Functional Unfolding of ��1-Antitrypsin Probed by Hydrogen-Deuterium Exchange Coupled with Mass Spectrometry

The native state of α₁-antitrypsin (α₁AT), a member of the serine protease inhibitor (serpin) family, is considered a kinetically trapped folding intermediate that converts to a more stable form upon complex formation with a target protease. Although previous structural and mutational studies of α₁AT revealed the structural basis of the native strain and the kinetic trap, the mechanism of how the native molecule overcomes the kinetic barrier to reach the final stable conformation during complex formation remains unknown. We hypothesized that during complex formation, a substantial portion of the molecule undergoes unfolding, which we dubbed functional unfolding. Hydrogen-deuterium exchange coupled with ESI-MS was used to analyze this serpin in three forms: native, complexing, and complexed with bovine β-trypsin. Comparing the deuterium content at the corresponding regions of these three samples, we probed the unfolding of α₁AT during complex formation. A substantial portion of the α₁AT molecule unfolded transiently during complex formation, including not only the regions expected from previous structural studies, such as the reactive site loop, helix F, and the following loop, but also regions not predicted previously, such as helix A, strand 6 of β-sheet B, and the N terminus. Such unfolding of the native interactions may elevate the free energy level of the kinetically trapped native serpin sufficiently to cross the transition state during complex formation. In the current study, we provide evidence that protein unfolding has to accompany functional execution of the protein molecule.The native strain of serine protease inhibitors (serpins)¹ is considered to be crucial to their biological functions, such as plasma protease inhibition (1, 2) and hormone delivery (3). Functional execution of serpins is accompanied by the conversion of the strained native structure into a more stable conformation (4). Because some of the strained native serpin structures are spontaneously converted into a more relaxed stable latent form under physiological conditions (5–7), the native structure is not the thermodynamically most stable conformation but is a kinetically trapped conformation. Upon binding a target protease, the scissile bond of the reactive site loop (RSL) is cleaved while the protease is covalently attached to the N-terminal part of the RSL (8, 9). During the conversion of the strained structure into the stable complex conformation (Fig. 1), RSL is inserted into the central β-sheet (A sheet) between strands 3 and 5 (s3A and s5A) to form strand 4 (s4A), and the covalently attached protease is concomitantly translocated to the opposite pole (10). Serpin inhibition occurs via a suicide substrate mechanism (4, 11, 12) in which serpins, upon binding proteases, partition between cleaved serpins and stable serpin-enzyme complexes.Open in a separate windowFig. 1.Structures of native α₁AT and α₁AT-trypsin complex. Left, structure of native α₁AT (Protein Data Bank code 1QLP) illustrated with secondary structural elements (1). Right, structure of α₁AT-trypsin complex (Protein Data Bank code 1EZX). The nine α-helices are colored dark gray, and the 16 β-strands are colored light gray.As a member of the serpin family, α₁-antitrypsin (α₁AT), which serves to modulate the activity of human leukocyte elastase in the lung, has been most extensively studied with regard to both structure and inhibition mechanism. Our previous studies with stabilizing mutations of α₁AT showed that the native strain is distributed throughout the molecule and that various unfavorable structural motifs, such as hydrophobic packing, cavity in the core, and surface hydrophobic patch, appear to maintain the native strain (13, 14). Indeed stabilizing mutations localized in the region of RSL insertion during complex formation affected the inhibitory function individually by retarding the loop insertion (15). Mutations in other regions did not affect the inhibitory function individually, but collectively these mutations affected the inhibitory function when the stabilization effect reached a certain threshold (16). Maintaining the kinetic trap appears to require sustaining RSL at the hydrophobic β-barrel composed of sheet B and sheet C (B/C β-barrel) because the conversion into the stable latent conformation occurs by destabilization of the B/C β-barrel (6) as well as by the extension of RSL length (17). Thus, upon binding a target protease, RSL cleavage appears to induce a conformational conversion, and the resultant strain throughout the molecule facilitates the opening of β-sheet A and the insertion of the RSL, which is critical for the inhibitory pathway as opposed to the substrate pathway (10).Although these structural and mutational studies revealed the structural basis for maintaining the kinetic trap and its relation to the inhibitory mechanism, several questions still remain. For example, what structural changes does the native serpin molecule undergo to overcome the kinetic barrier and reach the final stable conformation during the complex formation? In the present study, to probe the structural process of overcoming the kinetic barrier during complex formation with a target protease, amide hydrogen exchange (hydrogen-deuterium exchange (H/D-EX)) was explored during the conversion of the native α₁AT to the stable complex. H/D-EX coupled with ESI-MS is a powerful analytical tool for observing protein dynamics, transient conformational changes, and protein-protein interactions (18–22). These experiments demonstrated that transient structural unfolding occurred in many regions in the α₁AT molecule during formation of the complex with β-trypsin, and some of this unfolding was unpredicted from previous structural studies.     

Pseudomonas aeruginosa Eliminates Natural Killer Cells via Phagocytosis-Induced Apoptosis

Pseudomonas aeruginosa (PA) is an opportunistic pathogen that causes the relapse of illness in immunocompromised patients, leading to prolonged hospitalization, increased medical expense, and death. In this report, we show that PA invades natural killer (NK) cells and induces phagocytosis-induced cell death (PICD) of lymphocytes. In vivo tumor metastasis was augmented by PA infection, with a significant reduction in NK cell number. Adoptive transfer of NK cells mitigated PA-induced metastasis. Internalization of PA into NK cells was observed by transmission electron microscopy. In addition, PA invaded NK cells via phosphoinositide 3-kinase (PI3K) activation, and the phagocytic event led to caspase 9-dependent apoptosis of NK cells. PA-mediated NK cell apoptosis was dependent on activation of mitogen-activated protein (MAP) kinase and the generation of reactive oxygen species (ROS). These data suggest that the phagocytosis of PA by NK cells is a critical event that affects the relapse of diseases in immunocompromised patients, such as those with cancer, and provides important insights into the interactions between PA and NK cells.     

