Abstract
We present results from all-atom, fully unrestrained ab initio folding simulations for a stable protein with nontrivial secondary structure elements and a hydrophobic core. The construct, "trpcage", is a 20-residue sequence optimized by the Andersen group at University of Washington and is currently the smallest protein that displays two-state folding properties. Compared over the well-defined regions of the experimental structure, our prediction has a remarkably low 0.97 A Calpha root-mean-square-deviation (rmsd) and 1.4 A for all heavy atoms. The simulated structure family displays additional features that are suggested by experimental data, yet are not evident in the family of NMR-derived structures.
Keywords
ChemistryFolding (DSP implementation)Protein foldingAtom (system on chip)Protein structure predictionComputational chemistryChemical physicsCrystallographyProtein structureBiochemistry
Affiliated Institutions
Related Publications
Protein-Protein Interfaces: Architectures and Interactions in Protein-Protein Interfaces and in Protein Cores. Their Similarities and Differences
Protein structures generally consist of favorable folding motifs formed by specific arrangements of secondary structure elements. Similar architectures can be adopted by differe...
Accurate prediction of protein structures and interactions using a three-track neural network
Deep learning takes on protein folding In 1972, Anfinsen won a Nobel prize for demonstrating a connection between a protein’s amino acid sequence and its three-dimensional struc...
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
Abstract Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accurac...
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ<sub>1</sub> and χ<sub>2</sub> Dihedral Angles
While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the model with respect t...
Protein Folding Requires Crowd Control in a Simulated Cell
Macromolecular crowding has a profound effect upon biochemical processes in the cell. We have computationally studied the effect of crowding upon protein folding for 12 small do...
Publication Info
- Year
- 2002
- Type
- article
- Volume
- 124
- Issue
- 38
- Pages
- 11258-11259
- Citations
- 590
- Access
- Closed
External Links
Social Impact
Altmetric
PlumX Metrics
Social media, news, blog, policy document mentions
Citation Metrics
590
OpenAlex
Cite This
Carlos Simmerling,
Bentley Strockbine,
Adrián E. Roitberg
(2002).
All-Atom Structure Prediction and Folding Simulations of a Stable Protein.
Journal of the American Chemical Society
, 124
(38)
, 11258-11259.
https://doi.org/10.1021/ja0273851
Identifiers
- DOI
- 10.1021/ja0273851