Folding Stability Research Articles

Multiplanar (4-Dimension) Breast Augmentation—A Personal Surgical Concept for Dynamic Implant-Tissue Interaction Providing Sustainable Shape Stability

In esthetic breast augmentation long-term shape stability and natural appearance remain an ongoing challenge. The authors found that to reduce the incidence of secondary deformity and increase the natural feel and appearance, a standard multiplanar procedure combining a subfascial and dual plane approach with fasciotomies will provide long-term stability and esthetic quality. The technique involves a submuscular dissection, release of the infranipple portion of the pectoralis muscle combined with the wide subfascial release of the breast gland, and scoring of the deep plane of the superficial glandular fascia. For long-term stability, a firm fixation of the glandular fascia at the inframammary fold to the deep layer of the abdomino-pectoral fascia is critical. Long-term results were analyzed for up to 10 years. Postoperative measurements proved the intrinsic balance of the breasts without significant changes over time. The overall complication rate was <5%. Shape stability was observed over 10 years in more than 95% of the patients. Unsightly muscular animation could be avoided in almost every patient. Our results indicate that a technique of multiplane breast augmentation provides long-term stability and esthetic quality. By combining the benefits of well-established techniques of a submuscular dual plane, additional shaping through a controlled deep fasciotomy and stable inframammary fold fixation some of the existing tradeoffs of the different methods can be avoided.

Comparative Analysis of Protein Folding Stability-Based Profiling Methods for Characterization of Biological Phenotypes.

Recently, a new suite of mass spectrometry-based proteomic methods has been developed that enables evaluation of protein folding stability on the proteomic scale. These methods utilize chemical and thermal denaturation approaches (SPROX and TPP, respectively) as well as proteolysis strategies (DARTS, LiP, and PP) to assess protein folding stability. The analytical capabilities of these technique have been well-established for protein target discovery applications. However, less is known about the relative advantages and disadvantages of using these different strategies to characterize biological phenotypes. Reported here is a comparative study of SPROX, TPP, LiP, and conventional protein expression level measurements using both a mouse model of aging and a mammalian cell culture model of breast cancer. Analyses on proteins in brain tissue cell lysates derived from 1- and 18-month-old mice (n = 4-5 at each time point) and on proteins in cell lysates derived from the MCF-7 and MCF-10A cell lines revealed a majority of the differentially stabilized protein hits in each phenotype analysis had unchanged expression levels. In both phenotype analyses, TPP generated the largest number and fraction of differentially stabilized protein hits. Only a quarter of all the protein hits identified in each phenotype analysis had a differential stability that was detected using multiple techniques. This work also reports the first peptide-level analysis of TPP data, which was required for the correct interpretation of the phenotype analyses performed here. Studies on selected protein stability hits also uncovered phenotype-related functional changes.

CRNAsp12 Web Server for the Prediction of Circular RNA Secondary Structures and Stabilities

Circular RNAs (circRNAs) are a novel class of non-coding RNA that, unlike linear RNAs, form a covalently closed loop without the 5' and 3' ends. Growing evidence shows that circular RNAs play important roles in life processes and have great potential implications in clinical and research fields. The accurate modeling of circRNAs structure and stability has far-reaching impact on our understanding of their functions and our ability to develop RNA-based therapeutics. The cRNAsp12 server offers a user-friendly web interface to predict circular RNA secondary structures and folding stabilities from the sequence. Through the helix-based landscape partitioning strategy, the server generates distinct ensembles of structures and predicts the minimal free energy structures for each ensemble with the recursive partition function calculation and backtracking algorithms. For structure predictions in the limited structural ensemble, the server also provides users with the option to set the structural constraints of forcing the base pairs and/or forcing the unpaired bases, such that only structures that meet the criteria are enumerated recursively.

A riboswitch separated from its ribosome-binding site still regulates translation.

