Abstract
Cardiomyopathies are a severe and chronic cardiovascular burden worldwide, affecting a large cohort in the general population. Cysteine and glycine-rich protein 3 (CSRP3) is one of key proteins implicated in dominant dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM). In this study, we device a rapid in silico screening protocol that creates a mutational landscape map for all possible allowed and disallowed substitutions in the protein of interest. This map provides the structural and functional insights on the stability of LIM domains of CSRP3. Further, the sequence analysis delineates the eukaryotic CSRP3 protein orthologs which complements the mutational map, but provide limited information of amino acid exchanges. Next, we also evaluated the effect of HCM/DCM mutations on these domains. One of highly destabilising mutations—L44P (also disease causing) and a neutral mutation—L44M were further subjected to molecular dynamics (MD) simulations. The results establish that L44P substitution affects the LIM domain structure by altering secondary structure and due to loss of hydrophobic interaction with Phenylananine 35. The present study provides a useful perspective to our understanding of the role of mutations in the CSRP3 LIM domains and their evolution. This study provides a novel computational screening method for quick identification of key mutation sites for specific protein structures that can reduce the burden on experimental research.
Highlights
Cardiomyopathies are a severe and chronic cardiovascular burden worldwide, affecting a large cohort in the general population
For the sequence-based approach, the Polyphen[2] and PROVEAN sequence predictions showed that the majority of reported hypertrophic cardiomyopathy (HCM)/dilated cardiomyopathy (DCM) mutations are destabilising
Since the three-dimensional structure of LIM domains of Cysteine and glycine-rich protein 3 (CSRP3) alone are available for human CSRP3, this study focuses on mutations within LIM domains alone instead of the full-length protein structure
Summary
Cardiomyopathies are a severe and chronic cardiovascular burden worldwide, affecting a large cohort in the general population. We device a rapid in silico screening protocol that creates a mutational landscape map for all possible allowed and disallowed substitutions in the protein of interest. This map provides the structural and functional insights on the stability of LIM domains of CSRP3. Position was individually substituted by 19 other amino acid residues This mutational landscape map can be used to identify potentially deleterious mutations that have not been experimentally verified earlier. This approach coupled with sequence and structural analysis expands our overall knowledge on disease causing mutations and their effects on protein structures, which traditionally can be challenging to achieve by experimental approaches. We highlight the conservation of CSRP3 protein in representative eukaryotes, and differences in LIM1 and LIM2 that augment the disease-causing mutations and non-overlapping functional roles of the two LIM domains
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