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Computational Assessment of protein–protein Binding Affinity by Reversely Engineering the Energetics in protein Complexes

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Genomics, Proteomics & Bioinformatics 2021年第6期19卷 1012-1022页

作者： Bo Wang Zhaoqian Su Yinghao Wu Department of Systems and Computational Biology Albert Einstein College of MedicineBronxNY 10461USA

The cellular functions of proteins are maintained by forming diverse *** stability of these com-plexes is quantified by the measurement of binding affinity,and mutations that alter the binding affinity can cause various diseases such as cancer and *** a result,accurate estimation of the binding stability and the effects of mutations on changes of binding affinity is a crucial step to understanding the biological functions of proteins and their dysfunctional *** has been hypothesized that the stability of a protein complex is dependent not only on the residues at its binding interface by pairwise interactions but also on all other remaining residues that do not appear at the binding ***,we computationally reconstruct the binding affinity by decomposing it into the contributions of interfacial residues and other non-interfacial residues in a protein *** further assume that the contributions of both interfacial and non-interfacial residues to the binding affinity depend on their local structural environments such as solvent-accessible surfaces and secondary structural *** weights of all corresponding parameters are optimized by Monte-Carlo *** cross-validation against a large-scale dataset,we show that the model not only shows a strong correlation between the absolute values of the experimental and calculated binding affinities,but can also be an effective approach to predict the relative changes of binding affinity from ***,we have found that the optimized weights of many parameters can capture the first-principle chemical and physical features of molecular recognition,therefore re-versely engineering the energetics of protein *** results suggest that our method can serve as a useful addition to current computational approaches for predicting binding affinity and understanding the molecular mechanism of protein–protein interactions.

关键词： protein-protein interaction Binding affinity Non-interfacial residue Knowledge-based potential Monte-Carlo simulation

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MAGI3 Suppresses Glioma Cell Proliferation via Upregulation of PTEN Expression

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Biomedical and Environmental Sciences 2015年第7期28卷 502-509页

作者： MA Qian ZHANG Yan MENG Ran XIE Kun Ming XIONG Ying LIN Song HE Zong Lin K. TAO Tao YANG Ying ZHAO Ji Zong HE Jun Qi Department of Biochemistry and Molecular Biology Capital Medical University The Center of Prenatal Diagnosis First Affiliated HospitalCollege of MedicineZhengzhou Universit Department of Neurosurgery Beijing Tiantan Hospital Capital Medical University China National Clinical Research Center for Neurological Diseases UC Berkeley San Francisco Core Facilities Center Capital Medical University

Objective To investigate the role and molecular mechanism of membrane-associated guanylate kinase inverted 3 （MAGI3） in glioma cell proliferation. Methods The expression levels of MAGI3 and PTEN were assessed in glioma samples by Western blotting. MAGI3 was stably transfected into C6 glioma cells to obtain C6-MAGI3 cells. Then, the proliferation, the expression levels of MAGI3 and PTEN, and Akt phosphorylation were evaluated in C6 and C6-MAGI3 cells. Xenograft tumor models were established by subcutaneous injection of C6 and C6-MAGI3 cells into nude mice, and the growth rates of xenografts in the mice were compared. The potential role of MAGI3 expression in PI3K/Akt signaling activation was further investigated by examining the correlation between MAGI3 expression and the expression of PI3K/Akt signaling downstream target genes in a glioma dataset using gene set enrichment analysis （GSEA）. Results Expression levels of MAGI3 and PTEN were significantly downregulated in gliomas. Overexpression of MAGI3 in the glioma C6 cell line upregulated PTEN protein expression, inhibited the phosphorylation of Akt, and suppressed cell proliferation. MAGI3 overexpression also inhibited the growth of C6 glioma tumor xenografts in nude mice. Analysis based on the GEO database confirmed the negative correlation between activation of PI3K/Akt pathway and MAGI3 mRNA levels in human glioma samples. Conclusion The loss of MAGI3 expression in downregulation of PTEN expression, leading potential glioma suppressor. glioma may enhance the proliferation of glioma cells via to the activation of the PI3K/Akt pathway. MAGI3 is a

