Andreas Gaiser

The Non-canonical Hop Protein from Caenorhabditis elegans Exerts Essential Functions and Forms Binary Complexes with Either Hsc70 or Hsp90

Heat shock protein (Hsp) 70/Hsp90-organizing proteins (Hop/Sti1) are thought to function as adaptor proteins to link the two chaperone machineries Hsp70 and Hsp90 during the processing of substrate proteins in eukaryotes. Hop (Hsp70/Hsp90-organizing protein) is composed of three tetratricopeptide repeat (TPR) domains, of which the first (TPR1) binds to Hsp70, the second (TPR2A) binds to Hsp90, and the third (TPR2B) is of unknown function. Contrary to most other eukaryotes, the homologue closest to the Caenorhabditis elegans Hop homologue R09E12.3 (CeHop) lacks the TPR1 domain and the short linker region connecting it to TPR2A, questioning the reported function as an Hsp90/Hsp70 adaptor in vitro and in vivo. We observed high constitutive expression levels of CeHop and detected significant phenotypes upon knockdown, linking the protein to functions in gonad development. Interestingly, we observed physical interactions with both chaperones Hsp70 and Hsp90, albeit only the interaction with Hsp90 is strong and inhibition of the Hsp90 ATPase activity can be observed upon binding of CeHop. However, the formation of ternary complexes with both chaperone machineries is impaired, as Hsp70 and Hsp90 compete for CeHop interaction sites, in particular as Hsp90 binds to both TPR domains simultaneously and requires both TPR domains for ATPase regulation. These results imply that, at least in C. elegans, essential functions of Hop exist which apparently do not depend on the simultaneous binding of Hsp90 and Hsp70 to Hop.

Automata with generalized rabin pairs for probabilistic model checking and LTL synthesis

The model-checking problem for probabilistic systems crucially relies on the translation of LTL to deterministic Rabin automata (DRW). Our recent Safraless translation [KE12, GKE12] for the LTL(F,G) fragment produces smaller automata as compared to the traditional approach. In this work, instead of DRW we consider deterministic automata with acceptance condition given as disjunction of generalized Rabin pairs (DGRW). The Safraless translation of LTL(F,G) formulas to DGRW results in smaller automata as compared to DRW. We present algorithms for probabilistic model-checking as well as game solving for DGRW conditions. Our new algorithms lead to improvement both in terms of theoretical bounds as well as practical evaluation. We compare PRISM with and without our new translation, and show that the new translation leads to significant improvements.

Cdc37-Hsp90 Complexes Are Responsive to Nucleotide-induced Conformational Changes and Binding of Further Cofactors

Hsp90 is an ATP-dependent molecular chaperone, which facilitates the activation and stabilization of hundreds of client proteins in cooperation with a defined set of cofactors. Many client proteins are protein kinases, which are activated and stabilized by Hsp90 in cooperation with the kinase-specific co-chaperone Cdc37. Other Hsp90 co-chaperones, like the ATPase activator Aha1, also are implicated in kinase activation, and it is not yet clear how Cdc37 is integrated into Hsp90 co-chaperone complexes. Here, we studied the interaction between Cdc37, Hsp90, and other Hsp90 co-chaperones from the nematode Caenorhabditis elegans. Nematode Cdc37 binds with high affinity to Hsp90 and strongly inhibits the ATPase activity. In contrast to the human Hsp90 system, we observed binding of Cdc37 to open and closed Hsp90 conformations, potentially reflecting two different binding modes. Using a novel ultracentrifugation setup, which allows accurate analysis of multifactorial protein complexes, we show that cooperative and competitive interactions exist between other co-chaperones and Cdc37-Hsp90 complexes in the C. elegans system. We observed strong competitive interactions between Cdc37 and the co-chaperones p23 and Sti1, whereas the binding of the phosphatase Pph5 and the ATPase activator Aha1 to Cdc37-Hsp90 complexes is possible. The ternary Aha1-Cdc37-Hsp90 complex is disrupted by the nucleotide-induced closing reaction at the N terminus of Hsp90. This implies a carefully regulated exchange process of cofactors during the chaperoning of kinase clients by Hsp90.

Rabinizer: small deterministic automata for LTL (F,G)

We present Rabinizer, a tool for translating formulae of the fragment of linear temporal logic with the operators F (eventually) and G (globally) into deterministic Rabin automata. Contrary to tools like ltl2dstar, which translate the formula into a Buchi automaton and apply Safras determinization procedure, Rabinizer uses a direct construction based on the logical structure of the formulae. We describe a number of optimizations of the basic procedure, crucial for the good performance of Rabinizer, and present an experimental comparison.

