An open and shut case

A 1.3-A structure of zinc-bound N-terminal domain of calmodulin elucidates potential early ion-binding step

Calmodulin (CaM) is a 16.8-kDa calcium-binding protein involved in calcium-signal transduction. It is the canonical member of the EF-hand family of proteins, which are characterized by a helix-loop-helix calcium-binding motif. CaM is composed of N- and C-terminal globular domains (N-CaM and C-CaM), and within each domain there are two EF-hand motifs. Upon binding calcium, CaM undergoes a significant, global conformational change involving reorientation of the four helix bundles in each of its two domains. This conformational change upon ion binding is a key component of the signal transduction and regulatory roles of CaM, yet the precise nature of this transition is still unclear. Here, we present a 1.3-A structure of zinc-bound N-terminal calmodulin (N-CaM) solved by single-wavelength anomalous diffraction phasing of a selenomethionyl N-CaM. Our zinc-bound N-CaM structure differs from previously reported CaM structures and resembles calcium-free apo-calmodulin (apo-CaM), despite the zinc binding to both EF-hand motifs. Structural comparison with calcium-free apo-CaM, calcium-loaded CaM, and a cross-linked calcium-loaded CaM suggests that our zinc-bound N-CaM reveals an intermediate step in the initiation of metal ion binding at the first EF-hand motif. Our data also suggest that metal ion coordination by two key residues in the first metal-binding site represents an initial step in the conformational transition induced by metal binding. This is followed by reordering of the N-terminal region of the helix exiting from this first binding loop. This conformational switch should be incorporated into models of either stepwise conformational transition or flexible, dynamic energetic state sampling-based transition.

Computational studies of the binding mechanism of calmodulin with chrysin

Calmodulin (CaM) plays a crucial role in metabolism and physiology of eukaryotes by regulating biological activities. Multiple lines of evidences indicate that the phosphorylated flavonoids possess relatively stronger affinities for proteins by forming non-covalent complexes with them, and that the cellular functions are often triggered by this kind of interactions. Chrysin is one of the phosphorylated flavonoids that exist ubiquitously in plants and have remarkably beneficial pharmacological effects. In this study, the molecular docking tools were utilized to investigate the interactions of CaM with chrysin. Two different favorable binding modes have been observed. To complement the results obtained by the molecular docking study, an in-depth investigation into the binding modes was conducted with the molecular dynamics (MD) simulation to explore the binding profile and energy landscape. Based on the results thus obtained, a clear definition of the binding pocket for each of the two binding modes has been revealed. These findings may shed light upon the binding interactions of CaM with chrysin, providing a solid molecular basis for subset analysis of its pharmacological benefits.

The impact of X-ray crystallography and NMR on intracellular calcium signal transduction by EF-hand proteins: crossing the threshold from structure to biology and medicine

The use of x-ray crystallography and solution nuclear magnetic resonance (NMR) spectroscopy has revolutionized our understanding of the transduction of intracellular calcium signals into cellular responses. Indeed, the ability to cross a critical threshold from basic descriptive structural biochemistry to real-world applications in therapeutics and biotechnology now looms on the experimental horizon. The ~500 atomic resolution structures determined by x-ray and NMR approaches and deposited in the Protein Data Bank, many of which are of complexes of EF-hand proteins with peptide fragments of cellular targets, have yielded an extremely thorough description for how EF-hand proteins respond to the binding of calcium. Although this database of structures is a powerful structural tool to describe EF-hand protein function, it is limited in its ability to have a significant impact on biology and medicine because the structural effects on the downstream target are not determined. The opportunity that now lies before us is to extend this EF-hand-centric structural information so that the alterations in the target proteins are defined and the structural basis for functional consequences downstream is understood.

EF-hand protein dynamics and evolution of calcium signal transduction: an NMR view

Calcium signaling, one of the most widespread signaling mechanisms in cells, is generally carried out by EF-hand proteins, characterized by a helix-loop-helix motif paired in functional domains. EF-hand proteins may be viewed as molecular switches activated by calcium concentration transients. The EF-hand structural database has grown to a point where meaningful inferences on the functional conformational rearrangements upon calcium binding can be made by comparing a fair number of pairs of end points, i.e., the structures of the apo and calcium-bound forms. More compact descriptors of the movement associated with calcium binding, in terms of principal component analysis of the six interhelical angles, have also become available. Dynamic information obtained by NMR, also with the aid of calcium substitution with paramagnetic lanthanides, is shedding light on the intrinsic amplitude of the conformational degrees of freedom sampled by the various members of the EF-hand superfamily, as well as on the time scales of the motions. Particularly, NMR of lanthanide derivatives helps in capturing long time scale motions. Both static and dynamic pictures reveal a large variety of behaviors. It is increasingly recognized that the EF-hand machinery has differentiated its behavior during evolution in several ways, e.g., by modifying one of the loops, by undergoing a further duplication after the initial motif duplication that originated the functional domain, or by acquiring the ability to dimerize.

Calcium-binding proteins: intracellular sensors from the calmodulin superfamily

In all eukaryotic cells, and particularly in neurons, Ca(2+) ions are important second messengers in a variety of cellular signaling pathways. In the retina, Ca(2+) modulation plays a crucial function in the development of the visual system's neuronal connectivity and a regulatory role in the conversion of the light signal received by photoreceptors into an electrical signal transmitted to the brain. Therefore, the study of retinal Ca(2+)-binding proteins, which frequently mediate Ca(2+) signaling, has given rise to the important discovery of two subfamilies of these proteins, neuronal Ca(2+)-binding proteins (NCBPs) and calcium-binding proteins (CaBPs), that display similarities to calmodulin (CaM). These and other Ca(2+)-binding proteins are integral components of cellular events controlled by Ca(2+). Some members of these subfamilies also play a vital role in signal transduction outside of the retina. The expansion of the CaM-like protein family reveals diversification among Ca(2+)-binding proteins that evolved on the basis of the classic molecule, CaM. A large number of NCBP and CaBP subfamily members would benefit from their potentially specialized role in Ca(2+)-dependent cellular processes. Pinpointing the role of these proteins will be a challenging task for further research.