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学者姓名：李金宇
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Abstract ：
In this work, we investigate how nanoporous hexagonal boron nitride (hBN) membrane can achieve efficient water/ion separation using molecular dynamics simulations. In particular, it is interesting to figure out the transport mechanisms through slit-like orifices with different edge patterns, namely armchair, B-edged, and N-edged. It is observed that the water and ion conduction rates are sensitive to the edge patterns, which is attributed to the intriguing electrostatic interactions between hBN and solution particles. The armchair nanoslits barely discriminate ion from water molecules, whereas the nanoslits edged with zigzag patterns collaboratively impede ion permeation and allow fast water conduction. Our simulations not only support that hBN is a promising candidate for the development of permeable membrane for water desalination but also highlight the importance of nanoslit edge pattern. Together, this work will be helpful for the design of permeable membrane in the future.
Keyword ：
Desalination Desalination Hexagonal boron nitride Hexagonal boron nitride Molecular dynamics Molecular dynamics Nanoslit Nanoslit Permeable membrane Permeable membrane
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| GB/T 7714 | Liu, Lin , Liu, Yichang , Qi, Yingying et al. Hexagonal boron nitride with nanoslits as a membrane for water desalination: A molecular dynamics investigation [J]. | SEPARATION AND PURIFICATION TECHNOLOGY , 2020 , 251 . |
| MLA | Liu, Lin et al. "Hexagonal boron nitride with nanoslits as a membrane for water desalination: A molecular dynamics investigation" . | SEPARATION AND PURIFICATION TECHNOLOGY 251 (2020) . |
| APA | Liu, Lin , Liu, Yichang , Qi, Yingying , Song, Meiru , Jiang, Lizhi , Fu, Gang et al. Hexagonal boron nitride with nanoslits as a membrane for water desalination: A molecular dynamics investigation . | SEPARATION AND PURIFICATION TECHNOLOGY , 2020 , 251 . |
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Coronaviruses (CoV) have caused a number of major epidemics in humans and animals, including the current pandemic of coronavirus disease 2019 (COVID-19), which has brought a renewed focus on the evolution and interspecies transmission of coronaviruses. Swine acute diarrhea syndrome coronavirus (SADS-CoV), which was recently identified in piglets in southern China, is an alphacoronavirus that originates from the same genus of horseshoe bats as severe acute respiratory syndrome CoV (SARS-CoV) and that was reported to be capable of infecting cells from a broad range of species, suggesting a considerable potential for interspecies transmission. Given the importance of the coronavirus spike (S) glycoprotein in host range determination and viral entry, we report a cryo-electron microscopy (cryo-EM) structure of the SADS-CoV S trimer in the prefusion conformation at a 3.55-A resolution. Our structure reveals that the SADS-CoV S trimer assumes an intrasubunit quaternary packing mode in which the S1 subunit N-terminal domain (S1NTD) and the S1 subunit C-terminal domain (S1-CTD) of the same protomer pack together by facing each other in the lying-down state. SADS-CoV S has several distinctive structural features that may facilitate immune escape, such as a relatively compact architecture of the S trimer and epitope masking by glycan shielding. Comparison of SADS-CoV S with the spike proteins of the other coronavirus genera suggested that the structural features of SADS-CoV S are evolutionarily related to those of the spike proteins of the other genera rather than to the spike protein of a typical alphacoronavirus. These data provide new insights into the evolutionary relationship between spike glycoproteins of SADS-CoV and those of other coronaviruses and extend our understanding of their structural and functional diversity. IMPORTANCE In this article, we report the atomic-resolution prefusion structure of the spike protein from swine acute diarrhea syndrome coronavirus (SADS-CoV). SADS-CoV is a pathogenic alphacoronavirus that was responsible for a large-scale outbreak of fatal disease in pigs and that was reported to be capable of interspecies transmission. We describe the overall structure of the SADS-CoV spike protein and conducted a detailed analysis of its main structural elements. Our results and analyses are consistent with those of previous phylogenetic studies and suggest that the SADS-CoV spike protein is evolutionarily related to the spike proteins of betacoronaviruses, with a strong similarity in S1-NTDs and a marked divergence in S1-CTDs. Moreover, we discuss the possible immune evasion strategies used by the SADS-CoV spike protein. Our study provides insights into the structure and immune evasion strategies of the SADS-CoV spike protein and broadens the understanding of the evolutionary relationships between coronavirus spike proteins of different genera.
