Crown Domain Research Articles

Engineering the ADDobody protein scaffold for generation of high-avidity ADDomer super-binders

Adenovirus-derived nanoparticles (ADDomer) comprise 60 copies of adenovirus penton base protein (PBP). ADDomer is thermostable, rendering the storage, transport, and deployment of ADDomer-based therapeutics independent of a cold chain. To expand the scope of ADDomers for new applications, we engineered ADDobodies, representing PBP crown domain, genetically separated from PBP multimerization domain. We inserted heterologous sequences into hyper-variable loops, resulting in monomeric, thermostable ADDobodies expressed at high yields in Escherichia coli. The X-ray structure of an ADDobody prototype validated our design. ADDobodies can be used in ribosome display experiments to select a specific binder against a target, with an enrichment factor of ∼104-fold per round. ADDobodies can be re-converted into ADDomers by genetically reconnecting the selected ADDobody with the PBP multimerization domain from a different species, giving rise to a multivalent nanoparticle, called Chimera, confirmed by a 2.2Å electron cryo-microscopy structure. Chimera comprises 60 binding sites, resulting in ultra-high, picomolar avidity to the target.

Modular geodesics and wedge domains in non-compactly causal symmetric spaces

We continue our investigation of the interplay between causal structures on symmetric spaces and geometric aspects of Algebraic Quantum Field Theory. We adopt the perspective that the geometric implementation of the modular group is given by the flow generated by an Euler element of the Lie algebra (an element defining a 3-grading). Since any Euler element of a semisimple Lie algebra specifies a canonical non-compactly causal symmetric space M=G/H\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$M = G/H$$\\end{document}, we turn in this paper to the geometry of this flow. Our main results concern the positivity region W of the flow (the corresponding wedge region): If G has trivial center, then W is connected, it coincides with the so-called observer domain, specified by a trajectory of the modular flow which at the same time is a causal geodesic. It can also be characterized in terms of a geometric KMS condition, and it has a natural structure of an equivariant fiber bundle over a Riemannian symmetric space that exhibits it as a real form of the crown domain of G/K. Among the tools that we need for these results are two observations of independent interest: a polar decomposition of the positivity domain and a convexity theorem for G-translates of open H-orbits in the minimal flag manifold specified by the 3-grading.

Cryo-electron microscopy structures of capsids and in situ portals of DNA-devoid capsids of human cytomegalovirus

The portal-scaffold complex is believed to nucleate the assembly of herpesvirus procapsids. During capsid maturation, two events occur: scaffold expulsion and DNA incorporation. The portal-scaffold interaction and the conformational changes that occur to the portal during the different stages of capsid formation have yet to be elucidated structurally. Here we present high-resolution structures of the A- and B-capsids and in-situ portals of human cytomegalovirus. We show that scaffolds bind to the hydrophobic cavities formed by the dimerization and Johnson-fold domains of the major capsid proteins. We further show that 12 loop-helix-loop fragments—presumably from the scaffold domain—insert into the hydrophobic pocket of the portal crown domain. The portal also undergoes significant changes both positionally and conformationally as it accompanies DNA packaging. These findings unravel the mechanism by which the portal interacts with the scaffold to nucleate capsid assembly and further our understanding of scaffold expulsion and DNA incorporation.

На місці Жовкви та її околиць: документи до історії маєтності Висоцьких-Жолкевських у львівській землі в XV–XVI століттях (частина 1)

 The purpose of the work is to supplement the knowledge about the formation of noble estates in the Ruthenian voivodeship, since the late Middle Ages through the prism of historical geography. The research methodology is based on historical-critical, comparative (they were used in the analysis and comparison of original documents with their copies, which made it possible to identify signifi cant diff erences in the texts) and historical-geographical methods (to localize the proper names of geographical objects, listed in the acts). The scientifi c novelty of the research is to analyze the documents (including an Act, that was not previously published in a full), which established the boundaries of Jan Wysocki’s estate on the northwestern edge of Lviv land with its nearest neighbors: the private property of Jan Kulikowski (the demarcation in 1487) and the Yavoriv starosty (the deed of sale of crown domain to Piotr Szamotulski in 1456 with a text fragment, added in the 16th or 17th century). The documents were found in the form of copies in the Lviv castle court books and in the form of extracts from the same books. They are stored in the Central State Historical Archives of Ukraine in Lviv. The prospect of further research lies in the introduction into scientifi c circulation of the documents on the history of Ukrainian lands of the late Middle Ages and early modern times, in which the geographical nomenclature is recorded, with its further localization in space. Conclusions. Despite the fact, that the fi rst (the demarcation) and the second (the deed of sale of the land) documents were concluded for diff erent purposes, they both contain valuable information about the lands, owned by the above-mentioned persons (or land, they were going to own). Both in the fi rst and in the second document, this information is recorded in the form of an extensive list of microtoponyms, which in the Middle Ages and early modern times served as landmarks, when establishing boundaries of land holdings. The degree of importance of this information is shown by the fact, that in late copies of such acts we fi nd large fragments of the text with geographical nomenclature, that is absent in the original. Most likely, such insertions in the text were to serve as an additional «argument» for clarifying the ownership of a particular territory in the future.

