Protein p
K
a
prediction is essential
for the investigation of the pH-associated relationship between protein
structure and function. In this work, we introduce a deep learning-based
protein p
K
a
...predictor DeepKa, which is
trained and validated with the p
K
a
values
derived from continuous constant-pH molecular dynamics (CpHMD) simulations
of 279 soluble proteins. Here, the CpHMD implemented in the Amber
molecular dynamics package has been employed (
Huang
Y.
J. Chem. Inf. Model.
2018
,
58
,
1372
−
1383
29949356
). Notably, to avoid discontinuities at the boundary,
grid charges are proposed to represent protein electrostatics. We
show that the prediction accuracy by DeepKa is close to that by CpHMD
benchmarking simulations, validating DeepKa as an efficient protein
p
K
a
predictor. In addition, the training
and validation sets created in this study can be applied to the development
of machine learning-based protein p
K
a
predictors
in the future. Finally, the grid charge representation is general
and applicable to other topics, such as the protein–ligand
binding affinity prediction.
Primary hyperoxaluria (PH) is a rare inherited autosomal recessive disease caused by disturbed glyoxylate metabolism. The disease is characterized by calcium oxalate crystal deposition in various ...organs, especially in the kidney. Due to the lack of current understanding of PH, nearly all patients are only initially diagnosed with PH when recurrent lithiasis and progressive end-stage renal disease occur. Many cases are not diagnosed in patients until renal allograft insufficiency occurs after renal transplantation. This case report and literature review aim to emphasize the need for careful pre-transplant PH screening of patients with bilateral nephrocalcinosis or nephrolithiasis.
Renal allograft insufficiency was diagnosed as PH after kidney transplantation. Here, we detail the complete clinical course, including computed tomography images of the original kidney and renal graft, histopathological images of a biopsy of the transplanted kidney, the results of laboratory and molecular genetic tests, and the treatment. In addition, we reviewed the literature from 2000 to 2021 and analyzed 19 reported cases of PH diagnosed after kidney transplantation, and provide a summary of the characteristics, complications, treatment, and prognosis of these cases.
By reviewing and analyzing these cases, we concluded that patients with a history of nephrocalcinosis or nephrolithiasis in both kidneys need preoperative screening for PH and appropriate treatment before kidney transplantation. Delayed graft function caused by PH is easily misdiagnosed as acute rejection, and needle biopsy should be performed at an early stage.
1 Currently, there are 4468 renal allograft recipients located in Hubei province participating in follow-up at these hospitals. ...May 1, 2020, 31 recipients had been diagnosed with COVID-19 ...Supplementary Table 1, http://links.lww.com/CM9/A576. ...in a high risk area, stricter self-protection strategies should be adopted to avoid infection. Early admission to the hospital, lower dose of maintenance immunosuppressants following transplantation, and early reduction of immunosuppressants might account for the relatively lower incidence of death. ...although the use of corticosteroids in treating COVID-19 pneumonia remains controversial, a low dose of bolus corticosteroid (methylprednisolone 40–80 mg/day) was widely used in replacement of maintenance immunosuppressants in this cohort. According to experience from the management of cytomegalovirus infection, which is a common infectious complication after renal transplantation, a low dose of corticosteroid is a well-tolerable selection for the reduction of inflammation and cytokine release.
Tristetraprolin (TTP) is an RNA binding protein that plays a critical role in regulating proinflammatory immune responses by destabilizing target mRNAs via binding to their AU-rich elements (AREs) in ...the 3'-UTRs of mRNAs. A recent CLIP-seq study revealed that TTP-binding sites are enriched in the intronic regions of RNA. TTP is also a nuclear protein that exhibits putative DNA-binding activity. These features suggested that TTP might regulate gene transcription and/or alternative splicing of pre-mRNAs in the absence of stimulation.
