Single amino acid substitutions in Fibroblast Growth Factor Receptor 1 (FGFR1) destabilize protein and have been implicated in several genetic disorders like various forms of cancer, Kallamann syndrome, Pfeiffer syndrome, Jackson Weiss syndrome, etc. In order to gain functional insight into mutation caused by amino acid substitution to protein function and expression, special emphasis was laid on molecular dynamics simulation techniques in combination with in silico tools such as SIFT, PolyPhen 2.0, I-Mutant 3.0 and SNAP. It has been estimated that 68% nsSNPs were predicted to be deleterious by I-Mutant, slightly higher than SIFT (37%), PolyPhen 2.0 (61%) and SNAP (58%). From the observed results, P722S mutation was found to be most deleterious by comparing results of all in silico tools. By molecular dynamics approach, we have shown that P722S mutation leads to increase in flexibility, and deviated more from the native structure which was supported by the decrease in the number of hydrogen bonds. In addition, biophysical analysis revealed a clear insight of stability loss due to P722S mutation in FGFR1 protein. Majority of mutations predicted by these in silico tools were in good concordance with the experimental results.

Mucopolysaccharidosis (MPS) IIIA, also known as Sanfilippo syndrome type A, is a severe, progressive disease that affects the central nervous system (CNS). MPS IIIA is inherited in an autosomal recessive manner and is caused by a deficiency in the lysosomal enzyme sulfamidase, which is required for the degradation of heparan sulfate. The sulfamidase is produced by the Nsulphoglucosamine sulphohydrolase (SGSH) gene. In MPS IIIA patients, the excess of lysosomal storage of heparan sulfate often leads to mental retardation, hyperactive behavior, and connective tissue impairments, which occur due to various known missense mutations in the SGSH, leading to protein dysfunction. In this study, we focused on three mutations (R74C, S66W, and R245H) based on in silico pathogenic, conservation, and stability prediction tool studies. The three mutations were further subjected to molecular dynamic simulation (MDS) analysis using GROMACS simulation software to observe the structural changes they induced, and all the mutants exhibited maximum deviation patterns compared with the native protein.Conformational changes were observed in the mutants based on various geometrical parameters, such as conformational stability, fluctuation, and compactness, followed by hydrogen bonding, physicochemical properties, principal component analysis (PCA), and salt bridge analyses, which further validated the underlying cause of the protein instability. Additionally, secondary structure and surrounding amino acid analyses further confirmed the above results indicating the loss of protein function in the mutants compared with the native protein. The present results reveal the effects of three mutations on the enzymatic activity of sulfamidase, providing a molecular explanation for the cause of the disease. Thus, this study allows for a better understanding of the effect of SGSH mutations through the use of various computational approaches in terms of both structure and functions and provides a platform for the development of therapeutic drugs and potential disease treatments.

Larsen syndrome (LRS) is a rare genetic disease associated with variable manifestations including skeletal malformations, dislocations of the large joints, and notable changes in facial and limb features. Genetic variants in the Filamin B (FLNB) gene are associated with the development of LRS. We searched two literature databases (OMIM and PubMed) and three gene variant databases (HGMD, UniProt, & dbSNP) to capture all the possible variants associated with LRS phenotype, which may have an impact on the FLNB function. Our search yielded 77 variants that might impact the FLNB protein function in patients with LRS. We performed rigorous computational analysis such as conservational, biochemical, pathogenicity, and structural computational analyses to understand the deleterious effect of the G1691S variant. Further, the structural changes of the G1691S variant was compared with a null variant (G1691A) and the native protein through a molecular dynamic simulation study of 50 ns. We found that the variant G1691S was highly deleterious and destabilize the protein when compared to the native and variant G1691A. This might be due to the physicochemical changes in the variant G1691S when compared to the native and variant G1691A. The destabilization was further supported by transformation of bend to coil in variant G1691S whereas bend was retained in native and variant G1691A through molecular dynamics analysis. Our study shed light on the importance of computational methods to understand the molecular nature of genetic variants and structural insights on the function of the FLNB protein. J. Cell. Biochem. 118: 1900-1910, 2017. © 2017 Wiley Periodicals, Inc.

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