Cooperativity single-domain proteins

It has been shown that the hierarchical approach illustrated above for the case of a two-domain protein can be performed at a more fundamental level in order to account for the cooperative folding behavior of single-domain proteins (Freire and Murphy, 1991). This approach involves the use of the crystallographic structure of a pro-... 

The existence of the hydrophobic-core collapse, which is accompanied by the creation of a polar shell that screens the hydrophobic core from the solvent, renders the folding behavior of a heteropolymer different from crystalhzation or amorphous transitions of homopolymers. The reason is the disorder induced by the sequence of different monomer types. The hydrophobic-core formation is the main cooperative conformational transition which accompanies the tertiary folding process of a single-domain protein. 

Since the Gibbs energy difference of the native and denatured states determines the stability of a cooperative unit, it follows from Eq. (11) that the stability of a small globular protein (or a single domain) is maximal at the temperature at which the entropies of the native and denatured states are equal. At this temperature, the structure is stabilized only by the... 

Typically, the in vitro folding of a single domain globular protein resembles a first-order phase transition in the sense that the thermodynamic properties undergo an abrupt change, and the population of intermediates at equilibrium is very low. In other words, the process is cooperative and is well described by a two-state model [8]. The first attempts to explain protein folding cooperativity focused on the formation of secondary structure. Theoretical and experimental analysis of coil-helix transitions indeed proved that the process is cooperative [167]. However, the helix-coil transition is always continuous [168], and thus it cannot explain the two-state behavior of the protein folding transition. 

Cooperative folding units are defined from a functional rather than a purely structural point of view, even though in many cases a one-to-one correspondence can be found. Cooperative folding units can be as large as the entire protein (e.g., small globular proteins that exhibit two-state behavior effectively behave as cooperative folding units), entire protein domains, subdomains, and structural motifs, or as small as single a helices. The hierarchical level at which the description is made depends on the desired level of detail and is, in principle, only constrained by the availability of structural information. 

The Gibbs energy difference of the denatured and native states corresponds to the work required for the transition of a system from the native to the denatured state, i.e., the work of disruption of the native cooperative structure. Therefore, this quantity is usually considered as a measure of the stability of the cooperative structure, i.e., the stability of a small globular protein or cooperative domain. As for the large proteins, their stability cannot be expressed by a single value, but only by a set of values specifying the stability for each domain within these molecules and the interaction between the domains. 

The transition of a protein or a single cooperative domain from the native to the denatured state is always accompanied by a significant increase of its partial heat capacity (see, for reviews, Sturtevant, 1977 Privalov, 1979). The denaturationaJ increment of heat capacity A JCP = C° Cp amounts to 25-50% of the partial heat capacity of the native protein and does not depend noticeably on the environmental conditions under which denaturation proceeds (Fig. 1) or on the method of denaturation. However, it is different foi different proteins and seems to correlate with the number of contacts between nonpolar groups in native proteins (Table I). On the other hand, the partial specific heat capacities of denatured states of different proteins appear to be rather similar (Tiktopulo et... 

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