To elucidate the regulatory pattern of TTP, we cloned and overexpressed the human TTP-encoding gene, ZFP36, in HeLa cells in the absence of inflammatory stimuli. The transcriptomes of the control and ZFP36-overexpressing cells were sequenced and subjected to analysis and validation. Upon ZFP36 overexpression, the expression of genes associated with innate immunity, including those in the type I interferon signaling pathway and viral response, were specifically upregulated, implying a transcriptional regulatory mechanism associated with the predicted DNA binding activity of TTP. TTP preferentially regulated the alternative splicing of genes involved in the positive regulation of the I-κB/NF-κB cascade and the TRIF-dependent toll-like receptor, MAPK, TNF, and T cell receptor signaling pathways.
Our findings indicated that TTP may regulate the immune response via the regulation of alternative splicing and potentially transcription, which greatly expands the current understanding of the mechanisms of TTP-mediated gene regulation.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron is a major coronavirus variant, which was prevalent in China at the end of 2022 and caused widespread infection. As an ...immunosuppressed group, renal transplant recipients with SARS-CoV-2 infection are prone to developing serious pneumonia or an adverse outcome event if the infection is not treated in time. Here, we analyze the possible risk factors of infection severity.
92 cases of moderate and severe SARS-CoV-2 infection after renal transplantation were collected. Statistical methods, including Fisher's tests, F test, Spearman relative values, and multi-parameter logistic regression models, were used to analyze the risk factors for severe SARS-CoV-2 infection in renal transplant recipients.
44 cases complicated with hypertension were observed in the study cohort, among whom 30 were severe (OR: 4.63, p < 0.001). Out of 51 male patients infected with Omicron, 30 male patients presented with severe SARS-CoV-2 (OR: 2.45, p = 0.039). In renal transplant patients, hypertension comorbidity was closely correlated with clinical presentation (R = 0.369, p < 0.001). Blood routine test, chemistries, and additional indices showed increased neutrophils and C-reactive protein in patients with severe disease compared with the moderate group according to one-way analysis of variance (p = 0.004), while CD3 (p = 0.02) and CD4 (p = 0.04) showed lower expressional levels. We also observed meaningful correlations between neutrophil levels and hypertension comorbidity (R = 0.222, p = 0.034) and between interleukin-6 (IL-6) levels and diabetes comorbidity (R = 0.315, p = 0.011), with IL-6 considered a key factor in the context of coronavirus disease.
Renal transplant recipients were generally susceptible to infection with the Omicron variant, with a more pronounced incidence of severe illness observed in the group with hypertension comorbidity.
Long noncoding RNAs (lncRNAs) are persistently expressed and have been described as potential biomarkers and therapeutic targets in various diseases. However, there is limited information regarding ...lncRNA expression in the tissue of kidney exhibiting lupus nephritis (LN)a serious complication of systemic lupus erythematosus (SLE). In this study, RNA sequencing (RNA-seq) was performed to characterize the lncRNA and mRNA expression in kidney tissues from LN (MRL/lpr) and control mice. We identified 12,979 novel lncRNAs in mouse. The expression profiles of both mRNAs and lncRNAs were differed significantly between LN and control mice. In particular, there were more upregulated lncRNAs and mRNAs than downregulated ones in the kidney tissues of LN mice. However, GO analysis showed that more downregulated genes were enriched in immune and inflammatory response-associated pathways. KEGG analysis showed that both downregulated and upregulated genes were enriched in a number of pathways, including the SLE pathway, and approximately half of these SLE-associated genes encoded inflammatory factors. Moreover, we observed that 2,181 DElncRNAs may have targeted and regulated the expression of 778 mRNAs in LN kidney tissues. The results of this study showed that 11 DElncRNAs targeted and were co-expressed with six immune and SLE-associated genes. qPCR analysis confirmed that lncRNA Gm20513 positively regulated the expression of the SLE-associated gene H2-Aa. In conclusion, the results of our study demonstrates that lncRNAs influence the progression of LN and provide some cues for further study of lncRNAs in LN. These results regarding the lncRNA-mRNAregulatory network may have important value in LN diagnosis and therapy.
