Folding Efficiency Research Articles

Synthetic Studies of the Mutant Proinsulin Syndrome Demonstrate Correlation Between Folding Efficiency and Age of Diabetes Onset

Synthetic Studies of the Mutant Proinsulin Syndrome Demonstrate Correlation Between Folding Efficiency and Age of Diabetes Onset

Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds.

Peptides are an emerging modality for developing therapeutics that can either agonize or antagonize cellular pathways associated with disease, yet peptides often suffer from poor chemical and physical stability, which limits their potential. However, naturally occurring disulfide-constrained peptides (DCPs) and de novo designed Hyperstable Constrained Peptides (HCPs) exhibiting highly stable and drug-like scaffolds, making them attractive therapeutic modalities. Previously, we established a robust platform for discovering peptide therapeutics by utilizing multiple DCPs as scaffolds. However, we realized that those libraries could be further improved by considering the foldability of peptide scaffolds for library design. We hypothesized that specific sequence patterns within the peptide scaffolds played a crucial role in spontaneous folding into a stable topology, and thus, these sequences should not be subject to randomization in the original library design. Therefore, we developed a method for designing highly diverse DCP libraries while preserving the inherent foldability of each scaffold. To achieve this, we first generated a large-scale dataset from yeast surface display (YSD) combined with shotgun alanine scan experiments to train a machine-learning (ML) model based on techniques used for natural language understanding. Then we validated the ML model with experiments, showing that it is able to not only predict the foldability of peptides with high accuracy across a broad range of sequences but also pinpoint residues critical for foldability. Using the insights gained from the alanine scanning experiment as well as prediction model, we designed a new peptide library based on a de novo-designed HCP, which was optimized for enhanced folding efficiency. Subsequent panning trials using this library yielded promising hits having good folding properties. In summary, this work advances peptide or small protein domain library design practices. These findings could pave the way for the efficient development of peptide-based therapeutics in the future.

Mechanically rigid metallopeptide nanostructures achieved by highly efficient folding

AbstractNatural proteins must fold into complex three-dimensional structures to achieve excellent mechanical properties vital for biological functions, but this has proven to be exceptionally difficult to control in synthetic systems. As such, the long-standing issue of low mechanical rigidity and stability induced by misfolding constrains the physical and chemical properties of self-assembling peptide materials. Here we introduce a mixed-chirality strategy that enhances folding efficiency in topologically interlocked metallopeptide nanostructures. The orderly entanglement of heterochiral peptide-derived linkers can fold into a compact three-dimensional catenane. These folding-mediated secondary structural changes not only generate biomimetic binding pockets derived from individual peptide strands but also result in strong chiral amplification by the tight interlocking manner. Notably, this strategic ‘chirality mutation’ alters their arrangement into tertiary structures and is pivotal in achieving exceptional mechanical rigidity observed in the metallopeptide crystals, which exhibit a Young’s modulus of 157.6 GPa, approximately tenfold higher than the most rigid proteinaceous materials in nature. This unusual nature is reflected in enhanced peptide-binding properties and heightened antimicrobial activities relative to its unfolded counterpart.

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Chemical synthesis of mirror‐image D‐version of the immunoglobulin‐like domain of TrkA (DlgCTrkA), a protein molecule needed for mirror‐image screening of D‐peptide ligands targeting TrkA, was found to be difficult due to the poor efficiency of intermediate synthesis and final protein folding. To solve this problem, the strategy of removable glycosylation modification was used and found to effectively improve the yield of peptide segment synthesis and ligation. Interestingly, it is important to note that temporary glycosylation at distinct sites of DlgCTrkA led to significant differences in the process of protein folding. More details are discussed in the article by Li et al. on pages 2316—2322.image

Determining of the effect of reinforcing microrelief guides on the efficiency of folding integrated covers

