The initiation of adaptive immune responses relies on the precise recognition and interpretation of antigenic information. In this process, the specific binding of T cell receptors (TCRs) to peptide-major histocompatibility complex (pMHC) molecules represents one of the key molecular events in the initiation of adaptive immune responses. Accordingly, the structural features of TCR-pMHC complexes provide a fundamental basis for dissecting antigen recognition mechanisms and support rational vaccine design, therapeutic target discovery in TCR-based immunotherapy, and TCR identification and optimization. However, experimental determination of TCR-pMHC structures remains costly, time-consuming, and limited in coverage, making computational approaches essential for rapidly obtaining reliable structural information. Computational methods for predicting the structures of TCR-pMHC complexes have advanced rapidly in recent years, driven by progress in deep learning-based modeling frameworks and the increasing availability of structural and sequence resources. Despite these developments, most existing tools do not adequately distinguish the key structural and biophysical differences between MHC class I (MHC-I) and MHC class II (MHC-II) complexes during model construction. As a consequence, their predictive performance differs substantially between class I and class II complexes. In general, structural predictions for class I complexes outperform those for class II complexes. This discrepancy may be related to several fundamental differences between the two systems, including the architecture of the peptide-binding groove, the distribution of peptide lengths, and the properties of peptide flanking residues (PFRs). Compared with MHC-I molecules, MHC-II molecules usually bind longer antigenic peptides, which typically range from 13 to 25 amino acids in length. PFRs at both termini of these peptides participate in regulating the overall conformation of TCR-pMHC class II complexes and exert a pronounced effect on the geometric and physicochemical characteristics of the TCR-pMHC binding interface. Furthermore, within the TCR recognition interface, the complementarity-determining regions (CDRs) consist of segments that differ markedly in conformational behavior. They commonly include regions that are relatively rigid and structurally stable, together with highly flexible segments exhibiting substantial conformational plasticity. These rigidity-flexibility features constitute an essential structural basis enabling TCRs to recognize diverse peptide-MHC ligands and to accommodate conformational heterogeneity at the interface. However, many current modeling tools, in an effort to enforce global conformational stability or reduce structural noise, tend to over-constrain intrinsically flexible regions. Such oversimplification may lead to inappropriate rigidification of flexible CDR loops, resulting in local structural distortions, compromised interface geometry, or even complete modeling failure for specific complexes. Against this background, the review approaches the field from the perspective of computational differences between MHC-I and MHC-II complexes. We first systematically organize and summarize available resources related to TCRs and pMHCs, including structural datasets, sequence databases, prediction tools, and benchmarking studies. We then focus on five representative tools capable of predicting both class I and class II complexes—AlphaFold2, AlphaFold3, TCRmodel2, tFold-TCR, and TCR-pHLA_ModellerS. After excluding structures present in the training sets of these tools, we constructed a benchmark dataset comprising 25 class I and 10 class II TCR-pMHC complexes in the bound state and conducted a systematic evaluation using this dataset. We first employ widely used general evaluation metrics, including All-Atom Root Mean Square Deviation (All-Atom RMSD), Backbone RMSD, Template Modeling score (TM-score), and DockQ, to assess the global conformational accuracy and interface modeling quality of class I and class II complexes. For class II complexes, we propose for the first time a peptide flanking residue deviation index, including the PFRs-Deviation Index (PFRs-DI), N-PFR-Deviation Index (N-PFR-DI), and C-PFR-Deviation Index (C-PFR-DI), to quantitatively characterize conformational deviations in PFRs. In addition, we propose the CDR conformational consistency index (CCC) designed to qualitatively evaluate the ability of prediction tools to capture TCR CDR conformational flexibility. These metrics collectively assess a tool’s ability to model both overall conformation and critical functional regions, thereby addressing the limitations of existing evaluation criteria that overemphasize global structure while inadequately capturing modeling quality in key functional areas. This establishes a unified analytical framework for MHC-I and MHC-II complexes to guide data resource selection, modeling strategy formulation, and evaluation system development. The framework further advances computational modeling and provides crucial support for multi-scale analysis of TCR-pMHC recognition mechanisms and their biological functions.

