Predicting intrinsic disorder in proteins： an overview

The discovery of intrinsically disordered proteins （IDP） （i.e., biologically active proteins that do not possess stable secondary and/or tertiary structures） came as an unexpected surprise, as the existence of such proteins is in contradiction to the traditional ＂sequence →structure →function＂ paradigm. Accurate prediction of a protein＇s predisposition to be intrinsically disordered is a necessary prerequisite for the further understanding of principles and mechanisms of protein folding and function, and is a key for the elaboration of a new structural and functional hierarchy of proteins. Therefore, prediction of IDPs has attracted the attention of many researchers, and a number of prediction tools have been developed. Predictions of disorder, in turn, are playing major roles in directing laboratory experiments that are leading to the discovery of ever more disordered proteins, and thereby leading to a positive feedback loop in the investigation of these proteins. In this review of algorithms for intrinsic disorder prediction, the basic concepts of various prediction methods for IDPs are summarized, the strengths and shortcomings of many of the methods are analyzed, and the difficulties and directions of future development of IDP prediction techniques are discussed.

Minor fibrillar collagens,variable regions alternative splicing,intrinsic disorder,and tyrosine sulfation

Minor fibrillar collagen types V and XI,are those less abundant than the fibrillar collagen types I,II and III.The alpha chains share a high degree of similarity with respect to protein sequence in all domains except the variable region.Genomic variation and,in some cases,extensive alternative splicing contribute to the unique sequence characteristics of the variable region.While unique expression patterns in tissues exist,the functions and biological relevance of the variable regions have not been elucidated.In this review,we summarize the existing knowledge about expression patterns and biological functions of the collagen types V and XI alpha chains.Analysis of biochemical similarities among the peptides encoded by each exon of the variable region suggests the potential for a shared function.The alternative splicing,conservation of biochemical characteristics in light of low sequence conservation,and evidence for intrinsic disorder,suggest modulation of binding events between the surface of collagen fibrils and surrounding extracellular molecules as a shared function.

Prediction of Intrinsically Disordered Proteins with a Low Computational Complexity Method

The prediction of intrinsically disordered proteins is a hot research area in bio-information.Due to the high cost of experimental methods to evaluate disordered regions of protein sequences,it is becoming increasingly important to predict those regions through computational methods.In this paper,we developed a novel scheme by employing sequence complexity to calculate six features for each residue of a protein sequence,which includes the Shannon entropy,the topological entropy,the sample entropy and three amino acid preferences including Remark 465,Deleage/Roux,and Bfactor(2STD).Particularly,we introduced the sample entropy for calculating time series complexity by mapping the amino acid sequence to a time series of 0-9.To our knowledge,the sample entropy has not been previously used for predicting IDPs and hence is being used for the first time in our study.In addition,the scheme used a properly sized sliding window in every protein sequence which greatly improved the prediction performance.Finally,we used seven machine learning algorithms and tested with 10-fold cross-validation to get the results on the dataset R80 collected by Yang et al.and of the dataset DIS1556 from the Database of Protein Disorder(DisProt)(https://www.disprot.org)containing experimentally determined intrinsically disordered proteins(IDPs).The results showed that k-Nearest Neighbor was more appropriate and an overall prediction accuracy of 92%.Furthermore,our method just used six features and hence required lower computational complexity.

Prediction of Intrinsically Disordered Proteins Based on Deep Neural Network-ResNet18

Accurately,reliably and rapidly identifying intrinsically disordered(IDPs)proteins is essential as they often play important roles in various human diseases;moreover,they are related to numerous important biological activities.However,current computational methods have yet to develop a network that is sufficiently deep tomake predictions about IDPs and demonstrate an improvement in performance.During this study,we constructed a deep neural network that consisted of five identical variant models,ResNet18,combined with an MLP network,for classification.Resnet18 was applied for the first time as a deep model for predicting IDPs,which allowed the extraction of information fromIDP residues in greater detail and depth,and this information was then passed through the MLP network for the final identification process.Two well-known datasets,MXD494 and R80,were used as the blind independent datasets to compare their performance with that of our method.The simulation results showed that Matthew’s correlation coefficient obtained using our deep network model was 0.517 on the blind R80 dataset and 0.450 on the MXD494 dataset;thus,our method outperformed existing methods.

