A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

2017 ◽  
Vol 19 (21) ◽  
pp. 13629-13639 ◽  
Author(s):  
Jie Hu ◽  
Tao Chen ◽  
Moye Wang ◽  
Hue Sun Chan ◽  
Zhuqing Zhang
Keyword(s):  
Protein Folding ◽  
Force Fields ◽  
Coarse Grained ◽  
Unfolded Proteins ◽  
Critical Comparison ◽  
Atomic Models ◽  
Atomic Force

The predicted dimension of unfolded proteins is quite different using native-centric Gō-like models and transferrable (non-structure-based) models based on current atomic force fields.

scholarly journals Correction: A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding

2017 ◽  
Vol 19 (27) ◽  
pp. 18102-18102
Author(s):  
Jie Hu ◽  
Tao Chen ◽  
Moye Wang ◽  
Hue Sun Chan ◽  
Zhuqing Zhang
Keyword(s):  
Protein Folding ◽  
Chem Phys ◽  
Coarse Grained ◽  
Critical Comparison ◽  
Atomic Models ◽  
Phys Chem Chem Phys

Correction for ‘A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding’ by Jie Hu et al., Phys. Chem. Chem. Phys., 2017, 19, 13629–13639.

Pairwise energies for polypeptide coarse-grained models derived from atomic force fields

2009 ◽  
Vol 130 (19) ◽  
pp. 195103 ◽  
Author(s):  
Marcos R. Betancourt ◽  
Sheyore J. Omovie
Keyword(s):  
Force Fields ◽  
Coarse Grained ◽  
Atomic Force

Transferability of coarse-grained force fields: The polymer case

2008 ◽  
Vol 128 (6) ◽  
pp. 064904 ◽  
Author(s):  
Paola Carbone ◽  
Hossein Ali Karimi Varzaneh ◽  
Xiaoyu Chen ◽  
Florian Müller-Plathe
Keyword(s):  
Force Fields ◽  
Coarse Grained

scholarly journals Protein Folding by Domain V of Escherichia coli 23S rRNA: Specificity of RNA-Protein Interactions

2008 ◽  
Vol 190 (9) ◽  
pp. 3344-3352 ◽  
Author(s):  
Dibyendu Samanta ◽  
Debashis Mukhopadhyay ◽  
Saheli Chowdhury ◽  
Jaydip Ghosh ◽  
Saumen Pal ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Protein Folding ◽  
Carbonic Anhydrase ◽  
Protein Interactions ◽  
23S Rrna ◽  
Unfolded Proteins ◽  
Bovine Carbonic Anhydrase ◽  
Egg White Lysozyme ◽  
General Protein ◽  
Domain V

ABSTRACT The peptidyl transferase center, present in domain V of 23S rRNA of eubacteria and large rRNA of plants and animals, can act as a general protein folding modulator. Here we show that a few specific nucleotides in Escherichia coli domain V RNA bind to unfolded proteins and, as shown previously, bring the trapped proteins to a folding-competent state before releasing them. These nucleotides are the same for the proteins studied so far: bovine carbonic anhydrase, lactate dehydrogenase, malate dehydrogenase, and chicken egg white lysozyme. The amino acids that interact with these nucleotides are also found to be specific in the two cases tested: bovine carbonic anhydrase and lysozyme. They are either neutral or positively charged and are present in random coils on the surface of the crystal structure of both the proteins. In fact, two of these amino acid-nucleotide pairs are identical in the two cases. How these features might help the process of protein folding is discussed.

scholarly journals A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields

2018 ◽  
Vol 39 (28) ◽  
pp. 2360-2370 ◽  
Author(s):  
Adam K. Sieradzan ◽  
Artur Giełdoń ◽  
Yanping Yin ◽  
Yi He ◽  
Harold A. Scheraga ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Force Field ◽  
Force Fields ◽  
Coarse Grained ◽  
Protein Nucleic Acid ◽  
New Protein
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