COPD患者口腔和呼吸道内牙龈卟啉单胞菌、齿垢密螺旋体和福赛坦菌的同源性分析

目的分析慢性阻塞性肺疾病(COPD)患者口腔和呼吸道内牙龈卟啉单胞菌(Pg)、齿垢密螺旋体(Td)和福赛坦菌(Tf)的同源性,探讨牙周炎与COPD之间的关系。方法收集53例急性加重期COPD患者,采集龈下菌斑及呼吸道分泌物,同时进行牙周指标的检查。通过16S r DNA序列分析,构建患者口腔及呼吸道内Pg、Td和Tf的系统进化树,进行同源性分析。结果 53例患者中,5例患者口腔和呼吸道内Pg具有同源性,6例患者Td具有同源性,3例患者Tf具有同源性。结论 COPD患者口腔和呼吸道内Pg、Td和Tf具有同源性,COPD患者呼吸道内的这3种病原体均来自于口腔。     

Miropin,a Novel Bacterial Serpin from the Periodontopathogen Tannerella forsythia,Inhibits a Broad Range of Proteases by Using Different Peptide Bonds within the Reactive Center Loop

All prokaryotic genes encoding putative serpins identified to date are found in environmental and commensal microorganisms, and only very few prokaryotic serpins have been investigated from a mechanistic standpoint. Herein, we characterized a novel serpin (miropin) from the human pathogen Tannerella forsythia, a bacterium implicated in initiation and progression of human periodontitis. In contrast to other serpins, miropin efficiently inhibited a broad range of proteases (neutrophil and pancreatic elastases, cathepsin G, subtilisin, and trypsin) with a stoichiometry of inhibition of around 3 and second-order association rate constants that ranged from 2.7 × 10⁴ (cathepsin G) to 7.1 × 10⁵ m⁻¹s⁻¹ (subtilisin). Inhibition was associated with the formation of complexes that were stable during SDS-PAGE. The unusually broad specificity of miropin for target proteases is achieved through different active sites within the reactive center loop upstream of the P1-P1′ site, which was predicted from an alignment of the primary structure of miropin with those of well studied human and prokaryotic serpins. Thus, miropin is unique among inhibitory serpins, and it has apparently evolved the ability to inhibit a multitude of proteases at the expense of a high stoichiometry of inhibition and a low association rate constant. These characteristics suggest that miropin arose as an adaptation to the highly proteolytic environment of subgingival plaque, which is exposed continually to an array of host proteases in the inflammatory exudate. In such an environment, miropin may function as an important virulence factor by protecting bacterium from the destructive activity of neutrophil serine proteases. Alternatively, it may act as a housekeeping protein that regulates the activity of endogenous T. forsythia serine proteases.     

一株产碱性蛋白酶菌株的筛选鉴定及酶学特性研究

【目的】从丝茅草中筛选得到产蛋白酶菌株并研究驯化过程中微生物群落结构,以及探究该菌株的生长特性和蛋白酶的酶学特性。【方法】通过高通量测序探究来源于丝茅草的菌株在不同培养条件下细菌种类及丰度,通过选择性培养基来筛选能够分解酪素并产生蛋白酶的菌株,通过单因素试验方法确定环境因子对菌株生长和蛋白酶活性的影响。【结果】微生物群落结构在基础培养基和牛肉膏蛋白胨培养基中不同。通过含酪素的选择性培养基里筛选到1株产蛋白酶菌株H-16,经生理生化试验和16S r DNA鉴定知该菌株属于Escherichia marmotae,菌株H-16能产生分子量为70 k Da左右的单亚基蛋白酶。胰蛋白胨、蔗糖、30°C或35°C、p H 7分别为菌株生长的最适氮源、碳源、温度和p H。菌株H-16分泌的蛋白酶最适p H为6–8,在50°C及6%盐度以下酶活性几乎不受影响。此外,Cu(II)和Ag(I)等金属离子能够抑制蛋白酶的活性。【结论】该菌株H-16为嗜中温菌株,能够产生碱性蛋白酶。     

