Disorder and cysteines in proteins: A design for orchestration of conformational see-saw and modulatory functions

Michael Acceptors as Anti-Cancer Compounds: Coincidence or Causality?

Michael acceptors represent a class of compounds with potential anti-cancer properties. They act by binding to nucleophilic sites in biological molecules, thereby disrupting cancer cell function and inducing cell death. This mode of action, as well as their ability to be modified and targeted, makes them a promising avenue for advancing cancer therapy. We are investigating the molecular mechanisms underlying Michael acceptors and their interactions with cancer cells, in particular their ability to interfere with cellular processes and induce apoptosis. The anti-cancer properties of Michael acceptors are not accidental but are due to their chemical structure and reactivity. The electrophilic nature of these compounds allows them to selectively target nucleophilic residues on disease-associated proteins, resulting in significant therapeutic benefits and minimal toxicity in various diseases. This opens up new perspectives for the development of more effective and precise cancer drugs. Nevertheless, further studies are essential to fully understand the impact of our discoveries and translate them into clinical practice.

Accumulation and bio-oxidation of arsenite mediated by thermoacidophilic Cyanidiales: innate potential biomaterials toward arsenic remediation

Addressing geogenic and anthropogenic arsenic (As) pollution is critical for environmental health. This study explored arsenite [As(III)] removal using Cyanidiales, particularly Cyanidium caldarium (Cc) and Galdieria partita (Gp), under acidic to neutral pH, and determined As(III) detoxification mechanisms in relation to As speciation and protein secondary structure in Cyanidiales. Regarding As(III) sorption amounts, Cc outperformed Gp, reaching 83.2 mg g-1 of removal at pH 5.0. Wherein, 23.5 % of sorbed As on Cc presented as arsenate [As(V)] complexation with polysaccharides, alongside other predominant species including As(III)-cysteine (41.2 %) and As(III)-polysaccharides (35.3 %) complexes. This suggested that As(III) was directly transported into cells, rather than As(V). Coupled with the formation of As(III)-cysteine complexes within cells, these mechanisms may be key to efficiently accumulating As(III) in Cyanidiales during the 6-h incubation. These results highlight the potential of Cyanidiales for sustainable As(III) remediation and provide new insights into managing As(III) toxicity.

Protein structure-function continuum model: Emerging nexuses between specificity, evolution, and structure

The rationale for replacing the old binary of structure-function with the trinity of structure, disorder, and function has gained considerable ground in recent years. A continuum model based on the expanded form of the existing paradigm can now subsume importance of both conformational flexibility and intrinsic disorder in protein function. The disorder is actually critical for understanding the protein-protein interactions in many regulatory processes, formation of membrane-less organelles, and our revised notions of specificity as amply illustrated by moonlighting proteins. While its importance in formation of amyloids and function of prions is often discussed, the roles of intrinsic disorder in infectious diseases and protein function under extreme conditions are also becoming clear. This review is an attempt to discuss how our current understanding of protein function, specificity, and evolution fit better with the continuum model. This integration of structure and disorder under a single model may bring greater clarity in our continuing quest for understanding proteins and molecular mechanisms of their functionality.

A Proposal for a Consolidated Structural Model of the CagY Protein of Helicobacter pylori

CagY is the largest and most complex protein from Helicobacter pylori's (Hp) type IV secretion system (T4SS), playing a critical role in the modulation of gastric inflammation and risk for gastric cancer. CagY spans from the inner to the outer membrane, forming a channel through which Hp molecules are injected into human gastric cells. Yet, a tridimensional structure has been reported for only short segments of the protein. This intricate protein was modeled using different approaches, including homology modeling, ab initio, and deep learning techniques. The challengingly long middle repeat region (MRR) was modeled using deep learning and optimized using equilibrium molecular dynamics. The previously modeled segments were assembled into a 1595 aa chain and a 14-chain CagY multimer structure was assembled by structural alignment. The final structure correlated with published structures and allowed to show how the multimer may form the T4SS channel through which CagA and other molecules are translocated to gastric cells. The model confirmed that MRR, the most polymorphic and complex region of CagY, presents numerous cysteine residues forming disulfide bonds that stabilize the protein and suggest this domain may function as a contractile region playing an essential role in the modulating activity of CagY on tissue inflammation.