Sleep disorders and chronic kidney disease

Sleep disorders have a profound and well-documented impact on overall health and quality of life in the general population. In patients with chronic disease, sleep disorders are more prevalent, with an additional morbidity and mortality burden. The complex and dynamic relationship between sleep disorders and chronic kidney disease(CKD) remain relatively little investigated. This article presents an overview of sleep disorders in patients with CKD, with emphasis on relevant pathophysiologic underpinnings and clinical presentations. Evidence-based interventions will be discussed, in the context of individual sleep disorders, namely sleep apnea, insomnia, restless leg syndrome and excessive daytime sleepiness. Limitations of the current knowledge as well as future research directions will be highlighted, with a final discussion of different conceptual frameworks of the relationship between sleep disorders and CKD.

ipRGCs: possible causation accounts for the higher prevalence of sleep disorders in glaucoma patients

Sleep accounts for a third of one＇s lifetime, partial or complete deprivation of sleep could elicit sever disorders of body function. Previous studies have reported the higher prevalence of sleep disorders in glaucoma patients, but the definite mechanism for this phenomenon is unknown. On the other hand, it is well known by us that the intrinsically photosensitive retinal ganglion cells（ip RGCs） serve additional ocular functions, called non-image-forming（NIF） functions, in the regulation of circadian rhythm, melatonin secretion, sleep, mood and others. Specifically, ip RGCs can directly or indirectly innervate the central areas such as suprachiasmatic nucleus（SCN）, downstream pineal gland（the origin of melatonin）, sleep and wake-inducing centers and mood regulation areas, making NIF functions of ip RGCs relate to sleep. The more interesting thing is that previous research showed glaucoma not only affected visual functions such as the degeneration of classical retinal ganglion cells（RGCs）, but also affected ip RGCs. Therefore, we hypothesize that higher prevalence of sleep disorders in glaucoma patients maybe result from the underlying glaucomatous injuries of ip RGCs leading to the abnormalities of diverse NIF functions corresponding to sleep.

Nitric oxide-mediated S-nitrosylation of IAA17 protein in intrinsically disordered region represses auxin signaling

The phytohormone auxin plays crucial roles in nearly every aspect of plant growth and development.Auxin signaling is activated through the phytohormone-induced proteasomal degradation of the Auxin/INDOLE-3-ACETIC ACID(Aux/IAA)family of transcriptional repressors.Notably,many auxin-modulated physiological processes are also regulated by nitric oxide(NO)that executes its biological effects predominantly through protein S-nitrosylation at specific cysteine residues.However,little is known about the molecular mechanisms in regulating the interactive NO and auxin networks.Here,we show that NO represses auxin signaling by inhibiting IAA17 protein degradation.NO induces the S-nitrosylation of Cys-70 located in the intrinsically disordered region of IAA17,which inhibits the TIR1-IAA17 interaction and consequently the proteasomal degradation of IAA17.The accumulation of a higher level of IAA17 attenuates auxin response.Moreover,an IAA17^(C70W)nitrosomimetic mutation renders the accumulation of a higher level of the mutated protein,thereby causing partial resistance to auxin and defective lateral root development.Taken together,these results suggest that S-nitrosylation of IAA17 at Cys-70 inhibits its interaction with TIR1,thereby negatively regulating auxin signaling.This study provides unique molecular insights into the redox-based auxin signaling in regulating plant growth and development.

Prostate-associated gene 4 （PAGE4）, an intrinsically disordered cancer/testis antigen, is a novel therapeutic target for prostate cancer

Prostate-associated gene 4 （PAGE4） is a remarkably prostate-specific Cancer/Testis Antigen that is highly upregulated in the human fetal prostate and its diseased states but not in the adult normal gland. PAGE4 is an intrinsically disordered protein （IDP） that functions as a stress-response protein to suppress reactive oxygen species as well as prevent DNA damage. In addition, PAGE4 is also a transcriptional regulator that potentiates transactivation by the oncogene c-Jun, c-Jun forms the AP-1 complex by heterodimerizing with members of the Fos family and plays an important role in the development and pathology of the prostate gland, underscoring the importance of the PAGE4/c-Jun interaction. HIPK1, also a component of the stress-response pathway, phosphorylates PAGE4 at T51 which is critical for its transcriptional activity. Phosphorylation induces conformational and dynamic switching in the PAGE4 ensemble leading to a new cellular function. Finally, bioinformatics evidence suggests that the PAGE4 mRNA could be alternatively spliced resulting in four potential isoforms of the polypeptide alluding to the possibility of a range of conformational ensembles with latent functions. Considered together, the data suggest that PAGE4 may represent the first molecular link between stress and prostate cancer （PCa）. Thus, pharmacologically targeting PAGE4 may be a novel opportunity for treating and managing patients with PCa, especially patients with low-risk disease.

