A mechano-geometric framework to characterize macromolecular ensembles
Final Report Abstract
Macromolecules such as proteins, RNA, and DNA dynamically change their three-dimensional structure to perform their cellular functions. Understanding a molecule’s structural ensemble is crucial for revealing its key roles. While Molecular Dynamics (MD) simulations provide atomically trajectories, their computational cost is often prohibitive. In contrast, kinematic methods inspired by robotics can efficiently and fast model molecular motion, providing useful tools for data interpretation and integration. The objective in this project was to extend our existing kinematic molecular modeling method into a unified, mechano-geometric framework to study conformational ensembles of complex macromolecules. We combined geometric constraints and rigidity theory to study molecular flexibility and imposed a hierarchy of motions, enabling efficient conformation space and energy landscape sampling in an ultra-high-dimensional environment. We also identified allosteric hotspots for drug targeting through changes in dihedral degrees of freedom, steric or hydrophobic contacts, and constraint violations. A further objective was the validation and direct guidance with experimental data to bridge the gap between experimental and computational analysis. First, our method was extended for multi-chain proteins and molecular complexes. It is applied to identify key residues involved in allosteric communication, predicting mutation effects, and finding potential inhibitors. We found that the activation loop rigidified the active state kinases conformation, which is valuable for developing potential inhibitors. Furthermore, our method yields information about rigidified dihedral angles which affect molecular vibrational modes. We applied our method to the SARS CoV-2 main protease (Mpro ) and its mutation to analyze potential drugs. By analyzing 47 mutation sites for more than 3,300 different structures, we found that mutations generally increased the flexibility of Mpro. We also optimized the conformational transition motion planning for ultra-highdimensional conformation. We proposed dynamic Clash Constraints and a randomized Poisson-disk motion planner to address the challenge. Our results agreed with those from MD simulations. Second, for the data integration, we use a combination of techniques to study how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics. By using several methods such as X-ray free electron laser (XFEL), we demonstrate that Gly150 mutations that modify helical mobility decrease ICH catalytic. Additionally, we use site-specific cysteine photo-oxidation to investigate changes in protein structure. We analyzed the role of non-native contacts and identified energy barriers, helping us understand ligand. Our method bridges rigidity theory and elastic network models (ENM), revealing a protein-fold-specific, spatial hierarchy of motions encoded by the hydrogen bonding network and rationalizes experimental and simulated protein stiffness variations.
Publications
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Collision‐free poisson motion planning in ultra high‐dimensional molecular conformation spaces. Journal of Computational Chemistry, 39(12), 711-720.
Fonseca, Rasmus; Budday, Dominik & van, den Bedem Henry
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Kinematic Flexibility Analysis: Hydrogen Bonding Patterns Impart a Spatial Hierarchy of Protein Motion. Journal of Chemical Information and Modeling, 58(10), 2108-2122.
Budday, Dominik; Leyendecker, Sigrid & van, den Bedem Henry
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Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis. Proceedings of the National Academy of Sciences, 116(51), 25634-25640.
Dasgupta, Medhanjali; Budday, Dominik; de Oliveira Saulo, H. P.; Madzelan, Peter; Marchany-Rivera, Darya; Seravalli, Javier; Hayes, Brandon; Sierra, Raymond G.; Boutet, Sébastien; Hunter, Mark S.; Alonso-Mori, Roberto; Batyuk, Alexander; Wierman, Jennifer; Lyubimov, Artem; Brewster, Aaron S.; Sauter, Nicholas K.; Applegate, Gregory A.; Tiwari, Virendra K.; Berkowitz, David B. ... & Wilson, Mark A.
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Shining light on cysteine modification: connecting protein conformational dynamics to catalysis and regulation. Journal of Synchrotron Radiation, 26(4), 958-966.
van den Bedem, Henry & Wilson, Mark A.
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Kinematic Flexibility Analysis of Active and Inactive Kinase Conformations. PAMM, 20(1).
Chen, Xiyu; Leyendecker, Sigrid & van, den Bedem Henry
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Reproducibility of protein x-ray diffuse scattering and potential utility for modeling atomic displacement parameters. Structural Dynamics, 8(4).
Su, Zhen; Dasgupta, Medhanjali; Poitevin, Frédéric; Mathews, Irimpan I.; van den Bedem, Henry; Wall, Michael E.; Yoon, Chun Hong & Wilson, Mark A.
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Kinematic Vibrational Entropy Assessment and Analysis of SARS CoV-2 Main Protease. Journal of Chemical Information and Modeling, 62(11), 2869-2879.
Chen, Xiyu; Leyendecker, Sigrid & van, den Bedem Henry
