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Molecular Dynamics Simulations and Principal Component Analysis on Human Laforin Mutation W32G and W32G/K87A

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Abstract

Mutations in human laforin lead to an autosomal neurodegenerative disorder Lafora disease. In N-terminal carbohydrate binding domain of laforin, two mutations W32G and K87A are reported as highly disease causing laforin mutants. Experimental studies reported that mutations are responsible for the abolishment of glycogen binding which is a critical function of laforin. Our current computational study focused on the role of conformational changes in human laforin structure due to existing single mutation W32G and prepared double mutation W32G/K87A related to loss of glycogen binding. We performed 10 ns molecular dynamics (MD) simulation studies in the Gromacs package for both mutations and analyzed the trajectories. From the results, the global properties like root mean square deviation, root mean square fluctuation, radius of gyration, solvent accessible surface area and hydrogen bonds showed structural changes in atomic level observed in W32G and W32G/K87A laforin mutants. The conformational change induced by mutants influenced the loss of the overall stability of the native laforin. Moreover, the change in overall motion of protein was analyzed by principal component analysis and results showed protein clusters expanded more than native and also change in direction in case of double mutant in conformational space. Overall, our report provides theoretical information on loss of structure–function relationship due to flexible nature of laforin mutants. In conclusion, comparative MD simulation studies support the experimental data on W32G and W32G/K87A related to the lafora disease mechanism on glycogen binding.

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Abbreviations

MD:

Molecular dynamics

RMSD:

Root mean square deviation

RMSF:

Root means square fluctuation

Rg:

Radius of gyration

SASA:

Solvent accessible surface area

PCA:

Principal component analysis

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Authors and Affiliations

  1. Unit of Psychiatry, Faculty of Medicine, AIMST University, Bedong, Kedah Darul Aman, Malaysia

    P. S. Srikumar

  2. Unit of Biochemistry, Faculty of Medicine, AIMST University, Bedong, Kedah Darul Aman, Malaysia

    K. Rohini

  3. Unit of Microbiology, Faculty of Medicine, AIMST University, Bedong, Kedah Darul Aman, Malaysia

    Perumbilavil Kaithamanakallam Rajesh

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  1. P. S. Srikumar
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  2. K. Rohini
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  3. Perumbilavil Kaithamanakallam Rajesh
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Correspondence to K. Rohini.

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Srikumar, P.S., Rohini, K. & Rajesh, P.K. Molecular Dynamics Simulations and Principal Component Analysis on Human Laforin Mutation W32G and W32G/K87A. Protein J 33, 289–295 (2014). https://doi.org/10.1007/s10930-014-9561-2

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