关键词： Glioma PTEN MAGI3 PDZ protein-protein interaction PI3K/Akt

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Lipid phosphorylation by a diacylglycerol kinase suppresses ABA biosynthesis to regulate plant stress responses

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Molecular Plant 2024年第2期17卷 342-358页

作者： Jianwu Li Shuaibing Yao Sang-Chul Kim Xuemin Wang Department of Biology University of Missouri-St.LouisSt.LouisMO 63121USA Donald Danforth Plant Science Center St.LouisMO 63132USA

Lipid phosphorylation by diacylglycerol kinase(DGK)that produces phosphatidic acid(PA)plays important roles in various biological processes,including stress responses,but the underlying mechanisms remain ***,we show that DGK5 and its lipid product PA suppress ABA biosynthesis by interacting withABA-DEFICIENT2(ABA2),a key ABA biosynthesis enzyme,to negatively modulate plant responseto abiotic stress tested in Arabidopsis *** of DGK5 function rendered plants less damaged,whereas overexpression(OE)of DGK5 enhanced plant damage to water and salt *** dgk5 mutant plants exhibited decreased total cellular and nuclear levels of PA with increased levels of diacylglycerol,whereas DGK5-OE plants displayed the opposite ***,we found that both DGK5 and PA bind to the ABA-synthesizing enzyme ABA2 and suppress its enzymatic ***,the dgk5 mutant plants exhibited increased levels of ABA,while DGK5-OE plants showed reduced ABA *** addition,we showed that both DGK5 and ABA2 are detected in and outside the nuclei,and loss of DGK5 function decreased the nuclear association of *** found that both DGK5 activity and PA promote nuclear association of *** together,these results indicate that both DGK5 and PA interact with ABA2 to inhibit its enzymatic activity and promote its nuclear sequestration,thereby sup-pressing ABA production in response to abiotic *** study reveals a sophisticated mechanism by which DGK5 and PA regulate plant stress responses.

关键词： diacylglycerol kinase phosphatidic acid diacylglycerol lipid signaling stress responses lipid-protein binding protein-protein interaction Arabidopsis

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Dynamic Property is a Key Determinant for protein-protein interactions

Dynamic Property is a Key Determinant for Protein-protein In...

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第五届全国化学生物学学术会议

作者：白红军马文喆刘士勇来鲁华 Beijing National Laboratory for Molecular Sciences State Key Laboratory of Structural Chemistry for Stable and Unstable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871 Center for Theoretical BiologyPeking University Beijing National Laboratory for Molecular Sciences State Key Laboratory of Structural Chemistry for Stable and Unstable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871 Center for Theoretical BiologyPeking University Beijing National Laboratory for Molecular Sciences State Key Laboratory of Structural Chemistry for Stable and Unstable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871 Center for Theoretical BiologyPeking University Beijing National Laboratory for Molecular Sciences State Key Laboratory of Structural Chemistry for Stable and Unstable SpeciesCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing 100871 Center for Theoretical BiologyPeking University

＜正＞Dynamic property is highly correlated with the biological functions of macromolecules,such as the activity and specificity of enzymes and the allosteric regulation in the signal transduction *** of the dynamic property to protein function researches have been discussed a lot and encouraging progresses have been achieved,for example,in enzyme activity and protein-protein docking *** reveal its role in controlling protein-protein interactions,

关键词： Gaussian Network Model GNM protein-protein interaction Dynamic Property Dissociation Constant

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Bioinformatics analysis of metastasis-related proteins in hepatocellular carcinoma

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World Journal of Gastroenterology 2008年第38期14卷 5816-5822页

