ArticleBioMed research international2013
Dynamic folding pathway models of the Trp-cage protein.
Article in BioMed research international, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Protein Structure-Function Relationship: A Kernel-PCA Approach for Reaction Coordinate Identification.Journal of chemical theory and computation · 2025Article
- Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein.ACS omega · 2023Article
- Unperturbed Detection of the Dynamic Structure in the Hydrophobic Core of Trp-Cage via Two-Dimensional Infrared Spectroscopy.The journal of physical chemistry letters · 2020Article
- Tuning the Attempt Frequency of Protein Folding Dynamics via Transition-State Rigidification: Application to Trp-Cage.The journal of physical chemistry letters · 2015Article
- Folding dynamics and pathways of the trp-cage miniproteins.Biochemistry · 2014Article
- Assessment of local friction in protein folding dynamics using a helix cross-linker.The journal of physical chemistry. B · 2013Article
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Authors and funding
2 authors.
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Abstract
Using action-derived molecular dynamics (ADMD), we study the dynamic folding pathway models of the Trp-cage protein by providing its sequential conformational changes from its initial disordered structure to the final native structure at atomic details. We find that the numbers of native contacts and native hydrogen bonds are highly correlated, implying that the native structure of Trp-cage is achieved through the concurrent formations of native contacts and native hydrogen bonds. In early stage, an unfolded state appears with partially formed native contacts (~40%) and native hydrogen bonds (~30%). Afterward, the folding is initiated by the contact of the side chain of Tyr3 with that of Trp6, together with the formation of the N-terminal α -helix. Then, the C-terminal polyproline structure docks onto the Trp6 and Tyr3 rings, resulting in the formations of the hydrophobic core of Trp-cage and its near-native state. Finally, the slow adjustment processes of the near-native states into the native structure are dominant in later stage. The ADMD results are in agreement with those of the experimental folding studies on Trp-cage and consistent with most of other computational studies.
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