Suppressor of cytokine signaling 3 (SOCS3) is highly expressed in mice with renal ischemia/reperfusion (RI/R) injury and has the potential to regulate mitophagy. On this basis, this study further ...investigates the possible mechanism via which SOCS3 affects RI/R by regulating mitophagy.
After establishing a RI/R injury mouse model and a hypoxia/reoxygenation (H/R) cell model, the effects of silenced SOCS3 on injury and mitophagy in the above models were analyzed by ELISA, quantitative real-time polymerase chain reaction, Western blot, pathological sections, CCK-8 assay, flow cytometry, and JC-1 assay. Mechanistic studies were carried out with the help of database analysis and binding validation experiments (chromatin immunoprecipitation, dual-luciferase reporter assay, and co-immunoprecipitation). After the binding target was identified, the regulatory relationship between the target gene and SOCS3 was verified by rescue experiments.
The large increase in blood urea nitrogen (BUN) and creatinine (Cr) levels verified the success of the RI/R model. SOCS3 expression was up-regulated in RI/R mice. Silenced SOCS3 alleviated kidney damage and mitochondrial abnormalities in RI/R mice and inhibited mitophagy at the molecular level. Likewise, silenced SOCS3 alleviated H/R-induced cell damage and mitophagy. Finally, activating transcription factor 3 (ATF3) was determined to bind to the promoter of SOCS3, which interacted with insulin-like growth factor 1 receptor (IGF1R). Rescue experiments confirmed the effect of ATF3 on SOCS3 expression and the underlying regulatory mechanism.
ATF3 mediates SOCS3 expression to promote the activation of mitophagy, thereby aggravating renal ischemia-reperfusion injury.
pH regulates protein structures and the associated functions in many biological processes via protonation and deprotonation of ionizable side chains where the titration equilibria are determined by ...pKa's. To accelerate pH-dependent molecular mechanism research in the life sciences or industrial protein and drug designs, fast and accurate pKa prediction is crucial. Here we present a theoretical pKa data set PHMD549, which was successfully applied to four distinct machine learning methods, including DeepKa, which was proposed in our previous work. To reach a valid comparison, EXP67S was selected as the test set. Encouragingly, DeepKa was improved significantly and outperforms other state-of-the-art methods, except for the constant-pH molecular dynamics, which was utilized to create PHMD549. More importantly, DeepKa reproduced experimental pKa orders of acidic dyads in five enzyme catalytic sites. Apart from structural proteins, DeepKa was found applicable to intrinsically disordered peptides. Further, in combination with solvent exposures, it is revealed that DeepKa offers the most accurate prediction under the challenging circumstance that hydrogen bonding or salt bridge interaction is partly compensated by desolvation for a buried side chain. Finally, our benchmark data qualify PHMD549 and EXP67S as the basis for future developments of protein pKa prediction tools driven by artificial intelligence. In addition, DeepKa built on PHMD549 has been proven an efficient protein pKa predictor and thus can be applied immediately to, for example, pKa database construction, protein design, drug discovery, and so on.
DeepKa is a deep-learning-based protein pKa predictor proposed in our previous work. In this study, a web server was developed that enables online protein pKa prediction driven by DeepKa. The web ...server provides a user-friendly interface where a single step of entering a valid PDB code or uploading a PDB format file is required to submit a job. Two case studies have been attached in order to explain how pKa's calculated by the web server could be utilized by users. Finally, combining the web server with post processing as described in case studies, this work suggests a quick workflow of investigating the relationship between protein structure and function that are pH dependent.
DeepKa is a deep-learning-based protein pK a predictor proposed in our previous work. In this study, a web server was developed that enables online protein pK a prediction driven by DeepKa. The web ...server provides a user-friendly interface where a single step of entering a valid PDB code or uploading a PDB format file is required to submit a job. Two case studies have been attached in order to explain how pK a’s calculated by the web server could be utilized by users. Finally, combining the web server with post processing as described in case studies, this work suggests a quick workflow of investigating the relationship between protein structure and function that are pH dependent. The web server of DeepKa is freely available at http://www.computbiophys.com/DeepKa/main.
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