The initiation of adaptive immune responses relies on the precise recognition and interpretation of antigenic information. In this process, the specific binding of T cell receptors (TCRs) to peptide-major histocompatibility complex (pMHC) molecules represents one of the key molecular events in the initiation of adaptive immune responses. Accordingly, the structural features of TCR-pMHC complexes provide a fundamental basis for dissecting antigen recognition mechanisms and support rational vaccine design, therapeutic target discovery in TCR-based immunotherapy, and TCR identification and optimization. However, experimental determination of TCR-pMHC structures remains costly, time-consuming, and limited in coverage, making computational approaches essential for rapidly obtaining reliable structural information. Computational methods for predicting the structures of TCR-pMHC complexes have advanced rapidly in recent years, driven by progress in deep learning-based modeling frameworks and the increasing availability of structural and sequence resources. Despite these developments, most existing tools do not adequately distinguish the key structural and biophysical differences between MHC class I (MHC-I) and MHC class II (MHC-II) complexes during model construction. As a consequence, their predictive performance differs substantially between class I and class II complexes. In general, structural predictions for class I complexes outperform those for class II complexes. This discrepancy may be related to several fundamental differences between the two systems, including the architecture of the peptide-binding groove, the distribution of peptide lengths, and the properties of peptide flanking residues (PFRs). Compared with MHC-I molecules, MHC-II molecules usually bind longer antigenic peptides, which typically range from 13 to 25 amino acids in length. PFRs at both termini of these peptides participate in regulating the overall conformation of TCR-pMHC class II complexes and exert a pronounced effect on the geometric and physicochemical characteristics of the TCR-pMHC binding interface. Furthermore, within the TCR recognition interface, the complementarity-determining regions (CDRs) consist of segments that differ markedly in conformational behavior. They commonly include regions that are relatively rigid and structurally stable, together with highly flexible segments exhibiting substantial conformational plasticity. These rigidity-flexibility features constitute an essential structural basis enabling TCRs to recognize diverse peptide-MHC ligands and to accommodate conformational heterogeneity at the interface. However, many current modeling tools, in an effort to enforce global conformational stability or reduce structural noise, tend to over-constrain intrinsically flexible regions. Such oversimplification may lead to inappropriate rigidification of flexible CDR loops, resulting in local structural distortions, compromised interface geometry, or even complete modeling failure for specific complexes. Against this background, the review approaches the field from the perspective of computational differences between MHC-I and MHC-II complexes. We first systematically organize and summarize available resources related to TCRs and pMHCs, including structural datasets, sequence databases, prediction tools, and benchmarking studies. We then focus on five representative tools capable of predicting both class I and class II complexes—AlphaFold2, AlphaFold3, TCRmodel2, tFold-TCR, and TCR-pHLA_ModellerS. After excluding structures present in the training sets of these tools, we constructed a benchmark dataset comprising 25 class I and 10 class II TCR-pMHC complexes in the bound state and conducted a systematic evaluation using this dataset. We first employ widely used general evaluation metrics, including All-Atom Root Mean Square Deviation (All-Atom RMSD), Backbone RMSD, Template Modeling score (TM-score), and DockQ, to assess the global conformational accuracy and interface modeling quality of class I and class II complexes. For class II complexes, we propose for the first time a peptide flanking residue deviation index, including the PFRs-Deviation Index (PFRs-DI), N-PFR-Deviation Index (N-PFR-DI), and C-PFR-Deviation Index (C-PFR-DI), to quantitatively characterize conformational deviations in PFRs. In addition, we propose the CDR conformational consistency index (CCC) designed to qualitatively evaluate the ability of prediction tools to capture TCR CDR conformational flexibility. These metrics collectively assess a tool’s ability to model both overall conformation and critical functional regions, thereby addressing the limitations of existing evaluation criteria that overemphasize global structure while inadequately capturing modeling quality in key functional areas. This establishes a unified analytical framework for MHC-I and MHC-II complexes to guide data resource selection, modeling strategy formulation, and evaluation system development. The framework further advances computational modeling and provides crucial support for multi-scale analysis of TCR-pMHC recognition mechanisms and their biological functions.

