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1.
Protein & Cell ; (12): 553-567, 2018.
Article in English | WPRIM | ID: wpr-757973

ABSTRACT

ATP-sensitive potassium channels (K) are energy sensors on the plasma membrane. By sensing the intracellular ADP/ATP ratio of β-cells, pancreatic K channels control insulin release and regulate metabolism at the whole body level. They are implicated in many metabolic disorders and diseases and are therefore important drug targets. Here, we present three structures of pancreatic K channels solved by cryo-electron microscopy (cryo-EM), at resolutions ranging from 4.1 to 4.5 Å. These structures depict the binding site of the antidiabetic drug glibenclamide, indicate how Kir6.2 (inward-rectifying potassium channel 6.2) N-terminus participates in the coupling between the peripheral SUR1 (sulfonylurea receptor 1) subunit and the central Kir6.2 channel, reveal the binding mode of activating nucleotides, and suggest the mechanism of how Mg-ADP binding on nucleotide binding domains (NBDs) drives a conformational change of the SUR1 subunit.


Subject(s)
Animals , Mice , Adenosine Triphosphate , Metabolism , Amino Acid Sequence , Binding Sites , Cryoelectron Microscopy , Ligands , Mesocricetus , Models, Molecular , Nucleotides , Metabolism , Pancreas , Metabolism , Potassium Channels, Inwardly Rectifying , Chemistry , Metabolism , Protein Binding , Protein Multimerization , Protein Structure, Quaternary , Protein Subunits , Chemistry , Metabolism , Sf9 Cells , Spodoptera , Sulfonylurea Receptors , Chemistry , Metabolism
2.
Protein & Cell ; (12): 25-38, 2017.
Article in English | WPRIM | ID: wpr-757373

ABSTRACT

Mitophagy is an essential intracellular process that eliminates dysfunctional mitochondria and maintains cellular homeostasis. Mitophagy is regulated by the post-translational modification of mitophagy receptors. Fun14 domain-containing protein 1 (FUNDC1) was reported to be a new receptor for hypoxia-induced mitophagy in mammalian cells and interact with microtubule-associated protein light chain 3 beta (LC3B) through its LC3 interaction region (LIR). Moreover, the phosphorylation modification of FUNDC1 affects its binding affinity for LC3B and regulates selective mitophagy. However, the structural basis of this regulation mechanism remains unclear. Here, we present the crystal structure of LC3B in complex with a FUNDC1 LIR peptide phosphorylated at Ser17 (pS), demonstrating the key residues of LC3B for the specific recognition of the phosphorylated or dephosphorylated FUNDC1. Intriguingly, the side chain of LC3B Lys49 shifts remarkably and forms a hydrogen bond and electrostatic interaction with the phosphate group of FUNDC1 pS. Alternatively, phosphorylated Tyr18 (pY) and Ser13 (pS) in FUNDC1 significantly obstruct their interaction with the hydrophobic pocket and Arg10 of LC3B, respectively. Structural observations are further validated by mutation and isothermal titration calorimetry (ITC) assays. Therefore, our structural and biochemical results reveal a working model for the specific recognition of FUNDC1 by LC3B and imply that the reversible phosphorylation modification of mitophagy receptors may be a switch for selective mitophagy.


Subject(s)
Crystallography, X-Ray , Membrane Proteins , Chemistry , Metabolism , Microtubule-Associated Proteins , Chemistry , Metabolism , Mitophagy , Mitochondrial Proteins , Chemistry , Metabolism , Peptides , Chemistry , Metabolism , Phosphorylation , Protein Structure, Quaternary
3.
Protein & Cell ; (12): 675-685, 2017.
Article in English | WPRIM | ID: wpr-756968

ABSTRACT

The α3* nAChRs, which are considered to be promising drug targets for problems such as pain, addiction, cardiovascular function, cognitive disorders etc., are found throughout the central and peripheral nervous system. The α-conotoxin (α-CTx) LvIA has been identified as the most selective inhibitor of α3β2 nAChRs known to date, and it can distinguish the α3β2 nAChR subtype from the α6/α3β2β3 and α3β4 nAChR subtypes. However, the mechanism of its selectivity towards α3β2, α6/α3β2β3, and α3β4 nAChRs remains elusive. Here we report the co-crystal structure of LvIA in complex with Aplysia californica acetylcholine binding protein (Ac-AChBP) at a resolution of 3.4 Å. Based on the structure of this complex, together with homology modeling based on other nAChR subtypes and binding affinity assays, we conclude that Asp-11 of LvIA plays an important role in the selectivity of LvIA towards α3β2 and α3/α6β2β3 nAChRs by making a salt bridge with Lys-155 of the rat α3 subunit. Asn-9 lies within a hydrophobic pocket that is formed by Met-36, Thr-59, and Phe-119 of the rat β2 subunit in the α3β2 nAChR model, revealing the reason for its more potent selectivity towards the α3β2 nAChR subtype. These results provide molecular insights that can be used to design ligands that selectively target α3β2 nAChRs, with significant implications for the design of new therapeutic α-CTxs.


