O6-methylguanine repair by O6-alkylguanine-DNA alkyltransferase.

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.

Protection against radiation-induced DNA damage by amino acids: a DFT study.

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.

New bioinformatic strategies to rapidly characterize retroviral integration sites of gene therapy vectors.

OBJECTIVE: Increasing use of retroviral vector-mediated gene transfer created intense interest to characterize vector integrations on the genomic level. Techniques to determine insertion sites, mainly based on time-consuming manual data processing, are commonly applied. Since a high variability in processing methods hampers further data comparison, there is an urgent need to systematically process the data arising from such analysis. METHODS: To allow large-scale and standardized comparison of insertion sites of viral vectors we developed two programs, IntegrationSeq and IntegrationMap. IntegrationSeq can trim sequences, and valid integration sequences get further processed with IntegrationMap for automatic genomic mapping. IntegrationMap retrieves detailed information about whether integrations are located in or close to genes, the name of the gene, the exact localization in the transcriptional units, and further parameters like the distance from the transcription start site to the integration. RESULTS: We validated the method using 259 files originating from integration site analysis (LM-PCR). Sequences processed by IntegrationSeq led to an increased yield of valid integration sequence detection, which were shown to be more sensitive than conventional analysis and 15 times faster, while the specificities are equal. Output files generated by IntegrationMap were found to be 99.8% identical with results retrieved by much slower conventional mapping with the ENSEMBL alignment tool. CONCLUSION: Using IntegrationSeq and IntegrationMap, a validated, fast and standardized high-throughput analysis of insertion sites can be achieved for the first time.

ProtSweep, 2Dsweep and DomainSweep: protein analysis suite at DKFZ.

The wealth of transcript information that has been made publicly available in recent years has led to large pools of individual web sites offering access to bioinformatics software. However, finding out which services exist, what they can or cannot do, how to use them and how to feed results from one service to the next one in the right format can be very time and resource consuming, especially for non-experts. Automating this task, we present a suite of protein annotation pipelines (tasks) developed at the German Cancer Research Centre (DKFZ) oriented to protein annotation by homology (ProtSweep), by domain analysis (DomainSweep), and by secondary structure elements (2Dsweep). The aim of these tasks is to perform an exhaustive structural and functional analysis employing a wide variety of methods in combination with the most updated public databases. The three servers are available for academic users at the HUSAR open server http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar/

The electronic nonadiabatic coupling term: can it be ignored in dynamic calculations?

Whereas the search for the degeneracy points which are better known as conical intersections (or ci-points) is usually carried out with a lot of devotion, the nonadiabatic coupling terms (NACTs) which together with the adiabatic potential energy surfaces appear in the nuclear Born-Oppenheimer-Schrodinger equation are ignored in most dynamical calculations. In the present article we consider two well known frameworks, namely, the semiclassical surface hopping method and the vibrational coupling model Hamiltonian that avoid the NACTs and examine to what extent, this procedure is justified.

Two-state versus three-state quantization: an ab initio study of the three lower states of the {N,H2/A'} system.

In this article we present the first ab initio study of the conical intersections (cis) and their electronic nonadiabatic coupling terms (NACTs) for the {N,H2} system. Efforts were made to reveal the location of cis between the two lower, 1 2A' and 2 2A' states--to be designated as (1,2) cis--and the cis between the two upper, 2 2A' and 3 2A' states--to be designated as the (2,3) cis--of this system. We found that these cis are located along the collinear {NHH) arrangement. The study is carried out by analyzing two-state magnitudes such as the (1,2) and (2,3) adiabatic-to-diabatic transformation angles (known also as the mixing angles) and the corresponding topological phases (known also as the Berry phases or the Longuet-Higgins phases). In addition, a detailed three-state study is carried out. Here the emphasis is on driving the diagonal elements of the topological D matrix and analyzing situations for which the corresponding nonadiabatic coupling matrix is quantized. The reliability of two-state results is carefully examined by comparing them with corresponding outcomes derived for the three-state study. In addition we also calculated the potential-energy surfaces related to the two lower states and studied to what extent they are affected by the (1,2) ci. The results obtained in this treatment were found to be in full agreement with the NACT's calculations.

On diabatization and the topological D-matrix: theory and numerical studies of the H + H2 system and the C2H2 molecule.

