BMP-2 and BMP-9 binding specificities with ALK-3 in aqueous solution with dynamics

Signal ligands of the transforming growth factor-β (TGF-β) superfamily include the bone morphogenetic proteins (BMPs). BMPs bind to type I and type II serine-threonine kinase receptors and trigger the transphosphorylation cascade, wherein the active type II receptor phosphorylates the inactive type I receptor. This process further activates the cytoplasmic effectors of the pathway, such as SMAD proteins, which are homologs of both the Drosophila protein MAD (mothers against decapentaplegic) and the Caenorhabditis elegans protein SMA (small body size). Even though biological and medicinal studies have been performed on these complex species, we currently do not know the underlying molecular mechanisms of the signal ligand interactions with the receptors. Detailed understanding of these interactions increases our knowledge about these proteins, and also can provide the lacking information for successful mutation experiments. This study focuses on the computational analysis of binding affinities and structural binding specificities of two different types of BMPs (BMP-2 and BMP-9) to the activin receptor-like kinases (ALK-3) in solution. For studying the binding characteristics of BMP-2 or BMP-9 with ALK-3 in aqueous solution, we performed extensive molecular dynamics simulations coupled with thermodynamic calculations. The calculated thermodynamic properties show that the BMP-2/ALK-3 complex is thermodynamically more stable than a possible BMP-9/ALK-3 species in aqueous solution. The binding free energies indicate that ALK-3 preferably binds to BMP-2 instead of BMP-9. The structural analysis shows that ALK-3 binding with BMP-2 occurs in a perfectly symmetry pathway, whereas this symmetry is lost for possible ALK-3 interactions with BMP-9. The Phe49 to Val70 loop region of BMP-2 presents strong inter-molecular interactions with ALK-3. On the other hand, BMP-9 presents weaker interactions with ALK-3 via a non-continuous sequence. ALK-3-binding region of BMP-2 corresponds to the region predicted to be flexible by our intrinsic disorder analysis, whereas the related region of BMP-9 is expected to be noticeably less flexible. This study proposes that mutating the BMP-9 with the partial Phe49 to Val70 sequence of BMP-2 can help to increase the reactivity of BMP-9 towards stable ALK-3 binding, which in turn has the potential to develop new signaling pathways for improving the formation of tissues and to prevent or treat severe diseases. Furthermore, this study also demonstrates the usefulness of theoretical physical chemistry tools, such as molecular dynamics simulations and the ProtMet simulation software package in the structural characterization of the TGF-β superfamily proteins.