bioRxiv Science⌕ Search

Biology subjects

Tyagi, M.

Publications and source records attributed to Tyagi, M..

11 recordsLinked to original sources

HIV and Cocaine exposure promote Tau phosphorylation through RSK-1 in a GSK3β-independent manner.

HIV and cocaine are known to disrupt neuronal signaling and contribute to neurocognitive dysfunction, yet the underlying molecular mechanisms are not clear. In this study, we delineate the underlying molecular mechanism by which HIV and/or cocaine enhance Tau phosphorylation (p-Tau S396), a marker of Tau-mediated neuropathies. Furthermore, we elucidate how these two independent neuropathogenic factors, cocaine and HIV, exploit distinct yet convergent signaling pathways to drive this pathological event. We demonstrate that HIV robustly activates and upregulates RSK1, which functions upstream of AKT and promotes Tau phosphorylation through an AKT-independent mechanism while simultaneously inactivating GSK3{beta} via serine-9 phosphorylation (p-GSK3{beta} S9). However, cocaine not only activates RSK1 but also strongly stimulates AKT1, resulting in sustained GSK3{beta} inhibition and persistent Tau phosphorylation. Notably, Tau phosphorylation persists even under conditions of GSK3{beta} inactivation in both HIV and cocaine exposure, revealing a previously unrecognized GSK3{beta}-independent mechanism of Tau modification. Collectively, these findings identify RSK1 as the primary mediator of Tau phosphorylation upon HIV and/or cocaine exposure, and uncover a novel RSK1-driven, GSK3{beta}-independent pathway contributing to Tauopathy. Through a combination of immunofluorescence, immunoblotting, genetic knockout, and overexpression approaches, we establish RSK1 as a central signaling hub linking the AKT-GSK3{beta} pathway to Tau phosphorylation. We demonstrate that RSK1 operates as a critical upstream regulator of AKT and GSK3{beta} signaling, playing dual roles, both activating AKT and suppressing GSK3{beta}, thereby uncovering a novel layer of pathways that regulates Tau phosphorylation. The reproducibility of these main signaling pathways across SH-SY5Y neurons, mixed cell 3D spheroids, and human brain organoids underscores the robustness and biological relevance of this mechanism. Collectively, these findings reveal mechanistic convergence of HIV and cocaine on RSK1-dependent signaling and provide critical insight into how diverse neuropathic / neuropathological factors remodel neuronal signaling to drive Tau-associated dysfunction. These findings provide novel mechanistic insight into the molecular underpinnings of neuro-HIV and substance abuse associated Tauopathy. By identifying RSK1 as a master regulator and demonstrating that Tau phosphorylation can bypass GSK3{beta} inhibition, our study advances understanding of signaling complexity and highlights new opportunities for therapeutic intervention. Targeting RSK1 may represent a promising strategy to mitigate Tau pathology, induced due to insoluble aggregates of phosphorylated Tau, a common factor promoting cognitive decline not only in individuals with Alzheimers disease but also in those exposed to cocaine or/and infected with HIV. SignificancesThis study demonstrates that exposure to HIV and/or cocaine induces Tau phosphorylation at serine 396 (S396), a well-established marker of Tau pathology, and delineates how these two independent neuropathogenic factors engage distinct yet convergent signaling pathways to drive this pathogenic event. We show that HIV exposure drives robust RSK1 activation, positioning it upstream of AKT to promote Tau phosphorylation via an AKT-independent mechanism, while concurrently suppressing GSK3{beta} activity through serine-9 phosphorylation. In contrast, cocaine, while only moderately activating RSK1, primarily enhances AKT signaling, leading to sustained GSK3{beta} inhibition and increased Tau phosphorylation. Notably, Tau phosphorylation persists even under conditions of GSK3{beta} inactivation in both settings, revealing a previously unrecognized, RSK1-centered, GSK3{beta}-independent pathway of Tau modification. Overall, our findings demonstrate that Tau phosphorylation in the context of HIV infection and cocaine exposure is a complex, multi-layered regulatory process involving multiple signaling nodes. Importantly, we