[Show abstract][Hide abstract] ABSTRACT: The product ion spectra of proline-containing peptides are commonly dominated by y(n) ions generated by cleavage at the N-terminal side of proline residues. This proline effect is investigated in the current work by collision-induced dissociation (CID) of protonated Ala-Ala-Xxx-Pro-Ala (Xxx includes Ala, Ser, Leu, Val, Phe, and Trp) in an electrospray/quadrupole/time-of-flight (QqTOF) mass spectrometer and by quantum chemical calculations on protonated Ala-Ala-Ala-Pro-Ala. The CID spectra of all investigated peptides show a dominant y(2) ion (Pro-Ala sequence). Our computational results show that the proline effect mainly arises from the particularly low threshold energy for the amide bond cleavage N-terminal to the proline residue, and from the high proton affinity of the proline-containing C-terminal fragment produced by this cleavage. These theoretical results are qualitatively supported by the experimentally observed y(2)/b(3) abundance ratios for protonated Ala-Ala-Xxx-Pro-Ala (Xxx = Ala, Ser, Leu, Val, Phe, and Trp). In the post-cleavage phase of fragmentation the N-terminal oxazolone fragment with the Ala-Ala-Xxx sequence and Pro-Ala compete for the ionizing proton for these peptides. As the proton affinity of the oxazolone fragment increases, the y(2)/b(3) abundance ratio decreases.
Journal of the American Society for Mass Spectrometry 06/2011; 22(6):1032-9. · 3.59 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b(2) ions or facilely rearrange to form anhydrides from which both b(2) and b(2)+H(2)O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b(2) and b(2)+H(2)O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.; Suhai, S.; Somogyi, A.; Paizs, B. J. Am. Chem. Soc. 2009, 131, 14057-14065.). In addition to these findings we also report on the mechanisms for the formation of the b(1) ion, neutral loss (H(2)O, NH(3), guanidine) fragment ions, and the d(3) ion.
The Journal of Physical Chemistry B 10/2010; 114(46):15092-105. · 3.61 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: After a brief introduction to the use of the idempotent Dirac first-order density matrix (DM), its time-dependent generalization
is considered. Special attention is focused on the equation of motion for the time-dependent DM, which is characterized by
the one-body potential V(r, t) of time-dependent density functional theory. It is then shown how the force –∇
V(r, t) can be extracted explicitly from this equation of motion. Following a linear-response treatment in which a weak potential
V(r, t) is switched on to an initially uniform electron gas, the non-linear example of the two-electron spin-compensated Moshinsky
atom is a further focal point. We demonstrate explicitly how the correlated DM for this model can be constructed from the
idempotent Dirac DM, in this time-dependent example.
Journal of Mathematical Chemistry 01/2010; · 1.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The gas-phase structures and fragmentation pathways of the singly protonated peptide arginylglycylaspartic acid (RGD) are investigated by means of collision-induced-dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. It is demonstrated that despite the ionizing proton being strongly sequestered at the guanidine group, protonated RGD can easily be fragmented on charge directed fragmentation pathways. This is due to facile mobilization of the C-terminal or aspartic acid COOH protons thereby generating salt-bridge (SB) stabilized structures. These SB intermediates can directly fragment to generate b 2 ions or facilely rearrange to form anhydrides from which both b 2 and b 2 +H 2 O fragments can be formed. The salt-bridge stabilized and anhydride transition structures (TSs) necessary to form b 2 and b 2 +H 2 O are much lower in energy than their traditional charge solvated counterparts. These mechanisms provide compelling evidence of the role of SB and anhydride structures in protonated peptide fragmentation which complements and supports our recent findings for tryptic systems (Bythell, B. J.. In addition to these findings we also report on the mechanisms for the formation of the b 1 ion, neutral loss (H 2 O, NH 3 , guanidine) fragment ions, and the d 3 ion.
The Journal of Physical Chemistry B 01/2010; 114:15092–15105. · 3.61 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: O6-alkylguanine-DNA alkyltransferase (AGT) repairs O6-methylguanine (O6mG) in DNA that is known to cause mutation and cancer. On the basis of calculations performed using density functional theory involving the active site of AGT, a mechanism for catalytic demethylation of O6mG to guanine has been proposed. In this mechanism, roles of six amino acids, i.e., Cys145, His146, Glu172, Tyr114, Lys165, and Ser159 in catalytic demethylation of O6mG are involved. This mechanism has three steps as follows. At the first step, Cys145 in the Cys145-water-His146-Glu172 tetrad is converted to cysteine thiolate anion while at the second step, abstraction of the Tyr114 proton by the N3 site of O6mG occurs in a barrierless manner. In the third step, abstraction of Lys165 proton by deprotonated Tyr114 and transfer of the methyl group of O6mG to the thiolate group of Cys145 anion occur simultaneously. As AGT is a major target in cancer therapy, identification of the roles of the different amino acids in demethylation of O6mG is expected to be useful in designing efficient AGT inhibitors.