Subject(s)
Animals , Humans , Aplysia , Binding Sites , Conotoxins , Chemistry , Crystallography, X-Ray , Protein Structure, Quaternary , Receptors, Nicotinic , Chemistry
4.
Protein & Cell ; (12): 516-526, 2016.
Article in English | WPRIM | ID: wpr-757409

ABSTRACT

Protein phosphatase 2A (PP2A) accounts for the majority of total Ser/Thr phosphatase activities in most cell types and regulates many biological processes. PP2A holoenzymes contain a scaffold A subunit, a catalytic C subunit, and one of the regulatory/targeting B subunits. How the B subunit controls PP2A localization and substrate specificity, which is a crucial aspect of PP2A regulation, remains poorly understood. The kinetochore is a critical site for PP2A functioning, where PP2A orchestrates chromosome segregation through its interactions with BubR1. The PP2A-BubR1 interaction plays important roles in both spindle checkpoint silencing and stable microtubule-kinetochore attachment. Here we present the crystal structure of a PP2A B56-BubR1 complex, which demonstrates that a conserved BubR1 LxxIxE motif binds to the concave side of the B56 pseudo-HEAT repeats. The BubR1 motif binds to a groove formed between B56 HEAT repeats 3 and 4, which is quite distant from the B56 binding surface for PP2A catalytic C subunit and thus is unlikely to affect PP2A activity. In addition, the BubR1 binding site on B56 is far from the B56 binding site of shugoshin, another kinetochore PP2A-binding protein, and thus BubR1 and shugoshin can potentially interact with PP2A-B56 simultaneously. Our structural and biochemical analysis indicates that other proteins with the LxxIxE motif may also bind to the same PP2A B56 surface. Thus, our structure of the PP2A B56-BubR1 complex provides important insights into how the B56 subunit directs the recruitment of PP2A to specific targets.


Subject(s)
Humans , Amino Acid Motifs , Binding Sites , Cell Cycle Proteins , Chemistry , Crystallography, X-Ray , Multienzyme Complexes , Chemistry , Protein Phosphatase 2 , Chemistry , Protein Structure, Quaternary , Protein Serine-Threonine Kinases , Chemistry
5.
Protein & Cell ; (12): 854-865, 2016.
Article in English | WPRIM | ID: wpr-757378

ABSTRACT

Respirasome, a huge molecular machine that carries out cellular respiration, has gained growing attention since its discovery, because respiration is the most indispensable biological process in almost all living creatures. The concept of respirasome has renewed our understanding of the respiratory chain organization, and most recently, the structure of respirasome solved by Yang's group from Tsinghua University (Gu et al. Nature 237(7622):639-643, 2016) firstly presented the detailed interactions within this huge molecular machine, and provided important information for drug design and screening. However, the study of cellular respiration went through a long history. Here, we briefly showed the detoured history of respiratory chain investigation, and then described the amazing structure of respirasome.


Subject(s)
Animals , Humans , Electron Transport , Physiology , Electron Transport Chain Complex Proteins , Chemistry , History , Metabolism , History, 20th Century , History, 21st Century , Protein Structure, Quaternary , Structure-Activity Relationship
6.
Protein & Cell ; (12): 878-887, 2016.
Article in English | WPRIM | ID: wpr-757348

ABSTRACT

Mechanistic target of rapamycin (mTOR) complex 1 (mTORC1) integrates signals from growth factors, cellular energy levels, stress and amino acids to control cell growth and proliferation through regulating translation, autophagy and metabolism. Here we determined the cryo-electron microscopy structure of human mTORC1 at 4.4 Å resolution. The mTORC1 comprises a dimer of heterotrimer (mTOR-Raptor-mLST8) mediated by the mTOR protein. The complex adopts a hollow rhomboid shape with 2-fold symmetry. Notably, mTORC1 shows intrinsic conformational dynamics. Within the complex, the conserved N-terminal caspase-like domain of Raptor faces toward the catalytic cavity of the kinase domain of mTOR. Raptor shows no caspase activity and therefore may bind to TOS motif for substrate recognition. Structural analysis indicates that FKBP12-Rapamycin may generate steric hindrance for substrate entry to the catalytic cavity of mTORC1. The structure provides a basis to understand the assembly of mTORC1 and a framework to characterize the regulatory mechanism of mTORC1 pathway.