The object of research is the processes of strengthening the working surfaces of profile folding strips made of stainless steel AISI 347 and carbon steel AISI 1005 using laser formation of microrelief guides. The analytical and experimental studies are based on the technique of laser microrelief formation by pulsed laser effects. The main assumption of the study is that the use of laser microrelief formation could increase the hardness and wear resistance of the folding strips, improving the process of folding integrated covers. Analyzing the effect of different hardening methods on the mechanical properties and wear resistance of the working surfaces of folding strips is necessary to achieve this goal. A methodology for assessing microstructural changes and their impact on the mechanical properties of folding strips during laser hardening has been proposed. It has been shown that the formation of microrelief guides by laser pulse exposure reduces the thermal load on the material, increases the uniformity of hardening and wear resistance. The revealed wear rates calculated for carbon steel AISI 1005 are 0.875, and for stainless steel AISI 347 – 0.345. To improve the accuracy and efficiency of the folding process, a methodology has been devised for calculating the quantitative formation of microrelief guides on the working surface of profile folding strips. This will not only improve the wear resistance and mechanical properties of the strips but also optimize production processes. Differences in the results of hardening for stainless steel AISI 347 and carbon steel AISI 1005 were found: the hardness values for AISI 347 are 3,088–4,904 MPa at a load of 50–350 g with a deviation of 37.1 %, and for AISI 1005 – 2141–1665 MPa with a deviation of 22.3 %

Divergent folding-mediated epistasis among unstable membrane protein variants.

Many membrane proteins are prone to misfolding, which compromises their functional expression at the plasma membrane. This is particularly true for the mammalian gonadotropin-releasing hormone receptor GPCRs (GnRHR). We recently demonstrated that evolutionary GnRHR modifications appear to have coincided with adaptive changes in cotranslational folding efficiency. Though protein stability is known to shape evolution, it is unclear how cotranslational folding constraints modulate the synergistic, epistatic interactions between mutations. We therefore compared the pairwise interactions formed by mutations that disrupt the membrane topology (V276T) or tertiary structure (W107A) of GnRHR. Using deep mutational scanning, we evaluated how the plasma membrane expression of these variants is modified by hundreds of secondary mutations. An analysis of 251 mutants in three genetic backgrounds reveals that V276T and W107A form distinct epistatic interactions that depend on both the severity and the mechanism of destabilization. V276T forms predominantly negative epistatic interactions with destabilizing mutations in soluble loops. In contrast, W107A forms positive interactions with mutations in both loops and transmembrane domains that reflect the diminishing impacts of the destabilizing mutations in variants that are already unstable. These findings reveal how epistasis is remodeled by conformational defects in membrane proteins and in unstable proteins more generally.

Divergent folding-mediated epistasis among unstable membrane protein variants

Many membrane proteins are prone to misfolding, which compromises their functional expression at the plasma membrane. This is particularly true for the mammalian gonadotropin-releasing hormone receptor GPCRs (GnRHR). We recently demonstrated that evolutionary GnRHR modifications appear to have coincided with adaptive changes in cotranslational folding efficiency. Though protein stability is known to shape evolution, it is unclear how cotranslational folding constraints modulate the synergistic, epistatic interactions between mutations. We therefore compared the pairwise interactions formed by mutations that disrupt the membrane topology (V276T) or tertiary structure (W107A) of GnRHR. Using deep mutational scanning, we evaluated how the plasma membrane expression of these variants is modified by hundreds of secondary mutations. An analysis of 251 mutants in three genetic backgrounds reveals that V276T and W107A form distinct epistatic interactions that depend on both the severity and the mechanism of destabilization. V276T forms predominantly negative epistatic interactions with destabilizing mutations in soluble loops. In contrast, W107A forms positive interactions with mutations in both loops and transmembrane domains that reflect the diminishing impacts of the destabilizing mutations in variants that are already unstable. These findings reveal how epistasis is remodeled by conformational defects in membrane proteins and in unstable proteins more generally.

ER stress-induced transcriptional response reveals tolerance genes in yeast.

