51. Molecular basis of the functional differences between soluble human versus murine MD-2 : role of Val [sup] 135 in transfer of lipopolysaccharide from CD14 to MD-2Jožica Vašl, Alja Oblak, Tina Tinkara Peternelj, Javier Klett, Sonsoles Martín-Santamaría, Theresa L. Gioannini, Jerrold P. Weiss, Roman Jerala, 2016, original scientific article Keywords: MD-2, TLR-4, species specificity, innate immunology Published in DiRROS: 10.11.2016; Views: 4899; Downloads: 1062 Link to file |
52. Design principles for rapid folding of knotted DNA nanostructuresVid Kočar, John S. Schreck, Slavko Čeru, Helena Gradišar, Nino Bašić, Tomaž Pisanski, Jonathan P. K. Doye, Roman Jerala, 2016, original scientific article Abstract: Knots are some of the most remarkable topological features in nature. Self-assembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded through previously formed loops in an exactly defined order. Here we describe principles to guide the folding of highly knotted single-chain DNA nanostructures as demonstrated on a nano-sized square pyramid. Folding of knots is encoded by the arrangement of modules of different stability based on derived topological and kinetic rules. Among DNA designs composed of the same modules and encoding the same topology, only the one with the folding pathway designed according to the "free-end" rule folds efficiently into the target structure. Besides high folding yield on slow annealing, this design also folds rapidly on temperature quenching and dilution from chemical denaturant. This strategy could be used to design folding of other knotted programmable polymers such as RNA or proteins. Published in DiRROS: 13.04.2016; Views: 4385; Downloads: 1443 Full text (1,70 MB) This document has many files! More... |
53. Self-assembled structures composed of single polypeptide comprising at least three coiled-coil forming elements : patentRoman Jerala, Ota Fekonja, Jelka Pohar, Helena Gradišar, Mojca Benčina, Iva Hafner Bratkovič, Robert Bremšak, Špela Miklavič, Urška Jelerčič, Anja Lukan, Tibor Doles, Sabina Božič Abram, Marko Verce, Nika Debeljak, Jožica Friedrich, 2014, patent Keywords: self assembled structures, polipeptide chain, nenostructures Published in DiRROS: 13.05.2015; Views: 6188; Downloads: 915 Link to full text |
54. Postulates for validating TLR4 agonistsMateja Manček Keber, Roman Jerala, 2015, review article Abstract: TLRs play a central role in the innate immune response, recognizing a variety of molecular
structures characteristic of pathogens. Although TLR4, together with its co-receptor
myeloid differentiation-2 (MD-2), recognize bacterial LPS and therefore Gram-negative
bacterial infections, it also plays a key role in many other pathophysiological processes,
including sterile inflammation and viral infection. Specifically, numerous endogenous
agonists of TLR4 of notably diverse nature, ranging from proteins to metal ions, have
been reported. Direct activation of a single receptor by such a range of molecular signals
is very difficult to explain from a structural and mechanistic point of view. It is likely
that only a subset of these directly activate the TLR4–MD-2 complex. We propose three
postulates aimed at distinguishing the direct agonists of TLR4 from indirect activators.
These postulates are as follows: (i) that the agonist requires the TLR4/MD-2 receptor complex;
(ii) that agonist formed synthetically or in situ must activate the receptor complex
in order to eliminate artifacts of contamination by other agonists; and (iii) that a specific
molecular interaction between the agonist and TLR4/MD-2 must be identified. The same
type of postulates can be applied to pattern recognition receptors in general. Keywords: TLR4 agonists, molecular mechanism, ligand recognition Published in DiRROS: 26.01.2015; Views: 4965; Downloads: 468 Link to file |