identify RSK1 as a central integrative hub linking viral and substance-induced signaling to downstream Tau pathology. This work advances our understanding of the molecular mechanisms underlying neuroHIV and substance abuse-associated neurodegeneration. Furthermore, it highlights RSK1 as a novel and promising therapeutic target for mitigating Tauopathy in both cocaine-using and non-using people with HIV (PWH). Highlighted pointsO_LIRSK1 acts as a central regulator of Tau phosphorylation, capable of driving this process through a GSK3{beta}-independent mechanism. C_LIO_LIHIV promotes Tau phosphorylation primarily via robust upregulation and activation of RSK1, operating largely independent of AKT1, while concurrently inducing GSK3{beta} inactivation. C_LIO_LIDrugs of abuse, such as cocaine induces Tau phosphorylation through dual activation of AKT1 and RSK1, alongside sustained inactivation of GSK3{beta}. C_LIO_LITau phosphorylation persists despite GSK3{beta} inhibition, revealing a complex AKT1-RSK1 signaling axis and underscoring the dominant role of GSK3{beta}-independent mechanisms in Tau pathology following HIV and cocaine exposure. C_LIO_LIHIV and cocaine engage distinct yet convergent signaling pathways that disrupt neuronal homeostasis and drive tauopathy, providing mechanistic insight into neuroHIV and substance abuse-associated neurodegeneration. C_LIO_LIRSK1 functions as a key upstream modulator of AKT and GSK3{beta} pathways, positively regulating AKT signaling while negatively regulating GSK3{beta} activity. C_LIO_LIRSK1 emerges as a potential therapeutic target, offering new opportunities for intervention in HIV-associated neurocognitive disorders (HAND) and drug-induced neurodegeneration. C_LIO_LIEstablished and characterized H80 cells as a novel neuronal cell model and demonstrated their suitability for studying neuron-specific signaling pathways, including Tau phosphorylation. C_LIO_LIThe conserved and widespread nature of the signaling cascade driving Tau phosphorylation in response to HIV and/or cocaine exposure was validated across multiple model systems, including both 2D neuronal cell cultures and 3D systems such as human brain organoids and spheroids. C_LI Strength of the StudyThis original study provides novel mechanistic insight into how HIV and cocaine, two independent neuropathological factors, converge and diverge on intracellular signaling pathways to regulate Tau phosphorylation. By integrating immunofluorescence, immunoblotting, genetic knockout, and overexpression approaches, we identified RSK1 as a master regulator of Tau phosphorylation. Importantly, we discovered that HIV robustly upregulates and activates RSK1 to promote Tau phosphorylation through an AKT-independent route while simultaneously inactivating GSK3{beta}. On the other hand, cocaine exerts a moderate effect on RSK1 but strongly stimulates AKT to induce GSK3{beta} inactivation and drive Tau phosphorylation. A key strength of this work is the discovery that Tau phosphorylation persists despite GSK3{beta} inactivation, revealing a complex, GSK3{beta}-independent mechanism, involving RSK1 in Tau pathology. Moreover, our study, for the first time, identify RSK1 as an upstream regulator of AKT-GSK3{beta} signaling cascade, enhancing AKT signaling while simultaneously inhibiting GSK3{beta} activity, thereby underscoring the critical role of RSK1 in Tau phosphorylation and associated illnesses, such as HAND and Alzheimers disease. Together, these findings not only advance our understanding of the molecular underpinnings of neuroHIV and substance abuse associated tauopathy but also highlight RSK1 as a promising therapeutic target for not only HIV and cocaine induced neurotoxicity but also other neurodegenerative diseases, such as Alzheimers disease. Another key strength of this study is the establishment and characterization of H80 cells as a novel neuronal model, demonstrating their suitability for investigating neuron-specific signaling pathways, including Tau phosphorylation. The combination of comparative signaling analysis, genetic perturbations, and integrative mechanistic modeling makes this study both conceptually and technically novel, besides broadly relevant to the fields of neurovirology, addiction neuroscience, neurodegeneration, and cognitive impairments.

