Biomedical subjects

Marko Rozman

Publications and source records attributed to Marko Rozman.

7 recordsLinked to original sources

PubMed2006

Aspartic acid side chain effect-experimental and theoretical insight.

Gas-phase H/D exchange and density functional theory study of the Asp and Glu side-chain carboxylic group intrinsic reactivity is reported. H/D exchange site specific treatment and some additional theoretical calculations showed that a side-chain carboxylic group may initiate proton transfer along with bond formation to one of its oxygens, i.e., possibility to initiate selective of cleavage peptide bond ("aspartic acid effect"). That finding is used to select aspartic acid cleavage mechanisms (side-chain proton transfer either to backbone carbonyl or to amide nitrogen) for further computational study. B3LYP/6-31G(d) and G3(MP2)//B3LYP potential energy profiles of both mechanisms on a model system CH3CO-Asp-NHCH3 were constructed. Although energy employed in low-energy collision induced dissociation suffices for both mechanisms thresholds, energy transferred to specific modes suggests a complex one-step mechanism of proton transfer (from the side-chain carboxylic group to the backbone amide group), bond formation (between deprotonated carboxylic group and carbon atom of the backbone carbonyl), and peptide bond cleavage as favorable.

Aspartic Acid↗

PubMed2005

The gas-phase H/D exchange mechanism of protonated amino acids.

A mass spectrometry and Density Functional Theory study of gas-phase H/D exchange in protonated Ala, Cys, Ile, Leu, Met, and Val is reported. Site-specific rate constants were determined and results identify the alpha-amino group as the protonation site. Lack of exchange on the Cys thiol group is explained by the absence of strong intramolecular hydrogen bonding within the reaction complex. In aliphatic amino acids the presence of a methyl group at the beta-C atom was found to lower the site-specific H/D exchange rate for amino hydrogens. Study of the exchange mechanism showed that isotopic exchange occurs in two independent reactions: in one, only the carboxylic hydrogen is exchanged and in the other, both carboxylic and amino group hydrogens exchange. The proposed reaction mechanisms, calculated structures of various species, and a number of structural findings are consistent with experimental data.

Amino Acids↗

PubMed2005

Gas-phase structure of protonated histidine and histidine methyl ester: combined experimental mass spectrometry and theoretical ab initio study.

Gas-phase H/D exchange experiments with CD3OD and D2O and quantum chemical ab initio G3(MP2) calculations were carried out on protonated histidine and protonated histidine methyl ester in order to elucidate their bonding and structure. The H/D exchange experiments show that both ions have three equivalent fast hydrogens and one appreciably slower exchangeable hydrogen assigned to the protonated amino group participating in a strong intramolecular hydrogen bond (IHB) with the nearest N(sp2) nitrogen of the imidazole fragment and to the distal ring NH-group, respectively. It is taken for granted that the proton exchange in the IHB is much faster than the H/D exchange. Unlike in other protonated amino acids (glycine, proline, phenylalanine, tyrosine, and tryptophan) studied earlier, the exchange rate of the carboxyl group in protonated histidine is slower than that of the amino group. The most stable conformers and the enthalpies of neutral and protonated histidine and its methyl ester are calculated at the G3(MP2) level of theory. It is shown that strong intramolecular hydrogen bonding between the amino group and the imidazole ring nitrogen sites is responsible for the stability and specific properties of the protonated histidine. It is found that the proton fluctuates between the amino and imidazole groups in the protonated form across an almost vanishing barrier. Proton affinity (PA) of histidine calculated by the G3(MP2) method is 233.2 and 232.4 kcal mol(-1) for protonation at the imidazole ring and at the amino group nitrogens, respectively, which is about 3-5 kcal mol(-1) lower than the reported experimental value.

Gases↗

PubMed2005

Theoretical study of the gas-phase structures of sodiated and cesiated leucine and isoleucine: zwitterionic structure disfavored in kinetic method experiments.

The most stable charge-solvated (CS) and zwitterionic (ZW) structures of sodiated and cesiated leucine and isoleucine were studied by density functional theory methods. According to the Boltzmann distribution in gas phase, both forms of LeuNa+ and IleNa+ exist, but in LeuCs+ and IleCs+, the ZW forms are dominant. Results for the sodiated compounds are consistent with the relationship found between decrease in relative stability of CS versus ZW form and aliphatic amino acid side chain length. The observed degeneracy in energy for IleNa+ conformers is at odds with kinetic method results. Additional calculations showed that kinetic method structural determinations for IleNa+ do not reflect relative order of populations in the lowest energy conformers. Since complexation of cationized amino acids into ion-bound dimers disfavors ZW structure by approximately 8 kJ mol(-1), it is suggested that for energy close conformers of sodium-cationized amino acids, the kinetic method may not be reliable for structural determinations.