Degradation of immunoglobulins,protease inhibitors and interleukin-1 by a secretory proteinase of Acanthamoeba castellanii

The effect of a secretory proteinase from the pathogenic amoebae Acanthamoeba castellanii on host's defense-oriented or regulatory proteins such as immunoglobulins, interleukin-1, and protease inhibitors was investigated. The enzyme was found to degrade secretory immunoglobulin A (sIgA), IgG, and IgM. It also degraded interleukin-1 alpha (IL-1 alpha) and IL-1 beta. Its activity was not inhibited by endogenous protease inhibitors, such as alpha 2-macroglobulin, alpha 1-trypsin inhibitor, and alpha 2-antiplasmin. Furthermore, the enzyme rapidly degraded those endogenous protease inhibitors as well. The degradation of host's defense-oriented or regulatory proteins by the Acanthamoeba proteinase suggested that the enzyme might be an important virulence factor in the pathogenesis of Acanthamoeba infection.     

Crystal structure of a cross-reaction complex between an anti-HIV-1 protease antibody and an HIV-2 protease peptide

The monoclonal antibody 1696, elicited by HIV-1 protease, inhibits the activity of both HIV-1 and HIV-2 proteases with inhibition constants in the low nanomolar range. The antibody cross-reacts with peptides derived from the N-terminal region of both proteases. The crystal structure of the recombinant single-chain Fv fragment of 1696 complexed with an N-terminal peptide from the HIV-2 protease has been determined at 1.88A resolution. Interactions of the peptide with scFv1696 are compared with the previously reported structure of scFv1696 in complex with the corresponding peptide from HIV-1 protease. The origin of cross-reactivity of mAb1696 with HIV proteases is discussed.     

Design,synthesis and evaluation of 2,2-dimethyl-1,3-dioxolane derivatives as human rhinovirus 3C protease inhibitors

The human rhinovirus (HRV) is the most significant cause of the common cold all over the world. The maturation and replication of this virus entirely depend on the activity of a virus-encoded 3C protease. Due to the high conservation among different serotypes and the minimal homology existing between 3C protease and known mammalian enzymes, 3C protease has been regarded as an attractive target for the treatment of HRV infections. In this study, we identified a novel (4R,5R)-N⁴-(2-((3-methoxyphenyl)amino)ethyl)-2,2-dimethyl-N⁵-(naphthalen-2-yl)-1,3-dioxolane-4,5-dicarboxamide (7a) to be a HRV 3C protease inhibitor via virtual screening. Further research has been focused on the design, synthesis and in vitro biological evaluation of 7a derivatives. The studies revealed that compound 7d has an IC₅₀ value of 2.50 ± 0.7 µM against HRV 3C protease, and it thus could serve as a promising compound for the development of novel anti-rhinoviral medicines.     

Virtual screening-driven identification of human carbonic anhydrase inhibitors incorporating an original, new pharmacophore

Combinated ligand- and pharmacophore-based virtual screening approaches were used to discover novel potential pharmacophores acting as carbonic anhydrase (CA, EC 4.2.1.1) inhibitors (CAIs). A free database of commercially available compounds was screened through drug-like filters using a four-point pharmacophore, and followed by docking calculation within the active site of an X-ray structure of isoform CA II. One compound, bearing a trifluoro-dihydroxy-propanone moiety, showed an interesting, selective inhibitory activity in low micromolar range against this isoform versus CA I. The chemical originality of this new pharmacophore can represent an important bioisosteric alternative to the sulfonamido-based functionalities, thus leading to the development of a new class of CAIs.     

