Receptor-ligand interactions in blood flow are crucial to initiate such biological processes as inflammatory cascade,platelet thrombosis,as well as tumor metastasis.To mediate cell adhesion,the interacting receptors a...Receptor-ligand interactions in blood flow are crucial to initiate such biological processes as inflammatory cascade,platelet thrombosis,as well as tumor metastasis.To mediate cell adhesion,the interacting receptors and ligands must be anchored onto two apposing surfaces of two cells or a cell and a substratum,i.e.,two-dimensional（2D）binding,which is different from the binding of a soluble ligand in fluid phase to a receptor,i.e.,three-dimensional（3D） binding.While numerous works have been focused on3 D kinetics of receptor-ligand interactions in the immune system,2D kinetics and its regulations have been less understood,since no theoretical framework or experimental assays were established until 1993.Not only does the molecular structure dominate 2D binding kinetics,but the shear force in blood flow also regulates cell adhesion mediated by interacting receptors and ligands.Here,we provide an overview of current progress in 2D binding and regulations,mainly from our group.Relevant issues of theoretical frameworks,experimental measurements,kinetic rates and binding affinities,and force regulations are discussed.展开更多
Binding kinetic properties of protein–ligand complexes are crucial factors affecting the drug potency.Nevertheless,the current in silico techniques are insufficient in providing accurate and robust predictions for bi...Binding kinetic properties of protein–ligand complexes are crucial factors affecting the drug potency.Nevertheless,the current in silico techniques are insufficient in providing accurate and robust predictions for binding kinetic properties.To this end,this work develops a variety of binding kinetic models for predicting a critical binding kinetic property,dissociation rate constant,using eight machine learning(ML)methods(Bayesian Neural Network(BNN),partial least squares regression,Bayesian ridge,Gaussian process regression,principal component regression,random forest,support vector machine,extreme gradient boosting)and the descriptors of the van der Waals/electrostatic interaction energies.These eight models are applied to two case studies involving the HSP90 and RIP1 kinase inhibitors.Both regression results of two case studies indicate that the BNN model has the state-of-the-art prediction accuracy(HSP90:R^(2)_(test)=0:947,MAE_(test)=0.184,rtest=0.976,RMSE_(test)=0.220;RIP1 kinase:R^(2)_(test)=0:745,MAE_(test)=0.188,rtest=0.961,RMSE_(test)=0.290)in comparison with other seven ML models.展开更多
Objective To study the antibacterial mechanisms of berberine and try to understand the reasons why bacteria cells difficultly resisted to it.Methods Detecting the minimal inhibitory concentration(MIC) of bacterial cul...Objective To study the antibacterial mechanisms of berberine and try to understand the reasons why bacteria cells difficultly resisted to it.Methods Detecting the minimal inhibitory concentration(MIC) of bacterial cultures incubated under sub-MIC concentration of berberine,Huanglian,and Neomycin for more than 200 generations,in order to analyze the bacteria resistance.Detecting the binding kinetics of berberine to DNA,RNA,and proteins.Observing the changes in bacterial cell surface structure with scanning electron microscopy.Detecting the Ca2 +and K +released from berberine-treated bacterial cells with atomic absorption spectrum.Detection the absorption of methyl-3H-thymine ( 3 H-dT),3 H-uridine( 3 H-U),and 3 H-tyrosine( 3 H-Tyr)into berberine-treated bacterial cells.Results MICs of bacterial cultures,growing more than 200 generations in MH medium with 1/2 MIC of berberine(BA200) or Huanglian(HA200),did not increase compared to the control,while remarkably increased in MH medium with 1/2 MIC of Neomycin (NA200).In addition,from the culture NA200 it was easy to isolate resistant mutant strains which could grow in MH medium with more than four times MIC Neomycin,but from the culture BA200 and HA200 it was difficult to isolate berberine or Huanglian mutant strains could grow in MH medium with more than four times MIC berberine or Huanglian.The binding kinetics of berberine to DNA,RNA,and proteins illustrated that berberine could easily and tightly bind to DNA and RNA,and hardly dis-bind from DNA-and RNA-berberine complexes.Berberine could easily bind to protein too,but also easily dis-bind from berberine-protein complex.The bacterial cells treated with berberine sharply decreased the absorption of 3 H-dT,3 H-U,and 3 H-Tyr,as the radioactive precursors of DNA,RNA,and protein biosynthesis.Berberine could damage bacterial cell surface structure,especially for Gram-negative bacteria.Ca2 +and K + released from berberine-treated cells increased significantly compared to the control.Conclusion All of above results indicate that bacterial cells could not easily become resistant mutants to berberine.The mechanisms for the bactericidal effect of berberine include:inhibiting DNA duplication,RNA transcription,and protein biosynthesis;influencing or inhibiting enzyme activities;destructing the bacterial cell surface structure and resulting in Ca2 +and K +released from cells.All of the berberine bactericidal mechanisms are the most essential physiological functions for a live cell,if influenced any one such function,the mutation would be lethal mutation,so that it is difficult to get berberine resistant cells.The results in this paper also prefigure that berberine and its related Chinese medicines would provide a feasible way to control antibiotic resistance problem.展开更多
