Prediction of three dimensional structure of calmodulin

Interaction of the Melatonin/Ca2+-CaM Complex with Calmodulin Kinase II: Physiological Importance

Melatonin N-acetyl-5-methoxytriptamine is an ancient molecule which synchronizes the internal biologic activity with the environmental photoperiod. It is synthesized by the pineal gland during the night and released to the general circulation, where it reaches nanomolar concentrations. The indolamine acts through melatonin receptors and binds to different proteins such as calmodulin: a phylogenetically conserved protein which is the main transductor of the calcium signaling. In this review, we will describe evidence supporting that melatonin binds to calmodulin in presence of calcium, and we discuss the effects of this indolamine on the activity of calmodulin kinase II as an inhibitor and as stimulator of calmodulin-dependent protein kinase II activity. We also provide a literature review supporting the relevance of melatonin binding to calmodulin in the regulation of circadian rhythms in unicellular organisms, as well as in neuronal development in mammals as an ancient, conserved mechanism. Finally, we highlight the importance of antioxidant effects of melatonin on calmodulin preservation. SIGNIFICANCE STATEMENT: This review compiled evidence supporting that melatonin binds to calmodulin. We discuss the dual effect of melatonin on the activity of calmodulin kinase II, the possible mechanisms involved, and the relevance on regulation of circadian rhythms and neurodevelopment. Finally, we describe evidence supporting that the binding of melatonin to calmodulin hydrophobic pockets may prevent the oxidation of methionine species with a shielding effect that preserves the functionality of calmodulin.

Further Evidence of the Melatonin Calmodulin Interaction: Effect on CaMKII Activity

Melatonin (MEL) is a pleiotropic indolamine that reaches multiple intracellular targets. Among these, MEL binds to calmodulin (CaM) with high affinity. In presence of Ca²⁺, CaM binds to CaM-dependent kinase II (CaMKII). The Ca²⁺-CaM/CaMKII pathway regulates a myriad of brain functions in different cellular compartments. Evidence showing the regulation of this cellular pathway by MEL is scarce. Thus, our main objective was to study the interaction of MEL with CaM and its effects on CaMKII activity in two microenvironments (aqueous and lipidic) naturally occurring within the cell. In addition, colocalization of MEL with CaM in vivo was explored in mice brain hippocampus. In vitro CaM-MEL interaction and the structural conformations of CaM in the presence of this indoleamine were assessed through electrophoretic mobility and isoelectric point. The functional consequence of this interaction was evaluated by measuring CaMKII activity. Ca²⁺-CaM-MEL increased the activity of CaMKII in aqueous buffer but reduced the kinase activity in lipid buffer. Importantly, MEL colocalizes in vivo with Ca²⁺-CaM in the hippocampus. Our evidence suggests that MEL regulates the key cellular Ca²⁺-CaM/CaMKII pathway and might explain why physiological MEL concentrations reduce CaMKII activity in some experimental conditions, while in others it drives biological processes through activation of this kinase.

Efficient and automated large-scale detection of structural relationships in proteins with a flexible aligner

Background

The total number of known three-dimensional protein structures is rapidly increasing. Consequently, the need for fast structural search against complete databases without a significant loss of accuracy is increasingly demanding. Recently, TopSearch, an ultra-fast method for finding rigid structural relationships between a query structure and the complete Protein Data Bank (PDB), at the multi-chain level, has been released. However, comparable accurate flexible structural aligners to perform efficient whole database searches of multi-domain proteins are not yet available. The availability of such a tool is critical for a sustainable boosting of biological discovery.

Results

Here we report on the development of a new method for the fast and flexible comparison of protein structure chains. The method relies on the calculation of 2D matrices containing a description of the three-dimensional arrangement of secondary structure elements (angles and distances). The comparison involves the matching of an ensemble of substructures through a nested-two-steps dynamic programming algorithm. The unique features of this new approach are the integration and trade-off balancing of the following: 1) speed, 2) accuracy and 3) global and semiglobal flexible structure alignment by integration of local substructure matching. The comparison, and matching with competitive accuracy, of one medium sized (250-aa) query structure against the complete PDB database (216,322 protein chains) takes about 8 min using an average desktop computer. The method is at least 2–3 orders of magnitude faster than other tested tools with similar accuracy. We validate the performance of the method for fold and superfamily assignment in a large benchmark set of protein structures. We finally provide a series of examples to illustrate the usefulness of this method and its application in biological discovery.