OBJECTIVE: Gastric cancer (GC) is one of the most common malignancies seen in clinic and requires novel treatment options. Morin is a natural flavonoid extracted from the flower stalk of a highly valuable medicinal plant Prunella vulgaris L., which exhibits an anti-cancer effect in multiple types of tumors. However, the therapeutic effect and underlying mechanism of morin in treating GC remains elusive. The study aims to explore the therapeutic effect and underlying molecular mechanisms of morin in GC. METHODS: For in vitro experiments, the proliferation inhibition of morin was measured by cell counting kit-8 assay and colony formation assay in human GC cell line MKN45, human gastric adenocarcinoma cell line AGS, and human gastric epithelial cell line GES-1; for apoptosis analysis, microscopic photography, Western blotting, ubiquitination analysis, quantitative polymerase chain reaction analysis, flow cytometry, and RNA interference technology were employed. For in vivo studies, immunohistochemistry, biomedical analysis, and Western blotting were used to assess the efficacy and safety of morin in a xenograft mouse model of GC. RESULTS: Morin significantly inhibited the proliferation of GC cells MKN45 and AGS in a dose- and time-dependent manner, but did not inhibit human gastric epithelial cells GES-1. Only the caspase inhibitor Z-VAD-FMK was able to significantly reverse the inhibition of proliferation by morin in both GC cells, suggesting that apoptosis was the main type of cell death during the treatment. Morin induced intrinsic apoptosis in a dose-dependent manner in GC cells, which mainly relied on B cell leukemia/lymphoma 2 (BCL-2) associated agonist of cell death (BAD) but not phorbol-12-myristate-13-acetate-induced protein 1. The upregulation of BAD by morin was due to blocking the ubiquitination degradation of BAD, rather than the transcription regulation and the phosphorylation of BAD. Furthermore, the combination of morin and BCL-2 inhibitor navitoclax (also known as ABT-737) produced a synergistic inhibitory effect in GC cells through amplifying apoptotic signals. In addition, morin treatment significantly suppressed the growth of GC in vivo by upregulating BAD and the subsequent activation of its downstream apoptosis pathway. CONCLUSION Morin suppressed GC by inducing apoptosis, which was mainly due to blocking the ubiquitination-based degradation of the pro-apoptotic protein BAD. The combination of morin and the BCL-2 inhibitor ABT-737 synergistically amplified apoptotic signals in GC cells, which may overcome the drug resistance of the BCL-2 inhibitor. These findings indicated that morin was a potent and promising agent for GC treatment. Please cite this article as: Wang Y, Sun XY, Ma FQ, Ren MM, Zhao RH, Qin MM, Zhu XH, Xu Y, Cao ND, Chen YY, Dong TG, Pan YF, Zhao AG. Morin inhibits ubiquitination degradation of BCL-2 associated agonist of cell death and synergizes with BCL-2 inhibitor in gastric cancer cells. J Integr Med. 2025; 23(3): 320-332.
