Protein Energy Landscape

Atomic level studies of complex peptide and protein energy landscapes have become more detailed as computers have become faster, allowing for longer sampling simulations... 

Early attempts to calculate protein energy landscapes have been reported in the literature1,2 Spectroscopic studies of proteins, especially using atomic... 

Nevo R, Brumfeld V, Kapon R, Hinterdorfer P, Reich Z (2005) Direct measurement of protein energy landscape roughness. EMBO Reports 6(5) 482-486... 

Saven, Jeffery G. (2001), Designing protein energy landscapes, Chem. Rev. 101, 3113-3130. 

Levy Y, Becker OM (2002) Conformational polymorphism of wild-type and mutant prion proteins energy landscape analysis. Proteins Struct Funct Genet 47 458... 

Experimental evidence indicates that the local minima of protein energy landscapes have a complex, hierarchical structure [7], and computational methods have been developed for clustering local minima into hierarchies using various metrics for measuring the distance between them. Both... 

Xiao, H., Hoerner, J.K., Eyles, S.J., et al. (2(X)5) Mapping protein energy landscapes with amide hydrogen exchange and mass spectrometry I. A generalized model for a two-state protein and comparison with experiment. Protein Scierwe, 14 (2), 543-557. 

Wolynes P G 1997 Folding nucleus and energy landscapes of larger proteins within the capillarity approximation Proc. Natl Acad. Sci. (USA) 94 6170-5... 

Bryngelson J D, Onuchic J N, Socci N D and Wolynes P G 1995 Funnels, pathways, and the energy landscape of protein folding a synthesis Profe/ns 21 167-95... 

Figure 8 shows a one-dimensional sketch of a small fraction of that energy landscape (bold line) including one conformational substate (minimum) as well as, to the right, one out of the typically huge number of barriers separating this local minimum from other ones. Keeping this picture in mind the conformational dynamics of a protein can be characterized as jumps between these local minima. At the MD time scale below nanoseconds only very low barriers can be overcome, so that the studied protein remains in or close to its initial conformational substate and no predictions of slower conformational transitions can be made. 

Hans Prauenfelder, Sthephen G. Sligar, and Peter G. Wolynes. The energy landscape and motions of proteins. Science., 254 1598-1603, 1991. 

Fig. 10.27 Schematic representation of the energy landscape for protein folding. (Figure adapted from Onuchic ] N, Z Luthcy-Schulten and P Wolynes 1997. Theory of Protein Folding The Energy Landscape Perspective. Annual Reviews in Physical Chemistry 48 545-600.)...

Bryngelson J D, J N Onuchic, N D Socci and P G Wolynes 1995. Funnels, Pathways, and the Energy Landscape of Protein Folding A Synthesis. Proteins Structure, Function and Genetics 21 167-195. 

JM Troyer, EE Cohen. Protein conformational landscapes Energy minimization and clustering of a long molecular dynamics trajectory. Proteins 23 97-110, 1995. 

Figure 4 The energy landscape of the pnon protein (Pi P) (residues 124-226) in vacuum, obtained by principal coordinate analysis followed by the minimal energy envelope procedure. Two large basins are seen. One basin is associated with the native Pi P conformation the other is associated with partially unfolded conformations.

JN Onuchic, Z Luthey-Schulten, PG Wolynes. Theory of protein folding The energy landscape perspective. Annu Rev Phys Chem 48 545-600, 1997. 

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