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Mi Li

Publications and source records attributed to Mi Li.

At least 19 recordsLinked to original sources
PubMed2025

The impact of m6A methyltransferase METTL3 on airway remodeling in bronchial asthma.

BACKGROUND: Methyltransferase-like 3 (METTL3) is known to play a role in asthma airway remodeling and cell proliferation. Adenylate kinase 4 (AK4) regulates the proliferation of pulmonary artery smooth muscle cells and exerts its effects through the protein kinase B (AKT) pathway. However, the role of METTL3 and AK4-AKT in bronchial smooth muscle cells remains unclear. METHODS: Systemic METTL3 knockout mice and a mouse model of asthma were established. Airway remodeling was assessed using pulmonary function tests, histopathological staining, and Western blot analysis. RNA sequencing (RNA-seq) was performed to detect changes in gene expression following METTL3 knockdown. The 5-ethynyl-2'-deoxyuridine (EdU) assay was used to evaluate cell proliferation. Finally, the expression levels of relevant proteins were validated by Western blotting. RESULTS: Compared with the control model group, the METTL3 knockout group showed significantly reduced inflammatory cell infiltration, decreased collagen fiber deposition, and attenuated airway smooth muscle hyperplasia. RNA-seq revealed that the expression of numerous proliferation-related genes, including AK4, was upregulated following METTL3 knockdown. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that these genes were primarily enriched in the phosphatidylinositol 3-kinase (PI3K)/AKT signaling pathway. The EdU assay demonstrated that METTL3 knockdown inhibited cell proliferation. Western blot validation showed increased AK4 expression in lung tissues of the METTL3 knockout group compared to the control group, while phosphorylated AKT (p-AKT) levels were reduced. CONCLUSIONS: METTL3 knockout inhibits airway smooth muscle hyperplasia and alleviates airway remodeling in asthma. This effect may be mediated through the regulation of AK4 and the AKT signaling pathway.

Airway Remodeling↗
PubMed2006

Molecular replacement with pseudosymmetry and model dissimilarity: a case study.

Crystals of human T-cell leukemia virus protease (HTLV-1 PR) have been very difficult to prepare and only native data extending to 2.6 angstroms resolution could be collected. Initial attempts to solve the structure with a variety of low-sequence-identity models utilizing proteases from other retroviruses and using a number of molecular-replacement programs were unsuccessful. The structure was finally solved using Phaser, revealing extensive pseudosymmetry and significant deviations from the starting models, features that were likely to be responsible for the initial failures. The steps taken to solve this structure and some of its intriguing crystallographic aspects are discussed.

Aspartic Acid Endopeptidases↗
PubMed2006

Processing, catalytic activity and crystal structures of kumamolisin-As with an engineered active site.

Kumamolisin-As is an acid collagenase with a subtilisin-like fold. Its active site contains a unique catalytic triad, Ser278-Glu78-Asp82, and a putative transition-state stabilizing residue, Asp164. In this study, the mutants D164N and E78H/D164N were engineered in order to replace parts of the catalytic machinery of kumamolisin-As with the residues found in the equivalent positions in subtilisin. Unlike the wild-type and D164N proenzymes, which undergo instantaneous processing to produce their 37-kDa mature forms, the expressed E78H/D164N proenzyme exists as an equilibrated mixture of the nicked and intact forms of the precursor. X-ray crystallographic structures of the mature forms of the two mutants showed that, in each of them, the catalytic Ser278 makes direct hydrogen bonds with the side chain of Asn164. In addition, His78 of the double mutant is distant from Ser278 and Asp82, and the catalytic triad no longer exists. Consistent with these structural alterations around the active site, these mutants showed only low catalytic activity (relative k(cat) at pH 4.0 1.3% for D164N and 0.0001% for E78H/D164N). pH-dependent kinetic studies showed that the single D164N substitution did not significantly alter the logk(cat) vs. pH and log(k(cat)/Km) vs. pH profiles of the enzyme. In contrast, the double mutation resulted in a dramatic switch of the logk(cat) vs. pH profile to one that was consistent with catalysis by means of the Ser278-His78 dyad and Asn164, which may also account for the observed ligation/cleavage equilibrium of the precursor of E78H/D164N. These results corroborate the mechanistic importance of the glutamate-mediated catalytic triad and oxyanion-stabilizing aspartic acid residue for low-pH peptidase activity of the enzyme.

