scholarly journals Ascorbate peroxidase neofunctionalization at the origin of APx-R and APx-L: evidences from basal Archaeplastida

2020 ◽  
Author(s):  
Fernanda Lazzarotto ◽  
Paloma Koprovski Menguer ◽  
Luiz-Eduardo Del-Bem ◽  
Márcia Margis-Pinheiro
Keyword(s):  
Ascorbate Peroxidase ◽  
Peroxidase Activity ◽  
Binding Sites ◽  
The Other ◽  
Class I ◽  
Hybrid Proteins ◽  
Catalytic Sites ◽  
Molecular Phylogenetic ◽  
Binding Residues ◽  
L Proteins

AbstractAscorbate peroxidases (APx) are class I members of the non-animal peroxidases superfamily, a large group of evolutionarily related enzymes. Through mining in public databases, our group has previously identified two unusual subsets of APx homologs, disclosing the existence of two uncharacterized families of class I peroxidases, which were named ascorbate peroxidase-related (APx-R) and ascorbate peroxidase-like (APx-L). As APx, APx-R proteins possess all catalytic residues required for peroxidase activity. Nevertheless, these proteins do not contain residues known to be critical for ascorbate binding, implying that members of this family must use other substrates while reducing hydrogen peroxide. On the other hand, APx-L proteins not only lack ascorbate-binding residues, as do not contain any residue known to be essential for peroxidase activity, in contrast with every other member of the non-animal peroxidase superfamily, which is composed by over 10,000 proteins distributed among bacteria, archaea, fungi, algae, and plants. Through a molecular phylogenetic analysis performed with sequences derived from basal Archaeplastida, we now show the existence of hybrid proteins, which combine features of these three families. Analysis performed on public databases show that the prevalence of these proteins varies among distinct groups of organisms, accounting for up to 33% of total APx homologs in species of green algae. The analysis of this heterogeneous group of proteins sheds light on the origin of APx-R and APx-L, through a process characterized by the progressive deterioration of ascorbate-binding sites and catalytic sites towards neofunctionalization.

scholarly journals Ascorbate Peroxidase Neofunctionalization at the Origin of APX-R and APX-L: Evidence from Basal Archaeplastida

Antioxidants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 597
Author(s):  
Fernanda Lazzarotto ◽  
Paloma Koprovski Menguer ◽  
Luiz-Eduardo Del-Bem ◽  
Marcel Zámocký ◽  
Márcia Margis-Pinheiro
Keyword(s):  
Phylogenetic Analysis ◽  
Green Algae ◽  
Ascorbate Peroxidase ◽  
Peroxidase Activity ◽  
The Other ◽  
Hybrid Proteins ◽  
Catalytic Sites ◽  
Molecular Phylogenetic ◽  
Binding Residues ◽  
L Proteins

Ascorbate peroxidases (APX) are class I members of the Peroxidase-Catalase superfamily, a large group of evolutionarily related but rather divergent enzymes. Through mining in public databases, unusual subsets of APX homologs were identified, disclosing the existence of two yet uncharacterized families of peroxidases named ascorbate peroxidase-related (APX-R) and ascorbate peroxidase-like (APX-L). As APX, APX-R harbor all catalytic residues required for peroxidatic activity. Nevertheless, proteins of this family do not contain residues known to be critical for ascorbate binding and therefore cannot use it as an electron donor. On the other hand, APX-L proteins not only lack ascorbate-binding residues, but also every other residue known to be essential for peroxidase activity. Through a molecular phylogenetic analysis performed with sequences derived from basal Archaeplastida, the present study discloses the existence of hybrid proteins, which combine features of these three families. The results here presented show that the prevalence of hybrid proteins varies among distinct groups of organisms, accounting for up to 33% of total APX homologs in species of green algae. The analysis of this heterogeneous group of proteins sheds light on the origin of APX-R and APX-L and suggests the occurrence of a process characterized by the progressive deterioration of ascorbate-binding and catalytic sites towards neofunctionalization.

