysis of peptide hydrolysis. Based on results obtained from steady state kinetics, size exclusion chromatography, and velocity sedimentation, the hCMV protease exists in a monomer-dimer equilibrium. Dimerization of the protease is enhanced by the presence of glycerol and high concentrations of enzyme. Isolation of monomeric and dimeric species eluted from a size exclusion column, followed by immediate assay, identifies the dimer as the active species. Activity measurements conducted with a range of enzyme concentrations are also consistent with a kinetic model in which only the dimeric hCMV protease is active. Using this model, the dissociation constant of the protease is 6.6 microM in 10% glycerol and 0.55 microM in 20% glycerol at 30 degrees C and pH 7.5.

Elucidation of basic mechanistic and kinetic properties of influenza endonuclease using chemically synthesized RNAs

Influenza virus utilizes a unique mechanism for initiating the transcription of viral mRNA. The viral transcriptase ribonucleoprotein complex hydrolyzes host cell transcripts containing the cap 1 structure (m7GpppG(2'-OMe)-) to generate a capped primer for viral mRNA transcription. Basic aspects of this viral endonuclease reaction are elucidated in this study through the use of synthetic, radiolabeled RNA substrates and substrate analogs containing the cap 1 structure. Unlike most ribonucleases, this viral endonuclease is shown to catalyze the hydrolysis of the scissile phosphodiester, resulting in 5'-phosphate- and 3'-hydroxyl-containing fragments. Nevertheless, the 2'-OH adjacent to the released ribosyl 3'-OH is shown to be important for catalysis. In addition, while the endonuclease steady-state turnover rate is measured to be 2 h(-1), phosphodiester bond hydrolysis is not rate-limiting. The direct generation of a free 3'-OH and the subsequent slow release of this product are consistent with the viral need for efficient use of the capped primer in subsequent reactions of the influenza transcriptase complex.

Cleavage of oligoribonucleotides by the 2',5'-oligoadenylate- dependent ribonuclease L

RNase L, the 2',5' oligoadenylate-dependent ribonuclease, is one of the enzyme systems important in the cellular response to interferon. When activated in the presence of 2',5'-linked oligoadenylates, RNase L can catalyze the cleavage of synthetic oligoribonucleotides that contain dyad sequences of the forms UU, UA, AU, AA, and UG, but it cannot catalyze the cleavage of an oligoribonucleotide containing only cytosines. The primary site of the cleavage reaction with the substrate C11UUC7 has been defined to be 3' of the UU dyad by labeling either the 5' or the 3' end of the oligoribonucleotide and by examining the reaction products on polyacrylamide sequencing gels. Reaction time courses have been used to determine the kinetic parameters of the cleavage reactions. The effect of the overall length of the oligomeric substrate as well as the sequence of the bases around the position of the cleavage site on the kinetics of the cleavage reaction has been examined. The efficiency with which activated RNase L catalyzes the cleavage of the substrate C11UUC7 is 1.9 x 10(7) m-1 s-1. Because the cleavage of the synthetic oligoribonucleotide can be used to monitor the steady-state kinetics of catalysis by activated RNase L, this method offers an advantage over previous methods of assay for RNase L activity.

Stoichiometry of 2',5'-oligoadenylate-induced dimerization of ribonuclease L. A sedimentation equilibrium study

Ribonuclease L is an endoribonuclease that is activated by binding of 2',5'-linked oligoadenylates. Activation of ribonuclease L also induces dimerization. Here, we demonstrate using equilibrium sedimentation that dimerization requires the binding of one 5'-monophosphate 2',5'-(adenosine)3 molecule per ribonuclease L monomer. No dimerization was observed in the absence of activator up to a protein concentration of 18 microM, indicating that unliganded enzyme is unable to dimerize or the association is very weak. In parallel with dimerization, enzymatic activity is also maximized at a 1:1 activator: ribonuclease L stoichiometry. The same stoichiometry for dimerization is observed using a nonphosphorylated activator 2'-5'-(adenosine)3. Adenosine triphosphate or RNA oligonucleotide substrates do not induce dimerization. The observed stoichiometry supports a model for ribonuclease L dimerization in which activator binds to monomer, which subsequently dimerizes.