molecular biology↗

WRN helicase regulates mitophagy by resolving an intricate nexus of G-quadruplexes-R loops-ATG7 pre-mRNA maturation in cancer

Werner syndrome (WS) is a progeroid and cancer-predisposition disorder caused by loss of the Werner RECQ helicase-exonuclease (WRN), a key genome-maintenance enzyme essential for replication-stress signalling and DNA-repair. WS patients also develop metabolic abnormalities, including fatty-liver and diabetes, suggesting a link between WRN-deficiency and mitochondrial-dysfunction. WRN is frequently epigenetically silenced in cancers, yet its precise role in mitochondrial homeostasis in cancer remains unclear. Here, we define a role for WRN in regulating mitophagy and autophagy in cancer. WRN-deficient cells show defective mitochondrial respiration, morphology, and mitophagosome/autophagosome-maturation under basal and cisplatin-induced stress. Mechanistically, WRN-loss causes strong reduction of ATG7-protein, compromising autophagosome-biogenesis. Chromatin immunoprecipitation reveals accumulation of unresolved G-quadruplex structures (G4-DNA) across the ATG7-locus in WRN-deficient cells. Paradoxically, ATG7-mRNA expression is elevated despite reduced ATG7-protein in WRN-deficient cells, indicating a post-transcriptional defect. Further, we show that WRN resolves G4-DNA which prevent R-loops formation and interacts with the mRNA-processing factor U2AF35, independent of its helicase-exonuclease functions, to promote maturation of nascent ATG7 transcripts. In cancer patients, WRN level also inversely correlated with post-transcriptional defects in ATG7 mRNA. Collectively, our findings suggest pivotal association of WRN-loss in autophagy fidelity, which may further contribute to oncogenic transformation in WRN-deficient tissues and exacerbate cancer susceptibility in WS-patients. Significance statementWRN is well recognized for its roles in DNA repair and genome maintenance, which are essential for suppressing tumorigenesis and Werner syndrome (WS)-associated premature-aging. However, its functions in mitochondrial regulation remain underexplored, despite WS patients exhibiting severe metabolic defects and increased cancer risk. Here, we uncover a mechanistic link between WRN and autophagy/mitophagy, showing that WRN resolves G-quadruplexes and R-loops to enable proper post-transcriptional processing and translation of ATG7, a key autophagy enzyme. WRN-loss associated defective-autophagy may heighten the initiation of tumorigenesis in both WS-patients and in normal individual with mutated WRN in different tissue-types. As WRN is actively pursued as a synthetic-lethal target and multiple WRN inhibitors progress through clinical-development, our findings highlight mitochondrial quality-control defects as an additional determinant of WRN-targeted therapeutic-response.

cell biology↗

Arc mediates intercellular tau transmission via extracellular vesicles

Intracellular neurofibrillary tangles that consist of misfolded tau protein1 cause neurodegeneration in Alzheimers disease (AD) and frontotemporal dementia (FTD). Tau pathology spreads cell-to-cell2 but the exact mechanisms of tau release and intercellular transmission remain poorly defined. Tau is released from neurons as free protein or in extracellular vesicles (EVs)3-5 but the role of these different release mechanisms in intercellular tau transmission is unclear. Here, we show that the neuronal gene Arc is critical for packaging tau into EVs. Brain EVs purified from human tau (hTau) transgenic rTg4510 mice (rTgWT) contain high levels of hTau that are capable of seeding tau pathology. In contrast, EVs purified from rTgWT crossed with Arc knock-out mice (rTgArc KO) have significantly less hTau and cannot seed tau aggregation. Arc facilitates the release of hTau in EVs produced via the I-BAR protein IRSp53, but not free tau. Arc protein directly binds hTau to form a fuzzy complex that we identified in both mouse and human brain tissue. We find that pathological intracellular hTau accumulates in neurons in rTgArc KO mice, which correlates with accelerated neuron loss in the hippocampus. Finally, we find that intercellular tau transmission is significantly abrogated in Arc KO mice. We conclude that Arc-dependent release of tau in EVs plays a significant role in intracellular tau elimination and intercellular tau transmission.

neuroscience↗

Cocaine-induced DNA-PK relieves RNAP II pausing by promoting TRIM28 phosphorylation.

