Native state

About: Native state is a research topic. Over the lifetime, 2855 publications have been published within this topic receiving 138240 citations.

Protein denaturation. C. Theoretical models for the mechanism of denaturation.

Abstract: Publisher Summary This chapter reviews theoretical models that may be constructed and equations that may be derived from them to understand the process of protein denaturation. Given that the native state is stable under physiological conditions, the question arises whether the effects of environmental changes on the equilibrium between native and denatured states can be predicted, so as to account for the loss of stability of the native state and the appearance of different denatured states under specified conditions. This question involves not the absolute values for the free energies and other thermodynamic parameters for denaturation processes, but the changes in these parameters, along with changes in environmental variables. These changes can be predicted semiquantitatively. Furthermore, one can account both for the products formed under different conditions and for the character of the transitions from native to denatured state, at least for the simple proteins that have been studied in detail.

Energetics of protein structure.

Abstract: Publisher Summary This chapter summarizes the experimental information on protein energetics. This field is developing fast and the concept of the energetics of protein structure has changed considerably during the past few years based on new findings. The proteins which are presented in the chapter are selected from a large number of proteins for which the thermodynamics of unfolding are studied in laboratory. The analysis of protein energetics presented in this chapter is based on several assumptions: (1) protein groups contribute additively, and proportionally as their surfaces, to the overall thermodynamic effects of unfolding; (2) the protein interior closely resembles an organic crystal in the way groups are packed and the energetics of the interactions among these groups are similar to those in the organic crystals; and (3) under certain conditions the denatured protein can be regarded as unfolded. The main criteria in choosing these proteins have been the reversibility of the denaturation process modeling unfolding, the completeness of this unfolding, the reliability of thermodynamic data on this process, and the resolution of the three dimensional structure of the given protein. The latter is important to investigate the correlation between thermodynamic and structural characteristics of protein, including the water-ASA of various groups in the native and unfolded states, the number of hydrogen bonds, and the extent of van der Waals contacts in the native state.

Protein Folding Intermediates: Native-State Hydrogen Exchange

Abstract: The hydrogen exchange behavior of native cytochrome c in low concentrations of denaturant reveals a sequence of metastable, partially unfolded forms that occupy free energy levels reaching up to the fully unfolded state. The step from one form to another is accomplished by the unfolding of one or more cooperative units of structure. The cooperative units are entire omega loops or mutually stabilizing pairs of whole helices and loops. The partially unfolded forms detected by hydrogen exchange appear to represent the major intermediates in the reversible, dynamic unfolding reactions that occur even at native conditions and thus may define the major pathway for cytochrome c folding.

How does a protein fold

Abstract: THE number of all possible conformations of a polypeptide chain is too large to be sampled exhaustively. Nevertheless, protein sequences do fold into unique native states in seconds (the Levinthal paradox). To determine how the Levinthal paradox is resolved, we use a lattice Monte Carlo model in which the global minimum (native state) is known. The necessary and sufficient condition for folding in this model is that the native state be a pronounced global minimum on the potential surface. This guarantees thermodynamic stability of the native state at a temperature where the chain does not get trapped in local minima. Folding starts by a rapid collapse from a random-coil state to a random semi-compact globule. It then proceeds by a slow, rate-determining search through the semi-compact states to find a transition state from which the chain folds rapidly to the native state. The elements of the folding mechanism that lead to the resolution of the Levinthal paradox are the reduced number of conformations that need to be searched in the semi-compact globule (˜1010 versus ˜1016 for the random coil) and the existence of many (˜103) transition states. The results have evolutionary implications and suggest principles for the folding of real proteins.