Gromita: A Fully Integrated Graphical User Interface to Gromacs 4

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs package, while providing enhanced functionality by speeding up and simplifying the task of setting up molecular dynamics simulations of biological systems. Gromita can be freely downloaded from http://bio.demokritos.gr/gromita/

Short tandem repeats in the inhibitory domain of the mineralocorticoid receptor: prediction of a β-solenoid structure

BACKGROUND: The human mineralocorticoid receptor (MR) is one of the main components of the renin-angiotensin-aldosterone system (RAAS), the system that regulates the body exchange of water and sodium. The evolutionary origins of this protein predate those of renin and the RAAS; accordingly it has other roles, which are being characterized. The MR has two trans-activating ligand independent domains and one inhibitory domain (ID), which modulates the activity of the former. The structure of the ID is currently unknown. RESULTS: Here we report that the ID contains at least 15 tandem repeats of around 10 amino acids, which we computationally characterize in the human MR and in selected orthologs. This ensemble of repeats seems to have emerged around 450 million years ago, after the divergence of the MR from its close homolog, the glucocorticoid receptor, which does not possess the repeats. The region would have quickly expanded by successive duplication of the repeats stabilizing at its length in human MR shortly after divergence of tetrapoda from bony fishes 400 million years ago. Structural predictions, in combination with molecular dynamics simulations suggest that the repeat ensemble forms a {beta}-solenoid, namely a {beta}-helical fold with a polar core, stabilized by hydrogen-bonded ladders of polar residues. Our 3D-model, in conjunction with previous experimental data, implies a role of the {beta}-helical fold as a scaffold for multiple intra-and inter-molecular interactions and that these interactions are modulated via phosphorylation-dependent conformational changes. CONCLUSIONS: We, thus, propose that the structure of the repeat ensemble plays an important role in the coordination and sequential interactions of various MR partners and therefore in the functionality and specificity of MR

Establishment of computational biology in Greece and Cyprus: Past, present, and future.

We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

Evidence for disulfide bonds in SR Protein Kinase 1 (SRPK1) that are required for activity and nuclear localization

<div><p>Serine/arginine protein kinases (SRPKs) phosphorylate Arg/Ser dipeptide-containing proteins that play crucial roles in a broad spectrum of basic cellular processes. The existence of a large internal spacer sequence that separates the bipartite kinase catalytic core is a unique structural feature of SRPKs. Previous structural studies on a catalytically active fragment of SRPK1, which lacks the main part of the spacer domain, revealed that SRPK1 remains in an active state without any post-translational modifications or specific intra-protein interactions, while the spacer domain is depicted as a loop structure, outside the kinase core. Using systematic mutagenesis we now provide evidence that replacement of any individual cysteine residue in the spacer, apart from Cys414, or in its proximal flaking ends of the two kinase catalytic domains has an impact on kinase activity. Furthermore, the cysteine residues are critical for nuclear translocation of SRPK1 in response to genotoxic stress and SRPK1-dependent splicing of a reporter gene. While replacement of Cys207, Cys502 and Cys539 of the catalytic domains is predicted to distort the kinase active structure, our findings suggest that Cys356, Cys386, Cys427 and Cys455 of the spacer domain and Cys188 of the first catalytic domain are engaged in disulfide bridging. We propose that such a network of intramolecular disulfide bonds mediates the bending of the spacer region thus allowing the proximal positioning of the two catalytic subunits which is a prerequisite for SRPK1 activity.</p></div

Structural features of SRPK1.

<p>(A) Domain organization of SRPK1 as presented in ref. 8. The N- and C-terminal conserved kinase subdomains are colored purple and magenta, respectively. The N- and C-terminal spacer regions are colored yellow and green, respectively, while the remaining spacer domain is colored gray. SRPK1(FL): full-length SRPK1; SRPK1 ΔNS1: the crystallized fragment of SRPK1. (B) Overall structure of SRPK1 ΔNS1 as presented in refs 8 and 16. The coloring of the domains is as in (A). Note that the spacer domain is depicted as a loop outside the kinase core.</p

Effect of reducing agents on SRPK1 cysteine mutants electrophoretic mobility.

<p>Lysates from 293T cells transfected with wild-type SRPK1 and its mutant forms were analyzed under non-reducing conditions (i.e., without DTT) or reducing conditions (in the presence of 90 mM DTT) on 10% SDS-polyacrylamide gels. The proteins were then transferred to nitrocellulose and epitope-tagged wild-type or mutant SRPK1 was detected with the M5 anti-FLAG monoclonal antibody.</p

Nuclear translocation of SRPK1 and derived cysteine mutants in response to genotoxic stress.

<p>(A) Fluorescent pattern of wild-type FLAG-SRPK1 and mutant FLAG-SRPK1 188A, SRPK1 356G, SRPK1 386G, SRPK1 427G and SRPK1 455G in 5-FU-treated HeLa cells. SRPKs were detected using the M5 anti-FLAG monoclonal antibody, while nuclei were stained with propidium iodide (PI). Scale bar, 10 μm. (B) The ratio of average fluorescence intensity in the cell nucleus versus average intensity in the cell cytoplasm (N/C ratio) was quantified using ImageJ software. Each column represents the means ± SE of measurements from 20–30 cells.</p