Riboswitches regulate downstream gene expression by binding cellular metabolites. Regulation of translation initiation by riboswitches is posited to occur by metabolite-mediated sequestration of the Shine-Dalgarno sequence (SDS), causing bypass by the ribosome. Recently, we solved a co-crystal structure of a prequeuosine1-sensing riboswitch from Carnobacterium antarcticum that binds two metabolites in a single pocket. The structure revealed that the second nucleotide within the gene-regulatory SDS, G34, engages in a crystal contact, obscuring the molecular basis of gene regulation. Here, we report a co-crystal structure wherein C10 pairs with G34. However, molecular dynamics simulations reveal quick dissolution of the pair, which fails to reform. Functional and chemical probing assays inside live bacterial cells corroborate the dispensability of the C10-G34 pair in gene regulation, leading to the hypothesis that the compact pseudoknot fold is sufficient for translation attenuation. Remarkably, the C. antarcticum aptamer retained significant gene-regulatory activity when uncoupled from the SDS using unstructured spacers up to 10 nucleotides away from the riboswitch-akin to steric-blocking employed by sRNAs. Accordingly, our work reveals that the RNA fold regulates translation without SDS sequestration, expanding known riboswitch-mediated gene-regulatory mechanisms. The results infer that riboswitches exist wherein the SDS is not embedded inside a stable fold.

Mega-scale analysis of protein folding stability in biology and protein design.

Progress in DNA sequencing and machine learning have illuminated protein sequences and structures on an enormous scale, but protein thermodynamics remains invisible and largely unknown. New approaches are needed to reveal protein folding thermodynamics on the same enormous scale to overcome challenges in biology, medicine, and engineering. We present cDNA display proteolysis, a new method for measuring protein folding stability for up to 900,000 protein domains in a one-week experiment. From 1.7 million measurements in total, we curated a set of ∼800,000 high-quality folding stabilities comprehensively examining single amino acid variants of ∼350 natural and ∼250 de novo designed protein domains 40-72 amino acids in length. Using this immense dataset, we quantified (1) environmental factors influencing amino acid fitness, (2) thermodynamic couplings (including unexpected interactions) between protein sites, and (3) the global divergence between evolutionary amino acid usage and protein folding stability. We also demonstrated applications of our method and dataset to protein design. The unique scale, speed, and accuracy of cDNA display proteolysis hold the potential to reveal protein folding thermodynamics across the entire universe of protein domains.

Oncogenic mutations in the DNA-binding domain of FOXO1 that disrupt folding: Quantitative insights from experiments and molecular simulation.

FOXO1, a member of the family of winged-helix motif Forkhead box (FOX) transcription factors, is the most abundantly expressed FOXO member in mature B cells. Sequencing of diffuse large B-cell lymphoma (DLBCL) tumors and cell lines identified specific mutations in the forkhead domain linked to loss of function. Differential scanning calorimetry and thermal shift assays were used to characterize how eight of these mutations affect the stability of the FOX domain. Mutations L183P and L183R were found to be particularly destabilizing. Electrophoresis mobility shift assays show these same mutations also disrupt FOXO1 binding to their canonical DNA sequences, suggesting that the loss of function is due to destabilization of the folded structure. Computational modeling of the effect of mutations on FOXO1 folding was performed using alchemical free energy perturbation (FEP), and a Markov model of the entire folding reaction was constructed from massively parallel molecular simulations, which predicts folding pathways involving the late folding of helix α3. Although FEP can qualitatively predict the destabilization from L183 mutations, we find that a simple hydrophobic transfer model, combined with estimates of unfolded-state solvent-accessible surface areas from molecular simulations, is able to more accurately predict changes in folding free energies due to mutations. These results suggest that the atomic detail provided by simulations is important for the accurate prediction of mutational effects on folding stability. Corresponding disease-associated mutations in other FOX family members support further experimental and computational studies of the folding mechanism of FOX domains.

Folding stability at the anion-binding site distinguishes prestin from other SLC26 transporters as revealed by HDX-MS.

