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学者姓名：李春华
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摘要 ：
Dynamical properties of proteins play an essential role in their function exertion. The elastic network model (ENM) is an effective and efficient tool in characterizing the intrinsic dynamical properties encoded in biomacromolecule structures. The Gaussian network model (GNM) and anisotropic network model (ANM) are the two often-used ENM models. Here, we introduce an equally weighted multiscale ENM (equally weighted mENM) based on the original mENM (denoted as mENM), in which fitting weights of Kirchhoff/Hessian matrixes in mENM are removed since they neglect the details of pairwise interactions. Then, we perform its comparison with the mENM, traditional ENM, and parameter-free ENM (pfENM) in reproducing dynamical properties for the six representative proteins whose molecular dynamics (MD) trajectories are available in http://mmb.pcb.ub.es/MoDEL/. In the results, for B-factor prediction, mENM performs best, while the equally weighted mENM performs also well, better than the traditional ENM and pfENM models. As to the dynamical cross-correlation map calculation, mENM performs worst, while the results produced from the equally weighted mENM and pfENM models are close to those from MD trajectories with the latter a little better than the former. Furthermore, encouragingly, the equally weighted mANM displays the best performance in capturing the functional motional modes, followed by pfANM and traditional ANM models, while the mANM fails in all the cases. This work is helpful for strengthening the understanding of the elastic network model and provides a valuable guide for researchers to utilize the model to explore protein dynamics. © 2021 American Chemical Society.
关键词 ：
Molecular dynamics Molecular dynamics Proteins Proteins
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| GB/T 7714 | Gong, Weikang , Liu, Yang , Zhao, Yanpeng et al. Equally Weighted Multiscale Elastic Network Model and Its Comparison with Traditional and Parameter-Free Models [J]. | Journal of Chemical Information and Modeling , 2021 , 61 (2) : 921-937 . |
| MLA | Gong, Weikang et al. "Equally Weighted Multiscale Elastic Network Model and Its Comparison with Traditional and Parameter-Free Models" . | Journal of Chemical Information and Modeling 61 . 2 (2021) : 921-937 . |
| APA | Gong, Weikang , Liu, Yang , Zhao, Yanpeng , Wang, Shihao , Han, Zhongjie , Li, Chunhua . Equally Weighted Multiscale Elastic Network Model and Its Comparison with Traditional and Parameter-Free Models . | Journal of Chemical Information and Modeling , 2021 , 61 (2) , 921-937 . |
| 导入链接 | NoteExpress RIS BibTex |
摘要 ：
Transactive response DNA binding protein 43 (TDP-43), an alternative-splicing regulator, can specifically bind long UG-rich RNAs, associated with a range of neurodegenerative diseases. Upon binding RNA, TDP-43 undergoes a large conformational change with two RNA recognition motifs (RRMs) connected by a long linker rearranged, strengthening the binding affinity of TDP-43 with RNA. We extend the equally weighted multiscale elastic network model (ewmENM), including its Gaussian network model (ewmGNM) and Anisotropic network model (ewmANM), with the multiscale effect of interactions considered, to the characterization of the dynamics of binding interactions of TDP-43 and RNA. The results reveal upon RNA binding a loss of flexibility occurs to TDP-43's loop3 segments rich in positively charged residues and C-terminal of high flexibility, suggesting their anchoring RNA, induced fit and conformational adjustment roles in recognizing RNA. Additionally, based on movement coupling analyses, it is found that RNA binding strengthens the interactions among intra-RRM beta-sheets and between RRMs partially through the linker's mediating role, which stabilizes RNA binding interface, facilitating RNA binding efficiency. In addition, utilizing our proposed thermodynamic cycle method combined with ewmGNM, we identify the key residues for RNA binding whose perturbations induce a large change in binding free energy. We identify not only the residues important for specific binding, but also the ones critical for the conformational rearrangement between RRMs. Furthermore, molecular dynamics simulations are also performed to validate and further interpret the ENM-based results. The study demonstrates a useful avenue to utilize ewmENM to investigate the protein-RNA interaction dynamics characteristics.