Kinetic analysis of enhanced thermal stability of an alkaline protease with engineered twin disulfide bridges and calcium-dependent stability

The thermal stability of a cysteine-free alkaline protease (Alp) secreted by the eukaryote Aspergillus oryzae was improved both by the introduction of engineered twin disulfide bridges (Cys-69/Cys-101 and Cys-169/Cys-200), newly constructed as part of this study, and by the addition of calcium ions. We performed an extensive kinetic analysis of the increased thermal stability of the mutants as well as the role of calcium dependence. The thermodynamic activation parameters for irreversible thermal inactivation, the activation free energy (deltaG), the activation enthalpy (deltaH), and the activation entropy (deltaS) were determined from absolute reaction rate theory. The values of deltaH and deltaS were significantly and concomitantly increased as a result of introducing the twin disulfide bridges, for which the increase in the value of deltaH outweighed that of deltaS, resulting in significant increases in the value of deltaG. The enhancement of the thermal stability obtained by introducing the twin disulfide bridges is an example of the so-called low-temperature stabilization of enzymes. The stabilizing effect of calcium ions on wild-type Alp is similar to the results we obtained by introducing the engineered twin disulfide bridges.     

Thermodynamic dissection of the binding energetics of KNI-272, a potent HIV-1 protease inhibitor

KNI-272 is a powerful HIV-1 protease inhibitor with a reported inhibition constant in the picomolar range. In this paper, a complete experimental dissection of the thermodynamic forces that define the binding affinity of this inhibitor to the wild-type and drug-resistant mutant V82F/184V is presented. Unlike other protease inhibitors, KNI-272 binds to the protease with a favorable binding enthalpy. The origin of the favorable binding enthalpy has been traced to the coupling of the binding reaction to the burial of six water molecules. These bound water molecules, previously identified by NMR studies, optimize the atomic packing at the inhibitor/protein interface enhancing van der Waals and other favorable interactions. These interactions offset the unfavorable enthalpy usually associated with the binding of hydrophobic molecules. The association constant to the drug resistant mutant is 100-500 times weaker. The decrease in binding affinity corresponds to an increase in the Gibbs energy of binding of 3-3.5 kcal/mol, which originates from less favorable enthalpy (1.7 kcal/mol more positive) and entropy changes. Calorimetric binding experiments performed as a function of pH and utilizing buffers with different ionization enthalpies have permitted the dissection of proton linkage effects. According to these experiments, the binding of the inhibitor is linked to the protonation/deprotonation of two groups. In the uncomplexed form these groups have pKs of 6.0 and 4.8, and become 6.6 and 2.9 in the complex. These groups have been identified as one of the aspartates in the catalytic aspartyl dyad in the protease and the isoquinoline nitrogen in the inhibitor molecule. The binding affinity is maximal between pH 5 and pH 6. At those pH values the affinity is close to 6 x 10(10) M(-1) (Kd = 16 pM). Global analysis of the data yield a buffer- and pH-independent binding enthalpy of -6.3 kcal/mol. Under conditions in which the exchange of protons is zero, the Gibbs energy of binding is -14.7 kcal/mol from which a binding entropy of 28 cal/K mol is obtained. Thus, the binding of KNI-272 is both enthalpically and entropically favorable. The structure-based thermodynamic analysis indicates that the allophenylnorstatine nucleus of KNI-272 provides an important scaffold for the design of inhibitors that are less susceptible to resistant mutations.     

Demonstration of a relationship between talin and P235, a major substrate of the calcium-dependent protease in platelets