Keyword ：
coronavirus coronavirus cryo-EM cryo-EM protein structure-function protein structure-function spike protein spike protein virus entry virus entry
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| GB/T 7714 | Guan, Hongxin , Wang, Youwang , Perculija, Vanja et al. Cryo-electron Microscopy Structure of the Swine Acute Diarrhea Syndrome Coronavirus Spike Glycoprotein Provides Insights into Evolution of Unique Coronavirus Spike Proteins [J]. | JOURNAL OF VIROLOGY , 2020 , 94 (22) . |
| MLA | Guan, Hongxin et al. "Cryo-electron Microscopy Structure of the Swine Acute Diarrhea Syndrome Coronavirus Spike Glycoprotein Provides Insights into Evolution of Unique Coronavirus Spike Proteins" . | JOURNAL OF VIROLOGY 94 . 22 (2020) . |
| APA | Guan, Hongxin , Wang, Youwang , Perculija, Vanja , Saeed, Abdullah F. U. H. , Liu, Yichang , Li, Jinyu et al. Cryo-electron Microscopy Structure of the Swine Acute Diarrhea Syndrome Coronavirus Spike Glycoprotein Provides Insights into Evolution of Unique Coronavirus Spike Proteins . | JOURNAL OF VIROLOGY , 2020 , 94 (22) . |
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Fabrication of a multifunctional near-infrared (NIR) theranostic nanoplatform has attracted increasing attention. Indocyanine green (ICG), a clinic-approved NIR fluorescence-imaging agent, is an excellent photothermal agent candidate. However, the stability and tumor targeting are still great obstacles for its wide application. In this work, C-phycocyanin (CPC) as a tumor-associated macrophages (TAMs) targeted vehicle was used to fabricate noncovalent ICG conjugate of CPC (ICG@CPC) via self-assembly in aqueous media. Compared to free ICG, ICG@CPC displays improved stabilities in aqueous solutions and under light irradiation and threefold increase in photothermal conversion efficiency. The in vitro results indicated that ICG@CPC could be selectively internalized into J774A.1 cells via SR-A-mediated endocytosis and lead to enhanced photocytotoxicity against J774A.1 cells. In vivo results showed that ICG@CPC had significantly improved drug accumulation in the tumor and photothermal therapeutic efficacy relative to ICG alone. This study for the first time utilizes CPC as a TAMs-targeted nanocarrier for ICG and may promote further rational design of ICG-based photothermal nanodrugs for precise and efficient cancer theranosis.
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| GB/T 7714 | Wan, Dong-hua , Ma, Xin-Yue , Lin, Chen et al. Noncovalent Indocyanine Green Conjugate of C-Phycocyanin: Preparation and Tumor-Associated Macrophages-Targeted Photothermal Therapeutics [J]. | BIOCONJUGATE CHEMISTRY , 2020 , 31 (5) : 1438-1448 . |
| MLA | Wan, Dong-hua et al. "Noncovalent Indocyanine Green Conjugate of C-Phycocyanin: Preparation and Tumor-Associated Macrophages-Targeted Photothermal Therapeutics" . | BIOCONJUGATE CHEMISTRY 31 . 5 (2020) : 1438-1448 . |
| APA | Wan, Dong-hua , Ma, Xin-Yue , Lin, Chen , Zhu, Deng-hui , Li, Xingshu , Zheng, Bi-Yuan et al. Noncovalent Indocyanine Green Conjugate of C-Phycocyanin: Preparation and Tumor-Associated Macrophages-Targeted Photothermal Therapeutics . | BIOCONJUGATE CHEMISTRY , 2020 , 31 (5) , 1438-1448 . |
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Ly6/uPAR/alpha-neurotoxin domain (LU-domain) is characterized by the presence of 4-5 disulfide bonds and three flexible loops that extend from a core stacked by several conversed disulfide bonds (thus also named three-fingered protein domain). This highly structurally stable protein domain is typically a protein-binder at extracellular space. Most LU proteins contain only single LU-domain as represented by Ly6 proteins in immunology and alpha-neurotoxins in snake venom. For Ly6 proteins, many are expressed in specific cell lineages and in differentiation stages, and are used as markers. In this study, we report the crystal structures of the two LU-domains of human C4.4A alone and its complex with a Fab fragment of a monoclonal anti-C4.4A antibody. Interestingly, both structures showed that C4.4A forms a very compact globule with two LU-domain packed face to face. This is in contrast to the flexible nature of most LU-domain-containing proteins in mammals. The Fab combining site of C4.4A involves both LU-domains, and appears to be the binding site for AGR2, a reported ligand of C4.4A. This work reports the first structure that contain two LU-domains and provides insights on how LU-domains fold into a compact protein and interacts with ligands.