Ischemia–reperfusion alters cardiac lipoprotein lipase

Ischemia–reperfusion (I/R) is associated with changes in energy metabolism in the heart. However, the majority of studies have focused on examining rates and extent of fatty acid (FA) oxidation, with limited emphasis on FA delivery. We examined the influence of acute myocardial I/R on coronary lipoprotein lipase (LPL), the key enzyme responsible for triglyceride-lipoprotein hydrolysis and FA delivery to the heart. In a whole animal and an ex vivo model of I/R, we demonstrate increases in luminal LPL activity, an effect that involved signaling through nitric oxide. Given the damaging effect of excess FA utilization by the ischemic heart, strategies to restrict LPL at the vascular lumen would be an attractive therapeutic option in limiting I/R related cardiac injury.     

Cloning and endogenous expression of a Eucalyptus grandis UDP-glucose dehydrogenase cDNA

UDP-glucose dehydrogenase (UGDH) catalyzes the oxidation of UDP-glucose (UDP-Glc) to UDP-glucuronate (UDP-GlcA), a key sugar nucleotide involved in the biosynthesis of plant cell wall polysaccharides. A full-length cDNA fragment coding for UGDH was cloned from the cambial region of 6-month-old E. grandis saplings by RT-PCR. The 1443-bp-ORF encodes a protein of 480 amino acids with a predicted molecular weight of 53 kDa. The recombinant protein expressed in Escherichia coli catalyzed the conversion of UDP-Glc to UDP-GlcA, confirming that the cloned cDNA encodes UGDH. The deduced amino acid sequence of the cDNA showed a high degree of identity with UGDH from several plant species. The Southern blot assay indicated that more than one copy of UGDH is present in Eucalyptus. These results were also confirmed by the proteomic analysis of the cambial region of 3- and 22-year-old E. grandis trees by 2-DE and LC-MS/MS, showing that at least two isoforms are present. The cloned gene is mainly expressed in roots, stem and bark of 6-month-old saplings, with a lower expression in leaves. High expression levels were also observed in the cambial region of 3- and 22-year-old trees. The results described in this paper provide a further view of the hemicellulose biosynthesis during wood formation in E. grandis.     

A novel antiproliferative agent, phenylpyridineylbutenol, isolated from Streptomyces sp

A novel compound showing antiproliferative effect was isolated from Streptomyces sp. Its structure was determined based on the interpretation of the NMR spectra, and its conformation was elucidated using molecular modeling and 2D NOESY. It was determined to be (E)-4-phenyl-3-(pyridine-2-yl)but-2-en-1-ol.     

The development and validation of a charge-coupled device laser reflectance system to measure the complex cross-sectional shape and area of soft tissues

Determination of the stresses in soft tissues such as ligaments and tendons under uniaxial tension require accurate measurement of their cross-sectional area. Of the many methods available, there are concerns regarding contact methods which exert external loads and deform the cross-sectional shape of soft tissues. Hence, the area measurements are affected. On the other hand, non-contact methods have difficulties in dealing with complex shapes, especially with concavities. To address these problems, a new measurement system using a charge-coupled device (CCD) laser displacement sensor has been developed and tested. This system measures the complete surface profile of the object by rotating the laser 360° around the soft tissue. Then, the cross-sectional shape is reconstructed and the cross-sectional area determined via Simpson's rule. The system's accuracy was first verified with objects of various cross-sectional shapes and areas (cylinder: 23.1, 76.5, 510.3 mm²; cuboid: 34.3, 163.8, 316.7 mm², and cylinder with concavities: 121.4 mm²). The CCD laser reflectance system's accuracy was within 2.0% for these objects. To test biological application, the goat Achilles tendon and the anteromedial bundle of the porcine anterior cruciate ligament specimens were measured and compared to values obtained using another accepted technique, the laser micrometer system. The areas obtained using the CCD laser reflectance system were 4.4% and 9.7% lower than those obtained with the laser micrometer system respectively. These differences could be mainly attributed to concavities. Thus, the CCD laser reflectance system is an improved method for measuring the cross-sectional shape and area of soft tissues since it can detect and account for concavities without physically contacting the specimen.     

The effects of refreezing on the viscoelastic and tensile properties of ligaments

Biomechanical testing protocols for ligaments can be extensive and span two or more days. During this time, a specimen may have to undergo more than one cycle of freezing and thawing. Thus, the objective of this study was to evaluate the effects of refreezing on the viscoelastic and tensile properties of ligaments. The femur-medial collateral ligament-tibia complexes (FMTC) from six pairs of rabbit knees were used for this study. Following sacrifice, one leg in each pair was assigned to the fresh group and the FMTC was immediately dissected and prepared for testing. The contralateral knees were fresh-frozen at -20 degrees C for 3 weeks, thawed, dissected and then refrozen for one additional week before being tested as the refrozen group. The cross-sectional area and shape of the medial collateral ligament (MCL) was measured using a laser micrometer system. Stress relaxation and cyclic stress-relaxation tests in uniaxial tension were performed followed by a load to failure test. When the viscoelastic behavior of the MCL was described by the quasi-linear viscoelastic (QLV) theory, no statistically significant differences could be detected for the five constants (A, B, C, tau1, and tau2) between the fresh and refrozen groups (p > or = 0.07) based on our sample size. In addition, the structural properties of the FMTCs and the mechanical properties of the MCLs were also found to be similar between the two groups (p > or = 0.68). These results suggest that careful refreezing of the specimens had little or no effect on the biomechanical properties measured.