Essential domain motions in barnase revealed by MD simulations

Abstract

The wealth of data accumulated on the bacterial ribonuclease barnase is complemented by molecular dynamics trajectories starting from four different experimental structures and covering a total of >10 ns. Using principal component analysis, the simulations are interpreted in view of dynamic domains and hinges promoting relative motions of these domains. Two domains with residues 7-22 and 52-108 for the first domain and residues 25-51 for the second domain were consistently observed. Hinge regions consist primarily of Tyr24, Ser50, Ile51, and Gly52. Earlier mutation studies have demonstrated that the residues of the hinge regions play essential roles for the stability and activity of barnase. The domain motions are correlated to inter-domain interactions involving functionally important active site residues, such as Lys27 and Glu73. A model is presented that combines the observation of dynamic domains and their motions with the extensive mutation data from the literature. Enthalpic energy contributions originating from specific inter-domain interactions as well as entropic energy contributions due to the domain motions are discussed in the frame of this model and compared with destabilization energies measured for corresponding mutants.

An Online Approach for Mining Collective Behaviors from Molecular Dynamics Simulations

“…It is also important to note that many of the structures had the protein's substrate bound to it, hence small differences are visible in terms of the location of flexible regions; note that residues 71-81 are more flexible from our simulations. We were able to compare our results with previously published work based on Gaussian Network Model (GNM) [9], MD simulations and NMR experiments [37,48]. As illustrated in Fig.…”

“…The residues 21-48 exhibited different dynamical properties compared to the rest of the protein and hence this region was clustered into a separate region via DTA. Previous experimental work [37,48] also indicates that these residues are indeed dynamically distinct unit, forming a separate domain.…”

“…The maximally constrained residues namely Tyr24, Ala32, Gly52, Gly53, Arg87 and Thr103 are known to be important for barnase's folding with Ala30 being a nucleation site [19]. Similarly, Gly52 and Gly53 form a hinge-site of the protein, implicated in the stabilization of the protein's motions [37]. It is also interesting to note that the catalytically important residue Glu71 is also constrained [20,21], however Lys25 is not constrained to the extent of the residues that are implicated in protein folding or the functional hinge-site.…”

“…In another window (215), loop L1 had moved with respect to α1 helix compared to the predecessor window (214), illustrated in 6(b) (bottom). The collective displacement of these loops with respect to residues 21-48 is of importance since they represent inter-domain movements [37].…”

Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction

“…Clearly, if the manifold of interest is inherently nonlinear, the low-dimensional embedding obtained by means of PCA is severely distorted. PCA is commonly used in the analysis of near-equilibrium fluctuations sampled by molecular dynamics simulations (29)(30)(31)(32)(33)(34)(35)(36), because one can usually assume that the manifold of interest can be reasonably approximated by its tangent hyperplane around an equilibrium point. However, the extent of conformational changes involved in a folding process prohibits any a priori linearization of the manifold, and nonlinear techniques need to be used.…”