Atomic resolution structures of proteins indicate that the core is typically well packed, suggesting a densely connected network of interactions between amino acid residues. The combinatorial complexity of energetic interactions in such a network could be enormous, a problem that limits our ability to relate structure and function. Here, we report a case study of the complexity of amino acid interactions in a localized region within the core of the GFP, a particularly stable and tightly packed molecule. Mutations at three sites within the chromophore-binding pocket display an overlapping pattern of conformational change and are thermodynamically coupled, seemingly consistent with the dense network model. However, crystallographic and energetic analyses of coupling between mutations paint a different picture; pairs of mutations couple through independent ''hotspots'' in the region of structural overlap. The data indicate that, even in highly stable proteins, the core contains sufficient plasticity in packing to uncouple high-order energetic interactions of residues, a property that is likely general in proteins.A characteristic feature of natively folded proteins is a well ordered core consisting of amino acid residues in specific rotamer orientations making well defined packing interactions with neighboring residues. The quality of packing has been reported as uniformly high throughout the core of proteins (1), with mean side chain volumes slightly smaller than those observed in amino acid crystals (2, 3). The efficient packing of residues is often as important as the hydrophobic effect in determining the thermodynamic stability of the folded state (4-8) and may represent a key component of the overall evolutionary pressure guiding sequence variation of a protein fold (9, 10). Also, optimal packing of the core has been used as a design principle in creating artificial proteins, often with improved stability (11,12).What is the implication of these observations for the potential complexity of amino acid interactions in proteins? To define this problem, consider all of the ways that the free energy contribution of even one residue for fold stability (or any other thermodynamic property) might arise from the tertiary structure. In the simplest case, this residue might be energetically independent of all other residues; thus, its total free energy contribution is strictly an intrinsic property that involves no pairwise or higher-order interactions with other residues. More realistically, the energetics of the residue might depend on coupled interactions with other residues; in some cases, this might be rationalized as local packing against neighboring residues or through-space electrostatic interactions but may also derive from less intuitive cooperative interactions involving collections of residues that reach to distant sites (13,14). In the absence of prior knowledge, then, the total thermodynamic value of residue i is given by a combinatorial set of hierarchical structural interactions:where ⌬ЉG represents the n...
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.