Comparison of Algorithms for Checking Emptiness on Büchi Automata.

We re-investigate the problem of LTL model-checking for finite-state systems. Typical solutions, like in Spin, work on the fly, reducing the problem to Buchi emptiness. This can be done in linear time, and a variety of algorithms with this property exist. Nonetheless, subtle design decisions can make a great difference to their actual performance in practice, especially when used on-the-fly. We compare a number of algorithms experimentally on a large benchmark suite, measure their actual run-time performance, and propose improvements. Compared with the algorithm implemented in Spin, our best algorithm is faster by about 33 % on average. We therefore recommend that, for on-the-fly explicit-state model checking, nested DFS should be replaced by better solutions.

The Lid Domain of Caenorhabditis elegans Hsc70 Influences ATP Turnover, Cofactor Binding and Protein Folding Activity

Hsc70 is a conserved ATP-dependent molecular chaperone, which utilizes the energy of ATP hydrolysis to alter the folding state of its client proteins. In contrast to the Hsc70 systems of bacteria, yeast and humans, the Hsc70 system of C. elegans (CeHsc70) has not been studied to date. We find that CeHsc70 is characterized by a high ATP turnover rate and limited by post-hydrolysis nucleotide exchange. This rate-limiting step is defined by the helical lid domain at the C-terminus. A certain truncation in this domain (CeHsc70-Δ545) reduces the turnover rate and renders the hydrolysis step rate-limiting. The helical lid domain also affects cofactor affinities as the lidless mutant CeHsc70-Δ512 binds more strongly to DNJ-13, forming large protein complexes in the presence of ATP. Despite preserving the ability to hydrolyze ATP and interact with its cofactors DNJ-13 and BAG-1, the truncation of the helical lid domain leads to the loss of all protein folding activity, highlighting the requirement of this domain for the functionality of the nematodes Hsc70 protein.

Computing Least Fixed Points of Probabilistic Systems of Polynomials

We study systems of equations of the form X1 = f1(X1, ..., Xn), ..., Xn = fn(X1, ..., Xn), where each fi is a polynomial with nonnegative coefficients that add up to 1. The least nonnegative solution, say mu, of such equation systems is central to problems from various areas, like physics, biology, computational linguistics and probabilistic program verification. We give a simple and strongly polynomial algorithm to decide whether mu=(1, ..., 1) holds. Furthermore, we present an algorithm that computes reliable sequences of lower and upper bounds on mu, converging linearly to mu. Our algorithm has these features despite using inexact arithmetic for efficiency. We report on experiments that show the performance of our algorithms.

Probabilistic abstractions with arbitrary domains

Recent work by Hermanns et al. and Kattenbelt et al. has extended counterexample-guided abstraction refinement (CEGAR) to probabilistic programs. These approaches are limited to predicate abstraction. We present a novel technique, based on the abstract reachability tree recently introduced by Gulavani et al., that can use arbitrary abstract domains and widening operators (in the sense of Abstract Interpretation). We show how suitable widening operators can deduce loop invariants difficult to find for predicate abstraction, and propose refinement techniques.

A strongly polynomial algorithm for criticality of branching processes and consistency of stochastic context-free grammars☆

We provide a strongly polynomial algorithm for determining whether a given multi-type branching process is subcritical, critical, or supercritical. The same algorithm also decides consistency of stochastic context-free grammars.

On least fixed points of systems of positive polynomials

). Obviously, 1 = (1,...,1) is a solution for everySPrP. By Kleene’s theorem, every SPrP has a least nonnegative solution (called just least solution in what follows).SPrPsareimportantindifferentareasofthetheoryofstochasticprocessesandcomputationalmodels. Afundamentalresultof the theory of branching processes, with numerous applications in physics and biology (see e.g. [6, 1]), states that extinctionprobabilities of species are equal to the least solution of a SPrP. The same result has been recently shown for the probability ofterminationofcertainprobabilisticrecursiveprograms([5,4]). Theconsistencyofstochasticcontext-freegrammars,aproblemof interest in statistical natural language processing, also reduces to checking whether the least solution of a SPrP equals 1 (seee.g. [8]).We fix an SPrP with function f and denote its least solution by µ