作者： Pei-Ming Song Yang Zhang Yu-Fei He Hui-Min Bao Jian-Hua Luo Yin-Kun Liu Peng-Yuan Yang Xian Chen School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai 200030 China Institute of Biomedical Science Fudan University Shanghai 200320 China Department of Biochemistry and Biophysics University of North Carolina at Chapel Hill Chapel Hill North Carolina 27599 United States

AIM: To analyze the metastasis-related proteins in hepatocellular carcinoma (HCC) and discover the biomarker candidates for diagnosis and therapeutic intervention of HCC metastasis with bioinformatics tools. METHODS: Metastasis-related proteins were determined by stable isotope labeling and MS analysis and analyzed with bioinformatics resources, including Phobius, Kyoto encyclopedia of genes and genomes (KEGG), online mendelian inheritance in man (OMIM) and human protein reference database (HPRD). RESULTS: All the metastasis-related proteins were linked to 83 pathways in KEGG, including MAPK and p53 signal pathways. protein-protein interaction network showed that all the metastasis-related proteins were categorized into 19 function groups, including cell cycle, apoptosis and signal transduction. OMIM analysis linked these proteins to 186 OMIM entries. CONCLUSION: Metastasis-related proteins provide HCC cells with biological advantages in cell proliferation,migration and angiogenesis, and facilitate metastasis of HCC cells. The bird's eye view can reveal a global characteristic of metastasis-related proteins and many differentially expressed proteins can be identified as candidates for diagnosis and treatment of HCC.

关键词： Hepatocellular carcinoma Metastasis Bioinformatics protein-protein interaction Kyoto encyclopedia of genes and genomes

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A Peptide Binder of E3 Ligase Adaptor SPOP Disrupts Oncogenic SPOP-protein interactions in Kidney Cancer Cells

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Chinese Journal of Chemistry 2021年第2期39卷 274-280页

作者： Zhen Wang Hao Zhang Baoen Chen Sisheng Ouyang Tong Zheng Ran Zhou Ze Dong Yue Huang Tao Zhang Hualiang Jiang Jianhua Gan Cheng Luo Cai-Guang Yang School of Chinese Materia Medica Nanjing University of Chinese MedicineNanjingJiangsu210023 China State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai201203 China University of Chinese Academy of Sciences Beijing100049 China School of Pharmaceutical Science and Technology Hangzhou Institute for Advanced StudyUCASHangzhouZhejiang310024 China Shanghai Institute for Advanced Immunochemical Studies ShanghaiTech UniversityShanghai201210 China School of Life Sciences Fudan UniversityShanghai200433 China

The E3 ligase adaptor SPOP,overexpressed in the nucleus but frequently dislocated into the cytoplasm in all clear cell Renal Cell Carcinomas(ccRCC),serves as a regulatory hub to promote kidney cancer through the ubiquitination and degradation of multiple downstream cancer ***,our identification of a selective small-molecule inhibitor of the SPOP-phosphatase and tensin homolog(PTEN)interaction has demonstrated that the oncogenic SPOP-protein interaction would be a druggable target specific to ccRCC *** our knowledge,this is the first time such a small-molecule inhibitor has been ***,we have identified a peptide binder for the SPOP-MATH domain that disrupts the oncogenic SPOP-protein interactions in kidney cancer *** design and biophysical characterization yielded peptide Pep38 that binds to the MATH domain of SPOP and competes on PTEN-binding to SPOP in *** X-ray complex structure reveals that the peptide binder features the following combination:one,a mimic of the native peptide binder and two,an additionalβ-strand motif in sequence,which could contribute to increased binding *** order to improve cellular permeability,we fused Pep38 with the delivery peptide TAT to prepare peptide TAT38,which inhibits the endogenous substrate binding to SPOP and suppresses the proliferation of the ccRCC *** identification of the peptide inhibitors for SPOP-protein interactions provides further validation that the oncogenic SPOP-signaling pathway in ccRCC could be a druggable target specifically applicable to the therapy of kidney cancers.

