Extracellular matrix communicates to the nuclear environment by external stimuli that affect Lamina organization and chromatin distribution . It is known that integrins transmit mechanical stimuli to the actin filaments in turn connected to the LINC complex consisting of Nesprin and SUN proteins . SUN proteins are supposed to link the nuclear Lamina , that rearranges according to external impulse. Despite the relevance of SUN1-Lamin A/C in nuclear reshaping, their binding domains have not been identified yet.
We here designed computational protocol to study the SUN1-Lamin A/C binding domain that plays key role in lamina sensitivity to external load.
Computational protocol was designed to reconstruct the SUN1 nuclear domain (1-315aa according to Uniprot server). The secondary structure of SUN1 was predicted via a consensus study of eight different servers while I-TASSER server was used for tertiary structure. To stabilize the 3D selected model, molecular dynamic annealing test was implemented via NAMD software (from 300K to 500K deltat=5ns, deltaT=5K explicit water box; Charmrun force field). To predict SUN1-Lamin A/C interaction, Haddock server was used to perform molecular docking analysis between SUN1 predicted model and all the X-ray solved domains of Lamin A/C in order to cover its full length. Combining affinity energy values with cluster dimension we selected the most reliable 3D structure of SUN1-Lamin A/C complex. H-bonds analysis was performed with VMD server.
The secondary structure of SUN1 N-terminal domain was estimated with 87% of confidence value and it was used to predict 3D model. 3D model reliability was supported by 65.4% of similarity with expected secondary structure and its high stability during annealing simulation (90.2% of similarity). Testing SUN1 domain affinity to all the solved Lamin A/C domains we identified the Ig-fold domain (1IFR) as the most affine one due to its high energy interaction as supported by 4 H-bonds (aa 295,303,140,141 and 456,490,496 for SUN1 and Lamin, respectively).
We here estimated SUN1-Lamin A/C interaction structure required to elucidate its key role in force transmission from extra cellular matrix to the nucleus. The reliability of the developed protocol supported by the consistency between our data and the literature ones, introduces our strategy as new promising tool for 3D reconstruction of proteins . Moreover, the SUN1-Lamin A/C complex reconstruction represents the first step in deepen external force effects on nuclear shape. Considering the high occurrence of laminopathies-related single point mutations in Lamin A/C Ig-fold domain, we suggest that these mutations may alter SUN1-Lamin A/C interaction with consequences on nuclear sensitivity and thus gene activation. Further computational analyses could verify this hypothesis and X-ray technique will be used to validate the SUN1-Lamin complex.
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