Conclusions

The method is able to detect partial structure matching, rigid body shifts, conformational changes and tolerates substantial structural variation arising from insertions, deletions and sequence divergence, as well as structural convergence of unrelated proteins.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0866-8) contains supplementary material, which is available to authorized users.

The effect of calcium ions and peptide ligands on the relative stabilities of the calmodulin dumbbell and compact structures

A combination of ion mobility and mass spectrometry methods was used to characterize the molecular shape of the protein calmodulin (CaM) and its complexes with calcium and a number of peptide ligands. CaM, a calcium-binding protein composed of 148 amino acid residues, was found by X-ray crystallography to occur both in a globular shape and in the shape of an extended dumbbell. Here, it was found, as solutions of CaM and CaM complexes were sprayed into the solvent-free environment of the mass spectrometer, that major structural features of the molecule and the stoichiometry of the units constituting a complex in solution were preserved in the desolvation process. Two types of CaM structures were observed in our experiments: a compact and an extended form of CaM with measured cross sections in near-perfect agreement with those calculated for the known globular and extended dumbbell X-ray geometries. Calcium-free solutions yielded predominantly an extended CaM conformation. Ca(n)(2+)-CaM complexes were observed in calcium-containing solutions, n = 0-4, with the population of the compact conformation increasing relative to the elongated conformation as n increases. For n = 4, a predominantly compact globular conformation was observed. Solutions containing the peptide CaMKII(290-309), the CaM target domain of the Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) enzyme, yielded predominantly globular Ca(4)(2+)-CaM-CaMKII(290-309) complexes. Similar results were obtained with the 26-residue peptide melittin. For the 14-residue C-terminal melittin fragment, on the other hand, formation of both a 1:1 and a 1:2 CaM-peptide complex was detected. On the basis of the entirety of our results, we conclude that the collapse of extended (dumbbell-like) CaM structures into more compact globular structures occurs upon specific binding of four calcium ions. Furthermore, this calcium-induced structural collapse of CaM appears to be a prerequisite for formation of a particularly stable CaM-peptide complex involving peptides long enough to be engaged in interactions with both lobes of CaM.

The solution structure of the Mg2+ form of soybean calmodulin isoform 4 reveals unique features of plant calmodulins in resting cells

Soybean calmodulin isoform 4 (sCaM4) is a plant calcium-binding protein, regulating cellular responses to the second messenger Ca(2+). We have found that the metal ion free (apo-) form of sCaM4 possesses a half unfolded structure, with the N-terminal domain unfolded and the C-terminal domain folded. This result was unexpected as the apo-forms of both soybean calmodulin isoform 1 (sCaM1) and mammalian CaM (mCaM) are fully folded. Because of the fact that free Mg(2+) ions are always present at high concentrations in cells (0.5-2 mM), we suggest that Mg(2+) should be bound to sCaM4 in nonactivated cells. CD studies revealed that in the presence of Mg(2+) the initially unfolded N-terminal domain of sCaM4 folds into an alpha-helix-rich structure, similar to the Ca(2+) form. We have used the NMR backbone residual dipolar coupling restraints (1)D(NH), (1)D(C alpha H alpha), and (1)D(C'C alpha) to determine the solution structure of the N-terminal domain of Mg(2+)-sCaM4 (Mg(2+)-sCaM4-NT). Compared with the known structure of Ca(2+)-sCaM4, the structure of the Mg(2+)-sCaM4-NT does not fully open the hydrophobic pocket, which was further confirmed by the use of the fluorescent probe ANS. Tryptophan fluorescence experiments were used to study the interactions between Mg(2+)-sCaM4 and CaM-binding peptides derived from smooth muscle myosin light chain kinase and plant glutamate decarboxylase. These results suggest that Mg(2+)-sCaM4 does not bind to Ca(2+)-CaM target peptides and therefore is functionally similar to apo-mCaM. The Mg(2+)- and apo-structures of the sCaM4-NT provide unique insights into the structure and function of some plant calmodulins in resting cells.

