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Experimental and theoretical infrared spectra for tryptophan-[water.sub.n] complexes where n=1-6 are described. The evidence for a gradual transition to zwitterionic structures comes from tryptophan-methanol complexes up to n=9 and starting from n=5, the infrared spectra show increasing intensity in the diagnostic asymmetric CO[O.sup.-] stretch and in the weaker N[H.sup.>sub.3] bending modes as the cluster size increases.

The density functional theory (DFT) is used to study the binding of clusters of gold atoms (Au) with the guanine-cytosine (GC) and adenine-thymine (AT) Watson-Crick DNA base pairs. The analysis has shown that guanine and adenine have high affinity for Au clusters and the calculated adiabatic electron affinities (AEAs) of the GC-[Au.sub.n] complexes (n = 4, 8) are found to be much larger than those of the isolated base pairs.

Density functional theory (DFT) was used to study the adiabatic electron affinities (AEAs) of the adenine-thymine (AT) base pari surrounded by 5 and 13 water molecules. Geometries of neutral AT.nH2O and anionic (AT.nH2O)(super -) complexes (n=5 and 13) were fully optimized, and vibrational frequency analysis was performed at the B3LYP/6-31+G** level of theory.

A series of gas-phase experiments and extensive theoretical modeling was done on the family of singly protonated peptides AARAA, Ac-AARAA and AARAA-OMe to examine the effect of the initial water of hydration on the energetics, structures and the mechanism of H/D exchange on the peptides. It is concluded that (AARAA)H(super +) is capable of undergoing faster H/D exchange with D2O as compared to (AC-AARAA)H(super +) and (AARAA-OMe)H(super +).

Properties of isolated intercalators (ethidium (E), daunomycin (D), ellipticine (EL), and 4,6'-diaminide-2-phenylindole (DAPI)) and their stacking interactions with adenine...thymine (AT) and guanine...cytosine (GC) nucleic acid base pairs are investigated by means of a nonempirical correlated ab initio method. The intercalators exhibit large charge delocalization, and none of them contains sites with high charge concentration.

Several quantum mechanical methods were used to examine the electronic effects of a double bond rotation in protonated and neutral polyene Schiff bases. The performance of these methods is compared to one another to determine their efficiency. In the protonated case, the theoretical and experimental vibrational spectra were also compared to verify the methods. Results showed that the unrestricted natural orbital complete active space and UB3LYP frequencies were close to the experimental values.

Abstract Background The German cDNA Consortium has been cloning full length cDNAs and continued with their exploitation in protein localization experiments and cellular assays. However, the efficient use of large cDNA resources requires the development of strategies that are capable of a speedy selection of truly useful cDNAs from biological and experimental noise. To this end we have developed a new high-throughput analysis tool, CAFTAN, which simplifies these efforts and thus fills the gap between large-scale cDNA collections and their systematic annotation and application in functional genomics. Results CAFTAN is built around the mapping of cDNAs to the genome assembly, and the subsequent analysis of their genomic context. It uses sequence features like the presence and type of PolyA signals, inner and flanking repeats, the GC-content, splice site types, etc. All these features are evaluated in individual tests and classify cDNAs according to their sequence quality and likelihood to have been generated from fully processed mRNAs. Additionally, CAFTAN compares the coordinates of mapped cDNAs with the genomic coordinates of reference sets from public available resources (e.g., VEGA, ENSEMBL). This provides detailed information about overlapping exons and the structural classification of cDNAs with respect to the reference set of splice variants. The evaluation of CAFTAN showed that is able to correctly classify more than 85% of 5950 selected "known protein-coding" VEGA cDNAs as high quality multi- or single-exon. It identified as good 80.6 % of the single exon cDNAs and 85 % of the multiple exon cDNAs. The program is written in Perl and in a modular way, allowing the adoption of this strategy to other tasks like EST-annotation, or to extend it by adding new classification rules and new organism databases as they become available. We think that it is a very useful program for the annotation and research of unfinished genomes. Conclusion CAFTAN is a high-throughput sequence analysis tool, which performs a fast and reliable quality prediction of cDNAs. Several thousands of cDNAs can be analyzed in a short time, giving the curator/scientist a first quick overview about the quality and the already existing annotation of a set of cDNAs. It supports the rejection of low quality cDNAs and helps in the selection of likely novel splice variants, and/or completely novel transcripts for new experiments.

