Delineation of RAID1, the RACK1 interaction domain located within the unique N-terminal region of the cAMP-specific phosphodiesterase, PDE4D5

Background The cyclic AMP specific phosphodiesterase, PDE4D5 interacts with the β-propeller protein RACK1 to form a signaling scaffold complex in cells. Two-hybrid analysis of truncation and mutant constructs of the unique N-terminal region of the cAMP-specific phosphodiesterase, PDE4D5 were used to define a domain conferring interaction with the signaling scaffold protein, RACK1. Results Truncation and mutagenesis approaches showed that the RACK1-interacting domain on PDE4D5 comprised a cluster of residues provided by Asn-22/Pro-23/Trp-24/Asn-26 together with a series of hydrophobic amino acids, namely Leu-29, Val-30, Leu-33, Leu-37 and Leu-38 in a 'Leu-Xaa-Xaa-Xaa-Leu' repeat. This was done by 2-hybrid analyses and then confirmed in biochemical pull down analyses using GST-RACK1 and mutant PDE4D5 forms expressed in COS cells. Mutation of Arg-34, to alanine, in PDE4D5 attenuated its interaction with RACK1 both in 2-hybrid screens and in pull down analyses. A 38-mer peptide, whose sequence reflected residues 12 through 49 of PDE4D5, bound to RACK1 with similar affinity to native PDE4D5 itself (Ka circa 6 nM). Conclusions The RACK1 Interaction Domain on PDE4D5, that we here call RAID1, is proposed to form an amphipathic helical structure that we suggest may interact with the C-terminal β-propeller blades of RACK1 in a manner akin to the interaction of the helical G-γ signal transducing protein with the β-propeller protein, G-β

When move acceptance selection hyper-heuristics outperform Metropolis and elitist evolutionary algorithms and when not

Selection hyper-heuristics (HHs) are automated algorithm selection methodologies that choose between different heuristics during the optimisation process. Recently, selection HHs choosing between a collection of elitist randomised local search heuristics with different neighbourhood sizes have been shown to optimise standard unimodal benchmark functions from evolutionary computation in the optimal expected runtime achievable with the available low-level heuristics. In this paper, we extend our understanding of the performance of HHs to the domain of multimodal optimisation by considering a Move Acceptance HH (MAHH) from the literature that can switch between elitist and non-elitist heuristics during the run. In essence, MAHH is a non-elitist search heuristic that differs from other search heuristics in the source of non-elitism. We first identify the range of parameters that allow MAHH to hillclimb efficiently and prove that it can optimise the standard hillclimbing benchmark function OneMax in the best expected asymptotic time achievable by unbiased mutation-based randomised search heuristics. Afterwards, we use standard multimodal benchmark functions to highlight function characteristics where MAHH outperforms elitist evolutionary algorithms and the well-known Metropolis non-elitist algorithm by quickly escaping local optima, and ones where it does not. Since MAHH is essentially a non-elitist random local search heuristic, the paper is of independent interest to researchers in the fields of artificial intelligence and randomised search heuristics

Visualization of poly(ADP-ribose) bound to PARG reveals inherent balance between exo- and endo-glycohydrolase activities

Poly-ADP-ribosylation is a post-translational modification that regulates processes involved in genome stability. Breakdown of the poly(ADP-ribose) (PAR) polymer is catalysed by poly(ADP-ribose) glycohydrolase (PARG), whose endo-glycohydrolase activity generates PAR fragments. Here we present the crystal structure of PARG incorporating the PAR substrate. The two terminal ADP-ribose units of the polymeric substrate are bound in exo-mode. Biochemical and modelling studies reveal that PARG acts predominantly as an exo-glycohydrolase. This preference is linked to Phe902 (human numbering), which is responsible for low-affinity binding of the substrate in endo-mode. Our data reveal the mechanism of poly-ADP-ribosylation reversal, with ADP-ribose as the dominant product, and suggest that the release of apoptotic PAR fragments occurs at unusual PAR/PARG ratios

PhosIDP: a web tool to visualize the location of phosphorylation sites in disordered regions

From Springer Nature via Jisc Publications RouterHistory: received 2021-03-15, accepted 2021-04-19, registration 2021-04-20, online 2021-05-11, pub-electronic 2021-05-11, collection 2021-12Publication status: PublishedFunder: Agency for Science, Technology and Research; doi: http://dx.doi.org/10.13039/501100001348; Grant(s): IDs H17/01/a0/010, IDs H17/01/a0/010Funder: Engineering and Physical Sciences Research Council; doi: http://dx.doi.org/10.13039/501100000266; Grant(s): EP/N024796/1, EP/N024796/1Abstract: Charge is a key determinant of intrinsically disordered protein (IDP) and intrinsically disordered region (IDR) properties. IDPs and IDRs are enriched in sites of phosphorylation, which alters charge. Visualizing the degree to which phosphorylation modulates the charge profile of a sequence would assist in the functional interpretation of IDPs and IDRs. PhosIDP is a web tool that shows variation of charge and fold propensity upon phosphorylation. In combination with the displayed location of protein domains, the information provided by the web tool can lead to functional inferences for the consequences of phosphorylation. IDRs are components of many proteins that form biological condensates. It is shown that IDR charge, and its modulation by phosphorylation, is more tightly controlled for proteins that are essential for condensate formation than for those present in condensates but inessential