Aspartic Acid Endopeptidases↗
PubMed2006

[Effect of captopril on pulmonary vascular remodeling induced by left-to-right shunt in rats].

OBJECTIVE: To investigate the therapeutic effect of angiotensin converting enzyme inhibitor on pulmonary vascular remodeling of pulmonary hypertension induced by high pulmonary blood flow. METHODS: An arterial-venous shunt was surgically created between abdominal aorta and inferior vena cava in the rat of all groups except the control group. Captopril was given to all of the rats. Six weeks after the operation,pulmonary artery systolic pressure (PASP), pulmonary artery diastolic pressure (PADP) and right ventricular systolic pressure (RVSP) were measured. The rats' hearts were weighted to calculate the ratio of right ventricle mass to left ventricle plus septum mass. Immunohistochemical stains were used to identify alpha-actin and PCNA distribution in pulmonary arteries. Morphometric parameters (vascular wall thickness and muscularization) were used to assess the remodeling of small pulmonary arteries. RESULTS: The PASP, PADP, RVSP, RV/(LV+S), RV/BW, and (LV + S)/BW of the rats in the shunt group were significantly greater than those of the control group. Muscularization of small pulmonary arteries and pulmonary artery medial hypertrophy (wall thickness) were evident in the shunt group. The proliferation index of the smooth muscle cells of the small and medium-sized pulmonary arteries was significantly higher and the alpha-actin IOD was significantly lower in the rats of the shunt group than those of the control. By contrast, the levels of PASP, PADP, RVSP, RV/(LV+S), RV/BW, (LV+ S)/BW, and muscularization were lower in the rats of captopril group than those of the control. CONCLUSIONS: Captopril slows down pulmonary hypertension and remodeling development. Captopril and losartan may have preventive and therapeutic effects on pulmonary hypertension induced by congenital left-to-right shunts.

Angiotensin-Converting Enzyme Inhibitors↗
PubMed2005

Crystal structure of human T cell leukemia virus protease, a novel target for anticancer drug design.

The successful development of a number of HIV-1 protease (PR) inhibitors for the treatment of AIDS has validated the utilization of retroviral PRs as drug targets and necessitated their detailed structural study. Here we report the structure of a complex of human T cell leukemia virus type 1 (HTLV-1) PR with a substrate-based inhibitor bound in subsites P5 through P5'. Although HTLV-1 PR exhibits an overall fold similar to other retroviral PRs, significant structural differences are present in several loop areas, which include the functionally important flaps, previously considered to be structurally highly conserved. Potential key residues responsible for the resistance of HTLV-1 PR to anti-HIV drugs are identified. We expect that the knowledge accumulated during the development of anti-HIV drugs, particularly in overcoming drug resistance, will help in designing a novel class of antileukemia drugs targeting HTLV-1 PR and in predicting their drug-resistance profile. The structure presented here can be used as a starting point for the development of such anticancer therapies.

Amino Acid Sequence↗
PubMed2005

Crystal structure of the N-terminal domain of E. coli Lon protease.

We report here the first crystal structure of the N-terminal domain of an A-type Lon protease. Lon proteases are ubiquitous, multidomain, ATP-dependent enzymes with both highly specific and non-specific protein binding, unfolding, and degrading activities. We expressed and purified a stable, monomeric 119-amino acid N-terminal subdomain of the Escherichia coli A-type Lon protease and determined its crystal structure at 2.03 A (Protein Data Bank [PDB] code 2ANE). The structure was solved in two crystal forms, yielding 14 independent views. The domain exhibits a unique fold consisting primarily of three twisted beta-sheets and a single long alpha-helix. Analysis of recent PDB depositions identified a similar fold in BPP1347 (PDB code 1ZBO), a 203-amino acid protein of unknown function from Bordetella parapertussis, crystallized as part of a structural genomics effort. BPP1347 shares sequence homology with Lon N-domains and with a family of other independently expressed proteins of unknown functions. We postulate that, as is the case in Lon proteases, this structural domain represents a general protein and polypeptide interaction domain.

