Biomedical subjects

Ralf Bundschuh

Publications and source records attributed to Ralf Bundschuh.

17 recordsLinked to original sources

PubMed2025

Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.

Eukaryotic genomic DNA is repeatedly wrapped into nucleosome spools: the basic building block of chromatin. This organization regulates the physical accessibility of the genome to gene transcription, replication, and repair regulatory factors. Chromatin compaction is controlled by multivalent weak interactions, resulting in a complicated conformational landscape that remains challenging to characterize. This work reports a method for characterizing chromatin compaction, Free Energy Spectroscopy (FES), which is based on DNA nanotechnology and transmission electron microscopy. This method experimentally determines the chromatin compaction free energy landscape in terms of end-to-end distance and nucleosome stacking interactions. By deconvolving the free energy landscapes of partially and fully compact tetranucleosomes, FES revealed three separate mechanisms by which linker histones reshape the compaction energetics to condense chromatin. This study establishes FES as a method with the potential to help answer a broad range of mechanistic questions about genome and epigenome function.

DNA nanotechnology↗

PubMed2007

A structured viroid RNA serves as a substrate for dicer-like cleavage to produce biologically active small RNAs but is resistant to RNA-induced silencing complex-mediated degradation.

RNA silencing is a potent means of antiviral defense in plants and animals. A hallmark of this defense response is the production of 21- to 24-nucleotide viral small RNAs via mechanisms that remain to be fully understood. Many viruses encode suppressors of RNA silencing, and some viral RNAs function directly as silencing suppressors as counterdefense. The occurrence of viroid-specific small RNAs in infected plants suggests that viroids can trigger RNA silencing in a host, raising the question of how these noncoding and unencapsidated RNAs survive cellular RNA-silencing systems. We address this question by characterizing the production of small RNAs of Potato spindle tuber viroid (srPSTVds) and investigating how PSTVd responds to RNA silencing. Our molecular and biochemical studies provide evidence that srPSTVds were derived mostly from the secondary structure of viroid RNAs. Replication of PSTVd was resistant to RNA silencing, although the srPSTVds were biologically active in guiding RNA-induced silencing complex (RISC)-mediated cleavage, as shown with a sensor system. Further analyses showed that without possessing or triggering silencing suppressor activities, the PSTVd secondary structure played a critical role in resistance to RISC-mediated cleavage. These findings support the hypothesis that some infectious RNAs may have evolved specific secondary structures as an effective means to evade RNA silencing in addition to encoding silencing suppressor activities. Our results should have important implications in further studies on RNA-based mechanisms of host-pathogen interactions and the biological constraints that shape the evolution of infectious RNA structures.

Arabidopsis↗

PubMed2006

Model for folding and aggregation in RNA secondary structures.

We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the secondary structure and the energy gained by pairing drives the RNA to undergo a "temperature independent" second order phase transition from a molten to an aggregated phase. The aggregated phase thus obtained has a macroscopically large number of contacts between different RNAs. The partition function scaling exponent for this phase is theta approximately 1/2 and the crossover exponent of the phase transition is nu approximately 5/3. The relevance of these calculations to the aggregation of biological molecules is discussed.

Models, Chemical↗

PubMed2006

A practical approach to significance assessment in alignment with gaps.

Current numerical methods for assessing the statistical significance of local alignments with gaps are time consuming. Analytical solutions thus far have been limited to specific cases. Here, we present a new line of attack to the problem of statistical significance assessment. We combine this new approach with known properties of the dynamics of the global alignment algorithm and high performance numerical techniques and present a novel method for assessing significance of gaps within practical time scales. The results and performance of these new methods test very well against tried methods with drastically less effort.

Algorithms↗

PubMed2005

Quantification of the differences between quenched and annealed averaging for RNA secondary structures.

The analytical study of a disordered system is usually difficult due to the necessity to perform a quenched average over the disorder. Thus, one may resort to the easier annealed ensemble as an approximation to the quenched system. In the study of RNA secondary structures, we explicitly quantify the deviation of this approximation from the quenched ensemble by looking at the correlations between neighboring bases. This quantified deviation then allows us to propose a constrained annealed ensemble which predicts some physical quantities much closer to the results of the quenched ensemble without becoming technically intractable.

