Shruti Sharma, Kausik Chakraborty, Barbara K Müller, Nagore Astola, Yun-Chi Tang, Don C Lamb, Manajit Hayer-Hartl, F Ulrich Hartl[show abstract] [hide abstract]
ABSTRACT: The GroEL/GroES chaperonin system mediates protein folding in the bacterial cytosol. Newly synthesized proteins reach GroEL via transfer from upstream chaperones such as DnaK/DnaJ (Hsp70). Here we employed single molecule and ensemble FRET to monitor the conformational transitions of a model substrate as it proceeds along this chaperone pathway. We find that DnaK/DnaJ stabilizes the protein in collapsed states that fold exceedingly slowly. Transfer to GroEL results in unfolding, with a fraction of molecules reaching locally highly expanded conformations. ATP-induced domain movements in GroEL cause transient further unfolding and rapid mobilization of protein segments with moderate hydrophobicity, allowing partial compaction on the GroEL surface. The more hydrophobic regions are released upon subsequent protein encapsulation in the central GroEL cavity by GroES, completing compaction and allowing rapid folding. Segmental chain release and compaction may be important in avoiding misfolding by proteins that fail to fold efficiently through spontaneous hydrophobic collapse.Cell 05/2008; 133(1):142-53. · 32.40 Impact Factor
Feng Qiu, Sigrun Brendel, Paulo M F Cunha, Nagore Astola, Bauzhen Song, Eileen E M Furlong, Kevin R Leonard, Belinda Bullard[show abstract] [hide abstract]
ABSTRACT: Thick filaments in striated muscle are myosin polymers with a length and diameter that depend on the fibre type. In invertebrates, the length of the thick filaments varies widely in different muscles and additional proteins control filament assembly. Thick filaments in asynchronous insect flight muscle have an extremely regular structure, which is likely to be essential for the oscillatory contraction of these muscles. The factors controlling the assembly of thick filaments in insect flight muscle are not known. We previously identified a thick filament core protein, zeelin 1, in Lethocerus flight and non-flight muscles. This has been sequenced, and the corresponding proteins in Drosophila and Anopheles have been identified. The protein has been re-named myofilin. Zeelin 2, which is on the outside of Lethocerus flight muscle thick filaments, has been sequenced and because of the similarity to Drosophila flightin, is re-named flightin. In Drosophila flight muscle, myofilin has a molecular weight of 20 kDa and is one of five isoforms produced from a single gene. In situ hybridisation of Drosophila embryos showed that myofilin RNA is first expressed late in embryogenesis at stage 15, a little later than myosin. Antibody to myofilin labelled the entire A-band, except for the H-zone, in cryosections of flight and non-flight muscle. The periodicity of myofilin in Drosophila flight muscle thick filaments was found to be 30 nm by measuring the spacing of gold particles in labelled cryosections; this is about twice the 14.5 nm spacing of myosin molecules. The molar ratio of myofilin to myosin in indirect flight muscle is 1:2, which is the same as that of flightin. We propose a model for the association of these proteins in thick filaments, which is consistent with the periodicity and stoichiometry. Myofilin is probably needed for filament assembly in all muscles, and flightin for stability of flight muscle thick filaments in adult flies.Journal of Cell Science 05/2005; 118(Pt 7):1527-36. · 6.11 Impact Factor
Carolina Perez-Iratxeta, Nagore Astola, Francesca D Ciccarelli, Parantu K Sha, Peer Bork, Miguel A Andrade[show abstract] [hide abstract]
ABSTRACT: Entries in biological databases are usually linked to scientific references. To generate those links and to keep them up-to-date, database maintainers have to continuously scan the scientific literature to select references that are relevant for each single database entry. The continuous growth of both the corpus of scientific literature and the size of biological databases makes this task very hard. We present a protocol intended to assist the updating of an existing set of literature (abstract) links from a single database entry with new references. It consists of taking the set of MEDLINE neighbour references of the existing linked abstracts and evaluating their relevance according to the existing set of abstracts. To test the applicability of the algorithm, we did a simple benchmark of the system using the references associated with the entries of a protein domain database. Human experts found the references that the algorithm scored highly were more relevant to the database entry than those scored lowly, suggesting that the algorithm was useful.Applied Bioinformatics 02/2003; 2(3):189-91.