Limited proteolysis of glycogen phosphorylase a by subtilisin BPN'

The limited proteolysis of rabbit skeletal muscle phosphorylase a was undertaken with subtilisin BPN' immobilized to Sepharose 4B. The effect of substrates, activators and inhibitors of phosphorylase a was investigated by monitoring the changes in phosphorylase activity in the SDS gel electrophoretic pattern and in the 32P-content of 32P-labeled phosphorylase a. Phosphorylase a loses its activity upon subtilisin treatment. All ligands tested protect phosphorylase a activity against subtilisin action, probably by inducing structural changes in the tower loop of the enzyme. Glucose-6-P significantly accelerates [32P]peptide release from phosphorylase a through altering the structure of the N-terminal tail segment. The two subunits of dimeric phosphorylase a are held together by strong interactions--deduced from the correlation of the rate of proteolysis and the disappearance of catalytic activity.     

Limited proteolysis of thermolysin by subtilisin: isolation and characterization of a partially active enzyme derivative

Incubation of the neutral metalloendopeptidase thermolysin at pH 9-10 in the presence of 10 mM CaCl2 for 2 days at room temperature with subtilisin at a 50:1 molar ratio leads to a derivative possessing lower (approximately 3%) but intrinsic catalytic activity. This derivative, called thermolysin S, was isolated by gel filtration in approximately 80% yield and then separated from some residual intact thermolysin by an affinity chromatographic step on Sepharose-Gly-D-Phe. It was found that thermolysin S results from a tight association of two polypeptide fragments of apparent Mr of 24000 and 10000. Dissociation of the complex was achieved under strong denaturing conditions, such as gel filtration on a column equilibrated and eluted with 5 M guanidine hydrochloride. The positions of the clip sites were defined by amino acid analysis, end-group determination, and amino acid sequencing of the isolated fragments and shown to lie between Thr-4 and Ser-5, between Thr-224 and Gln-225, and also between Gln-225 and Asp-226. Thermolysin S, which is therefore a stable complex of fragments 5-224(225) and 225(226)-316, shows a shift in optimum pH of about 1 unit toward the acid range with respect to intact thermolysin and a Km essentially unchanged, with furylacryloyl-Gly-Leu-NH2 as substrate. Inhibitors of thermolysin such as ethoxyformic anhydride and Zn2+ ions inactivate also the nicked enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)     

Modification of yeast phosphofructokinase by trypsin and subtilisin in the presence of effectors.

Yeast phosphofructokinase was subjected to limited proteolysis by trypsin in the presence of different effectors. It could be demonstrated that the substrates MgATP and fructose-6-phosphate are able to protect the enzyme from inactivation by trypsin. Other effectors like AMP, ADP, phosphoenolpyruvate, citrate and ammonium ions exhibit only negligible effects. During the first step of degradation consisting in the conversion of the subunits from Mr 120,000 to 90,000 no significant effects of the substrates and effectors on the proteolytic inactivation of yeast phosphofructokinase can be observed. In the presence of ATP as well as of ADP the sensitivity of the enzyme against ATP inhibition is either not or only slightly influenced by proteolytic modification. The modified enzyme retains its sensitivity against activation by AMP, independently of whether effectors are present or absent during proteolysis. The kinetic parameters of the enzyme modified by subtilisin in the presence of ATP or of fructose-6-phosphate have been determined.     

Limited proteolysis by subtilisin reveals structural differences between phosphorylase a and b

The limited proteolysis of rabbit skeletal muscle phosphorylase a and b was studied with subtilisin BPN' immoblized to Sepharose 4B. The activity of phosphorylase b is nearly resistant to subtilisin under the conditions (pH 7.0, 30 degrees C) where phosphorylase a rapidly loses its activity. The pH profile of phosphorylase a and b digestion is different. Proteolytic fragments of mol. wt 70,000 and 30,000 generated from phosphorylase a, while mol. wt 80,000 and 70,000 generated from phosphorylase b can be detected by SDS gel electrophoresis. Addition of AMP to phosphorylase b favours a conformation similar to--but not identical with--phosphorylase a as recognised by subtilisin action.     

Some properties of Escherichia coli glutamine synthetase after limited proteolysis by subtilisin.

Escherichia coli glutamine synthetase is inactivated by subtilisin. Protection against inactivation is afforded by glutamine and ammonium ions. One large fragment (Mr = 35,000) is identified by sodium dodecyl sulfate-gel electrophoresis and carries adenylylation site. Smaller quantities of two other fragments (Mr = 17,000 and 15,000, respectively) are als observed oo observed on the gel. tthe nicked protein remains dodecameric, as evidenced by electrophoresis and centrifugation. It has retained the binding properties toward ADP and Ci-bacron blue and undergoes conformation changes upon binding, as does the intact protein. It is recognized by the antiserum raised against the native enzyme. The nicked protein also remains an excellent substrate of E. coli adenylyltransferase.     

Complementation of soluble phosphofructokinase activity in yeast mutants.

