Little is known about how proteins begin to unfold. In particular, how and when water molecules penetrate into the protein interior during unfolding, thereby enabling the dissolution of specific structure, is poorly understood. The hypothesis that the native state expands initially into a dry molten globule, in which tight packing interactions are broken, but whose hydrophobic core has not expanded sufficiently to be able to absorb water molecules, has very little experimental support. Here, we report our analysis of the earliest observable events during the unfolding of single chain monellin ( Two models are commonly invoked to describe the rate-limiting step during protein unfolding. The commonly accepted model is that the rate-limiting step is controlled by the extensive rearrangement of native structure upon the entry of water into the hydrophobic core (1-5). In the alternative model, based on the dry molten globule hypothesis (6), the rate-limiting step is an initial concerted rupture of the tight side-chain packing in the interior, without any entry of water. The free energy barrier arises because the loss of enthalpy in the dry globular transition state has not yet been compensated for by a gain in conformational entropy (7,8). Experimental evidence in support of this hypothesis is, however, scarce and moreover, indirect (9-11). The dry molten globule model posits that the tight packing interactions are lost cooperatively when thermal fluctuations cause secondary structural elements to move marginally apart from each other (7). But small displacements of individual secondary structural units have not been detected as the initial steps of the unfolding of any protein. In particular, the detection of the rotation or translation of an ␣-helix or the fraying movement of a ␤-strand during the formation of a dry molten globule, which would constitute the most direct evidence in support of the dry molten globule hypothesis, has been difficult to capture in experiments.Multisite FRET measurements allow determination of the displacements of specific segments of a protein structure, during folding or unfolding (12)(13)(14)(15)(16)(17)(18)(19). In this study, 2-site FRET measurements of the unfolding of single-chain monellin (MNEI), in both equilibrium and kinetic unfolding experiments, have been carried out to determine how an intramolecular distance, spanning the Nand C-termini of the sole helix in the protein changes, compared with an intramolecular distance corresponding to the end-to-end distance of the protein. MNEI is an intensely sweet, small plant protein in which the sole ␣-helix is packed against a 5-stranded ␤-sheet in a ␤-grasp fold (Fig. 1A). In earlier studies, the folding and unfolding of MNEI have been characterized in detail (20)(21)(22). The folding and unfolding reactions of MNEI appear to be multistate, with multiple intermediates populating on parallel pathways (21). It is shown here that the unfolding of the protein begins with an initial expansion of the protein into a dry molten globular st...

Stress-induced misfolding and intraneuronal aggregation of the highly conserved nucleic acid binding protein TDP-43 (transactive response DNA binding protein 43 kDa) and its fragments have been implicated in amyotrophic lateral sclerosis and several other neurodegenerative diseases. However, the physicochemical mechanism of its misfolding from the functional folded state is poorly understood. TDP-43 is a four-domain protein and performs the essential nucleic acid binding function with the help of its two tandem RNA recognition motif domains naturally tethered by a linker (called here the tethered RRM domain of TDP-43 or TDP-43 tRRM ). Here, we show that the monomeric native form of TDP-43 tRRM remains in a pH-dependent and reversible thermodynamic equilibrium with a protonated, nanosized, 40-meric form (the A form). Under the stress-like low-pH condition, the A form becomes predominantly populated. In the A form, protein molecules have restricted dynamics of surface side-chain residues but native-like secondary structure. This self-assembled form possesses a loosely packed core in which the intrinsically disordered and aggregation-prone regions are in the proximity. The A form is metastable and swiftly aggregates into a highly stable amyloid-like protofibrillar form (β form) mediated by the disorder-to-order transition of intrinsically disordered regions upon small environmental perturbations. Interestingly, the A form and the β form are not formed when TDP-43 tRRM is bound to DNA, indicating that the nucleic acid binding regions of the protein participate in their formation. Our results reveal how the energy landscapes of folding and aggregation of TDP-43 tRRM are coupled by a metastable molten-globule like oligomeric form and modulated by stress-like conditions.

