Secondary structure evolution, as a function of time, for the LOX-1 region (140–165) including strands 0 (red bar with middle point around 150) and 1 (red bar with middle point around 156)

<p><b>Copyright information:</b></p><p>Taken from "Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant"</p><p>http://www.biomedcentral.com/1472-6807/7/73</p><p>BMC Structural Biology 2007;7():73-73.</p><p>Published online 7 Nov 2007</p><p>PMCID:PMC2194713.</p><p></p> Colour code identifying the secondary structure is shown in the figure

Dynamic cross-correlation maps calculated for the wild-type and the mutant LOX-1 proteins

<p><b>Copyright information:</b></p><p>Taken from "Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant"</p><p>http://www.biomedcentral.com/1472-6807/7/73</p><p>BMC Structural Biology 2007;7():73-73.</p><p>Published online 7 Nov 2007</p><p>PMCID:PMC2194713.</p><p></p> Panels A and C reports the intra-subunit motion correlations in the wild-type, while panels B and D the intra-subunit motion correlations in the mutant. The black and grey squares represent the Cmotion correlations wit

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-2

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p> 12 amino acids, on a cellulose membrane using the SPOT synthesis method [21]. The membrane was incubated with the EH domain of POB1 fused to the GST and probed with an anti-GST antibody. The groups of spots considered to be positives are indicated as a, b, c and d. Positives controls, binding to secondary antibodies, are indicated with rectangles. (B) Amino acid sequence of human Eps15. The N-terminal region comprising the three EH domains is underlined, sequences corresponding to the spots considered to be positives are outlined. Residues corresponding to the indicated regions are: a (aa 623–633), b (aa 647–674), c (aa 592–606) and d (aa 796–813)

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-0

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>er plate and incubated with the EH domain of POB1 fused to GST and GST alone as negative control. The bound domain was identified with an anti-GST antibody and a secondary antibody linked to alkaline phosphatase; wt is a phage not exposing any ectopic peptide. Below: sequences of the selected peptides are aligned with respect to the NPF and DPF motifs

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-7

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>er plate and incubated with the EH domain of POB1 fused to GST and GST alone as negative control. The bound domain was identified with an anti-GST antibody and a secondary antibody linked to alkaline phosphatase; wt is a phage not exposing any ectopic peptide. Below: sequences of the selected peptides are aligned with respect to the NPF and DPF motifs

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-5

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>e: (A), Eps15 EH1, PDB code: (B) and POB1, PDB code: (C) EH domains. Residues in the hydrophobic groove are coloured in red, residues which line the edge of the binding pocket are in green while the gate charged residues are in blue. (B) : representation of the classical binding pocket of Eps15 EH1 domain. : residues distant from the binding pocket, which have been discussed in the text, are mapped on the molecular surface of Eps15. Lys 21 indicates the position of the binding pocket. (C) : representation of the classical binding pocket of POB1 EH domain. : residues mutated in this study are mapped on the molecular surface of POB1. Lys 307 indicates the position of the binding pocket. Lysine residues are coloured in blue, Phe344 and Ile347 in red and Gln289 in orange. Molecular surfaces were generated with PyMol

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-4

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>g 10 DPF tripeptides, as described in Figure 3, were incubated with a cell extract from Hek293. Bound proteins were resolved by SDS-PAGE and analyzed by western-blotting using an anti-Eps15 antibody

Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction-3

<p><b>Copyright information:</b></p><p>Taken from "Binding to DPF-motif by the POB1 EH domain is responsible for POB1-Eps15 interaction"</p><p>http://www.biomedcentral.com/1471-2091/8/29</p><p>BMC Biochemistry 2007;8():29-29.</p><p>Published online 21 Dec 2007</p><p>PMCID:PMC2238750.</p><p></p>ins (EH1-EH2-EH3) were tested in a pull-down experiment from Hek293 to evaluate the relative binding efficiency towards endogenous Eps15. (B) The isolated GST-EH domains (EH1, EH2, EH3) and the N-terminal region of Eps15 were tested in a similar experiment. The input lane corresponds to 0,1% of the lysate. Relative binding efficiencies represent the quantification of the Western blotting using the Image Quant Software. In the lower panel, the GST fusions are visualized by Coomassie staining

Molecular dynamics simulations show how the FMRP Ile304Asn mutation destabilizes the KH2 domain structure and affects its function

<div><p>Mutations or deletions of FMRP, involved in the regulation of mRNA metabolism in brain, lead to the Fragile X syndrome (FXS), the most frequent form of inherited intellectual disability. A severe manifestation of the disease has been associated with the Ile304Asn mutation, located on the KH2 domain of the protein. Several hypotheses have been proposed to explain the possible molecular mechanism responsible for the drastic effect of this mutation in humans. Here, we performed a molecular dynamics simulation and show that the Ile304Asn mutation destabilizes the hydrophobic core producing a partial unfolding of two α-helices and a displacement of a third one. The affected regions show increased residue flexibility and motion. Molecular docking analysis revealed strongly reduced binding to a model single-stranded nucleic acid in agreement with known data that the two partially unfolded helices form the RNA-binding surface. The third helix, which we show here to be also affected, is involved in the PAK1 protein interaction. These two functional binding sites on the KH2 domain do not overlap spatially, and therefore, they can simultaneously bind their targets. Since the Ile304Asn mutation affects both binding sites, this may justify the severe clinical manifestation observed in the patient in which both mRNA metabolism activity and cytoskeleton remodeling would be affected.</p></div

Simulative and Experimental Characterization of a pH-Dependent Clamp-like DNA Triple-Helix Nanoswitch

Here we couple experimental and simulative techniques to characterize the structural/dynamical behavior of a pH-triggered switching mechanism based on the formation of a parallel DNA triple helix. Fluorescent data demonstrate the ability of this structure to reversibly switch between two states upon pH changes. Two accelerated, half microsecond, MD simulations of the system having protonated or unprotonated cytosines, mimicking the pH 5.0 and 8.0 conditions, highlight the importance of the Hoogsteen interactions in stabilizing the system, finely depicting the time-dependent disruption of the hydrogen bond network. Urea-unfolding experiments and MM/GBSA calculations converge in indicating a stabilization energy at pH 5.0, 2-fold higher than that observed at pH 8.0. These results validate the pH-controlled behavior of the designed structure and suggest that simulative approaches can be successfully coupled with experimental data to characterize responsive DNA-based nanodevices