Hydration Behavior along the Folding Pathways of Trpzip4, Trpzip5 and Trpzip6

Response of Foldable Protein Conformations to Non-Physiological Perturbations: Interplay of Thermal Factors and Confinement

Technological advances frequently interface biomolecules with nanomaterials at non-physiological conditions, necessitating response characterization of key processes. Similar encounters are expected in cellular contexts. We report in silico investigations of the response of diverse protein conformational states to lowering of temperature and imposition of spatial constraints. Conformational states are represented by folded form of the Albumin binding domain (ABD) protein, its compact denatured form, and structurally disordered nascent folding elements. Data from extensive simulations are evaluated to elicit structural, thermodynamic and dynamic responses of the states and their associated environment. Analyses reveal alterations to folding propensity with reduced thermal energy and confinement, with signatures of trend reversal in highly disordered states. Across temperatures, confinement has restrictive effects on volume and energetic fluctuations, leading to narrowing of differences in isothermal compressibility (κ) and heat capacities (Cp). While excess (over ideal gas) entropy of the hydration layer marks dependence on the conformational state at bulk, confinement triggers erasure of differences. These observations are largely consistent with timescales of protein-water hydrogen bonding dynamics. The results implicate multi-factorial associations within a simple bio-nano complex. We expect the current study to motivate investigations of more biologically relevant interfaces towards mechanistic understanding and potential applications.

MANUSCRIPT Local Crowd, Local Probe: Strengths and Drawbacks of Azidohomoalanine as a Site-Specific Crowding Probe

Every residue on a protein can be characterized by its interaction with water, in lack or in excess, as water is the matrix of biological systems. Infrared spectroscopy and the implementation of local azidohomoalanine (AHA) probes allow us to move beyond an ensemble or surface-driven conceptualization of water behavior and toward a granular, site-specific picture. In this paper, we examined the role of crowding in modulating both global and local behavior on the β-hairpin, TrpZip2 using a combination of Fourier-transform infrared spectroscopy (FTIR) spectroscopy, two-dimensional infrared (2D IR) spectroscopy, and molecular dynamics simulations. We found that, at the amino acid level, crowding drove dehydration of both sheet and turn peptide sites as well as free AHA. However, the subpicosecond dynamics showed highly individualized responses based on the local environment. Interestingly, while steady-state FTIR measurements revealed similar responses at the amino-acid level to hard versus soft crowding (dehydration), we found that PEG and glucose had opposite stabilizing and destabilizing effects on the protein secondary structure, emphasizing an important distinction in understanding the impact of crowding on protein structure as well as the role of crowding across length scales.

Opposing roles of organic salts on mini-protein structure

We investigated the effects of 1-ethyl-3-methylimidazolium chloride ([EMIM][Cl]) and choline chloride ([Chol][Cl]) on the local environment and conformational landscapes of Trp-cage and Trpzip4 mini-proteins using experimental and computational approaches. Fluorescence experiments and computational simulations revealed distinct behaviors of the mini-proteins in the presence of these organic salts. [EMIM][Cl] showed a strong interaction with Trp-cage, leading to fluorescence quenching and destabilization of its native structural interactions. Conversely, [Chol][Cl] had a negligible impact on Trp-cage fluorescence at low concentrations but increased it at high concentrations, indicating a stabilizing role. Computational simulations elucidated that [EMIM][Cl] disrupted the hydrophobic core packing and decreased proline-aromatic residue contacts in Trp-cage, resulting in a more exposed environment for Trp residues. In contrast, [Chol][Cl] subtly influenced the hydrophobic core packing, creating a hydrophobic environment near the tryptophan residues. Circular dichroism experiments revealed that [Chol][Cl] stabilized the secondary structure of both mini-proteins, although computational simulations did not show significant changes in secondary content at the explored concentrations. The simulations also demonstrated a more rugged free energy landscape for Trp-cage and Trpzip4 in [EMIM][Cl], suggesting destabilization of the tertiary structure for Trp-cage and secondary structure for Trpzip4. Similar fluorescence trends were observed for Trpzip4, with [EMIM][Cl] quenching fluorescence and exhibiting stronger interaction, while [Chol][Cl] increased the fluorescence at high concentrations. These findings highlight the interplay between [EMIM][Cl] and [Chol][Cl] with the mini-proteins and provide a detailed molecular-level understanding of how these organic salts impact the nearby surroundings and structural variations. Understanding such interactions is valuable for diverse applications, from biochemistry to materials science.

