Hydrophilic Linkers and Polar Contacts Affect Aggregation of FG Repeat Peptides

Transport of large proteins into the nucleus involves two events, binding of the cargo protein to a transport receptor in the cytoplasm and passage of the cargo-transporter complex through the selective permeability barrier of the nuclear pore complex. The permeability barrier is formed by largely disordered polypeptides, each containing a number of conserved hydrophobic phenylalanine-glycine (FG) sequence motifs, connected by hydrophilic linkers of varying sequence (FG nups). How the motifs interact to form the permeability barrier, however, is not yet known. We have, therefore, carried out molecular dynamics simulations on various model FG repeat peptides to study the aggregation propensity of FG nups and the specific roles of the hydrophobic FG motifs and the hydrophilic linkers. Our simulations show spontaneous aggregation of the model nups into hydrated aggregates, which exhibit structural features assumed to be part of the permeability barrier. Our simulations suggest that short β-sheets are an important structural feature of the aggregates and that Phe residues are sufficiently exposed to allow rapid binding of transport receptors. A surprisingly large influence of the amino acid composition of the hydrophilic linkers on aggregation is seen, as well as a major contribution of hydrogen-bonding patterns

Influence of the g conformation of Ser and Thr on the structure of transmembrane helices

In order to study the influence of Ser and Thr on the structure of transmembrane helices we have analyzed a database of helix stretches extracted from crystal structures of membrane proteins and an ensemble of model helices generated by molecular dynamics simulations. Both complementary analyses show that Ser and Thr in the g conformation induce and/or stabilize a structural distortion in the helix backbone. Using quantum mechanical calculations, we have attributed this effect to the electrostatic repulsion between the side chain Oc atom of Ser and Thr and the backbone carbonyl oxygen at position i 3. In order to minimize the repulsive force between these negatively charged oxygens, there is a modest increase of the helix bend angle as well as a local opening of the helix turn preceding Ser/Thr. This small distortion can be amplified through the helix, resulting in a significant displacement of the residues located at the other side of the helix. The crystal structures of aquaporin Z and the b2-adrenergic receptor are used to illustrate these effects. Ser/Thr-induced structural distortions can be implicated in processes as diverse as ligand recognition, protein function and protein folding

Structural basis for interdomain communication in SHIP2 providing high phosphatase activity

SH2-containing-inositol-5-phosphatases (SHIPs) dephosphorylate the 5-phosphate of phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P3) and play important roles in regulating the PI3K/Akt pathway in physiology and disease. Aiming to uncover interdomain regulatory mechanisms in SHIP2, we determined crystal structures containing the 5-phosphatase and a proximal region adopting a C2 fold. This reveals an extensive interface between the two domains, which results in significant structural changes in the phosphatase domain. Both the phosphatase and C2 domains bind phosphatidylserine lipids, which likely helps to position the active site towards its substrate. Although located distant to the active site, the C2 domain greatly enhances catalytic turnover. Employing molecular dynamics, mutagenesis and cell biology, we identify two distinct allosteric signaling pathways, emanating from hydrophobic or polar interdomain interactions, differentially affecting lipid chain or headgroup moieties of PI(3,4,5)P3. Together, this study reveals details of multilayered C2-mediated effects important for SHIP2 activity and points towards interesting new possibilities for therapeutic interventions.We thank Jose´ Terro´ n Bautista for help with MD analysis. We thank the ESRF and ALBA for provid- ing the synchrotron-radiation facilities and the staff for their assistance in the data collection. We are grateful to the Barcelona Supercomputing Centre and National Supercomputing Centre (BSC-CNS) for allocating computer time to run the reported simulations. The work was supported by the Span- ish Ministry of Economy, Industry and Competitiveness (MEIC) Grants BFU2010-15923 (DL) and MEIC Project Retos BFU2016-77665-R co-funded by the European Regional Development Fund (ERDF) (DL), the Comunidad Auto´ noma de Madrid Grant S2010/BMD-2457 (DL), and by the National Cancer Research Centre. DL is also a recipient of awards from the Volkswagen Foundation (Az: 86 416–1) and Worldwide Cancer Research (15-1177).S

List of c-Abl point mutants investigated in this study with summary of the effect of mutations.

<p>Mutants were tested for c-Abl activity via immunoblotting of HEK293 lysates or immunoprecipitates (IP) and via kinase activity assay. The numbering of residues is in agreement with the sequence of the isoform Ib. Activity scoring (effect of the mutation):, nt, not tested, − inactive (mutation disruptive), + weakly active (mutation mildly disruptive), ++ activity similar to wild-type (mutation neutral), +++ hyperactive (mutation activating) (See also Supplemental Table S1).</p><p>List of c-Abl point mutants investigated in this study with summary of the effect of mutations.</p

Domain organization and crystal structures of Abl kinase.

<p><b>A</b> The c-Abl isoform Ib is characterized by myristoylation (Myr) on Gly-2 of the N-terminal capping region (cap). The tyrosine kinase domain is preceded by the SH3 and SH2 domains and a connecting linker. The last exon region contains nuclear localization signals and a C-terminal actin binding domain (ABD). <b>B</b> In the down-regulated state (PDB entry 2FO0), the SH2 domain binds the C-lobe of the kinase domain, the myristate is bound in its cognate pocket and the SH3 domain binds the SH2-CD linker. <b>C</b> In the active “top-hat” conformation (PDB entry 1OPL), the SH2 domain moves to interact with the N-lobe of the kinase domain. The αC helix and the activation loop are highlighted in red and pink, respectively. <b>D</b> Positions of the most important point mutations at the SH2-CD interface and in the β3-αC loop.</p

Allosteric coupling and flexibility of c-Abl.

<p><b>A</b> Allosteric couplings of residues in the CD to the SH2 domain. High values (yellow and red) indicate strong allosteric interactions (See also Supplemental <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003863#pcbi.1003863.s001" target="_blank">Figure S1</a> A–C). <b>B</b> Free CD colored by RMSF from MD simulations. <b>C</b> SH2-CD construct colored by RMSF. (See also <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003863#pcbi.1003863.s002" target="_blank">Figure S2</a>).</p