Amino Acid Sequence↗
PubMed2005

Crystal structure of cockroach allergen Bla g 2, an unusual zinc binding aspartic protease with a novel mode of self-inhibition.

The crystal structure of Bla g 2 was solved in order to investigate the structural basis for the allergenic properties of this unusual protein. This is the first structure of an aspartic protease in which conserved glycine residues, in two canonical DTG triads, are substituted by different amino acid residues. Another unprecedented feature revealed by the structure is the single phenylalanine residue insertion on the tip of the flap, with the side-chain occupying the S1 binding pocket. This and other important amino acid substitutions in the active site region of Bla g 2 modify the interactions in the vicinity of the catalytic aspartate residues, increasing the distance between them to approximately 4A and establishing unique direct contacts between the flap and the catalytic residues. We attribute the absence of substantial catalytic activity in Bla g 2 to these unusual features of the active site. Five disulfide bridges and a Zn-binding site confer stability to the protein, which may contribute to sensitization at lower levels of exposure than other allergens.

Amino Acid Sequence↗
PubMed2005

Structural basis for the function of stringent starvation protein a as a transcription factor.

Stringent starvation protein A (SspA) of Escherichia coli is an RNA polymerase-associated transcriptional activator for the lytic development of phage P1 and is essential for stationary phase-induced acid tolerance of E. coli. We report the crystal structure of Yersinia pestis SspA, which is 83% identical to E. coli SspA in amino acid sequence and is functionally complementary in supporting the lytic growth of phage P1 and acid resistance of an E. coli sspA mutant. The structure reveals that SspA assumes the characteristic fold of glutathione S-transferase (GST). However, SspA lacks GST activity and does not bind glutathione. Three regions of SspA are flexible, the N and C termini and the alpha2-helix. The structure also reveals a conserved surface-exposed pocket composed of residues from a loop between helices alpha3 and alpha4. The functional roles of these structural features were investigated by assessing the ability of deletion and site-directed mutants to confer acid resistance of E. coli and to activate transcription from a phage P1 late promoter, thereby supporting the lytic growth of phage P1. The results indicate that the flexible regions are not critical for SspA function, whereas the surface pocket is important for both transcriptional activation of the phage P1 late promoter and acid resistance of E. coli. The size, shape, and property of the pocket suggest that it mediates protein-protein interactions. SspA orthologs from Y. pestis, Vibrio cholerae, and Pseudomonas aeruginosa are all functional in acid resistance of E. coli, whereas only Y. pestis SspA supports phage P1 growth.

Adhesins, Bacterial↗
PubMed2005

Effects of amphetamine-CNS depressant combinations and of other CNS stimulants in four-choice drug discriminations.