Subject(s)
Humans , Cell Line , Cryoelectron Microscopy , Methods , Mechanistic Target of Rapamycin Complex 1 , Multiprotein Complexes , Chemistry , Protein Structure, Quaternary , TOR Serine-Threonine Kinases , Chemistry
7.
Protein & Cell ; (12): 403-416, 2016.
Article in English | WPRIM | ID: wpr-757127

ABSTRACT

YfiBNR is a recently identified bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) signaling system in opportunistic pathogens. It is a key regulator of biofilm formation, which is correlated with prolonged persistence of infection and antibiotic drug resistance. In response to cell stress, YfiB in the outer membrane can sequester the periplasmic protein YfiR, releasing its inhibition of YfiN on the inner membrane and thus provoking the diguanylate cyclase activity of YfiN to induce c-di-GMP production. However, the detailed regulatory mechanism remains elusive. Here, we report the crystal structures of YfiB alone and of an active mutant YfiB(L43P) complexed with YfiR with 2:2 stoichiometry. Structural analyses revealed that in contrast to the compact conformation of the dimeric YfiB alone, YfiB(L43P) adopts a stretched conformation allowing activated YfiB to penetrate the peptidoglycan (PG) layer and access YfiR. YfiB(L43P) shows a more compact PG-binding pocket and much higher PG binding affinity than wild-type YfiB, suggesting a tight correlation between PG binding and YfiB activation. In addition, our crystallographic analyses revealed that YfiR binds Vitamin B6 (VB6) or L-Trp at a YfiB-binding site and that both VB6 and L-Trp are able to reduce YfiB(L43P)-induced biofilm formation. Based on the structural and biochemical data, we propose an updated regulatory model of the YfiBNR system.


Subject(s)
Amino Acid Sequence , Bacterial Proteins , Chemistry , Genetics , Metabolism , Binding Sites , Biofilms , Crystallography, X-Ray , Cyclic GMP , Metabolism , Dimerization , Molecular Dynamics Simulation , Molecular Sequence Data , Mutagenesis , Protein Structure, Quaternary , Pseudomonas aeruginosa , Metabolism , Sequence Alignment , Tryptophan , Chemistry , Metabolism , Vitamin B 6 , Chemistry , Metabolism
8.
Braz. dent. j ; 26(2): 105-109, Mar-Apr/2015. tab, graf
Article in English | LILACS | ID: lil-741217

ABSTRACT

Dried, fresh and glycolic extracts of Zingiber officinale were obtained to evaluate the action against G. mellonella survival assay against Enterococcus faecalis infection. Eighty larvae were divided into: 1) E. faecalis suspension (control); 2) E. faecalis + fresh extract of Z. officinale (FEO); 3) E. faecalis + dried extract of Z. officinale (DEO); 4) E. faecalis + glycolic extract of Z. officinale (GEO); 5) Phosphate buffered saline (PBS). For control group, a 5 μL inoculum of standardized suspension (107 cells/mL) of E. faecalis (ATCC 29212) was injected into the last left proleg of each larva. For the treatment groups, after E. faecalis inoculation, the extracts were also injected, but into the last right proleg. The larvae were stored at 37 °C and the number of dead larvae was recorded daily for 168 h (7 days) to analyze the survival curve. The larvae were considered dead when they did not show any movement after touching. E. faecalis infection led to the death of 85% of the larvae after 168 h. Notwithstanding, in treatment groups with association of extracts, there was an increase in the survival rates of 50% (GEO), 61% (FEO) and 66% (DEO) of the larvae. In all treatment groups, the larvae exhibited a survival increase with statistically significant difference in relation to control group (p=0.0029). There were no statistically significant differences among treatment groups with different extracts (p=0.3859). It may be concluded that the tested extracts showed antimicrobial activity against E. faecalis infection by increasing the survival of Galleria mellonella larvae.


