Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
Explore this paper's citation graph
Summary
The folding mechanism of a three-helix bundle protein is studied at atomic resolution, including effects of explicit water, and the kinetic bottlenecks for folding can be determined from the thermal ensembles of structures on the free energy barriers, provided the kinetically determined transition-state ensembled are similar to those determined fromfree energy barriers.
- Type
- article
- Published
- 2003-11-17
- Cited by
- 308
- References
- 48
- Access
- Open access
- OpenAlex
- https://openalex.org/W1970900907
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:8494848
Keywords
Protein folding, Chemical physics, Folding funnel, Downhill folding, Contact order
References
- Folding dynamics and mechanism of β-hairpin formation
- Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.
- Fast events in protein folding: helix melting and formation in a small peptide.
- An information theory model of hydrophobic interactions.
- Protein folding funnels: a kinetic approach to the sequence-structure relationship.
- High populations of non-native structures in the denatured state are compatible with the formation of the native folded state.
- Characterization of the folding kinetics of a three-helix bundle protein via a minimalist Langevin model.
- A SYNTHETIC RETROTRANSITION (BACKWARD READING) SEQUENCE OF THE RIGHT-HANDED THREE-HELIX BUNDLE DOMAIN (10-53) OF PROTEIN A SHOWS SIMILARITY IN CONFOMA TION AS PREDICTED BY COMPUTATION
- Staphylococcal protein A: unfolding pathways, unfolded states, and differences between the B and E domains.
- Probing the folding free energy landscape of the src-SH3 protein domain
- Exploring the folding free energy surface of a three-helix bundle protein.
- Folding of a small helical protein using hydrogen bonds and hydrophobicity forces
- Absolute comparison of simulated and experimental protein-folding dynamics
- Mapping the transition state and pathway of protein folding by protein engineering
- α-Helical stabilization by side chain shielding of backbone hydrogen bonds
- The complete folding pathway of a protein from nanoseconds to microseconds
- New perspectives on hydrophobic effects
- Molecular dynamics with coupling to an external bath
- Characterisation of the transition states for protein folding: towards a new level of mechanistic detail in protein engineering analysis.
- Measuring the rate of intramolecular contact formation in polypeptides.
Cited by
- Atomic Simulations of Protein Folding, Using the Replica Exchange Algorithm
- Designing generalized statistical ensembles for numerical simulations of biopolymers.
- Ensuring Mixing Efficiency of Replica-Exchange Molecular Dynamics Simulations.
- Computational study of DNA in non-canonical environment
- Computational methods for studying serpin conformational change and structural plasticity.
- Boundary value approaches to molecular dynamics simulation
- Peptide Microarrays: Methods and Protocols
- Caractérisation et modélisation de structures nucléiques auto-assemblées fonctionnalisables
- Reviews in Computational Chemistry, Volume 32
- All-atom protein folding with free-energy forcefields.
- From Solution into Vacuum - Structural Transitions in Proteins
- Hydration water dynamics of the tau protein in its native and amyloid states. (Dynamique de l'eau d'hydratation de la protéine tau dans des formes native et amyloïde)
- Challenges in protein folding simulations: Timescale, representation, and analysis
- Influence of temperature, friction, and random forces on folding of the B‐domain of staphylococcal protein A: All‐atom molecular dynamics in implicit solvent
- Mean Force Simulation of the Adsorption of Aqueous Dilute Solutions
- Multiple replica repulsion technique for efficient conformational sampling of biological systems.
- A test of implicit solvent models on the folding simulation of the GB1 peptide.
- Correction to the article “Study of the Villin Headpiece folding dynamics by combining coarse‐grained Monte Carlo evolution and all‐atom molecular dynamics”
- Three-body interactions improve the prediction of rate and mechanism in protein folding models.
- Conformational flexibility of soluble cellulose oligomers: chain length and temperature dependence.
Related papers
- Unification of the folding mechanisms of non-two-state and two-state proteins.
- Unification of the Folding Mechanisms of Non-two-state and Two-state Proteins
- Energy barriers, cooperativity, and hidden intermediates in the folding of small proteins.
- The “Beacon” Structural Model of Protein Folding: Application for Trp-Cage in Water
- The energy landscape of a fast-folding protein mapped by Ala→Gly Substitutions
- Local interactions and the optimization of protein folding
- Trp Cage Folding in Confinement
- Temperature dependence of the free energy landscape of the src‐SH3 protein domain
- On the role of conformational geometry in protein folding
- Folding of the four-helix bundle FF domain from a compact on-pathway intermediate state is governed predominantly by water motion