The outer hair cell protein prestin (SLC26A5) responds to transmembrane voltage fluctuations by changing its cross-sectional area. This process, known as electromotility, is fundamental to mammalian cochlear amplification. Though prestin belongs to the SLC26 family of membrane transporters, it is the only member capable of displaying electromotility. Prestin's associated charge movement is driven by the helical dipole between TM3 and TM10, the charged residue R399, and the bound anion, but the relative roles remain to be determined. Here, we investigated these issues by interrogating the dynamics of prestin and SLC26A9, a typical SLC26 anion transporter, using hydrogen-deuterium exchange mass spectrometry (HDX-MS). We show that the folding stability of the anion-binding site of prestin is at least 2.8 kcal/mol weaker than SLC26A9 while the remaining regions have similar stability. Anion binding to prestin reversibly folds the binding site by joining the TM3 and TM10 helices, ensuing allosteric modulation of the TMD dynamics. In contrast, anion binding minimally affects the stability of SLC26A9, including the TM3-TM10 dielectric gap. We find helix fraying at the binding site but cooperative unfolding for multiple peripheral helices, with potential structural and functional relevance. Our HDX-MS data not only validate recent cryo-EM structures, but also highlight the unique role of the bound anion driving the folding of prestin's anion-binding site. This phenomenon may have implications to prestin's voltage-sensing mechanism in the outer hair cells.

Monitoring the structural stability of the isolated 'Mg2+-sensor' of MgtE by spectroscopic and computational approaches.

MgtE is the primary magnesium transport system in ∼50% of bacteria, and its eukaryotic homologs are SLC41 family of solute carriers. The full-length MgtE from T. thermophilus is a homodimeric Mg2+ channel, which contains transmembrane and cytosolic domains. The cytoplasmic domain, which is connected to transmembrane domain through the plug helix, is proposed to primarily function as a Mg2+ sensor. We have monitored the folding and structural stability of the isolated cytoplasmic domain of MgtE (MgtETT-CD) under protein denaturing conditions using sophisticated spectroscopic approaches. Despite being a soluble protein, our results from size-exclusion chromatography, dynamic light scattering, CD measurements and various intrinsic tryptophan fluorescence approaches strongly demonstrate that MgtETT-CD is resistant to chemical and thermal denaturation. This is supported by the tryptophan lifetime distributions using MEM analysis of fluorescence decay and fluorescence quenching measurements. Interestingly, instead of denaturing the protein, it appears that chemical denaturants make the protein stably compact by modifying the secondary structural elements of MgtETT-CD. Like chemical denaturants, high temperature (>80 °C) also stabilizes the folded state, however, in contrast to denaturants, high temperature retains the α-helical nature of MgtETT-CD, suggesting that the mechanism of stabilization of the folded state of MgtETT-CD by chemical and physical means are different. Truncated versions of MgtETT-CD are also resistant to denaturation suggesting that the plug helix is not responsible for this unique behaviour of the Mg2+ sensor. An all-atom molecular dynamics simulation is currently underway to understand the nature of interaction of MgtETT-CD with denaturants. Taken together, our results show that the folded state organization of MgtETT-CD is not compromised under denaturing conditions. Overall, our results are relevant not only for understanding the nature of Mg2+-sensor of MgtE, but also in designing stable proteins.

Damage resistance of gamma crystallins: Weathering heat, UV, and ionizing radiation.

The γ-crystallins are structural and refractive proteins of the vertebrate lens. They belong to the βγ-crystallin superfamily, which is characterized by an exceptionally stable double-Greek key fold. In the context of the lens, these proteins must remain stable and soluble for the lifetime of the organism. Recent work in my group focuses on understanding how γ-crystallins maintain functionality in the face of damage caused by aging and oxidation. I will present results on the impact of heat, UV light, and ionizing radiation on human γS-crystallin and cataract-associated variants. We find that the γ-crystallins are not particularly resistant to damage; on the contrary, they appear to be selected for the ability to remain soluble even when the protein surface is significantly modified and transient unfolding intermediates are populated. These have been investigated using a variety of biophysical techniques, including circular dichroism, mass spectrometry, fluorescence, and NMR spectroscopy. In particular, mass spectrometry measurements on irradiated samples show evidence of both deamidation and oxidative damage, while high-resolution NMR data allow us to locate protein regions and specific residues that are involved in conformational changes, altered dynamics, and protein-protein contacts. We will discuss proposed aggregation mechanisms mediated by different types of protein modification, as well as the relevance of these findings to human cataract disease.

CHalf: Folding Stability Made Simple.