Assay for influenza virus endonuclease using DNA polymerase extension of a specific cleavage product

The synthesis of influenza virus mRNA requires primers generated by cleavage of host cell transcripts 10-13 nucleotides from the 5' end by a virally encoded endonuclease. This novel enzyme is an attractive target for the development of antiviral agents. An assay for the influenza virus endonuclease has been developed that monitors the substrate cleavage reaction only at the correct position in the sequence, thereby discriminating against nonspecific RNA cleavage products. The influenza endonuclease assay is sensitive enough to detect 200 amol of product. The assay employs a DNA polymerase-catalyzed extension of the endonuclease cleavage product using radiolabeled dGTP and a DNA template containing a 3' region complementary to the product joined to a 5' region consisting of 10 dC residues. The influenza endonuclease assay does not involve gel electrophoretic separation and is amenable to high volume screening of potential inhibitors. The assay may also be employed to determine the site of influenza endonucleolytic cleavage in the substrate.

Three-dimensional structure of a mutant HIV-1 protease displaying cross-resistance to all protease inhibitors in clinical trials

Analysis of mutational effects in the human immunodeficiency virus type-1 (HIV-1) provirus has revealed that as few as four amino acid side-chain substitutions in the HIV-1 protease (M46I/L63P/V82T/I84V) suffice to yield viral variants cross-resistant to a panel of protease inhibitors either in or being considered for clinical trials (Condra, J. H., Schleif, W. A., Blahy, O. M., Gadryelski, L. J., Graham, D. J., Quintero, J. C., Rhodes, A., Robbins, H. L., Roth, E., Shivaprakash, M., Titus, D., Yang, T., Teppler, H., Squires, K. E., Deutsch, P. J., and Emini, E. A. (1995) Nature 374, 569-571). As an initial effort toward elucidation of the molecular mechanism of drug resistance in AIDS therapies, the three-dimensional structure of the HIV-1 protease mutant containing the four substitutions has been determined to 2.4-A resolution with an R factor of 17.1%. The structure of its complex with MK639, a protease inhibitor of the hydroxyaminopentane amide class of peptidomimetics currently in Phase III clinical trials, has been resolved at 2.0 A with an R factor of 17.0%. These structures are compared with those of the wild-type enzyme and its complex with MK639 (Chen, Z., Li, Y., Chen, E., Hall, D. L., Darke, P. L., Culberson, C., Shafer, J., and Kuo, L. C. (1994) J. Biol. Chem. 269, 26344-26348). There is no gross structural alteration of the protease due to the site-specific mutations. The C alpha tracings of the two native structures are identical with a root-mean-square deviation of 0.5 A, and the four substituted side chains are clearly revealed in the electron density map. In the MK639-bound form, the V82T substitution introduces an unfavorable hydrophilic moiety for binding in the active site and the I84V substitution creates a cavity (unoccupied by water) that should lead to a decrease in van der Waals contacts with the inhibitor. These changes are consistent with the observed 70-fold increase in the Ki value (approximately 2.5 kcal/mol) for MK639 as a result of the mutations in the HIV-1 protease. The role of the M46I and L63P substitutions in drug resistance is not obvious from the crystallographic data, but they induce conformational perturbations (0.9-1.1 A) in the flap domain of the native enzyme and may affect the stability and/or activity of the enzyme unrelated directly to binding.