Extratos seco, fresco e glicólico de Zingiber officinale foram obtidos para avaliar suas ações por meio de ensaio de sobrevivência em G. mellonella contra infecção por Enterococcus faecalis. Oitenta larvas foram divididas em: 1) Suspensão de E. faecalis (controle); 2) E. faecalis + extrato fresco de Z. officinale (FEO); 3) E. faecalis + extrato seco de Z. officinale (DEO); 4) E. faecalis + extrato glicólico de Z. officinale (GEO); 5) Solução tampão fosfato salina (PBS). Para o grupo de controle, 5 µL de inóculo de suspensão padronizada (107 células/mL) de E. faecalis (ATCC 29212) foi injetado na última proleg esquerda de cada lagarta. Para os grupos com tratamento, após a injeção de E. faecalis, os extratos foram injetados na última proleg direita. Após as injeções, as lagartas foram armazenadas a 37 °C e o número de animais mortos foi registrado diariamente em 168 h (7 dias) para analisar a curva de sobrevivência. As lagartas foram consideradas mortas quando elas não mostraram qualquer movimento após o toque. A infecção por E. faecalis levou à morte de 85% das lagartas após 168 h. Não obstante, nos grupos de tratamento com associação dos extratos, houve um aumento nas taxas de sobrevivência de 50% (GEO), 61% (FEO) e 66% (DEO) das lagartas. Em todos os grupos com tratamento, as lagartas apresentaram um aumento na sobrevivência, com diferença estatisticamente significativa em relação ao grupo controle (p=0,0029). Não houve diferença estatisticamente significativa entre os tratamentos com os diferentes extratos (p=0,3859). Pode concluir-se que os extratos testados mostraram atividade antimicrobiana contra a infecção por E. faecalis, aumentando a sobrevivência das lagartas de G. mellonella.


Subject(s)
Humans , Receptors, GABA-A/chemistry , Binding Sites , Benzamidines/chemistry , Benzamidines/metabolism , Benzamidines/pharmacology , Conserved Sequence , Crystallography, X-Ray , Cell Membrane/chemistry , Cell Membrane/metabolism , Drug Design , GABA-A Receptor Agonists/chemistry , GABA-A Receptor Agonists/metabolism , GABA-A Receptor Agonists/pharmacology , Genetic Predisposition to Disease , Glycosylation , Models, Molecular , Mutation/genetics , Protein Structure, Quaternary , Protein Structure, Tertiary , Protein Subunits , Polysaccharides/chemistry , Polysaccharides/metabolism , Receptors, GABA-A/genetics , Synaptic Transmission
9.
Protein & Cell ; (12): 445-455, 2013.
Article in English | WPRIM | ID: wpr-757792

ABSTRACT

Severe fever with thrombocytopenia syndrome virus (SFTSV), a member of the Phlebovirus genus from the Bunyaviridae family endemic to China, is the causative agent of life-threatening severe fever with thrombocytopenia syndrome (SFTS), which features high fever and hemorrhage. Similar to other negative-sense RNA viruses, SFTSV encodes a nucleocapsid protein (NP) that is essential for viral replication. NP facilitates viral RNA encapsidation and is responsible for the formation of ribonucleoprotein complex. However, recent studies have indicated that NP from Phlebovirus members behaves in inhomogeneous oligomerization states. In the present study, we report the crystal structure of SFTSV NP at 2.8 Å resolution and demonstrate the mechanism by which it processes a ringshaped hexameric form to accomplish RNA encapsidation. Key residues essential for oligomerization are identified through mutational analysis and identified to have a significant impact on RNA binding, which suggests that correct formation of highly ordered oligomers is a critical step in RNA encapsidation. The findings of this work provide new insights into the discovery of new antiviral reagents for Phlebovirus infection.


Subject(s)
Binding Sites , Crystallography, X-Ray , Mutation , Nucleocapsid Proteins , Chemistry , Genetics , Metabolism , Phlebovirus , Metabolism , Protein Binding , Protein Multimerization , Protein Structure, Quaternary , RNA, Viral , Metabolism , Recombinant Proteins , Chemistry , Genetics
10.
Protein & Cell ; (12): 432-444, 2013.
Article in English | WPRIM | ID: wpr-757791

ABSTRACT

Group II chaperonins, which assemble as double-ring complexes, assist in the refolding of nascent peptides or denatured proteins in an ATP-dependent manner. The molecular mechanism of group II chaperonin assembly and thermal stability is yet to be elucidated. Here, we selected the group II chaperonins (cpn-α and cpn-β), also called thermosomes, from Acidianus tengchongensis and investigated their assembly and thermal stability. We found that the binding of ATP or its analogs contributed to the successful assembly of thermosomes and enhanced their thermal stabilities. Cpn-β is more thermally stable than cpn-α, while the thermal stability of the hetero thermosome cpn-αβ is intermediate. Cryo-electron microscopy reconstructions of cpn-α and cpn-β revealed the interwoven densities of their non-conserved flexible N/C-termini around the equatorial planes. The deletion or swapping of their termini and pH-dependent thermal stability assays revealed the key role of the termini electrostatic interactions in the assembly and thermal stability of the thermosomes.


