scholarly journals Incorporating Knowledge of Secondary Structures in a L-System-Based Encoding for Protein Folding

2006 ◽  
pp. 247-258 ◽  
Author(s):  
Gabriela Ochoa ◽  
Gabi Escuela ◽  
Natalio Krasnogor
Keyword(s):  
Protein Folding ◽  
Secondary Structures ◽  
L System

Protein folding intermediates with rapidly exchangeable amide protons contain authentic hydrogen-bonded secondary structures

Biochemistry ◽  
1995 ◽  
Vol 34 (9) ◽  
pp. 2998-3008 ◽  
Author(s):  
J. Inaki Guijarro ◽  
Michael Jackson ◽  
Alain F. Chaffotte ◽  
Muriel Delepierre ◽  
Henry H. Mantsch ◽  
...  
Keyword(s):  
Protein Folding ◽  
Secondary Structures ◽  
Folding Intermediates ◽  
Amide Protons ◽  
Hydrogen Bonded

scholarly journals Statistical Evidence for a Helical Nascent Chain

Biomolecules ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 357
Author(s):  
Leonor Cruzeiro ◽  
Andrew C. Gill ◽  
J. Chris Eilbeck
Keyword(s):  
Amino Acids ◽  
Protein Folding ◽  
Amino Acid ◽  
Secondary Structures ◽  
Initial Structure ◽  
The Novel ◽  
Nascent Chain ◽  
Equilibrium Process ◽  
Β Sheets ◽  
Α Helix

We investigate the hypothesis that protein folding is a kinetic, non-equilibrium process, in which the structure of the nascent chain is crucial. We compare actual amino acid frequencies in loops, α-helices and β-sheets with the frequencies that would arise in the absence of any amino acid bias for those secondary structures. The novel analysis suggests that while specific amino acids exist to drive the formation of loops and sheets, none stand out as drivers for α-helices. This favours the idea that the α-helix is the initial structure of most proteins before the folding process begins.

scholarly journals An Alternative Approach to Protein Folding

2013 ◽  
Vol 2013 ◽  
pp. 1-10
Author(s):  
Yeona Kang ◽  
Charles M. Fortmann
Keyword(s):  
Protein Folding ◽  
Ab Initio ◽  
Diffusion Model ◽  
Diffusion Theory ◽  
Secondary Structures ◽  
Drift Diffusion Model ◽  
Drift Diffusion ◽  
Desktop Computer ◽  
Tertiary Structures ◽  
Protein Secondary Structures

A diffusion theory-based, all-physicalab initioprotein folding simulation is described and applied. The model is based upon the drift and diffusion of protein substructures relative to one another in the multiple energy fields present. Without templates or statistical inputs, the simulations were run at physiologic and ambient temperatures (including pH). Around 100 protein secondary structures were surveyed, and twenty tertiary structures were determined. Greater than 70% of the secondary core structures with over 80% alpha helices were correctly identified on protein ranging from 30 to 200 amino-acid sequence. The drift-diffusion model predicted tertiary structures with RMSD values in the 3–5 Angstroms range for proteins ranging 30 to 150 amino acids. These predictions are among the best for an allab initioprotein simulation. Simulations could be run entirely on a desktop computer in minutes; however, more accurate tertiary structures were obtained using molecular dynamic energy relaxation. The drift-diffusion model generated realistic energy versus time traces. Rapid secondary structures followed by a slow compacting towards lower energy tertiary structures occurred after an initial incubation period in agreement with observations.

scholarly journals A multifunnel energy landscape encodes the competing α-helix and β-hairpin conformations for a designed peptide

2020 ◽  
Vol 22 (3) ◽  
pp. 1359-1370 ◽  
Author(s):  
Debayan Chakraborty ◽  
Yassmine Chebaro ◽  
David J. Wales
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Energy Landscape ◽  
Secondary Structures ◽  
Free Energy Landscape ◽  
Conformational Switching ◽  
Α Helix

The propensities to form different secondary structures are encoded in the multifunnel nature of the underlying free energy landscape, and conformational switching between such structures is a key element of protein folding and aggregation.

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