Crystal structure at 1.9-A resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases

L-735,524 is a potent, orally bioavailable inhibitor of human immunodeficiency virus (HIV) protease currently in a Phase II clinical trial. We report here the three-dimensional structure of L-735,524 complexed to HIV-2 protease at 1.9-A resolution, as well as the structure of the native HIV-2 protease at 2.5-A resolution. The structure of HIV-2 protease is found to be essentially identical to that of HIV-1 protease. In the crystal lattice of the HIV-2 protease complexed with L-735,524, the inhibitor is chelated to the active site of the homodimeric enzyme in one orientation. This feature allows an unambiguous assignment of protein-ligand interactions from the electron density map. Both Fourier and difference Fourier maps reveal clearly the closure of the flap domains of the protease upon L-735,524 binding. Specific interactions between the enzyme and the inhibitor include the hydroxy group of the hydroxyaminopentane amide moiety of L-735,524 ligating to the carboxyl groups of the essential Asp-25 and Asp-25' enzymic residues and the amide oxygens of the inhibitor hydrogen bonding to the backbone amide nitrogen of Ile-50 and Ile-50' via an intervening water molecule. A second bridging water molecule is found between the amide nitrogen N2 of L-735,524 and the carboxyl oxygen of Asp-29'. Although other hydrogen bonds also add to binding, an equally significant contribution to affinity arises from hydrophobic interactions between the protease and the inhibitor throughout the pseudo-symmetric S1/S1', S2/S2', and S3/S3' regions of the enzyme. Except for its pyridine ring, all lipophilic moieties (t-butyl, indanyl, benzyl, and piperidyl) of L-735,524 are rigidly defined in the active site.

Purification of active herpes simplex virus-1 protease expressed in Escherichia coli

Assembly of viral capsids for replication of herpes simplex virus requires the proteolytic processing of the assembly protein ICP35. The protease responsible for this process is encoded within the 635-amino acid open reading frame of the UL26 gene of the virus. A simple purification scheme is given in this report for the native, mature form of the protease expressed in Escherichia coli. The scheme allows the preparation of milligram quantities of purified enzyme for elucidation of kinetic mechanism as well as for structural studies. Utilizing a 13-residue peptide substrate representing the natural cleavage site that releases the protease, kcat and Km values of the purified native enzyme are 2.0 min-1 and 0.88 mM, respectively. Thus, peptide cleavage is less efficient than reported for other viral proteases. The possibility exists that viral or cellular factors are involved in vivo for activation of the protease for herpes capsid maturation.

Effect of template secondary structure on the inhibition of HIV-1 reverse transcriptase by a pyridinone non-nucleoside inhibitor

The importance of RNA secondary structure on HIV-1 reverse transcriptase catalyzed polymerization and on the potency of the pyridin-2-one inhibitor 3-(4,7-dichlorobenzoxazol-2-ylmethylamino)-5-ethyl-6-meth ylpyridin-2(1H)-one, L-697,661, were investigated by employing heteromeric primer-template systems. Our data revealed that a stem-loop hairpin secondary structure in the RNA template could lead to strong hindrance of reverse transcription in the reaction catalyzed by HIV-1 reverse transcriptase resulting in the build up of intermediate-length (pause) polymerization products. The presence of L-697,661 greatly enhanced the accumulation of the pause products suggesting that the rate of enzyme translocation from the pause product might be more potently inhibited than polymerization up to the pause site. Model experiments using a synthetic RNA template containing a stem-loop hairpin revealed that the inhibitory potency of L-697, 661 increased 2-fold upon polymerization to within four bases of the secondary structure. Inhibitor potency was enhanced over 6-fold when primer-extension proceeded through the duplex region of the stem-loop.