Intrinsic disorder may drive the interaction of PROS1 and MERTK in uveal melanoma

BACKGROUND

Class 2 uveal melanomas are associated with the inactivation of the BRCA1 ((breast cancer type 1 susceptibility protein)-associated protein 1 (BAP1)) gene. Inactivation of BAP1 promotes the upregulation of vitamin K-dependent protein S (PROS1), which interacts with the tyrosine-protein kinase Mer (MERTK) receptor on M2 macrophages to induce an immunosuppressive environment.

METHODS

We simulated the interaction of PROS1 with MERTK with ColabFold. We evaluated PROS1 and MERTK for the presence of intrinsically disordered protein regions (IDPRs) and disorder-to-order (DOT) regions to understand their protein-protein interaction (PPI). We first evaluated the structure of each protein with AlphaFold. We then analyzed specific sequence-based features of the PROS1 and MERTK with a suite of bioinformatics tools.

RESULTS

With high-resolution, moderate confidence, we successfully modeled the interaction between PROS1 and MERTK (predicted local distance difference test score (pDLLT) = 70.68). Our structural analysis qualitatively demonstrated IDPRs (i.e., spaghetti-like entities) in PROS1 and MERK. PROS1 was 23.37 % disordered, and MERTK was 23.09 % disordered, classifying them as moderately disordered and flexible proteins. PROS1 was significantly enriched in cysteine, the most order-promoting residue (p-value <0.05). Our IUPred analysis demonstrated that there are two disorder-to-order transition (DOT) regions in PROS1. MERTK was significantly enriched in proline, the most disorder-promoting residue (p-value <0.05), but did not contain DOT regions. Our STRING analysis demonstrated that the PPI network between PROS1 and MERTK is more complex than their assumed one-to-one binding (p-value <2.0 × 10-6).

CONCLUSION

Our findings present a novel prediction for the interaction between PROS1 and MERTK. Our findings show that PROS1 and MERTK contain elements of intrinsic disorder. PROS1 has two DOT regions that are attractive immunotherapy targets. We recommend that IDPRs and DOT regions found in PROS1 and MERTK should be considered when developing immunotherapies targeting this PPI.

IFF: Identifying key residues in intrinsically disordered regions of proteins using machine learning

Conserved residues in protein homolog sequence alignments are structurally or functionally important. For intrinsically disordered proteins or proteins with intrinsically disordered regions (IDRs), however, alignment often fails because they lack a steric structure to constrain evolution. Although sequences vary, the physicochemical features of IDRs may be preserved in maintaining function. Therefore, a method to retrieve common IDR features may help identify functionally important residues. We applied unsupervised contrastive learning to train a model with self-attention neuronal networks on human IDR orthologs. Parameters in the model were trained to match sequences in ortholog pairs but not in other IDRs. The trained model successfully identifies previously reported critical residues from experimental studies, especially those with an overall pattern (e.g., multiple aromatic residues or charged blocks) rather than short motifs. This predictive model can be used to identify potentially important residues in other proteins, improving our understanding of their functions. The trained model can be run directly from the Jupyter Notebook in the GitHub repository using Binder (mybinder.org). The only required input is the primary sequence. The training scripts are available on GitHub (https://github.com/allmwh/IFF). The training datasets have been deposited in an Open Science Framework repository (https://osf.io/jk29b).

Click chemistry-based thiol redox proteomics reveals significant cysteine reduction induced by chronic ethanol consumption

