Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility

Abstract

The identification of the factors that enable normally folded proteins to remain in their soluble and functional states is crucial for a comprehensive understanding of any biological system. We have determined a series of energy landscapes of the acylphosphatase from Drosophila melanogaster under a variety of conditions by combining NMR measurements with restrained molecular dynamics simulations. We thus analyzed the differences in the structures, dynamics, and energy surfaces of the protein in its soluble state or in situations where it aggregates through conformational states that have native-like structure, folding stability, and enzymatic activity. The study identifies the nature of the energy barriers that under normal physiological conditions prevent the protein ensemble from populating dangerous aggregation-prone states. We found that such states, although similar to the native conformation, have altered surface charge distribution, alternative topologies of the β-sheet region, and modified solvent exposure of hydrophobic surfaces and aggregation-prone regions of the sequence. The identified barriers allow the protein to undergo functional dynamics while remaining soluble and without a significant risk of misfolding and aggregation into nonfunctional and potentially toxic species.protein misfolding | free energy barriers | avoidance of protein aggregation | molecular simulations

Intrinsic disorder modulates protein self-assembly and aggregation

“…In particular, we suggest that in specific cases large flexible loops in proteins may act to inhibit aggregation as a result of their high values of conformational entropy. It is well established that the aggregation propensity of proteins depends on the properties and population of all the conformational states within the ensemble, including the N* aggregation-prone species (14,15). The present results may provide a clear example of this concept by demonstrating that the flexibility of the ground state of EAS (the highly soluble state in bulk solution) is remarkably different from that of the aggregation-prone state (at the air-water interface).…”

“…The dynamic properties of proteins can play key roles in influencing their propensity for self-ssembly and aggregation (14) and have considerable significance in many aspects of their function (27)(28)(29)(30)(31). More generally, a range of factors discriminate between aggregation-prone and aggregation-resistant states of proteins, including charge effects, negative design elements and accessibility of aggregation-prone sequences (7,16).…”

“…The principal means for controlling misfolding and aggregation are, however, intrinsic factors that proteins have optimized throughout evolution and have encoded in their amino-acid sequences (13) to define specific energy barriers that prevent their solution states from adopting aggregation-prone conformations (that we denote here as "N*") under normal circumstances (14). The population of N* within the conformational ensemble of a protein state has a crucial impact on its rate of aggregation (15) and in this context it has been shown that negative design is an important feature of protein structures that have been specifically optimized to prevent unwanted intermolecular association (16).…”

Bacterial Cell Division Regulation by Ser/Thr Kinases: A Structural Perspective

“…A comparative analysis of the structure of this domain with other Ig-fold domains clearly unveils that the Ig-domain of PrkC lacks the N-terminal strand. Although further studies are needed to define the role of this new type of incomplete Ig-fold domains, it has been suggested that the exposure of an anomalously large number of backbone -strand hydrogen-bond donors and acceptors may endow these domains with adhesive properties [86][87][88]. On analogy with the E. coli pilus subunit PapG, PrkC Ig-like domain may be involved in peptidoglycan binding [30,85].…”

Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies

“…It is also becoming increasingly evident, however, that some normally folded proteins can aggregate from native-like states (N*) that are directly accessible from the native state (N) without the need for a transition across the major energy barrier for unfolding (reviewed in (7)). Formation of N* states may be promoted by mutations or subtle changes in solution conditions, for example, inducing the displacement of an edge b-strand and the subsequent exposure of aggregationprone regions of the protein (8)(9)(10)(11)(12)(13). As an alternative possibility, the release of a ligand may expose an aggregation-prone binding site (14)(15)(16).…”