Abstract
Normal mode analysis (NMA) in internal (dihedral) coordinates naturally reproduces the collective functional motions of biological macromolecules. iMODS facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules. The distinctive internal coordinate formulation improves the efficiency of NMA and extends its applicability while implicitly maintaining stereochemistry. Vibrational analysis, motion animations and morphing trajectories can be easily carried out at different resolution scales almost interactively. The server is versatile; non-specialists can rapidly characterize potential conformational changes, whereas advanced users can customize the model resolution with multiple coarse-grained atomic representations and elastic network potentials. iMODS supports advanced visualization capabilities for illustrating collective motions, including an improved affine-model-based arrow representation of domain dynamics. The generated all-heavy-atoms conformations can be used to introduce flexibility for more advanced modeling or sampling strategies. The server is free and open to all users with no login requirement at http://imods.chaconlab.org.
Highlights
The main functions of living cells are usually governed by large macromolecular complexes
Normal mode analysis (NMA) in internal coordinates naturally reproduces the collective functional motions of biological macromolecules. iMod server (iMODS) facilitates the exploration of such modes and generates feasible transition pathways between two homologous structures, even with large macromolecules
We have shown how approaches based on Cartesian NMA can accumulate important geometrical distortions when used for the flexible fitting of atomic structures into electron microscopy maps [11]
Summary
The main functions of living cells (replication, transcription, translation, folding and protein turnover) are usually governed by large macromolecular complexes (polymerases, ribosomes, chaperonins and proteasomes). Normal mode analysis (NMA) is a popular approach for describing the collective functional motions of such macromolecules [1,2,3]. NMA in Cartesian coordinates has been used for many years in online modeling of protein flexibility. NMA in dihedral space is a more natural and effective approach than the Cartesian formulation for modeling macromolecular conformational changes. The method has been improved, including the implementation of a faster eigenproblem solver [13] This improvement permitted the computation of the lowest-frequency modes almost interactively for standard-size systems while extending the application range to large macromolecules. The iMod server (iMODS) provides a user-friendly interface for this enhanced NMA methodology in internal coordinates. The generated conformations and pathways can be downloaded and used as inputs in more sophisticated sampling or modeling techniques
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