关键词 ：
binding dynamics binding dynamics ewmENM ewmENM key residues key residues TDP-43-RNA interactions TDP-43-RNA interactions
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| GB/T 7714 | Deng, Xueqing , Wang, Shihao , Han, Zhongjie et al. Dynamics of binding interactions of TDP-43 and RNA: An equally weighted multiscale elastic network model study [J]. | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , 2021 . |
| MLA | Deng, Xueqing et al. "Dynamics of binding interactions of TDP-43 and RNA: An equally weighted multiscale elastic network model study" . | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2021) . |
| APA | Deng, Xueqing , Wang, Shihao , Han, Zhongjie , Gong, Weikang , Liu, Yang , Li, Chunhua . Dynamics of binding interactions of TDP-43 and RNA: An equally weighted multiscale elastic network model study . | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , 2021 . |
| 导入链接 | NoteExpress RIS BibTex |
摘要 ：
Aminoacyl-tRNA synthetases (aaRSs), a family of ubiquitous and essential enzymes, can bind target tRNAs and catalyze the aminoacylation reaction in genetic code translation. In this work, we explore the dynamic properties and allosteric communication of human mitochondrial phenylalanyl-tRNA synthetase (hmPheRS) in free and bound states to understand the mechanisms of its tRNA(Phe) recognition and allostery using molecular dynamics simulations combined with the torsional mutual information-based network model. Our results reveal that hmPheRS's residue mobility and inter-residue motional coupling are significantly enhanced by tRNA(Phe) binding, and there occurs a strong allosteric communication which is critical for the aminoacylation reaction, suggesting the vital role of tRNA(Phe) binding in the enzyme's function. The identified signaling pathways mainly make the connections between the anticodon binding domain (ABD) and catalytic domain (CAD), as well as within the CAD composed of many functional fragments and active sites, revealing the co-regulation role of them to act coordinately and achieve hmPheRS's aminoacylation function. Besides, several key residues along the communication pathways are identified to be involved in mediating the coordinated coupling between anticodon recognition at the ABD and activation process at the CAD, showing their pivotal role in the allosteric network, which are well consistent with the experimental observation. This study sheds light on the allosteric communication mechanism in hmPheRS and can provide important information for the structure-based drug design targeting aaRSs.
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| GB/T 7714 | Shao, Qi , Han, Zhongjie , Cheng, Jingmin et al. Allosteric Mechanism of Human Mitochondrial Phenylalanyl-tRNA Synthetase: An Atomistic MD Simulation and a Mutual Information-Based Network Study [J]. | JOURNAL OF PHYSICAL CHEMISTRY B , 2021 , 125 (28) : 7651-7661 . |
| MLA | Shao, Qi et al. "Allosteric Mechanism of Human Mitochondrial Phenylalanyl-tRNA Synthetase: An Atomistic MD Simulation and a Mutual Information-Based Network Study" . | JOURNAL OF PHYSICAL CHEMISTRY B 125 . 28 (2021) : 7651-7661 . |
| APA | Shao, Qi , Han, Zhongjie , Cheng, Jingmin , Wang, Qiankun , Gong, Weikang , Li, Chunhua . Allosteric Mechanism of Human Mitochondrial Phenylalanyl-tRNA Synthetase: An Atomistic MD Simulation and a Mutual Information-Based Network Study . | JOURNAL OF PHYSICAL CHEMISTRY B , 2021 , 125 (28) , 7651-7661 . |
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摘要 ：
Human P-glycoprotein (P-gp) belongs to ATP-Binding Cassette (ABC) transporter, which can export varieties of anti-cancer drugs out of tumor cells, resulting in multidrug resistance (MDR) of tumor cells. We utilized targeted molecular dynamics simulation to explore the allosteric transition of human P-gp from outward- to inward-facing state. The results show that NBDs experience translational and rotational movement, caused by the successive hydrolysis of ATP molecules. The reorientation of the TMDs begins with the closing of the extracellular gate, followed by the opening of the cytoplasmic gate. The opening delay of the cytoplasmic gate is due to the extensive electrostatic interactions here. The sequence conservation analysis reveals that charged residues in TM3, 4 are highly conserved for achieving the unidirectional transport property. Our results give detailed movement and energy analyses to the reverse allosteric process of human P-gp and are helpful to the understanding of the working mechanism of human P-gp.
