Allosteric transitions of supramolecular systems explored by network models: application to chaperonin GroEL.
Identification of pathways involved in the structural transitions of biomolecular systems is often complicated by the transient nature of the conformations visited across energy barriers and the multiplicity of paths accessible in the multidimensional energy landscape. This task becomes even more challenging in exploring molecular systems on the order of megadaltons. Coarse-grained models that lend themselves to analytical solutions appear to be the only possible means of approaching such cases. Motivated by the utility of elastic network models for describing the collective dynamics of biomolecular systems and by the growing theoretical and experimental evidence in support of the intrinsic accessibility of functional substates, we introduce a new method, adaptive anisotropic network model (aANM), for exploring functional transitions. Application to bacterial chaperonin GroEL and comparisons with experimental data, results from action minimization algorithm, and previous simulations support the utility of aANM as a computationally efficient, yet physically plausible, tool for unraveling potential transition pathways sampled by large complexes/assemblies. An important outcome is the assessment of the critical inter-residue interactions formed/broken near the transition state(s), most of which involve conserved residues.
Yang
Zheng
Z
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.
Májek
Peter
P
Bahar
Ivet
I
D018834:Chaperonin 60 / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D007536:Isomerism; D008956:Models, Chemical; D008958:Models, Molecular; D046912:Multiprotein Complexes / Q000737:chemistry / Q000648:ultrastructure; D011487:Protein Conformation
D018834:Chaperonin 60; D046912:Multiprotein Complexes