Talin is a 225,000-Dalton protein we have purified from smooth muscle. In chick embryo fibroblasts talin is found in adhesion plaques (focal contacts), areas where the cell is closely apposed to the substratum. In comparison with other cytoskeletal proteins, we found talin to be unusually susceptible to proteolysis and have identified a 190,000-Dalton proteolytic fragment of talin in the immunoblots of many tissues. These observations raised the possibility that the cleavage of talin to this fragment has physiological relevance. One system that we have investigated in which significant proteolysis occurs is platelets. During platelet activation several high-molecular-weight proteins are cleaved to lower-molecular-weight forms. Here we demonstrate that talin is closely related to one of these platelet high-molecular-weight proteins, P235. The purification of talin is comparable to that developed for P235, and the two proteins have similar biophysical properties. In addition, antibodies raised against chicken gizzard talin recognize P235 in purified form as well as in crude platelet extracts. The platelet protein also resembles smooth-muscle talin in its susceptibility to endogenous proteolysis: P235 is rapidly cleaved to a 190-200 kD polypeptide by a calcium-activated protease found in platelet extracts. Moreover, partial proteolysis of P235 and talin with chymotrypsin, elastase, or trypsin also generates remarkably similar one-dimensional peptide maps. Because of their similar biophysical properties, immunological crossreactivity, and similar one-dimensional partial peptide maps, we conclude that P235 is the platelet form of talin.     

β-Propeller repeats and a PDZ domain in the tricorn protease: predicted self-compartmentalisation and C-terminal polypeptide-binding strategies of substrate selection

Prokaryotic proteases demonstrate a variety of substrate-selection strategies that prevent uncontrolled protein degradation. Proteasomes and ClpXP-like proteases form oligomeric structures that exclude large substrates from central solvated chambers containing their active sites. Monomeric prolyl oligopeptidases have been shown to contain beta-propeller structures that similarly reduce access to their catalytic residues. By contrast, Tsp-like enzymes contain PDZ domains that are thought to specifically target C-terminal polypeptides. We have investigated the sequence of Thermoplasma acidophilum tricorn protease using recently-developed database search methods. The tricorn protease is known to associate into a 20 hexamer capsid enclosing an extremely large cavity that is 37 nm in diameter. It is unknown, however, how this enzyme selects its small oligopeptide substrates. Our results demonstrate the presence in tricorn protease of a PDZ domain and two predicted six-bladed beta-propeller domains. We suggest that the PDZ domain is involved in targeting non-polar C-terminal peptides, similar to those generated by the T. acidophilum proteasome, whereas the beta-propeller domains serve to exclude large substrates from the tricorn protease active site in a similar manner to that previously indicated for prolyl oligopeptidase.     

Purification and characterization of a digestive alkaline protease from the larvae of Spilosoma obliqua

A digestive protease from Spilosoma obliqua (Lepidoptera: Arctiidae) fifth instar larval guts was purified and characterized. The protease was purified using ammonium sulfate fractionation, ion-exchange chromatography, and hemoglobin-sepharose affinity chromatography. The purification procedure resulted in a 37-fold increase in the specific activity of the protease. Protease thus obtained was found to be electrophoretically pure under native and denaturing conditions. The purified protease had a molecular mass of 90 kDa as determined by gel filtration, and a pH optimum of 11.0. The purified protease optimally hydrolyzed casein at 50 degrees C. A Km of 2 x10(-6) M was obtained using BApNA as a substrate for the purified alkaline protease. The ability of S. obliqua protease and bovine trypsin to hydrolyze various synthetic substrates (BApNA, BAEE, and BAME), and the inhibition patterns of S. obliqua and bovine trypsin with "classical" trypsin inhibitors are also reported.     

Determination of L-756 423, a novel HIV protease inhibitor, in human plasma and urine using high-performance liquid chromatography with fluorescence detection

A method for the determination of L-756 423, a novel HIV protease inhibitor, in human plasma and urine is described. Plasma and urine samples were extracted using 3M Empore extraction disk cartridges in the C₁₈ and MPC (mixed-phase cation-exchange) formats, respectively. The extract was analyzed using HPLC with fluorescence detection (ex 248 nm, em 300 nm), and included a column switching procedure to reduce run-time. The assay was linear in the concentration range 5 to 1000 ng/ml when 1-ml aliquots of plasma and urine were extracted. Recoveries of L-756 423 were greater than 84% over the calibration curve range using the described sample preparation procedures. Intra-day precision and accuracy for this assay was less than 9% RSD and within 7%, respectively. Inter-day variabilities for the plasma (n=17) and urine (n=10) were less than 5% and 3% for low (15 ng/ml) and high (750 ng/ml) quality control samples. Bovine serum albumin (0.5%) was used as an additive to urine to prevent precipitation of L-756 423 during the storage of clinical samples. The assay was used in support of human clinical trials.     

