Folding pathways simulations

Figure 3. The folding pathway simulated for SVl 1 RNA. (Adapted with permission from reference 45. Copyright 1995 Academic.)...

Bond C ], K-B Wong, ] Clarke, A R Ferscht and V Daggett 1997. Characterisation of Residual Structure in the Tliermally Denatured State of Barnase by Simulation and Experiment Description of the Folding Pathway. Proceedings of the National Academy of Sciences USA 94 13409-13413. 

Godzik A, J Skolnick and A Kolinski 1992. Simulations of the Folding Pathway of Triose Phosj Lsomerase-type a// Barrel Proteins. Proceedings of the National Academy of Sciences USA 89 1 2633. 

Liwo A, Khalili M, Scheraga HA (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc. Natl. Acad. Sci. 

To see if monitoring these variables acmally yields any useful information on the folding pathway, multiple simulated annealing runs with all parameter monitoring facihties implemented were carried out on a family of vitamin D molecules (Figure 4) [23]. The classical biological responses for l,25(OH)2-vitamin D3 are now well established. The vitamin D hormone is known to mediate intestinal calcium absorption and bone calcium metabolism via its receptor. More recently, non-traditional activities have been discovered including cell differentiation and prohferation. 

Other theoretical structure prediction methods, such as simulating folding pathways, lattice models, simulations and predictions, inverse folding (i.e. designing the best sequence for a fold/structure), physical methods (based on finding minimum energy conformations for realistic physicochemical potentials), are not discussed here. 

Zhang, Z., Boyle, PC., Lu, B.Y, Chang, J.Y, Wriggers, W. Entropic folding pathway of human epidermal growth factor explored by disulfide scrambling and amplified collective motion simulations, Biochem. 2006,45,15269. 

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