ArticleThe journal of physical chemistry. B2016
Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on α-Helix Folding.
Article in The journal of physical chemistry. B, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Estimation of binding rates and affinities from multiensemble Markov models and ligand decoupling.The Journal of chemical physics · 2022Article
- Unprotected peptide macrocyclization and stapling via a fluorine-thiol displacement reaction.Nature communications · 2022Article
- Molecular dynamics simulations of an engineered T4 lysozyme exclude helix to sheet transition, and provide insights into long distance, intra-protein switchable motion.Protein science : a publication of the Protein Society · 2020Article
- Exposing the Nucleation Site in α-Helix Folding: A Joint Experimental and Simulation Study.The journal of physical chemistry. B · 2019Article
- Mechanisms of Lipid Scrambling by the G Protein-Coupled Receptor Opsin.Structure (London, England : 1993) · 2018Article
- Bridging Microscopic and Macroscopic Mechanisms of p53-MDM2 Binding with Kinetic Network Models.Biophysical journal · 2017Article
- A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter.Scientific reports · 2017Article
- Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking.Scientific reports · 2016Article
- Conformational Heterogeneity in the Michaelis Complex of Lactate Dehydrogenase: An Analysis of Vibrational Spectroscopy Using Markov and Hidden Markov Models.The journal of physical chemistry. B · 2016Article
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Authors and funding
2 authors.
Funding
Abstract
Salt-bridge interactions play an important role in stabilizing many protein structures, and have been shown to be designable features for protein design. In this work, we study the effects of non-native salt bridges on the folding of a soluble alanine-based peptide (Fs peptide) using extensive all-atom molecular dynamics simulations performed on the Folding@home distributed computing platform. Using Markov State Models, we show how non-native salt-bridges affect the folding kinetics of Fs peptide by perturbing specific conformational states. Furthermore, we present methods for the automatic detection and analysis of such states. These results provide insight into helix folding mechanisms and useful information to guide simulation-based computational protein design.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.