In the U.S., alcohol-associated liver disease (ALD) impacts millions of people and is a major healthcare burden. While the pathology of ALD is unmistakable, the molecular mechanisms underlying ethanol hepatotoxicity are not fully understood. Hepatic ethanol metabolism is intimately linked with alterations in extracellular and intracellular metabolic processes, specifically oxidation/reduction reactions. The xenobiotic detoxification of ethanol leads to significant disruptions in glycolysis, β-oxidation, and the TCA cycle, as well as oxidative stress. Perturbation of these regulatory networks impacts the redox status of critical regulatory protein thiols throughout the cell. Integrating these key concepts, our goal was to apply a cutting-edge approach toward understanding mechanisms of ethanol metabolism in disrupting hepatic thiol redox signaling. Utilizing a chronic murine model of ALD, we applied a cysteine targeted click chemistry enrichment coupled with quantitative nano HPLC-MS/MS to assess the thiol redox proteome. Our strategy reveals that ethanol metabolism largely reduces the cysteine proteome, with 593 cysteine residues significantly reduced and 8 significantly oxidized cysteines. Ingenuity Pathway Analysis demonstrates that ethanol metabolism reduces specific cysteines throughout ethanol metabolism (Adh1, Cat, Aldh2), antioxidant pathways (Prx1, Mgst1, Gsr), as well as many other biochemical pathways. Interestingly, a sequence motif analysis of reduced cysteines showed a correlation for hydrophilic, charged amino acids lysine or glutamic acid nearby. Further research is needed to determine how a reduced cysteine proteome impacts individual protein activity across these protein targets and pathways. Additionally, understanding how a complex array of cysteine-targeted post-translational modifications (e.g., S-NO, S-GSH, S-OH) are integrated to regulate redox signaling and control throughout the cell is key to the development of redox-centric therapeutic agents targeted to ameliorate the progression of ALD.

Chaetocin disrupts the SUV39H1-HP1 interaction independent of SUV39H1 methyltransferase activity

Chemical tools to control the activities and interactions of chromatin components have broad impact on our understanding of cellular and disease processes. It is important to accurately identify their molecular effects to inform clinical efforts and interpretations of scientific studies. Chaetocin is a widely used chemical that decreases H3K9 methylation in cells. It is frequently attributed as a specific inhibitor of the histone methyltransferase activities of SUV39H1/SU(VAR)3-9, although prior observations showed chaetocin likely inhibits methyltransferase activity through covalent mechanisms involving its epipolythiodixopiperazine disulfide 'warhead' functionality. The continued use of chaetocin in scientific studies may derive from the net effect of reduced H3K9 methylation, irrespective of a direct or indirect mechanism. However, there may be other molecular impacts of chaetocin on SUV39H1 besides inhibition of H3K9 methylation levels that could confound the interpretation of past and future experimental studies. Here, we test a new hypothesis that chaetocin may have an additional downstream impact aside from inhibition of methyltransferase activity. Using a combination of truncation mutants, a yeast two-hybrid system, and direct in vitro binding assays, we show that the human SUV39H1 chromodomain (CD) and HP1 chromoshadow domain (CSD) directly interact. Chaetocin inhibits this binding interaction through its disulfide functionality with some specificity by covalently binding with the CD of SUV39H1, whereas the histone H3-HP1 interaction is not inhibited. Given the key role of HP1 dimers in driving a feedback cascade to recruit SUV39H1 and to establish and stabilize constitutive heterochromatin, this additional molecular consequence of chaetocin should be broadly considered.

Metallothionein-2: An emerging target in inflammatory diseases and cancers

Metallothionein-2 (MT-2) was originally discovered as a mediator of zinc homeostasis and cadmium detoxification. However, MT-2 has recently received increased attention because altered expression of MT-2 is closely related to various diseases such as asthma and cancers. Several pharmacological strategies have been developed to inhibit or modify MT-2, revealing its potential as drug target in diseases. Therefore, a better understanding of the mechanisms of MT-2 action is warranted to improve drug development for potential clinical applications. In this review, we highlight recent advances in determining the protein structure, regulation, binding partners, and new functions of MT-2 in inflammatory diseases and cancers.

Removal and concurrent reduction of Cr(VI) by thermoacidophilic Cyanidiales: a novel extreme biomaterial enlightened for acidic and neutral conditions