Exploring Heterogeneous Dynamical Environment around an Ensemble of Aβ42 Peptide Monomer Conformations

Exploring the conformational properties of amyloid β (Aβ) peptides and the role of solvent (water) in guiding the dynamical environment at their interfaces is crucial for microscopic understanding of Aβ misfolding, which is involved in causing the most common neurodegenerative disorder, i.e., Alzheimer's disease. While numerous studies in the past have emphasized examining the conformational states of Aβ peptides, the role of water has not received much attention. Here, we have performed all-atom molecular dynamics simulations of several full-length Aβ₄₂ peptide monomers with different initial configurations. Our efforts are directed toward probing the origin of the heterogeneous dynamics of water around various segments of the Aβ peptide, identified as the two terminal segments (N-term and C-term) and the two hydrophobic segments (hp1 and hp2), along with the central turn region interconnecting hp1 and hp2. Our results revealed that water hydrating hp1, hp2, and turn (nonterminal segments) and C-term segments exhibit nonuniformly restricted translational as well as rotational motions. The degree of such restriction has been found to be correlated with the hydrogen bond relaxation time scales at the interface. Importantly, it is revealed that the water molecules around hp1 and, to some extent, around hp2, form relatively rigid hydration layers, compared to that around the other segments. Such rigid hydration layers arise due to relatively more solid-like caging motions resulting in relatively lesser hydration entropy. As hp1 and hp2 have been demonstrated to play a central role in Aβ aggregation, we believe that distinct water dynamics in the vicinity of these two segments, as outlined in this study, can provide vital information in understanding the early stages of the onset of the aggregation process of such peptides at higher concentration that can further aid toward advances in AD therapeutics.

Hydration of a small protein under carbon nanotube confinement: Adsorbed substates induce selective separation of the dynamical response

The co-involvement of biological molecules and nanomaterials has increasingly come to the fore in modern-day applications. While the "bio-nano" (BN) interface presents physico-chemical characteristics that are manifestly different from those observed in isotropic bulk conditions, the underlying molecular reasons remain little understood; this is especially true of anomalies in interfacial hydration. In this paper, we leverage atomistic simulations to study differential adsorption characteristics of a small protein on the inner (concave) surface of a single-walled carbon nanotube whose diameter exceeds dimensions conducive to single-file water movement. Our findings indicate that the extent of adsorption is decided by the degree of foldedness of the protein conformational substate. Importantly, we find that partially folded substates, but not the natively folded one, induce reorganization of the protein hydration layer into an inner layer water closer to the nanotube axis and an outer layer water in the interstitial space near the nanotube walls. Further analyses reveal sharp dynamical differences between water molecules in the two layers as observed in the onset of increased heterogeneity in rotational relaxation and the enhanced deviation from Fickian behavior. The vibrational density of states reveals that the dynamical distinctions are correlated with differences in crucial bands in the power spectra. The current results set the stage for further systematic studies of various BN interfaces vis-à-vis control of hydration properties.

Effects of Metal Ions on Aβ42 Peptide Conformations from Molecular Simulation Studies

In this study, we investigate the conformational characteristics of full-length Aβ₄₂ peptide monomers in the presence of Na⁺ and Zn²⁺ metal ions using atomistic molecular dynamics (MD) simulations with an aim to explore the possible driving forces behind enhanced aggregation rates of the peptides in the presence of salts. The calculations reveal that the presence of metal ions shifts the conformational equilibrium more toward the compact ordered Aβ structures. Such compact ordered structures stabilized by distant nonlocal contacts between two crucial hydrophobic segments, hp1 and hp2, primarily through two important hydrophobic aromatic residues, Phe-19 and Phe-20, are expected to trigger the aggregation process at a faster rate by populating and stabilizing the aggregation prone structures. Formation of a significant number of such distant contacts in the presence of Na⁺ ions has also been found to result in breaking of the N-terminal helix. On the contrary, binding of Zn²⁺ ion to Aβ peptide is highly specific, which stabilizes the N-terminal helix instead of breaking it. This explains why the aggregation rate of Aβ peptides is higher in the presence of divalent Zn²⁺ ions than monovalent Na⁺ ions. Relatively higher overall stability of the most populated Aβ peptide monomers in the presence of Zn²⁺ ions has been found to be associated with specific Zn²⁺-Aβ binding and significant free energy gain.

Dynamical crossover of water confined within the amphiphilic nanocores of aggregated amyloid β peptides

It is believed that the self-assembly of amyloid beta (Aβ) peptides in the brain is the cause of Alzheimer's disease. Atomistic molecular dynamics simulations of aqueous solutions of Aβ protofilaments of different sizes at room temperature have been carried out to explore the dynamic properties of water confined within the core and at the exterior surface of the protofilaments. Attempts have been made to understand how the non-uniform distortion of the protofilaments associated with their structural crossover influences the diffusivity and the hydrogen bonding environment of the confined water molecules. In contrast to the homogeneous solvent dynamical environment at the exterior surface, the calculations revealed heterogeneously restricted motions of water confined within the distorted cores of the protofilaments. Importantly, it is demonstrated that the structural crossover of the aggregates observed for the decamer is associated with a dynamical transition of water confined within its core. A direct one-to-one correlation between the heterogeneously restricted core water motions and the kinetics of the breaking and formation of hydrogen bonds quantitatively demonstrated that a modified hydrogen bond arrangement within the cores of higher order Aβ protofilaments is the origin behind the crossover in core water mobility. A fraction of the water molecules forming short-lived water-water hydrogen bonds within the core of the crossover protofilament decamer are believed to diffuse away easily from the core and thus play a crucial role in further growth of the protofilament by facilitating the binding of new peptide monomers.