Sensitivity of HIV-1 reverse transcriptase and its mutants to inhibition by azidothymidine triphosphate

HIV-1 reverse transcriptase can catalyze the addition of either azidothymidine monophosphate (AZTMP) or thymidine monophosphate (dTMP) to a primer strand opposite template adenosine bases. The ratio of incorporation of AZTMP to dTMP as catalyzed by HIV-1 reverse transcriptase has been determined to be 0.4 using an RNA-DNA duplex substrate prepared from oligonucleotides with sequences taken from the HIV-1 genome sequence. Slight variations are found for the incorporation ratio of the two nucleotides on other substrates. Substrates containing more than one adenosine in the single-stranded part of the template allow for more chances to incorporate AZTMP and less full-length product. Variations in the intensity of bands on an autoradiograph of a DNA sequencing gel corresponding to different positions of incorporation of AZTMP suggest that not all template adenosine positions offer the same level of discrimination against incorporation of AZTMP. A reverse transcriptase containing a set of four mutations (D67N, K70R, T215Y, K219Q) known to cause resistance to AZT in cell culture assays has a ratio of incorporation that is 0.77 +/- 0.03 times the ratio for the wild-type reverse transcriptase opposite one specific template adenosine. In contrast, a hybrid mutant containing the same four mutations that cause resistance to AZT and an additional mutation, Y181C, which by itself causes resistance to the non-nucleoside inhibitor L-697,661 [Sardana et al. (1992), J. Biol. Chem. 267, 17526-17530], has a ratio of incorporation that is 1.34 +/- 0.01 times that of the wild-type, indicating that the hybrid mutant enzyme is more susceptible to inhibition by AZTTP than the wild-type reverse transcriptase.(ABSTRACT TRUNCATED AT 250 WORDS)

Dissociation and association of the HIV-1 protease dimer subunits: equilibria and rates

The kinetics and equilibrium properties were investigated for the interconversion between the active dimer of human immunodeficiency virus 1 (HIV-1) protease and its inactive monomeric subunits. The equilibrium dissociation constant (Kd) of the dimeric protease as well as the monomer association rate were obtained by monitoring the fluorescence change of an active-site-directed fluorescent probe (L-737244) upon its binding to the protease. The Kd of the HIV-1 protease is strongly pH dependent. At pH 5.5 where the enzyme is most active catalytically, the extrapolated values of Kd are 0.75 and 3.4 nM at 30 and 37 degrees C, respectively. The rate constant for HIV-1 monomer association, approximately 4 x 10(5) M-1 s-1, is within the range commonly observed for protein-protein interactions. Dimer dissociation was further scrutinized in the presence of an inactive, point mutant form of the enzyme. As a result of subunit exchange between the native and mutant enzymes and the formation of an inactive heterodimer, there was a time-dependent decrease in the activity of the native protease. Enzyme activity could be reinstated with the addition of an active-site-directed inhibitor (L-365862) which selectively binds active dimers. The rate of dimer dissociation was found to also decrease with pH. At pH 5.5 and 30 degrees C, the half-life for subunit dissociation is about 0.5 h. The slow dissociation, coupled with the high stability for dimer association, attests to the importance of allowing sufficient time for dimer-monomer equilibration in kinetic assays in order to avoid reaching erroneous conclusions in studies of dimer dissociation.

Solution oligomerization of the rev protein of HIV-1: implications for function

rev is an RNA-binding protein of human immunodeficiency virus-1 and is required for the expression of incompletely spliced viral transcripts. Oligomerization of rev is thought to be associated with RNA binding and rev function. Here, we have characterized the oligomerization of rev using equilibrium analytical centrifugation. rev is predominantly monomeric at low concentrations, but reversibly polymerizes to produce large aggregates at higher concentrations. The data fit well to an unlimited isodesmic self-association model in which the association constants for the addition of a monomer to each aggregate are equal [K = 1.08 x 10(6) M-1 at 4 degrees C]. The association constant is essentially independent of monovalent salt concentration from 0.15 to 2 M at pH 6-9. Thermodynamic parameters derived from the temperature dependence of the association constant over the limited range of 0-30 degrees C reveal that the primary contribution to the free energy of oligomerization is a large negative enthalpy. Binding of rev to the rev-responsive element of RNA was characterized under the same conditions as the centrifugation experiments using a nitrocellulose filter assay. rev binds to the RRE at a protein concentration where rev is predominantly monomeric, suggesting that solution multimerization of rev is not required for rev function.