Thermoacidophilic Cyanidiales maintain a competitive edge in inhabiting extreme environments enriched with metals. Here, species of Cyanidioschyzon merolae (Cm), Cyanidium caldarium (Cc), and Galdieria partita (Gp) were exploited to remove hexavalent chromium [Cr(VI)]. Cm and Gp could remove 168.1 and 93.7 mg g^-1 of Cr(VI) at pH 2.0 and 7.0, respectively, wherein 89% and 62% of sorbed Cr on Cm and Gp occurred as trivalent chromium [Cr(III)]. Apart from surface-sorbed Cr(VI), the in vitro Cr(III) bound with polysaccharide and in vivo chromium(III) hydroxide [Cr(OH)₃] attested to the reduction capability of Cyanidiales. The distribution of Cr species varied as a function of sorbed Cr amount, yet a relatively consistent proportion of Cr(OH)₃, irrespective of Cr sorption capacity, was found only on Cm and Cc at pH 2.0. In conjunction with TXM (transmission X-ray microscopy) images that showed less impaired cell integrity and possible intracellular Cr distribution on Cm and Cc at pH 2.0, the in vivo Cr(OH)₃ might be the key to promoting the Cr sorption capacity (≥ 152 mg g^-1). Cyanidiales are promising candidates for the green and sustainable remediation of Cr(VI) due to their great removal capacity, the spontaneous reduction under oxic conditions, and in vivo accumulation.

A Trajectory of Discovery: Metabolic Regulation by the Conditionally Disordered Chloroplast Protein, CP12

The chloroplast protein CP12, which is widespread in photosynthetic organisms, belongs to the intrinsically disordered proteins family. This small protein (80 amino acid residues long) presents a bias in its composition; it is enriched in charged amino acids, has a small number of hydrophobic residues, and has a high proportion of disorder-promoting residues. More precisely, CP12 is a conditionally disordered proteins (CDP) dependent upon the redox state of its four cysteine residues. During the day, reducing conditions prevail in the chloroplast, and CP12 is fully disordered. Under oxidizing conditions (night), its cysteine residues form two disulfide bridges that confer some stability to some structural elements. Like many CDPs, CP12 plays key roles, and its redox-dependent conditional disorder is important for the main function of CP12: the dark/light regulation of the Calvin-Benson-Bassham (CBB) cycle responsible for CO₂ assimilation. Oxidized CP12 binds to glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase and thereby inhibits their activity. However, recent studies reveal that CP12 may have other functions beyond the CBB cycle regulation. In this review, we report the discovery of this protein, its features as a disordered protein, and the many functions this small protein can have.

Mass-spectrometric identification of oxidative modifications in plasma-purified plasminogen: Association with hypofibrinolysis in patients with acute pulmonary embolism

OBJECTIVES

Mechanisms behind disturbed fibrinolysis in pulmonary embolism (PE) are poorly understood. We hypothesized that oxidative stress-induced changes in plasminogen contribute to impaired fibrinolysis in patients with acute PE.

METHODS

Oxidative and other modifications were investigated using mass-spectrometry in plasminogen purified from pooled plasma of 5 acute PE patients on admission and after 3 months of anticoagulant treatment, along with plasma clot lysis time, a measure of global efficiency of fibrinolysis, and a stable oxidative stress marker, plasma 8-isoprostane.

RESULTS

Twenty sites of oxidation, 3 sites of carbonylation and 4 sites of S-nitrosylation were identified in plasminogen. The intensity of peptides oxidized at cysteine residues with respect to unmodified peptides decreased after 3 months of anticoagulation (p = 0.018). This was not observed for oxidized methionine residues (p = 0.9). Oxidized tryptophan (n = 4) and proline (n = 2), as well as carbonylation at 3 threonine residues were selectively identified in acute PE episode, not after 3 months. This was accompanied by 12.8% decrease in clot lysis time (p = 0.043). Deamidation occurred at the arginine, previously identified to undergo the cleavage by plasminogen activator. Methylated were two lysine-binding sites important for an interaction of plasminogen with fibrin. Other identified modifications involved: glycation, acetylation, phosphorylation, homocysteinylation, carbamylation and dichlorination (88 modifications at 162 sites).

CONCLUSIONS

Data suggest that oxidative stress-induced changes in plasminogen molecules may contribute to less effective global fibrinolysis in patients with acute PE. The comprehensive library of posttranslational modifications in plasminogen molecules was provided, including modifications of sites reported to be involved in important biological functions.

