Monkey pepsinogens and pepsins. VI. One-step activation of Japanese monkey pepsinogen to pepsin

When Japanese monkey pepsinogen was activated at pH 2.0 in the absence of pepstatin, the activation segment of the amino(N)-terminal 47 residues was released as a single intact polypeptide. This clearly shows that the pepsinogen was activated to pepsin directly. This direct activation was called a 'one-step' process. On the other hand, when pepsinogen was activated at pH 2.0 in the presence of pepstatin, an appreciable amount of pepsinogen was converted to an intermediate form between pepsinogen and pepsin, although a part of pepsinogen was activated directly to pepsin. The intermediate form was generated by releasing the N-terminal 25 residues of pepsinogen. This activation through the intermediate form is thought to be a 'two-step' or 'stepwise-activating' process involving a bimolecular reaction between pepstatin-bound pepsinogen and free pepsin.     

Activation mechanism of calcium-activated neutral protease. Evidence for the existence of intramolecular and intermolecular autolyses

The activation mechanism through limited autolysis of a calcium-activated neutral protease (CANP) with a high sensitivity to calcium ions (microCANP) was analyzed. The rate of autolysis was dependent on microCANP concentration. The reaction was inhibited by high concentrations of digestible substrates but not by a nondigestible substrate. Incubation of microCANP inactivated by N-ethylmaleimide with a small amount of activated microCANP caused the degradation of the former in a manner similar to the autolysis of native microCANP. Immobilized microCANP bound to an anti-microCANP immunoglobulin G column autolyzed on addition of calcium ions. These results show that activation of microCANP through limited autolysis involves both intramolecular and intermolecular reactions.     

Comparison of intramolecular and intermolecular reactions in protein folding

The intrinsic component of the standard free energy change for the formation of a disulfide bond in a protein molecule is compared to that for an analogous chemical reaction. The former reaction, which represents theintramolecular formation of a disulfide bond in a protein molecule from a cysteine group containing a mixed disulfide bond with glutathione, and a free cysteine residue, is a unimolecular reaction. In contrast, its chemical analogue is a bimolecular reaction, and corresponds to theintermolecular disulfide interchange between a mixed disulfide-bonded compound between a cysteine residue and glutathione, and a free cysteine molecule. The difference in the intrinsic free energy of the above two reactions is estimated by two different approaches. First, a theoretical estimate of the magnitude of the difference in free energy of the two reactions (for a standard state of 1 M) is obtained using a gas-phase statistical thermodynamic approach, which indicates that the intramolecular reaction is energetically favored over its intermolecular counterpart by as much as 15.6 kcal/mole. For comparison, an experimentally derived value is also obtained, using experimental data from a study by Konishi et al. of the regeneration of the protein ribonuclease A (RNase A) from its reduced form by reduced and oxidized glutathiones. The intrinsic component of the free energy change of the intramolecular reaction, as it occurs in the protein molecule, is obtained from such experimental data by accounting explicitly for the free energy change (assumed to be solely an entropy change) pertaining to the conformational changes (ring closure) that the protein molecule undergoes in the course of the reaction. On the basis of the value derived from such an experimental approach, the intramolecular reaction is also energetically more favorable as compared to its intermolecular analogue, but only by a difference of 2.3 kcal/mole (for a standard state of 1 M). The large apparent discrepancy between the two values estimated from the theoretical and experimental approaches is rationalized by the postulation of several additional factors not inherent in the gas-phase theoretical estimate, such as dehydration and intramolecular hydrogen-bonding effects, which can largely compensate for the otherwise favorable energetics of the intramolecular reaction.     

Quantitative relation between intermolecular and intramolecular binding of pro-rich peptides to SH3 domains

Flexible linkers are often found to tether binding sequence motifs or connect protein domains. Here we analyze three usages of flexible linkers: 1), intramolecular binding of proline-rich peptides (PRPs) to SH3 domains for kinase regulation; 2), intramolecular binding of PRP for increasing the folding stability of SH3 domains; and 3), covalent linking of PRPs and other ligands for high-affinity bivalent binding. The basis of these analyses is a quantitative relation between intermolecular and intramolecular binding constants. This relation has the form K(i) = K(e0)p for intramolecular binding and K(e) = K(e01)K(e02)p for bivalent binding. The effective concentration p depends on the length of the linker and the distance between the linker attachment points in the bound state. Several applications illustrate the usefulness of the quantitative relation. These include intramolecular binding to the Itk SH3 domain by an internal PRP and to a circular permutant of the alpha-spectrin SH3 domain by a designed PRP, and bivalent binding to the two SH3 domains of Grb2 by two linked PRPs. These and other examples suggest that flexible linkers and sequence motifs tethered to them, like folded protein domains, are also subject to tight control during evolution.     