The biogenesis of autophagosomes provides the basis for macroautophagy to capture and degrade intracellular cargoes.Binding of the autophagy-related protein ATG8/LC3 to autophagic membranes is essential to autophagoso...The biogenesis of autophagosomes provides the basis for macroautophagy to capture and degrade intracellular cargoes.Binding of the autophagy-related protein ATG8/LC3 to autophagic membranes is essential to autophagosome formation,which involves the specific and dynamic processing of ATG8/LC3 by cysteine protease ATG4.However,to date,the mechanism whereby ATG4 is recruited to the membranes,the interaction of ATG4 and ATG8/LC3 on the membranes,and its role in the growth of phagophore are not completely understood.Here,we used fluorescence recovery after photobleaching to monitor the turnover of GFP-tagged ATG4B and LC3B in living animal cells.The data show that ATG4B localizes to early autophagic membranes in an LC3B-dependent manner.During autophagy,ATG4B and LC3B undergo rapid cytosol/isolation membrane exchange but not at the cytosol/completed autophagosome.In addition,ATG4B activity controls the efficiency of autophagosome formation by impacting the membrane binding/dissociation of LC3B.These data suggest that ATG4 and LC3 play interdependent roles in the formation of autophagosomes.展开更多
As a general mechanism for governing the bioactivity of membrane receptors,allosteric modulation is critical in cell signaling and cell communication but remains difficult to measure in situ.Herein,we introduce a data...As a general mechanism for governing the bioactivity of membrane receptors,allosteric modulation is critical in cell signaling and cell communication but remains difficult to measure in situ.Herein,we introduce a data mining-integrated tracking microscopy(DMITM)to investigate allosteric modulation of membrane receptors in the native state in live cells.Using Kmeans clustering-based hidden Markov modeling to uncover the ligand binding and unbinding events with diffusivity variations of ligand-conjugated nanoprobes as observations.展开更多
基金supported by Natural Science Foundation of China(grants 10042001,10072071,10128205,30225027, 10332060,30730032,11072251,and 31110103918)National Key Basic Research Foundation of China(grants 2006CB910303 and 2011CB710904)+2 种基金National High Technology Research and Development Program of China(grants 2007AA02Z306 and 2011AA020109)Chinese Academy of Sciences(grants KJCX2-L02,KJCX2-SW-L06, 2005-1-16,KJCX2-YW-L08,Y2010030,XDA01030102,XDA04073 801)NIH Fogarty International Research Collaboration Award TW 05774-01
文摘Receptor-ligand interactions in blood flow are crucial to initiate such biological processes as inflammatory cascade,platelet thrombosis,as well as tumor metastasis.To mediate cell adhesion,the interacting receptors and ligands must be anchored onto two apposing surfaces of two cells or a cell and a substratum,i.e.,two-dimensional（2D）binding,which is different from the binding of a soluble ligand in fluid phase to a receptor,i.e.,three-dimensional（3D） binding.While numerous works have been focused on3 D kinetics of receptor-ligand interactions in the immune system,2D kinetics and its regulations have been less understood,since no theoretical framework or experimental assays were established until 1993.Not only does the molecular structure dominate 2D binding kinetics,but the shear force in blood flow also regulates cell adhesion mediated by interacting receptors and ligands.Here,we provide an overview of current progress in 2D binding and regulations,mainly from our group.Relevant issues of theoretical frameworks,experimental measurements,kinetic rates and binding affinities,and force regulations are discussed.
基金financial supports of“the Fundamental Research Funds for the Central Universities”(DUT22YG218),NSFC(22278053,22078041)China Postdoctoral Science Foundation(2022M710578)“the Dalian High-level Talents Innovation Support Program”(2021RQ105).
文摘Binding kinetic properties of protein–ligand complexes are crucial factors affecting the drug potency.Nevertheless,the current in silico techniques are insufficient in providing accurate and robust predictions for binding kinetic properties.To this end,this work develops a variety of binding kinetic models for predicting a critical binding kinetic property,dissociation rate constant,using eight machine learning(ML)methods(Bayesian Neural Network(BNN),partial least squares regression,Bayesian ridge,Gaussian process regression,principal component regression,random forest,support vector machine,extreme gradient boosting)and the descriptors of the van der Waals/electrostatic interaction energies.These eight models are applied to two case studies involving the HSP90 and RIP1 kinase inhibitors.Both regression results of two case studies indicate that the BNN model has the state-of-the-art prediction accuracy(HSP90:R^(2)_(test)=0:947,MAE_(test)=0.184,rtest=0.976,RMSE_(test)=0.220;RIP1 kinase:R^(2)_(test)=0:745,MAE_(test)=0.188,rtest=0.961,RMSE_(test)=0.290)in comparison with other seven ML models.
