Received: 2 January 2018 | Accepted: 9 March 2018 DOI: 10.1002/jcb.26834 RESEARCH ARTICLE Protein phenotype diagnosis of autosomal dominant calmodulin mutations causing irregular heart rhythms Noor A. Shaik 1,2 | Zuhier A. Awan 3 | Prashant K. Verma 1 | Ramu Elango 1,2 | Babajan Banaganapalli 1,2 1 Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia 2 Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah, Saudi Arabia 3 Department of Clinical Biochemistry, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia Correspondence Babajan Banaganapalli, Princess Al- Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER- HD), King Abdulaziz University, P.O. Box 80205, Jeddah-21589, Saudi Arabia. Email: bbabajan@kau.edu.sa Funding information Deanship of Scientific Research, King Abdulaziz University, Grant number: G- 553-140-38 Abstract The life-threatening group of irregular cardiac rhythmic disorders also known as Cardiac Arrhythmias (CA) are caused by mutations in highly conserved Calmodulin (CALM/CaM) genes. Herein, we present a multidimensional approach to diagnose changes in phenotypic, stability, and Ca 2+ ion binding properties of CA-causing mutations. Mutation pathogenicity was determined by diverse computational machine learning approaches. We further modeled the mutations in 3D protein structure and analyzed residue level phenotype plasticity. We have also examined the influence of torsion angles, number of H-bonds, and free energy dynamics on the stability, near-native simulation dynamic potential of residue fluctuations in protein structures, Ca 2+ ion binding potentials, of CaM mutants. Our study recomends to use M-CAP method for measuring the pathogenicity of CA causing CaM variants. Interestingly, most CA-causing variants we analyzed, exists in either third (V/H-96, S/I-98, V-103) or fourth (G/V-130, V/E/H-132, H-134, P-136, G-141, and L-142) EF- hands located in carboxyl domains of the CaM molecule. We observed that the minor structural fluctuations caused by these variants are likely tolerable owing to the highly flexible nature of calmodulin's globular domains. However, our molecular docking results supports that these variants disturb the affinity of CaM toward Ca 2+ ions and corroborate previous findings from functional studies. Taken together, these computational findings can explain the molecular reasons for subtle changes in structure, flexibility, and stability aspects of mutant CaM molecule. Our comprehensive molecular scanning approach demonstrates the utility of computa- tional methods in quick preliminary screening of CA- CaM mutations before undertaking time consuming and complicated functional laboratory assays. KEYWORDS Ca2+ binding, calmodulin, CaM, heart rhythm, molecular docking 1 | INTRODUCTION Calmodulin (CaM; calcium modulated protein) is a well- known multifunctional Ca 2+ binding protein in eukaryotic cells. This protein is usually found in the cytosol or on cellular Noor A. Shaik and Zuhier A. Awan contributed equally in this paper. J Cell Biochem. 2018;1–16. wileyonlinelibrary.com/journal/jcb © 2018 Wiley Periodicals, Inc. | 1