Dry molten globular (DMG) intermediates, an expanded form of the native protein with a dry core, have been observed during denaturant-induced unfolding of many proteins. These observations are counterintuitive because traditional models of chemical denaturation rely on changes in solvent-accessible surface area, and there is no notable change in solvent-accessible surface area during the formation of the DMG. Here we show, using multisite fluorescence resonance energy transfer, far-UV CD, and kinetic thiol-labeling experiments, that the guanidinium chloride (GdmCl)-induced unfolding of RNase H also begins with the formation of the DMG. Population of the DMG occurs within the 5-ms dead time of our measurements. We observe that the size and/or population of the DMG is linearly dependent on [GdmCl], although not as strongly as the second and major step of unfolding, which is accompanied by core solvation and global unfolding. This rapid GdmCl-dependent population of the DMG indicates that GdmCl can interact with the protein before disrupting the hydrophobic core. These results imply that the effect of chemical denaturants cannot be interpreted solely as a disruption of the hydrophobic effect and strongly support recent computational studies, which hypothesize that chemical denaturants first interact directly with the protein surface before completely unfolding the protein in the second step (direct interaction mechanism).protein unfolding | dry molten globule | steady-state FRET D enaturants such as guanidinium chloride (GdmCl) and urea are classic perturbants used to probe the thermodynamics and kinetics of protein conformational changes, although their mechanism of action is poorly understood (1-15). In some of these studies, a dry molten globular (DMG) state has been observed on the native side of the free-energy barrier (16-18). The DMG is an expanded form of the native protein in which at least some of the side-chain packing interactions are disrupted without solvation of the hydrophobic core; it was originally postulated to explain heat-induced unfolding of proteins (19,20). Recently, unfolding intermediates resembling the DMG have also been observed in the absence of denaturants, and it has been suggested that the DMG exists in rapid equilibrium with the native state (21-23). The fact that the DMG can be observed by the addition of denaturants is, however, counterintuitive, because traditional models of chemical denaturation rely on changes in solvent-accessible surface area (SASA) (3,24,25) and there is no notable change in SASA during the formation of the DMG.Recent computational studies have suggested an alternative model of chemical denaturation in which denaturants first interact directly with the protein surface, causing the protein to swell, and then penetrate the core (the so-called "direct interaction" mechanism) (9,11,12,26). One of the consequences of this model is that denaturants unfold proteins in two steps (9, 12). In the first step, denaturant molecules displace water molecules within the fir...

Understanding how electric fields and their fluctuations in the active site of enzymes affect efficient catalysis represents a critical objective of biochemical research. We have directly measured the dynamics of the electric field in the active site of a highly proficient enzyme, Δ 5 -3-ketosteroid isomerase (KSI), in response to a sudden electrostatic perturbation that simulates the charge displacement that occurs along the KSI catalytic reaction coordinate. Photoexcitation of a fluorescent analog (coumarin 183) of the reaction intermediate mimics the change in charge distribution that occurs between the reactant and intermediate state in the steroid substrate of KSI. We measured the electrostatic response and angular dynamics of four probe dipoles in the enzyme active site by monitoring the time-resolved changes in the vibrational absorbance (IR) spectrum of a spectator thiocyanate moiety (a quantitative sensor of changes in electric field) placed at four different locations in and around the active site, using polarization-dependent transient vibrational Stark spectroscopy. The four different dipoles in the active site remain immobile and do not align to the changes in the substrate electric field. These results indicate that the active site of KSI is preorganized with respect to functionally relevant changes in electric fields.enzyme catalysis | electrostatic preorganization | Stark effect | visible-pump IR probe | time-resolved anisotropy E nzymes catalyze the vast majority of biochemical reactions and accelerate the rate of these reactions by many orders of magnitude compared to the uncatalyzed reactions in solution. The origins of the enormous catalytic power of enzymes are still not well understood despite enormous effort (1-6). In particular, the functional role of fast picosecond protein motions in catalysis and the dynamic nature of the transition state barrier crossing is a subject of ongoing and current debate (7-13). Theoretical studies have suggested that fast vibrations in enzymes might generate transition state conformations conducive to the chemical reaction (7,8,(14)(15)(16)(17)(18)(19)(20)(21), a familiar concept for reactions in ordinary solvents (22). In an alternative viewpoint, preorganization effects have been suggested to be a major contributing factor to enzyme catalysis (23-28). It has been postulated that enzymes have partially oriented dipoles of polar and charged groups in the active site that interact with electrostatic features present in the catalytic transition state more favorably than water can. Such preorganization of active site dipoles and charges has been suggested to result in a reduction in the reorganization energy and provide enormous catalytic advantage over the reaction in solution, where water molecules must rearrange in order to solvate charge rearrangements during the chemical reaction (24,(29)(30)(31). The relative merits of these opposing viewpoints remains unclear largely because of the paucity of direct experimental assessment of the key discrepancies betwee...