Cesium↗

PubMed2003

Kinetics of gas-phase hydrogen/deuterium exchange and gas-phase structure of protonated phenylalanine, proline, tyrosine and tryptophan.

Site-specific rate constants for the gas-phase hydrogen/deuterium (H/D) exchange of four, three, five and five hydrogen atoms in protonated phenylalanine (Phe), proline (Pro), tyrosine (Tyr) and tryptophan (Trp), respectively, were determined from matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (MALDI-FTICRMS) experiments with D(2)O, D(2)S, and CH(3)OD as deuterating agents. No H/D exchange was observed with D(2)S. For exchange with both CD(3)OD and D(2)O, which is about ten times slower in the latter, results indicate for all compounds protonation of the alpha-amino group in agreement with theoretical results. Also, with both reagents, all compounds exchange at the COOH site more than ten times faster than at the protonation site, with OH and NH sites of Tyr and Trp, respectively, exchanging slowest. The observation of H/D exchange despite the high differences in proton affinities between the amino acids and deuterating agent exceeding 200 kJ mol(-1) is in agreement with lowering of the barrier for proton transfer through hydrogen bonding proposed by Lebrilla and coworkers.

Amino Acids↗

PubMed2003

Mass spectrometric investigation of N-sulfonylated purine nucleic bases and nucleosides.

The gas/phase behaviour of N-sulfonylated purine nucleic bases and nucleosides towards electron impact (EI) and matrix-assisted laser desorption/ionization (MALDI) occurring in a ion trap of a Fourier transform ion cyclotron resonance mass spectrometer is investigated. The influence of the storage time on the protonated molecule ([M+H](+)) abundance under EI conditions confirms that the formation of these ions proceeds through ion/molecule reactions. Using stored-waveform inverse Fourier transform (SWIFT) selective isolation of M(+.) or H(3)O(+), self-chemical ionization, M(+.)/M, and chemical ionization, H(3)O(+)/M, are detected. Investigation of specific EI expulsion of SO(2), SO(2)H and/or SO(2)H(2) from M(+.) and/or [M+H](+) shows that oxygen protonation in bond;SO(2)bond; proceeds faster than nitrogen protonation. Expulsion of SO(2) from molecular ions is not observed in MALDI mass spectra of nucleosides.

Fourier Analysis↗

PubMed2003

[Matrix-assisted laser desorption ionization].

Since its invention, matrix-assisted laser desorption ionization (MALDI) has found wide application in mass spectrometry of high molecular weight compounds such as synthetic polymers and biopolymers. Despite widespread application of MALDI, the fundamental processes of ion formation and desorption are still poorly understood. The chemistry of the MALDI process, occurring both during sample preparation and during ionization is reflected in the mass spectrum. As the MALDI technique now stands a low concentration of analyte molecules, which usually exhibit only moderate absorption per molecules, is embedded in matrix crystals consisting of a small, highly absorbing species. In this manner the efficient and controllable energy transfer is retained while the analyte molecules are separated from excessive energy that would lead to their decomposition. The matrix is believed to serve two major functions: adsorption of energy from the laser light and the isolation of analyte molecules from each other. There are 3 major methods for the preparation of samples for analysis which are quite quick and simple: dried droplet, surface and sandwich preparation. Experiments with pH indicator dyes serve as proof that analyte's charge state in the matrix crystals is the same as in solution. Upon laser desorption a sudden and explosive phase transition occurs and a dense plume of desorbed material is formed. The initial velocity of analyte ions in the plume depends only on the matrix used. Initial species formed as a result of laser desorption are tiny clusters. They consist of a matrix, analyte and other ionic species embedded in the matrix crystals all held together by hydrogen bonds and coulombic interactions. The first essential charging and thus ionization process is the statistical occurrence of clusters with a deficit/excess of anions of cations. Very small initial clusters are likely to be highly charged. Highly charged initial clusters cannot survive in the matrix plume and their charge drops. Clusters shrink by evaporation of neutral molecules. This paper presents only those cases leading to analyte ions and compares MALDI and the electrospray ionization technique.

Spectrometry, Mass, Matrix-Assisted Laser Desorpti↗