The structure of a protein defines its function and integrity and correlates with the protein folding stability (PFS). Quantifying PFS allows researchers to assess differential stability of proteins in different disease or ligand binding states, providing insight into protein efficacy and potentially serving as a metric of protein quality. There are a number of mass spectrometry (MS)-based methods to assess PFS, such as Thermal Protein Profiling (TPP), Stability of Proteins from Rates of Oxidation (SPROX), and Iodination Protein Stability Assay (IPSA). Despite the critical value that PFS studies add to the understanding of mechanisms of disease and treatment development, proteomics research is still primarily dominated by concentration-based studies. We found that a major reason for the lack of PFS studies is the lack of a user-friendly data processing tool. Here we present the first user-friendly software, CHalf, with a graphical user interface for calculating PFS. Besides calculating site-specific PFS of a given protein from chemical denature folding stability assays, CHalf is also compatible with thermal denature folding stability assays. CHalf also includes a set of data visualization tools to help identify changes in PFS across protein sequences and in between different treatment conditions. We expect the introduction of CHalf to lower the barrier of entry for researchers to investigate PFS, promoting the usage of PFS in studies. In the long run, we expect this increase in PFS research to accelerate our understanding of the pathogenesis and pathophysiology of disease.

De novo protein fold design through sequence-independent fragment assembly simulations

De novo protein design generally consists of two steps, including structure and sequence design. Many protein design studies have focused on sequence design with scaffolds adapted from native structures in the PDB, which renders novel areas of protein structure and function space unexplored. We developed FoldDesign to create novel protein folds from specific secondary structure (SS) assignments through sequence-independent replica-exchange Monte Carlo (REMC) simulations. The method was tested on 354 non-redundant topologies, where FoldDesign consistently created stable structural folds, while recapitulating on average 87.7% of the SS elements. Meanwhile, the FoldDesign scaffolds had well-formed structures with buried residues and solvent-exposed areas closely matching their native counterparts. Despite the high fidelity to the input SS restraints and local structural characteristics of native proteins, a large portion of the designed scaffolds possessed global folds completely different from natural proteins in the PDB, highlighting the ability of FoldDesign to explore novel areas of protein fold space. Detailed data analyses revealed that the major contributions to the successful structure design lay in the optimal energy force field, which contains a balanced set of SS packing terms, and REMC simulations, which were coupled with multiple auxiliary movements to efficiently search the conformational space. Additionally, the ability to recognize and assemble uncommon super-SS geometries, rather than the unique arrangement of common SS motifs, was the key to generating novel folds. These results demonstrate a strong potential to explore both structural and functional spaces through computational design simulations that natural proteins have not reached through evolution.

Direct Observation and Real-Time Tracking of an Extraordinarily Stable Folding Intermediate in Mitotic Arrest Deficient Protein 2 Folding by Single-Molecule Fluorescence Resonance Energy Transfer.

Although ensemble experiments have suggested that mitotic arrest deficient protein 2 (Mad2), a metamorphic protein, has folding intermediates, direct evidence and characterization are not available. It remains an outstanding challenge to capture the folding intermediates in real time, which is crucial to elucidate the folding mechanism, but the folding intermediates are normally unstable and only exist transiently. By combining confocal-microscopy-based and total internal reflection fluorescence (TIRF)-microscopy-based single-molecule Förster resonance energy transfer (sm-FRET) techniques, we have investigated the folding/unfolding process of Mad2 and captured its folding intermediate at the single-molecule level. This provides direct evidence for the existence of an intermediate along the folding pathway of Mad2. The folding intermediate proved to be extraordinarily stable, with an extremely long average dwell time of 2.3 s under the conditions of 3 M GdmCl at ambient temperature. The folding trajectories obtained from TIRF experiments further suggest that the intermediate is on-pathway to native Mad2.

Multi-omics analysis revealed the role of CCT2 in the induction of autophagy in Alzheimer's disease.