Humans ; Flavonoids/therapeutic use* ; Stomach Neoplasms/pathology* ; Animals ; Proto-Oncogene Proteins c-bcl-2/metabolism* ; Cell Line, Tumor ; Apoptosis/drug effects* ; Cell Proliferation/drug effects* ; Ubiquitination/drug effects* ; Mice ; Drug Synergism ; Mice, Inbred BALB C ; Mice, Nude ; Xenograft Model Antitumor Assays ; Flavones

This study was analyzed the spatial-temporal distribution and aggregation characteristics of Yersinia pestispositive host animals and vector pathogens in marmot natural foci in the Qilian-Altun mountains,Gansu Province,to provide a scientific basis for precise plague prevention and control.Y.pestissurveillance data for marmot natural foci in Qilian-Altun Mountains of Gansu Province from 2014 to 2023 were obtained from the Disease Control and Prevention Center of Gansu Province.Origin 2024 software was used for data visualization and presentation.Global and local spatial autocorrelation analyses and trend analyses were conducted in ArcGIS 10.8 software,with townships as the spatial scale.Cumulatively,440 strains of Y.pestis were isolated from the natural marmot foci in the Qilian-Altun mountainsof Gansu Province from 2014 to 2023.Most strains was isolated from marmots(345 strains,78.41%),and the remainder were isolated from vectors.Temporal distribution analysis indicated that the highest number of detected bacteria was reported in July and August(both 121 strains,27.50%).Regional distribution analysis revealed that Aksai County reported the highest number of detected bacteria(255 strains,57.95%).Global spatial autocorrelation analysis showed a spatially clustered distribution of the number of bacteria detected annually in the townships containing natural foci,except in2014,2016,and 2021-2023.The strongest spatial clustering was observed in 2020(Moran's I=0.521 2,Z=14.397 0,P<0.001).Local spatial autocorrelation analysis indicated a"high-high"aggregation area in the natural foci every year from 2014 to 2023,primarily in Hongliuwan Town of Aksai County and Dangchengwan Town of Subei County.The distribution of the"low-low"aggregation area was essentially consistent with the low activity area of the Yersinia pestisepidemic.The trend in annual total bacterial count gradually increased from east to west,and peaked in the western part of the epidemic focus.Clear spatial aggregation characteristics of the number of Y.pestis were detected in the marmot natural foci in the Qilian-Altun mountains at the townshiplevel as a whole in Gansu Province from 2014 to 2023.The aggregation area was mainly in the western section of Qilian Mountain to the Altun mountain section of the epidemic source area.Monitoring and prevention and control efforts should be focused in this key area,with prevention and control measures tailored to the local conditions,and classified guidance to decrease the risk of plague occurrence and spread.

Objective To observe the efficacy of self-made auxiliary reduction device combined with sinus tarsi approach(STA)in the treatment of Sanders type Ⅱ to Ⅳ calcaneal fractures.Methods A total of 40 patients with Sanders type Ⅱ to Ⅳ calcaneal fractures admitted to our hospital from January to June 2023 were selected and divided into the control group and the observation group by the random number table method,with 20 cases in each group.Patients in the control group underwent surgical treatment with the heel extensile lateral approach(ELA),while patients in the observation group underwent surgical treatment with the auxiliary reduction device combined with STA.The surgical-related indicators,postoperative complications and ankle-foot anatomical indicators of patients in the two groups were compared.The recovery of limb function was evaluated by the American Orthopaedic Foot and Ankle Society(AOFAS)ankle-hindfoot scale and Maryland foot function score.Results There was no statistically significant difference in the operation time,postoperative incision drying time,or duration of postoperative pain between the two groups(P>0.05).The postoperative suture removal time of the patients in the observation group was shorter than that of the control group,and the difference was statistically significant(P<0.05).The incidence of skin edge necrosis of incision and the total incidence of complications of patients in the observation group were significantly lower than those in the control group(P<0.05).The B?hler angle and Gissane angle of patients in both groups increased after surgery compared with those before surgery(P<0.05);there was no statistically significant difference in the B?hler angle or Gissane angle after surgery of patients between the two groups(P>0.05).The AOFAS score1 week after surgery of the patients in the observation group was higher than that in the control group(P<0.05),while there were no statistically significant differences in the AOFAS scores or Maryland scores of patients at other time points between the two groups(P>0.05).Conclusion The use of the auxiliary reduction device in surgical treatment with STA for Sanders type Ⅱ to Ⅳ calcaneal fractures can effectively restore the function of the foot and ankle,with short postoperative suture removal time and low incidence of postoperative complications.

