Proton transfer in arginine-carboxylate interactions

Exponential averaging versus umbrella sampling for computing the QM/MM free energy barrier of the initial step of the desuccinylation reaction catalyzed by sirtuin 5

The computational characterization of enzymatic reactions poses a great challenge which arises from the high dimensional and often rough potential energy surfaces commonly explored by static QM/MM methods such as adiabatic mapping (AM). The present study highlights the difficulties in estimating free energy barriers via exponential averaging over AM pathways. Based on our previous study [von der Esch et al., J. Chem. Theory Comput., 2019, 15, 6660-6667], where we analyzed the first reaction step of the desuccinylation reaction catalyzed by human sirtuin 5 (SIRT5) by means of QM/MM adiabatic mapping and machine learning, we use, here, umbrella sampling to compute the free energy profile of the initial reaction step. The computational investigations show that the initial step of the desuccinylation reaction proceeds via an S_N2-type reaction mechanism in SIRT5, suggesting that the first step of the deacylation reactions catalyzed by sirtuins is highly conserved. In addition, the direct comparison of the extrapolated free energy barrier from minimal energy paths and the computed free energy path from umbrella sampling further underlines the importance of extensive sampling.

Formation of (bn-1 + H2O) ions by collisional activation of MALDI-formed peptide [M + H]+ ions in a QqTOF mass spectrometer

Collisional activation of [M + H](+) parent ions from peptides of n amino acid residues may yield a rearrangement that involves loss of the C-terminal amino acid residue to produce (b(n-1) + H(2)O) daughters. We have studied this reaction by a retrospective examination of the m/z spectra of two collections of data. The first set comprised 398 peptides from coat protein digests of a number of plant viruses by various enzymes, where conditions in the tryptic digests were chosen so as to produce many missed cleavages. In this case, a large effect was observed-323 (b(n-1) + H(2)O) daughter ions (approximately 81%), including 185 (approximately 46%) "strong" decays with ratios (b(n-1) + H(2)O)/(b(n-1)) > 1. The second set comprised 1200 peptides, all from tryptic digests, which were carried out under more stringent conditions, resulting in relatively few missed cleavages. Even here, 190 (b(n-1) + H(2)O) ions (approximately 16%) were observed, including 87 (> 7%) "strong" decays, so the effect is still appreciable. The results suggest that the tendency for (b(n-1) + H(2)O) ion formation is promoted by the protonated side chain of a non-C-terminal basic amino acid residue, in the order arginine >> lysine > or = histidine, and that its (non-C-terminal) position is not critical. The results can be interpreted by a mechanism in which hydrogen bonding between the protonated side chain and the (n - 1) carbonyl oxygen facilitates loss of the C-terminal amino acid residue to give a product ion having a carboxyl group at the new C-terminus.

Design and synthesis of potent, orally active, inhibitors of carboxypeptidase U (TAFIa)

A series of 3-mercapto-propionic acid derivatives that function as reversible inhibitors of carboxypeptidase U have been prepared. We present a successful design strategy using cyclic, low basicity guanidine mimetics resulting in potent, selective and bioavailable inhibitors of carboxypeptidase U (TAFIa).

Proton Motion and Proton Transfer in the Formamidine-Formic Acid Complex: An Ab Initio Projector Augmented Wave Molecular Dynamics Study

An ab initio molecular dynamics study performed with the projector augmented wave method (PAW) on proton motion and (double) proton transfer in the formamidine-formic acid complex is reported. The PAW trajectories were calculated with a time interval of 0.12 fs, for a total evolution time period of 36ps, and for temperatures in the range 500-600 K. All proton-transfer processes start with a proton transition at the O-H...N group, and are followed by a second proton transition, either at the same group ("single crossing-recrossing transitions") or at the other group, namely the N-H...O group ("double proton transfers"). According to the delay between the two transitions (more or less than 15 fs), one may distinguish between "concerted" (42%) or "successive" (16%) single crossing-recrossing transitions, and between "simultaneous" (7%) or "successive" (35%) double proton transfers. Successive processes take place via a zwitterionic intermediate, which remains stable for up to approximately 120 fs ("ionic regions"). The findings are in excellent agreement with the results of ab initio (HF, MP2) and density functional theory (DFT; B3LYP, B3P86) calculations, according to which the zwitterionic intermediate that results from the first proton transition is a true local minimum. Furthermore, it is shown that the optimized geometries of stationary points (ground state, transition state, and zwitterion) comply well with corresponding average data obtained from the PAW trajectories for normal periods, crossover points, and ionic regions.

Salt bridge interactions: stability of the ionic and neutral complexes in the gas phase, in solution, and in proteins

A theoretical study on the stability of the salt bridges in the gas phase, in solution, and in the interior of proteins is presented. The study is mainly focused on the interaction between acetate and methylguanidinium ions, which were used as model compounds for the salt bridge between Asp (Glu) and Arg. Two different solvents (water and chloroform) were used to analyze the effect of varying the dielectric constant of the surrounding media on the salt bridge interaction. Calculations in protein environments were performed by using a set of selected protein crystal structures. In all cases attention was paid to the difference in stability between the ion pair and neutral hydrogen-bonded forms. Comparison of the results determined in the gas phase and in solution allows us to stress the large influence of the environment on the binding process, as well as on the relative stability between the ionic and neutral complexes. The high anisotropy of proteins and the local microenvironment in the interior of proteins make a decisive contribution in modulating the energetics of the salt bridge. In general, the formation of salt bridges in proteins is not particularly favored, with the ion pair structure being preferred over the interaction between neutral species.