Destabilization of Hydrophobic Core of Chicken Villin Headpiece in Guanidinium Chloride Induced Denaturation: Hint of π-Cation Interaction

Osmolyte-induced conformational stabilization of a hydrophobic polymer

Elucidating the mechanistic role of osmolytes on conformations of hydrophobic prototypical macromolecules in principle is the stepping stone towards understanding the effect of osmolytes on proteins. Motivated by this, we use equilibrium simulations and umbrella sampling techniques to dissect the underlying mechanism of osmolyte-induced conformational stability of a hydrophobic polymer. Our results unveil a remarkable osmolyte-dependent conformational stabilization of the polymer. In an aqueous solution of 4 M choline chloride (ChCl), the polymer has an even more compact structure than in water. On the other hand, an aqueous solution of 8 M urea stabilizes the extended state of the polymer. Interestingly, the polymer adopts an intermediate hairpin conformation in a mixed osmolyte solution of 4 M ChCl and 8 M urea in water due to the interplay of ChCl and urea. Our simulations identify the relative accumulation of water and the hydrophilic part of choline or preferential binding of urea near the collapsed and the extended states, respectively. Analyses split out the enthalpic and entropic contributions to the overall free energy. This decides the stabilization of the preferred conformation in the chosen osmolyte solution. Our simulations show that in an aqueous solution of ChCl, the hairpin state is stabilized by entropy gain. In contrast, the enthalpic contribution stabilizes the hairpin state in mixed environments. However, a collapsed state is energetically not favored in the presence of urea. In brief, via employing an in silico approach, the current findings indicate the importance of osmolytes in stabilizing the conformational states of hydrophobic polymers.

Optimized Collective Variable for Collapse Transition in Linear Hydrophobic Polymers: Importance of Hydration Water and End-to-End Distance

Choosing an appropriate collective variable (CV) for any biomolecular process is a challenging task. Researchers are developing methods to solve this issue using a variety of methodologies, most recently using machine learning (ML) methods. In this work, we investigate the mechanism of collapse transition across various lengths of polymer systems through adaptively sampled multiple short trajectories utilizing the Time Lagged Independent Component Analysis (TICA) framework. From TICA analysis, it is revealed that the radius of gyration (Rg) and end-to-end distance serve as good order parameters (OPs) for these systems describing overall energy landscapes. Markov state model (MSM) and mean first passage time (MFPT) analysis suggest that hydration water (Nw) plays a determining role in dictating the time scale and barrier for the collapsed transition for the C40 system. P-fold analysis on identifying transition state ensembles (TSE) identified by committor analysis also strengthens the role of Nw in such a transition. TICA, MSM, and committor analyses on the collapse transition for C45 reveal similarities with C40 systems in different aspects. Furthermore, we propose a pipeline integrating XGBoost regression along with an interpretable ML model, Shapley Additive exPlanation (SHAP) to precisely elucidate the contribution of each OP locally at the TSE. Through this approach, we observe that the collapse transition is primarily driven by Nw for both polymer systems. A carefully designed protocol for the collapsed transition of C60 systems indirectly reiterates the above result. Overall, our results suggest that while the end-to-end distance should be considered for better resolution of metastable states in the landscape, Nw is the crucial coordinate to be used in enhanced sampling for the exploration of actual collapse transitions for linear hydrophobic polymer systems. The Python code for analyzing the contribution of different OPs in the TSE using an ML-aided protocol is available on GitHub (https://github.com/saikat-ai/linear_polymer_project).

Expression, purification, and characterisation of the p53 binding domain of Retinoblastoma binding protein 6 (RBBP6)

RBBP6 is a 250 kDa eukaryotic protein known to be a negative regulator of p53 and essential for embryonic development. Furthermore, RBBP6 is a critical element in carcinogenesis and has been identified as a potential biomarker for certain cancers. RBBP6's ability to interact with p53 and cause its degradation makes it a potential drug target in cancer therapy. Therefore, a better understating of the p53 binding domain of RBBP6 is needed. This study presents a three-part purification protocol for the polyhistidine-tagged p53 binding domain of RBBP6, expressed in Escherichia coli bacterial cells. The purified recombinant domain was shown to have structure and is functional as it could bind endogenous p53. We characterized it using clear native PAGE and far-UV CD and found that it exists in a single form, most likely monomer. We predict that its secondary structure is predominantly random coil with 19% alpha-helices, 9% beta-strand and 14% turns. When we exposed the recombinant domain to increasing temperature or known denaturants, our investigation suggested that the domain undergoes relatively small structural changes, especially with increased temperature. Moreover, we notice a high percentage recovery after returning the domain close to starting conditions. The outcome of this study is a pure, stable, and functional recombinant RBBP6-p53BD that is primarily intrinsically disordered.

