Massive conformation change in the prion protein: Using dual-basin structure-based models to find misfolding pathways

Exploring the structural acrobatics of fold-switching proteins using simplified structure-based models

Metamorphic proteins are a paradigm of the protein folding process, by encoding two or more native states, highly dissimilar in terms of their secondary, tertiary, and even quaternary structure, on a single amino acid sequence. Moreover, these proteins structurally interconvert between these native states in a reversible manner at biologically relevant timescales as a result of different environmental cues. The large-scale rearrangements experienced by these proteins, and their sometimes high mass interacting partners that trigger their metamorphosis, makes the computational and experimental study of their structural interconversion challenging. Here, we present our efforts in studying the refolding landscapes of two quintessential metamorphic proteins, RfaH and KaiB, using simplified dual-basin structure-based models (SBMs), rigorously footed on the energy landscape theory of protein folding and the principle of minimal frustration. By using coarse-grained models in which the native contacts and bonded interactions extracted from the available experimental structures of the two native states of RfaH and KaiB are merged into a single Hamiltonian, dual-basin SBM models can be generated and savvily calibrated to explore their fold-switch in a reversible manner in molecular dynamics simulations. We also describe how some of the insights offered by these simulations have driven the design of experiments and the validation of the conformational ensembles and refolding routes observed using this simple and computationally efficient models.

Metamorphic proteins under a computational microscope: Lessons from a fold-switching RfaH protein

Metamorphic proteins constitute unexpected paradigms of the protein folding problem, as their sequences encode two alternative folds, which reversibly interconvert within biologically relevant timescales to trigger different cellular responses. Once considered a rare aberration, metamorphism may be common among proteins that must respond to rapidly changing environments, exemplified by NusG-like proteins, the only transcription factors present in every domain of life. RfaH, a specialized paralog of bacterial NusG, undergoes an all-α to all-β domain switch to activate expression of virulence and conjugation genes in many animal and plant pathogens and is the quintessential example of a metamorphic protein. The dramatic nature of RfaH structural transformation and the richness of its evolutionary history makes for an excellent model for studying how metamorphic proteins switch folds. Here, we summarize the structural and functional evidence that sparked the discovery of RfaH as a metamorphic protein, the experimental and computational approaches that enabled the description of the molecular mechanism and refolding pathways of its structural interconversion, and the ongoing efforts to find signatures and general properties to ultimately describe the protein metamorphome.

Lowered pH Leads to Fusion Peptide Release and a Highly Dynamic Intermediate of Influenza Hemagglutinin

Hemagglutinin (HA), the membrane-bound fusion protein of the influenza virus, enables the entry of virus into host cells via a structural rearrangement. There is strong evidence that the primary trigger for this rearrangement is the low pH environment of a late endosome. To understand the structural basis and the dynamic consequences of the pH trigger, we employed explicit-solvent molecular dynamics simulations to investigate the initial stages of the HA transition. Our results indicate that lowered pH destabilizes HA and speeds up the dissociation of the fusion peptides (FPs). A buried salt bridge between the N-terminus and Asp1122 of HA stem domain locks the FPs and may act as one of the pH sensors. In line with recent observations from simplified protein models, we find that, after the dissociation of FPs, a structural order-disorder transition in a loop connecting the central coiled-coil to the C-terminal domains produces a highly mobile HA. This motion suggests the existence of a long-lived asymmetric or "symmetry-broken" intermediate during the HA conformational change. This intermediate conformation is consistent with models of hemifusion, and its early formation during the conformational change has implications for the aggregation seen in HA activity.