Three pigeons were trained to discriminate among 5 mg/kg pentobarbital, 2 mg/kg amphetamine, a combination of these two drugs at these doses, and saline using a four-choice procedure (amphetamine-pentobarbital group). Three other pigeons were trained to discriminate among 5 mg/kg morphine, 2 mg/kg methamphetamine, a combination of these two drugs at these doses, and saline (methamphetamine-morphine group). After 10 to 13 months of training, the pigeons averaged more than 90% of their responses on the appropriate key during training sessions. In subsequent testing, dose-response curves were determined for the individual drugs, for a wide range of dose combinations of the training drugs, and for two drugs to which the pigeons had not been exposed previously (pseudoephedrine and nicotine). After low test doses of the training drugs, pigeons responded on the saline key. As the dose increased, responding on the key associated with that drug during training sessions increased. When training drugs were combined at doses that were not discriminable when given alone, responding occurred on the saline key. When a discriminable dose of one training drug was combined with a nondiscriminable dose of the other training drug, responding occurred on the key associated with the discriminable dose. When both drugs were given at discriminable doses, responding almost always occurred on the drug-combination key. The response-rate decreasing effects of pentobarbital and amphetamine were mutually antagonized when the drugs were combined, but the rate-decreasing effects of morphine and methamphetamine were not. After low doses of pseudoephedrine and nicotine, pigeons in both groups responded on the saline key. After higher doses of pseudoephedrine and nicotine, responding in the amphetamine-pentobarbital group occurred primarily on the amphetamine key. In the methamphetamine-morphine group, higher doses of pseudoephedrine and especially nicotine engendered more responding on the combination key than had occurred in the other group. The four-choice procedure can reveal subtle effects in the discrimination of individual drugs and drug combinations that are not apparent with procedures offering fewer response alternatives.

Amphetamine↗
PubMed2005

[Effects of Losartan on expression of heme oxygenases in volume-overloaded rats with left-to-right shunt].

OBJECTIVE: To study the expression of heme oxygenase-1 mRNA and pulmonary remodeling before and after surgical establishment of left-to-right shunt in volume-overloaded SD rats and rats with Losartan intervention. METHODS: Left-to-right shunt volume-overloaded SD rat models were established by aortocaval shunt operation. Seven rats with shunt were placed on Losartan (Losartan group), 7 rats with but not given Losartan were included in the operation group, and 4 rats after sham operation served as controls. Pulmonary pressure and right ventricular pressure were measured during catheterization. The relative weights ventricles were determined after execution of the rats. Pulmonary vascular remodeling parameters, including percentage arterial wall thickness and percentage muscularized small arteries, were assessed by morphometry. Heme oxygenase-1 (HO-1) mRNA expression and heme oxygenase-2 (HO-2) mRNA expression were detected RT-PCR method. RESULTS: Pulmonary artery pressure and right ventricular relative weight decreased significantly in the rats of Losartan group; in addition, the percentage arterial wall thickness and percentage of muscularized small arteries in the Losartan group were reduced as compared with those in the operation group. The level 1 mRAN expression in rats with shunt was significantly higher than that in rats without shunt. The level mRNA expression in the Losartan group decreased remarkably as compared against that in the operation The level of HO-1 mRNA expression in lungs was significantly higher than that in ventricles. There statistically significant differences in HO-2 mRNA expression levels between the three rat groups. CONCLUSION: Losartan intervention can markedly reduce pulmonary pressure, inhibit vascular remodeling in volume-overloaded left-to-right shunt rats, and result in down-regulation of HO-1 mRNA expression.

Animals↗
PubMed2005

[A pilot study of using pure albumin as a dialysate in the treatment of liver failure].

OBJECTIVE: To observe the effect of a new extracorporeal hepatic support-hemodialysis with albumin-based dialysate on patient with liver failure, and to compare the result with that of molecular absorbent recycling system (MARS). METHODS: Eighteen patients with liver failure were enrolled and treated intermittently with artificial liver on the basis of conventional regime. Among them, 12 of them were treated with single albumin dialysis (SAD) for 6 hours each period, and 6 with MARS for 6 hours. During each session of SAD, 4,000 ml albumin-based dialysate (45 g/L) was circulated in the dialysate route at a flow rate of 10 L/h with the blood flow rate of 250 ml/min. Liver and renal function, prothrombin activity (PTA), serum ammonia (NH(3)), endotoxin were monitored before and after the treatment, and the serial bilirubin content was measured in the serum and the albumin dialysate of all patients respectively 1-hour, 3-hour, 6-hour after the treatment with SAD. RESULTS: After treatment with SAD, the clinical symptoms and signs were improved and the hemodynamics were stabilized, complications were ameliorated partially, in particular hepatic encephalopathy was improved, with low incidence of adverse reaction, and the effective rate and survival rate were high. The serum PTA was increased obviously (P<0.05), and the serum blood urea nitrogen (BUN), serum creatinine (SCr), total bilirubin (TB), total bile acid (TBA), NH(3), endotoxin were decreased significantly (all P<0.05), and elimination of bilirubin slowed down gradually. The results showed that SAD was as effective as MARS, with a lower cost, and simpler and more convenient than MARS. CONCLUSION: Single albumin dialysis may eliminate protein-bound and water-soluble hepatic toxins, improve clinical symptoms and liver function in the treatment of liver failure, and worth further clinical study.

