Molecular mechanism of multispecific recognition of Calmodulin through conformational changes

Abstract

Calmodulin (CaM) is found to have the capability to bind multiple targets. Investigations on the association mechanism of CaM to its targets are crucial for understanding protein-protein binding and recognition. Here, we developed a structure-based model to explore the binding process between CaM and skMLCK binding peptide. We found the cooperation between nonnative electrostatic interaction and nonnative hydrophobic interaction plays an important role in nonspecific recognition between CaM and its target. We also found that the conserved hydrophobic anchors of skMLCK and binding patches of CaM are crucial for the transition from high affinity to high specificity. Furthermore, this association process involves simultaneously both local conformational change of CaM and global conformational changes of the skMLCK binding peptide. We found a landscape with a mixture of the atypical "induced fit," the atypical "conformational selection," and "simultaneously binding-folding," depending on the synchronization of folding and binding. Finally, we extend our discussions on multispecific binding between CaM and its targets. These association characteristics proposed for CaM and skMLCK can provide insights into multispecific binding of CaM. structure-based model | Calmodulin | mixture binding mechanism | multispecific recognition M any biological processes are driven by protein-protein binding. The large-scale domain rearrangements in proteins have long been recognized to have a critical role in biological function. This flexibility or conformational dynamics also provide a new viewpoint of binding. In addition to the "lock-andkey" binding mechanism, proposed by Fischer to describe the rigid binding in enzyme catalysis (1), two scenarios, considering flexibility during binding, emerged and are referred as "induced fit" and "conformational selection," addressing the critical roles of flexibility in protein recognition (2-6).Calmodulin (CaM) is an ubiquitous Ca 2+ binding protein that is involved in a wide range of cellular Ca 2+ -dependent signaling pathways. With incorporating Ca 2+ ions, Ca 2+ -CaM regulates the activity of many kinds of proteins including protein phosphatase, inositol triphosphate kinase, nitric oxide synthase, protein kinases, nicotinamide adenine dinucleotide kinase, Ca 2+ pumps, and proteins involved in motility (7-9). The binary complex Ca 2+ -CaM is found to have the capability to bind over 300 targets (7)(8)(9). Exploring the molecular mechanism of Ca 2+ -CaM binding to the different targets is crucial for understanding protein-protein multispecific recognition. X-ray crystallography experiments have been performed to resolve Ca 2+ -loaded CaM structure (10). However, complexes of CaM with target enzymes are difficult to study by NMR and the crystallization method, due to the spatial resolution in the experiments. Alternatively, short peptide sequences corresponding to CaM-binding domains are often used to explore CaM-target protein interactions and several studies suggest that these CaM-peptide in...

Calmodulin fishing with a structurally disordered bait triggers CyaA catalysis

“…The ability of individual N- and C-terminal lobes of CaM to independently associate to either distinct sites on the same protein or to the same site on two distinct polypeptides, thus facilitating their dimerization, have been described for numerous CaM targets, although in many instances, the affinity of individual lobes with their target sequence is lower than that with the AC H-helix. Our data further highlight the remarkable conformational diversity of CaM upon binding to its targets [ 44 – 49 ].…”

Calmodulin regulates MGRN1‐GP78 interaction mediated ubiquitin proteasomal degradation system

“…CaM is an important calcium sensor studied extensively due to its flexibility and structural plasticity toward numerous substrates (29,30). Structural and computational studies have explored the interactions between CaM and a diverse heterogeneous group of interacting proteins.…”

“…These conformational changes expose nonpolar surfaces of CaM, which then bind to nonpolar regions on the target proteins. Target proteins have CaM-binding sites that may vary in their amino acid sequences but share common features of having bulky hydrophobic residues separated by a specific number of residues and a helix-forming propensity (28)(29)(30). Furthermore, a recent report elucidates how CaM regulates the interaction of the ER Ca 2+ sensor, the stromal interaction molecule (STIM), with the plasma membrane pore-forming subunit, Orai1 (31).…”

A high-affinity calmodulin-binding site in the CyaA toxin translocation domain is essential for invasion into eukaryotic cells

“…We have previously shown that the P454 peptide, residues 454-484 from the CyaA translocation region, exhibits membrane-active properties similar to antimicrobial peptides (AMPs) 67 . As with certain AMPs, the P454 peptide displays biophysical properties that are similar to that of many calmodulin-binding peptides: they can form amphiphilic helices, they are positively charged and contain a few aromatic or hydrophobic residues involved in complex stabilization [68][69][70] . Indeed, we found that P454 binds calmodulin (CaM) in solution in a calcium-dependent manner as shown by analytical ultracentrifugation and far-UV circular dichroism spectroscopy ( Figure S2 and Table S1).…”