Drug abuse continues to pose a significant challenge in HIV control efforts. In our investigation, we discovered that cocaine not only upregulates the expression of DNA-dependent protein kinase (DNA-PK) but also augments DNA-PK activation by enhancing its phosphorylation at S2056. Moreover, DNA-PK phosphorylation triggers the translocation of DNA-PK into the nucleus. The finding that cocaine promotes nuclear translocation of DNA-PK further validates our observation of enhanced DNA-PK recruitment at the HIV long terminal repeat (LTR) following cocaine exposure. By activating and facilitating the nuclear translocation of DNA-PK, cocaine effectively orchestrates multiple stages of HIV transcription, thereby promoting HIV replication. Additionally, our study indicates that cocaine-induced DNA-PK promotes hyper-phosphorylation of RNA polymerase II (RNAP II) carboxyl-terminal domain (CTD) at Ser5 and Ser2 sites, enhancing both initiation and elongation phases, respectively, of HIV transcription. Cocaines enhancement of transcription initiation and elongation is further supported by its activation of cyclin-dependent kinase 7 (CDK7) and subsequent phosphorylation of CDK9, thereby promoting positive transcriptional elongation factor b (P-TEFb) activity. We demonstrate for the first time that cocaine, through DNA-PK activation, promotes the specific phosphorylation of TRIM28 at Serine 824 (p-TRIM28, S824). This modification converts TRIM28 from a transcriptional inhibitor to a transactivator for HIV transcription. Additionally, we observe that phosphorylation of TRIM28 (p-TRIM28, S824) promotes the transition from the pausing phase to the elongation phase of HIV transcription, thereby facilitating the production of full-length HIV genomic transcripts. This finding corroborates the observed enhanced RNAP II CTD phosphorylation at Ser2, a marker of transcriptional elongation, following cocaine exposure. Accordingly, upon cocaine treatment, we observed elevated recruitment of p-TRIM28-(S824) at the HIV LTR. Overall, our results have unraveled the intricate molecular mechanisms underlying cocaine-induced HIV transcription and gene expression. These findings hold promise for the development of highly targeted therapeutics aimed at mitigating the detrimental effects of cocaine in individuals living with HIV. Highlights of the studyO_LICocaine upregulates both the expression and activity of DNA-PK. C_LIO_LICocaine augments the phosphorylation of DNA-PK selectively at S2056, a post-translational modification that marks functionally active form of DNA-PK. C_LIO_LICocaine enhances the nuclear translocation of DNA-PK. C_LIO_LIThe DNA-PK inhibition severely impairs HIV transcription, replication, and latency reactivation. C_LIO_LICocaine facilitates the initiation and elongation phases of HIV by enhancing RNAPII CTD phosphorylation at Ser5 and Ser2, respectively, by stimulating DNA-PK. C_LIO_LICocaine also supports initiation and elongation phases of HIV transcription by stimulating CDK7 (the kinase of TFIIH) and CDK9 (the kinase subunit of P-TEFb), respectively. C_LIO_LICocaine-mediated activation of DNA-PK relieves RNAP II pausing by reversing the inhibitory effect of pausing factor TRIM28 and converting it into a transactivator by catalyzing its phosphorylation at S824 site. C_LIO_LIThus, cocaine, by activating DNA-PK, facilitates the multiple phases of HIV transcription, namely, initiation, RNAP II pause-release, and elongation. C_LI

molecular biology↗

Comparative vitreous proteomic profiling of proliferative diabetic retinopathy and diabetic with no-retinopathy subjects implicates impaired autophagy in DR pathogenesis

PurposeDiabetic retinopathy (DR) is a neurovascular complication of diabetes (DM) causing the loss of neurons (ganglion cells) in the retina. The disease etiology and potential pathogenic mechanisms in this disease remains unclear. In the present study, we aimed to further understand the key and novel pathogenic mechanisms involved in DR pathogenesis by taking cues from our global proteomics data. MethodologyThe study was approved by the institutional review board (IRB) of LVPEI, Hyderabad, India. Vitreous humour samples (PDR; n=3, DM; n=3, Control; n=3) were collected from patients undergoing vitrectomy and subjected to LC-MS-MS analysis. The acquired raw data were searched against the human vitreous proteome and was further analysed by various bioinformatic and proteomic tools. Western blotting and IHC was performed to validate crucial pathways. Blood samples from patients (DM, PDR & NPDR) and controls (n=50); cadaveric retinas from diabetic and non-diabetic donors (n=10) and epiretinal membranes (ERM, n=10) from DR cases and controls were collected and RNA was isolated. Quantitative expression of genes involved in autophagy were performed. CT was compared across different categories and significance estimated using a student t-test. ResultA total of 1079 proteins were identified with 16 completely novel proteins in eye proteome. Top pathways identified were autophagy, inflammation, LXR/RXR activation (lipid metabolism), ROS generation by macrophages, apoptosis and protein degradation. Regulatory proteins identified were associated with cell death, phagocytic activation, angiogenesis and apoptosis. Autophagy inducers such as ROS was found to be accumulated in the DR vitreous. TREM2, microglial receptor was identified as a novel protein in PDR vitreous. The expression of TREM2, an autophagy-associated gene was significantly (p-value = 0.05) upregulated in all categories as compared to control (NDM and/or NDM/No-DR). TREM2 protein also seemed to colocalise with microglial marker F4/80 in retinal tissues and intense expression was observed near the blood vessels in case of PDR retina. Other autophagy-associated markers were also differentially regulated in DR as compared to controls. ConclusionThis study emphasises on the strong role of autophagy pathways and its associated genes in the development of DR.

genomics↗

Arc mediates intercellular synaptic plasticity via IRSp53-dependent extracellular vesicle biogenesis.