Saccharomyces cerevisiae is important for protein secretion studies, yet the complexities of protein synthesis and secretion under endoplasmic reticulum (ER) stress conditions remain not fully understood. ER stress, triggered by alterations in the ER protein folding environment, poses substantial challenges to cells, especially during heterologous protein production. In this study, we used RNA-seq to analyze the transcriptional responses of yeast strains to ER stress induced by reagents such as tunicamycin (Tm) or dithiothreitol (DTT). Our gene expression analysis revealed several crucial genes, such as HMO1 and BIO5, that are involved in ER-stress tolerance. Through metabolic engineering, the best engineered strain R23 with HMO1 overexpression and BIO5 deletion, showed enhanced ER stress tolerance and improved protein folding efficiency, leading to a 2.14-fold increase in α-amylase production under Tm treatment and a 2.04-fold increase in cell density under DTT treatment. Our findings contribute to the understanding of cellular responses to ER stress and provide a basis for further investigations into the mechanisms of ER stress at the cellular level.

Investigating the Effect of RNA Scaffolds on the Multicolor Fluorogenic Aptamer Pepper in Different Bacterial Species.

RNA synthetic biology tools have primarily been applied in E. coli; however, many other bacteria are of industrial and clinical significance. Thus, the multicolor fluorogenic aptamer Pepper was evaluated in both Gram-positive and Gram-negative bacteria. Suitable HBC-Pepper dye pairs were identified that give blue, green, or red fluorescence signals in the E. coli, Bacillus subtilis, and Salmonella enterica serovar Typhimurium (S. Typhimurium). Furthermore, we found that different RNA scaffolds have a drastic effect on in vivo fluorescence, which did not correlate with the in vitro folding efficiency. One such scaffold termed DF30-tRNA displays 199-fold greater fluorescence than the Pepper aptamer alone and permits simultaneous dual color imaging in live cells.

A uniquely efficacious type of CFTR corrector with complementary mode of action.

Three distinct pharmacological corrector types (I, II, III) with different binding sites and additive behavior only partially rescue the F508del-cystic fibrosis transmembrane conductance regulator (CFTR) folding and trafficking defect observed in cystic fibrosis. We describe uniquely effective, macrocyclic CFTR correctors that were additive to the known corrector types, exerting a complementary "type IV" corrector mechanism. Macrocycles achieved wild-type-like folding efficiency of F508del-CFTR at the endoplasmic reticulum and normalized CFTR currents in reconstituted patient-derived bronchial epithelium. Using photo-activatable macrocycles, docking studies and site-directed mutagenesis a highly probable binding site and pose for type IV correctors was identified in a cavity between lasso helix-1 (Lh1) and transmembrane helix-1 of membrane spanning domain (MSD)-1, distinct from the known corrector binding sites. Since only F508del-CFTR fragments spanning from Lh1 until MSD2 responded to type IV correctors, these likely promote cotranslational assembly of Lh1, MSD1, and MSD2. Previously corrector-resistant CFTR folding mutants were also robustly rescued, suggesting substantial therapeutic potential for type IV correctors.

A growth type pathway for improving the folding of BPTI.

The in vitro oxidative folding of the protein bovine pancreatic trypsin inhibitor (BPTI) with oxidized dithiothreitol or glutathione has served as a paradigm for protein folding but could take weeks at physiological pH because of the need to escape from kinetic traps via a rearrangement type pathway. The two major kinetic traps are called N' and N* and contain two of the three native disulfide bonds, which occur between residues 5 and 55, 30 and 51, and 14 and 38. N' is missing the disulfide bond between residues 5 and 55 while N* is missing the disulfide bond between residues 30 and 51. By determining rate constant for the reactions of the kinetic traps N* and N' and their mixed disulfides with glutathione and glutathione disulfide, many for the first time, we demonstrate that growth type pathways are feasible and could even be more efficient than rearrangement type pathways. Thus, formally unproductive pathways became productive. Interestingly, under physiological redox conditions both rearrangement and growth type pathways are important highlighting the redundancy of oxidative protein folding. With the new set of rate constants, modeling indicated that in vitro oxidative protein folding of BPTI via a growth type pathway using an oxidation, reduction and oxidation cycle would significantly improve protein folding efficiency, albeit under non-physiological redox conditions. With these changing conditions 91 ± 2% of native BPTI was achieved in 12 h compared to 83% native protein in 24 h using our previous best conditions of 5 mM GSSG and 5 mM GSH. Therefore, changing redox conditions via an oxidation, reduction and oxidation cycle may become an additional methodology for enhancing in vitro protein folding in aqueous solution.

