The Protein Unfolded State: One, No One and One Hundred Thousand

Mitochondria and MICOS - function and modeling

An extensive review is presented on mitochondrial structure and function, mitochondrial proteins, the outer and inner membranes, cristae, the role of F1FO-ATP synthase, the mitochondrial contact site and cristae organizing system (MICOS), the sorting and assembly machinery morphology and function, and phospholipids, in particular cardiolipin. Aspects of mitochondrial regulation under physiological and pathological conditions are outlined, in particular the role of dysregulated MICOS protein subunit Mic60 in Parkinson's disease, the relations between mitochondrial quality control and proteins, and mitochondria as signaling organelles. A mathematical modeling approach of cristae and MICOS using mechanical beam theory is introduced and outlined. The proposed modeling is based on the premise that an optimization framework can be used for a better understanding of critical mitochondrial function and also to better map certain experiments and clinical interventions.

High-Throughput Molecular Modeling and Evaluation of the Anti-Inflammatory Potential of Açaí Constituents against NLRP3 Inflammasome

The search for bioactive compounds in natural products holds promise for discovering new pharmacologically active molecules. This study explores the anti-inflammatory potential of açaí (Euterpe oleracea Mart.) constituents against the NLRP3 inflammasome using high-throughput molecular modeling techniques. Utilizing methods such as molecular docking, molecular dynamics simulation, binding free energy calculations (MM/GBSA), and in silico toxicology, we compared açaí compounds with known NLRP3 inhibitors, MCC950 and NP3-146 (RM5). The docking studies revealed significant interactions between açaí constituents and the NLRP3 protein, while molecular dynamics simulations indicated structural stabilization. MM/GBSA calculations demonstrated favorable binding energies for catechin, apigenin, and epicatechin, although slightly lower than those of MCC950 and RM5. Importantly, in silico toxicology predicted lower toxicity for açaí compounds compared to synthetic inhibitors. These findings suggest that açaí-derived compounds are promising candidates for developing new anti-inflammatory therapies targeting the NLRP3 inflammasome, combining efficacy with a superior safety profile. Future research should include in vitro and in vivo validation to confirm the therapeutic potential and safety of these natural products. This study underscores the value of computational approaches in accelerating natural product-based drug discovery and highlights the pharmacological promise of Amazonian biodiversity.

Elucidating the influence of electrostatic force on the re-arrangement of H-bonds of protein polymers in the presence of salts

Polyampholytes/proteins have an intriguing network of hydrogen bonds (H-bonds), especially their secondary structure, which plays a crucial role in determining the conformational stability of the polymer. The changes in protein secondary structure in the protein-salt system have been extensively deciphered by researchers, yet their pathways for breakage and recreation are unknown. Understanding the mechanism of protein conformational changes towards their biological activities, like protein folding, remains one of the main challenges and requires multiscale analysis of this strongly correlated system. Herein, salts have been used to reveal the re-arrangement behavior in the H-bond network of proteins under the influence of electrostatic interactions, as the strength of electrostatic forces is much stronger than that of H-bonds. At lower salt concentrations, there are negligible changes in the secondary structures as the electrostatic forces induced by the salt ions are less. Later, the existing H-bonds break and reconstruct new H-bonds at higher salt concentrations due to the influence of the stronger electrostatic interaction induced by the large number of salt ions. Molecular dynamics (MD) simulations and FTIR studies have been used rigorously to decipher the reason behind the re-arrangement of the H-bonds within gelatin (protein). The re-arrangement in the H-bond has also been observed with time from simulations and experiments. Thus, this study could provide a fresh perspective on the conformational changes of polyampholytes/proteins and will also influence the studies of protein folding-unfolding interaction in the presence of salt ions.

Understanding the heterogeneity intrinsic to protein folding

Relating the native fold of a protein to its amino acid sequence remains a fundamental problem in biology. While computer algorithms have demonstrated recently their prowess in predicting what structure a particular amino acid sequence will fold to, an understanding of how and why a specific protein fold is achieved remains elusive. A major challenge is to define the role of conformational heterogeneity during protein folding. Recent experimental studies, utilizing time-resolved FRET, hydrogen-exchange coupled to mass spectrometry, and single-molecule force spectroscopy, often in conjunction with simulation, have begun to reveal how conformational heterogeneity evolves during folding, and whether an intermediate ensemble of defined free energy consists of different sub-populations of molecules that may differ significantly in conformation, energy and entropy.

Unfolding under Pressure: An NMR Perspective

This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.

yGPS-P: A Yeast-Based Peptidome Screen for Studying Quality Control-Associated Proteolysis

Quality control-associated proteolysis (QCAP) is a fundamental mechanism that maintains cellular homeostasis by eliminating improperly folded proteins. In QCAP, the exposure of normally hidden cis-acting protein sequences, termed degrons, triggers misfolded protein ubiquitination, resulting in their elimination by the proteasome. To identify the landscape of QCAP degrons and learn about their unique features we have developed an unbiased screening method in yeast, termed yGPS-P, which facilitates the determination of thousands of proteome-derived sequences that enhance proteolysis. Here we describe the fundamental features of the yGPS-P method and provide a detailed protocol for its use as a tool for degron search. This includes the cloning of a synthetic peptidome library in a fluorescence-based reporter system, and data acquisition, which entails the combination of Fluorescence-Activated Cell Sorting (FACS) and Next-Generation Sequencing (NGS). We also provide guidelines for data extraction and analysis and for the application of a machine-learning algorithm that established the evolutionarily conserved amino acid preferences and secondary structure propensities of QCAP degrons.