Keyword ：
C4.4A C4.4A LU-domain LU-domain three-fingered fold three-fingered fold uPAR uPAR
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| GB/T 7714 | Jiang, Yunbin , Lin, Lin , Chen, Shanli et al. Crystal Structures of Human C4.4A Reveal the Unique Association of Ly6/uPAR/alpha-neurotoxin Domain [J]. | INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES , 2020 , 16 (6) : 981-993 . |
| MLA | Jiang, Yunbin et al. "Crystal Structures of Human C4.4A Reveal the Unique Association of Ly6/uPAR/alpha-neurotoxin Domain" . | INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES 16 . 6 (2020) : 981-993 . |
| APA | Jiang, Yunbin , Lin, Lin , Chen, Shanli , Jiang, Longguang , Kriegbaum, Mette C. , Grdsvoll, Henrik et al. Crystal Structures of Human C4.4A Reveal the Unique Association of Ly6/uPAR/alpha-neurotoxin Domain . | INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES , 2020 , 16 (6) , 981-993 . |
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The Holliday junction (HJ) is a key intermediate during homologous recombination and DNA double-strand break repair. Timely HJ resolution by resolvases is critical for maintaining genome stability. The mechanisms underlying sequence-specific substrate recognition and cleavage by resolvases remain elusive. The monokaryotic chloroplast 1 protein (MOC1) specifically cleaves four-way DNA junctions in a sequence-specific manner. Here, we report the crystal structures of MOC1 from Zea mays, alone or bound to HJ DNA. MOC1 uses a unique beta-hairpin to embrace the DNA junction. A base-recognition motif specifically interacts with the junction center, inducing base flipping and pseudobase-pair formation at the strand-exchanging points. Structures of MOC1 bound to HJ and different metal ions support a two-metal ion catalysis mechanism. Further molecular dynamics simulations and biochemical analyses reveal a communication between specific substrate recognition and metal ion-dependent catalysis. Our study thus provides a mechanism for how a resolvase turns substrate specificity into catalytic efficiency.
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| GB/T 7714 | Lin, Huajian , Zhang, Danping , Zuo, Ke et al. Structural basis of sequence-specific Holliday junction cleavage by MOC1 [J]. | NATURE CHEMICAL BIOLOGY , 2019 , 15 (12) : 1241-, . |
| MLA | Lin, Huajian et al. "Structural basis of sequence-specific Holliday junction cleavage by MOC1" . | NATURE CHEMICAL BIOLOGY 15 . 12 (2019) : 1241-, . |
| APA | Lin, Huajian , Zhang, Danping , Zuo, Ke , Yuan, Cai , Li, Jinyu , Huang, Mingdong et al. Structural basis of sequence-specific Holliday junction cleavage by MOC1 . | NATURE CHEMICAL BIOLOGY , 2019 , 15 (12) , 1241-, . |
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Matriptase is a type II transmembrane serine protease, which has been suggested to play critical roles in numerous pathways of biological developments. Matriptase is the activator of several oncogenic proteins, including urokinase-type plasminogen activator (uPA), hepatocyte growth factor (HGF) and protease-activated receptor 2 (PAR-2). The activations of these matriptase substrates subsequently lead to the generation of plasmin, matrix metalloproteases (MMPs), and the triggers for many other signaling pathways related to cancer proliferation and metastasis. Accordingly, matriptase is considered an emerging target for the treatments of cancer. Thus far, inhibitors of matriptase have been developed as potential anti-cancer agents, which include small-molecule inhibitors, peptide-based inhibitors, and monoclonal antibodies. This review covers established literature to summarize the chemical and biochemical aspects, especially the inhibitory mechanisms and structure-activity relationships (SARs) of matriptase inhibitors with the goal of proposing the strategies for their future developments in anti-cancer therapy.
