ArticleProceedings of the National Academy of Sciences of the United States of America2014
Equilibrium simulations of proteins using molecular fragment replacement and NMR chemical shifts.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Energy Landscape Analysis of Membrane Proteins Using NMR-Based Hybrid Restraint Potentials.Journal of chemical theory and computation · 2026Article
- Hierarchical Assembly of Single-Stranded RNA.Journal of chemical theory and computation · 2024Article
- Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure.JACS Au · 2022Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
- Combining Experimental Data and Computational Methods for the Non-Computer Specialist.Molecules (Basel, Switzerland) · 2020Review
- Efficient Ensemble Refinement by Reweighting.Journal of chemical theory and computation · 2019Article
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- A Generative Angular Model of Protein Structure Evolution.Molecular biology and evolution · 2017Article
- UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling.Bioinformatics (Oxford, England) · 2016Article
- Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation.Biophysical journal · 2016Article
- Article
- Disordered Regions Flanking Ordered Domains Modulate Signaling Transduction.Biophysical journal · 2015Article
- A robust algorithm for optimizing protein structures with NMR chemical shifts.Journal of biomolecular NMR · 2015Article
- Limitations and extensions of the lock-and-key principle: differences between gas state, solution and solid state structures.International journal of molecular sciences · 2015Review
- Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction.Journal of chemical theory and computation · 2015Article
- Article
- Integrating solid-state NMR and computational modeling to investigate the structure and dynamics of membrane-associated ghrelin.PloS one · 2015Article
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7 authors.
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Abstract
Methods of protein structure determination based on NMR chemical shifts are becoming increasingly common. The most widely used approaches adopt the molecular fragment replacement strategy, in which structural fragments are repeatedly reassembled into different complete conformations in molecular simulations. Although these approaches are effective in generating individual structures consistent with the chemical shift data, they do not enable the sampling of the conformational space of proteins with correct statistical weights. Here, we present a method of molecular fragment replacement that makes it possible to perform equilibrium simulations of proteins, and hence to determine their free energy landscapes. This strategy is based on the encoding of the chemical shift information in a probabilistic model in Markov chain Monte Carlo simulations. First, we demonstrate that with this approach it is possible to fold proteins to their native states starting from extended structures. Second, we show that the method satisfies the detailed balance condition and hence it can be used to carry out an equilibrium sampling from the Boltzmann distribution corresponding to the force field used in the simulations. Third, by comparing the results of simulations carried out with and without chemical shift restraints we describe quantitatively the effects that these restraints have on the free energy landscapes of proteins. Taken together, these results demonstrate that the molecular fragment replacement strategy can be used in combination with chemical shift information to characterize not only the native structures of proteins but also their conformational fluctuations.
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