Adult↗
PubMed2004

Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity.

Kumamolisin-As (previously called ScpA) is the first known example of a collagenase from the sedolisin family (MEROPS S53). This enzyme is active at low pH and in elevated temperatures. In this study that used x-ray crystallographic and biochemical methods, we investigated the structural basis of the preference of this enzyme for collagen and the importance of a glutamate residue in the unique catalytic triad (Ser(278)-Glu(78)-Asp(82)) for enzymatic activity. Crystal structures of the uninhibited enzyme and its complex with a covalently bound inhibitor, N-acetyl-isoleucyl-prolyl-phenylalaninal, showed the occurrence of a narrow S2 pocket and a groove that encompasses the active site and is rich in negative charges. Limited endoproteolysis studies of bovine type-I collagen as well as kinetic studies using peptide libraries randomized at P1 and P1', showed very strong preference for arginine at the P1 position, which correlated very well with the presence of a negatively charged residue in the S1 pocket of the enzyme. All of these features, together with those predicted through comparisons with fiddler crab collagenase, a serine peptidase, rationalize the enzyme's preference for collagen. A comparison of the Arrhenius plots of the activities of kumamolisin-As with either collagen or peptides as substrates suggests that collagen should be relaxed before proteolysis can occur. The E78H mutant, in which the catalytic triad was engineered to resemble that of subtilisin, showed only 0.01% activity of the wild-type enzyme, and its structure revealed that Ser(278), His(78), and Asp(82) do not interact with each other; thus, the canonical catalytic triad is disrupted.

Amino Acid Sequence↗
PubMed2004

Two inhibitor molecules bound in the active site of Pseudomonas sedolisin: a model for the bi-product complex following cleavage of a peptide substrate.

High-resolution crystallographic analysis of a complex of the serine-carboxyl proteinase sedolisin with pseudo-iodotyrostatin revealed two molecules of this inhibitor bound in the active site of the enzyme, marking subsites from S3 to S3('). The mode of binding represents two products of the proteolytic reaction. Substrate specificity of sedolisin was investigated using peptide libraries and a new peptide substrate for sedolisin, MCA-Lys-Pro-Pro-Leu-Glu#Tyr-Arg-Leu-Gly-Lys(DNP)-Gly, was synthesized based on the results of the enzymatic and crystallographic studies and was shown to be efficiently cleaved by the enzyme. The kinetic parameters for the substrate, measured by the increase in fluorescence upon relief of quenching, were: k(cat)=73+/-5 s(-1), K(m)=0.12+/-0.011 microM, and k(cat)/K(m)=608+/-85 s(-1)microM(-1).

Binding Sites↗
PubMed2003

A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases.

BACKGROUND: Tripeptidyl-peptidase I, also known as CLN2, is a member of the family of sedolisins (serine-carboxyl peptidases). In humans, defects in expression of this enzyme lead to a fatal neurodegenerative disease, classical late-infantile neuronal ceroid lipofuscinosis. Similar enzymes have been found in the genomic sequences of several species, but neither systematic analyses of their distribution nor modeling of their structures have been previously attempted. RESULTS: We have analyzed the presence of orthologs of human CLN2 in the genomic sequences of a number of eukaryotic species. Enzymes with sequences sharing over 80% identity have been found in the genomes of macaque, mouse, rat, dog, and cow. Closely related, although clearly distinct, enzymes are present in fish (fugu and zebra), as well as in frogs (Xenopus tropicalis). A three-dimensional model of human CLN2 was built based mainly on the homology with Pseudomonas sp. 101 sedolisin. CONCLUSION: CLN2 is very highly conserved and widely distributed among higher organisms and may play an important role in their life cycles. The model presented here indicates a very open and accessible active site that is almost completely conserved among all known CLN2 enzymes. This result is somehow surprising for a tripeptidase where the presence of a more constrained binding pocket was anticipated. This structural model should be useful in the search for the physiological substrates of these enzymes and in the design of more specific inhibitors of CLN2.

