Computer-Aided Drug Design by Unknown

Author:Unknown
Language: eng
Format: epub
ISBN: 9789811568152
Publisher: Springer Singapore

7.7.2 RMSF

The root mean square fluctuation (RMSF) is the best way to study the residue-wise fluctuation of the protein from the MD trajectory. It describes the fluctuation of each residue or domain in a protein. The RMSF can be plotted as RMSF (nm) vs. residue number (Kuzmanic and Zagrovic 2010). The RMSF of a protein is measured by the deviation between the position of particle i with its reference position, and T represents the time, and riref is the reference position of particle i.

Well organized and rigid structures, like helix and sheets, show low RMSF, while loosely structure like bends and coils showed higher RMSF value because atom can have more fluctuation in the bends and coils as compared to helix and sheet. RMSF of the Cα atoms for native and mutant MtbICL was calculated from the MD trajectory to compare the residue-wise fluctuations (Fig. 7.6b). A high degree of residue-wise fluctuations observed in mutant MtbICL as compared to the native structure, and this happens due to a single mutation L148A, which causes more fluctuations and instability in the mutant. This mutation can also deform the shape of the binding site and which in turn can prevent the function of the enzyme (Shukla et al. 2018c).

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