Two-state protein folding

This schematic view is the current frame work for understanding two-state protein folding [5]. For several reviews of the extensive literature on the theory of folding, and folding statistical mechanics see e.g. [5,12,14]. 

K. W. Plaxco, K. T. Simons, I. Ruczinski, and D. Baker, Topology, stability, sequence, and length Defining the determinants of two-state protein folding kinetics. Biochemistry 39, 11177-11183... 

Depending on the protein, the free energy landscape differs as is illustrated in Fig. 6. For some two-state proteins, with an independently stable secondary structure, the diffusion-collision mechanism is preferred. Other proteins,for which the secondary structure is less stable on its own, fold cooperatively using the nucleation-condensation pathway. In all cases there is still two state behavior, because there is only one rate limiting barrier. 

B. F. (2008) Interconversion between two unrelated protein folds in the lymphotactin native state. Proceeding of the National Academy of Sciences of the United States of America, 105, 5057-5062. 

Protein Folding Nuclei and the Transition State Ensemble in Two-state Proteins. 

In biochemistry, when dealing with huge molecules such as proteins or nucleic acids, it is often convenient to treat the system as being a quasi-two-state system. For instance, a protein may be viewed as having two states the folded F (or native) and the unfolded U (or denatured) states. Clearly, each of these states consists of many quantum-mechanical states. It is convenient to define the Helmholtz energy of each of these combined states as follows ... 

Relation Between Stability and Folding Rate for Six Two-State Proteins Ibat Have Been Mutated Extensively"... 

The fact that the folding (and unfolding) kinetics of relatively small, two-state proteins can be predicted with reasonable accuracy from global features of the native state like the contact order, stability, and number of contacts supports the idea that the details of protein structure are not required to capture the key features of protein folding, so that reduced representations should be adequate. However, the most widely used simple heteropolymer models, those restricted to a simple cubic lattice, predict that stability is more important than native structure, in contrast to the experimental data for proteins. In this section we seek to understand why lattice models differ from proteins in this regard. Doing so is of importance because complete details of the folding trajectories of such models... 

Measuring Protein Sta.bihty, Protein stabihty is usually measured quantitatively as the difference in free energy between the folded and unfolded states of the protein. These states are most commonly measured using spectroscopic techniques, such as circular dichroic spectroscopy, fluorescence (generally tryptophan fluorescence) spectroscopy, nmr spectroscopy, and absorbance spectroscopy (10). For most monomeric proteins, the two-state model of protein folding can be invoked. This model states that under equihbrium conditions, the vast majority of the protein molecules in a solution exist in either the folded (native) or unfolded (denatured) state. Any kinetic intermediates that might exist on the pathway between folded and unfolded states do not accumulate to any significant extent under equihbrium conditions (39). In other words, under any set of solution conditions, at equihbrium the entire population of protein molecules can be accounted for by the mole fraction of denatured protein, and the mole fraction of native protein,, ie. 

NOESY NMR spectroscopy is a homonuclear two-dimensional experiment that identifies proton nuclei that are close to each other in space. If one has already identified proton resonances in one-dimensional NMR spectroscopy or by other methods, it is then possible to determine three dimensional structure through NOESY. For instance, it is possible to determine how large molecules such as proteins fold themselves in three-dimensional space using the NOESY technique. The solution structures thus determined can be compared with solid-state information on the same protein obtained from X-ray crystallographic studies. The pulse sequence for a simple NOESY experiment is shown in Figure 3.23 as adapted from Figure 8.12 of reference 19. 

---