No abstract

The fragmentation pathways of protonated peptides are reviewed in the present paper paying special attention to classification of the known fragmentation channels into a simple hierarchy defined according to the chemistry involved. It is shown that the 'mobile proton' model of peptide fragmentation can be used to understand the MS/MS spectra of protonated peptides only in a qualitative manner rationalizing differences observed for low-energy collision induced dissociation of peptide ions having or lacking a mobile proton. To overcome this limitation, a deeper understanding of the dissociation chemistry of protonated peptides is needed. To this end use of the 'pathways in competition' (PIC) model that involves a detailed energetic and kinetic characterization of the major peptide fragmentation pathways (PFPs) is proposed. The known PFPs are described in detail including all the pre-dissociation, dissociation, and post-dissociation events. It is our hope that studies to further extend PIC will lead to semi-quantative understanding of the MS/MS spectra of protonated peptides which could be used to develop refined bioinformatics algorithms for MS/MS based proteomics. Experimental and computational data on the fragmentation of protonated peptides are reevaluated from the point of view of the PIC model considering the mechanism, energetics, and kinetics of the major PFPs. Evidence proving semi-quantitative predictability of some of the ion intensity relationships (IIRs) of the MS/MS spectra of protonated peptides is presented.

We extend an approximate density functional theory (DFT) method for the description of long-range dispersive interactions which are normally neglected by construction, irrespective of the correlation function applied. An empirical formula, consisting of an R−6 term is introduced, which is appropriately damped for short distances; the corresponding C6 coefficient, which is calculated from experimental atomic polarizabilities, can be consistently added to the total energy expression of the method. We apply this approximate DFT plus dispersion energy method to describe the hydrogen bonding and stacking interactions of nucleic acid base pairs. Comparison to MP2/6-31G*(0.25) results shows that the method is capable of reproducing hydrogen bonding as well as the vertical and twist dependence of the interaction energy very accurately.

We present an EST sequence assembler that specializes in reconstruction of pristine mRNA transcripts, while at the same time detecting and classifying single nucleotide polymorphisms (SNPs) occuring in different variations thereof. The assembler uses iterative multipass strategies centered on high-confidence regions within sequences and has a fallback strategy for using low-confidence regions when needed. It features special functions to assemble high numbers of highly similar sequences without prior masking, an automatic editor that edits and analyzes alignments by inspecting the underlying traces, and detection and classification of sequence properties like SNPs with a high specificity and a sensitivity down to one mutation per sequence. In addition, it includes possibilities to use incorrectly preprocessed sequences, routines to make use of additional sequencing information such as base-error probabilities, template insert sizes, strain information, etc., and functions to detect and resolve possible misassemblies. The assembler is routinely used for such various tasks as mutation detection in different cell types, similarity analysis of transcripts between organisms, and pristine assembly of sequences from various sources for oligo design in clinical microarray experiments.On the way to understand the function of all genes of an organism, it is now clear that the genome sequence alone may be not enough, especially if the organism shows a high degree of complexity. Analysis of the genome must be supported by efforts on understanding its transcription-the transcriptome-occurring in cells. Citing Camargo et al. (2001), the "most definitive approach to the elucidation of transcripts remains their direct sequencing." This corresponds with earlier findings of Bonfield et al. (1998), who concluded that "direct sequencing is required to define the precise location and nature of any [mutation] change", as this method ensures the highest reliability and quality regarding the definition of single nucleotide polymorphisms (SNPs).Several approaches have been proposed to assemble ESTs and detect SNPs in the resulting alignments, among these are TRACE-DIFF by Bonfield et al. (1998) Barker et al. (2003). The most significant shortcoming common to all of these methods is the fact that they determine potential SNP positions from assemblies that align all available sequences together, regardless of whether they contain differing SNP positions or originate from different sources such as, for example, organisms, strains, cell types, etc. Unfortunately, the intrinsic properties of alignment algorithms can, and do lead to misassemblies, especially when the sequences involved are highly similar. This, in turn, leads to wrongly assembled transcripts, and these can cause false or nonexistent proteins to be predicted as is shown in Figure 1. As a side effect, nonexistent SNP positions are also generated.To address these problems, the method we have devised and implemented, the miraEST assembler, consists of an iterative multiple-pass...

No abstract

The present status of development of the density-functional-based tightbinding (DFTB) method is reviewed. As a two-centre approach to densityfunctional theory (DFT), it combines computational efficiency with reliability and transferability. Utilizing a minimal-basis representation of Kohn-Sham eigenstates and a superposition of optimized neutral-atom potentials and related charge densities for constructing the effective many-atom potential, all integrals are calculated within DFT. Self-consistency is included at the level of Mulliken charges rather than by self-consistently iterating electronic spin densities and effective potentials. Excited-state properties are accessible within the linear response approach to time-dependent (TD) DFT. The coupling of electronic and ionic degrees of freedom further allows us to follow the non-adiabatic structure evolution via coupled electron-ion molecular dynamics in energetic particle collisions and in the presence of ultrashort intense laser pulses. We either briefly outline or give references describing examples of applications to ground-state and excited-state properties. Addressing the scaling problems in size and time generally and for biomolecular systems in particular, we describe the implementation of the parallel 'divide-and-conquer' order-N method with DFTB and the coupling of the DFTB approach as a quantum method with molecular mechanics force fields.

In this paper we propose an extension of the self-consistent charge-density-functional tight-binding ͑SCC-DFTB͒ method ͓M. Elstner et al., Phys. Rev. B 58, 7260 ͑1998͔͒, which allows the calculation of the optical properties of finite systems within time-dependent density-functional response theory ͑TD-DFRT͒. For a test set of small organic molecules low-lying singlet excitation energies are computed in good agreement with first-principles and experimental results. The overall computational cost of this parameter-free method is very low and thus it allows us to examine large systems: we report successful applications to C 60 and the polyacene series.

No abstract