Evidence for the adaptation of protein pH-dependence to subcellular pH

<p>Abstract</p> <p>Background</p> <p>The availability of genome sequences, and inferred protein coding genes, has led to several proteome-wide studies of isoelectric points. Generally, isoelectric points are distributed following variations on a biomodal theme that originates from the predominant acid and base amino acid sidechain pKas. The relative populations of the peaks in such distributions may correlate with environment, either for a whole organism or for subcellular compartments. There is also a tendency for isoelectric points averaged over a subcellular location to not coincide with the local pH, which could be related to solubility. We now calculate the correlation of other pH-dependent properties, calculated from 3D structure, with subcellular pH.</p> <p>Results</p> <p>For proteins with known structure and subcellular annotation, the predicted pH at which a protein is most stable, averaged over a location, gives a significantly better correlation with subcellular pH than does isoelectric point. This observation relates to the cumulative properties of proteins, since maximal stability for individual proteins follows the bimodal isoelectric point distribution. Histidine residue location underlies the correlation, a conclusion that is tested against a background of proteins randomised with respect to this feature, and for which the observed correlation drops substantially.</p> <p>Conclusion</p> <p>There exists a constraint on protein pH-dependence, in relation to the local pH, that is manifested in the pKa distribution of histidine sub-proteomes. This is discussed in terms of protein stability, pH homeostasis, and fluctuations in proton concentration.</p

Volume-based solvation models out-perform area-based models in combined studies of wild-type and mutated protein-protein interfaces

<p>Abstract</p> <p>Background</p> <p>Empirical binding models have previously been investigated for the energetics of protein complexation (ΔG models) and for the influence of mutations on complexation (i.e. differences between wild-type and mutant complexes, ΔΔG models). We construct binding models to directly compare these processes, which have generally been studied separately.</p> <p>Results</p> <p>Although reasonable fit models were found for both ΔG and ΔΔG cases, they differ substantially. In a dataset curated for the absence of mainchain rearrangement upon binding, non-polar area burial is a major determinant of ΔG models. However this ΔG model does not fit well to the data for binding differences upon mutation. Burial of non-polar area is weighted down in fitting of ΔΔG models. These calculations were made with no repacking of sidechains upon complexation, and only minimal packing upon mutation. We investigated the consequences of more extensive packing changes with a modified mean-field packing scheme. Rather than emphasising solvent exposure with relatively extended sidechains, rotamers are selected that exhibit maximal packing with protein. This provides solvent accessible areas for proteins that are much closer to those of experimental structures than the more extended sidechain regime. The new packing scheme increases changes in non-polar burial for mutants compared to wild-type proteins, but does not substantially improve agreement between ΔG and ΔΔG binding models.</p> <p>Conclusion</p> <p>We conclude that solvent accessible area, based on modelled mutant structures, is a poor correlate for ΔΔG upon mutation. A simple volume-based, rather than solvent accessibility-based, model is constructed for ΔG and ΔΔG systems. This shows a more consistent behaviour. We discuss the efficacy of volume, as opposed to area, approaches to describe the energetic consequences of mutations at interfaces. This knowledge can be used to develop simple computational screens for binding in comparative modelled interfaces.</p

Survival of elderly patients with stage 5 CKD: comparison of conservative management and renal replacement therapy

Background. Elderly patients with end-stage renal disease and severe extra-renal comorbidity have a poor prognosis on renal replacement therapy (RRT) and may opt to be managed conservatively (CM). Information on the survival of patients on this mode of therapy is limited

Successful stabilisation of nephropathy in a patient with POEMS (polyneuropathy, organomegaly, endocrinopathy, M-band, skin changes) syndrome on treatment with mycophenolate and steroids: a case report

<p>Abstract</p> <p>Introduction</p> <p>Renal involvement in POEMS (polyneuropathy, organomegaly, endocrinopathy, M-band, skin changes) syndrome is considered to be an under-diagnosed phenomenon with no clear treatment path. The limited literature suggests steroids to be the drug of choice, although improvements are limited and usually reverse on withdrawal of the drug.</p> <p>Case presentation</p> <p>A 52-year-old Caucasian woman presenting with features consistent with POEMS syndrome developed progressive renal impairment with proteinuria. Renal biopsy revealed a membranoproliferative glomerulonephritis. She was treated with relatively low dose oral mycophenolate mofetil and prednisolone which stabilised her nephropathy and neuropathy.</p> <p>Conclusion</p> <p>We describe an alternative therapeutic option in patients with this serious but poorly understood condition.</p

Diffraction from the beta-sheet crystallites in spider silk

We analyze the wide angle x-ray scattering from oriented spider silk fibers in terms of a quantitative scattering model, including both structural and statistical parameters of the $\beta$-sheet crystallites of spider silk in the amorphous matrix. The model is based on kinematic scattering theory and allows for rather general correlations of the positional and orientational degrees of freedom, including the crystallite's size, composition and dimension of the unit cell. The model is evaluated numerically and compared to experimental scattering intensities allowing us to extract the geometric and statistical parameters. We show explicitly that for the experimentally found mosaicity (width of the orientational distribution) inter-crystallite effects are negligible and the data can be analyzed in terms of single crystallite scattering, as is usually assumed in the literature.Comment: 15 pages, 14 figures, on average 0.93 figures per pag