Diselenide-bond replacement of the external disulfide bond of insulin increases its oligomerization leading to sustained activity

Seleno-insulin, a class of artificial insulin analogs, in which one of the three disulfide-bonds (S-S’s) of wild-type insulin (Ins) is replaced by a diselenide-bond (Se-Se), is attracting attention for its unique chemical and physiological properties that differ from those of Ins. Previously, we pioneered the development of a [C7UA,C7UB] analog of bovine pancreatic insulin (SeIns) as the first example, and demonstrated its high resistance against insulin-degrading enzyme (IDE). In this study, the conditions for the synthesis of SeIns via native chain assembly (NCA) were optimized to attain a maximum yield of 72%, which is comparable to the in vitro folding efficiency for single-chain proinsulin. When the resistance of BPIns to IDE was evaluated in the presence of SeIns, the degradation rate of BPIns became significantly slower than that of BPIns alone. Furthermore, the investigation on the intermolecular association properties of SeIns and BPIns using analytical ultracentrifugation suggested that SeIns readily forms oligomers not only with its own but also with BPIns. The hypoglycemic effect of SeIns on diabetic rats was observed at a dose of 150 μg/300 g rat. The strategy of replacing the solvent-exposed S-S with Se-Se provides new guidance for the design of long-acting insulin formulations.

Synthesis of biologically active proteins as L6KD-SUMO fusions forming inclusion bodies in Escherichia coli.

A new platform has been developed to facilitate the production of biologically active proteins and peptides in Escherichia coli. The platform includes an N-terminal self-associating L6 KD peptide fused to the SUMO protein (small ubiquitin-like protein modifier) from the yeast Saccharomyces cerevisiae, which is known for its chaperone activity. The target proteins are fused at the C termini of the L6 KD-SUMO fusions, and the resulting three-component fusion proteins are synthesized and self-assembled in E. coli into so-called active inclusion bodies (AIBs). In vivo, the L6 KD-SUMO platform facilitates the correct folding of the target proteins and directs them into AIBs, greatly simplifying their purification. In vitro, the platform facilitates the effective separation of AIBs by centrifugation and subsequent target protein release using SUMO-specific protease. The properties of the AIBs were determined using five proteins with different sizes, folding efficiencies, quaternary structure, and disulfide modifications. Electron microscopy shows that AIBs are synthesized in the form of complex fibrillar structures resembling "loofah sponges" with unusually thick filaments. The obtained results indicate that the new platform has promising features and could be developed to facilitate the synthesis and purification of target proteins and protein complexes without the use of renaturation.

Merging non-covalent and covalent crosslinking: En route to single chain nanoparticles

Single-chain nanoparticles represent an emerging class of nanomaterials designed to mimic protein's folding paradigm. Intrachain covalent crosslinking toward the formation of single-chain nanoparticles encounters complex energy landscapes, leading to the potential occurrence of misfolding issues. While non-covalent crosslinking can circumvent this issue, the resulting single-chain nanoparticles exhibit lower structural stability compared to their covalently crosslinked counterparts. In this study, we present a novel approach for the synthesis of single-chain nanoparticles, achieved through the combination of non-covalent and covalent intramolecular crosslinking. Cyanostilbenes grafted onto the linear polymer form intrachain non-covalent stacks aided by hydrogen bonds, leading to the formation of non-covalently crosslinked single-chain nanoparticles. These nanoparticles undergo conversion to covalently crosslinked nanostructures through subsequent photo-irradiation using [2 + 2] photocycloaddition, a process facilitated by the supramolecular confinement effect. Consequently, the resulting single-chain nanoparticles demonstrate both intrachain folding efficiency and substantial stability, offering significant potential for advancing applications across diverse fields.

