Stereochemical aspects of peptide hydrolysis catalyzed by serine proteases of the chymotrypsin type

Bizzozero, Spartaco A.; Dutler, Hans

doi:10.1016/0045-2068(81)90042-0

Cited by 60 publications

(51 citation statements)

References 27 publications

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“…Hydrogen bonds from the flap to the charged oxygen may serve to orientate the orbitals so that there is a lone pair antiperiplanar to the C-N bond but not to the hydroxyl C-O bond, thereby ensuring that on collapse of the tetrahedral intermediate, the leaving group is the free amine rather than the original nucleophile [23]. Pyrimidalisation of the peptide nitrogen may be favoured by the binding-induced peptide rotation, which would direct the free lone pair generally towards the catalytic groups, and consequently no inversion of the lone pair and proton directions would be required for protonation of the NH leaving group, in contrast to that suggested for the serine proteinases [24]. Release of the neutral products, and binding of a new water molecule, restores the enzyme.…”

Section: Catalytic Mechanismmentioning

confidence: 98%

The catalytic mechanism of aspartic proteinases

Pearl

1987

FEBS Letters

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The highly symmetric active site of an aspartic proteinase, endothiapepsin, binds a water molecule ideally situated for nucleophilic attack on a substrate peptide bond whose distortion from planarity is stabilised by interactions of the substrate with the extended binding cleft. The apparent electrophilicity of the catalysis results from this distortion. The scissile peptide bond is orientated with the carbonyl oxygen hydrogen bonding to the tip of the p-hairpin 'flap' which lies over the cleft. Nucleophilic attack by the bound water leads to a tetrahedral intermediate similar to observed complexes with hydroxyl inhibitors and stabilised by hydrogen bonds with the flap.

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Section: Catalytic Mechanismmentioning

confidence: 98%

The catalytic mechanism of aspartic proteinases

Pearl

1987

FEBS Letters

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“…The second alternative was proved to be correct by showing that Ac-Phe-Sar-NH2 is also unreactive. Detailed stereochemical analysis of the structural events occurring during catalysis indicated that unreactivity arises from an unfavourable interaction between the N-alkyl substituent and the imidazole ring of His-57 during formation of the tetrahedral intermediate [26].…”

Section: Discussionmentioning

confidence: 99%

“…The resulting conformation of this part of the substrate appears to be similar to that observed for the complex between trypsin and bovine pancreatic trypsin inhibitor, a model of which was constructed for comparison. The modifications needed to transform a model of an enzyme-substrate complex into one of the corresponding tetrahedral intermediate were carried out as described in detail previously [26].…”

Section: Discussionmentioning

confidence: 99%

Kinetic Investigation of the a‐Chymotrypsin‐Catalyzed Hydrolysis of Peptide Substrates

Bizzozero¹,

Baumann²,

Dutler³

1982

European Journal of Biochemistry

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Peptide substrates of the general structure Ac-Tyr-Lyl-Lyz-. . -Ly,-NH2 and Ac-Phe-L,,-NHz have been synthesized and subjected to cr-chymotrypsin-catalyzed hydrolysis to collect information on the interactions between the enzyme active site and the amino-acid residues Lyl, Ly2, etc., C-terminal to the susceptible bond of the peptide. For this purpose changes in the dissociation constants of the enzyme-substrate complexes and in the rate constants of acylation have been related to the structural variations of the substrates. The results indicate that interactions occur with the two residues next to the scissible bond, L,1 and Lyz, but not with residue Ly3. Structural description of individual interactions was carried out with the aid of skeletal models of the active site. From such combination of kinetic and structural data a plausible interaction scheme for the substrate side C-terminal to the scissible bond has been deduced. This interaction scheme, which defines conformation and orientation of this part of the substrate within the active site, is characterized by the presence of a single hydrogen bond occurring between NH(Ly2) and . No donor interacting with the back-bone carbonyl groups of residues Lyl and LY2 could be detected in the model of a-chymotrypsin. The effect of modification of the side chains of residues Lyl and LY2 on the kinetic constants was shown to be consistent with the interactions assumed to occur between the side chains of these residues and the active site. The interpretation of the results obtained from these specificity studies have led to refined concepts concerning the relative importance of different sets of enzyme-substrate interactions in determining reactivity.Endopeptidases possess extended active sites which can accommodate between five and seven amino-acid residues of peptide substrates 11-51, Since they usually display a marked specificity for the side chain of the residue containing the reactive carbonyl group, the interactions of this residue with the enzyme are often termed primary interactions. For some serine proteases, as for trypsin, chymotrypsin and elastase, the structural basis of these interactions is clearly discernible from the known three-dimensional structures of the active sites. The other interacting residues of the substrate are said to form secondary interactions with the enzyme. On account of differences in the way these secondary interactions affect the rate of hydrolysis, they can be subdivided into two sets: those originating from the invariant part and those originating from the variable part of the peptide substrate. The invariant part includes the atoms of the backbone and the p carbons of the side chains, which are present in all amino acids but glycine. It is reasonable to assume that this invariant part, together with the specific residue, leads to interactions occurring according to a well defined interaction scheme which henceforth will be called the 'cardinal' interaction scheme. For chymotrypsin, such an interaction scheme regarding the substr...

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“…The prevailing orientation of histidine H + -440 is the one promoting leaving group departure in ACh-AChE. This orientation has also been found in the molecular dynamics simulations of acyl-chymotrypsin by Nakagawa et al [39] and by Bizzozero and Dutler [40]. Whereas the molecular dynamics simulations involve reaction intermediates and not transition states, their results point to unambiguous preferences for proton transfer just preceding the formation of transition states.…”

Section: Interactions Of Histidine H + -440mentioning

confidence: 66%

Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants

Enyedy

Kovach

Bencsura

2001

Biochemical Journal

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The role of active-site residues in the dealkylation reaction in the P S C S diastereomer of 2-(3,3-dimethylbutyl)methylphosphonofluoridate (soman)-inhibited Torpedo californica acetylcholinesterase (AChE) was investigated by full-scale molecular dynamics simulations using CHARMM : 400 ps equilibration was followed by 150-200 ps production runs with the fully solvated tetracoordinate phosphonate adduct of the wild-type, Trp84Ala and Gly199Gln mutants of AChE. Parallel simulations were carried out with the tetrahedral intermediate formed between serine-200 Oγ of AChE and acetylcholine. We found that the NεH in histidine H + -440 is positioned to protonate the oxygen in choline and thus promote its departure. In contrast, NεH in histidine H + -440 is not aligned for a favourable proton transfer to the pinacolyl O to promote dealkylation, but electrostatic stabilization by histidine H + -440 of the developing anion on the phosphonate monoester occurs. Destabilizing interactions between residues and the alkyl fragment

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Stereochemical aspects of peptide hydrolysis catalyzed by serine proteases of the chymotrypsin type

Cited by 60 publications

References 27 publications

The catalytic mechanism of aspartic proteinases

The catalytic mechanism of aspartic proteinases

Kinetic Investigation of the a‐Chymotrypsin‐Catalyzed Hydrolysis of Peptide Substrates

Molecular dynamics study of active-site interactions with tetracoordinate transients in acetylcholinesterase and its mutants

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