Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet.

By Eugene I. Shakhnovich. 2006

345 citations recorded by the source corpus.

Subfields: Molecular Biology

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In Molecular Biology

1. Jinbo Xu
2. Yang Zhang
3. Sheng Wang
4. Michael Feig
5. Andrej Sali
6. Feng Zhao
7. Min-Yi Shen
8. Jianlin Cheng

Citations in the corpus

• A position-specific distance-dependent statistical potential for protein structure and functional study (2012, background): “, 1997; Sippl, 1990; Tanaka and Scheraga, 1976; Zhang and Zhang, 2010; Zhou and Zhou, 2002) compare favorably to physics-based potentials (Brooks et al., 2009; Bryngelson et al., 1995; Case et al., 2005; Dill, 1985, 1997; Dobson et al., 1998; Schuler et al., 2001; Shakhnovich, 2006) in many applicat”
• All-atom ab initio folding of a diverse set of proteins. (2006, background): “This is an important conclusion which is consistent with basic theoretical understanding that diversity of intramolecular and solvent interactions is necessary to provide energy gaps that enable a polypeptide chain to be stable in native conformation (Shakhnovich, 2006).”
• Computational protein structure refinement: Almost there, yet still so far to go (2017, background): “10,11 14 While much has been learned at the fundamental level about protein structures and the folding process, 13 pure ab initio methods that do not use any information from known structures largely fail to accurately and reliably predict the structures of all but very small proteins.”
• Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations (2011, background): “Statistical mechanics of two-state protein folding (21, 22) would predict the relationship between protein stability and intracellular abundance of folded proteins to follow the Boltzmann law:”
• Statistical potential for assessment and prediction of protein structures (2006, background): “Therefore, an accurate free energy function would enable the is to also prediction and assessment of protein structures (Dill 1985, 1997; Bryngelson et al. 1995; Dobson et al. 1998; Shakhnovich 2006).”
• How a protein searches for its site on DNA: the mechanism of facilitated diffusion (2009, background): “The speed-stability paradox in protein folding is resolved by designing sequences that have a pronounced energy gap between the native folded conformation and the bulk of unfolded ones [35, 36].”