An ESR study of the peroxidase reaction catalyzed by human methaemoglobin and methaemoglobin-haptoglobin complex

1991 ◽  
Vol 56 (4) ◽  
pp. 923-932
Author(s):  
Jana Stejskalová ◽  
Pavel Stopka ◽  
Zdeněk Pavlíček
Keyword(s):  
Hydrogen Peroxide ◽  
Ascorbic Acid ◽  
Amino Acid ◽  
Peroxidase Activity ◽  
Amino Acid Analysis ◽  
Superoxide Radical ◽  
Esr Spectra ◽  
The Other ◽  
Delocalized Electron

The ESR spectra of peroxidase systems of methaemoglobin-ascorbic acid-hydrogen peroxide and methaemoglobin-haptoglobin complex-ascorbic acid-hydrogen peroxide have been measured in the acetate buffer of pH 4.5. For the system with methaemoglobin an asymmetrical signal with g ~ 2 has been observed which is interpreted as the perpendicular region of anisotropic spectrum of superoxide radical. On the other hand, for the system with methaemoglobin-haptoglobin complex the observed signal with g ~ 2 is symmetrical and is interpreted as a signal of delocalized electron. After realization of three repeatedly induced peroxidase processes the ESR signal of the perpendicular part of anisotropic spectrum of superoxide radical is distinctly diminished, whereas the signal of delocalized electron remains practically unchanged. An amino acid analysis of methaemoglobin along with results of the ESR measurements make it possible to derive a hypothesis about the role of haptoglobin in increasing of the peroxidase activity of methaemoglobin.

THE MOLECULAR ORGANIZATION OF HUMAN ALPHA 2-MACROGLOBULIN. AN IMMUNO ELECTRON MICROSCOPIC STUDY WITH MONOCLONAL ANTIBODIES

1987 ◽  
Author(s):  
E Delain ◽  
M Barrav ◽  
J Tapon-Bretaudière ◽  
F Pochon ◽  
F Van Leuven
Keyword(s):  
Monoclonal Antibodies ◽  
Binding Sites ◽  
Divalent Cations ◽  
The Other ◽  
Molecular Organization ◽  
Cellular Receptor ◽  
Electron Microscopic ◽  
Microscopic Method ◽  
Bait Region ◽  
Electron Microscopic Method

Electron microscopy is a very convenient method to localize the epitopes of monoclonal antibodies (mAbs) at the surface of macromolecules for studying their tree-dimensional organization.We applied this immuno-electron microscopic method to human ct2-macroglobulin (ct2M). 29 anti-α2M mAbs have been tested with the four different forms of a2M : native and chymotrypsin-transformed tetramers, and the corresponding dimers, obtained by dissociation with divalent cations. These mAbs can be classified in three types : those which are specific for 1) the H-like transformed molecules, 2) the native molecules, and 3) those which can react with both forms of α2M.1) Among the H-like α2M specific mAbs, several react with the 20 kD-domain which is recognized by the cellular receptor of transformed a2M. This domain is located at the carboxyterminal end of each monomer. One IgG binds to the end of two adjacent tips of the H-like form.The other mAbs of this type bind to the α2M tips at non-terminal positions. Intermolecular connections built polymers of alternating α2M and IgG molecules.2) Among the native a2M-specific mAbs some are able to inhibit the protease-induced transformation of the native α2M. The binding sites of these mAbs are demonstrated on the native half-molecules. One of these mAbs was also able to react with transformed dimers, in a region corresponding very likely to an inaccessible epitope in the tetrameric transformed α2M molecule.3) Among the mAbs of this type, only two were able to inhibit the protease-induced transformation of α2M. Obviously, their epitopes should be close to the bait region of α2M. The other mAbs reacting with both α2M forms did not inhibit the α2M transformation.All these mAbs can be distinguished by the structure of the immune complexes formed with all forms of α2M. The epitopes are more easily located on the dimers and on the H-like transformed α2M than on the native molecules.From these observations, we propose a new model of the tree-dimensional organization of the human α2M in its native and transformed configurations, and of its protease-induced transformation.