The Journal of Physical Chemistry B 11/2009; 113(51):16285-90. · 3.61 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The mobile proton model (Dongre, A. R., Jones, J. L., Somogyi, A. and Wysocki, V. H. J. Am. Chem. Soc. 1996, 118 , 8365-8374) of peptide fragmentation states that the ionizing protons play a critical role in the gas-phase fragmentation of protonated peptides upon collision-induced dissociation (CID). The model distinguishes two classes of peptide ions, those with or without easily mobilizable protons. For the former class mild excitation leads to proton transfer reactions which populate amide nitrogen protonation sites. This enables facile amide bond cleavage and thus the formation of b and y sequence ions. In contrast, the latter class of peptide ions contains strongly basic functionalities which sequester the ionizing protons, thereby often hindering formation of sequence ions. Here we describe the proton-driven amide bond cleavages necessary to produce b and y ions from peptide ions lacking easily mobilizable protons. We show that this important class of peptide ions fragments by different means from those with easily mobilizable protons. We present three new amide bond cleavage mechanisms which involve salt-bridge, anhydride, and imine enol intermediates, respectively. All three new mechanisms are less energetically demanding than the classical oxazolone b(n)-y(m) pathway. These mechanisms offer an explanation for the formation of b and y ions from peptide ions with sequestered ionizing protons which are routinely fragmented in large-scale proteomics experiments.
Journal of the American Chemical Society 09/2009; 131(39):14057-65. · 10.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: As an illustration of the applicability of the coherent potential approximation (CPA) method to the treatment of aperiodic biopolymers (DNA and proteins) the results of a calculation with a k-dependent self-energy are presented in the case of the (SN)x and (SN—H)x mixed system. Further we give ab initio SCF LCAO band structures for polyglycine, which were corrected with the aid of the electron polaron model for long-range correlation and with the help of the ÔÂÔ method for excitonic effects. Finally, on the basis of the electronic structure of DNA and proteins, different possible mechanisms of chemical carcinogenesis are described.
International Journal of Quantum Chemistry 06/2009; 14(S5):35 - 49. · 1.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A minimal basis set ab initio calculation has been performed for the four nucleotide bases and for the infinite polycytosine chain. The LEMO levels have been corrected using the ǑǍǑ procedure. Long-range correlation effects on the band structure of polyC have been computed using the electron polaron model.Using these calculated quantities and assuming that the other three homopolynucleotides have a similar band structure as polyC, the positions and widths of their valence and exciton bands have been approximated. Finally, by the superposition of the band structures of the homopolynucleotides the physically interesting bands of poly(G-C) and poly(A-T) have been estimated.
International Journal of Quantum Chemistry 06/2009; 12(S4):55 - 63. · 1.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Bacteriorhodopsin is a proton-pumping membrane protein found in the plasma membrane of the archaeon Halobacterium salinarium. Light-induced isomerization of the retinal chromophore from all-trans to 13-cis leads to a sequence of five conformation-coupled proton transfer steps and the net transport of one proton from the cytoplasmic to the extracellular side of the membrane. The mechanism of the long-distance proton transfer from the primary acceptor Asp85 to the extracellular proton release group during the O --> bR is poorly understood. Experiments suggest that this long-distance transfer could involve a transient state [O] in which the proton resides on the intermediate carrier Asp212. To assess whether the transient protonation of Asp212 participates in the deprotonation of Asp85, we performed hybrid Quantum Mechanics/Molecular Mechanics proton transfer calculations using different protein structures and with different retinal geometries and active site water molecules. The structural models were assessed by computing UV-vis excitation energies and C=O vibrational frequencies. The results indicate that a transient [O] conformer with protonated Asp212 could indeed be sampled during the long-distance proton transfer to the proton release group. Our calculations suggest that, in the starting proton transfer state O, the retinal is strongly twisted and at least three water molecules are present in the active site.
