Discrete Molecular Dynamics Simulation of Biomolecules - Computational Modeling of Biological Systems - page 71

Fig. 9 Mechanism of regulation by iFKBP; Src regulation. ( a ) The portion of the FAK catalytic
domain targeted for insertion of iFKBP ( blue ) and the G-loop ( red ). ( b ) Dynamic correlation anal-
ysis of the wild-type FAK catalytic domain ( red , positive correlation; blue , negative correlation).
The circled region indicates strong negative correlation between the movement of the insertion loop
and the G-loop. ( c ) Tube representation depicting changes in the dynamics of the N-terminal lobe
of the FAK catalytic domain, based on DMD simulations. Warmer colors and thicker backbone
correspond to higher root mean squared fluctuation (RMSF) values, reflecting the degree of free
movement within the structure. The red arrows point to the G-loop

sample the conformational dynamics of complicated systems, DMD simulations
will play an important role in our understanding of biology and the effort to combat
human diseases.

References

1. Bernado, P., Blackledge, M.: Structural biology: proteins in dynamic equilibrium. Nature 468 ,
1046-1048 (2010)
2. Hvidt, A., Nielsen, S.O.: Hydrogen exchange in proteins. Adv. Protein. Chem. 21 ,

287-386 (1966)
3. Linderstrom-Lang, K.U.: Deuterium exchange and protein structure. Methuen, London 1958
4. Englander, S.W., Kallenbach, N.R.: Hydrogen exchange and structural dynamics of proteins
and nucleic acids. Q Rev. Biophys. 16 , 521-655 (1983)
5. Ishima, R., Torchia, D.A.: Protein dynamics from NMR. Nat. Struct. Biol. 7 , 740-743 (2000)
6. Karplus, M., McCammon, J.A.: Molecular dynamics simulations of biomolecules. Nat. Struct.
Biol. 9 , 646-652 (2002)