Structural and nucleic acid binding properties of hepatitis delta virus small antigen

AIM To further characterize the structure and nucleic acid binding properties of the 195 amino acid small delta antigen, S-HDAg, a study was made of a truncated form of S-HDAg, comprising amino acids 61-195(?60HDAg), thus lacking the domain considered necessary for dimerization and higher order multimerization.METHODS Circular dichroism, and nuclear magnetic resonance experiments were used to assess the structure of ?60HDAg. Nucleic acid binding properties were investigated by gel retardation assays. RESULTS Results showed that the truncated ?60HDAg protein is intrinsically disordered but compact, whereas the RNA binding domain, comprising residues 94-146, adopts a dynamic helical conformation. We also found that ?60HDAg fails to multimerize but still contains nucleic acid binding activity, indicating that multimerization is not essential for nucleic acid binding. Moreover, in agreement with what has been previously reported for full-length protein, no apparent specificity was found for the truncated protein regarding nucleic acid binding.CONCLUSION Taken together these results allowed concluding that ?60HDAg is intrinsically disordered but compact; ?60HDAg is not a multimer but is still capable of nucleic acid binding albeit without apparent specificity.

Unfoldomics of prostate cancer： on the abundance and roles of intrinsically disordered proteins in prostate cancer

Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease. We also hope that the results of our analysis can potentially lead to future experimental studies of these proteins to find novel pathways associated with this disease.

Molecular signaling involving intrinsically disordered proteins in prostate cancer

Investigations on cellular protein interaction networks （PINs） reveal that proteins that constitute hubs in a PIN are notably enriched in Intrinsically Disordered Proteins （IDPs） compared to proteins that constitute edges, highlighting the role of IDPs in signaling pathways. Most IDPs rapidly undergo disorder-to-order transitions upon binding to their biological targets to perform their function. Conformational dynamics enables IDPs to be versatile and to interact with a broad range of interactors under normal physiological conditions where their expression is tightly modulated. IDPs are involved in many cellular processes such as cellular signaling, transcriptional regulation, and splicing; thus, their high-specificity/low-affinity interactions play crucial roles in many human diseases including cancer. Prostate cancer （PCa） is one of the leading causes of cancer-related mortality in men worldwide. Therefore, identifying molecular mechanisms of the oncogenic signaling pathways that are involved in prostate carcinogenesis is crucial. In this review, we focus on the aspects of cellular pathways leading to PCa in which IDPs exert a Iorimary role.

Liquid–liquid phase separation in plants:Advances and perspectives from model species to crops

Membraneless biomolecular condensates play important roles in both normal biological activities and re-sponses to environmental stimuli in living organisms.Liquid‒liquid phase separation(LLPS)is an organi-zational mechanism that has emerged in recent years to explain the formation of biomolecular conden-sates.In the past decade,advances in LLPS research have contributed to breakthroughs in diseasefields.By contrast,although LLPS research in plants has progressed over the past 5 years,it has been concentrated on the model plant Arabidopsis,which has limited relevance to agricultural production.In this review,we provide an overview of recently reported advances in LLPS in plants,with a particular focus on photomorphogenesis,flowering,and abiotic and biotic stress responses.We propose that many potential LLPS proteins also exist in crops and may affect crop growth,development,and stress resistance.This possibility presents a great challenge as well as an opportunity for rigorous scientific research on the biological functions and applications of LLPS in crops.

Phenotypic plasticity in prostate cancer： role of ntrinsically disordered proteins

A striking characteristic of cancer ceLls is their remarkable phenotypic plasticity, which is the ability to switch states or phenotypes in response to environmental fluctuations. Phenotypic changes such as a partial or complete epithelial to mesenchymal transition （EMT） that play important roles in their survival and proliferation, and development of resistance to therapeutic treatments, are widely believed to arise due to somatic mutations in the genome. However, there is a growing concern that such a deterministic view is not entirely consistent with multiple lines of evidence, which indicate that stochasticity may also play an important role in driving phenotypic plasticity. Here, we discuss how stochasticity in protein interaction networks （PINs） may play a key role in determining phenotypic plasticity in prostate cancer （PCa）. Specifically, we point out that the key players driving transitions among different phenotypes （epithelial, mesenchymal, and hybrid epithelial/mesenchymal）, including ZEB1, SNAIl, OVOL1, and OVOL2, are intrinsically disordered proteins （IDPs） and discuss how plasticity at the molecular level may contribute to stochasticity in phenotypic switching by rewiring PINs. We conclude by suggesting that targeting iDPs implicated in EMT in PCa may be a new strategy to gain additional insights and develop novel treatments for this disease, which is the most common form of cancer in adult men.

