Abstract:
:The functional properties of proteins are decided not only by their relatively rigid overall structures, but even more importantly, by their dynamic properties. In a protein, some regions of structure exhibit highly correlated or anti-correlated motions with others, some are highly dynamic but uncorrelated, while other regions are relatively static. The residues with correlated or anti-correlated motions can form a so-called dynamic cross-correlation network, through which information can be transmitted. Such networks have been shown to be critical to allosteric transitions, and ligand binding, and have also been shown to be able to mediate epistatic interactions between mutations. As a result, they are likely to play a significant role in the development of new enzyme engineering strategies. In this chapter, protocols are provided for the assessment of dynamic cross-correlation networks, and for their application in protein engineering. Transketolase from E. coli is used as a model and the software GROMACS is applied for carrying out MD simulations to generate trajectories containing structural ensembles. The trajectory is then used for a dynamic cross correlation analysis using the R package, Bio3D. A matrix of all atom-wise cross-correlation coefficients is finally obtained, which can be displayed in a graphical representation termed a dynamical cross-correlation matrix.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Yu H,Dalby PAdoi
10.1016/bs.mie.2020.04.020subject
Has Abstractpub_date
2020-01-01 00:00:00pages
15-49eissn
0076-6879issn
1557-7988pii
S0076-6879(20)30148-8journal_volume
643pub_type
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