Chapter 8. Computer Simulations of Protein Folding

2008 ◽  
pp. 161-187 ◽  
Author(s):  
Vijay S. Pande ◽  
Eric J. Sorin ◽  
Christopher D. Snow ◽  
Young Min Rhee
Keyword(s):  
Protein Folding ◽  
Computer Simulations

Bridging the Gap Between Optical Spectroscopic Experiments and Computer Simulations for Fast Protein Folding Dynamics

2012 ◽  
Vol 2 (1) ◽  
pp. 45-58 ◽  
Author(s):  
Raymond Z. Cui ◽  
Daniel-Adriano Silva ◽  
Jian Song ◽  
Gregory R. Bowman ◽  
Wei Zhuang ◽  
...  
Keyword(s):  
Protein Folding ◽  
Computer Simulations ◽  
Folding Dynamics

Computer Simulations of Protein Folding

2012 ◽  
Vol 14 (2) ◽  
pp. 97-103 ◽  
Author(s):  
Leili Javidpour
Keyword(s):  
Protein Folding ◽  
Computer Simulations

scholarly journals Computer Simulations of Alzheimers Amyloid β-Protein Folding and Assembly

2006 ◽  
Vol 3 (5) ◽  
pp. 493-504 ◽  
Author(s):  
Brigita Urbanc ◽  
Luis Cruz ◽  
David Teplow ◽  
H. Eugene Stanley
Keyword(s):  
Protein Folding ◽  
Computer Simulations ◽  
Protein Folding And Assembly

Bridging the Gap Between Optical Spectroscopic Experiments and Computer Simulations for Fast Protein Folding Dynamics

2012 ◽  
Vol 2 (1) ◽  
pp. 45-58 ◽  
Author(s):  
Raymond Z. Cui ◽  
Daniel-Adriano Silva ◽  
Jian Song ◽  
Gregory R. Bowman ◽  
Wei Zhuang ◽  
...  
Keyword(s):  
Protein Folding ◽  
Computer Simulations ◽  
Folding Dynamics

scholarly journals Topological descriptions of protein folding

2019 ◽  
Vol 116 (19) ◽  
pp. 9360-9369 ◽  
Author(s):  
Erica Flapan ◽  
Adam He ◽  
Helen Wong
Keyword(s):  
Protein Folding ◽  
Crystal Structures ◽  
Computer Simulations ◽  
Haloacid Dehalogenase ◽  
Topological Description ◽  
The Future ◽  
Experimental Approaches ◽  
Knotted Proteins ◽  
Plos Comput Biol ◽  
Fingerprint Data

How knotted proteins fold has remained controversial since the identification of deeply knotted proteins nearly two decades ago. Both computational and experimental approaches have been used to investigate protein knot formation. Motivated by the computer simulations of Bölinger et al. [Bölinger D, et al. (2010) PLoS Comput Biol 6:e1000731] for the folding of the 61-knotted α-haloacid dehalogenase (DehI) protein, we introduce a topological description of knot folding that could describe pathways for the formation of all currently known protein knot types and predicts knot types that might be identified in the future. We analyze fingerprint data from crystal structures of protein knots as evidence that particular protein knots may fold according to specific pathways from our theory. Our results confirm Taylor’s twisted hairpin theory of knot folding for the 31-knotted proteins and the 41-knotted ketol-acid reductoisomerases and present alternative folding mechanisms for the 41-knotted phytochromes and the 52- and 61-knotted proteins.

PROTEIN FOLDING STAGES AND UNIVERSAL EXPONENTS

2010 ◽  
Vol 24 (20) ◽  
pp. 2113-2115 ◽  
Author(s):  
KERSON HUANG
Keyword(s):  
Protein Folding ◽  
Hydrogen Bonding ◽  
Computer Simulations ◽  
Power Law ◽  
Molten Globule ◽  
Hydrophobic Effect ◽  
Radius Of Gyration ◽  
Three Stages ◽  
Self Avoiding Walk

We propose three stages in protein folding, based on physical arguements involving the interplay between the hydrophobic effect and hydrogen bonding, and computer simulations using the CSAW (conditioned self-avoiding walk) model. These stages are characterized by universal exponents ν = 3/5, 3/7, 2/5 in the power law R ~ Nν, where R is the radius of gyration and N is the number of residues. They correspond to the experimentally observed stages: unfolded, preglobule, molten globule.

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