Subject(s)
Acidianus , Metabolism , Adenosine Triphosphate , Metabolism , Amino Acid Sequence , Cryoelectron Microscopy , Hydrogen-Ion Concentration , Molecular Sequence Data , Mutation , Nucleotides , Metabolism , Protein Binding , Protein Folding , Protein Stability , Protein Structure, Quaternary , Sequence Alignment , Static Electricity , Temperature , Thermosomes , Chemistry , Genetics , Metabolism
11.
Protein & Cell ; (12): 695-701, 2013.
Article in English | WPRIM | ID: wpr-757771

ABSTRACT

The F-BAR domain containing proteins PACSINs are cytoplasmic phosphoproteins involved in various membrane deformations, such as actin reorganization, vesicle transport and microtubule movement. Our previous study shows that all PACSINs are composed of crescent shaped dimers with two wedge loops, and the wedge loop-mediated lateral interaction between neighboring dimers is important for protein packing and tubulation activity. Here, from the crystal packing of PACSIN 2, we observed a tight tip-to-tip interaction, in addition to the wedge loop-mediated lateral interaction. With this tip-to-tip interaction, the whole packing of PACSIN 2 shows a spiral-like assembly with a central hole from the top view. Elimination of this tip-to-tip connection inhibited the tubulation function of PACSIN 2, indicating that tip-to-tip interaction plays an important role in membrane deformation activity. Together with our previous study, we proposed a packing model for the assembly of PACSIN 2 on membrane, where the proteins are connected by tip-to-tip and wedge loop-mediated lateral interactions on the surface of membrane to generate various diameter tubules.


Subject(s)
Humans , Adaptor Proteins, Signal Transducing , Chemistry , Genetics , Cell Membrane , Chemistry , Crystallography, X-Ray , Liposomes , Chemistry , Models, Molecular , Mutagenesis, Site-Directed , Protein Interaction Domains and Motifs , Protein Multimerization , Protein Structure, Quaternary , Recombinant Proteins , Chemistry , Genetics , Static Electricity
12.
Protein & Cell ; (12): 687-694, 2013.
Article in English | WPRIM | ID: wpr-757763

ABSTRACT

TRAF4 is a unique member of TRAF family, which is essential for innate immune response, nervous system and other systems. In addition to be an adaptor protein, TRAF4 was identified as a regulator protein in recent studies. We have determined the crystal structure of TRAF domain of TRAF4 (residues 292-466) at 2.60 Å resolution by X-ray crystallography method. The trimericly assembled TRAF4 resembles a mushroom shape, containing a super helical "stalk" which is made of three right-handed intertwined α helixes and a C-terminal "cap", which is divided at residue L302 as a boundary. Similar to other TRAFs, both intermolecular hydrophobic interaction in super helical "stalk" and hydrogen bonds in "cap" regions contribute directly to the formation of TRAF4 trimer. However, differing from other TRAFs, there is an additional flexible loop (residues 421-426), which contains a previously identified phosphorylated site S426 exposing on the surface. This S426 was reported to be phosphorylated by IKKα which is the pre-requisite for TRAF4-NOD2 complex formation and thus to inhibit NOD2-induced NF-κB activation. Therefore, the crystal structure of TRAF4-TRAF is valuable for understanding its molecular basis for its special function and provides structural information for further studies.


Subject(s)
Humans , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Hydrophobic and Hydrophilic Interactions , Models, Molecular , Phosphorylation , Protein Conformation, alpha-Helical , Protein Domains , Protein Structure, Quaternary , Recombinant Proteins , Chemistry , Sequence Homology, Amino Acid , TNF Receptor-Associated Factor 4 , Chemistry
13.
Protein & Cell ; (12): 833-845, 2013.
Article in English | WPRIM | ID: wpr-757562