This article is divided into two main parts: (1) The theoretical part contains a new derivation of the topological matrix D (M. Baer and A. Alijah, Chem. Phys. Lett., 2000, 319, 489) which is based, solely, on the spatial dependent electronic manifold. This derivation enables more intimate relations between the adiabatic and the diabatic frameworks as is discussed in detail in the manuscript. (2) The numerical part is also divided into two parts: (a) In the first part we extend our previous study on the H + H2 system (G. Halasz, A. Vibok, A. M. Mebel and M. Baer, J. Chem. Phys., 2003, 118, 3052) by calculating the topological matrix for five states (instead of three) and for configuration spaces four times larger than before. These studies are expected to yield detailed information on the possibility of diabatization of this system. (b) We report on preliminary results concerning the C2H2 molecule. So far we established the existence of one (1,2) conical intersection and we have good reasons to believe that this system contains several (2,3) and (3,4) conical intersections as well.

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.

SUMMARY: The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single web portal. The 'Guided Solution Finder' which is available through the HNB portal helps users to locate the appropriate resources to answer their queries by employing a detailed, tree-like questionnaire. Furthermore, automated complex tool cascades ('tasks'), involving resources located on different servers, have been implemented, allowing users to perform comprehensive data analyses without the requirement of further manual intervention for data transfer and re-formatting. Currently, automated cascades for the analysis of regulatory DNA segments as well as for the prediction of protein functional properties are provided. AVAILABILITY: The HNB portal is available at http://www.hnbioinfo.de

Proton mobility and main fragmentation pathways of protonated lysylglycine.

Theoretical model calculations were performed to validate the 'mobile proton' model for protonated lysylglycine (KG). Detailed scans carried out at various quantum chemical levels of the potential energy surface (PES) of protonated KG resulted in a large number of minima belonging to various protonation sites and conformers. Transition structures corresponding to proton transfer reactions between different protonation sites were determined, to obtain some energetic and structural insight into the atomic details of these processes. The rate coefficients of the proton transfer reactions between the isomers were calculated using the Rice-Ramsperger-Kassel-Marcus (RRKM) method in order to obtain a quantitative measure of the time-scale of these processes. Our results clearly indicate that the added proton is less mobile for protonated KG than for peptides lacking a basic amino acid residue. However, the energy needed to reach the energetically less favorable but-from the point of view of backbone fragmentation-critical amide nitrogen protonation sites is available in tandem mass spectrometers operated under low-energy collision conditions. Using the results of our scan of the PES of protonated KG, the dissociation pathways corresponding to the main fragmentation channels for protonated KG were also determined. Such pathways include loss of ammonia and formation of a protonated alpha-amino-epsilon-caprolactam. The results of our theoretical modeling, which revealed all the atomic details of these processes, are in agreement with the available experimental results.

Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N'-methyl amide conformational states.

Density-functional theory (DFT) calculations utilizing the Becke 3LYP hybrid functional have been carried out for N-acetyl L-alanine N'-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA), vibrational circular dichroism (VCD), Raman spectra, and Raman optical activity (ROA) intensities. The large changes due to hydration in the structures, and the relative stability of the conformer, reflected in the VA, VCD, Raman spectra, and ROA spectra observed experimentally, are reproduced by the DFT calculations. A neural network has been constructed for reproducing the inverse scattering data (we infer the structural coordinates from spectroscopic data) that the DFT method could produce. The purpose of the network has also been to generate the large set of conformational states associated with each set of spectroscopic data for a given conformer of the molecule by interpolation. Finally the neural network performances are used to monitor a sensitivity analysis of the importance of secondary structures and the influence of the solvent. The neural network is shown to be good in distinguishing the different conformers of the small alanine peptide, especially in the gas phase.

Proton mobility in protonated glycylglycine and N-formylglycylglycinamide: a combined quantum chemical and RKKM study.

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.

Theoretical study of the main fragmentation pathways for protonated glycylglycine.

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.

Formation of a2+ ions of protonated peptides. An ab initio study.

The mechanism of the formation of a2+ ions from b2+ ions occurring during fragmentation of protonated peptides is investigated using quantum chemical methods. The geometries of the stationary structures involved in two possible mechanisms, namely, a two-step mechanism via an open-chain acylium ion and a concerted pathway involving rupture of two covalent bonds of the cyclic isomer of the b2+ ion, as well as the energetics of the reactions, were calculated at the MP2 and B3LYP levels, both combined with the 6-31G(d,p) as well as the 6-31++G(d,p) basis sets for the simplest analog of the b2+ ion. The energetically favored path is the direct expulsion of the CO molecule from the cyclic b2+ ion. The ZPE-corrected barrier height for this reaction is 26.2 kcal mol(-1) at the MP2/6-31G(d,p) level, while the highest barrier along the two step path is 31.4 kcal mol(-1). The barrier height for the reverse reaction is 3.8 kcal mol(-1), significantly smaller than the average kinetic energy release (KER) measured for larger b2+ ions. The barrier height for the reverse reactions of the MeCO-NH-CHMeCO+, NH2-iBuCH-CO-NH-CH2CO+, and NH2-CH2-CO-NH-CH(i-Bu)CO+ b2+ ions was found to be 11.3, 9.6, and 18.4 kcal mol(-1), in reasonable agreement with the measured KER for these reactions, indicating that the simplest model compound has unique properties in this respect. Based on comparisons with G2-MP2 calculations, comments are made on the applicability of various levels of theory for the description of the reaction.