The carbohydrate moiety of Japanese monkey pepsinogens. Its composition and site of attachment to protein.

Identification and determination of the carbohydrate component of Japanese monkey pepsinogens have been performed, and the amino acid sequence around the carbohydrate chain has been investigated. Glycopeptides were prepared by successive digestion of pepsinogens with thermolysin and aminopeptidases. Analyses of their carbohydrate composition by paper and gas-liquid chromatography showed the presence of 4 glucosamine, 6 galactose, 6–8 mannose, and 8–10 fucose residues per molecule of the carbohydrate chain, among which the high content of fucose is especially unique. The amino acid sequence of a major glycopeptide was deduced to be Ile-Gly-Ile-Gly-Thr-Pro-Gln-Ala-Asn, in which the asparagine residue is the site of attachment of the carbohydrate chain.     

Monkey pepsinogens and pepsins. III. Carbohydrate moiety of Japanese monkey pepsinogens and the amino acid sequence around the site of its attachment to protein.

Purified Japanese monkey pepsinogens I and II contain carbohydrate as a part of the enzyme molecule. By gel filtration on Sephadex G-100, chromatography on DE-32 cellulose, and polyacrylamide disc gel electrophoresis, the carbohydrate moiety could not be separated from the enzyme protein, and the content did not decrease on repeated chromatography. Glycopeptides were obtained by successive digestion of pepsinogens with thermolysin and aminopeptidases and isolated by chromatography on Sephadex G-25 and G-50. Identification and determination of carbohydrate components was performed by paper and gas-liquid chromatographies. The presence of 4 glucosamines, 6 galactoses, 6--8 mannoses, and 8--11 fucoses per molecule of the glycopeptide of both pepsinogens was observed, of which the high content of fucose is especially unique. The molecular weight of the carbohydrate chains should be around 4,000--5,000. The amino acid sequence of a major glycopeptide was deduced to be Ile-Gly-Ile-Gly-Thr-Pro-Gln-Ala-Asn, in which the asparagine residue is the site of attachment of the carbohydrate chain.     

Monkey pepsinogens and pepsins. VII. Analysis of the activation process and determination of the NH2-terminal 60-residue sequence of Japanese monkey progastricsin, and molecular evolution of pepsinogens

Japanese monkey progastricsin was shown to be activated to gastricsin exclusively by a two-step process through an intermediate form. The occurrence of this process was substantiated by the isolation of the intermediate form and released peptides. By NH2-terminal sequence analyses of these protein and peptide species, the amino acid sequence of the 43-residue activation segment (propart) was determined to be as follows: (Formula: see text) The NH2-terminal 26-residue peptide was released first, resulting in generation of the intermediate form. The subsequent release of peptides, residues Nos. 27-40 and 27-43, generated two gastricsins as the final products. This two-step process of activation of Japanese monkey progastricsin is in striking contrast to the one-step activation process occurring exclusively for pepsinogen A of the same monkey species. The course of molecular evolution of pepsinogens including progastricsins was deduced from the amino acid sequences of their activation segments by constructing phylogenic trees. The trees divided pepsinogens into 3 clusters, i.e., pepsinogens A, progastricsins and prochymosin, showing that these three groups diverged from one another very early on in the course of the evolution of pepsinogens.     

A model-independent approach to assigning bacteriorhodopsin''s intramolecular reactions to photocycle intermediates.

By using factor analysis and decomposition, bacteriorhodopsin's intramolecular reactions have been assigned to photocycle intermediates. Independent of specific kinetic models, the pure BR-L, BR-M, BR-N, and BR-O difference spectra were calculated by analyzing simultaneously two different measurements in the visible and infrared spectral region performed at pH 6.5, 298 K, 1 M KCl, and pH 7.5, 288 K, 1 M KCl. Even though after M formation L, M, N, and O intermediates kinetically overlap under physiological conditions, their pure spectra have been separated by this analysis in contrast to other approaches at which unphysiological conditions or mutants have been used or specific photocycle models have been assumed. The results now provide a set reference spectra for further studies. The following conclusions for physiologically relevant reactions are drawn: (a) the catalytic proton release binding site, asp 85, is protonated in the L to M transition and remains protonated in the intermediates N and O; (b) the catalytic proton uptake binding site asp 96 is deprotonated in the M to N transition and already reprotonated in the N to O transition; (c) proton transfer between asp 96 and the Schiff base is facilitated by backbone movements of a few peptide carbonyl groups in the M to N transition.     

