Understanding the specificity of serpin–protease complexes through interface analysis

Serpins such as antithrombin, heparin cofactor II, plasminogen activator inhibitor, antitrypsin, antichymotrypsin, and neuroserpin are involved in important biological processes by inhibiting specific serine proteases. Initially, the protease recognizes the mobile reactive loop of the serpin eliciting conformational changes, where the cleaved loop together with the protease inserts into β-sheet A, translocating the protease to the opposite side of inhibitor leading to its inactivation. Serpin interaction with proteases is governed mainly by the reactive center loop residues (RCL). However, in some inhibitory serpins, exosite residues apart from RCL have been shown to confer protease specificity. Further, this forms the basis of multi-specificity of some serpins, but the residues and their dimension at interface in serpin-protease complexes remain elusive. Here, we present a comprehensive structural analysis of the serpin-protease interfaces using bio COmplexes COntact MAPS (COCOMAPS), PRotein Interface Conservation and Energetics (PRICE), and ProFace programs. We have carried out interface, burial, and evolutionary analysis of different serpin-protease complexes. Among the studied complexes, non-inhibitory serpins exhibit larger interface region with greater number of residue involvement as compared to the inhibitory serpins. On comparing the multi-specific serpins (antithrombin and antitrypsin), a difference in the interface area and residue number was observed, suggestive of a differential mechanism of action of these serpins in regulating their different target proteases. Further, detailed study of these multi-specific serpins listed few essential residues (common in all the complexes) and certain specificity (unique to each complex) determining residues at their interfaces. Structural mapping of interface residues suggested that individual patches with evolutionary conserved residues in specific serpins determine their specificity towards a particular protease.     

Quantitative analysis of the bacteriophage Qβ infection cycle

In this study, the infection cycle of bacteriophage Qβ was investigated. Adsorption of bacteriophage Qβ to Escherichia coli is explained in terms of a collision reaction, the rate constant of which was estimated to be 4 × 10^− 10 ml/cells/min. In infected cells, approximately 130 molecules of β-subunit and 2 × 10⁵ molecules of coat protein were translated in 15 min. Replication of Qβ RNA proceeded in 2 steps—an exponential phase until 20 min and a non-exponential phase after 30 min. Prior to the burst of infected cells, phage RNAs and coat proteins accumulated in the cells at an average of up to 2300 molecules and 5 × 10⁵ molecules, respectively. An average of 90 infectious phage particles per infected cell was released during a single infection cycle up to 105 min.     

Different roles of TGF-β in the multi-lineage differentiation of stem cells

Stem cells are a population of cells that has infinite or long-term self-renewal ability and can produce various kinds of descendent cells.Transforming growth factor β(TGF-β) family is a superfamily of growth factors,including TGF-β1,TGF-β2 and TGF-β3,bone morphogenetic proteins,activin/inhibin,and some other cytokines such as nodal,which plays very important roles in regulating a wide variety of biological processes,such as cell growth,differentiation,cell death.TGF-β,a pleiotropic cytokine,has been proved to be differentially involved in the regulation of multi-lineage differentiation of stem cells,through the Smad pathway,non-Smad pathways including mitogen-activated protein kinase pathways,phosphatidylinositol-3-kinase/AKT pathways and Rholike GTPase signaling pathways,and their cross-talks.For instance,it is generally known that TGF-β promotes the differentiation of stem cells into smooth muscle cells,immature cardiomyocytes,chondrocytes,neurocytes,hepatic stellate cells,Th17 cells,and dendritic cells.However,TGF-β inhibits the differentiation of stem cells into myotubes,adipocytes,endothelial cells,and natural killer cells.Additionally,TGF-β can provide competence for early stages of osteoblastic differentiation,but at late stages TGF-β acts as an inhibitor.The three mammalian isoforms(TGF-β1,2 and 3) have distinct but overlapping effects on hematopoiesis.Understanding the mechanisms underlying the regulatory effect of TGF-β in the stem cell multi-lineage differentiation is of importance in stem cell biology,and will facilitate both basic research and clinical applications of stem cells.In this article,we discuss the current status and progress in our understanding of different mechanisms by which TGF-β controls multi-lineage differentiation of stem cells.     

