1,721,081 research outputs found
Interazione di piccoli neuropeptidi con membrane modello: studi spettroscopici e computazionali.
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Molecular Modelling of the Interaction of Myelin Basic Protein (MBP) Peptides with Signalling Proteins and Effects of Post-Translational Modifications
No full textMyelin Basic Protein (MBP) is a multifunctional protein involved in maintaining the stability and integrity of the myelin sheath by a variety of interactions with membranes, and with cytoskeletal and other proteins. In this chapter the interactions of MBP with two signalling proteins, the calmodulin (CaM) and an SH3-domain containing protein, and their modulation by post-translational modifications (PTMs) were investigated at an atomic level by means of the docking simulation approach, to gain further structural insight on the putative signalling role of MBP. Based on previously obtained experimental results, three CaM and one SH3-domain putative targets were identified in the classic 18.5 kDa MBP isoform and their interaction with the binding site of the receptor was modelled. The ability of CaM and of the SH3-domain to bind the MBP peptides was confirmed and the strength of the interaction seems to be of the same order of magnitude. The docking results on CaM highlight the conformational adaptability of MBP. The target peptides can adopt different binding modes, adapting the orientations of their side chains in such a way that the basic residues interact with the negatively-charged clusters at the extremities of the CaM binding tunnel and the hydrophobic ones anchor the MBP segments to its hydrophobic pockets. Thus it seems that CaM induces the binding mode that is most favourable for it, promoting the -helical conformation of its targets. On the contrary, the polyproline type II helical conformation that is a characteristic of SH3-domain ligands is already present on the MBP target in vitro under physiological conditions. The MBP - SH3-domain interaction occurs by means of salt bridges and cation-π interactions between the basic residues in the peptide and the negatively-charged and aromatic residues in the receptor, but the molecular recognition and association seems to be mediated by weak CH∙∙∙ interactions of the ligand prolyl residues with the aromatic residues in the binding site. The effects of PTMs on MBP peptides show a lowering of the CaM-MBP affinity after deimination, while phosphorylation seems to have only a minor effect. Phosphorylation or methylation of the MBP ligand did not cause any major inhibition of binding with the SH3-domain, beyond a somewhat less favourable interaction for phosphorylated peptides. Although the conformation of the MBP peptide in the SH3-domain pocket changed significantly, new interactions were able to substitute for those lost, in order to stabilize the complex
Molecular dynamics simulations in the presence of lipids on a functionally relevant fragment of myelin basic protein.
No full textInside the mechanism of SMN-SmD1 protein complex formation: effects of the Spinal Muscular Atrophy - causing E134K mutation. A molecular dynamics simulation study.
No full textSpinal muscular atrophy (SMA) is a motor neuron disease that leads to muscle atrophy due to motor neurons degeneration. SMA is a major genetic cause of early childhood mortality and results from mutations in the Survival of Motor Neuron (SMN) gene1. The SMN protein plays a crucial role in the assembly of spliceosomal small nuclear ribonucleoprotein complexes via binding to the spliceosomal Sm core proteins, in particular to their arginine-glycine (RG) rich C-terminal tails. SMN contains a central Tudor domain, directly involved in the SMN–Sm protein interaction by the recognition of symmetrically dimethylated arginine (DMR) residues in the RG repeats. In particular, an aromatic cage on Tudor domain seems to mediate this binding (1–3).
Six of the pathogenic mutations causing SMA occur in the SMN Tudor domain. The only one that prevents the binding to the Sm proteins without a perturbation of the domain fold is E134K, that is the cause of the more severe type I SMA (3).
To gain more understanding about the mechanism by which SMN interacts with the Sm proteins, and which are the structural effects on binding of its deleterious mutation E134K, we investigated the behavior of the native and mutated structure of the SMN Tudor domain in the presence of the C-terminal tail of SmD1, by means of molecular dynamics simulations.
The interaction of the SmD1 tail with the Tudor domain is electrostatic driven by the acidic residues near the entrance of the aromatic cage. A central DMR of the tail enters into the cage rapidly and stably, forming a network of cationic-pi interactions, both in stacking and T-shaped. The complex is stabilized also by the salt-bridges formed by the other DMRs and arginine residues wrapped around the acidic surface of the domain.
The E134K mutation destabilizes the cage, not only with the disruption of the strong 134-136-127 H-bonds network, but also with the formation of new electrostatic and cationic-pi interactions. The cage collapses and expands, preventing a stable binding of the DMR. This is impeded also by the detachment of the C-terminal region of the tail from the Tudor domain, caused by the E134K charge inversion.
The results are in agreement with what experimentally observed (1–3) and clarify the key role of E134 in the interaction of the SmD1 tail to the Tudor domain. The loss of a strong Tudor-SmD1 interaction, if by one side causes the loss of a functional splicing machinery, by the other side causes the exposition of the detached Sm tails, that could stimulate the recognition by anti-Sm autoantibodies, as is reported for other diseases as lupus erithematosus (4), giving rise to the innovative hypothesis of SMA as an autoimmune disease.
1. P. Selenko et al., Nat. Struct. Biol. 8, 27–31 (2001).
2. R. Sprangers et al., J. Mol. Biol. 327, 507–520 (2003).
3. K. Tripsianes et al., Nat. Struct. Mol. Biol. 18, 1414–20 (2011).
4. H. Brahms et al., J. Biol. Chem. 275, 17122–17129 (2000)
The Tridimensional Model of the STAS Domain of the Bacillus Subtilis YtvA Protein: a Step Towards the Comprehension of a Putative Regulatory Function
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