Journal of the American Chemical Society 05/2009; 131(20):7064-78. · 10.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Direct and indirect radiation-induced DNA damage is associated with the formation of radical cations (G(+)) and radical anions (G(-)) of guanine, respectively. Deprotonation of G(+) and dehydrogenation of G(-) generate guanine neutral radical [G(-H)] and guanine anion [G(-H)(-)], respectively. These products are of worrisome concern, as they are involved in reactions that are related to certain lethal diseases. It has been observed that guanyl radicals can be repaired by amino acids having strong reducing properties that are believed to be the residues of DNA-bound proteins such as histones. As a result, repair of G(-H) and G(-H)(-) by the amino acids cysteine and tyrosine has been studied here in detail by density functional theory in both the gas phase and aqueous medium using the polarized continuum and Onsager solvation models of self-consistent reaction field theory. Solvation in aqueous medium using three explicit water molecules was also studied. Four equivalent tautomers of each the above radical and anion that will be formed through proton and hydrogen loss from all of the nitrogen centers of guanine radical cation and guanine radical anion, respectively, were considered in the present study. It was found that in both the gas phase and aqueous medium, normal guanine can be retrieved from its radical-damaged form by a hydrogen-atom-transfer (HT) mechanism. Normal guanine can also be retrieved from its anionic damaged form in both the gas phase and aqueous medium through a two-electron-coupled proton-transfer (TECPT) mechanism or a one-step hydrogen-atom- and electron-transfer (OSHET) mechanism. The present results are discussed in light of the experimental findings.
The Journal of Physical Chemistry B 04/2009; 113(16):5633-44. · 3.61 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s).
We have developed a new tool called DoOPSearch http://doopsearch.abc.hu for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program.
We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that might provide a clue on the function of the motifs and genes.
[Show abstract][Hide abstract] ABSTRACT: Ab initio supermolecule calculations have been performed for the glyoxal–formamide and for the H2S–formamide charge transfer complexes in their ground states. According to the results obtained with Mulliken's population analysis, glyoxal acts always as an electron acceptor against formamide which we have used as model compound for a peptide group. The results indicate also that the amount of transferred charge depends strongly on the intermolecular distance and on the relative orientation of the molecular planes. On the other hand we have found that H2S against our expectation acts at most relative geometrical positions as an electron acceptor with respect to formamidc.
International Journal of Quantum Chemistry 01/2009; 12:451-457. · 1.17 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The gas-phase structures and fragmentation pathways of the N-terminal b and a fragments of YAGFL-NH(2), AGLFY-NH(2), GFLYA-NH(2), FLYAG-NH(2), and LYAGF-NH(2) were investigated using collision-induced dissociation (CID) and detailed molecular mechanics and density functional theory (DFT) calculations. Our combined experimental and theoretical approach allows probing of the scrambling and rearrangement reactions that take place in CID of b and a ions. It is shown that low-energy CID of the b(5) fragments of the above peptides produces nearly the same dissociation patterns. Furthermore, CID of protonated cyclo-(YAGFL) generates the same fragments with nearly identical ion abundances when similar experimental conditions are applied. This suggests that rapid cyclization of the primarily linear b(5) ions takes place and that the CID spectrum is indeed determined by the fragmentation behavior of the cyclic isomer. This can open up at various amide bonds, and its fragmentation behavior can be understood only by assuming a multitude of fragmenting linear structures. Our computational results fully support this cyclization-reopening mechanism by showing that protonated cyclo-(YAGFL) is energetically favored over the linear b(5) isomers. Furthermore, the cyclization-reopening transition structures are energetically less demanding than those of conventional bond-breaking reactions, allowing fast interconversion among the cyclic and linear isomers. This chemistry can lead in principle to complete loss of sequence information upon CID, as documented for the b(5) ion of FLYAG-NH(2). CID of the a(5) ions of the above peptides produces fragment ion distributions that can be explained by assuming b-type scrambling of their parent population and a --> a*-type rearrangement pathways ( Vachet , R. W. , Bishop , B. M. , Erickson , B. W. , and Glish , G. L. J. Am. Chem. Soc. 1997, 119, 5481 ). While a ions easily undergo cyclization, the resulting macrocycle predominantly reopens to regenerate the original linear structure. Computational data indicate that the a --> a*-type rearrangement pathways of the linear a isomers involve post-cleavage proton-bound dimer intermediates in which the fragments reassociate and the originally C-terminal fragment is transferred to the N-terminus.