Antibody array analysis of labelled proteomes: how should we control specificity?

Researchers who use protein binders in multiplexed assays can be divided into two camps. One believes that arrays with proteome-wide coverage will become a reality once we have developed binders for all proteins. The sceptics claim that detection with immobilized protein binders and sample labelling will not provide the required specificity. In this article, we review the evidence showing that antibody array analysis of labelled samples can provide meaningful data and discuss the issues raised by the sceptics. We argue that direct the evidence for monospecificity has yet to be published. This will require assays designed to resolve the proteins captured by each binder. One option is to combine array measurement with protein separation. We have developed an assay where labelled sample proteins are separated by size exclusion chromatography (SEC) before contact with microsphere-based arrays (Size-MAP; size exclusion chromatography-resolved microsphere-based affinity proteomics). The effect is an 'antibody array Western blot' where reactivity of immobilized binders is resolved against the size of the proteins in the sample. We show that Size-MAP is useful to discriminate monospecific- and polyreactive antibodies and for automatic detection of reacting with the same target. The possibility to test specificity directly in array-based measurement should be useful to select the best binders and to determine whether the DNA microarray for the proteome is a realistic goal or not.     

Reconciling the different roles of Gsk3β in “naïve” and “primed” pluripotent stem cells

Signaling pathways orchestrated by PI3K/Akt, Raf/Mek/Erk and Wnt/β-catenin are known to play key roles in the self-renewal and differentiation of pluripotent stem cells. The serine/threonine protein kinase Gsk3β has roles in all three pathways, making its exact function difficult to decipher. Consequently, conflicting reports have implicated Gsk3β in promoting self-renewal, while others suggest that it performs roles in the activation of differentiation pathways. Different thresholds of Gsk3β activity also have different biological effects on pluripotent cells, making this situation even more complex. Here, we describe a further level of complexity that is most apparent when comparing “naïve” murine and “primed” human pluripotent stem cells. In naïve cells, Gsk3β activity is restrained by PI3K/Akt, but when released from inhibitory signals it antagonizes self-renewal pathways by targeting pluripotency factors such as Myc and Nanog. This situation also applies in primed cells, but, in addition, a separate pool of Gsk3β is required to suppress canonical Wnt signaling. These observations suggest that different Gsk3β-protein complexes shift the balance between naïve and primed pluripotent cells and identify fundamental differences in their cell signaling. Altogether, these findings have important implications for the mechanisms underpinning the establishment of different pluripotent cell states and for the control of self-renewal and differentiation.     

Reconciling the different roles of Gsk3β in “na?ve” and “primed” pluripotent stem cells

Signaling pathways orchestrated by PI3K/Akt, Raf/Mek/Erk and Wnt/β-catenin are known to play key roles in the self-renewal and differentiation of pluripotent stem cells. The serine/threonine protein kinase Gsk3β has roles in all three pathways, making its exact function difficult to decipher. Consequently, conflicting reports have implicated Gsk3β in promoting self-renewal, while others suggest that it performs roles in the activation of differentiation pathways. Different thresholds of Gsk3β activity also have different biological effects on pluripotent cells, making this situation even more complex. Here, we describe a further level of complexity that is most apparent when comparing “naïve” murine and “primed” human pluripotent stem cells. In naïve cells, Gsk3β activity is restrained by PI3K/Akt, but when released from inhibitory signals it antagonizes self-renewal pathways by targeting pluripotency factors such as Myc and Nanog. This situation also applies in primed cells, but, in addition, a separate pool of Gsk3β is required to suppress canonical Wnt signaling. These observations suggest that different Gsk3β-protein complexes shift the balance between naïve and primed pluripotent cells and identify fundamental differences in their cell signaling. Altogether, these findings have important implications for the mechanisms underpinning the establishment of different pluripotent cell states and for the control of self-renewal and differentiation.     