Keyword ：
Cancer Cancer Inhibitor Inhibitor Invasion Invasion Matriptase Matriptase Migration Migration Structure-activity relationship Structure-activity relationship
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| GB/T 7714 | Zuo, Ke , Qi, Yingying , Yuan, Cai et al. Specifically targeting cancer proliferation and metastasis processes: the development of matriptase inhibitors [J]. | CANCER AND METASTASIS REVIEWS , 2019 , 38 (3) : 507-524 . |
| MLA | Zuo, Ke et al. "Specifically targeting cancer proliferation and metastasis processes: the development of matriptase inhibitors" . | CANCER AND METASTASIS REVIEWS 38 . 3 (2019) : 507-524 . |
| APA | Zuo, Ke , Qi, Yingying , Yuan, Cai , Jiang, Longguang , Xu, Peng , Hu, Jianping et al. Specifically targeting cancer proliferation and metastasis processes: the development of matriptase inhibitors . | CANCER AND METASTASIS REVIEWS , 2019 , 38 (3) , 507-524 . |
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Cell surface receptors play a critical role in modulating intracellular signal transduction, making them important drug targets. However, it remains challenging to develop a selective and efficient strategy for regulating receptor function. Herein, we develop a strategy, called bispecific aptamer induced artificial protein-pairing, to selectively regulate receptor function. In this strategy, bispecific aptamer probes act as molecular mediators to bind to both a target receptor protein and a paired protein, which brings the two proteins into close proximity on the living cell membrane. Importantly, the paired proteins work not only as a cancer biomarker for enhancing cell selectivity but also as a blocking assistant to inhibit target receptor function via strong steric hindrance effect. Compared with single-aptamer-mediated regulation, the proposed bispecific aptamer probes afford substantial improvement in selective and efficient regulation of receptor function and downstream signaling pathways. This work offers a versatile methodology to design molecular mediators that can modulate receptor function, thereby providing a new way for developing novel therapeutic drugs.
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| GB/T 7714 | Wang, Liping , Liang, Hong , Sun, Jin et al. Bispecific Aptamer Induced Artificial Protein-Pairing: A Strategy for Selective Inhibition of Receptor Function [J]. | JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 2019 , 141 (32) : 12673-12681 . |
| MLA | Wang, Liping et al. "Bispecific Aptamer Induced Artificial Protein-Pairing: A Strategy for Selective Inhibition of Receptor Function" . | JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 141 . 32 (2019) : 12673-12681 . |
| APA | Wang, Liping , Liang, Hong , Sun, Jin , Liu, Yichang , Li, Jinyu , Li, Jingying et al. Bispecific Aptamer Induced Artificial Protein-Pairing: A Strategy for Selective Inhibition of Receptor Function . | JOURNAL OF THE AMERICAN CHEMICAL SOCIETY , 2019 , 141 (32) , 12673-12681 . |
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Intramembrane proteases hydrolyze peptide bonds within the cell membrane as the decision-making step of various signaling pathways. Sporulation factor IV B protease (SpoIVB) and C-terminal processing proteases B (CtpB) play central roles in cellular differentiation via regulated intramembrane proteolysis (RIP) process which activates pro-sigma(K) processing at the sigma(K) checkpoint during spore formation. SpoIVB joins CtpB in belonging to the widespread family of PDZ-proteases, but much remains unclear about the molecular mechanisms and structure of SpoIVB. In this study, we expressed inactive SpoIVB (SpoIVB(S378A)) fused with maltose binding protein (MBP)-tag and obtained the solution structure of SpoIVB(S378A) from its small angle X-ray scattering (SAXS) data. The fusion protein is more soluble, stable, and yields higher expression compared to SpoIVB without the tag. MBP-tag not only facilitates modeling of the structure in the SAXS envelope but also evaluates reliability of the model. The solution structure of SpoIVB(S378A) fits closely with the experimental scattering data (chi(2) = 1.76). Comparing the conformations of PDZ-proteases indicates that SpoIVB adopts a PDZ-protease pattern similar to the high temperature requirement A proteases (HtrAs) rather than CtpB. We not only propose that SpoIVB uses a more direct and simple way to cleave the substrates than that of CtpB, but also that they work together as signal amplifiers to activate downstream proteins in the RIP pathway.
