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