Homeostatic regulation of ribosomal proteins by ubiquitin-independent cotranslational degradation

Ribosomes are the workplace for protein biosynthesis. Protein production required for normal cell function is tightly linked to ribosome abundance. It is well known that ribosomal genes are actively transcribed and ribosomal messenger RNAs (mRNAs) are rapidly translated, and yet ribosomal proteins have relatively long half-lives. These observations raise questions as to how homeostasis of ribosomal proteins is controlled. Here, we show that ribosomal proteins, while posttranslationally stable, are subject to high-level cotranslational protein degradation (CTPD) except for those synthesized as ubiquitin (Ub) fusion precursors. The N-terminal Ub moiety protects fused ribosomal proteins from CTPD. We further demonstrate that cotranslational folding efficiency and expression level are two critical factors determining CTPD of ribosomal proteins. Different from canonical posttranslational degradation, we found that CTPD of all the ribosomal proteins tested in this study does not require prior ubiquitylation. This work provides insights into the regulation of ribosomal protein homeostasis and furthers our understanding of the mechanism and biological significance of CTPD.

Design, mechanical characteristics evaluation, and energy absorption of multi-story Kresling origami-inspired structures

This study investigates how combination of different stories in a Kresling origami-inspired structure design can improve the desired mechanical characteristics such as fatigue, stability, modal, energy analyses, and folding pattern. Because of the possibility of fatigue failure and axial buckling, we provide a crease modeling approach that could improve the mechanical characteristics as well as the folding efficiency. In the first step, we observe the folding pattern of an origami structure design composed of multiple stories. It is shown that every two stories have a similar folding pattern. If the number of stories is odd, the middle one experiences different behavior. In the next step, we employ different heights, length ratios, and rotation directions of stories in the designs to demonstrate how these variations affect origami’s mechanical properties. It is indicated that the structure with the same story height can enhance the life cycles while decreasing the stories’ height can postpone the buckling failure. Although the stability of the structure can be compromised if there are more stories with greater length ratios, it can achieve the highest total strain energy level in the folding operation and improves fatigue life. Furthermore, it is determined that the stories’ rotation does not affect the folding process. In the reverse rotation, the stability is decreased substantially, but the life cycles are slightly reduced.

Use of the redox-dependent intein system for enhancing production of the cyclic green fluorescent protein

To expand the reported redox-dependent intein system application, in this work, we used the split intein variant with highly trans-splicing efficiency and minimal extein dependence to cyclize the green fluorescent protein variant reporter in vitro. The CPG residues were introduced adjacent to the intein's catalytic cysteine for reversible formation of a disulfide bond to retard the trans-splicing reaction under the oxidative environment. The cyclized reporter protein in Escherichia coli cells was easily prepared by organic extraction and identified by the exopeptidase digestion. The amounts of extracted cyclized protein reporter in BL21 (DE3) cells were higher than those in hyperoxic SHuffle T7 coexpression system for facilitating the disulfide bond formation. The double His6-tagged precursor was purified for in vitro cyclization of the protein for 3 h. Compared with the purified linear counterpart, the cyclic reporter showed about twofold increase in fluorescence intensity, exhibited thermal and hydrolytic stability, and displayed better folding efficiency in BL21 (DE3) cells at the elevated temperature. Taken together, the developed redox-dependent intein system will be used for producing other cyclic disulfide-free proteins. The cyclic reporter is a potential candidate applied in certain thermophilic aerobes.

MeJA-mediated enhancement of salt-tolerance of Populus wutunensis by 5-aminolevulinic acid

Background5-Aminolevulinic acid (ALA) is a natural and environmentally benign multifunctional plant growth regulator involved in the regulation of plant tolerance to various environmental stresses. This research aimed to explore the molecular mechanisms of salt tolerance in Populus wutunensis induced by exogenous ALA using physiological and transcriptomic analyses.ResultsPhysiological results showed that 50 mg·L− 1 ALA-treatment significantly reduced the malondialdehyde (MDA) content and the relative electrical conductivity (REC) and enhanced antioxidant activities of enzymes such as SOD, POD and CAT in salt-stressed P. wutunensis seedlings. Transcriptome analysis identified ALA-induced differentially expressed genes (DEGs) associating with increased salt-tolerance in P. wutunensis. GO and KEGG enrichment analyses showed that ALA activated the jasmonic acid signaling and significantly enhanced the protein processing in endoplasmic reticulum and the flavonoid biosynthesis pathways. Results of the hormone-quantification by LC-MS/MS-based assays showed that ALA could increase the accumulation of methyl jasmonate (MeJA) in salt-stressed P. wutunensis. Induced contents of soluble proteins and flavonoids by exogenous ALA in salt-treated seedlings were also correlated with the MeJA content.Conclusion5-aminolevulinic acid improved the protein-folding efficiency in the endoplasmic reticulum and the flavonoid-accumulation through the MeJA-activated jasmonic acid signaling, thereby increased salt-tolerance in P. wutunensis.

