Structural Aspects and Prediction of Calmodulin-Binding Proteins

Abstract

Calmodulin (CaM) is an important intracellular protein that binds Ca²⁺ and functions as a critical second messenger involved in numerous biological activities through extensive interactions with proteins and peptides. CaM's ability to adapt to binding targets with different structures is related to the flexible central helix separating the N- and C-terminal lobes, which allows for conformational changes between extended and collapsed forms of the protein. CaM-binding targets are most often identified using prediction algorithms that utilize sequence and structural data to predict regions of peptides and proteins that can interact with CaM. In this review, we provide an overview of different CaM-binding proteins, the motifs through which they interact with CaM, and shared properties that make them good binding partners for CaM. Additionally, we discuss the historical and current methods for predicting CaM binding, and the similarities and differences between these methods and their relative success at prediction. As new CaM-binding proteins are identified and classified, we will gain a broader understanding of the biological processes regulated through changes in Ca²⁺ concentration through interactions with CaM.

Keywords: CaMBP; IQ motif; SVM; calmodulin; machine learning; peptide; prediction; random forest.

Figure 1

All CaM structures shown in blue, and CaMBPs are shown in red or tan. (A). Apo-CaM (PDB ID 1cfd) with central helix unwound/extended. (B). Holo-CaM (PDB ID 4bw8) with 4 Ca²⁺ ions in EF-Hand sites 1–4. (C). Ca²⁺/CaM/MARCKS (myristoylated alanine-rich C kinase substrate) complex (PDB ID 1iwq). The N-lobe of CaM is not involved in binding [10]. (D). Ca²⁺/CaM/CaMKIIα complex (PDB ID 1cm1) exhibiting 1-5-10 binding mode with collapsed CaM [11]. (E). Ca²⁺/CaM/RyR1 complex (PDB ID 2bcx) exhibiting unusual 1-17 binding mode with collapsed CaM [12]. (F). Ca²⁺/CaM bound to peptide analog of CaM-binding region of chicken smooth muscle myosin light-chain kinase (PDB ID 1cdl) [13]. (G). Apo-CaM/Myosin V 2:1 complex (PDB ID 2ix7). Each CaM C- lobe is partially open to grip the first part of the IQ motif (IQxxxR), while the closed N-terminal lobes interact weakly with the second part of the motif (GxxxR) [14]. (H). Apo-CaM (blue) bound to zebrafish IQCG protein (red) (PDB ID 4lzx), exhibiting lower affinity than the Ca²⁺-bound state [15]. Sidechain interactions with CaM include residues highlighted in bold from the IQCG sequence 400-410 (LQAWWRGTMIR). (I). Ca²⁺/CaM/Glutamate decarboxylase chains B and C (PDB ID 1nwd) [16].

Figure 2

HMM logo as a visualization of profile HMM for IQ motif, from EMBL-EBI, family IQ (PF00612). The IQ motif is identified by letters at positions 7 and 8 in the logo, where increasing height of the letter represents greater distribution of the amino acid in the sequences analyzed through multiple sequence alignment.