Prediction of flexible/rigid regions from protein sequences using k-spaced amino acid pairs

Background

Traditionally, it is believed that the native structure of a protein corresponds to a global minimum of its free energy. However, with the growing number of known tertiary (3D) protein structures, researchers have discovered that some proteins can alter their structures in response to a change in their surroundings or with the help of other proteins or ligands. Such structural shifts play a crucial role with respect to the protein function. To this end, we propose a machine learning method for the prediction of the flexible/rigid regions of proteins (referred to as FlexRP); the method is based on a novel sequence representation and feature selection. Knowledge of the flexible/rigid regions may provide insights into the protein folding process and the 3D structure prediction.

Results

The flexible/rigid regions were defined based on a dataset, which includes protein sequences that have multiple experimental structures, and which was previously used to study the structural conservation of proteins. Sequences drawn from this dataset were represented based on feature sets that were proposed in prior research, such as PSI-BLAST profiles, composition vector and binary sequence encoding, and a newly proposed representation based on frequencies of k-spaced amino acid pairs. These representations were processed by feature selection to reduce the dimensionality. Several machine learning methods for the prediction of flexible/rigid regions and two recently proposed methods for the prediction of conformational changes and unstructured regions were compared with the proposed method. The FlexRP method, which applies Logistic Regression and collocation-based representation with 95 features, obtained 79.5% accuracy. The two runner-up methods, which apply the same sequence representation and Support Vector Machines (SVM) and Naïve Bayes classifiers, obtained 79.2% and 78.4% accuracy, respectively. The remaining considered methods are characterized by accuracies below 70%. Finally, the Naïve Bayes method is shown to provide the highest sensitivity for the prediction of flexible regions, while FlexRP and SVM give the highest sensitivity for rigid regions.

Conclusion

A new sequence representation that uses k-spaced amino acid pairs is shown to be the most efficient in the prediction of the flexible/rigid regions of protein sequences. The proposed FlexRP method provides the highest prediction accuracy of about 80%. The experimental tests show that the FlexRP and SVM methods achieved high overall accuracy and the highest sensitivity for rigid regions, while the best quality of the predictions for flexible regions is achieved by the Naïve Bayes method.

Quantitative analysis of the conservation of the tertiary structure of protein segments

The publication of the crystallographic structure of calmodulin protein has offered an example leading us to believe that it is possible for many protein sequence segments to exhibit multiple 3D structures referred to as multi-structural segments. To this end, this paper presents statistical analysis of uniqueness of the 3D-structure of all possible protein sequence segments stored in the Protein Data Bank (PDB, Jan. of 2003, release 103) that occur at least twice and whose lengths are greater than 10 amino acids (AAs). We refined the set of segments by choosing only those that are not parts of longer segments, which resulted in 9297 segments called a sponge set. By adding 8197 signature segments, which occur uniquely in the PDB, into the sponge set we have generated a benchmark set. Statistical analysis of the sponge set demonstrates that rotating, missing and disarranging operations described in the text, result in the segments becoming multi-structural. It turns out that missing segments do not exhibit a change of shape in the 3D-structure of a multi-structural segment. We use the root mean square distance for unit vector sequence (URMSD) as an improved measure to describe the characteristics of hinge rotations, missing, and disarranging segments. We estimated the rate of occurrence for rotating and disarranging segments in the sponge set and divided it by the number of sequences in the benchmark set which is found to be less than 0.85%. Since two of the structure changing operations concern negligible number of segment and the third one is found not to have impact on the structure, we conclude that the 3D-structure of proteins is conserved statistically for more than 98% of the segments. At the same time, the remaining 2% of the sequences may pose problems for the sequence alignment based structure prediction methods.