ABSTRACT

Cytomegalovirus (CMV) is distinct among members of the Herpesviridae family for having the largest dsDNA genome (230 kb). Packaging of large dsDNA genome is known to give rise to a highly pressurized viral capsid, but molecular interactions conducive to the formation of CMV capsid resistant to pressurization have not been described. Here, we report a cryo electron microscopy (cryoEM) structure of the murine cytomegalovirus (MCMV) capsid at a 9.1 Å resolution and describe the molecular interactions among the ∼3000 protein molecules in the MCMV capsid at the secondary structure level. Secondary structural elements are resolved to provide landmarks for correlating with results from sequence-based prediction and for structure-based homology modeling. The major capsid protein (MCP) upper domain (MCPud) contains α-helices and β-sheets conserved with those in MCPud of herpes simplex virus type 1 (HSV-1), with the largest differences identified as a "saddle loop" region, located at the tip of MCPud and involved in interaction with the smallest capsid protein (SCP). Interactions among the bacteriophage HK97-like floor domain of MCP, the middle domain of MCP, the hook and clamp domains of the triplex proteins (hoop and clamp domains of TRI-1 and clamp domain of TRI-2) contribute to the formation of a mature capsid. These results offer a framework for understanding how cytomegalovirus uses various secondary structural elements of its capsid proteins to build a robust capsid for packaging its large dsDNA genome inside and for attaching unique functional tegument proteins outside.


Subject(s)
Amino Acid Sequence , Capsid Proteins , Chemistry , Metabolism , Cryoelectron Microscopy , Models, Molecular , Molecular Sequence Data , Muromegalovirus , Chemistry , Protein Binding , Protein Multimerization , Protein Structure, Quaternary , Protein Structure, Tertiary
14.
Experimental & Molecular Medicine ; : e22-2013.
Article in English | WPRIM | ID: wpr-158223

ABSTRACT

The accumulation of abnormal protein aggregates is a major characteristic of many neurodegenerative disorders, including Parkinson's disease (PD). The intracytoplasmic deposition of alpha-synuclein aggregates and Lewy bodies, often found in PD and other alpha-synucleinopathies, is thought to be linked to inefficient cellular clearance mechanisms, such as the proteasome and autophagy/lysosome pathways. The accumulation of alpha-synuclein aggregates in neuronal cytoplasm causes numerous autonomous changes in neurons. However, it can also affect the neighboring cells through transcellular transmission of the aggregates. Indeed, a progressive spreading of Lewy pathology among brain regions has been hypothesized from autopsy studies. We tested whether inhibition of the autophagy/lysosome pathway in alpha-synuclein-expressing cells would increase the secretion of alpha-synuclein, subsequently affecting the alpha-synuclein deposition in and viability of neighboring cells. Our results demonstrated that autophagic inhibition, via both pharmacological and genetic methods, led to increased exocytosis of alpha-synuclein. In a mixed culture of alpha-synuclein-expressing donor cells with recipient cells, autophagic inhibition resulted in elevated transcellular alpha-synuclein transmission. This increase in protein transmission coincided with elevated apoptotic cell death in the recipient cells. These results suggest that the inefficient clearance of alpha-synuclein aggregates, which can be caused by reduced autophagic activity, leads to elevated alpha-synuclein exocytosis, thereby promoting alpha-synuclein deposition and cell death in neighboring neurons. This finding provides a potential link between autophagic dysfunction and the progressive spread of Lewy pathology.


Subject(s)
Animals , Humans , Mice , Adenine/analogs & derivatives , Autophagy/drug effects , Cell Line , Exocytosis/drug effects , Extracellular Space/metabolism , Mice, Knockout , Microtubule-Associated Proteins/deficiency , Phagosomes/drug effects , Protein Structure, Quaternary , Protein Transport/drug effects , alpha-Synuclein/chemistry
15.
Protein & Cell ; (12): 769-780, 2012.
Article in English | WPRIM | ID: wpr-757857

ABSTRACT

Enolase is a conserved cytoplasmic metalloenzyme existing universally in both eukaryotic and prokaryotic cells. The enzyme can also locate on the cell surface and bind to plasminogen, via which contributing to the mucosal surface localization of the bacterial pathogens and assisting the invasion into the host cells. The functions of the eukaryotic enzymes on the cell surface expression (including T cells, B cells, neutrophils, monocytoes, neuronal cells and epithelial cells) are not known. Streptococcus suis serotype 2 (S. suis 2, SS2) is an important zoonotic pathogen which has recently caused two large-scale outbreaks in southern China with severe streptococcal toxic shock syndrome (STSS) never seen before in human sufferers. We recently identified the SS2 enolase as an important protective antigen which could protect mice from fatal S.suis 2 infection. In this study, a 2.4-angstrom structure of the SS2 enolase is solved, revealing an octameric arrangement in the crystal. We further demonstrated that the enzyme exists exclusively as an octamer in solution via a sedimentation assay. These results indicate that the octamer is the biological unit of SS2 enolase at least in vitro and most likely in vivo as well. This is, to our knowledge, the first comprehensive characterization of the SS2 enolase octamer both structurally and biophysically, and the second octamer enolase structure in addition to that of Streptococcus pneumoniae. We also investigated the plasminogen binding property of the SS2 enzyme.