Surgical repair of atrial septal rupture due to blunt trauma

We report a case of atrial septal rupture and surgical cure after blunt chest trauma. Review of the literature indicates that this rare lesion results from severe forces applied to the chest and is often associated with other serious and life-threatening injuries. The defect may not be recognized for several months or even years in patients who survive concomitant initial trauma. When operative repair is undertaken, a favorable outcome can be anticipated.

Amorphous silicon and amorphous silicon nitride films prepared by a plasma-enhanced chemical vapor deposition process as optical coating materials

Durable, uniform, and reproducible amorphous silicon and amorphous silicon nitride thin films deposited by plasma-enhanced chemical vapor deposition that are appropriate for the design and fabrication of optical interference filters in the near-infrared region are found. Optical and physicalk properties of single-layer films are discussed. The durability and performance of Fabry-Perot interference filters and a 15-layer long-pass edge filter in the near-infrared region designed and fabricated with these two thin-film materials are also reported.

Utilization of conformational flexibility in enzyme action-linkage between binding, isomerization, and catalysis

An intimate relationship between protein conformational changes and catalysis has often been suggested. The present study employs ligand-induced ultraviolet difference spectra and kinetic parameters determined for Escherichia coli ornithine transcarbamoylase and its site-specific mutants to evaluate the linkage between binding, isomerization, and reaction rate. For the wild-type enzyme, the lead substrate carbamoyl phosphate introduces a large difference absorbance in the enzyme upon binding (delta epsilon max approximately 1,800 M-1 cm-1; Miller, A. W., and Kuo, L. C. (1990) J. Biol. Chem. 265, 15023-15027). The spectrum is the same in lineshape as that produced by the bisubstrate analog N-(phosphonacetyl)-L-ornithine and is 80% as intense. Both substrate and analog cause gross protein conformational rearrangements as evident by swift and severe cracking of enzyme crystals in their presence. For the mutants, the difference spectra actuated by the substrate are the same in lineshape as that of the wild type but vary in intensity. A wide range of substrate affinity and steady-state kinetic constants are also observed for the mutants. When the binding energy of carbamoyl phosphate and the activation energy for transcarbamoylation are calculated for the wild-type and mutant enzymes, they are found to be inversely correlated to the intensity of protein difference absorbance elicited by the lead substrate. Together with analyses of steady-state kinetic parameters derived for various plausible reaction schemes, the experimental data suggest that carbamoyl phosphate induces the committed isomerization in ornithine transcarbamoylase for transition state binding. Our results provide a unique demonstration that an induced-fit isomerization, triggered by binding, either controls or contributes significantly to the rate of an enzyme-catalyzed reaction.

Protonation of arginine 57 of Escherichia coli ornithine transcarbamoylase regulates substrate binding and turnover

The amino acid residue Arg57 of Escherichia coli ornithine transcarbamoylase is located in the carbamoyl phosphate-binding domain of the enzyme. This residue has been implicated to be critical for efficient carbamoylation and is linked to an induced-fit protein isomerization elicited by the lead substrate carbamoyl phosphate. To elucidate its role in substrate binding and catalysis, Arg57 has been substituted by one of two amino acids, glycine and histidine, varying in size and charge. Elimination of the positive charge and steric bulk on residue 57 with an arginine-to-glycine substitution results in an enzyme which binds its substrates in a random order (Kuo, L. C., Miller, A. W., Lee, S., and Kozuma, C. (1988) Biochemistry 27, 8823-8832). Replacement of Arg57 by histidine provides a substantial portion of the steric bulk at this residue position and also brings the pKa of this residue into an experimentally observable window. Kinetic and pH titration experiments reveal that when His57 is deprotonated the enzyme binds its substrates randomly. However, when His57 is protonated the enzyme observes the obligatory substrate binding order as seen for the wild type. Both the Gly57 and His57 point mutants are incapable of undergoing the carbamoyl phosphate-induced protein conformational changes apparent in the wild type. These results reveal that the induced-fit isomerization of ornithine transcarbamoylase does not contribute to the order in which the substrates bind. A comparison of the reaction schemes and pH profiles of the wildtype and His57 enzymes further indicates that protonation of residue 57 facilitates formation of the binary enzyme-carbamoyl phosphate complex and augments the turnover rate of the reaction. Together with steady-state kinetic parameters derived in terms of microscopic rate constants, our results provide additional support to our earlier suggestion (Zambidis, I. and Kuo, L. C. (1990) J. Biol. Chem. 265, 2620-2623) that the turnover rate of the wild-type ornithine transcarbamoylase in the forward reaction is largely dictated by the rate of the carbamoyl phosphate-induced isomerization.

