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    Molecular Dynamics: An in Silico Analysis of JD and Its Mutant

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    Jonathan Chan
    The document summarizes a molecular dynamics simulation analysis comparing a Jd wild type protein to a Jd D35N mutant. The simulation results suggest the mutant is more rigid and stable based on lower RMSD values and requiring more force in constant velocity pulling simulations. However, this contradicts published experimental studies showing the mutant is less rigid, requiring a revision of the simulation parameters.

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    Molecular Dynamics: An in Silico Analysis of JD and Its Mutant

    Uploaded by

    Jonathan Chan
    40 views7 pages
    The document summarizes a molecular dynamics simulation analysis comparing a Jd wild type protein to a Jd D35N mutant. The simulation results suggest the mutant is more rigid and stable based on lower RMSD values and requiring more force in constant velocity pulling simulations. However, this contradicts published experimental studies showing the mutant is less rigid, requiring a revision of the simulation parameters.

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    Bioinformatics

    Original Title

    In Silico Analysis

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    The document summarizes a molecular dynamics simulation analysis comparing a Jd wild type protein to a Jd D35N mutant. The simulation results suggest the mutant is more rigid and stable based on lower RMSD values and requiring more force in constant velocity pulling simulations. However, this contradicts published experimental studies showing the mutant is less rigid, requiring a revision of the simulation parameters.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    40 views7 pages

    Molecular Dynamics: An in Silico Analysis of JD and Its Mutant

    Uploaded by

    Jonathan Chan
    The document summarizes a molecular dynamics simulation analysis comparing a Jd wild type protein to a Jd D35N mutant. The simulation results suggest the mutant is more rigid and stable based on lower RMSD values and requiring more force in constant velocity pulling simulations. However, this contradicts published experimental studies showing the mutant is less rigid, requiring a revision of the simulation parameters.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 7

    Molecular Dynamics

    An in silico analysis of Jd and its mutant


    Buban, J., Chan, J.

    RMSD

    Jd Wild Type

    Jd D35N

    >RMSD approximates residue mobility and protein stability.


    >In this picture, Red indicates greater mobility while Blue indicates less mobility
    >Eyeballing suggests that the mutant has less mobility

    RMSD

    >RMSD approximates residue mobility and protein stability.


    >Average JD RMSD: 1.24397 ; Average JD D35N: 1.1356
    >RMSD indicates that mutant is less mobile and more stable

    Constant Velocity Pulling Video

    Jd Wild Type

    JdD35N

    Constant Velocity Pulling

    >The stability of the proteins were also tested using constant velocity pulling.
    >The graph hints that more force is needed to pull JdD35N
    >Average force value is consistent with this observation
    (Jd: 543.841 piconewtons JdD35N: 799.40 piconewtons)

    Conclusion
    >in silico analysis suggests that Jd D35N is structurally
    more rigid than Jd wild type
    >This is in stark contrast to published studies, which found
    that JdD35N is less rigid than the Jd wild type (Bascos, 2009). A
    revision of the parameters in the molecular dynamics
    simulation script is recommended.

    Reference
    Landry SJ, Bascos NA (2009) Protein flexural
    dysfunction: Loss of structural rigidity in a Hsp40
    J-domain mutant correlates with loss of Hsp70
    activation. The FASEB Journal

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