Scaffold Hopping and Screening for Potent Small Molecule Agonists for GRP94: Implications to Alleviate ER Stress-Associated Pathogenesis.

Disparity in the activity of Endoplasmic reticulum (ER) leads to degenerative diseases, mainly associated with protein misfolding and aggregation leading to cellular dysfunction and damage, ultimately contributing to ER stress. ER stress activates the complex network of Unfolded Protein Response (UPR) signaling pathways mediated by transmembrane proteins IRE1, ATF6, and PERK. In addition to UPR, many ER chaperones have evolved to optimize the output of properly foldedsecretory and membrane proteins. Glucose-regulated protein 94 (GRP94), an ER chaperone of heat shock protein HSP90 family, directs protein folding through interaction with other components of the ER protein folding machinery and assists in ER-associated degradation (ERAD). Activation of GRP94 would increase the efficacy of protein folding machinery and regulate the UPR pathway toward homeostasis. The present study aims to screen for novel agonists for GRP94 based on Core hopping, pharmacophore hypothesis, 3D-QSAR, and virtual screening with small-molecule compound libraries in order to improve the efficiency of native protein folding by enhancing GRP94 chaperone activity, therefore to reduce protein misfolding and aggregation. In this study, we have employed the strategy of small molecule-dependent ER programming to enhance the chaperone activity of GRP94 through scaffold hopping-based screening approach to identify specific GRP94 agonists. New scaffolds generated by altering the cores of NECA, the known GRP94 agonist, were validated by employing pharmacophore hypothesis testing, 3D-QSAR modeling, and molecular dynamics simulations. This facilitated the identification of small molecules to improve the efficiency of native protein folding by enhancing GRP94 activity. High-throughput virtual screening of the selected pharmacophore hypothesis against Selleckchem and ZINC databases retrieved a total of 2,27,081 compounds. Further analysis on docking and ADMET properties revealed Epimedin A, Narcissoside, Eriocitrin 1,2,3,4,6-O-Pentagalloylglucose, Secoisolariciresinol diglucoside, ZINC92952357, ZINC67650204, and ZINC72457930 as potential lead molecules. The stability and interaction of these small molecules were far better than the known agonist, NECA indicating their efficacy in selectively alleviating ER stress-associated pathogenesis. These results substantiate the fact that small molecule-dependent ER reprogramming would activate the ER chaperones and therefore reduce the protein misfolding as well as aggregation associated with ER stress in order to restore cellular homeostasis.

Examining the importance of termini location in successful protein folding with HaloTag circular permutants in vitro, in E. coli, and in mammalian cells.

Though in vitro studies have produced insight into mechanisms underlying protein folding, determining how cellular factors modulate folding remains challenging. Proteins have the opportunity to fold when synthesized from N- to C-terminus by the ribosome at a rate of around five to ten residues per second in cells. This is much slower than the average folding rate of most small proteins, giving the nascent chain time to sample many conformations during translation. When refolding in vitro, HaloTag populates an aggregation-prone intermediate that contains structure from both the N- and C-termini, but this intermediate does not form co-translationally. Could altering the chain connectivity of HaloTag decrease its folding efficiency? We have shown how changing the vectorial synthesis of HaloTag through circular permutation affects folding efficiency in vitro and in vivo. We assessed all 298 circular permutants of HaloTag in E. coli cell lysate and showed that circular permutation positions differentially affect protein solubility and function. FACS experiments in live mammalian HEK293T cells demonstrate that many circular permutants retain function in an alternative cellular environment. Combining these data with both standard in vitro protein folding assays and hydrogen-exchange MS studies to map the folding process yields insight into how circular permutation alters the folding landscape of HaloTag and the role of co-translational folding in this process.