We describe here the genetic and biochemical analyses of two classes of mutations in the soluble phosphofructokinase (PFK I) of Saccharomyces cerevisiae: those leading to the loss of activity and those giving rise to a kinetically altered enzyme. Complementation and allele-testing between these two classes of mutants show that loss of enzyme activity in vitro can come about not only by mutations in the catalytic subunit but also in the regulatory subunit. Also, a mutation in the catalytic subunit can give rise to an enzyme altered in its kinetic properties in a manner phenomenologically similar to that caused by a mutation in the regulatory subunit. The results of the complementation studies in diploids suggest that, in spite of their distinct functions, both the subunits are essential for activity to be detected in vitro. This is confirmed by the reconstitution of an active PFK I enzyme by mixing cell-free extracts of two complementing parents, each of which lacks the enzyme activity. PFK activity appears in the mixture, reaching a maximum value of 60-100% of that of the diploid in 15-30 min at 24 degrees C. Unlike the catalytic subunit which exists in various multimeric states in cell-free extracts of the mutant bearing only this subunit, the regulatory subunit exists largely as a monomer in a mutant devoid of the catalytic subunit. The reconstituted enzyme, however, is indistinguishable from that of the wild type, as analysed by sedimentation studies and Western blot analysis, demonstrating that only the heteromeric complex of the two subunits is active, while neither of the individual subunits displays activity in vitro.     

Limited proteolysis analysis of the ribosome is affected by subunit association

Our understanding of the structural organization of ribosome assembly intermediates, in particular those intermediates that result from misfolding leading to their eventual degradation within the cell, is limited because of the lack of methods available to characterize assembly intermediate structures. Because conventional structural approaches, such as NMR, X‐ray crystallography, and cryo‐EM, are not ideally suited to characterize the structural organization of these flexible and sometimes heterogeneous assembly intermediates, we have set out to develop an approach combining limited proteolysis with matrix‐assisted laser desorption/ionization mass spectrometry (MALDI‐MS) that might be applicable to ribonucleoprotein complexes as large as the ribosome. This study focuses on the limited proteolysis behavior of appropriately assembled ribosome subunits. Isolated subunits were analyzed using limited proteolysis and MALDI‐MS and the results were compared with previous data obtained from 70S ribosomes. Generally, ribosomal proteins were found to be more stable in 70S ribosomes than in their isolated subunits, consistent with a reduction in conformational flexibility on subunit assembly. This approach demonstrates that limited proteolysis combined with MALDI‐MS can reveal structural changes to ribosomes on subunit assembly or disassembly, and provides the appropriate benchmark data from 30S, 50S, and 70S proteins to enable studies of ribosome assembly intermediates. © 2009 Wiley Periodicals, Inc. Biopolymers 91: 410–422, 2009. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Limited proteolysis of streptokinase and properties of some fragments.

Limited proteolysis of streptokinase (Sk) by trypsin and thermolysin was performed under various incubation conditions and analysed by polyacrylamide gel electrophoresis. Several fragments (Sk1, Tr27, Tr17, Th26, and Th16) were isolated and characterized further. The N-terminal sequences of Tr27, Tr17, Th26, Th16 and the C-terminal sequences of Tr27 and Th26 were determined by partial sequencing. The evidence available allows the positioning of these fragments within the Sk sequence. Fragment Sk1 is obtained by carefully standardized tryptic digestion of Sk and gel chromatography under non-denaturing conditions. Sk1 is formed by a large polypeptide Ser60-Lys293 and non-covalently bonded smaller polypeptides composed of amino acids from the N-terminal region Ile1-Lys59 of Sk. Fragment Tr27 consists of the large polypeptide Ser60-Lys293 of Sk1, and can be obtained from Sk1 by removal of the smaller N-terminal polypeptides under denaturing conditions. Fragment Th26 is composed of amino acids Phe63-His291. The N-termini of fragments Tr17 and Th16 start with Glu148 and Ile151. From their electrophoretically-determined sizes it can be concluded that they most probably have the same C-terminal amino acids, Lys293 and His291, as fragments Tr27 and Th26, respectively. Secondary structure elements of similar composition were found in all the fragments studied using circular dichroism (c.d.) and infrared (i.r.) measurements. Differential scanning calorimetric (d.s.c.) measurements were performed in order to correlate the sequence regions of Sk to energetic folding units of the protein. Fragments Sk1, Tr27, Th26, Tr17, and Th16 show one melting peak in the temperature range from 42.8 to 46.1 degrees C (thermal unfolding stage). For fragment Sk1, this melting peak can be separated by deconvolution into two transitions at T1 = 46.1 degree C and T2 = 47.3 degrees C with delta H1 = 450 kJ/mol and delta H2 = 219 kJ/mol, respectively. Fragments Tr17 and Th16 show one two-state transition at T = 42.8 degrees C with delta H = 326 kJ/mol.     

Stimulation of yeast phosphofructokinase activity by Fructose 2,6-bisphosphate

Fructose 2,6-bisphosphate is a powerful activator of yeast phosphofructokinase when assayed at pH levels of ≥7.0. Half maximal stimulation of enzyme activity occurs at 10^?7 M levels of Fru 2,6-P₂ concentration. This stimulating effect by Fru 2,6-P₂ can be synergistic to that exerted by AMP in counteracting the inhibition of phosphofructokinase activity by ATP. The affinity (S_0.5) of the yeast enzyme to fructose 6-phosphate changes from 1.5 mM in the absence of Fru 2,6-P₂ to 40 μM in its presence.     

