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Screening of mutations affecting protein stability and dynamics of FGFR1 — A simulation analysis

View Article: PubMed Central - PubMed

ABSTRACT

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.

No MeSH data available.


Molecular dynamics simulation of native and mutant model protein at 6000 ps.A. Time evolution of backbone RMSDs is shown as a function of time of the wild and mutant structures at 6000 ps. The symbol coding scheme is as follows: wild (black color), mutant P722S (Green color), V607M (red color) and V513G (blue color).B. RMSF of the backbone carbon alpha over the entire simulation. The ordinate is RMSF (nm), and the abscissa is atom. The symbol coding scheme is as follows: wild (black color), mutant P722S (green color), V607M (red color) and V513G (blue color).C. Average number of intermolecular hydrogen bond in native and mutant versus time. The symbol coding scheme is as follows: wild (black color), mutant P722S (green color), V607M (red color) and V513G (blue color).
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f0010: Molecular dynamics simulation of native and mutant model protein at 6000 ps.A. Time evolution of backbone RMSDs is shown as a function of time of the wild and mutant structures at 6000 ps. The symbol coding scheme is as follows: wild (black color), mutant P722S (Green color), V607M (red color) and V513G (blue color).B. RMSF of the backbone carbon alpha over the entire simulation. The ordinate is RMSF (nm), and the abscissa is atom. The symbol coding scheme is as follows: wild (black color), mutant P722S (green color), V607M (red color) and V513G (blue color).C. Average number of intermolecular hydrogen bond in native and mutant versus time. The symbol coding scheme is as follows: wild (black color), mutant P722S (green color), V607M (red color) and V513G (blue color).

Mentions: To examine the extent to which mutation effects protein structure, RMSD values were determined for native and mutant protein structure. We calculated the RMSD for all the atoms from the initial structure, which were considered as a central criterion to measure the convergence of the protein system concerned. It is evident that the native (3RHX) and mutant structures (V513G, V607M, P7222S) remain close to its starting conformation till 200 ps resulting in a backbone RMSD of about 0.14 nm (Fig. 2A). Between ranges of 500–2000 ps, wild type structure attained a maximum RMSD value of about 0.25 nm and among mutants 607 attained a maximum deviation of about 0.28 nm. From 2000 ps till end, mutant P722S retained a large deviation from other structure attaining a maximum RMSD of about 0.35 nm around 3600 ps. Throughout the analysis, mutant model P722S showed maximum deviation, while mutant model V607M exhibited intermediated deviated and native and mutant model V513G showed least deviation. A small variation in the average RMSD values of native and mutants after the relaxation period (~ 0.14 nm) lead to the conclusion that the mutations could affect the dynamic behavior of mutant protein, thus providing a suitable basis for further analyses. For determining the mutation affects dynamic behavior of residues, RMSF values of mutant and native structure were calculated. RMSF value of native residues fluctuates from a range of 0.08–0.28 nm in the entire simulation period. Moreover, mutant model V513G and V607M exhibited flexibility of ~ 0.35 nm and ~ 0.36 nm, while mutant P722S showed a maximum flexibility of about 0.38 nm (Fig. 2B). Analysis of the fluctuations revealed that the greatest degree of flexibility was shown by mutant model P722S. The reason for deviation in flexibility of residues was further validated by hydrogen bond analysis. Native protein exhibited maximum number of hydrogen bond 178–235, while the mutant model V513G and V607M showed an intermediate number of hydrogen bonds in the range of 180–235 (Fig. 2C). P722S exhibited least number of hydrogen bond ranging from ~ 170 to 213, which was in agreement with the stability of mutant models observed from the RMSD and RMSF analyses. These results imply that mutations might destroy the ability of hydrogen bond formation.


Screening of mutations affecting protein stability and dynamics of FGFR1 — A simulation analysis
Molecular dynamics simulation of native and mutant model protein at 6000 ps.A. Time evolution of backbone RMSDs is shown as a function of time of the wild and mutant structures at 6000 ps. The symbol coding scheme is as follows: wild (black color), mutant P722S (Green color), V607M (red color) and V513G (blue color).B. RMSF of the backbone carbon alpha over the entire simulation. The ordinate is RMSF (nm), and the abscissa is atom. The symbol coding scheme is as follows: wild (black color), mutant P722S (green color), V607M (red color) and V513G (blue color).C. Average number of intermolecular hydrogen bond in native and mutant versus time. The symbol coding scheme is as follows: wild (black color), mutant P722S (green color), V607M (red color) and V513G (blue color).
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Show All Figures
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f0010: Molecular dynamics simulation of native and mutant model protein at 6000 ps.A. Time evolution of backbone RMSDs is shown as a function of time of the wild and mutant structures at 6000 ps. The symbol coding scheme is as follows: wild (black color), mutant P722S (Green color), V607M (red color) and V513G (blue color).B. RMSF of the backbone carbon alpha over the entire simulation. The ordinate is RMSF (nm), and the abscissa is atom. The symbol coding scheme is as follows: wild (black color), mutant P722S (green color), V607M (red color) and V513G (blue color).C. Average number of intermolecular hydrogen bond in native and mutant versus time. The symbol coding scheme is as follows: wild (black color), mutant P722S (green color), V607M (red color) and V513G (blue color).
Mentions: To examine the extent to which mutation effects protein structure, RMSD values were determined for native and mutant protein structure. We calculated the RMSD for all the atoms from the initial structure, which were considered as a central criterion to measure the convergence of the protein system concerned. It is evident that the native (3RHX) and mutant structures (V513G, V607M, P7222S) remain close to its starting conformation till 200 ps resulting in a backbone RMSD of about 0.14 nm (Fig. 2A). Between ranges of 500–2000 ps, wild type structure attained a maximum RMSD value of about 0.25 nm and among mutants 607 attained a maximum deviation of about 0.28 nm. From 2000 ps till end, mutant P722S retained a large deviation from other structure attaining a maximum RMSD of about 0.35 nm around 3600 ps. Throughout the analysis, mutant model P722S showed maximum deviation, while mutant model V607M exhibited intermediated deviated and native and mutant model V513G showed least deviation. A small variation in the average RMSD values of native and mutants after the relaxation period (~ 0.14 nm) lead to the conclusion that the mutations could affect the dynamic behavior of mutant protein, thus providing a suitable basis for further analyses. For determining the mutation affects dynamic behavior of residues, RMSF values of mutant and native structure were calculated. RMSF value of native residues fluctuates from a range of 0.08–0.28 nm in the entire simulation period. Moreover, mutant model V513G and V607M exhibited flexibility of ~ 0.35 nm and ~ 0.36 nm, while mutant P722S showed a maximum flexibility of about 0.38 nm (Fig. 2B). Analysis of the fluctuations revealed that the greatest degree of flexibility was shown by mutant model P722S. The reason for deviation in flexibility of residues was further validated by hydrogen bond analysis. Native protein exhibited maximum number of hydrogen bond 178–235, while the mutant model V513G and V607M showed an intermediate number of hydrogen bonds in the range of 180–235 (Fig. 2C). P722S exhibited least number of hydrogen bond ranging from ~ 170 to 213, which was in agreement with the stability of mutant models observed from the RMSD and RMSF analyses. These results imply that mutations might destroy the ability of hydrogen bond formation.

View Article: PubMed Central - PubMed

ABSTRACT

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.

No MeSH data available.