11 research outputs found
Effects of membrane and biological target on the structural and allosteric properties of recoverin: a computational approach
Recoverin (Rec) is a prototypical calcium sensor protein primarily expressed in the vertebrate retina. The binding of two Ca2+ ions to the functional EF-hand motifs induces the extrusion of a myristoyl group that increases the affinity of Rec for the membrane and leads to the formation of a complex with rhodopsin kinase (GRK1). Here, unbiased all-atom molecular dynamics simulations were performed to monitor the spontaneous insertion of the myristoyl group into a model multicomponent biological membrane for both isolated Rec and for its complex with a peptide from the GRK1 target. It was found that the functional membrane anchoring of the myristoyl group is triggered by persistent electrostatic protein-membrane interactions. In particular, salt bridges between Arg43, Arg46 and polar heads of phosphatidylserine lipids are necessary to enhance the myristoyl hydrophobic packing in the Rec-GRK1 assembly. The long-distance communication between Ca2+-binding EF-hands and residues at the interface with GRK1 is significantly influenced by the presence of the membrane, which leads to dramatic changes in the connectivity of amino acids mediating the highest number of persistent interactions (hubs). In conclusion, specific membrane composition and allosteric interactions are both necessary for the correct assembly and dynamics of functional Rec-GRK1 complex
caf2 nanoparticles as surface carriers of gcap1 a calcium sensor protein involved in retinal dystrophies
CaF2 nanoparticles constitute biocompatible nano-carriers for the calcium sensor protein GCAP1 preserving its biological function
Revealing druggable cryptic pockets in the Nsp1 of SARS-CoV-2 and other β-coronaviruses by simulations and crystallography
Non-structural protein 1 (Nsp1) is a main pathogenicity factor of α- and β-coronaviruses. Nsp1 of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) suppresses the host gene expression by sterically blocking 40S host ribosomal subunits and promoting host mRNA degradation. This mechanism leads to the downregulation of the translation-mediated innate immune response in host cells, ultimately mediating the observed immune evasion capabilities of SARS-CoV-2. Here, by combining extensive molecular dynamics simulations, fragment screening and crystallography, we reveal druggable pockets in Nsp1. Structural and computational solvent mapping analyses indicate the partial crypticity of these newly discovered and druggable binding sites. The results of fragment-based screening via X-ray crystallography confirm the druggability of the major pocket of Nsp1. Finally, we show how the targeting of this pocket could disrupt the Nsp1-mRNA complex and open a novel avenue to design new inhibitors for other Nsp1s present in homologous β-coronaviruses
SWISH-X, an Expanded Approach to Detect Cryptic Pockets in Proteins and at Protein–Protein Interfaces
Protein–protein interactions mediate most molecular
processes
in the cell, offering a significant opportunity to expand the set
of known druggable targets. Unfortunately, targeting these interactions
can be challenging due to their typically flat and featureless interaction
surfaces, which often change as the complex forms. Such surface changes
may reveal hidden (cryptic) druggable pockets. Here, we analyze a
set of well-characterized protein–protein interactions harboring
cryptic pockets and investigate the predictive power of current computational
methods. Based on our observations, we developed a new computational
strategy, SWISH-X (SWISH Expanded), which combines the established
cryptic pocket identification capabilities of SWISH with the rapid
temperature range exploration of OPES MultiThermal. SWISH-X is able
to reliably identify cryptic pockets at protein–protein interfaces
while retaining its predictive power for revealing cryptic pockets
in isolated proteins, such as TEM-1 β-lactamase