Exploring the role of hydrophilic amino acids in unfolding of protein in aqueous ethanol solution

Hydrophobic association is the key contributor behind the formation of well packed core of a protein which is often believed to be an important step for folding from an unfolded chain to its compact functional form. While most of the protein folding/unfolding studies have evaluated the changes in the hydrophobic interactions during chemical denaturation, the role of hydrophilic amino acids in such processes are not discussed in detail. Here we report the role of the hydrophilic amino acids behind ethanol induced unfolding of protein. Using free energy simulations, we show that chicken villin head piece (HP-36) protein unfolds gradually in presence of water-ethanol binary mixture with increasing composition of ethanol. However, upon mutation of hydrophilic amino acids by glycine while keeping the hydrophobic amino acids intact, the compact state of the protein is found to be stable at all compositions with gradual flattening of the free energy landscape upon increasing compositions. The local environment around the protein in terms of ethanol/water number significantly differs in wild type protein compared to the mutated protein. The calculated Wyman-Tanford preferential binding coefficient of ethanol for wild type protein reveals that a greater number of cosolutes (here ethanol) bind to the unfolded state compared to its folded state. However, no significant increase in binding coefficient of ethanol at the unfolded state is found for mutated protein. Local-bulk partition coefficient calculation also suggests similar scenarios. Our results reveal that the weakening of hydrophobic interactions in aqueous ethanol solution along with larger preferential binding of ethanol to the unfolded state mediated by hydrophilic amino acids combinedly helps unfolding of protein in aqueous ethanol solution.

Factors Promoting the Formation of Clathrate-Like Ordering of Water in Biomolecular Structure at Ambient Temperature and Pressure

Clathrate hydrate forms when a hydrophobic molecule is entrapped inside a water cage or cavity. Although biomolecular structures also have hydrophobic patches, clathrate-like water is found in only a limited number of biomolecules. Also, while clathrate hydrates form at low temperature and moderately higher pressure, clathrate-like water is observed in biomolecular structure at ambient temperature and pressure. These indicate presence of other factors along with hydrophobic environment behind the formation of clathrate-like water in biomolecules. In the current study, we presented a systematic approach to explore the factors behind the formation of clathrate-like water in biomolecules by means of molecular dynamics simulation of a model protein, maxi, which is a naturally occurring nanopore and has clathrate-like water inside the pore. Removal of either confinement or hydrophobic environment results in the disappearance of clathrate-like water ordering, indicating a coupled role of these two factors. Apart from these two factors, clathrate-like water ordering also requires anchoring groups that can stabilize the clathrate-like water through hydrogen bonding. Our results uncover crucial factors for the stabilization of clathrate-like ordering in biomolecular structure which can be used for the development of new biomolecular structure promoting clathrate formation.

Molecular Insights into the Unusual Structure of an Antifreeze Protein with a Hydrated Core

The primary driving force for protein folding is the formation of a well-packed, anhydrous core. However, recently, the crystal structure of an antifreeze protein, maxi, has been resolved where the core of the protein is filled with water, which apparently contradicts the existing notion of protein folding. Here, we have performed standard molecular dynamics (MD) simulation, replica exchange MD (REMD) simulation, and umbrella sampling using TIP4P water at various temperatures (300, 260, and 240 K) to explore the origin of this unusual structural feature. It is evident from standard MD and REMD simulations that the protein is found to be stable at 240 K in its unusual state. The core of protein has two layers of semi-clathrate water separating the methyl groups of alanine residues from different helical strands. However, with increasing temperature (260 and 300 K), the stability decreases as the core becomes dehydrated, and methyl groups of alanine are tightly packed driven by hydrophobic interactions. Calculation of the potential of mean force by an umbrella sampling technique between a pair of model hydrophobes resembling maxi protein at 240 K shows the stabilization of second solvent-separated minima (SSM), which provides a thermodynamic rationale of the unusual structural feature in terms of weakening of the hydrophobic interaction. Because the stabilization of SSMs is implicated for cold denaturation, it suggests that the maxi protein is so designed by nature where the cold denatured-like state becomes the biologically active form as it works near or below the freezing point of water.

Towards Rational Chemosensor Design through Improved Understanding of Experimental Parameter Variation and Tolerance in Cyclodextrin-Promoted Fluorescence Detection

We have previously developed a highly efficient fluorescence-based toxicant-detection method that operates in complex environments to detect aromatic toxicants and toxicant metabolites with high sensitivity and selectivity. This method relies on the ability of γ-cyclodextrin to act as a supramolecular scaffold, and uses a variety of non-covalent interactions between the cyclodextrin, toxicant, and fluorophore to enable efficient detection. Reported herein is an investigation of the effect of various experimental parameters, including host concentration, temperature, pH, salt, and solvent, on the observed energy-transfer efficiencies. These results advance our understanding of γ-cyclodextrin-based association complexes and provide crucial information for the development of fluorescence-based sensors using such complexation and the resultant fluorescence-based detection.

Protein unfolding mechanisms and their effects on folding experiments

In this review, I discuss the various methods researchers use to unfold proteins in the lab in order to understand protein folding both in vitro and in vivo. The four main techniques, chemical-, heat-, pressure- and force-denaturation, produce distinctly different unfolded conformational ensembles. Recent measurements have revealed different folding kinetics from different unfolding mechanisms. Thus, comparing these distinct unfolded ensembles sheds light on the underlying free energy landscape of folding.