scholarly journals A hybrid, bottom-up, structurally accurate, Go¯-like coarse-grained protein model

2019 ◽  
Vol 151 (4) ◽  
pp. 044111 ◽  
Author(s):  
Tanmoy Sanyal ◽  
Jeetain Mittal ◽  
M. Scott Shell
Keyword(s):  
Coarse Grained ◽  
Bottom Up ◽  
Protein Model

scholarly journals Temperature and Phase Transferable Bottom-up Coarse-Grained Models

2020 ◽  
Vol 16 (11) ◽  
pp. 6823-6842 ◽  
Author(s):  
Jaehyeok Jin ◽  
Alvin Yu ◽  
Gregory A. Voth
Keyword(s):  
Coarse Grained ◽  
Bottom Up

Coarse-grained protein model, cooperativity of folding and subdomain structure

2006 ◽  
Vol 422 (4-6) ◽  
pp. 429-433 ◽  
Author(s):  
Hiroo Kenzaki ◽  
Macoto Kikuchi
Keyword(s):  
Coarse Grained ◽  
Protein Model

scholarly journals A Coarse-Grained Protein Model in a Water-like Solvent

2013 ◽  
Vol 3 (1) ◽  
Author(s):  
Sumit Sharma ◽  
Sanat K. Kumar ◽  
Sergey V. Buldyrev ◽  
Pablo G. Debenedetti ◽  
Peter J. Rossky ◽  
...  
Keyword(s):  
Coarse Grained ◽  
Protein Model

Self-Assembly of the β2-Microglobulin NHVTLSQ Peptide Using a Coarse-Grained Protein Model Reveals a β-Barrel Species

2008 ◽  
Vol 112 (14) ◽  
pp. 4410-4418 ◽  
Author(s):  
Wei Song ◽  
Guanghong Wei ◽  
Normand Mousseau ◽  
Philippe Derreumaux
Keyword(s):  
Self Assembly ◽  
Coarse Grained ◽  
Β2 Microglobulin ◽  
Protein Model

scholarly journals Quantitative Prediction of pH-Controlled Ionization of Oligopeptides

2020 ◽  
Author(s):  
Raju Lunkad ◽  
Anastasiia Murmiliuk ◽  
Pascal Hebbeker ◽  
Milan Boublík ◽  
Zdeněk Tošner ◽  
...  
Keyword(s):  
Electrostatic Interactions ◽  
Weak Acid ◽  
Coarse Grained ◽  
Quantitative Prediction ◽  
Bottom Up ◽  
Coarse Grained Model ◽  
Flexible Polymer ◽  
Acid And Base ◽  
Base Side ◽  
Capillary Zone

Weak ampholytes are ubiquitous in nature and commonly found in artificial pH-responsive systems. However, our limited understanding of their ionisation response and the lack of predictive capabilities hinder the bottom-up design of such systems. Here, we used a coarse-grained model of a flexible polymer with weakly ionisable monomer units to quantitatively analyse the ionisation behaviour of two oligopeptides. Differences in ionisation response between oligopeptides and monomeric amino acids showed that electrostatic interactions between weak acid and base side chains play a key role in oligopeptide ionisation, as predicted by our model. Moreover, by comparing our simulations with experimental results from potentiometric titration, capillary zone electrophoresis and NMR, we demonstrated that our model reliably predicts the ionisation response and electrophoretic mobilities of various peptide sequences. Ultimately, our model is the first step towards using predictive bottom-up design of responsive ampholytes to tailor their properties as a function of charge and pH.<br>

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