Chaperonin containing TCP1 subunit 2 (CCT2) is essential in various neurodegenerative diseases, albeit its role in the pathogenesis of Alzheimer's disease (AD) remains elusive. This study aimed to evaluate the role of CCT2 in Alzheimer's disease. First, bioinformatics database analysis revealed that CCT2 was significantly downregulated in patients with Alzheimer's disease and associated with autophagic clearance of β-amyloid. The 789 differentially expressed genes overlapped in AD-group and CCT2-low/high group, and the CCT2-high-associated genes screened by Pearson coefficients were enriched in protein folding, autophagy, and messenger RNA stability regulation pathways. These results suggest that CCT2 is significantly and positively associated with multiple pathways linked to autophagy and negatively associated with neuronal death. The logistic prediction model with 13 key genes, such as CCT2, screened in this study better predicts Alzheimer's disease occurrence (AUC = 0.9671) and is a favorable candidate for predicting potential biological targets of Alzheimer's disease. Additionally, this study predicts reciprocal micro RNAs and small molecule drugs for hub genes. Our findings suggest that low CCT2 expression may be responsible for the autophagy suppression in Alzheimer's disease, providing an accurate explanation for its pathogenesis and new targets and small molecule inhibitors for its treatment.

DMSO-Induced Unfolding of the Antifungal Disulfide Protein PAF and Its Inactive Variant: A Combined NMR and DSC Study.

PAF and related antifungal proteins are promising antimicrobial agents. They have highly stable folds around room temperature due to the presence of 3-4 disulfide bonds. However, unfolded states persist and contribute to the thermal equilibrium in aqueous solution, and low-populated states might influence their biological impact. To explore such equilibria during dimethyl sulfoxide (DMSO)-induced chemical unfolding, we studied PAF and its inactive variant PAFD19S using nuclear magnetic resonance (NMR) and differential scanning calorimetry (DSC). According to the NMR monitoring at 310 K, the folded structures disappear above 80 v/v% DMSO concentration, while the unfolding is completely reversible. Evaluation of a few resolved peaks from viscosity-compensated 15N-1H HSQC spectra of PAF yielded ∆G = 23 ± 7 kJ/M as the average value for NMR unfolding enthalpy. The NMR-based structures of PAF and the mutant in 50 v/v% DMSO/H2O mixtures were more similar in the mixed solvents then they were in water. The 15N NMR relaxation dynamics in the same mixtures verified the rigid backbones of the NMR-visible fractions of the proteins; still, enhanced dynamics around the termini and some loops were observed. DSC monitoring of the Tm melting point showed parabolic dependence on the DMSO molar fraction and suggested that PAF is more stable than the inactive PAFD19S. The DSC experiments were irreversible due to the applied broad temperature range, but still suggestive of the endothermic unfolding of PAF.

Evaluation of exogenous therapeutic protein activity under confinement and crowding effects.

Dysfunction of intracellular proteins is frequently associated with various diseases, such as cancer. The exogenous proteins in cells are usually assembled with specific configurations due to physiological confinement/crowding to exhibit novel features in the protein structure, folding or conformational stability, distinguished with their behaviors in buffer solutions. Here, we synthesized exogenous proteins under confined/crowded conditions, to explore protein activity within cells. The findings suggested that the confinement and crowding effects on protein activity are heterogeneous; they showed an inhibitory effect on HRP by decreasing Km from ∼9.5- and ∼21.7-fold and Vmax from ∼6.8- and ∼20.2-fold lower than that of dilute solutions. Interestingly, the effects on Cyt C seem to be more complicated, and crowding exerts a positive effect by increasing Km ∼ 3.6-fold and Vmax ∼ 1.5-fold higher than that of dilute solutions; however, confinement exhibits a negative effect by decreasing Km ∼2.0 and Vmax ∼8.3 times. Additionally, in contrast to traditional nanoparticle-based confinement models, we synthesized a biodegradable nanoparticle to mimic the confined space, and the biggest advantage of this novel model is that the particles can be degraded and thus it can provide more intuitive observations of the properties of the target proteins under confinement and after release. Furthermore, we also evaluated protein activity in different cellular environments, indicating that the exogenous protein activity was closely related to the crowdedness of cellular environments, and the inhibition of protein activity in MDA-MB-231 cancer cells was more obvious than in HEK293 normal cells. Finally, SAXS analysis revealed the correlation between the protein conformation and the different environments. Our work will provide a unique method for precisely assessing whether the target cellular environments are native matrix in which specific exogenous protein drugs are delivered to function or whether they display a therapeutic role, which is of great significance for screening and development of new drugs.