Difference of activation processes and structure of activation peptides in human pepsinogens A and progastricsin

The activation processes of two human pepsinogens A (pepsinogens 3 and 5) and progastricsin were compared with special attention to pepsinogens 3 and 5. Each zymogen was converted to pepsin in a stepwise manner through intermediate forms. In pepsinogens A, the major cleavage site was the Leu23-Lys24 bond and this cleavage was suggested to occur intramolecularly. When each of the pepsins A was added to the corresponding pepsinogen A exogenously, the latter was rapidly converted to pepsin, releasing the 47-residue intact activation segment. In this case, the Leu47-Val48 bond connecting the activation segment with the pepsin moiety was cleaved by an intermolecular reaction. On the other hand, when the pepsinogen A-pepstatin complex was attacked by each corresponding pepsin A added exogenously, significant cleavage by an intermolecular reaction occurred at the Asp25-Phe26 bond, generating the Phe26-intermediate form. These shifts of the cleavage sites in pepsinogens A depending on the activation conditions are likely to correlate with the conformation of the activation segment. These results can be explained consistently in terms of a proposed molecular model of activation.     

Occurrence of two different pathways in the activation of porcine pepsinogen to pepsin

Activation of porcine pepsinogen at pH 2.0 was found to proceed simultaneously by two different pathways. One pathway is the direct conversion process of pepsinogen to pepsin, releasing the intact activation segment. The isolation of the released 44-residue segment was direct evidence of this one-step process. At pH 5.5 the segment bound tightly to pepsin to form a 1:1 pepsin-activation segment complex, which was chromatographically indistinguishable from pepsinogen. The other is a stepwise-activating or sequential pathway, in which pepsinogen is activated to pepsin through intermediate forms, releasing activation peptides stepwisely. These intermediate forms were isolated and characterized. The major intermediate form was shown to be generated by removal of the amino-terminal 16 residues from pepsinogen. The released peptide mixture was composed of two major peptides comprising residues 1-16 and 17-44, and hence the stepwise-activating process was deduced to be mainly a two-step process.     

Regulatory mechanism of length-dependent activation in skinned porcine ventricular muscle: role of thin filament cooperative activation in the Frank-Starling relation

Cardiac sarcomeres produce greater active force in response to stretch, forming the basis of the Frank-Starling mechanism of the heart. The purpose of this study was to provide the systematic understanding of length-dependent activation by investigating experimentally and mathematically how the thin filament “on–off” switching mechanism is involved in its regulation. Porcine left ventricular muscles were skinned, and force measurements were performed at short (1.9 µm) and long (2.3 µm) sarcomere lengths. We found that 3 mM MgADP increased Ca²⁺ sensitivity of force and the rate of rise of active force, consistent with the increase in thin filament cooperative activation. MgADP attenuated length-dependent activation with and without thin filament reconstitution with the fast skeletal troponin complex (sTn). Conversely, 20 mM of inorganic phosphate (Pi) decreased Ca²⁺ sensitivity of force and the rate of rise of active force, consistent with the decrease in thin filament cooperative activation. Pi enhanced length-dependent activation with and without sTn reconstitution. Linear regression analysis revealed that the magnitude of length-dependent activation was inversely correlated with the rate of rise of active force. These results were quantitatively simulated by a model that incorporates the Ca²⁺-dependent on–off switching of the thin filament state and interfilament lattice spacing modulation. Our model analysis revealed that the cooperativity of the thin filament on–off switching, but not the Ca²⁺-binding ability, determines the magnitude of the Frank-Starling effect. These findings demonstrate that the Frank-Starling relation is strongly influenced by thin filament cooperative activation.     

A novel tetrafunctional reagent for simultaneous intramolecular and intermolecular cross-linking of bovine hemoglobin

A novel tetrafunctional reagent, alpha,gamma,alpha',gamma'-tetra-succinimidyl-hexanediamide-di-glutamate ester (HDG(OSu)(4)), was successfully synthesized, and a well-defined cross-linked bovine hemoglobin (mainly 128 kDa) was prepared with this reagent. Due to the spatial structure of this cross-linking reagent, the intramolecular and intermolecular cross-linking of bovine hemoglobin was formed simultaneously in one reaction. Although the cross-linked bovine hemoglobin showed a slight decrease in half-saturated O(2) pressure value (P(50), from 28.1 mm Hg to 21.7 mm Hg) and Hill coefficient (from 2.5 to 2), due to the cross-linkage, it still performed well for O(2) delivery.     

The energetics of intramolecular reactions and enzyme catalysis.