基金The National Natural Sciences of Chinese(81041089)
文摘Objective To study the antibacterial mechanisms of berberine and try to understand the reasons why bacteria cells difficultly resisted to it.Methods Detecting the minimal inhibitory concentration(MIC) of bacterial cultures incubated under sub-MIC concentration of berberine,Huanglian,and Neomycin for more than 200 generations,in order to analyze the bacteria resistance.Detecting the binding kinetics of berberine to DNA,RNA,and proteins.Observing the changes in bacterial cell surface structure with scanning electron microscopy.Detecting the Ca2 +and K +released from berberine-treated bacterial cells with atomic absorption spectrum.Detection the absorption of methyl-3H-thymine ( 3 H-dT),3 H-uridine( 3 H-U),and 3 H-tyrosine( 3 H-Tyr)into berberine-treated bacterial cells.Results MICs of bacterial cultures,growing more than 200 generations in MH medium with 1/2 MIC of berberine(BA200) or Huanglian(HA200),did not increase compared to the control,while remarkably increased in MH medium with 1/2 MIC of Neomycin (NA200).In addition,from the culture NA200 it was easy to isolate resistant mutant strains which could grow in MH medium with more than four times MIC Neomycin,but from the culture BA200 and HA200 it was difficult to isolate berberine or Huanglian mutant strains could grow in MH medium with more than four times MIC berberine or Huanglian.The binding kinetics of berberine to DNA,RNA,and proteins illustrated that berberine could easily and tightly bind to DNA and RNA,and hardly dis-bind from DNA-and RNA-berberine complexes.Berberine could easily bind to protein too,but also easily dis-bind from berberine-protein complex.The bacterial cells treated with berberine sharply decreased the absorption of 3 H-dT,3 H-U,and 3 H-Tyr,as the radioactive precursors of DNA,RNA,and protein biosynthesis.Berberine could damage bacterial cell surface structure,especially for Gram-negative bacteria.Ca2 +and K + released from berberine-treated cells increased significantly compared to the control.Conclusion All of above results indicate that bacterial cells could not easily become resistant mutants to berberine.The mechanisms for the bactericidal effect of berberine include:inhibiting DNA duplication,RNA transcription,and protein biosynthesis;influencing or inhibiting enzyme activities;destructing the bacterial cell surface structure and resulting in Ca2 +and K +released from cells.All of the berberine bactericidal mechanisms are the most essential physiological functions for a live cell,if influenced any one such function,the mutation would be lethal mutation,so that it is difficult to get berberine resistant cells.The results in this paper also prefigure that berberine and its related Chinese medicines would provide a feasible way to control antibiotic resistance problem.
基金the National Natural Science Foundation of China(31671434,31701203,81420108017,81525010,and 91749203)the National Key Research and Development Program of China(2016YFA0100602,2017YFA0103302,2020YFA0112404,and 2018YFC2000705)+1 种基金the Program for Guangdong Introducing Innovative and Entrepreneurial Teams(2017ZT07S347)the Fundamental Research Funds for the Central Universities(21617336).
文摘The biogenesis of autophagosomes provides the basis for macroautophagy to capture and degrade intracellular cargoes.Binding of the autophagy-related protein ATG8/LC3 to autophagic membranes is essential to autophagosome formation,which involves the specific and dynamic processing of ATG8/LC3 by cysteine protease ATG4.However,to date,the mechanism whereby ATG4 is recruited to the membranes,the interaction of ATG4 and ATG8/LC3 on the membranes,and its role in the growth of phagophore are not completely understood.Here,we used fluorescence recovery after photobleaching to monitor the turnover of GFP-tagged ATG4B and LC3B in living animal cells.The data show that ATG4B localizes to early autophagic membranes in an LC3B-dependent manner.During autophagy,ATG4B and LC3B undergo rapid cytosol/isolation membrane exchange but not at the cytosol/completed autophagosome.In addition,ATG4B activity controls the efficiency of autophagosome formation by impacting the membrane binding/dissociation of LC3B.These data suggest that ATG4 and LC3 play interdependent roles in the formation of autophagosomes.
基金supported by theNationalNatural Science Foundation of China(grant nos.21874039,21605045,21890744,and 21521063)Fundamental Research Funds for Central Universities at Hunan University。
文摘As a general mechanism for governing the bioactivity of membrane receptors,allosteric modulation is critical in cell signaling and cell communication but remains difficult to measure in situ.Herein,we introduce a data mining-integrated tracking microscopy(DMITM)to investigate allosteric modulation of membrane receptors in the native state in live cells.Using Kmeans clustering-based hidden Markov modeling to uncover the ligand binding and unbinding events with diffusivity variations of ligand-conjugated nanoprobes as observations.
