Solution structure of the β‐subunit of the translation initiation factor aIF2 from archaebacteria <i>Sulfolobus solfataricus</i>

Pechkova, Eugenia; Nicolini, Claudio

doi:10.1002/prot.21797

Cited by 13 publications

(7 citation statements)

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“…aIF2β of Sulfolobus solfataricus is an intrinsically disordered protein consisting of both ordered and disordered regions (Figure S5, see additional file 1). The N-terminus of aIF2β has been shown to be disordered [62] and also in the homologous protein from Methanobacterium thermoautotrophicum [63]. However, this region is responsible for mediating binding to aIF2γ through a MoRF-type interaction.…”

Section: Resultsmentioning

confidence: 99%

Archaic chaos: intrinsically disordered proteins in Archaea

et al. 2010

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BackgroundMany proteins or their regions known as intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) lack unique 3D structure in their native states under physiological conditions yet fulfill key biological functions. Earlier bioinformatics studies showed that IDPs and IDRs are highly abundant in different proteomes and carry out mostly regulatory functions related to molecular recognition and signal transduction. Archaea belong to an intriguing domain of life whose members, being microbes, are characterized by a unique mosaic-like combination of bacterial and eukaryotic properties and include inhabitants of some of the most extreme environments on the planet. With the expansion of the archaea genome data (more than fifty archaea species from five different phyla are known now), and with recent improvements in the accuracy of intrinsic disorder prediction, it is time to re-examine the abundance of IDPs and IDRs in the archaea domain.ResultsThe abundance of IDPs and IDRs in 53 archaea species is analyzed. The amino acid composition profiles of these species are generally quite different from each other. The disordered content is highly species-dependent. Thermoproteales proteomes have 14% of disordered residues, while in Halobacteria, this value increases to 34%. In proteomes of these two phyla, proteins containing long disordered regions account for 12% and 46%, whereas 4% and 26% their proteins are wholly disordered. These three measures of disorder content are linearly correlated with each other at the genome level. There is a weak correlation between the environmental factors (such as salinity, pH and temperature of the habitats) and the abundance of intrinsic disorder in Archaea, with various environmental factors possessing different disorder-promoting strengths. Harsh environmental conditions, especially those combining several hostile factors, clearly favor increased disorder content. Intrinsic disorder is highly abundant in functional Pfam domains of the archaea origin. The analysis based on the disordered content and phylogenetic tree indicated diverse evolution of intrinsic disorder among various classes and species of Archaea.ConclusionsArchaea proteins are rich in intrinsic disorder. Some of these IDPs and IDRs likely evolve to help archaea to accommodate to their hostile habitats. Other archaean IDPs and IDRs possess crucial biological functions similar to those of the bacterial and eukaryotic IDPs/IDRs.

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Section: Resultsmentioning

confidence: 99%

Archaic chaos: intrinsically disordered proteins in Archaea

et al. 2010

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“…Oscillations in the concentrations of proteins are a response of the cell to external stimuli that has been observed in several cellular contexts [1][2][3][4][22][23][24]. Even one of the simplest system displaying oscillations, that is a two-node delayed feedback loop, can be difficult to study because one has little control over the numerical values of the parameters which control the model.…”

Section: Discussionmentioning

confidence: 99%

How likely are oscillations in a genetic feedback loop with delay?

2017

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Some genetic control networks display temporal oscillations as a result of delays in their homeostatic control. A relevant question about these systems is whether the oscillating regime is a rare feature, or it corresponds to a sizeable volume of the space of parameters. The answer is not trivial mainly due to the large number of parameters controlling the rate equations which describe the network. We have developed an efficient sampling scheme of the parameter space, based on a Monte Carlo algorithm, and applied it to a two-node system with delay, characterised by a 8-dimension parameter space. The result is that the volume fraction of the parameter space associated with oscillations is small but not negligible, and it is weakly dependent on the duration of the delay. The most critical parameter to control oscillations is the coupling production rates, which must have opposite sign, giving rise to a negative feedback loop. The oscillating regions are connected except along the equilibrium constants between the two species, not allowing neutral evolution along this parameter.

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“…All NMR spectra were registered on Bruker Avance III 400 MHz and Avance 600 MHz using 7–9 mM solutions of ligands in deuterated phosphate buffer (pH 7.4). The assignment was performed through one- and two-dimensional 1 H and 13 C NMR spectra by the standard manual method [ 33 , 34 ]. The complete assignment of the molecules and the list of NOEs are reported in Tables S1 and S2 of Supplementary Materials .…”

Section: Methodsmentioning

confidence: 99%

A Combined NMR-Computational Study of the Interaction between Influenza Virus Hemagglutinin and Sialic Derivatives from Human and Avian Receptors on the Surface of Transfected Cells

Panigada

Siccardi

Potenza

et al. 2018

IJMS

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The development of small-molecule inhibitors of influenza virus Hemagglutinin could be relevant to the opposition of the diffusion of new pandemic viruses. In this work, we made use of Nuclear Magnetic Resonance (NMR) spectroscopy to study the interaction between two derivatives of sialic acid, Neu5Ac-α-(2,6)-Gal-β-(1–4)-GlcNAc and Neu5Ac-α-(2,3)-Gal-β-(1–4)-GlcNAc, and hemagglutinin directly expressed on the surface of recombinant human cells. We analyzed the interaction of these trisaccharides with 293T cells transfected with the H5 and H1 variants of hemagglutinin, which thus retain their native trimeric conformation in such a realistic environment. By exploiting the magnetization transfer between the protein and the ligand, we obtained evidence of the binding event, and identified the epitope. We analyzed the conformational features of the glycans with an approach combining NMR spectroscopy and data-driven molecular dynamics simulations, thus obtaining useful information for an efficient drug design.

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Solution structure of the β‐subunit of the translation initiation factor aIF2 from archaebacteria Sulfolobus solfataricus

Cited by 13 publications

References 18 publications

Archaic chaos: intrinsically disordered proteins in Archaea

Archaic chaos: intrinsically disordered proteins in Archaea

How likely are oscillations in a genetic feedback loop with delay?

A Combined NMR-Computational Study of the Interaction between Influenza Virus Hemagglutinin and Sialic Derivatives from Human and Avian Receptors on the Surface of Transfected Cells

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