The relative rates of reactions should always be examined by an awareness of differential effects. The magnitude and variation of the relative rates of intramolecular reactions can be rationalized by the differences in entropy and strain energy. The relative rates of enzyme-catalysed reactions are sometimes due to groundstate effects. The beta-lactamase-catalysed hydrolysis of beta-lactam antibiotics may require a unique disposition of catalytic groups owing to an unusual process of bond fission in the four membered ring.     

Three-dimensional structure of porcine pancreatic procarboxypeptidase A. A comparison of the A and B zymogens and their determinants for inhibition and activation.

The three-dimensional structure of procarboxypeptidase A (PCPA) from porcine pancreas has been determined at 2 A resolution and refined to a crystallographic R-factor of 0.198, with a root-mean-square deviation from ideal values for bond lengths of 0.015 A and for angles of 2.1 degrees. It is compared with procarboxypeptidase B (PCPB) from the same tissue. The 94/95 residue activation segments of PCPA/PCPB have equivalent folds: an N-terminal globular region with an open sandwich antiparallel alpha/antiparallel beta topology, followed by an extended alpha-helical segment, the connection to the enzyme. Alignment of the secondary structures of the activation segments of PCPA and PCPB (residues A1 to A99) indicates a two residue insertion between residues A34 and A35 and a C-terminal helix that is two turns longer in PCPA compared to PCPB. A deletion is observed between residues A43 to A45, the region containing the short 3(10) helix that covers the active site in PCPB. The globular region (A4 to A80) shields the preformed active center of carboxypeptidase A (CPA), but none of the residues involved in catalysis makes direct contacts with the activation segment. In contrast, subsites S2, S3 and S4 of the enzyme, involved in the binding of peptidic substrates, are blocked by specific contacts with residues AspA36, TrpA38, ArgA47, AspA53 and GluA86 of the activation segment. It has been described that several residues of CPA exhibit different conformations in the free enzyme compared to when substrate is bound: Arg127, Arg145, Glu270 and Tyr248. In PCPA all of these residues are found in the "active" conformation, as if substrate were actually bound. The presence of a ligand, tentatively interpreted as a free amino acid (Val) in the active center could explain this fact. The connecting region (A80 to A99), the target for proteolytic activation, establishes fewer contacts with the enzyme in PCPA than in PCPB. The activation segment of PCPA (A4 to A99) remains bound to the enzyme after the first trypsin cleavage between ArgA99-Ala1 probably due to the stability conferred on it by the alpha-helix (alpha 3) of the connecting segment. These and other structural features may explain the differences in intrinsic activity and different rates or proteolytic activation of each zymogen.     

Peroxidase and pseudoperoxidase reactions in relation to sudanophilia.

A selective staining of hemoglobin in erythroid cell series was achieved by use of Sudan Black B (modified method of Sheehan and Storey) if optimal amount of hydrogen peroxide was added to the staining mixture. The effect of some inhibitory agents (KCN, wet heat, pH) on this staining as well as on the Lepehne's pseudoperoxidase reaction for hemoglobin was similar. Both reactions were more resistant to these factors than the peroxidase reactions and sudanophilia in granulocytes in which both could be blocked by the pretreatment with absolute methanol. Moreover the effect of some extraction procedures for lipids on both myeloperoxidase reactions and sudanophilia was investigated. The results support the view that the sudanophilia in granulocytes is due to their peroxidase activity and for the staining of hemoglobin by use of Sudan Black B with H2O2 its pseudoperoxidase activity is responsible. In addition the effect of the substitution of phenolphosphate by dihydroxybenzenes on granulocyte sudanophilia is reported.     

Conversion of pepsinogen to pepsin. Further evidence for intramolecular and pepsin-catalyzed activation.

Exposure of pepsinogen to acid for less than 2 min yields a product with proteolytic activity. This activity is due to intramolecular and intermolecular formation of pepsin from pepsinogen. We find no evidence for intermolecular proteolytic activity in the zymogen. These conclusions are based upon two sets of experiments. First, chemical cleavage of pepsinogen during short activation is demonstrated by quantitative analysis of the NH2-terminal 2 residues of the pepsin and pepsinogen in an activation mixture. In addition, quantitative NH2-terminal analyses after activation under different conditions confirm our previous inference that the product of unimolecular pepsinogen activation is homogeneous whereas bimolecular activation produces a pepsin product with a variety of NH2 termini. Second, spectral changes which occur upon acidification of a pepsinogen solution and are reversed by neutralization are shown to be consistent with the chemical cleavage of pepsinogen during acidification. The first order rate constant for pepsinogen activation, calculated from these spectral experiments, agrees well with the value we had determined previously.