Origins of life: first came evolutionary dynamics.

When life arose from prebiotic molecules 3.5 billion years ago, what came first? Informational molecules (RNA, DNA), functional ones (proteins), or something else? We argue here for a different logic: rather than seeking a molecule type, we seek a dynamical process. Biology required an ability to evolve before it could choose and optimise materials. We hypothesise that the evolution process was rooted in the peptide folding process. Modelling shows how short random peptides can collapse in water and catalyse the elongation of others, powering both increased folding stability and emergent autocatalysis through a disorder-to-order process.

Abstract 2748: Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues

Abstract 2748: Protein folding stabilities are a major determinant of oxidation rates for buried methionine residues

Redox processes in Cu-binding proteins: the "in-between" states in intrinsically disordered peptides.

We report on a concept that some of us first described a decade ago for pure electron transfer [V. Balland, C. Hureau and J.-M. Savéant, Proc. Natl. Acad. Sci. U. S. A., 2010, 107, 17113]. In the present viewpoint, based on more recent results, we refine and extend this "in-between state" concept to explain the formation of reactive oxygen species by copper ions bound to the amyloid-β (Aβ) peptide involved in Alzheimer's disease. In such intrinsically disordered peptides, the Cu coordination is versatile due to the lack of stable folding and the presence of multiple possible binding anchors. Hence, the Cu(I) and Cu(II) ions do impose their favoured sites, with Cu(I) bound in a linear fashion between two His residues and Cu(II) in a square-based pyramid bound to Asp1 amine and carbonyl groups and two His residues in the equatorial plane. Hence a direct electron transfer is prevented and alternatively an in-between state (IBS) mechanism applies, whose description and analysis with respect to other electron transfer processes is the topic of the present viewpoint.

Extension Peptide of Plant Ferritin from Setaria italica Presents a Novel Fold

The extension peptide (EP) is the most distinctive feature of mature plant ferritin. Some EPs have exhibited serine-like protease activity, which is associated with iron uptake and release. EP forms a helix and a long loop, followed by a conserved core helical bundle. However, whether the EP adopts a stable or uniform folding pattern in all plants remains unclear. To clarify this, we investigated the crystal structure of ferritin-1 from Setaria italica (SiFer1), a type of monocotyledon. In our structure of SiFer1, the EP is different from other EPs in other solved structures of plant ferritins and consisted of a pair of β-sheets, a shorter helix, and two loops, which masks two hydrophobic pockets on the outer surface of every subunit. Furthermore, sequence analysis and structure comparison suggest that the EPs in ferritins from monocotyledons may adopt a novel fold pattern, and the conformations of EPs in ferritins are alterable among different plant species. Furthermore, additional eight iron atoms were first founded binding in the fourfold channels, demonstrating the vital function of fourfold channels in iron diffusion. In all, our structure provides new clues for understanding plant ferritins and the functions of the EP.

Simplified modelling of self-piercing riveted joints and application in crashworthiness analysis for steel-aluminium hybrid beams

In this paper, an equivalent simplified model of self-piercing riveting (SPR-ESM) validated by tests is constructed to characterize the macroscopic mechanical responses of SPR joints under quasi-static and dynamic loading conditions. The application of SPR-ESM in the crashworthiness analysis of steel-aluminium hybrid beam is investigated. The results reveal that the failure of the riveting point in the test specimen is accurately simulated by the numerical model connected by SPR-ESM, and relative errors of mechanical responses between simulation and test are controlled within 7 %. Parametric study is performed to explore the effect of the riveting point failure on the mechanical performance of steel-aluminium hybrid beam under different loading angles. The results indicate that: (1) a severe instability deformation mode of steel-aluminium hybrid beam is easily to happen when the loading angles increases; (2) the effect of riveting point failure on the mechanical performance of steel-aluminium hybrid beam is limited when the beam has a stable folding deformation; and (3) a significant decrease in the ability of resisting deformation and energy absorption is easily to happen when the steel-aluminium hybrid beam has a severe instability deformation mode.