Inhibition of HIV-1 reverse transcriptase by pyridinone derivatives. Potency, binding characteristics, and effect of template sequence

The inhibition of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase by pyridinone compounds has been investigated using as templates synthetic RNA with sequences based on the HIV-1 genome sequence. In reactions catalyzed by the enzyme that incorporated more than one nucleotide per primer, inhibition by a representative pyridinone inhibitor, 3-[2-(1,3-benzoxazol-2-yl)ethyl]-5-ethyl-6-methyl-pyridin-2(1H)one (L-696,229), was noncompetitive against deoxynucleotide triphosphate. For reactions that incorporated one deoxynucleotide per primer, IC50 values ranged from 20 to 200 nM, depending on the position of incorporation of the incoming deoxynucleotide base on the template. Inhibition of synthesis on a set of four templates differing only at the template base complementary to the incoming nucleotide had similar IC50 values. These results demonstrate that inhibitory potency is dependent on the primary structure of the template and that inhibitory potency is largely independent of the identity of the incoming nucleotide base. The inhibition of HIV-1 reverse transcription by L-696,229 also displayed slow-binding characteristics. The slow-binding aspect was exploited to gauge the interaction between inhibitor and enzyme. By titrating the reduction in the extent of the burst of synthesis observed in a reaction incorporating dideoxythymidine monophosphate into poly(rA)-oligo(dT)18, the apparent equilibrium constant for dissociation of the reverse transcriptase-L-696,229 complex was estimated to be 400 nM.

Activity and dimerization of human immunodeficiency virus protease as a function of solvent composition and enzyme concentration

The activity of human immunodeficiency virus 1 (HIV-1) protease has been examined as a function of solvent composition, incubation time, and enzyme concentration at 37 degrees C in the pH 4.5-5.5 range. Glycerol and dimethyl sulfoxide inhibit the enzyme, while polyethylene glycol and bovine serum albumin activate the enzyme. When incubated at a concentration of 50-200 nM, the activity of the protease decreases irreversibly with an apparent first-order rate constant of 4-9 x 10(-3) min-1. The presence of 0.1% (w/v) polyethylene glycol or bovine serum albumin in the reaction buffer dramatically stabilizes enzyme activity. In the absence of prolonged incubation of the enzyme at submicromolar concentration, the specific activity of HIV-1 protease in buffers of either high or low ionic strength is constant over the enzyme concentration range of 0.25-5 nM, indicating that dissociation of the dimeric protease, if occurring, can only be governed by a picomolar dissociation constant. Similarly, the variation of the specific activity of HIV-2 protease over the enzyme concentration of 4-85 nM is consistent only with a dimer dissociation constant of less than 10 nM. We conclude that: 1) the assumption of a nondissociating HIV-1 protease is a valid one for kinetic studies of tight-binding inhibitors where nanomolar concentrations of the enzymes are employed; 2) stock protease solutions of submicromolar concentration in the absence of activity-stabilizing compounds may lead to erroneous kinetic data and complicate mechanistic interpretations.