scholarly journals Novel Interactions of ESCRT-III with LIP5 and VPS4 and their Implications for ESCRT-III Disassembly

2008 ◽  
Vol 19 (6) ◽  
pp. 2661-2672 ◽  
Author(s):  
Soomin Shim ◽  
Samuel A. Merrill ◽  
Phyllis I. Hanson
Keyword(s):  
Atpase Activity ◽  
Binding Site ◽  
Binding Sites ◽  
Essential Role ◽  
Multivesicular Body ◽  
The Other ◽  
Aaa Atpase ◽  
Direct Binding ◽  
Novel Interactions

The AAA+ ATPase VPS4 plays an essential role in multivesicular body biogenesis and is thought to act by disassembling ESCRT-III complexes. VPS4 oligomerization and ATPase activity are promoted by binding to LIP5. LIP5 also binds to the ESCRT-III like protein CHMP5/hVps60, but how this affects its function remains unclear. Here we confirm that LIP5 binds tightly to CHMP5, but also find that it binds well to additional ESCRT-III proteins including CHMP1B, CHMP2A/hVps2–1, and CHMP3/hVps24 but not CHMP4A/hSnf7–1 or CHMP6/hVps20. LIP5 binds to a different region within CHMP5 than within the other ESCRT-III proteins. In CHMP1B and CHMP2A, its binding site encompasses sequences at the proteins' extreme C-termini that overlap with “MIT interacting motifs” (MIMs) known to bind to VPS4. We find unexpected evidence of a second conserved binding site for VPS4 in CHMP2A and CHMP1B, suggesting that LIP5 and VPS4 may bind simultaneously to these proteins despite the overlap in their primary binding sites. Finally, LIP5 binds preferentially to soluble CHMP5 but instead to polymerized CHMP2A, suggesting that the newly defined interactions between LIP5 and ESCRT-III proteins may be regulated by ESCRT-III conformation. These studies point to a role for direct binding between LIP5 and ESCRT-III proteins that is likely to complement LIP5's previously described ability to regulate VPS4 activity.

Cell adhesion and phagocytosis promoted by monoclonal antibodies not directed against fibronectin receptors

1988 ◽  
Vol 90 (2) ◽  
pp. 201-214 ◽  
Author(s):  
F. Grinnell ◽  
C.H. Ho ◽  
T.L. Tuan
Keyword(s):  
Monoclonal Antibodies ◽  
Cell Adhesion ◽  
Binding Sites ◽  
Cell Spreading ◽  
The Other ◽  
Immunofluorescence Staining ◽  
Baby Hamster Kidney ◽  
Bhk Cells ◽  
Reducing Conditions ◽  
Latex Beads

In this report we describe cell adhesion and phagocytosis promoted by two monoclonal antibodies that were selected for immunofluorescence staining of non-permeabilized baby hamster kidney (BHK) cells. Anti-BHK1 staining was heaviest along cell margins, whereas anti-BHK2 staining was continuous along cell margins. Neither antibody stained elongated plaque structures such as were observed when cells were reacted with antibodies to fibronectin (FN) receptors. The monoclonal antibodies functioned as adhesion ligands in four different assays: attachment to culture dishes, spreading, binding of latex beads and phagocytosis. Anti-BHK1 and anti-BHK2 promoted attachment to culture dishes similarly, but anti-BHK2 was more effective at promoting cell spreading. Antibody-promoted cell spreading was inhibited by the peptides Ser-Asp-Gly-Arg and Gly-Arg-Gly-Asp-Ser-Pro but not by other, related, peptides tested. The monoclonal antibodies also promoted binding of latex beads, and the bead binding sites were motile, on the basis of their ‘capping’ response. Nevertheless, anti-BHK2 beads were phagocytosed by cells 5- to 20-fold more efficiently than anti-BHK1 beads. The binding sites for anti-BHK1 and anti-BHK2 were characterized by immunoprecipitation experiments. Anti-BHK1 binding sites contained 50K (K = 10(3) Mr) and 88K components under non-reducing conditions that migrated as a 51/53K doublet and a 93K component under reducing conditions. On the other hand, anti-BHK2 binding sites contained 88K and 110K components under non-reducing conditions that shifted to apparent 107K and 128K values when measured under reducing conditions.