关键词： SPOP protein-protein interaction Clear cell Renal Cell Carcinomas Crystal structure Peptide inhibitor

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Atomistic characterization of binding modes and affinity of peptide inhibitors to amyloid-β protein

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Frontiers of Chemical Science and Engineering 2014年第4期8卷 433-444页

作者： Fufeng LIU Wenjie DU Yan SUN Jie ZHENG Xiaoyan DONG Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology Tianjin University Tianjin 300072 China Department of Chemical and Biomolecular Engineering The University of Akron Akron OH 44325 USA Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) Tianjin 300072 China

Abstract The aggregation of amyloid β-protein （Aβ） is tightly linked to the pathogenesis of Alzheimer＇s disease. Previous studies have found that three peptide inhibitors （i.e., KLVFF, VVIA, and LPFFD） can inhibit Aβ aggregation and alleviate Aβ-induced neurotoxicity. How- ever, atomic details of binding modes and binding affinities between these peptide inhibitors and Aβ have not been revealed. Here, using molecular dynamics simulations and molecular mechanics Poisson Boltzmann surface area （MM/PBSA） analysis, we examined the effect of three peptide inhibitors （KLVFF, VVIA, and LPFFD） on their sequence-specific interactions with Aβ and the molecular basis of their inhibition. All inhibitors exhibit varied binding affinity to Aβ, in which KLVFF has the highest binding affinity, whereas LPFFD has the least. MM/PBSA analysis further revealed that different peptide inhibitors have different modes of interaction with Aβ, consequently hotspot binding residues, and underlying driving forces. Specific residue-based interactions between inhibitors and Aβ were determined and compared for illustrating different binding and inhibition mechanisms. This work provides structure-based binding information for further modifica- tion and optimization of these three peptide inhibitors to enhance their binding and inhibitory abilities against Aβ aggregation.

关键词： Alzheimer's disease amyloid β-protein pep-tide inhibitors protein-protein interaction moleculardynamics simulation

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Spectro-Microscopy of Living Plant Cells

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Molecular Plant 2012年第1期5卷 14-26页

作者： Klaus Hatter Alfred J. Meixner Frank Schleifenbaum Center for Plant Molecular Biology （ZMBP） Plant Physiology and Biophysical Chemistry University of Tubingen Auf der Morgenstelle 1 72076 Tuebingen Germany Institute for Physical and Theoretical Chemistry （IPTC） Nano-Optics University of Tubingen Auf der Morgenstelle 8 72076 Tubingen Germany

Spectro-microscopy, a combination of fluorescence microscopy with spatially resolved spectroscopic techni- ques, provides new and exciting tools for functional cell biology in living organisms. This review focuses on recent devel- opments in spectro-microscopic applications for the investigation of living plant cells in their native tissue context. The application of spectro-microscopic methods led to the recent discovery of a fast signal response pathway for the brassi- nosteroide receptor BRI1 in the plasma membrane of living plant cells. Moreover, the competence of different plant cell types to respond to environmental or endogenous stimuli was determined in vivo by correlation analysis of different optical and spectroscopic readouts such as fluorescence lifetime （FLT）. Furthermore, a new spectro-microscopic technique, fluorescence intensity decay shape analysis microscopy （FIDSAM）, has been developed. FIDSAM is capable of imaging low- expressed fluorophore-tagged proteins at high spatial resolution and precludes the misinterpretation of autofluorescence artifacts. In addition, FIDSAM provides a very effective and sensitive tool on the basis of F6rster resonance energy transfer （FRET） for the qualitative and quantitative determination of protein-protein interaction. Finally, we report on the quan- titative analysis of the photosystem I and II （PSI/PSII） ratio in the chloroplasts of living Arabidopsis plants at room tem- perature, using high-resolution, spatially resolved fluorescence spectroscopy. With this technique, it was not only possible to measure PSI/PSII ratios, but also to demonstrate the differential competence of wild-type and carbohydrate-deficient plants to adapt the PSI/PSII ratio to different light conditions. In summary, the information content of standard microscopic images is extended by several dimensions by the use of spectro-microscopic approaches. Therefore, novel cell physiolog- ical and molecular topics can be addressed and valuable insigh

关键词： Fluorescence microscopy FLIM FRET photosystems protein-protein interaction FIDSAM.

