Chapter 13 Principal Components Analysis: A Review of its Application on Molecular Dynamics Data

A comparative study of structural and conformational properties of casein kinase-1 isoforms: Insights from molecular dynamics and principal component analysis

“…Furthermore, we also conclude that the specific internal motions in the 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 proteins empower them for their biological functions. Such internal motions are responsible for different conformational changes that allow the proteins to bind with their substrates with high specificity (Stein et al, 2006). In order to validate the conformational subspaces during dynamics of CK1 isoforms, we performed potential energy surface (PES) study for each trajectory (Fig.…”

“…Here, we present a comparative study of three isoforms (α, δ and ε) of human CK1 with a particular emphasis on their dynamic etiquette under physiological condition in aqueous medium. Moreover, principal component analysis (PCA) of MD data was performed to reveal the conformational substates sampled during the dynamics of these kinases (Hayward and Go, 1995;Stein et al, 2006;Hayward and de Groot, 2008;Du et al, 2006;Li et al, 2009). Potential energy surfaces (PES), a contour map of potential energy as a function of conformational coordinates, were employed to confirm the conformational substates (Frauenfelder et al, 1991).…”

Probing Protein Folding Dynamics Using Multivariate Statistical Techniques

“…Recent studies explore the energy landscape and the conformational states (Alakent, Doruker et al 2005;Mu, Nguyen et al 2005), identify modes contributing to protein fluctuations in MD simulation of apoadenylate kinase (Lou and Cukier 2006), and extract key mechanistic features from simulations of chemotrypsin inhibitor 2 (Palazoglu, Gursoy et al 2004). One can also refer to a comprehensive review article for further details (Stein, Loccisano et al 2006).…”

Comparative MD analysis of the stability of transthyretin providing insight into the fibrillation mechanism

“…43,44 Particularly, in this case, PCA is used to analyze the large amplitude motions that are difficult to visualize from a lengthy MD trajectory due to frequent small amplitude motions. We have analyzed all of the trajectories in a series of different ways.…”

“…The index of selectivity only includes the a-carbon atoms as we are interested in conformational changes involving the backbone. It has been reported that the choice of index of selectivity has a great influence on PCA 44 and therefore we have performed a scree test (scree plot) to determine how successful the reduction in dimensionality is. The scree plot shows a kink after the third eigenvector (data not shown), which means that the data is highly correlated.…”