Novel small synthetic HIV-1 V3 crown variants: CCR5 targeting ligands.

The CC chemokine receptor 5 (CCR5) antagonism represents a promising pharmacological strategy for therapeutic intervention as it plays a significant role in reducing the severity and progression of a wide range of pathological conditions. Here we designed and generated peptide ligands targeting the chemokine receptor, CCR5, that were derived from the critical interaction sites of the V3 crown domain of envelope protein glycoprotein gp120 (TRKSIHIGPGRAFYTTGEI) of HIV-1 using computational biology approach and the peptide sequence corresponding to this region was taken as the template peptide, designated as TMP-1. The peptide variants were synthesized by employing Fmoc chemistry using polymer support and were labelled with rhodamine B to study their interaction with the CCR5 receptor expressed on various cells. TMP-1 and TMP-2 were selected as the high-affinity ligands from in vitro receptor-binding assays. Specific receptor-binding experiments in activated peripheral blood mononuclear cells and HOS.CCR5 cells indicated that TMP-1 and TMP-2 had significant CCR5 specificity. Further, the functional analysis of TMP peptides using chemotactic migration assay showed that both peptides did not mediate the migration of responsive cells. Thus, template TMP-1 and TMP-2 represent promising CCR5 targeting peptide candidates.

The adapted hyper-Kähler structure on the crown domain

Let $$\Xi $$ be the crown domain associated with a non-compact irreducible Hermitian symmetric space G / K. We give an explicit description of the unique G-invariant adapted hyper-Kahler structure on $$\Xi $$ , i.e., compatible with the adapted complex structure $$J_\mathrm{ad}$$ and with the G-invariant Kahler structure of G / K. We also compute invariant potentials of the involved Kahler metrics and the associated moment maps.

Structure of a Bacterial Virus DNA-Injection Protein Complex Reveals a Decameric Assembly with a Constricted Molecular Channel.

The multi-layered cell envelope structure of Gram-negative bacteria represents significant physical and chemical barriers for short-tailed phages to inject phage DNA into the host cytoplasm. Here we show that a DNA-injection protein of bacteriophage Sf6, gp12, forms a 465-kDa, decameric assembly in vitro. The electron microscopic structure of the gp12 assembly shows a ~150-Å, mushroom-like architecture consisting of a crown domain and a tube-like domain, which embraces a 25-Å-wide channel that could precisely accommodate dsDNA. The constricted channel suggests that gp12 mediates rapid, uni-directional injection of phage DNA into host cells by providing a molecular conduit for DNA translocation. The assembly exhibits a 10-fold symmetry, which may be a common feature among DNA-injection proteins of P22-like phages and may suggest a symmetry mismatch with respect to the 6-fold symmetric phage tail. The gp12 monomer is highly flexible in solution, supporting a mechanism for translocation of the protein through the conduit of the phage tail toward the host cell envelope, where it assembles into a DNA-injection device.

Invariant envelopes of holomorphy in the complexification of a Hermitian symmetric space

In this paper we investigate invariant domains in $\, \Xi^+$, a distinguished $\,G$-invariant, Stein domain in the complexification of an irreducible Hermitian symmetric space $\,G/K$. The domain $\,\Xi^+$, recently introduced by Kr\otz and Opdam, contains the crown domain $\,\Xi\,$ and it is maximal with respect to properness of the $\,G$-action. In the tube case, it also contains $\,S^+$, an invariant Stein domain arising from the compactly causal structure of a symmetric orbit in the boundary of $\,\Xi$. We prove that the envelope of holomorphy of an invariant domain in $\,\Xi^+$, which is contained neither in $\,\Xi\,$ nor in $\,S^+$, is univalent and coincides with $\,\Xi^+$. This fact, together with known results concerning $\,\Xi\,$ and $\,S^+$, proves the univalence of the envelope of holomorphy of an arbitrary invariant domain in $\,\Xi^+\,$ and completes the classification of invariant Stein domains therein.