关键词 ：
Human P-glycoprotein Human P-glycoprotein Interaction energy Interaction energy Movement coupling Movement coupling Reverse allosteric process Reverse allosteric process Targeted molecular dynamics simulation Targeted molecular dynamics simulation
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| GB/T 7714 | Zhang, Yue , Han, Zhongjie , Li, Chunhua . Molecular insight into human P-glycoprotein allosteric transition from outward- to inward-facing state [J]. | CHEMICAL PHYSICS , 2020 , 538 . |
| MLA | Zhang, Yue et al. "Molecular insight into human P-glycoprotein allosteric transition from outward- to inward-facing state" . | CHEMICAL PHYSICS 538 (2020) . |
| APA | Zhang, Yue , Han, Zhongjie , Li, Chunhua . Molecular insight into human P-glycoprotein allosteric transition from outward- to inward-facing state . | CHEMICAL PHYSICS , 2020 , 538 . |
| 导入链接 | NoteExpress RIS BibTex |
摘要 ：
Background The maintenance of protein structural stability requires the cooperativity among spatially neighboring residues. Previous studies have shown that conserved residues tend to occur clustered together within enzyme active sites and protein-protein/DNA interfaces. It is possible that conserved residues form one or more local clusters in protein tertiary structures as it can facilitate the formation of functional motifs. In this work, we systematically investigate the spatial distributions of conserved residues as well as hot spot ones within protein-RNA interfaces. Results The analysis of 191 polypeptide chains from 160 complexes shows the polypeptides interacting with tRNAs evolve relatively rapidly. A statistical analysis of residues in different regions shows that the interface residues are often more conserved, while the most conserved ones are those occurring at protein interiors which maintain the stability of folded polypeptide chains. Additionally, we found that 77.8% of the interfaces have the conserved residues clustered within the entire interface regions. Appling the clustering characteristics to the identification of the real interface, there are 31.1% of cases where the real interfaces are ranked in top 10% of 1000 randomly generated surface patches. In the conserved clusters, the preferred residues are the hydrophobic (Leu, Ile, Met), aromatic (Tyr, Phe, Trp) and interestingly only one positively charged Arg residues. For the hot spot residues, 51.5% of them are situated in the conserved residue clusters, and they are largely consistent with the preferred residue types in the conserved clusters. Conclusions The protein-RNA interface residues are often more conserved than non-interface surface ones. The conserved interface residues occur more spatially clustered relative to the entire interface residues. The high consistence of hot spot residue types and the preferred residue types in the conserved clusters has important implications for the experimental alanine scanning mutagenesis study. This work deepens the understanding of the residual organization at protein-RNA interface and is of potential applications in the identification of binding site and hot spot residues.
关键词 ：
Binding site identification Binding site identification Clustering characteristics Clustering characteristics Conserved residues Conserved residues Hot spot residues Hot spot residues Protein-RNA interfaces Protein-RNA interfaces
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| GB/T 7714 | Yang, Zhen , Deng, Xueqing , Liu, Yang et al. Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification [J]. | BMC BIOINFORMATICS , 2020 , 21 (1) . |
| MLA | Yang, Zhen et al. "Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification" . | BMC BIOINFORMATICS 21 . 1 (2020) . |
| APA | Yang, Zhen , Deng, Xueqing , Liu, Yang , Gong, Weikang , Li, Chunhua . Analyses on clustering of the conserved residues at protein-RNA interfaces and its application in binding site identification . | BMC BIOINFORMATICS , 2020 , 21 (1) . |
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摘要 ：
BackgroundInfluenza A virus (IAV) infection is a serious public health problem not only in South East Asia but also in European and African countries. Scientists are using network biology to dig deep into the essential host factors responsible for regulation of virus infections. Researchers can explore the virus invasion into the host cells by studying the virus-host relationship based on their protein-protein interaction network.MethodsIn this study, we present a comprehensive IAV-host protein-protein interaction network that is obtained based on the literature-curated protein interaction datasets and some important interaction databases. The network is constructed in Cytoscape and analyzed with its plugins including CytoHubba, CytoCluster, MCODE, ClusterViz and ClusterOne. In addition, Gene Ontology and KEGG enrichment analyses are performed on the highly IAV-associated human proteins. We also compare the current results with those from our previous study on Hepatitis C Virus (HCV)-host protein-protein interaction network in order to find out valuable information.ResultsWe found out 1027 interactions among 829 proteins of which 14 are viral proteins and 815 belong to human proteins. The viral protein NS1 has the highest number of associations with human proteins followed by NP, PB2 and so on. Among human proteins, LNX2, MEOX2, TFCP2, PRKRA and DVL2 have the most interactions with viral proteins. Based on KEGG pathway enrichment analysis of the highly IAV-associated human proteins, we found out that they are enriched in the KEGG pathway of basal cell carcinoma. Similarly, the result of KEGG analysis of the common host factors involved in IAV and HCV infections shows that these factors are enriched in the infection pathways of Hepatitis B Virus (HBV), Viral Carcinoma, measles and certain other viruses.ConclusionIt is concluded that the list of proteins we identified might be used as potential drug targets for the drug design against the infectious diseases caused by Influenza A Virus and other viruses.