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Implementation and application of FRET-FLIM technology

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Journal of Innovative Optical Health Sciences 2019年第5期12卷 57-68页

作者： Shiqi Wang Binglin Shen Sheng Ren Yihua Zhao Silu Zhang Junle Qu Liwei Liu Key Laboratory of Optoelectronic Devices and Systems of Guangdong Province College of Physics and Optoelectronic Engineering Shenzhen University Shenzhen518060P.R.China

With the development of the new detection methods and the function of fluorescent molecule,researchers hope to further explore the internal mechanisms of organisms,monitor changes in the intracellular microenvironment,and dynamic processes of molecular interactions in ***-rescence resonance energy transfer(FRET)describes the energy transfer process between donor fluorescent molecules and acceptor fluorescent *** is an important means to detect protein-protein interactions and protein conformation changes in *** lifetime imaging microscopy(FLIM)enables noninvasive measurement of the fAuorescence lifetime of fluorescent particles in *** FRET-FLIM technology,which is use FLIM to quantify and analyze FRET,enables real-time monitoring of dynamic changes of proteins in biological cells and analysis of protein interaction *** distance between donor and acceptor and their respective fAuorescent lifetime,which are of great importance for studying the mechanism of intracellular activity can be obtained by data analysis and algorithm ftting.

关键词： Fluorescence resonance energy transfer fuorescenc-lifetime imaging microscopy protein-protein interaction

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Expression profile analysis to identify potential gene changes induced by dexamethasone in the trabecular meshwork

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International Journal of Ophthalmology(English edition) 2022年第8期15卷 1240-1248页

作者： Miao Wei Lu-Ming Chen Ze-Yu Huang Guo-Wei Zhang Huai-Jin Guan Min Ji Eye Institute Affiliated Hospital of Nantong UniversityNantong 226001Jiangsu ProvinceChina Dalian Medical University Dalian 116000Liaoning ProvinceChina

AIM:To investigate potential gene changes in trabecular meshwork(TM)induced by dexamethasone(DEX)in steroidinduced glaucoma(SIG).METHODS:The expression data of 24 cases from a public functional genomics data were sorted to identify the mechanisms of action of DEX on the *** relationships of the differentially expressed genes(DEGs)were enriched using Gene Ontology(GO)and Kyoto Encyclopedia of Genes and Genomes(KEGG)*** addition,the hub genes were screened by the Search Tool for the Retrieval of Interacting Genes Database(STRING)and Cytoscape ***,human TM cells(HTMCs)were treated with DEX to preliminarily explore the function of hub ***:Totally 47 DEGs,including 21 downregulated and 26 upregulated genes were *** primary enriched results of the DEGs consisted of inflammatory response,extracellular matrix(ECM),negative regulation of cell proliferation,TNF signalling pathway and the regulation of tr yptophan channels by inflammator y ***,pro-melanin-enriched hormone(PMCH)and Bradykinin B1 receptor(BDKRB1)were screened as hub *** is verified in GSE37474 data *** blot and quantitative real-time polymerase chain reaction(q PCR)results showed that protein and RNA expression levels of BDKRB1 were significantly decreased after DEX treatment,while PMCH was not significantly ***:BDKRB1 may be a key gene involved in SIG onset,providing a suitable therapeutic target for improving the prognosis of SIG patients.

关键词： dexamethasone trabecular meshwork cells steroid-induced glaucoma differentially expressed genes protein-protein interaction

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