Activation by phosphate of yeast phosphofructokinase.

The activity of yeast phosphofructokinase assayed in vitro at physiological concentrations of known substrates and effectors is 100-fold lower than the glycolytic flux observed in vivo. Phosphate synergistically with AMP activates the enzyme to a level within the range of the physiological needs. The activation by phosphate is pH-dependent: the activation is 100-fold at pH 6.4 while no effect is observed at pH 7.5. The activation by AMP, phosphate, or both together is primarily due to changes in the affinity of the enzyme for fructose-6-P. Under conditions similar to those prevailing in glycolysing yeast (pH 6.4, 1 mM ATP, 10 mM NH4+) the apparent affinity constant for fructose-6-P (S0.5) decreases from 3 to 1.4 mM upon addition of 1 mM AMP or 10 mM phosphate; if both activators are present together, S0.5 is further decreased to 0.2 mM. In all cases the cooperativity toward fructose-6-P remains unchanged. These results are consistent with a model for phosphofructokinase where two conformations, with different affinities for fructose-6-P and ATP, will present the same affinity for AMP and phosphate. AMP would diminish the affinity for ATP at the regulatory site and phosphate would increase the affinity for fructose-6-P. The results obtained indicate that the activity of phosphofructokinase in the shift glycolysis-gluconeogenesis is mainly regulated by changes in the concentration of fructose-6-P.     

Dynamic properties of in vitro enzyme systems containing phosphofructokinase.

The dynamic properties of a series of in vitro reaction systems with increasing complexity and containing phosphofructokinase as central enzyme have been investigated. An experimental strategy and a principal mathematical treatment was elaborated to search for the minimum requirements with respect to the enzyme composition of a reaction system for generating limit cycle behaviour. As a criterion, such models have been developed which permit experimental realization by application of a specially designed flow-through equipment. In addition to phosphofructokinase, the following enzymes have been stepwise included into the reaction systems composing the Models 1 through 6: pyruvate kinase, adenylate kinase, hexokinase, and glucose 6-phosphate isomerase. It turned out that only a minimum dynamic system containing phosphofructokinase and pyruvate kinase as well as excesses of adenylate kinase and glucose 6-phosphate isomerase for maintaining equilibrium conditions between the respective reacting species, acquires the property of limit cycle behaviour and, hence, to generate sustained self-oscillations. The approach permits to compute the region of the experimentally variable parameters (influx rates of fructose 6-phosphate and ATP, maximum rate of pyruvate kianse) for which self-oscillatory behaviour can be predicted.     

Some kinetic and molecular properties of yeast phosphofructokinase

Yeast PFK had a sedimentation coefficient of 16.7 S both in the absence and in the presence of ATP, and did not dissociate even at very low protein concentrations. Sodium dodecyl-sulphate caused dissociation of the protein to sub-units of 3.2 S.The effects of pH on substrate affinities are described. In the presence of UTP, acting as non-inhibiting phosphate donor, the behaviour of the enzyme towards F-6-P was co-operative, with a Hill coefficient of 2.2.     

Purification of yeast cytochrome c oxidase with a subunit composition resembling the mammalian enzyme.

Yeast cytochrome c oxidase has been isolated by ion exchange chromatography using lauryl maltoside (n-dodecyl beta-D-maltoside) as the solubilizing detergent. The enzyme prepared in this way has a heme aa3 concentration of 8-9 nmol/mg of protein and a turnover number in the range of 180-210 s-1 at pH 6.2 in 0.01% lauryl maltoside at 20 degrees C. Yeast cytochrome c oxidase prepared by any of several previously published methods which use Triton X-100 contains nine subunits. The enzyme isolated in lauryl maltoside contains these same nine different polypeptides and three others, including homologues of subunits VIa and VIb of the mammalian enzyme.     

Limited proteolysis by trypsin influences activity of maize phosphoenolpyruvate carboxylase

Maize phosphoenolpyruvate carboxylase (PEPC) was rapidly and completely inactivated by very low concentrations of trypsin at 37 degrees C. PEP+Mg2+ and several other effectors of PEP carboxylase offered substantial protection against trypsin inactivation. Inactivation resulted from a fairly specific cleavage of 20 kDa peptide from the enzyme subunit. Limited proteolysis under catalytic condition (in presence of PEP, Mg2+ and HCO3) although yielded a truncated subunit of 90 kDa, did not affect the catalytic function appreciably but desensitized the enzyme to the effectors like glucose-6-phosphate glycine and malate. However, under non-catalytic condition, only malate sensitivity was appreciably affected. Significant protection of the enzyme activity against trypsin during catalytic phase could be either due to a conformational change induced on substrate binding. Several lines of evidence indicate that the inactivation caused by a cleavage at a highly conserved C-terminal end of the subunit.