The unfolding kinetics of many small proteins appears to be first order, when measured by ensemble-averaging probes such as fluorescence and circular dichroism. For one such protein, monellin, it is shown here that hidden behind this deceptive simplicity is a complexity that becomes evident with the use of experimental probes that are able to discriminate between different conformations in an ensemble of structures. In this study, the unfolding of monellin has been probed by measurement of the changes in the distributions of 4 different intramolecular distances, using a multisite, time-resolved fluorescence resonance energy transfer methodology. During the course of unfolding, the protein molecules are seen to undergo slow and continuous, diffusive swelling. The swelling process can be modeled as the slow diffusive swelling of a Rouse-like chain with some additional noncovalent, intramolecular interactions. Here, we show that specific structure is lost during the swelling process gradually, and not in an all-or-none manner, during unfolding.diffusive swelling ͉ distance distribution ͉ gradual unfolding ͉ Rouse model ͉ time-resolved FRET

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The role of van der Waals (vdW) packing interactions compared to the hydrophobic effect in stabilizing the functional structure of proteins is poorly understood. Here we show, using fluorescence resonance energy transfer, dynamic fluorescence quenching, red-edge excitation shift, and near- and far-UV circular dichroism, that the pH-induced structural perturbation of a multidomain protein leads to the formation of a state in which two out of the three domains have characteristics of dry molten globules, that is, the domains are expanded compared to the native protein with disrupted packing interactions but have dry cores. We quantitatively estimate the energetic contribution of vdW interactions and show that they play an important role in the stability of the native state and cooperativity of its structural transition, in addition to the hydrophobic effect. Our results also indicate that during the pH-induced unfolding, side-chain unlocking and hydrophobic solvation occur in two distinct steps and not in a concerted manner, as commonly believed.

TDP-43 protein travels between the cytosol and the nucleus to perform its nucleic acid binding functions through its two tandem RNA recognition motif domains (TDP-43tRRM). When exposed to various environmental stresses, it forms abnormal aggregates in the cytosol of neurons, which are the hallmarks of amyotrophic lateral sclerosis and other TDP-43 proteinopathies. However, the nature of early structural changes upon stress sensing and the consequent steps during the course of aggregation are not well understood. In this study, we show that under low-pH conditions, mimicking starvation stress, TDP-43tRRM undergoes a conformational opening reaction linked to the protonation of buried ionizable residues and grows into a metastable oligomeric assembly (called the “low-pH form” or the “L form”). In the L form, the protein molecules have disrupted tertiary structure, solvent-exposed hydrophobic patches, and mobile side chains but the native-like secondary structure remains intact. The L form structure is held by weak interactions and has a steep dependence on ionic strength. In the presence of as little as 15 mM KCl, it fully misfolds and further oligomerizes to form a β-sheet rich “β form” in at least two distinct steps. The β form has an ordered, stable structure that resembles worm-like amyloid fibrils. The unstructured regions of the protein gain structure during L ⇌ β conversion. Our results suggest that TDP-43tRRM could function as a stress sensor and support a recent model in which stress sensing during neurodegeneration occurs by assembly of proteins into metastable assemblies that are precursors to the solid aggregates.