Binding Sites↗

PubMed2005

Coupled dynamics of RNA folding and nanopore translocation.

The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base pairing theoretically, using kinetic Monte Carlo simulations and analytical methods. We find that the transient formation of base pairs that do not occur in the ground state can significantly speed up translocation.

Base Pairing↗

PubMed2005

Numerical method for accessing the universal scaling function for a multiparticle discrete time asymmetric exclusion process.

In the universality class of the one-dimensional Kardar-Parisi-Zhang (KPZ) surface growth, Derrida and Lebowitz conjectured the universality of not only the scaling exponents, but of an entire scaling function. Since and Derrida and Lebowitz's original publication [Phys. Rev. Lett. 80, 209 (1998)] this universality has been verified for a variety of continuous-time, periodic-boundary systems in the KPZ universality class. Here, we present a numerical method for directly examining the entire particle flux of the asymmetric exclusion process (ASEP), thus providing an alternative to more difficult cumulant ratios studies. Using this method, we find that the Derrida-Lebowitz scaling function (DLSF) properly characterizes the large-system-size limit (N--> infinity) of a single-particle discrete time system, even in the case of very small system sizes (N< or =22). This fact allows us to not only verify that the DLSF properly characterizes multiple-particle discrete-time asymmetric exclusion processes, but also provides a way to numerically solve for quantities of interest, such as the particle hopping flux. This method can thus serve to further increase the ease and accessibility of studies involving even more challenging dynamics, such as the open-boundary ASEP.

Journal Article↗

PubMed2005

Modeling DNA unzipping in the presence of bound proteins.

Unzipping force analysis of protein association is a technique to investigate protein-DNA interactions by mechanically unzipping DNA. We computationally investigate the limits of this technique under quasistatic conditions. We find the minimum binding energy of a protein for which the protein can be detected using this technique and the minimum distance between the binding sites of two proteins of varying binding energies that can be resolved unambiguously with this technique.

Binding Sites↗

PubMed2005

Discovery of new genes and deletion editing in Physarum mitochondria enabled by a novel algorithm for finding edited mRNAs.

Gene finding is complicated in organisms that exhibit insertional RNA editing. Here, we demonstrate how our new algorithm Predictor of Insertional Editing (PIE) can be used to locate genes whose mRNAs are subjected to multiple frameshifting events, and extend the algorithm to include probabilistic predictions for sites of nucleotide insertion; this feature is particularly useful when designing primers for sequencing edited RNAs. Applying this algorithm, we successfully identified the nad2, nad4L, nad6 and atp8 genes within the mitochondrial genome of Physarum polycephalum, which had gone undetected by existing programs. Characterization of their mRNA products led to the unanticipated discovery of nucleotide deletion editing in Physarum. The deletion event, which results in the removal of three adjacent A residues, was confirmed by primer extension sequencing of total RNA. This finding is remarkable in that it comprises the first known instance of nucleotide deletion in this organelle, to be contrasted with nearly 500 sites of single and dinucleotide addition in characterized mitochondrial RNAs. Statistical analysis of this larger pool of editing sites indicates that there are significant biases in the 2 nt immediately upstream of editing sites, including a reduced incidence of nucleotide repeats, in addition to the previously identified purine-U bias.

Algorithms↗

PubMed2005

Model for codon position bias in RNA editing.

RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with a certain bias in choosing the positions of the editing sites. In the mitochondrial genes of Physarum polycephalum, many more editing events have been observed at the third codon position than at the first and second, while in some plant mitochondria the second codon position dominates. Here we propose an evolutionary model that explains this bias as the basis of selection at the protein level. The model predicts a distribution of the three positions rather close to the experimental observation in Physarum. This suggests that the codon position bias in Physarum is mainly a consequence of selection at the protein level.

Animals↗

PubMed2004

Finite width model sequence comparison.

Sequence comparison is a widely used computational technique in modern molecular biology. In spite of the frequent use of sequence comparisons, the important problem of assigning statistical significance to a given degree of similarity is still outstanding. Analytical approaches to filling this gap usually make use of an approximation that neglects certain correlations in the disorder underlying the sequence comparison algorithm. Here, we use the longest common subsequence problem, a prototype sequence comparison problem, to analytically establish that this approximation does make a difference to certain sequence comparison statistics. In the course of establishing this difference we develop a method that can systematically deal with these disorder correlations.