Objective To explore the efficacy of"internet+"family doctor contract service model on controlling risk factors related to atherosclerotic cardiovascular disease(ASCVD)such as hypertension,dyslipidemia,and diabetes in young and middle-aged patients in the community.Methods A total of 231 young and middle-aged patients with ASCVD who were contracted and treated regularly in Shanghai Yangpu District Xinjiangwancheng Community Health Service Center from Jan to Dec 2020.According to the different intervention models,they were divided into the traditional group receiving the conventional family doctor contract service and the Internet group taking"internet+"family doctor contract service mode for intervention.The systolic blood pressure,diastolic blood pressure,fasting plasma glucose(FPG),low density lipoprotein(LDL-C),triglyceride(TG)and total cholesterol(TC)were compared within and between the two groups before intervention,three months after intervention,and one year after intervention,to evaluate the control effects of the two intervention modes.Results The 231 patients,of which 113 cases in traditional group and 118 cases in Internet group,were recruited in the study.there were no significant differences in gender,age and proportions of hypertension,diabetes and dyslipidemia between the two groups.Before intervention,there were no significant differences in systolic blood pressure,diastolic blood pressure,FPG,LDL-C,TG and TC between the two groups.Three months after intervention,the systolic blood pressure,diastolic blood pressure,FPG,LDL-C,TG and TC of the two groups were significantly lower than those before the intervention(all P<0.05),and the systolic blood pressure and diastolic blood pressure of the Internet group were significantly lower than those of the traditional group(all P<0.05),but there was no significant difference between the two groups in FPG,LDL-C,TG and TC.One year after the intervention,the systolic blood pressure,diastolic blood pressure,FPG,LDL-C,TG and TC of the patients in the two groups decreased significantly compared with those before intervention(all P<0.05),while the Internet group decreased more significantly(all P<0.05).Conclusion Compared with the traditional contract model,"internet+"family doctor contract service had better management effect on ASCVD-related risk factors in young and middle-aged patients in the community,and benefits the patients to a higher degree.

Objective To explore the application value of fractional anisotropy(FA)analysis of RGB component transformation in different directions of fibers in substantia nigra in Parkinson's disease(PD).Methods There were 35 cases of PD and 37 cases of normal control group.After being performed by brain diffusion tensor imaging(DTI)scanning,the sequence was imported into 3DSlicense 5.6.0,and the diffusion module was used to implement pseudo color mapping based on FA,locate and segment substantia nigra,and use the substantia nigra mask as the tracking starting point.After forming tracing,fibers were imported into DTIANALYSIS 1.51,converting the RGB components into FA values for analysis,and visualized the analysis result.At the same time,fiber length,fiber density,and segmented FA point cloud percentage were compared.Results Compared with the normal group,the length of substantia nigra fibers in the PD group was shorter[(95.14±19.85)mm vs(115.99±21.39)mm,P＜0.01],and there was a statistical difference between the two groups.There was no statistical difference in fiber density[(0.07±0.05)/mm3 vs(0.10±0.12)/mm3,P＞0.05]between control group and PD group.The percentage of FA segment point clouds in the PD group was lower than that in the normal group at 0.9-1,but the principal component characteristics of the point cloud ratios in each FA segment were not significant.Conclusion Based on the transformation of RGB components into FA analysis,the length,density,and FA values of substantia nigra nerve fibers in PD patients can be quantified and visualized,providing a basis for the study of PD neural pathways.

Objective To explore the visualization effect of different walking fibers and anatomical positions of the basal nucleus in the postcentral gyrus based on the diffusion tensor imaging(DTI)fiber bundle of the precentral gyrus and internal capsule reconstruction model.Methods A set of diffusion tensor volume(DTV)data was used to visualize and export a mesh model by a 3DSlicense 5.6.2 software.The basal nucleus were reconstructed by 3DSlicense through T1W1 data from the same scan,and exported the mesh model,and thus imported the above model into DTIANALYSIS 1.51 software for visualization.By adjusting the RGB component threshold,the fiber bundles were screened to obtain fiber bundles that mainly run left and right,front and back,and up and down.The anatomical relationship between the fiber bundles and the basal nucleus was observed.Results The fiber bundles originating from the precentral gyrus were mainly distributed in the inner and lower parts,and run above and outside the basal nucleus;The fiber bundles that mainly run forward and backward are distributed on the outer side and run on the outer side of the basal nucleus;The fiber bundles that mainly run up and down were distributed in the upper and middle parts of the precentral gyrus,with some fibers running towards the hypothalamus.They intersect in the corpus callosum and ventral pons,and run along the posterior part of the space between the lentiform nucleus and the dorsal thalamus.Conclusion Based on the RGB components in DTI,fibers with different walking directions in the precentral gyrus can be screened to display their anatomical position relationship with the basal ganglia.