Glycation Contributes to Interaction Between Human Bone Alkaline Phosphatase and Collagen Type I.

Bone is a biological composite material comprised primarily of collagen type I and mineral crystals of calcium and phosphate in the form of hydroxyapatite (HA), which together provide its mechanical properties. Bone alkaline phosphatase (ALP), produced by osteoblasts, plays a pivotal role in the mineralization process. Affinity contacts between collagen, mainly type II, and the crown domain of various ALP isozymes were reported in a few in vitro studies in the 1980s and 1990s, but have not attracted much attention since, although such interactions may have important implications for the bone mineralization process. The objective of this study was to investigate the binding properties of human collagen type I to human bone ALP, including the two bone ALP isoforms B1 and B2. ALP from human liver, human placenta and E. coli were also studied. A surface plasmon resonance-based analysis, supported by electrophoresis and blotting, showed that bone ALP binds stronger to collagen type I in comparison with ALPs expressed in non-mineralizing tissues. Further, the B2 isoform binds significantly stronger to collagen type I in comparison with the B1 isoform. Human bone and liver ALP (with identical amino acid composition) displayed pronounced differences in binding, revealing that post-translational glycosylation properties govern these interactions to a large extent. In conclusion, this study presents the first evidence that glycosylation differences in human ALPs are of crucial importance for protein-protein interactions with collagen type I, although the presence of the ALP crown domain may also be necessary. Different binding affinities among the bone ALP isoforms may influence the mineral-collagen interface, mineralization kinetics, and degree of bone matrix mineralization, which are important factors determining the material properties of bone.

Molecular Evolution of the Tissue-nonspecific Alkaline Phosphatase Allows Prediction and Validation of Missense Mutations Responsible for Hypophosphatasia

ALPL encodes the tissue nonspecific alkaline phosphatase (TNSALP), which removes phosphate groups from various substrates. Its function is essential for bone and tooth mineralization. In humans, ALPL mutations lead to hypophosphatasia, a genetic disorder characterized by defective bone and/or tooth mineralization. To date, 275 ALPL mutations have been reported to cause hypophosphatasia, of which 204 were simple missense mutations. Molecular evolutionary analysis has proved to be an efficient method to highlight residues important for the protein function and to predict or validate sensitive positions for genetic disease. Here we analyzed 58 mammalian TNSALP to identify amino acids unchanged, or only substituted by residues sharing similar properties, through 220 millions years of mammalian evolution. We found 469 sensitive positions of the 524 residues of human TNSALP, which indicates a highly constrained protein. Any substitution occurring at one of these positions is predicted to lead to hypophosphatasia. We tested the 204 missense mutations resulting in hypophosphatasia against our predictive chart, and validated 99% of them. Most sensitive positions were located in functionally important regions of TNSALP (active site, homodimeric interface, crown domain, calcium site, …). However, some important positions are located in regions, the structure and/or biological function of which are still unknown. Our chart of sensitive positions in human TNSALP (i) enables to validate or invalidate at low cost any ALPL mutation, which would be suspected to be responsible for hypophosphatasia, by contrast with time consuming and expensive functional tests, and (ii) displays higher predictive power than in silico models of prediction.

Catalytic Signature of a Heat-Stable, Chimeric Human Alkaline Phosphatase with Therapeutic Potential

Recombinant alkaline phosphatases are becoming promising protein therapeutics to prevent skeletal mineralization defects, inflammatory bowel diseases, and treat acute kidney injury. By substituting the flexible crown domain of human intestinal alkaline phosphatase (IAP) with that of the human placental isozyme (PLAP) we generated a chimeric enzyme (ChimAP) that retains the structural folding of IAP, but displays greatly increased stability, active site Zn2+ binding, increased transphosphorylation, a higher turnover number and narrower substrate specificity, with comparable selectivity for bacterial lipopolysaccharide (LPS), than the parent IAP isozyme. ChimAP shows promise as a protein therapeutic for indications such as inflammatory bowel diseases, gut dysbioses and acute kidney injury.

Quotients of the crown domain by a proper action of a cyclic group

LetG/KG/Kbe an irreducible Riemannian symmetric space of the non-compact type and denote byΞ\Xithe associated crown domain. We show that for any proper action of a cyclic groupΓ\Gammathe quotientΞ/Γ\Xi /\Gammais Stein. An analogous statement holds true for discrete nilpotent subgroups of a maximal split-solvable subgroup ofGG. We also show thatΞ\Xiis taut.