Keyword ：
PDZ-protease PDZ-protease regulated intramembrane proteolysis regulated intramembrane proteolysis SAXS SAXS SpoIVB SpoIVB sporulation sporulation
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| GB/T 7714 | Xie, Xie , Guo, Nannan , Xue, Guangpu et al. Solution Structure of SpoIVB Reveals Mechanism of PDZ Domain-Regulated Protease Activity [J]. | FRONTIERS IN MICROBIOLOGY , 2019 , 10 . |
| MLA | Xie, Xie et al. "Solution Structure of SpoIVB Reveals Mechanism of PDZ Domain-Regulated Protease Activity" . | FRONTIERS IN MICROBIOLOGY 10 (2019) . |
| APA | Xie, Xie , Guo, Nannan , Xue, Guangpu , Xie, Daoqing , Yuan, Cai , Harrison, Joshua et al. Solution Structure of SpoIVB Reveals Mechanism of PDZ Domain-Regulated Protease Activity . | FRONTIERS IN MICROBIOLOGY , 2019 , 10 . |
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The urokinase-type plasminogen activator receptor (uPAR) is a cell surface receptor that is capable of binding to a range of extracellular proteins and triggering a series of proteolytic and signaling events. Previous structural studies of uPAR with its ligands uPA and vitronectin revealed that its three domains (DI, DII, and DIII) form a large hydrophobic cavity to accommodate uPA. In the present study, the structure of unoccupied murine uPAR (muPAR) is determined. The structure of DII and DIII of muPAR is well defined and forms a compact globular unit, while DI could not be traced. Molecular dynamic simulations further confirm the rigid binding interface between DII and DIII. This study shows overall structural flexibility of uPAR in the absence of uPA.
Keyword ：
crystal structure crystal structure molecular dynamics molecular dynamics rigid rigid unoccupied unoccupied uPAR uPAR
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| GB/T 7714 | Liu, Min , Lin, Lin , Hoyer-Hansen, Gunilla et al. Crystal structure of the unoccupied murine urokinase-type plasminogen activator receptor (uPAR) reveals a tightly packed DII-DIII unit [J]. | FEBS LETTERS , 2019 , 593 (11) : 1236-1247 . |
| MLA | Liu, Min et al. "Crystal structure of the unoccupied murine urokinase-type plasminogen activator receptor (uPAR) reveals a tightly packed DII-DIII unit" . | FEBS LETTERS 593 . 11 (2019) : 1236-1247 . |
| APA | Liu, Min , Lin, Lin , Hoyer-Hansen, Gunilla , Ploug, Michael , Li, Hanlin , Jiang, Longguang et al. Crystal structure of the unoccupied murine urokinase-type plasminogen activator receptor (uPAR) reveals a tightly packed DII-DIII unit . | FEBS LETTERS , 2019 , 593 (11) , 1236-1247 . |
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The secondary structure content of proteins and their complexes may change significantly on passing from aqueous solution to the gas phase (as in mass spectrometry experiments). In this work, we investigate the impact of hydrophobic residues on the formation of the secondary structure of a real protein complex in the gas phase. We focus on a well-studied protein complex, the amyloid- (1-40) dimer (2A). Molecular dynamics simulations reproduce the results of ion mobility-mass spectrometry experiments. In addition, a helix (not present in the solution) is identified involving (19)FFAED(23), consistent with infrared spectroscopy data on an A segment. Our simulations further point to the role of hydrophobic residues in the formation of helical motifs - hydrophobic sidechains shield helices from being approached by residues that carry hydrogen bond sites. In particular, two hydrophobic phenylalanine residues, F19 and F20, play an important role for the helix, which is induced in the gas phase in spite of the presence of two carboxyl-containing residues.
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| GB/T 7714 | Liu, Lin , Dong, Xin , Liu, Yichang et al. Role of hydrophobic residues for the gaseous formation of helical motifs [J]. | CHEMICAL COMMUNICATIONS , 2019 , 55 (35) : 5147-5150 . |
| MLA | Liu, Lin et al. "Role of hydrophobic residues for the gaseous formation of helical motifs" . | CHEMICAL COMMUNICATIONS 55 . 35 (2019) : 5147-5150 . |
| APA | Liu, Lin , Dong, Xin , Liu, Yichang , Osterlund, Nicklas , Graslund, Astrid , Carloni, Paolo et al. Role of hydrophobic residues for the gaseous formation of helical motifs . | CHEMICAL COMMUNICATIONS , 2019 , 55 (35) , 5147-5150 . |
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