Exploring Potential Signals of Selection for Disordered Residues in Prokaryotic and Eukaryotic Proteins

Intrinsically disordered proteins(IDPs)are an important class of proteins in all domains of life for their functional importance.However,how nature has shaped the disorder potential of prokaryotic and eukaryotic proteins is still not clearly known.Randomly generated sequences are free of any selective constraints,thus these sequences are commonly used as null models.Considering different types of random protein models,here we seek to understand how the disorder potential of natural eukaryotic and prokaryotic proteins differs from random sequences.Comparing proteomewide disorder content between real and random sequences of 12 model organisms,we noticed that eukaryotic proteins are enriched in disordered regions compared to random sequences,but in prokaryotes such regions are depleted.By analyzing the position-wise disorder profile,we show that there is a generally higher disorder near the N-and C-terminal regions of eukaryotic proteins as compared to the random models;however,either no or a weak such trend was found in prokaryotic proteins.Moreover,here we show that this preference is not caused by the amino acid or nucleotide composition at the respective sites.Instead,these regions were found to be endowed with a higher fraction of protein-protein binding sites,suggesting their functional importance.We discuss several possible explanations for this pattern,such as improving the efficiency of protein-protein interaction,ribosome movement during translation,and post-translational modification.However,further studies are needed to clearly understand the biophysical mechanisms causing the trend.

Computational Analysis of Position-dependent Disorder Content in DisProt Database

A bioinformatics analysis of disorder content of proteins from the DisProt database has been performed with respect to position of dis- ordered residues. Each protein chain was divided into three parts： N- and C- terminal parts with each containing 30 amino acid （AA） residues and the middle region containing the remaining AA residues. The results show that in terminal parts, the percentage of disor- dered AA residues is higher than that of all AA residues （17% of disordered AA residues and 11% of all）. We analyzed the percentage of disorder for each of 20 AA residues in the three parts of proteins with respect to their hydropathy and molecular weight. For each AA, the percentage of disorder in the middle part is lower than that in terminal parts which is comparable at the two termini. A new scale of AAs has been introduced according to their disorder content in the middle part of proteins： CIFWMLYHRNVTAGQDSKEP. All big hydrophobic AAs are less frequently disordered, while almost all small hydrophilic AAs are more frequently disordered. The results obtained may be useful for construction and improving predictors for protein disorder.

Condensation of STM is critical for shoot meristem maintenance and salt tolerance in Arabidopsis

The shoot meristem generates the entire shoot system and is precisely maintained throughout the life cycle under various environmental challenges.In this study,we identified a prion-like domain(PrD)in the key shoot meristem regulator SHOOT MERISTEMLESS(STM),which distinguishes STM from other related KNOX1 proteins.We demonstrated that PrD stimulates STM to form nuclear condensates,which are required for maintaining the shoot meristem.STM nuclear condensate formation is stabilized by selected PrD-containing STM-interacting BELL proteins in vitro and in vivo.Moreover,condensation of STM promotes its interaction with the Mediator complex subunit MED8 and thereby enhances its transcriptional activity.Thus,condensate formation emerges as a novel regulatory mechanism of shoot meristem functions.Furthermore,we found that the formation of STM condensates is enhanced upon salt stress,which allows enhanced salt tolerance and increased shoot branching.Our findings highlight that the transcription factor partitioning plays an important role in cell fate determination and might also act as a tunable environmental acclimation mechanism.

