Conformational dynamics of supramolecular protein assemblies

Abstract

Supramolecular protein assemblies including molecular motors, cytoskeletal filaments, chaperones, and ribosomes play a central role in a broad array of cellular functions ranging from cell division and motility to RNA and protein synthesis and folding. Single-particle reconstructions of such assemblies have been growing rapidly in recent years, providing increasingly high resolution structural information under native conditions. While the static structure of these assemblies provides essential insight into their mechanism of biological function, their dynamical motions provide additional important information that cannot be inferred from structure alone. Here we present an unsupervised computational framework for the analysis of high molecular weight assemblies and use it to analyze the conformational dynamics of structures deposited in the Electron Microscopy Data Bank. Protein assemblies are modeled using a recently introduced coarse-grained modeling framework based on the finite element method, which is used to compute equilibrium thermal fluctuations, elastic strain energy distributions associated with specific conformational transitions, and dynamical correlations in distant molecular domains. Results are presented in detail for the ribosome-bound termination factor RF2 from Escherichia coli, the nuclear pore complex from Dictyostelium discoideum, and the chaperonin GroEL from E. coli. Elastic strain energy distributions reveal hinge-regions associated with specific conformational change pathways, and correlations in collective molecular motions reveal dynamical coupling between distant molecular domains that suggest new, as well as confirm existing, allosteric mechanisms. Results are publically available for use in further investigation and interpretation of biological function including cooperative transitions, allosteric communication, and molecular mechanics, as well as in further classification and refinement of electron microscopy based structures.

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures

“…The final solution shape is computed iteratively using the commercial finite element software program ADINA (Automatic Dynamic Incremental Non-linear Analysis, ADINA R&D Inc., Watertown, MA, USA) using a geometrically non-linear finite element formulation to reach mechanical equilibrium. Normal mode analysis (15,16) is performed at this mechanical free energy minimum to compute the mechanical flexibility of the folded structure. Root-mean-square fluctuations of basepairs are computed at 298 K for the final solution shape using 200 lowest normal modes and the equipartition theorem of statistical thermodynamics (17).…”

Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps

“…Normal mode analysis on coarse grain representation of cryo-EM maps have been used previously to decipher functionally relevant conformational changes. 61,62 NMA results suggested that regions corresponding to proteins SF3b130 (mode 1), SF3b14b (mode 3) and p14 (mode 4) are highly flexible ( Fig. 2A).…”

Modeling of the mechano-chemical behaviour of the nuclear pore complex: current research and perspectives

“…For example, how the mechanical strains that are transmitted to the NPC regulate pore activation, and thus the translocation of molecules? Several studies have started to look into these mechanisms, 15,79 however there is still a long way to go before gaining a full understanding of this complex correlation. The mechanics of the NPC and its specific response to the deformation of the NE, due to the cell's mechanosensitive loop, may be key to understanding a plethora of vital processes such as cell remodeling, proliferation, mechanotransduction and cell adaptation.…”

“…Modal analysis simulations are useful when searching for more mechanically favorable modes of the deformation of complex protein structures, which have direct implications on selective cargo translocation. 75,79 An agent-based model was also proposed in ref. 80 and 81 to analyze nucleocytoplasmic molecular diffusion through the NPC.…”