Current models of learning and memory have focused on cell-autonomous regulation of synaptic strength; however, intercellular signaling between cells in the brain is important for normal cognition. The immediate early gene Arc is a repurposed retrotransposon critical for long-term forms of synaptic plasticity and memory. Arc protein forms virus-like capsids released in extracellular vesicles (EVs) that mediate intercellular signaling of unknown function. Here, we find that long-term potentiation stimuli induce the biogenesis of Arc EVs by recruiting the I-BAR protein IRSp53, which facilitates Arc capsid assembly, trafficking, and release from actin-rich filopodial structures in dendrites. Arc EVs transfer Arc protein and mRNA to neighboring dendrites, where translation of transferred Arc mRNA induces a loss of surface AMPA-type glutamate receptors. These results show that Arc EVs mediate an intercellular form of synaptic plasticity that may be critical for memory consolidation and reveals a new neuronal EV biogenesis pathway.

neuroscience↗

Decoupling of the Onset of Anharmonicity between a Protein and Its Surface Water around 200 K

The protein dynamical transition at [~] 200 K, where the biomolecule transforms from a harmonic, non-functional form to an anharmonic, functional state, has been thought to be slaved to the thermal activation of dynamics in its surface hydration water. Here, by selectively probing the dynamics of protein and hydration water using elastic neutron scattering and isotopic labelling, we found that the onset of anharmonicity in the two components around 200 K are decoupled. The one in protein is an intrinsic transition, whose characteristic temperature is independent of the instrumental resolution time, but varies with the biomolecular structure and the amount of hydration, while the one of water is merely a resolution effect.

biophysics↗

A systematic investigation on the involvement of complement pathway in diabetic retinopathy

BackgroundComplement system play a crucial role in retinal homeostasis. Several proteomic studies have shown deposition of complement protein in ocular tissues from diabetic retinopathy, however, their exact involvement in pathogenesis of DR remains unclear.\n\nMethodsWe evaluated major complement pathway proteins in the classical and alternative pathway including C1q, C4b, C3, CFB and CFH in vitreous humor and serum samples from PDR patients and controls by western blotting. Quantitative real time (QRT) PCR was done for PDR, NPDR and no-DM controls for correlating the expression of several key pro and anti -angiogenic genes with their correspondingprotein levels. Inflammation in the vitreous humor samples was assessed by ELISA and metalloproteinase activity measured by gelatin zymography. Glial activation and its association with complement activation in diabetic eyes was assessed by immunohistochemistry.\n\nResultsA significant increase in C3 proteins, its activated fragment C3b (110kDa) along with a concurrent up regulation of CFH was observed for PDR vitreous. QRT identified a significant upregulation of angiogenic genes and downregulation of antiangiogenic genes in PDR and NPDR cases. PDR vitreous had increased MMP9 activity and upregulation of inflammatory markers IL8, sPECAM and down regulation of anti-inflammatory marker IL-10. Increased C3 deposition and CFH upregulation were observed in DM retina. CFH was found co-localizing with CD11b+ve activated microglial cells in inner nuclear layer of DM retina.\n\nConclusionsThe present study confirms increased activation of alternative complement pathway in PDR. The co-localization of CFH in CD11b +ve cells further suggests microglia as a source of CFH in diabetic retina. Increased CFH levels could be a feedback mechanism for arresting excessive complement activation DR eyes.

immunology↗

DNA-PK facilitates HIV transcription by regulating the activity of RNA polymerase II and the recruitment of transcription machinery at HIV LTR