Proton mobility in protonated peptides: a joint molecular orbital and RRKM study.

The mobile proton model was critically evaluated by using purely theoretical models which include quantum mechanical calculations to determine stationary points on the potential energy surface (PES) of a model compound, and Rice-Ramsperger-Kassel-Marcus (RRKM) calculations to determine the rate constants of various processes (conformational changes, proton transfer reactions) which occur during mass analysis of protonated peptides. Extensive mapping of the PES of protonated N-formylglycinamide resulted in various minima which were stabilized by one or more of the following types of interaction: internal hydrogen bond, charge transfer interaction, charge delocalization, and ring formation. The relative energies of most of the investigated minima are less then 20 kcal mol(-1) compared with the most stable species. More importantly, the relative energies of the transition structures connecting these minima are fairly low, allowing facile transitions among the energetically low-lying species. It is demonstrated that a path can be found leading from the energetically most stable species, protonated on an amide oxygen, to the structure from which the energetically most favorable fragmentation occurs. It is also shown that the added proton can sample all protonation sites prior to fragmentation. The RRKM calculations applied the results of ab initio computations (structures, energetics, vibrational frequencies) to the reactions (internal rotations, proton transfers) occurring in protonated N-formylglycinamide, and clearly lend additional evidence to the mobile proton model. Based on the results of the PES search on protonated N-formylglycinamide, we also comment on the mechanism proposed by Arnot et al. (Arnot D, Kottmeier D, Yates N, Shabanowitz J, Hunt D F. 42(nd) ASMS Conference on Mass Spectrometry, 1994; 470) and Reid et al. (Reid G E, Simpson R J, O'Hair R A J. J. Am. Soc. Mass Spectrom. 1998; 9:945) for the formation of b(2)(+) ions. According to the high level ab initio results, the mechanism relying on amide oxygen protonated species seems to be less feasible than the one which involves N-protonated species.

Molecular dynamics study of the nature and origin of retinal's twisted structure in bacteriorhodopsin.

The planarity of the polyene chain of the retinal chromophore in bacteriorhodopsin is studied using molecular dynamics simulation techniques and applying different force-field parameters and starting crystal structures. The largest deviations from a planar structure are observed for the C(13)==C(14) and C(15)==N(16) double bonds in the retinal Schiff base structure. The other dihedral angles along the polyene chain of the chromophore, although having lower torsional barriers in some cases, do not significantly deviate from the planar structure. The results of the simulations of different mutants of the pigment show that, among the studied amino acids of the binding pocket, the side chain of Trp-86 has the largest impact on the planarity of retinal, and the mutation of this amino acid to alanine leads to chromophore planarity. Deletion of the methyl C(20), removal of a water molecule hydrogen-bonded to H(15), or mutation of other amino acids to alanine did not show any significant influence on the distortion of the chromophore. The results from the present study suggest the importance of the bulky residue of Trp-86 in the isomerization process, in both ground and excited states of the chromophore, and in fine-tuning of the pK(a) of the retinal protonated Schiff base in bacteriorhodopsin. The dark adaptation of the pigment and the last step of the bacteriorhodopsin photocycle imply low barriers against the rotation of the double bonds in the Schiff base region. The twisted double bonds found in the present study are consistent with the proposed mechanism of these ground state isomerization events.

QM/MM study of the active site of free papain and of the NMA-papain complex.