Computational prediction and validation of specific EmbR binding site on PknH

Tuberculosis drug resistance continues to threaten global health but the underline molecular mechanisms are not clear.Ethambutol(EMB),one of the well-known first-line drugs in tuberculosis treatment is,unfortunately,not free from drug resistance problems.Genomic studies have shown that some genetic mutations in Mycobacterium tuberculosis(Mtb)EmbR,and EmbC/A/B genes cause EMB resistance.EmbR-PknH pair controls embC/A/B operon,which encodes EmbC/A/B genes,and EMB interacts with EmbA/B proteins.However,the EmbR binding site on PknH was unknown.We conducted molecular simulation on the EmbR-peptides binding structures and discovered phosphorylated PknH 273-280(N′-HEALS^(P)DPD-C′)makesβstrand with the EmbR FHA domain,asβ-MoRF(MoRF;molecular recognition feature)does at its binding site.Hydrogen bond number analysis also supported the peptides’β-MoRF forming activity at the EmbR FHA domain.Also,we discovered that previously known phosphorylation residues might have their chronological order according to the phosphorylation status.The discovery validated that Mtb PknH 273-280(N′-HEALSDPD-C′)has reliable EmbR binding affinity.This approach is revolutionary in the computer-aided drug discovery field,because it is the first trial to discover the protein-protein interaction site,and find binding partner in nature from this site.

Steroid hormone receptors and prostate cancer： role of structural dynamics in therapeutic targeting

Steroid hormone receptors （SHRs） act in cell type- and gene-specific manner through interactions with coregulatory proteins to regulate numerous physiological and pathological processes at the level of gene regulation. Binding of steroid receptor modulator （SRM） ligand leads to allosteric changes in SHR to exert positive or negative effects on the expression of target genes. Due, in part, to the fact that current SRMs generally target ligand binding domain （LBD）/AF2 and neglect intrinsically disordered （ID） N-terminal domain （NTD）/AF1, clinically relevant SRMs lack selectivity and are also prone to the development of resistance over time. Therefore, to maximize the efficacy of SHR-based therapeutics, the possibility of developing unique modulators that act to control AF1 activity must be considered. Recent studies targeting androgen receptor＇s （AR＇s） ID AF1 domain for the castration-resistant prostate cancer has provided the possibility of therapeutically targeting ID NTD/AF1 surfaces by allosteric modulations to achieve desired effects. In this review article, we discuss how inter- and intra- molecular allosteric regulations controlled by AR＇s structural flexibility and dynamics particularly the ID NTD/AF1 is an emerging area of investigation, which could be exploited for drug development and therapeutic targeting of prostate cancer.

A sting in the tail： the N-terminal domain of the androgen receptor as a drug target

The role of androgen receptor （AR） in the initiation and progression of prostate cancer （PCa） is well established. Competitive inhibition of the AR ligand-binding domain （LBD） has been the staple of antiandrogen therapies employed to combat the disease in recent years. However, their efficacy has often been limited by the emergence of resistance, mediated through point mutations, and receptor truncations. As a result, the prognosis for patients with malignant castrate resistant disease remains poor. The amino-terminal domain （NTD） of the AR has been shown to be critical for AR function. Its modular activation function （AF-1） is important for both gene regulation and participation in protein-protein interactions. However, due to the intrinsically disordered structure of the domain, its potential as a candidate for therapeutic intervention has been dismissed in the past. The recent emergence of the small molecule EPI-O01 has provided evidence that AR-NTD can be targeted therapeutically, independent of the LBD. Targeting of AR-NTD has the potential to disrupt multiple intermolecular interactions between AR and its coregulatory binding partners, in addition to intramolecular cross-talk between the domains of the AR. Therapeutics targeting these protein-protein interactions or NTD directly should also have efficacy against emerging AR splice variants which may play a role in PCa progression. This review will discuss the role of intrinsic disorder in AR function and illustrate how emerging therapies might target NTD in PCa.

Mechanisms and regulation underlying membraneless organelle plasticity control

Evolution has enabled living cells to adopt their structural and functional complexity by organizing intricate cellular compartments,such as membrane-bound and membraneless organelles(MLOs),for spatiotemporal catalysis of physiochemical reactions essential for cell plasticity control.Emerging evidence and view support the notion that MLOs are built by multivalent interactions of biomolecules via phase separation and transition mechanisms.In healthy cells,dynamic chemical modifications regulate MLO plasticity,and reversible phase separation is essential for cell homeostasis.Emerging evidence revealed that aberrant phase separation results in numerous neurodegenerative disorders,cancer,and other diseases.In this review,we provide molecular underpinnings on(i)mechanistic understanding of phase separation,(ii)unifying structural and mechanistic principles that underlie this phenomenon,(iii)various mechanisms that are used by cells for the regulation of phase separation,and(iv)emerging therapeutic and other applications.