Breast cancer cells attract the migration of adipose tissue-derived stem cells via the PDGF-BB/PDGFR-β signaling pathway

The origin of vascular cells in tumors is unknown, but it is believed that tumors use cells from the host to build new vessels. To determine whether adipose tissue stem cells (ASCs) could be attracted by cancer cells, we performed migration assays in which ASCs were seeded on a transwell migration system top chamber and tumor-conditioned medium was placed in the bottom chamber. Our data showed that a significant number of ASCs migrated toward the tumor-conditioned medium (p < 0.0001), and migration of human ASCs significantly (p < 0.0001) increased in response to increased concentrations of recombinant PDGF-BB. In addition, neutralizing antibodies to PDGF receptor (PDGFR)-β decreased migration of ASCs toward a breast cancer-conditioned medium to the level of serum-free control. These data suggest that tumor cell-derived PDGF-BB is an important factor in governing the microenvironment interaction between tumor cells and local tissue-resident stem cells.     

Enzyme specificity: “pseudopolymorphism” of lactate dehydrogenase in Drosophila melanogaster

An electrophoretic variant in the LDH (l-lactate:NAD oxidoreductase, E.C.1.1.1.27) of Drosophila melanogaster was observed on starch (or polyacrylamide) gels. This variant was found to exhibit an identical isozymic pattern (three isozymes with a decreasing staining density) on starch gel and map position as the Adh locus. On the other hand, anodal polyacrylamide gel electrophoresis in crude extracts has shown LDH to consist of nine bands and ADH of four bands. We have shown that ADH (Alcohol:NAD oxidoreductase, E.C.1.1.1.1) also oxidizes l(+)-lactate or d(–)-lactate with the NAD, while LDH oxidizes ethanol. By using various genetic and biochemical techniques, we have shown that the observed Ldh electrophoretic variant was not a real one and could be attributed to the presence of ADH. We have called this phenomenon pseudopolymorphism, and the problem of enzyme specificity has been examined. The appearance of a band in an assay using lactic acid as a substrate is not sufficient evidence for the presence of LDH. Hence, caution is called for before characterizing an electrophoretic band on a gel as being equivalent to the presence of a genetic locus. Out of the nine electrophoretic zones of activity observed on polyacrylamide gel (or out of the six previously observed) using crude extract, only two (one major and one minor) belong to LDH, as revealed by purified enzyme preparations. Furthermore, purified LDH exhibits activity in two bands on starch gel (out of three observed in crude extracts), which appear in different positions as compared with those of ADH. Finally, one band which responds to the presence of d(–)-lactate but not to l(+)-lactate has been revealed.     

Mutations in the gene for the E1β subunit: a novel cause of pyruvate dehydrogenase deficiency

We describe two unrelated patients with pyruvate dehydrogenase (PDH) deficiency attributable to mutations in the gene encoding the E1 subunit of the complex. This is a previously unrecognised form of PDH deficiency, which most commonly results from mutations in the X-linked gene for the E1 subunit. Both patients had reduced immunoreactive E1 protein and both had missense mutations in the E1 gene. Activity of the PDH complex was restored in cultured fibroblasts from both patients by transfection and expression of the normal E1 coding sequence.     

A morphometric analysis of the subcellular distribution of LHβ and FSHβ in secretory granules in the pituitary gonadotrophs of the frog (Rana japonica)

Immunohistochemical localization of lutropin (LH) and follitropin (FSH) in the pituitary gland of the frog Rana japonica was studied by the peroxidase-anti-peroxidase method and the two-face, double-labeling method with different-sized gold particles at the light-and electron-microscopic levels, respectively, using monoclonal antibodies against bullfrog LH and FSH. Light-microscopic immunohistochemistry indicated that approximately 66.0% of all the gonadotrophs in the pituitary contained both LH and FSH, whereas 33.4% of gonadotrophs contained only LH, and 0.6% contained only FSH. The staining intensity of LH and FSH varied from cell to cell. The gonadotrophs were classified into four types (Types I–IV) in terms of their ultrastructural and immunolabeling characteristics. Moreover, several secretory granule types were recognized according to differences in their shape and electron density. In all the cell types, both LH and FSH were often seen in the same secretory granules, but the proportion of granules bearing both hormones ranged from 5.5% in Type I to 32.7% in Type IV. Most secretory granules in Types I and II were immunolabeled with LH alone, whereas a small number of granules were immunolabeled with FSH alone. More immunolabeled FSH granules were present in Types III and IV than in Types I and II.     