Subject(s)
Humans , Amino Acid Sequence , Binding Sites , Crystallography, X-Ray , Models, Molecular , Molecular Sequence Data , Phosphopyruvate Hydratase , Chemistry , Metabolism , Plasminogen , Metabolism , Protein Multimerization , Protein Structure, Quaternary , Solutions , Species Specificity , Streptococcus suis
16.
Protein & Cell ; (12): 864-874, 2012.
Article in English | WPRIM | ID: wpr-757842

ABSTRACT

In addition to DNA repair pathways, cells utilize translesion DNA synthesis (TLS) to bypass DNA lesions during replication. During TLS, Y-family DNA polymerase (Polη, Polκ, Polı and Rev1) inserts specific nucleotide opposite preferred DNA lesions, and then Polζ consisting of two subunits, Rev3 and Rev7, carries out primer extension. Here, we report the complex structures of Rev3-Rev7-Rev1(CTD) and Rev3-Rev7-Rev1(CTD)-Polκ(RIR). These two structures demonstrate that Rev1(CTD) contains separate binding sites for Polκ and Rev7. Our BIAcore experiments provide additional support for the notion that the interaction between Rev3 and Rev7 increases the affinity of Rev7 and Rev1. We also verified through FRET experiment that Rev1, Rev3, Rev7 and Polκ form a stable quaternary complex in vivo, thereby suggesting an efficient switching mechanism where the "inserter" polymerase can be immediately replaced by an "extender" polymerase within the same quaternary complex.


Subject(s)
Humans , Binding Sites , Crystallography, X-Ray , DNA Repair , DNA-Binding Proteins , Chemistry , Genetics , Metabolism , DNA-Directed DNA Polymerase , Chemistry , Genetics , Metabolism , Fluorescence Resonance Energy Transfer , Mad2 Proteins , Nuclear Proteins , Chemistry , Genetics , Metabolism , Nucleotidyltransferases , Chemistry , Genetics , Metabolism , Protein Binding , Protein Structure, Quaternary , Protein Structure, Tertiary , Proteins , Chemistry , Genetics , Metabolism , Recombinant Proteins , Chemistry , Genetics
17.
Protein & Cell ; (12): 123-131, 2012.
Article in English | WPRIM | ID: wpr-757289

ABSTRACT

D-psicose 3-epimerase (DPEase) is demonstrated to be useful in the bioproduction of D-psicose, a rare hexose sugar, from D-fructose, found plenty in nature. Clostridium cellulolyticum H10 has recently been identified as a DPEase that can epimerize D-fructose to yield D-psicose with a much higher conversion rate when compared with the conventionally used DTEase. In this study, the crystal structure of the C. cellulolyticum DPEase was determined. The enzyme assembles into a tetramer and each subunit shows a (β/α)(8) TIM barrel fold with a Mn(2+) metal ion in the active site. Additional crystal structures of the enzyme in complex with substrates/products (D-psicose, D-fructose, D-tagatose and D-sorbose) were also determined. From the complex structures of C. cellulolyticum DPEase with D-psicose and D-fructose, the enzyme has much more interactions with D-psicose than D-fructose by forming more hydrogen bonds between the substrate and the active site residues. Accordingly, based on these ketohexose-bound complex structures, a C3-O3 proton-exchange mechanism for the conversion between D-psicose and D-fructose is proposed here. These results provide a clear idea for the deprotonation/protonation roles of E150 and E244 in catalysis.


Subject(s)
Binding Sites , Biocatalysis , Catalytic Domain , Clostridium cellulolyticum , Hexoses , Chemistry , Manganese , Chemistry , Protein Structure, Quaternary , Racemases and Epimerases , Chemistry , Metabolism , Substrate Specificity
18.
Protein & Cell ; (12): 781-789, 2012.
Article in English | WPRIM | ID: wpr-757222

ABSTRACT

Dimerization among the EGFR family of tyrosine kinase receptors leads to allosteric activation of the kinase domains of the partners. Unlike other members in the family, the kinase domain of HER3 lacks key amino acid residues for catalytic activity. As a result, HER3 is suggested to serve as an allosteric activator of other EGFR family members which include EGFR, HER2 and HER4. To study the role of intracellular domains in HER3 dimerization and activation of downstream signaling pathways, we constructed HER3/HER2 chimeric receptors by replacing the HER3 kinase domain (HER3-2-3) or both the kinase domain and the C-terminal tail (HER3-2-2) with the HER2 counterparts and expressed the chimeric receptors in Chinese hamster ovary (CHO) cells. While over expression of the intact human HER3 transformed CHO cells with oncogenic properties such as AKT/ERK activation and increased proliferation and migration, CHO cells expressing the HER3-2-3 chimeric receptor showed significantly reduced HER3/HER2 dimerization and decreased phosphorylation of both AKT and ERK1/2 in the presence of neuregulin-1 (NRG-1). In contrast, CHO cells expressing the HER3-2-2 chimeric receptor resulted in a total loss of downstream AKT activation in response to NRG-1, but maintained partial activation of ERK1/2. The results demonstrate that the intracellular domains play a crucial role in HER3's function as an allosteric activator and its role in downstream signaling.