关键词 ：
Cytoscape Cytoscape Hepatitis C virus Hepatitis C virus Influenza a virus Influenza a virus KEGG KEGG Protein-protein interaction networks Protein-protein interaction networks
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| GB/T 7714 | Farooq, Qurat ul Ain , Shaukat, Zeeshan , Aiman, Sara et al. A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host [J]. | BMC INFECTIOUS DISEASES , 2020 , 20 (1) . |
| MLA | Farooq, Qurat ul Ain et al. "A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host" . | BMC INFECTIOUS DISEASES 20 . 1 (2020) . |
| APA | Farooq, Qurat ul Ain , Shaukat, Zeeshan , Aiman, Sara , Zhou, Tong , Li, Chunhua . A systems biology-driven approach to construct a comprehensive protein interaction network of influenza A virus with its host . | BMC INFECTIOUS DISEASES , 2020 , 20 (1) . |
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摘要 ：
We constructed a non-redundant non-ribosomal protein-RNA interface dataset (including 694 structures) from the Protein Data Bank (PDB). The interface preferences of amino acids, nucleotides and the secondary structure elements of protein and RNA were computed based on the dataset. The results show that beta-ladder, beta-bridge and 3(10)-helix of proteins and the unpaired nucleotides of RNA, especially those irregularly arranged nucleotides have remarkably high interface propensities. Based on these, we classified the secondary structure elements, constructed the 60x12 amino acid-nucleotide pairwise potential, and used it as a scoring function in protein-RNA docking to select the near native structures. The results show the 60x12 pairwise potential has a scoring success rate of 65.77%, better than those of the pairwise potentials with secondary structure information of protein or RNA considered, as well as better than that of our previously constructed 60x 8* potential based on the 251 protein-RNA complex structures. This work is helpful for strengthening the understanding of protein-RNA specific interactions and can advance the progress of protein-RNA complex structure prediction.
关键词 ：
interface preference interface preference molecular docking molecular docking secondary structure secondary structure statistical potential statistical potential
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| GB/T 7714 | Lu Lin , Liu Yang , Li Chun-Hua . Preferences of Sequence and Structure for Protein-RNA Interfaces and Its Application in Scoring Potential Construction for Docking [J]. | PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS , 2020 , 47 (7) : 634-644 . |
| MLA | Lu Lin et al. "Preferences of Sequence and Structure for Protein-RNA Interfaces and Its Application in Scoring Potential Construction for Docking" . | PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS 47 . 7 (2020) : 634-644 . |
| APA | Lu Lin , Liu Yang , Li Chun-Hua . Preferences of Sequence and Structure for Protein-RNA Interfaces and Its Application in Scoring Potential Construction for Docking . | PROGRESS IN BIOCHEMISTRY AND BIOPHYSICS , 2020 , 47 (7) , 634-644 . |
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摘要 ：
RNA molecules play important roles in biological processes, their functions are intimately related to structural dynamics. Elastic network model (ENM) has achieved great success in predicting the large-amplitude collective behavior of proteins. However, for loosely-packed RNA structures, ENM models can not reproduce their dynamics as accurate as the densely-packed ones. In this work, the multiscale Gaussian network model (mGNM) is extended to predict dynamic properties of RNAs. All tests are performed on a non-redundant RNA structure database we constructed. In results, for B-factor reproduction, encouragingly mGNM achieves a significant improvement with the average value of Pearson correlation coefficient (PCC) between theoretical and experimental B-factors being 0.732, much higher than 0.494 and 0.321 obtained by conventional GNM and parameter-free GNM (pfGNM) models, respectively. Furtherly, mGNM attains a larger improvement in B-factor prediction for loosely-packed parts. Additionally, based on the analysis of functional movements, mGNM can properly make domain decompositions for tRNA(Asp) and xrRNA. This work can strengthen the understanding of the intrinsic dynamics of RNAs, and mGNM is expected to have a bright prospect in dynamic analyses for loosely folded biomolecules, especially RNAs.