Compositional Bias of Intrinsically Disordered Proteins and Regions and Their Predictions

Intrinsically disordered regions (IDRs) carry out many cellular functions and vary in length and placement in protein sequences. This diversity leads to variations in the underlying compositional biases, which were demonstrated for the short vs. long IDRs. We analyze compositional biases across four classes of disorder: fully disordered proteins; short IDRs; long IDRs; and binding IDRs. We identify three distinct biases: for the fully disordered proteins, the short IDRs and the long and binding IDRs combined. We also investigate compositional bias for putative disorder produced by leading disorder predictors and find that it is similar to the bias of the native disorder. Interestingly, the accuracy of disorder predictions across different methods is correlated with the correctness of the compositional bias of their predictions highlighting the importance of the compositional bias. The predictive quality is relatively low for the disorder classes with compositional bias that is the most different from the “generic” disorder bias, while being much higher for the classes with the most similar bias. We discover that different predictors perform best across different classes of disorder. This suggests that no single predictor is universally best and motivates the development of new architectures that combine models that target specific disorder classes.

Topological dynamics of an intrinsically disordered N‐terminal domain of the human androgen receptor

Human androgen receptor contains a large N‐terminal domain (AR‐NTD) that is highly dynamic and this poses a major challenge for experimental and computational analysis to decipher its conformation. Misfolding of the AR‐NTD is implicated in prostate cancer and Kennedy's disease, yet our knowledge of its structure is limited to primary sequence information of the chain and a few functionally important secondary structure motifs. Here, we employed an innovative combination of molecular dynamics simulations and circuit topology (CT) analysis to identify the tertiary structure of AR‐NTD. We found that the AR‐NTD adopts highly dynamic loopy conformations with two identifiable regions with distinct topological make‐up and dynamics. This consists of a N‐terminal region (NR, residues 1–224) and a C‐terminal region (CR, residues 225–538), which carries a dense core. Topological mapping of the dynamics reveals a traceable time‐scale dependent topological evolution. NR adopts different positioning with respect to the CR and forms a cleft that can partly enclose the hormone‐bound ligand‐binding domain (LBD) of the androgen receptor. Furthermore, our data suggest a model in which dynamic NR and CR compete for binding to the DNA‐binding domain of the receptor, thereby regulating the accessibility of its DNA‐binding site. Our approach allowed for the identification of a previously unknown regulatory binding site within the CR core, revealing the structural mechanisms of action of AR inhibitor EPI‐001, and paving the way for other drug discovery applications.

In-depth analysis of amino acid and nucleotide sequences of Hsp60: how conserved is this protein?

Chaperonin Hsp60, as a protein found in all organisms, is of great interest in medicine, since it is present in many tissues and can be used both as a drug and as an object of targeted therapy. Hence, Hsp60 deserves a fundamental comparative analysis to assess its evolutionary characteristics. It was found that the percent identity of Hsp60 amino acid sequences both within and between phyla was not high enough to identify Hsp60s as highly conserved proteins. However, their ATP binding sites are largely conserved. The amino acid composition of Hsp60s remained relatively constant. At the same time, the analysis of the nucleotide sequences showed that GC content in the Hsp60 genes was comparable to or greater than the genomic values, which may indicate a high resistance to mutations due to tight control of the nucleotide composition by DNA repair systems. Natural selection plays a dominant role in the evolution of Hsp60 genes. The degree of mutational pressure affecting the Hsp60 genes is quite low, and its direction does not depend on taxonomy. Interestingly, for the Hsp60 genes from Chordata, Arthropoda, and Proteobacteria the exact direction of mutational pressure could not be determined. However, upon further division into classes, it was found that the direction of the mutational pressure for Hsp60 genes from Fish differs from that for other chordates. The direction of the mutational pressure affects the synonymous codon usage bias. The number of high and low represented codons increases with increasing GC content, which can improve codon usage. Special server has been created for bioinformatics analysis of Hsp60: http://oka.protres.ru:4202/.