Abstract Background In the last years several high-throughput cDNA sequencing projects have been funded worldwide with the aim of identifying and characterizing the structure of complete novel human transcripts. However some of these cDNAs are error prone due to frameshifts and stop codon errors caused by low sequence quality, or to cloning of truncated inserts, among other reasons. Therefore, accurate CDS prediction from these sequences first require the identification of potentially problematic cDNAs in order to speed up the posterior annotation process. Results cDNA2Genome is an application for the automatic high-throughput mapping and characterization of cDNAs. It utilizes current annotation data and the most up to date databases, especially in the case of ESTs and mRNAs in conjunction with a vast number of approaches to gene prediction in order to perform a comprehensive assessment of the cDNA exon-intron structure. The final result of cDNA2Genome is an XML file containing all relevant information obtained in the process. This XML output can easily be used for further analysis such us program pipelines, or the integration of results into databases. The web interface to cDNA2Genome also presents this data in HTML, where the annotation is additionally shown in a graphical form. cDNA2Genome has been implemented under the W3H task framework which allows the combination of bioinformatics tools in tailor-made analysis task flows as well as the sequential or parallel computation of many sequences for large-scale analysis. Conclusions cDNA2Genome represents a new versatile and easily extensible approach to the automated mapping and annotation of human cDNAs. The underlying approach allows sequential or parallel computation of sequences for high-throughput analysis of cDNAs.

The proton-driven amide bond cleavages are described that are required to produce b and y ions from peptide ions lacking easily mobilizable protons. Three new amide bond cleavage mechanisms are presented that involve salt-bridge, anhydride and imine enol intermediates.

Hybrid quantum mechanics/molecular mechanics proton transfer calculations are performed using different protein structures and with different retinal geometries and active site water molecules in order to assess whether the transient protonation of Asp212 has participated in deprotonation of Asp85. The results have shown that a transient [O] conformer with protonated Asp212 is sampled during the long-distance proton transfer to the proton release group.

The gas-phase structures and fragmentation pathways of the N-terminal b and a fragments of YAGFL-N[H.sub.2], AGLFY-N[H.sub.2], GFLYA-N[H.sub.2], FLYAG-N[H.sub.2] and LYAGF-N[H.sub.2] are examined by using collision-induced dissociation (CID) and molecular mechanics and density functional theory (DFT) calculations. The studies have shown that the a -> a*-type rearrangement pathways of the linear a isomers have involved post-cleavage proton-bound dimer intermediates in which the fragments reassociates and the originally C-terminal fragment is transferred to the N-terminus.

The conformational structures of protonated polyalanine peptides, [Ala.sub.n][H.sup.+] are investigated in the gas phase. Results show that the peptide [Ala.sub.3][H.sup.+] exhibits an unfolded shape with likely dynamic interconversion between different conformations.

Density functional theory was used to study the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical. Results reveal that water molecules surrounding the GC base pair have significant effect on the geometry of the GC base pair and promote nonplanarity in the GC base pair.

Infrared multiple-photon dissociation (IR-MPD) spectroscopy and detailed molecular mechanics and density function theory (DFT) calculations are used to investigate the gas-phase structures of the photonated pentapeptide Leu-enkephalin and its main collision-induced dissociation (CID) product ions, [b.sub.4] and [a.sub.4]. The results have shown that the presence of cyclic [b.sub.4] and [a.sub.4] fragment ions are very important, thus supporting the peptide fragmentation pathways that result in scrambling of the amino acid sequence upon CID.

Quantum mechanical/molecular mechanical (QM/MM) reaction-path calculations were used for examining the protein photocycle. The barrier for the thermal cis-trans back-isomerization is lowered by retinal twisting and the rate-limiting barrier for back-isomerization is 5-6 kcal/mol larger than the barrier for the first proton-transfer step.

The application of infrared photofragment spectroscopy to the amino acids tyrosine and phenylalanine, and two pentapeptides, bradykinin fragment 1-5 and [Leu]-enkephalin, all bound to a potassium cation is presented. The striking feature in the [Leu]-enkephalin spectrum is the high infrared activity of the tyrosine side-chain modes, which can be clearly identified from comparison to the experimental spectrum, but which is not reproduced by the DFT calculations.

The proton transfer energy profiles in bacteriorhodopsin for various retinal isomeric states are investigated by employing quantum mechanics (QM)/ molecular mechanics (MM) minimum-energy path calculations. The proton transfer energy profiles are determined by two opposite-sign contributions, first the interaction between Asp85 and the 13-cis retinal, strongly favoring proton transfer, and the other arising from the protein electrostatic environment that stabilizes the ion pair state and gives rise to a proton transfer barrier.

Protein identification in proteomics is mostly achieved by tandem mass spectrometry (MS/MS) analysis of peptides produced by enzymatic digestion. In the MS/MS experiments, protonated peptides undergo collision-induced dissociation (CID), and the fragment ion spectrum is used to assign their amino acid sequence.

Infrared multiple-photon dissociation (IR-MPD) is applied to demonstrate the fragmentation formed by sustained collision-induced dissociation(CID) from the singly protonated peptide [Leu]-enkephalin (Tyr-Gly-Gly-Phe-Leu). Three distinct oxazolone cyclic structures are identified, indicating IR-MPD as an important tool in the elucidation of peptide fragment ions.