关键词 ：
B-factor B-factor Divide domain Divide domain Intramolecular interactions Intramolecular interactions Multiscale Gaussian network model (mGNM) Multiscale Gaussian network model (mGNM) RNA molecules RNA molecules
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| GB/T 7714 | Wang, Shihao , Gong, Weikang , Deng, Xueqing et al. Exploring the dynamics of RNA molecules with multiscale Gaussian network model [J]. | CHEMICAL PHYSICS , 2020 , 538 . |
| MLA | Wang, Shihao et al. "Exploring the dynamics of RNA molecules with multiscale Gaussian network model" . | CHEMICAL PHYSICS 538 (2020) . |
| APA | Wang, Shihao , Gong, Weikang , Deng, Xueqing , Liu, Yang , Li, Chunhua . Exploring the dynamics of RNA molecules with multiscale Gaussian network model . | CHEMICAL PHYSICS , 2020 , 538 . |
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摘要 ：
The allosteric regulation during the binding interactions between small nuclear RNAs (snRNAs) and the associated protein factors is critical to the function of spliceosomes in alternative RNA splicing. Although network models combined with molecular dynamics simulations have shown to be powerful tools for the analysis of protein allostery, the atomic-level simulations are, however, too expensive and with limited accuracy for the large-size systems. In this work, we use a residual network model combined with a coarse-grained Gaussian network model (GNM) to investigate the binding interactions between the snRNA and the human U1A protein which is a major component of the spliceosomal U1 small nuclear ribonucleoprotein particle, and to identify the residues that play an important role in the allosteric communication in U1A during this process. We also utilize the Girvan-Newman method to detect the structural organization in U1A-snRNA recognition and interactions. Our results reveal that: (I) not only the residues at the binding sites that are traditionally considered to play a major role in U1A-snRNA association, but those residues that are far away from the RNA binding interface participate in the U1A's allosteric signal transmission induced by the RNA binding; (H) the structure of U1A protein is well organized with different communities acting different roles for its RNA binding and allosteric regulation. The study demonstrates that the combination of the residual network and elastic network models is an effective and efficient method which can be readily extended to the investigation of the allosteric communication for other macromolecular interaction systems.
关键词 ：
Allosteric communication Allosteric communication Complex network model Complex network model Gaussian network model Gaussian network model Key residues Key residues U1A-snRNA interactions U1A-snRNA interactions
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| GB/T 7714 | Shao, Qi , Gong, Weikang , Li, Chunhua . A study on allosteric communication in U1A-snRNA binding interactions: network analysis combined with molecular dynamics data [J]. | BIOPHYSICAL CHEMISTRY , 2020 , 264 . |
| MLA | Shao, Qi et al. "A study on allosteric communication in U1A-snRNA binding interactions: network analysis combined with molecular dynamics data" . | BIOPHYSICAL CHEMISTRY 264 (2020) . |
| APA | Shao, Qi , Gong, Weikang , Li, Chunhua . A study on allosteric communication in U1A-snRNA binding interactions: network analysis combined with molecular dynamics data . | BIOPHYSICAL CHEMISTRY , 2020 , 264 . |
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摘要 ：
Human P-glycoprotein (P-gp), a kind of ATP-Binding Cassette transporter, can export a diverse variety of anti-cancer drugs out of the tumor cell. Its overexpression is one of the main reasons for the multidrug resistance (MDR) of tumor cells. It has been confirmed that during the substrate transport process, P-gp experiences a large-scale structural rearrangement from the inward- to outward-facing states. However, the mechanism of how the nucleotide-binding domains (NBDs) control the transmembrane domains (TMDs) to open towards the periplasm in the outward-facing state has not yet been fully characterized. Herein, targeted molecular dynamics simulations were performed to explore the conformational rearrangement of human P-gp. The results show that the allosteric process proceeds in a coupled way, and first the transition is driven by the NBDs, and then transmitted to the cytoplasmic parts of TMDs, finally to the periplasmic parts. The trajectories show that besides the translational motions, the NBDs undergo a rotation movement, which mainly occurs in xy plane and ensures the formation of the correct ATP-binding pockets. The analyses on the interaction energies between the six structure segments (cICLs) from the TMDs and NBDs reveal that their subtle energy differences play an important role in causing the periplasmic parts of the transmembrane helices to separate from each other in the established directions and in appropriate amplitudes. This conclusion can explain the two experimental phenomena about human P-gp in some extent. These studies have provided a detailed exploration into human P-gp rearrangement process and given an energy insight into the TMD reorientation during P-gp transition.
关键词 ：
conformational rearrangement conformational rearrangement human P-glycoprotein human P-glycoprotein interaction energy interaction energy movement coupling movement coupling targeted molecular dynamic simulation targeted molecular dynamic simulation
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| GB/T 7714 | Zhang, Yue , Gong, Weikang , Wang, Yan et al. Exploring movement and energy in human P-glycoprotein conformational rearrangement [J]. | JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS , 2019 , 37 (5) : 1104-1119 . |
| MLA | Zhang, Yue et al. "Exploring movement and energy in human P-glycoprotein conformational rearrangement" . | JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS 37 . 5 (2019) : 1104-1119 . |
| APA | Zhang, Yue , Gong, Weikang , Wang, Yan , Liu, Yang , Li, Chunhua . Exploring movement and energy in human P-glycoprotein conformational rearrangement . | JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS , 2019 , 37 (5) , 1104-1119 . |
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