Subject(s)
Animals , Cricetinae , Humans , Amino Acid Sequence , CHO Cells , Cell Movement , Cell Proliferation , Cricetulus , Extracellular Signal-Regulated MAP Kinases , Metabolism , Intracellular Space , MAP Kinase Signaling System , Models, Molecular , Molecular Sequence Data , Phosphatidylinositol 3-Kinases , Metabolism , Protein Multimerization , Protein Structure, Quaternary , Protein Structure, Tertiary , Proto-Oncogene Proteins c-akt , Metabolism , Receptor, ErbB-2 , Chemistry , Receptor, ErbB-3 , Chemistry , Genetics , Metabolism , Recombinant Fusion Proteins , Chemistry , Genetics , Metabolism , Signal Transduction
19.
Protein & Cell ; (12): 55-63, 2011.
Article in English | WPRIM | ID: wpr-757664

ABSTRACT

The importance of NAC (named as NAM, ATAF1, 2, and CUC2) proteins in plant development, transcription regulation and regulatory pathways involving protein-protein interactions has been increasingly recognized. We report here the high resolution crystal structure of SNAC1 (stress-responsive NAC) NAC domain at 2.5 Å. Although the structure of the SNAC1 NAC domain shares a structural similarity with the reported structure of the ANAC NAC1 domain, some key features, especially relating to two loop regions which potentially take the responsibility for DNA-binding, distinguish the SNAC1 NAC domain from other reported NAC structures. Moreover, the dimerization of the SNAC1 NAC domain is demonstrated by both soluble and crystalline conditions, suggesting this dimeric state should be conserved in this type of NAC family. Additionally, we discuss the possible NAC-DNA binding model according to the structure and reported biological evidences.


Subject(s)
Amino Acid Motifs , Amino Acid Sequence , Conserved Sequence , Crystallography, X-Ray , DNA , Metabolism , Models, Molecular , Molecular Sequence Data , Oryza , Metabolism , Physiology , Plant Proteins , Chemistry , Metabolism , Promoter Regions, Genetic , Genetics , Protein Multimerization , Protein Structure, Quaternary , Protein Structure, Tertiary , Stress, Physiological
20.
Protein & Cell ; (12): 223-236, 2011.
Article in English | WPRIM | ID: wpr-757109

ABSTRACT

Amyotrophic lateral sclerosis (ALS) is a fatal disease characterized by the premature loss of motor neurons. While the underlying cellular mechanisms of neuron degeneration are unknown, the cytoplasmic aggregation of several proteins is associated with sporadic and familial forms of the disease. Both wild-type and mutant forms of the RNA-binding proteins FUS and TDP-43 accumulate in cytoplasmic inclusions in the neurons of ALS patients. It is not known if these so-called proteinopathies are due to a loss of function or a gain of toxicity resulting from the formation of cytoplasmic aggregates. Here we present a model of FUS toxicity using the yeast Saccharomyces cerevisiae in which toxicity is associated with greater expression and accumulation of FUS in cytoplasmic aggregates. We find that FUS and TDP-43 have a high propensity for co-aggregation, unlike the aggregation patterns of several other aggregation-prone proteins. Moreover, the biophysical properties of FUS aggregates in yeast are distinctly different from many amyloidogenic proteins, suggesting they are not composed of amyloid.


Subject(s)
Humans , Amyotrophic Lateral Sclerosis , Metabolism , Pathology , Cell Proliferation , Cytoplasm , Metabolism , DNA-Binding Proteins , Genetics , Metabolism , Detergents , Pharmacology , Kinetics , Peptides , Metabolism , Prions , Chemistry , Metabolism , Protein Binding , Protein Multimerization , Protein Structure, Quaternary , Protein Transport , RNA-Binding Protein FUS , Chemistry , Genetics , Metabolism , Saccharomyces cerevisiae , Cell Biology , Genetics , Metabolism , Saccharomyces cerevisiae Proteins , Chemistry , Metabolism
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