Soluble aggregates of the amyloid-β peptide are trapped by serum albumin to enhance amyloid-β activation of endothelial cells

Background  

Self-assembly of the amyloid-β peptide (Aβ) has been implicated in the pathogenesis of Alzheimer's disease (AD). As a result, synthetic molecules capable of inhibiting Aβ self-assembly could serve as therapeutic agents and endogenous molecules that modulate Aβ self-assembly may influence disease progression. However, increasing evidence implicating a principal pathogenic role for small soluble Aβ aggregates warns that inhibition at intermediate stages of Aβ self-assembly may prove detrimental. Here, we explore the inhibition of Aβ_1–40 self-assembly by serum albumin, the most abundant plasma protein, and the influence of this inhibition on Aβ_1–40 activation of endothelial cells for monocyte adhesion.     

In vivo activation of autoreactive cytotoxic T lymphocytes after bone marrow transplantation: evidence for the prethymic specificity of T cells?

The light density fraction (A + B, i.e., remaining above the 26% concentration in the discontinuous BSA gradient) of BCF1 (H-2b X H-2k) mouse bone marrow contains cells that after injection into irradiated syngeneic recipients give rise to autoreactive Lyt-2+, Thy-1+ CTL. After injection of unfractionated bone marrow cells, the levels of these CTL were low or undetectable, suggesting that either the precursors were highly enriched in the A + B fraction or that bone marrow cells with higher density have a suppressive function. The specificity of the killing was not directed toward all the available class I MHC antigens: only targets carrying H-2Kb-coded determinants were killed. There was no overlapping between the autoreactive and alloreactive precursors: cells from the A + B fraction could not respond to an alloantigen in vitro, not even in the presence of an interleukin 2-containing supernatant, and the autoreactive CTL activated in vivo could not kill allogeneic targets. The induction of the autoreactive CTL did not require the presence of the appropriate MHC antigen in the maturation environment, thus differing from the activation of mature T cells. The observed CTL specificity, together with the previous findings showing that prethymic T cells are locating in the same BSA fraction as the precursors for these autoreactive cells, support the idea that the prethymic T cell repertoire is, at least partially, directed to recognize self-MHC antigens.     

Is the “soluble” phase of cells structured?

Evidence suggesting that small molecular-weight precursors as well as polymers such as proteins and RNA, are not homogeneously distributed in the "soluble" phase of the cell, and that there may be, on one hand, hitherto unidentified barriers to normal diffusion within the cell and, on the other, channels through which certain molecular species may move in the cell sap much faster than their diffusion coefficients will permit, is discussed. Some implications of such barriers and channels, if they exist, are stated.     

The specificity of monoglyceride–protein interactions and mechanism of the protein induced Lβ to coagel phase transition

This study aims at gaining insight into the specificity and molecular mechanism of monoglyceride–protein interactions. We used β-lactoglobulin (β-LG) and lysozyme as model proteins and both monostearoylglycerol and monopalmitoylglycerol as defined gel phase monoglycerides. The monoglycerides were used in different combinations with the two negatively charged amphiphiles dicetylphosphate and distearylphosphate. The interactions were characterized using the monolayer technique, isothermal titration calorimetry, ²H-nuclear magnetic resonance (NMR) using deuterium labelled monoglycerides and freeze fracture electron microscopy (EM). Our results show that lysozyme inserts efficiently into all monolayers tested, including pure monoglyceride layers. The insertion of β-LG depends on the lipid composition of the monolayer and is promoted when the acylchains of the negatively charged amphiphile are shorter than that of the monoglyceride. The binding parameters found for the interaction of β-LG and lysozyme with monoglyceride bilayers were generally similar. Moreover, in all cases a large exothermic binding enthalpy was observed which was found to depend on the nature of the monoglycerides but not of the proteins. ²H-NMR and freeze fracture EM showed that this large enthalpy results from a protein mediated catalysis of the monoglyceride L_β to coagel phase transition. The mechanism of this phase transition consists of two steps, an initial protein mediated vesicle aggregation step which is followed by stacking and probably fusion of the bilayers.