Interdomain Contacts Control Native State Switching of RfaH on a Dual-Funneled Landscape

RfaH is a virulence factor from Escherichia coli whose C-terminal domain (CTD) undergoes a dramatic α-to-β conformational transformation. The CTD in its α-helical fold is stabilized by interactions with the N-terminal domain (NTD), masking an RNA polymerase binding site until a specific recruitment site is encountered. Domain dissociation is triggered upon binding to DNA, allowing the NTD to interact with RNA polymerase to facilitate transcription while the CTD refolds into the β-barrel conformation that interacts with the ribosome to activate translation. However, structural details of this transformation process in the context of the full protein remain to be elucidated. Here, we explore the mechanism of the α-to-β conformational transition of RfaH in the full-length protein using a dual-basin structure-based model. Our simulations capture several features described experimentally, such as the requirement of disruption of interdomain contacts to trigger the α-to-β transformation, confirms the roles of previously indicated residues E48 and R138, and suggests a new important role for F130, in the stability of the interdomain interaction. These native basins are connected through an intermediate state that builds up upon binding to the NTD and shares features from both folds, in agreement with previous in silico studies of the isolated CTD. We also examine the effect of RNA polymerase binding on the stabilization of the β fold. Our study shows that native-biased models are appropriate for interrogating the detailed mechanisms of structural rearrangements during the dramatic transformation process of RfaH.

To carry out their biological functions, proteins must fold into defined three-dimensional structures. In most proteins, a single fold determined by the amino acid sequence, and sometimes influenced by environmental conditions, is believed to be suited for each protein’s dedicated task. However, some proteins challenge this broadly accepted paradigm, adopting different structures that can enable diverse roles or trigger pathological responses, such as prion diseases. Escherichia coli RfaH constitutes a dramatic example of this atypical behavior. RfaH C-terminal domain folds into either a helical bundle that binds to the N-terminal domain and inhibits unregulated recruitment to the transcription complex or, in the presence of a specific DNA target, into a stand-alone β-barrel structure that binds to the ribosome and couples transcription and translation of RfaH-dependent genes. To understand the mechanism of this structural rearrangement, we performed molecular dynamics using a model where the stabilizing interactions from both folds are integrated. Our results argue that this transformation requires destabilization of the domain interface, is favored by interactions between the N-terminal domain of RfaH and RNA polymerase, and proceeds via a bound intermediate state that connects both folds.

Order and disorder control the functional rearrangement of influenza hemagglutinin

Influenza hemagglutinin (HA), a homotrimeric glycoprotein crucial for membrane fusion, undergoes a large-scale structural rearrangement during viral invasion. X-ray crystallography has shown that the pre- and postfusion configurations of HA2, the membrane-fusion subunit of HA, have disparate secondary, tertiary, and quaternary structures, where some regions are displaced by more than 100 Å. To explore structural dynamics during the conformational transition, we studied simulations of a minimally frustrated model based on energy landscape theory. The model combines structural information from both the pre- and postfusion crystallographic configurations of HA2. Rather than a downhill drive toward formation of the central coiled-coil, we discovered an order-disorder transition early in the conformational change as the mechanism for the release of the fusion peptides from their burial sites in the prefusion crystal structure. This disorder quickly leads to a metastable intermediate with a broken threefold symmetry. Finally, kinetic competition between the formation of the extended coiled-coil and C-terminal melting results in two routes from this intermediate to the postfusion structure. Our study reiterates the roles that cracking and disorder can play in functional molecular motions, in contrast to the downhill mechanical interpretations of the "spring-loaded" model proposed for the HA2 conformational transition.

Balancing bond, nonbond, and gō-like terms in coarse grain simulations of conformational dynamics

Characterization of the protein conformational landscape remains a challenging problem, whether it concerns elucidating folding mechanisms, predicting native structures or modeling functional transitions. Coarse-grained molecular dynamics simulation methods enable exhaustive sampling of the energetic landscape at resolutions of biological interest. The general utility of structure-based models is reviewed along with their differing levels of approximation. Simple Gō models incorporate attractive native interactions and repulsive nonnative contacts, resulting in an ideal smooth landscape. Non-Gō coarse-grained models reduce the parameter set as needed but do not include bias to any desired native structure. While non-Gō models have achieved limited success in protein coarse-graining, they can be combined with native structured-based potentials to create a balanced and powerful force field. Recent applications of such Gō-like models have yielded insight into complex folding mechanisms and conformational transitions in large macromolecules. The accuracy and usefulness of reduced representations are also revealed to be a function of the mathematical treatment of the intrinsic bonded topology.