Amino Acid Sequence↗
PubMed2003

Retention of sequential drug discriminations under fixed-interval schedules for long time periods without training.

The experiments showed that sequential drug discriminations can be learned and retained under a fixed-interval (FI) schedule for more than 18 months without additional training under a complex three-choice procedure. Pigeons were trained to discriminate among 5 mg/kg pentobarbital, 2 mg/kg D-amphetamine, and saline. After responding stabilized, dose-response curves were determined for other drugs. Subsequently, pentobarbital was replaced with 5 mg/kg morphine as a training drug, and D-amphetamine was replaced with 30 mg/kg caffeine. After the pigeons learned these new discriminations, dose-response curves were redetermined. Initially, chlordiazepoxide substituted for pentobarbital, cocaine substituted for D-amphetamine, and nicotine partially substituted for D-amphetamine. Morphine, Delta9-tetrahydrocannabinol, and caffeine did not substitute for either drug. After retraining with morphine and caffeine, responding occurred on the pentobarbital/morphine key after pentobarbital, chlordiazepoxide and morphine and on the D-amphetamine/caffeine key after D-amphetamine, cocaine and caffeine. After nicotine and Delta9-tetrahyrdocannabinol, responding occurred on the saline key. These data show that drug discriminations learned under fixed-interval schedules are retained for long time periods, even when discrimination training with other drugs occurs during the retention period.

Animals↗
PubMed2003

Characterization of four orthologs of stringent starvation protein A.

Orthologous proteins can be beneficial for X-ray crystallographic studies when a protein from an organism of choice fails to crystallize or the crystals are not suitable for structure determination. Their amino-acid sequences should be similar enough that they will share the same fold, but different enough so that they may crystallize under alternative conditions and diffract to higher resolution. This multi-species approach was employed to obtain diffraction-quality crystals of the RNA polymerase (RNAP) associated stringent starvation protein A (SspA). Although Escherichia coli SspA could be crystallized, the crystals failed to diffract well enough for structure determination. Therefore, SspA proteins from Yersinia pestis, Vibrio cholerae and Pseudomonas aeruginosa were cloned, expressed, purified and subjected to crystallization trials. The V. cholerae SspA protein failed to crystallize under any conditions tested and the P. aeruginosa SspA protein did not form crystals suitable for data collection. On the other hand, Y. pestis SspA crystallized readily and the crystals diffracted to 2.0 A.

Amino Acid Sequence↗
PubMed2003

Structural and enzymatic properties of the sedolisin family of serine-carboxyl peptidases.

Sedolisins (serine-carboxyl peptidases) are proteolytic enzymes whose fold resembles that of subtilisin; however, they are considerably larger, with the mature catalytic domains containing approximately 375 amino acids. The defining features of these enzymes are a unique catalytic triad, Ser-Glu-Asp, as well as the presence of an aspartic acid residue in the oxyanion hole. High-resolution crystal structures have now been solved for sedolisin from Pseudomonas sp. 101, as well as for kumamolisin from a thermophilic bacterium, Bacillus novo sp. MN-32. The availability of these crystal structures enabled us to model the structure of mammalian CLN2, an enzyme which, when mutated in humans, leads to a fatal neurodegenerative disease. This review compares the structural and enzymatic properties of this newly defined MEROPS family of peptidases, S53, and introduces their new nomenclature.

Amino Acid Sequence↗