Hybrid quantum mechanical/molecular mechanical (QM/MM) calculations using restricted and unrestricted Hartree-Fock and B3LYP ab initio (QM) and Amber force field (MM), respectively, have been applied to study the catalytic site of papain in both free and substrate bonded forms. Ab initio geometry optimizations have been performed for the active site of papain and the N-methyl-acetamide (NMA)-papain complex within the molecular mechanical treatment of the protein environment. A covalent tetrahedral intermediate structure could be obtained only when the amide N atom of the substrate molecule was protonated through a proton transfer from the His-159 in the catalytic site. Our results support the previous assumption that a proton transfer from His-159 to the amide N atom of the substrate occurs prior to or concerted with the nucleophilic attack of the Cys-25 sulfur atom to the carbonyl group of the substrate. The electron correlation effect will reduce the proton transfer barrier. Therefore, this proton transfer can be easily observed in the B3LYP/6-31G* calculations. The HF/6-31G* method overestimates the reaction barrier against this proton transfer. The sulfur atom of Cys-25 and the imidazole ring of His-159 are found to be coplanar in the free form of the enzyme. However, the rotation of the imidazole ring of His-159 was observed during the formation of the tetrahedral intermediate. Without the papain environment, the coplanar thiolate-imidazolium ion pair RS-...ImH+ is much less stable than the neutral form of RSH....Im. Within the protein environment, however, the thiolate-imidazolium ion pair becomes more stable than its neutral form by 4.1 and 0.4 kcal/mol in HF/6-31G* and B3LYP/6-31G* calculations, respectively. The barrier of proton transfer from S-H group of Cys-25 to the imidazole ring of His-159 was reduced from 22.0 kcal/mol to 15.2 kcal/mol by the protein environment in HF/6-31G* calculations. This barrier is found to be much smaller (2.5 kcal/mol) in B3LYP/6-31G* calculations.

Estimating linkage disequilibrium between a polymorphic marker locus and a trait locus in natural populations.

Positional cloning of gene(s) underlying a complex trait requires a high-resolution linkage map between the trait locus and genetic marker loci. Recent research has shown that this may be achieved through appropriately modeling and screening linkage disequilibrium between the candidate marker locus and the major trait locus. A quantitative genetics model was developed in the present study to estimate the coefficient of linkage disequilibrium between a polymorphic genetic marker locus and a locus underlying a quantitative trait as well as the relevant genetic parameters using the sample from randomly mating populations. Asymptotic covariances of the maximum-likelihood estimates of the parameters were formulated. Convergence of the EM-based statistical algorithm for calculating the maximum-likelihood estimates was confirmed and its utility to analyze practical data was exploited by use of extensive Monte-Carlo simulations. Appropriateness of calculating the asymptotic covariance matrix in the present model was investigated for three different approaches. Numerical analyses based on simulation data indicated that accurate estimation of the genetic parameters may be achieved if a sample size of 500 is used and if segregation at the trait locus explains not less than a quarter of phenotypic variation of the trait, but the study reveals difficulties in predicting the asymptotic variances of these maximum-likelihood estimates. A comparison was made between the statistical powers of the maximum-likelihood analysis and the previously proposed regression analysis for detecting the disequilibrium.

Protein fold class prediction: new methods of statistical classification.

Feed forward neural networks are compared with standard and new statistical classification procedures for the classification of proteins. We applied logistic regression, an additive model and projection pursuit regression from the methods based on a posterior probabilities; linear, quadratic and a flexible discriminant analysis from the methods based on class conditional probabilities, and the K-nearest-neighbors classification rule. Both, the apparent error rate obtained with the training sample (n = 143) and the test error rate obtained with the test sample (n = 125) and the 10-fold cross validation error were calculated. We conclude that some of the standard statistical methods are potent competitors to the more flexible tools of machine learning.

W2H: WWW interface to the GCG sequence analysis package.

MOTIVATION: The user-friendly, graphical X-windows interface (WPI) to the GCG sequence analysis package can often not be used due to the lack of an X-server on PC or Macintosh computers. Because Web browsers like Netscape are much more common on those platforms, we decided to develop W2H, a WWW interface to the GCG Sequence Analysis Software Package with nearly the same functionality as the X-windows interface WPI. RESULTS: The new WWW interface (W2H) to the GCG Sequence Analysis Software Package (Wisconsin Package) supports modern Web technologies, like client-pull method, or embedded scripting language, and provides a reasonable platform independence. The interface is quite comprehensive with advanced features like sequence selector, search set builder, enzyme chooser, access to sequence databases, uploading client files to the GCG server or displaying and manipulating graphical outputs in addition to GCG analysis programs. W2H also manages secure access to both GCG server and user data. For special environments, like workshops, conferences and company intranets, there is a special mode (Intranet mode) with less security constraints. The behaviour of W2H is mostly controlled by meta-data files describing the applications and giving a base for dynamic creation of HTML documents. This paper presents mainly the development approaches used, and architectural design aspects of W2H. AVAILABILITY: W2H is available by ftp://ftp.ebi.ac. uk/pub/software/unix/w2h or ftp://genome.dkfz-heidelberg.de/pub/w2h CONTACT: m.senger@ebi.ac.uk