Algorithms↗

PubMed2004

Analytical description of finite size effects for RNA secondary structures.

The ensemble of RNA secondary structures of uniform sequences is studied analytically. We calculate the partition function for very long sequences and discuss how the crossover length, beyond which asymptotic scaling laws apply, depends on thermodynamic parameters. For realistic choices of parameters this length can be much longer than natural RNA molecules. This has to be taken into account when applying asymptotic theory to interpret experiments or numerical results.

Base Pairing↗

PubMed2004

Translocation of structured polynucleotides through nanopores.

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the translocation process. We show that this circumstance may be exploited to determine the full basepairing pattern of polynucleotides, including RNA pseudoknots. The crucial requirement is that the translocation dynamics (i.e. the length of the translocated molecular segment) needs to be recorded as a function of time with a spatial resolution of a few nucleotides. This could be achieved, for instance, by applying a mechanical driving force for translocation and recording force-extension curves (FECs) with a device such as an atomic force microscope or optical tweezers. Our analysis suggests that, with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids.

Animals↗

PubMed2003

Mechanically probing the folding pathway of single RNA molecules.

We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating the experimentally determined free energy rules for RNA secondary structure, whereas exterior single-stranded regions are modeled as freely jointed chains. For exemplary RNA sequences (hairpins and the Tetrahymena thermophila group I intron), we compute the quasiequilibrium fluctuations in the end-to-end distance as the molecule is unfolded by pulling on opposite ends. Unlike the average quasiequilibrium force-extension curves, these fluctuations reveal clear signatures from the unfolding of individual structural elements. We find that the resolution of these signatures depends on the spring constant of the force-measuring device, with an optimal value intermediate between very rigid and very soft. We compare and relate our results to recent experiments by Liphardt et al. (2001).

Animals↗

PubMed2002

Delocalization transitions of semiflexible manifolds.

Semiflexible manifolds such as fluid membranes or semiflexible polymers undergo delocalization transitions if they are subject to attractive interactions. We study manifolds with short-ranged interactions by field-theoretic methods based on the operator product expansion of local interaction fields. We apply this approach to manifolds in a random potential. Randomness is always relevant for fluid membranes, while for semiflexible polymers there is a first-order transition to the strong coupling regime at a finite temperature.

Journal Article↗

PubMed2002

Rapid significance estimation in local sequence alignment with gaps.

In order to assess the significance of sequence alignments, it is crucial to know the distribution of alignment scores of pairs of random sequences. For gapped local alignment, it is empirically known that the shape of this distribution is of the Gumbel form. However, the determination of the parameters of this distribution is a computationally very expensive task. We present a new algorithmic approach which allows estimation of the more important of the Gumbel parameters at least five times faster than the traditional methods. Actual runtimes of our algorithm between less than a second and a few minutes on a workstation bring significance estimation into the realm of interactive applications.

Algorithms↗

PubMed2002

Hybrid alignment: high-performance with universal statistics.

The score statistics of a recently introduced 'hybrid alignment' algorithm is studied in detail numerically. An extensive survey across the 2216 models of protein domains contained in the Pfam v5.4 database (Bateman et al., Nucleic Acids Res., 28, 263-266, 2000) verifies the theoretical predictions: For the position-specific scoring functions used in the Pfam models, the score statistics of hybrid alignment obey the Gumbel distribution, with the key Gumbel parameter lambda taking on the asymptotic value 1 universally for all models. Thus, the use of hybrid alignment eliminates the time-consuming computer simulations normally needed to assign p-values to alignment scores, freeing the users to experiment with different scoring parameters and functions. The performance of the hybrid algorithm in detecting sequence homology is also studied. For protein sequences from the SCOP database (Murzin et al., J. Mol. Biol., 247, 536-540, 1995) using uniform scoring functions, the performance is found to be comparable to the best of the existing methods. Preliminary results using the PfamA database suggest that the hybrid algorithm achieves similar performance as existing methods for position-specific scoring systems as well. Hybrid alignment is thereby established as a high performance alignment algorithm with well-characterized, universal statistics.

Algorithms↗