Despite the use of highly effective antiretroviral therapy (HAART), the presence of latent or transcriptionally silent proviruses prevents cure and eradication of HIV infection. These transcriptionally silent proviruses are well protected from both the immune system and HAART regimens. Thus, in order to tackle the problem of latent HIV reservoirs, it is a prerequisite to define all the pathways that regulate HIV transcription. We have previously reported that DNA-PK facilitates HIV transcription by interacting with the RNA polymerase II (RNAP II) complex recruited at HIV LTR. To extend those studies further, here we demonstrate that DNA-PK promotes HIV transcription by supporting it at several stages, including initiation, pause-release and elongation. We discovered that DNA-PK increases phosphorylation of RNAP II C-terminal domain (CTD) at serine 5 (Ser5) and serine 2 (Ser2) by both directly catalyzing and by augmenting the recruitment of P-TEFb at HIV LTR. We found that DNA-PK facilitates the establishment of euchromatin structure at HIV LTR, which further supports HIV gene expression. DNA-PK inhibition or knockdown leads to the severe impairment of HIV gene expression and conversion of euchromatin to heterochromatin at HIV LTR. It also profoundly restricts HIV replication and reactivation of latent provirus. DNA-PK promotes the recruitment of TRIM28 at LTR and facilitates the release of paused RNAP II through TRIM28 phosphorylation. The results were reproduced in cell lines belonging to both lymphoid and myeloid lineages and were confirmed in primary CD4+ T cells and peripheral blood mononuclear cells (PBMCs) from HIV-infected patients.\n\nIMPORTANCEOur results reveal the important role of DNA-PK in supporting HIV transcription, replication and latent proviral reactivation. Intriguingly, this study sheds light on an important pathway that affects HIV gene expression. These findings provide strong rationale for developing and using transcriptional inhibitors, such as DNA-PK inhibitors, as supplement to HAART regimens in order to further enhance their effectiveness and to suppress toxicity due to HIV proteins.

molecular biology↗

CBF-1 promotes the establishment and maintenance of HIV latency by recruiting Polycomb repressive complexes, PRC1 and PRC2, at HIV LTR

The C-promoter binding factor-1 (CBF-1) is a potent and specific inhibitor of the HIV-1 LTR promoter. Here we demonstrate that the knockdown of endogenous CBF-1 in latently infected primary CD4+ T cells, using specific small hairpin RNAs (shRNA), resulted in the reactivation of latent HIV proviruses. Chromatin immunoprecipitation (ChIP) assays using latently infected primary T cells and Jurkat T-cell lines demonstrated that CBF-1 induces the establishment and maintenance of HIV latency by recruiting Polycomb Group (PcG/PRC) corepressor complexes or Polycomb repressive complexes 1 and 2 (PRC1 and PRC2). Knockdown of CBF-1 resulted in the dissociation of PRCs corepressor complexes enhancing the recruitment of RNA polymerase II (RNAP II) at HIV LTR. Knockdown of certain components of PRC1 and PRC2 also led to the reactivation of latent proviruses. Similarly, treatment of latently infected primary CD4+ T cells with the EZH2 inhibitor, 3-deazaneplanocin A (DZNep), led to their reactivation.

molecular biology↗

PB-kPRED: Knowledge-Based Prediction Of Protein Backbone Conformation Using A Structural Alphabet

Libraries of structural prototypes that abstract protein local structures are known as structural alphabets and have proven to be very useful in various aspects of protein structure analyses and predictions. One such library, Protein Blocks (PBs), is composed of 16 standard 5-residues long structural prototypes. This form of analyzing proteins involves drafting its structure as a string of PBs. Thus, predicting the local structure of a protein in terms of protein blocks is a step towards the objective of predicting its 3-D structure. Here a new approach, kPred, is proposed towards this aim that is independent of the evolutionary information available. It involves (i) organizing the structural knowledge in the form of a database of pentapeptide fragments extracted from all protein structures in the PDB and (ii) apply a purely knowledge-based algorithm, not relying on secondary structure predictions or sequence alignment profiles, to scan this database and predict most probable backbone conformations for the protein local structures.\n\nBased on the strategy used for scanning the database, the method was able to achieve efficient mean Q16 accuracies between 40.8% and 66.3% for a non-redundant subset of the PDB filtered at 30% sequence identity cut-off. The impact of these scanning strategies on the prediction was evaluated and is discussed. A scoring function that gives a good estimate of the accuracy of prediction was further developed. This score estimates very well the accuracy of the algorithm (R2 of 0.82). An online version of the tool is provided freely for non-commercial usage at http://www.bo-protscience.fr/kpred/.

bioinformatics↗