Bioinformatic Analysis of Lytic Polysaccharide Monooxygenases Reveals the Pan-Families Occurrence of Intrinsically Disordered C-Terminal Extensions

Lytic polysaccharide monooxygenases (LPMOs) are monocopper enzymes secreted by many organisms and viruses. LPMOs catalyze the oxidative cleavage of different types of polysaccharides and are today divided into eight families (AA9-11, AA13-17) within the Auxiliary Activity enzyme class of the CAZy database. LPMOs minimal architecture encompasses a catalytic domain, to which can be appended a carbohydrate-binding module. Intriguingly, we observed that some LPMO sequences also display a C-terminal extension of varying length not associated with any known function or fold. Here, we analyzed 27,060 sequences from different LPMO families and show that 60% have a C-terminal extension predicted to be intrinsically disordered. Our analysis shows that these disordered C-terminal regions (dCTRs) are widespread in all LPMO families (except AA13) and differ in terms of sequence length and amino-acid composition. Noteworthily, these dCTRs have so far only been observed in LPMOs. LPMO-dCTRs share a common polyampholytic nature and an enrichment in serine and threonine residues, suggesting that they undergo post-translational modifications. Interestingly, dCTRs from AA11 and AA15 are enriched in redox-sensitive, conditionally disordered regions. The widespread occurrence of dCTRs in LPMOs from evolutionarily very divergent organisms, hints at a possible functional role and opens new prospects in the field of LPMOs.

Revealing Intrinsic Disorder and Aggregation Properties of the DPF3a Zinc Finger Protein

Double PHD fingers 3 (DPF3) is a human epigenetic factor found in the multiprotein BRG1-associated factor (BAF) chromatin remodeling complex. It has two isoforms: DPF3b and DPF3a, but very little is known about the latter. Despite the lack of structural data, it has been established that DPF3a is involved in various protein-protein interactions and that it is subject to phosphorylation. These features are typical of intrinsically disordered proteins (IDPs) for which the disorder is essential to their functionality. IDPs are also prone to aggregation and can assemble into cytotoxic amyloid fibrils in specific pathological contexts. In the present work, the DPF3a disordered nature and propensity to aggregation have been investigated using a combination of disorder predictors and biophysical methods. The DPF3a-predicted disordered character has been correlated to a characteristic random coil signal in far-UV circular dichroism (CD) and to a fluorescence emission band typical of Trp residues fully exposed to the solvent. After DPF3a purification and 24 h of incubation at room temperature, dynamic light scattering confirmed the presence of DPF3a aggregates whose amyloid nature have been highlighted by a specific deep-blue autofluorescence signature, as well as by an increase in thioflavin T fluorescence upon binding. These results are supported by an enrichment in twisted β-sheets as observed in far-UV CD and a blue shift in intrinsic Trp fluorescence. Both indicate that DPF3a spontaneously tends to orderly aggregate into amyloid fibrils. The diversity of optical signatures originates from dynamical transitions between the disordered and aggregated states of the protein during the incubation. Transmission electron microscopy micrographs reveal that the DPF3a fibrillation process leads to the formation of short needle-shape filaments.

Are granulins copper sequestering proteins?

Granulins (GRN 1-7) are short (~6 kDa), cysteine-rich proteins that are generated upon the proteolytic processing of progranulin (PGRN). These peptides, along with their precursor, have been implicated in multiple pathophysiological roles, especially in neurodegenerative diseases. Previously we showed that GRN-3 and GRN-5 are fully disordered in the reduced form implicating redox sensitive attributes to the proteins. Redox-based modulations are often carried out by metalloproteins in mitigating oxidative stress and maintaining metal-homeostasis within cells. To probe whether GRNs play a role in metal sequestration, we tested the metal binding propensity of the reduced forms of GRNs -3 and - 5 under neutral and acidic pH mimicking cytosolic and lysosomal conditions, respectively. We found, at neutral pH, both GRNs selectively bind Cu and no other divalent metal cations, with a greater specificity for Cu(I). Binding of Cu did not result in a disorder-to-order structural transition but partly triggered the multimerization of GRNs via uncoordinated cystines at both pH conditions. Overall, the results indicate that GRNs -3 and - 5 have surprisingly strong affinity for Cu in the pM range, comparable to other known copper sequestering proteins. The results also hint at a potential of GRNs to reduce Cu(II) to Cu(I), a process that has significance in mitigating Cu-induced ROS cytotoxicity in cells. Together, this report uncovers metal-coordinating property of GRNs for the first time, which may have profound significance in their structure and pathophysiological functions.