Crystal structure of rat intestinal alkaline phosphatase – Role of crown domain in mammalian alkaline phosphatases

Intestinal alkaline phosphatases (IAPs) are involved in the cleavage of phosphate prodrugs to liberate the drug for absorption in the intestine. To facilitate in vitro characterization of phosphate prodrugs, we have cloned, expressed, purified and characterized IAPs from rat and cynomolgus monkey (rIAP and cIAP respectively) which are important pre-clinical species for drug metabolism studies. The recombinant rat and monkey enzymes expressed in Sf9 insect cells (IAP-Ic) were found to be glycosylated and active. Expression of rat IAP in Escherichia coli (rIAP-Ec) led to ~200-fold loss of activity that was partially recovered by the addition of external Zn(2+) and Mg(2+) ions. Crystal structures of rIAP-Ec and rIAP-Ic were determined and they provide rationale for the discrepancy in enzyme activities. Rat IAP-Ic retains its activity in presence of both Zn(2+) and Mg(2+) whereas activity of most other alkaline phosphatases (APs) including the cIAP was strongly inhibited by excess Zn(2+). Based on our crystal structure, we hypothesized the residue Q317 in rIAP, present within 7 Å of the Mg(2+) at M3, to be important for this difference in activity. The Q317H rIAP and H317Q cIAP mutants showed reversal in effect of Zn(2+), corroborating the hypothesis. Further analysis of the two structures indicated a close linkage between glycosylation and crown domain stability. A triple mutant of rIAP, where all the three putative N-linked glycosylation sites were mutated showed thermal instability and reduced activity.

Establishment of crown–root domain borders in mouse incisor

Teeth are composed of two domains, the enamel-covered crown and the enamel-free root. The understanding of the initiation and regulation of crown and root domain formation is important for the development of bioengineered teeth. In most teeth the crown develops before the root, and erupts to the oral cavity whereas the root anchors the tooth to the jawbone. However, in the continuously growing mouse incisor the crown and root domains form simultaneously, the crown domain forming the labial and the root domain the lingual part of the tooth. While the crown–root border on the incisor distal side supports the distal enamel extent, reflecting an evolutionary diet adaptation, on the incisor mesial side the root-like surface is necessary for the attachment of the interdental ligament between the two incisors. Therefore, the mouse incisor exhibits a functional distal–mesial asymmetry. Here, we used the mouse incisor as a model to understand the mechanisms involved in the crown–root border formation. We analyzed the cellular origins and gene expression patterns leading to the development of the mesial and distal crown–root borders. We discovered that Barx2, En1, Wnt11, and Runx3 were exclusively expressed on the mesial crown–root border. In addition, the distal border of the crown–root domain might be established by cells from a different origin and by an early Follistatin expression, factor known to be involved in the root domain formation. The use of different mechanisms to establish domain borders gives indications of the incisor functional asymmetry.

Rational Design of Murine Secreted Alkaline Phosphatase for Enhanced Performance as a Reporter Gene in Mouse Gene Therapy Preclinical Studies

Many preclinical gene therapy studies use a reporter gene to evaluate vector design and performance in mouse models of human disease. Unfortunately, most commonly used reporter genes are immunogenic in mice, which confounds accurate evaluation of vector function. In previous studies, we showed that the murine secreted alkaline phosphatase (mSEAP) gene functions well as a simple and sensitive reporter gene in mice. In this study, we have used rational design to enhance mSEAP performance. The majority of native mSEAP remains attached to the outer surface of the cell through glycan phosphatidylinositol linkage; removal of the carboxy-terminal tail of mSEAP resulted in a dramatic enhancement of release of the protein into cell culture medium and into mouse plasma in whole animal experiments. We increased the heat stability of mSEAP through mutation of a key residue in the crown domain of the protein (H451E), thus allowing us to reduce endogenous, background AP activity through heat inactivation for enhanced sensitivity. We show that these alterations in mSEAP result in enhanced performance in tissue culture and mouse studies. Taken together, these data illustrate that mSEAP is a sensitive, nonimmunogenic reporter for preclinical mouse studies.

