Abstract
Mass-spring models have been a standard approach in molecular modeling for the last few decades, such as elastic network models (ENMs) that are widely used for normal mode analysis. In this work, we present a vastly different elastic solid model (ESM) of macromolecules that shares the same simplicity and efficiency as ENMs in producing the equilibrium dynamics and moreover, offers some significant new features that may greatly benefit the research community. ESM is different from ENM in that it treats macromolecules as elastic solids. Our particular version of ESM presented in this work, named αESM, captures the shape of a given biomolecule most economically using alpha shape, a well-established technique from the computational geometry community. Consequently, it can produce most economical coarse-grained models while faithfully preserving the shape and thus makes normal mode computations and visualization of extremely large complexes more manageable. Secondly, as a solid model, ESM’s close link to finite element analysis renders it ideally suited for studying mechanical responses of macromolecules under external force. Lastly, we show that ESM can be applied also to structures without atomic coordinates such as those from cryo-electron microscopy. The complete MATLAB code of αESM is provided.
Highlights
Great strides have been made in the last few decades in determining the structure and dynamics of macromolecules
elastic solid model (ESM) is different from Elastic network models (ENMs) in that it treats macromolecules as elastic solids
Our particular version of ESM model presented in this work, named αESM, captures the shape of a given biomolecule most economically using alpha shape, a well-established technique from the computational geometry community
Summary
Great strides have been made in the last few decades in determining the structure and dynamics of macromolecules. They are currently over 160,000 structures deposited in the PDB [1] and structures of increasingly larger molecular assemblies are becoming available. The cryoelectron microscopy, as one example, has brought much excitement to the field of structural biology, being able to determine at near-atomic accuracy the structures of extremely large complexes and capture their dynamics through the determination of many conformations. Normal mode analysis in general and elastic network models in particular have been widely used in the last several decades for studying the equilibrium dynamics of macromolecules. For a recent review on elastic network or coarse-grained models of macromolecules, see Refs. Shape, or symmetry to be more precisely, was shown to be the sole determinant of their motion patterns [18]
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