Purification and characterization of a thermostable, haloalkaliphilic extracellular serine protease from the extreme halophilic archaeon Halogeometricum borinquense strain TSS101

A novel haloalkaliphilic, thermostable serine protease was purified from the extreme halophilic archaeon, Halogeometricum borinquense strain TSS101. The protease was isolated from a stationary phase culture, purified 116-fold with 18% yield and characterized biochemically. The molecular mass of the purified enzyme was estimated to be 86 kDa. The enzyme showed the highest activity at 60 degrees C and pH 10.0 in 20% NaCl. The enzyme had high activity over the pH range from 6.0 to 10.0. Enzymatic activity was strongly inhibited by 1 mM phenyl methylsulfonyl fluoride, but activity was increased 59% by 0.1% cetyltrimethylammonium bromide. The enzyme exhibited relatively high thermal stability, retaining 80% of its activity after 1 h at 90 degrees C. Thermostability increased in the presence of Ca2+. The stability of the enzyme was maintained in 10% sucrose and in the absence of NaCl.     

Chlamydia trachomatis and Chlamydophila abortus induce the expression of secretory leukocyte protease inhibitor in cells of the human female reproductive tract

C. trachomatis and C. abortus are related Gram‐negative intracellular bacteria that cause reproductive failure due to infertility (C. trachomatis) or abortion (C. abortus). These organisms target epithelial cells in the reproductive tract and/or placenta, but the innate immune mechanisms that lead to protection or pathology and disease are poorly understood. SLPI is an innate immune molecule which protects mucosal surfaces from infection and injury. C. trachomatis and C. abortus were found to induce SLPI mRNA and peptide expression in HeLa (cervical epithelium) and JEG‐3 cells (trophoblast) respectively. Both cell lines constitutively expressed SLPI and, although infection enhanced this expression, killed organisms did not. These data demonstrate that Chlamydia/Chlamydophila grow in cells that express SLPI, suggesting that SLPI does not exert antimicrobial effects against these organisms. However, SLPI has multiple functions, and we speculate that it may play a role in controlling tissue inflammation and pathology.     

The inhibitory effects of the cysteine protease inhibitor, oryzacystatin, on digestive proteases and on larval survival and development of the southern corn rootworm (Diabrotica undecimpunctata howardi)

At least eight proteolytic activities have been identified in the midgut contents of larval Southern corn rootworm (Diabrotica undecimpunctata howardi). Around 70% of protease activity could be arrested by the cysteine protease inhibitors E-64 and chicken egg-white cystatin, while the aspartic acid protease inhibitor pepstatin caused 30% inhibition. The cysteine protease activity was found to be highly sensitive to inhibition by both chicken egg-white cystatin and the rice cystatin, oryzacystatin I. Oryzacystatin I, expressed as a fully functional fusion protein in E. coli, was found to strongly inhibit larval gut protease activity. This recombinant oryzacystatin, incorporated into artificial diet at concentrations of 10 mM and above, caused significant decreases in larval survival and weight gain. E-64 was also shown to cause a significant antimetabolic in vivo effect. These results demonstrate the great potential for cysteine protease inhibitors, such as oryzacystatin, as tools for exploitation in the control of the Southern corn rootworm.     

