Protein unfolding simulations

Finkelslain A V 1997. Can Protein Unfolding Simulate Protein Folding Protein Engineering 10 843... 

R. Walser, A. E. Mark, and W. F. van Gunsteren, Biophys. J., 78, 2752 (2000). On the Temperature and Pressure Dependence of a Range of Properties of a Type of Water Model Commonly Used in High-Temperature Protein Unfolding Simulations. 

To facilitate conformational transitions in the before-mentioned adenylate kinase, Elamrani and co-workers scaled all atomic masses by a large factor thus allowing the use of a high effective simulation temperature of 2000K ([Elamrani et al. 1996]). To prevent protein unfolding, elements of secondary structure had to be constrained. 

Alonso D O V and V Daggett 1995. Molecular Dynamics Simulations of Protein Unfolding and Limited Refolding Characterisation of Partially Unfolded States of Ubiquitm in 60% Methanol and in Water. Journal of Molecular Biology 247 501-520. 

Daggett, V. (2002). Molecular dynamics simulations of the protein unfolding/folding reaction. Acc. Chem. Res. 35, 422-429. Available at http //pubs.acs.org. 

B. Chowdhry, S. Leharne. Simulation andAnalysis of Differential Scanning Calorimetry Output Protein Unfolding Studies 1. J. Chem. Educ. 1997, 74, 236-241. 

All-atom Simulations of Protein Unfolding and Short Peptide Folding... 

Lazaridis T. and Karplus M. New view of protein folding reconciled with the old through multiple unfolding simulations. Science (1997) 278(N5345) 1928-1931. 

Alonso D. O. V. and Daggett V. Molecular dynamics simulations of protein unfolding and limited refolding characterization of partially unfolded states of ubiquitin in 60 % methanol and in water. J. Mol. Biol. (1995) 247 501-520. 

Daggett, V., Validation of protein-unfolding transition states identified in molecular dynamics simulations. Biochem Soc Symp, 2001(68) 83-93. 

Simulation and Analysis of Differential Scanning Calorimetry Output Protein Unfolding Studies 1 87... 

We carried out two series of unfolding MD simulations, one for the authentic form and the other for the recombinant form of goat a-lactalbumin at 398 K. The unfolding simulations reasonably reproduced the experimentally observed difference between the proteins, i.e., the faster rate of unfolding of the recombinant protein. 

Brooks, C. L. Molecular simulations of peptide and protein unfolding in quest of a molten globule Curr. Op. Struc. Biol. 1993 3, 92-98. 

Fig. 2. Simulated DSC endotherm, (bold line), for a monomeric protein unfolding reversibly via a two-state transition (Jm = 60°, A/f° = 50 kcal/mol, A//cal/Aff = 1.0). The sigmoidal heat capacity baseline, (dashed line), shifts from the native to unfolded due to a ACp of 750 cal/...

---