ArticleBiophysical journal2016
Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.
Article in Biophysical journal, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Solvent Environment Influences Molecular Conformation and Electron Transport in Peptides.The journal of physical chemistry letters · 2026Article
- Learning data-efficient coarse-grained molecular dynamics from forces and noise.Nature communications · 2026Article
- Unveiling hidden intermediate states in protein folding with AI-based conditional transition clustering.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Discovering cryptic pocket opening and binding of a stimulant derivative in a vestibular site of the 5-HTScience advances · 2025Article
- Adaptive sampling-based structural prediction reveals opening of a GABAScience advances · 2025Article
- The Arabidopsis AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition.Communications biology · 2024Article
- Analysis of Protein Folding Simulation with Moving Root Mean Square Deviation.Journal of chemical information and modeling · 2023Article
- Role of internal loop dynamics in antibiotic permeability of outer membrane porins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets.Nature communications · 2021Article
- Protein-Folding Analysis Using Features Obtained by Persistent Homology.Biophysical journal · 2020Article
- pH-Induced Local Unfolding of the Phl p 6 Pollen Allergen From cpH-MD.Frontiers in molecular biosciences · 2020Article
- Dynamics Rationalize Proteolytic Susceptibility of the Major Birch Pollen Allergen Bet v 1.Frontiers in molecular biosciences · 2020Article
- Detecting early stage structural changes in wild type, pathogenic and non-pathogenic prion variants using Markov state model.RSC advances · 2019Article
- Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water.Frontiers in chemistry · 2019Article
- Characterizing the Diversity of the CDR-H3 Loop Conformational Ensembles in Relationship to Antibody Binding Properties.Frontiers in immunology · 2018Article
- Optimized parameter selection reveals trends in Markov state models for protein folding.The Journal of chemical physics · 2016Article
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3 authors.
Funding
Abstract
After reanalyzing simulations of NuG2-a designed mutant of protein G-generated by Lindorff-Larsen et al. with time structure-based independent components analysis and Markov state models as well as performing 1.5 ms of additional sampling on Folding@home, we found an intermediate with a register-shift in one of the β-sheets that was visited along a minor folding pathway. The minor folding pathway was initiated by the register-shifted sheet, which is composed of solely nonnative contacts, suggesting that for some peptides, nonnative contacts can lead to productive folding events. To confirm this experimentally, we suggest a mutational strategy for stabilizing the register shift, as well as an infrared experiment that could observe the nonnative folding nucleus.
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