Journal of the American Chemical Society 01/2009; 130(52):17774-89. · 10.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: The functional mechanism of the light-driven proton pump protein bacteriorhodopsin depends on the location of water molecules in the active site at various stages of the photocycle and on their roles in the proton-transfer steps. Here, free energy computations indicate that electrostatic interactions favor the presence of a cytoplasmic-side water molecule hydrogen bonding to the retinal Schiff base in the state preceding proton transfer from the retinal Schiff base to Asp85. However, the nonequilibrium nature of the pumping process means that the probability of occupancy of a water molecule in a given site depends both on the free energies of insertion of the water molecule in this and other sites during the preceding photocycle steps and on the kinetic accessibility of these sites on the time scale of the reaction steps. The presence of the cytoplasmic-side water molecule has a dramatic effect on the mechanism of proton transfer: the proton is channeled on the Thr89 side of the retinal, whereas the transfer on the Asp212 side is hindered. Reaction-path simulations and molecular dynamics simulations indicate that the presence of the cytoplasmic-side water molecule permits a low-energy bacteriorhodopsin conformer in which the water molecule bridges the twisted retinal Schiff base and the proton acceptor Asp85. From this low-energy conformer, proton transfer occurs via a concerted mechanism in which the water molecule participates as an intermediate proton carrier.
The Journal of Physical Chemistry B 11/2008; 112(47):14729-41. · 3.61 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Exonic splicing enhancers (ESEs) activate nearby splice sites and promote the inclusion (vs. exclusion) of exons in which they reside, while being a binding site for SR proteins. To study the impact of ESEs on alternative splicing it would be useful to have a possibility to detect them in exons. Identifying SR protein-binding sites in human DNA sequences by machine learning techniques is a formidable task, since the exon sequences are also constrained by their functional role in coding for proteins.
The choice of training examples needed for machine learning approaches is difficult since there are only few exact locations of human ESEs described in the literature which could be considered as positive examples. Additionally, it is unclear which sequences are suitable as negative examples. Therefore, we developed a motif-oriented data-extraction method that extracts exon sequences around experimentally or theoretically determined ESE patterns. Positive examples are restricted by heuristics based on known properties of ESEs, e.g. location in the vicinity of a splice site, whereas negative examples are taken in the same way from the middle of long exons. We show that a suitably chosen SVM using optimized sequence kernels (e.g., combined oligo kernel) can extract meaningful properties from these training examples. Once the classifier is trained, every potential ESE sequence can be passed to the SVM for verification. Using SVMs with the combined oligo kernel yields a high accuracy of about 90 percent and well interpretable parameters.
The motif-oriented data-extraction method seems to produce consistent training and test data leading to good classification rates and thus allows verification of potential ESE motifs. The best results were obtained using an SVM with the combined oligo kernel, while oligo kernels with oligomers of a certain length could be used to extract relevant features.
[Show abstract][Hide abstract] ABSTRACT: Very recent criticisms of existing exchange-correlation functionals by Wanko et al. applied to systems of biological interest have led us to reopen the question of the ground-state conformer of glycine: the simplest amino acid. We immediately show that the global minimum of the Hartree–Fock (HF) ground-state leads to a planar structure of the five non-hydrogenic nuclei, in the non-ionized form NH2–CH2–COOH. This is shown to lie lower in energy than the zwitterion structure NHB3 –CH2–COO, as required by experiment. Refinement of the nuclear geometry using second-order Møller–Plesset perturbation theory (MP2) is also carried out, and bond lengths are found to accord satisfactorily with experimentally determined values. The ground-state electron density for the MP2 geometry is then redetermined by HF theory and equidensity contours are displayed. The HF first-order density matrix γ(r, r ′) is then used to obtain similar exchange-energy density (εx(r)) contours for the lowest conformer of glycine. At first sight, their shape looks almost the same as for the density ρ(r), which seems to vindicate the LDA proportional to ρ(r). However, by way of an analytically soluble model for an atomic ion, it is shown that this has to be corrected to obtain an accurate HF exchange energy Ex as the volume integral of εx(r). Finally, recognizing that for larger amino acids, the use of HF plus MP2 perturbation corrections will become prohibitive, we have used the HF information for εx(r) and ρ(r) to plot the truly non-local exchange potential proposed by Slater, from the density matrix γ(r, r ′). This latter calculation should be practicable for large amino acids, but there adopting Becke's one-parameter form of εx(r) correcting LDA exchange. Some future directions are suggested.
Physics and Chemistry of Liquids 06/2008; 46(3):242-254. · 0.52 Impact Factor