Purification and stability characteristics of an alkaline serine protease from a newly isolated Haloalkaliphilic bacterium sp. AH-6

An alkaline protease secreting Haloalkaliphilic bacterium (Gene bank accession number EU118361) was isolated from the Saurashtra Coast in Western India. The alkaline protease was purified by a single step chromatography on phenyl sepharose 6 FF with 28% yield. The molecular mass was 40 kDa as judged by SDS-PAGE. The enzyme displayed catalysis and stability over pH 8–13, optimally at 9–11. It was stable with 0–4 M NaCl and required 150 mM NaCl for optimum catalysis at 37 °C; however, the salt requirement for optimal catalysis increased with temperature. While crude enzyme was active at 25–80 °C (optimum at 50 °C), the purified enzyme had temperature optimum at 37 °C, which shifted to 80 °C in the presence of 2 M NaCl. The NaCl not only shifted the temperature profile but also enhanced the substrate affinity of the enzyme as reflected by the increase in the catalytic constant (K _cat). The enzyme was also calcium dependent and with 2 mM Ca⁺², the activity reached to maximum at 50 °C. The crude enzyme was highly thermostable (37–90 °C); however, the purified enzyme lost its stability above 50 °C and its half life was enhanced by 30 and sevenfold at 60 °C with 1 M NaCl and 50 mM Ca⁺², respectively. The activity of the enzyme was inhibited by PMSF, indicating its serine type. While the activity was slightly enhanced by Tween-80 (0.2%) and Triton X-100 (0.05%), it marginally decreased with SDS. In addition, the enzyme was highly stable with oxidizing-reducing agents and commercial detergents and was affected by metal ions to varying extent. The study assumes significance due to the enzyme stability under the dual extremities of pH and salt coupled with moderate thermal tolerance. Besides, the facts emerged on the enzyme stability would add to the limited information on this enzyme from Haloalkaliphilic bacteria.     

The role of calcium ions in the stability and instability of a thermolysin-like protease

Thermolysin and other secreted broad-specificity proteases, such as subtilisin or alpha-lytic protease, are produced as pre-pro-proteins that stay at least partially unfolded while in the cytosol. After secretion, the pro-proteases fold to their active conformations in a process that includes the autolytic removal of the pro-peptide. We review the life cycle of the thermolysin-like protease from Bacillus stearothermophilus in light of the calcium dependent stability and instability of the N-terminal domain. The protease binds calcium ions in the regions that are involved in the autolytic maturation process. It is generally assumed that the calcium ions contribute to the extreme stability of the protease, but experimental evidence for TLP-ste indicates that at least one of the calcium ions plays a regulatory role. We hypothesize that this calcium ion plays an important role as a switch that modulates the protease between stable and unstable states as appropriate to the biological need.     

Foot and mouth disease leader protease (Lbpro): Investigation of prime side specificity allows the synthesis of a potent inhibitor

Foot and mouth disease virus expresses its genetic information as a single polyprotein that is translated from the single-stranded RNA genome. Proteinases contained within the polyprotein then generate the mature viral proteins. The leader protease (Lb^pro) performs the initial cleavage by freeing itself from the growing polypeptide chain; subsequently, Lb^pro cleaves the two homologues of the host cell protein eukaryotic initiation factor 4G (eIF4G). We showed that Lb^pro possesses specific binding sites at the non prime side from S₁ down to S₇ [Santos et al. (2009) Biochemistry, 48, 7948–7958]. Here, we demonstrate that Lb^pro has high prime side specificity at least down to the S′₅ site. Lb^pro is thus not only one of the smallest papain-like cysteine peptidases but also one of the most specific. It can still however cleave between both K↓G and G↓R pairs. We further determined the two-step irreversible inhibition (E + I ↔ EI→ E − I) kinetic parameters of two known irreversible epoxide-based inhibitors of cysteine proteinases, E64 and CA074 on Lb^pro that show for the reversible step (E + I ↔ EI) K_i = 3.4 μM and 11.6 μM, and for the irreversible step (EI→E−I) k₄ = 0.16 and 0.06 min⁻¹, respectively. Knowledge of the Lb^pro specificity led us to extend E64 by addition of the dipeptide R–P. This compound, termed E64-R-P-NH₂, irreversibly inhibited Lb^pro with a K_i = 30 nM and k₄ = 0.01 min⁻¹ and can serve as the basis for design of specific inhibitors of FMDV replication.