Energy-refined structures

Figure 4. Comparison of energy refined structures A, B, and C with NMR structures A", B", and C". (Reproduced with permission from ref. 24. Copyright 1988 Wiley.)...

The favoured dihedral angles for protein main chains were derived from energy considerations of steric clashes in peptides giving the well known Ramachandran plot (Ramachandran and Sasisekharan, 1968). These phi/psi combinations characterize the elements of secondary structure. Accurate main chain models can be constructed from spare parts, that is short pieces of helices, sheets, turns, and random coils taken from highly refined structures, provided a series of C-alpha positions can be established from the electron density map... 

In conjunction with a study on the reactivity of dimeric quinone me-thides, Elder et al. (56) examined the physical and electronic structure of guaiacylglycerol-/ -coniferyl ether, which is substituted in a manner representative of the lignin polymer. Calculations were performed using AMBER (Assisted Model Building with Energy Refinement) (24), which is a force-field method, and the energetic minimum was determined to be a folded structure similar to that reported by Gravitis and Erins (55). 

Continued Quantum and Molecular Mechanical Simulations, In this technique, a molecular dynamics simulation includes the treatment of some part of the system wilh a quantum mechanical technique. This approach. yMf.MM. is similar to programs that Use quantum mechanical methods to treat the n-systems of the structures in question separately from the sigma framework. The results are combined ai ihe end to render a slructure which is optimized and energy-refined in satisfy both self-consistent field (SCF) and force field energy convergence. 

Structures determined by spectroscopic means are generally underdetermined in that the number of variables is similar to or greater than the number of observations. In such cases, the energy-minimized structures can be used to aid in the refinement of the structure or as a check on the geometry[51]. Applications of molecular mechanics modeling to the determination of solution structures is described in detail in Chapters 6, 7, and 9. Such approaches are fundamental to the determination of macromolecu-lar structures by NMR spectroscopy. 

Fig. 5. Stereoview of one energy-refined model structure proposed for the G G -interstrand-crosslinked duplex d(CATAG CTATG)2 (coordinates were kindly supplied by Prof. Gary...

M. Billeter, Th. Schaumann, W. Braun, and K. Wiithrich, Biopolymers, 29, 695 (1989). Restrained Energy Refinement with Two Different Algorithms and Force Fields of the Structure of the a-Amylase Inhibitor Tendamistat Determined by NMR in Solution. 

Figure 9. Refined structure of patellamide C - ensemble of 14 lowest energy structures...

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