Control of L-ornithine specificity in Escherichia coli ornithine transcarbamoylase. Site-directed mutagenic and pH studies

Escherichia coli ornithine transcarbamoylase displays a strict specificity toward its second substrate L-ornithine. After forming a binary complex with carbamoyl phosphate and undergoing an induced-fit isomerization (Miller, A. W., and Kuo, L. C. (1990) J. Biol. Chem. 265, 15023-15027), the enzyme selects only the minor, zwitterionic ornithine with an uncharged delta-amino group for transcarbamoylation. Formation of the productive ternary complex is linked to two enzymic ionizations (pK alpha 6.2 approximately 6.3 and 9.1 approximately 9.3) and two ornithine ionizations (pK alpha 8.5 and 10.6) (Kuo, L. C., Herzberg, W., and Lipscomb, W. N. (1985) Biochemistry 24, 4754-4761). To elucidate the mechanism through which substrate specificity is achieved, the binding of L-ornithine to two site-specific point mutants (Arg-57----Gly and Cys-273----Ala) of the enzyme has been examined. For the Gly-57 mutant enzyme, which does not undergo the induced-fit isomerization, affinity for ornithine drops by a factor of 500. The pH profile of the apparent equilibrium constant governing the association of L-ornithine to the binary complex of this mutant reveals that only two enzymic ionizations affect ornithine binding. The ionizations linked to L-ornithine are not detected. Hence, the preisomerized binary complex binds not only poorly but also indiscriminately all ionic species of L-ornithine. For the Ala-273 mutant enzyme, which exhibits the induced-fit isomerization, affinity of the amino acid is decreased by an order of magnitude. Ionizations of L-ornithine to yield a zwitterion for binding are detected in pH analyses for this mutant, but the pK alpha of 6.2 associated with the enzymic deprotonation in the wild type is absent. Therefore, Cys-273 is a binding site of L-ornithine. The D-isomer of ornithine is a very weak, deadend ligand to all three forms of the enzyme with affinities in the millimolar range. Employing the estimated affinities of D- and L-ornithine, the binding stereospecificity of the wild-type and mutant binary complexes toward the amino acid substrate may be evaluated. L-Ornithine binds preferentially over D-ornithine by two and four orders of magnitude in the absence and presence of protein isomerization, respectively.(ABSTRACT TRUNCATED AT 400 WORDS)

Ligand-induced isomerizations of Escherichia coli ornithine transcarbamoylase. An ultraviolet difference analysis

Ligand-induced ultraviolet difference spectra have been determined for Escherichia coli ornithine transcarbamoylase. The most prominent feature of the spectra is an absorbance difference which resembles a single period of a sine wave spanning the 245-320 nm region with a maximum at approximately 270 nm and a minimum at around 295-300 nm. This broad absorbance difference is typical of a blue-shift 1La band of tryptophan. Superimposed on the broad band in the 275-310 nm region is a series of smaller, narrow peaks resulted from red-shifted 1Lb bands of tryptophan and tyrosine residues. At pH 8.5, only carbamoyl phosphate and its analog phosphonacetamide yield a large ultraviolet difference absorbance (approximately 1800 M-1 cm-1) when bound to the enzyme. The spectra obtained are essentially the same in lineshape to and 80% in intensity of that produced by the bisubstrate analogy, N-(phosphonacetyl)-L-ornithine. In contrast, inorganic phosphate, a product of the reaction, induces small protein absorbance changes (approximately 300 M-1 cm-1) mainly in the 275-310 nm range. When complexed to the free enzyme, L-ornithine yields a marginally discernible ultraviolet difference spectrum in the 275-310 nm region, and its analogs L-norvaline and L-citrulline provide no absorbance change. However, inorganic phosphate in combination with any of the L-amino acids produces a difference spectrum similar to that given by carbamoyl phosphate alone. Collectively, these spectra suggest that carbamoyl phosphate elicits an isomerization required for the formation of the ternary complex and are consistent with the compulsory ordered mechanism of the enzyme at pH 8.5 with carbamoyl phosphate being the first substrate bound. Below pH 8, there is a kinetically discernible amount of random binding, but ordered addition is still the preferred pathway (Wargnies B., Legrain, C., and Stalon, V. (1978) Eur J. Biochem. 89, 203-212). Reflecting this change, the difference absorbance of the enzyme bound with carbamoyl phosphate is also pH dependent. The 1La band in the carbamoyl phosphate difference spectrum diminishes by approximately 20% at low pH. The PALO-induced changes, however, are pH invariant suggesting that full extent of the induced-fit isomerization is always reached in the ternary complex.