Structural and Biochemical Characterization of a Halophilic Archaeal Alkaline Phosphatase

Phosphate is an essential component of all cells that must be taken up from the environment. Prokaryotes commonly secrete alkaline phosphatases (APs) to recruit phosphate from organic compounds by hydrolysis. In this study, the AP from Halobacterium salinarum, an archaeon that lives in a saturated salt environment, has been functionally and structurally characterized. The core fold and the active-site architecture of the H. salinarum enzyme are similar to other AP structures. These generally form dimers composed of dominant β-sheet structures sandwiched by α-helices and have well-accessible active sites. The surface of the enzyme is predicted to be highly negatively charged, like other proteins of extreme halophiles. In addition to the conserved core, most APs contain a crown domain that strongly varies within species. In the H. salinarum AP, the crown domain is made of an acyl-carrier-protein-like fold. Different from other APs, it is not involved in dimer formation. We compare the archaeal AP with its bacterial and eukaryotic counterparts, and we focus on the role of crown domains in enhancing protein stability, regulating enzyme function, and guiding phosphoesters into the active-site funnel.

Analysis on the Crown Domain

This paper is a further development of complex methods in harmonic analysis on semi-simple Lie groups [AG], [BeR], [KrS1,2]. We study the growth behaviour of the holomorphic extension of the orbit map of the spherical vector of an irreducible spherical representation of a real reductive group G when approaching the boundary of the crown domain of the Riemannian symmetric space G/K. As an application, we prove that Maas cusp forms have exponential decay.

Molecular basis of perinatal hypophosphatasia with tissue‐nonspecific alkaline phosphatase bearing a conservative replacement of valine by alanine at position 406

Hypophosphatasia, a congenital metabolic disease related to the tissue-nonspecific alkaline phosphatase gene (TNSALP), is characterized by reduced serum alkaline phosphatase levels and defective mineralization of hard tissues. A replacement of valine with alanine at position 406, located in the crown domain of TNSALP, was reported in a perinatal form of hypophosphatasia. To understand the molecular defect of the TNSALP (V406A) molecule, we examined this missense mutant protein in transiently transfected COS-1 cells and in stable CHO-K1 Tet-On cells. Compared with the wild-type enzyme, the mutant protein showed a markedly reduced alkaline phosphatase activity. This was not the result of defective transport and resultant degradation of TNSALP (V406A) in the endoplasmic reticulum, as the majority of newly synthesized TNSALP (V406A) was conveyed to the Golgi apparatus and incorporated into a cold detergent insoluble fraction (raft) at a rate similar to that of the wild-type TNSALP. TNSALP (V406A) consisted of a dimer, as judged by sucrose gradient centrifugation, suggestive of its proper folding and correct assembly, although this mutant showed increased susceptibility to digestion by trypsin or proteinase K. When purified as a glycosylphosphatidylinositol-anchorless soluble form, the mutant protein exhibited a remarkably lower Kcat/Km value compared with that of the wild-type TNSALP. Interestingly, leucine and isoleucine, but not phenylalanine, were able to substitute for valine, pointing to the indispensable role of residues with a longer aliphatic side chain at position 406 of TNSALP. Taken together, this particular mutation highlights the structural importance of the crown domain with respect to the catalytic function of TNSALP.

Corner view on the crown domain

In this paper we raise a question about the boundary of the crown domain of a Riemannian symmetric space X. In case X is of Hermitian type we give an affirmative answer.

A Novel Glycosylphosphatidylinositol-Anchored Alkaline Phosphatase Dwells in the Hepatic Duct of the Pearl Oyster, Pinctada fucata

Alkaline phosphatases are ubiquitous enzymes involved in many important biological processes. Mammalian tissue-nonspecific alkaline phosphatase (TNAP) has long been thought to play an important role in bone mineralization. In this study, we identified a full-length cDNA encoding a potential alkaline phosphatse from pearl oyster Pinctada fucata by RT-PCR and RACE and designated the encoded protein as PFAP. The sequence of PFAP shares an overall similarity of 67% with that of human TNAP. Prediction and analysis of its secondary and tertiary structure revealed that the PFAP contains two mammalian-specific regions, the crown domain, involved in collagen binding, and the calcium binding domain, which hint its potential ability to participate in biomineralization. RT-PCR and in situ hybridization showed that the PFAP mRNA distributes specifically in the hepatic duct of the digestive diverticula. These findings implied its possible role in calcium absorption and transportation. In vivo, PFAP could be specifically released by phosphatidylinositol-specific phospholipase C (PIPLC), suggesting it is glycophosphatidylinositol-anchored to the plasma membrane. Therefore, a human growth hormone-PFAP fusion was constructed to locate the cleavage/attachment site. Immunofluorescent labeling and immunoblotting showed that Asn-477 is the cleavage/attachment site and the 25-residue peptide COOH-terminal to Asn-477 is removed during glycophosphatidylinositol anchoring. This research will hopefully pave the way to illustrate the role PFAP plays in calcium transportation related to pearl biomineralization.