Influence of stereochemistry on proton transfer in protonated tripeptide models.
ABSTRACT Vectorial proton transfer among carbonyl oxygen atoms was studied in two models of tripeptide via quantum chemical calculations using the hybrid B3LYP functional and the 6-31++G basis set. Two principal proton transfer pathways were found: a first path involving isomerization of the proton around the double bond of the carbonyl group, and a second based on the large conformational flexibility of the tripeptide model where all carbonyl oxygen atoms cooperate. The latter pathway has a rate-determining step energy barrier that is only around half of that for the first pathway. As conformational flexibility plays a crucial role in second pathway, the effect of attaching methyl groups to the alpha carbon atoms was studied. The results obtained are presented for all four possible stereochemical configurations.
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ABSTRACT: The catalytic mechanism for peptide hydrolysis by thermolysin has been investigated using the B3LYP hybrid density functional method. The starting structure for the calculations was based on the X-ray crystal structure of the enzyme inhibited with the ZF (p)LA phosphonamidate transition-state analogue. Besides the three Zn ligands His142, His146 and Glu166, a few additional residues were also included in the model. Following the order of importance, the outer-sphere ligands Glu143, His231 and Asp226 were shown to play significant catalytic roles, well correlated with results from site-directed mutagenesis experiments. A single-step reaction mechanism was obtained starting from the initial enzyme-substrate complex with a pentacoordinated metal center and proceeding to the enzyme-carboxylate complex as a final product, following a proposal by Matthews and co-workers. The transition state combines a nucleophilic water oxygen attack on the peptide carbon and a proton transfer from the water to the peptide nitrogen, mediated by the Glu143 carboxylate. A free activation energy of 15.2 kcal/mol was obtained, compared to the experimental 12.4-16.3 kcal/mol range for various peptide substrates. An interesting aspect of the present single-step mechanism is that the Glu143 carboxylate moves a significant distance of ~1.0 A. Different chemical models were examined, both related to the system size and proper side-chain modeling. The significance of the protein frame rigidity around the active site was estimated by fixing and subsequently releasing the edge atom positions. Finally, alternative mechanistic proposals are briefly summarized.JBIC Journal of Biological Inorganic Chemistry 04/2002; 7(3):284-98. · 3.35 Impact Factor
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ABSTRACT: Theoretical model calculations were performed to investigate the degree of validity of the mobile proton model of protonated peptides. The structures and energies of the most important minima corresponding to different structural isomers of protonated diglycine and their conformers, as well as the barriers separating them, were determined by DFT calculations. The rate coefficients of the proton transfer reactions between the isomers were calculated using the RRKM method in order to obtain a quantitative measure of the time scale of these processes. The proton transfer reactions were found to be very fast already at and above the threshold to the lowest energy decomposition pathway. Two possible mechanisms of b2+-ion formation via water loss from the dipeptide are also discussed. The rate-determining step of the proton migration along a peptide chain is also investigated using the model compound N-formylglycylglycinamide. The investigations revealed that this process very possibly occurs via the protonation of the carbonyl oxygens of the amide bonds, and its rate-determining step is an internal rotation-type transition of the protonated C=O-H group between two adjacent C=O-HellipsisO=C bridges.Rapid Communications in Mass Spectrometry 02/2001; 15(8):637-50. · 2.51 Impact Factor
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ABSTRACT: Quantum chemical and RRKM calculations were carried out on protonated glycylglycine in order to determine the atomic details of the main fragmentation pathways leading to formation of a1 and y1 ions. Two possible mechanisms were considered. The first path results in elimination of aziridinone as a neutral counterpart of the y1 ion formed. Our calculations show that this pathway has a relatively high threshold energy (48.6 kcal/mol) and the corresponding unimolecular rate constants are quite small even at large internal energy. An alternative pathway (a1-y1) proposed in the present paper seems, however, to be favored against the above 'aziridinone' one from the points of view of both energetics and kinetics. The 'a1-y1' pathway leads to simultaneous formation of a1 and y1 ions, the ratio of which depends on the energy distribution of the fragmenting species for a particular dipeptide. However, even if y1 ions are formed via the 'a1-y1' pathway, the corresponding neutrals eliminated do not have a strained cyclic aziridinone structure. Instead, in a two-step process, CO and NHCH2 are formed leading to neutral products energetically more favored than aziridinone. The available experimental data reevaluated in the present paper lend support to the 'a1-y1' pathway.Rapid Communications in Mass Spectrometry 02/2001; 15(8):651-63. · 2.51 Impact Factor