Substrate specificity and protonation state of Escherichia coli ornithine transcarbamoylase as determined by pH studies. Binding of carbamoyl phosphate

Binding of carbamoyl phosphate to Escherichia coli ornithine transcarbamoylase and its relation to turnover have been examined as a function of pH under steady-state conditions. The pH profile of the dissociation constant of carbamoyl phosphate (Kiacp) shows that the affinity of the substrate increases as pH decreases. Two ionizing groups are involved in carbamoyl phosphate binding. Protonation of an enzymic group with pKa 9.6 results in productive binding of the substrate with a moderate affinity of Kiacp approximately 30 microM. Protonation of a second group further enhances binding by roughly another order of magnitude. This ionization occurs with a pKa that shifts from less than 6 in the free enzyme to 7.3 in the binary complex. However, tighter binding of carbamoyl phosphate due to this ionization does not contribute to catalysis. The turnover rate (kcat) of the enzyme diminishes in the acidic pH range and is governed by an ionization with a pKa of 7.2. Both the catalytic pKa of 7.2 and the productive binding pKa of 9.6 appear in the pH profile of kcat/KMcp. Together with earlier kinetic results (Kuo, L. C., Herzberg, W., and Lipscomb, W. N. (1985) Biochemistry 24, 4754-4761), these data suggest that the step which modulates kcat may occur prior to the binding of the second substrate L-ornithine.

Zn2+ regulation of ornithine transcarbamoylase. II. Metal binding site

Two types of conformational changes are mediated in Escherichia coli ornithine transcarbamoylase by the metal ion zinc. Upon binding of zinc in rapid equilibrium, the enzyme undergoes an allosteric transition. In the absence of substrates, the zinc-bound enzyme further undergoes a slow isomerization with a concomitant activity loss. Three metal ions are tightly complexed in the isomerized enzyme as determined by gel chromatography and atomic absorption spectroscopy. Since the enzyme is a trimer composed of identical subunits, one zinc ion is bound per enzyme monomer. With the application of site-directed mutagenesis, the cysteinyl residue at position 273 of the enzyme has been identified as a metal ligand. When this residue is replaced by an alanine, zinc is no longer a tight-binding inhibitor and does not promote isomerization. The alteration in the action of zinc on the mutant enzyme is attributed to a reduced metal affinity. The mutant enzyme, when saturated by the metal, displays an intrinsic allostery unchanged from that of the wild-type; an identical Hill coefficient of 1.5 is found for zinc binding to the Ala273 and wild-type enzymes. Cys273 is also a binding site of L-ornithine. At pH 8.5, the Ala273 enzyme binds the substrate analog L-norvaline ten times more weakly and exhibits a kcat/Kmorn that is 27 times less than that of the wild-type enzyme. This finding supports our earlier interpretation that the zinc-induced ornithine co-operativity of ornithine transcarbamoylase is caused by direct competition between L-ornithine and the metal for the same site. As controls, each of the remaining three cysteinyl residues of the bacterial ornithine transcarbamoylase has also been replaced with alanine. These sulfhydryl groups are found not to be related to zinc complexation, ornithine binding or enzyme allostery.