Folding process elucidation

Given that a sequence folds to a known native stmcture, what are the mechanisms in the transition from the unfolded confonnation to the folded state This is a kinetics problem, the solution of which requires elucidation of the pathways and transition states in the folding process. 

TRIR methods have also found utility in the elucidation of reaction mechanisms involved in biological systems, most notably photosynthetic and respiratory proteins. In addition, TRIR spectroscopy has also been used to enhance our understanding of the dynamics of protein folding processes. ... 

The protein folding problem is of fundamental importance in modern structural biology. Recent advances in experimental techniques have helped to elucidate thermodynamic and kinetic mechanisms that underlie different stages of the folding process [1-6]. Computer simulations performed at various levels of molecular detail have played a central role in the interpretation of experimental studies. Molecular simulations using models based on fully atomic representations are becoming more accurate and more practical and are increasingly... 

Experimental studies generally yield only limited amounts of information of the actual molecular details of the motion experienced by a peptide or protein, any conformational transitions it undergoes, and the full conformational ensemble. Therefore, there is a need for theoretical studies to better elucidate these events. Complicated macromolecules cannot be studied using analytical methods. Instead, computer simulation methods are used, particularly molecular dynamics, which by providing atomic positions as a function of time, in principle, provides a realistic and complete picture of protein motion. To be most effective, experimental and theoretical studies should be linked. In this way, the experimental results are used to test the validity of the simulations, and when simulations accurately mimic reality they can be used in a predictive manner. Simulations can provide detailed information in these areas that often cannot be obtained experimentally, especially in the case of protein folding where it has proved difficult to characterize proteins during the folding process. 

Use of Simplified Lattice Models to Elucidate Features of the Protein Folding Process... 

Carotenoid accumulation during fruit ripening in tomato has been studied extensively and is a good model system to elucidate the regulation of the process. During ripening the concentration of carotenoids increases between 10 and 15-fold due mainly to a 500-fold increase in the concentration of lycopene (Fraser et al, 1994 Table 13.5). Accumulation of lycopene begins... 

Fig. 6.4. Illustration of the unfolded nature of the phosphorylated kinase-inducible domain (pKID) of CREB (left) and its conformation after folding upon binding to the KIX domain of CBP (right). The mechanism of this process has recently been elucidated by NMR [28] and is discussed more fully in Chap. 1 (Wright). Adapted by permission from [5] (Macmillan Publishers Ltd., copyright 2005)...

Until very recently, metabolic stability screening and metabolite identification (metabolite ID) have been sequential processes that is, the metabolic stability assays are typically performed hrst to identify rapidly metabolized compounds and a follow-up metabolite ID study is performed next, typically at a 10-fold higher substrate concentration to ensure generation of sufficiently high-quality MS/MS information to support structure elucidation. 

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