The HML mating-type cassette of Saccharomyces cerevisiae is regulated by two separate but functionally equivalent silencers

1989 ◽  
Vol 9 (11) ◽  
pp. 4621-4630
Author(s):  
D J Mahoney ◽  
J R Broach
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mating Type ◽  
Binding Sites ◽  
The Other ◽  
Functional Domains ◽  
Gene Products ◽  
Cis Acting ◽  
Full Expression ◽  
Mating Type Genes ◽  
Chromosome Iii

Mating-type genes resident in the silent cassette HML at the left arm of chromosome III are repressed by the action of four SIR gene products, most likely mediated through two cis-acting sites located on opposite sides of the locus. We showed that deletion of either of these two cis-acting sites from the chromosome did not yield any detectable derepression of HML, while deletion of both sites yielded full expression of the locus. In addition, each of these sites was capable of exerting repression of heterologous genes inserted in their vicinity. Thus, HML expression is regulated by two independent silencers, each fully competent for maintaining repression. This situation was distinct from the organization of the other silent locus, HMR, at which a single silencer served as the predominant repressor of expression. Examination of identifiable domains and binding sites within the HML silencers suggested that silencing activity can be achieved by a variety of combinations of various functional domains.

Chemotaxis-associated properties of separated prestalk and prespore cells of Dictyostelium discoideum

1986 ◽  
Vol 64 (8) ◽  
pp. 722-732 ◽  
Author(s):  
J. D. Mee ◽  
D. M. Tortolo ◽  
M. B. Coukell
Keyword(s):  
Light Scattering ◽  
Cell Surface ◽  
Dictyostelium Discoideum ◽  
Binding Sites ◽  
Large Fraction ◽  
Cell Types ◽  
The Other ◽  
Deficient Mutant ◽  
Camp Phosphodiesterase ◽  
Intracellular Cgmp

During development, prestalk and prespore cells of Dictyostelium discoideum become organized in multicellular structures. This physical association makes it difficult to characterize the two cell types biochemically and physiologically. In the present study, we have separated prestalk and prespore cells from 16-h slugs by the method of Tsang and Bradbury and have examined a number of chemotaxis-associated properties of these cells. When assayed on phosphate-buffered agar under both gradient and nongradient conditions, isolated prestalk cells responded chemotactically to cAMP and, unexpectedly, to folate and certain folate derivatives. In contrast, separated prespore cells failed to respond appreciably to any of these compounds. Neither prestalk nor prespore cells of strain HC91 exhibited a cAMP-induced increase in intracellular cGMP. However, a cGMP response was observed in both prestalk and prespore cells of strain NP368, a cGMP phosphodiesterase deficient mutant. Both cell types exhibited comparable cAMP-mediated light-scattering changes and possessed similar levels of surface cAMP- and folate-binding sites. On the other hand, prestalk cells had at least fourfold higher cAMP phosphodiesterase and folate deaminase activities than prespore cells, and a large fraction of both activities was on the cell surface. Therefore, the greater chemotactic response of prestalk cells to cAMP and folate on agar might be due, in part, to their increased capacity to generate a chemoattractant gradient. Results obtained in this study demonstrate that prestalk and prespore cells separated by this procedure can be used in certain physiological as well as biochemical experiments.

scholarly journals ProPred1: prediction of promiscuous MHC Class-I binding sites

2003 ◽  
Vol 19 (8) ◽  
pp. 1009-1014 ◽  
Author(s):  
H. Singh ◽  
G.P.S. Raghava
Keyword(s):  
Mhc Class I ◽  
Binding Sites ◽  
Class I

scholarly journals The structure of the native cardiac thin filament at systolic Ca2+ levels

2021 ◽  
Vol 118 (13) ◽  
pp. e2024288118
Author(s):  
Cristina M. Risi ◽  
Ian Pepper ◽  
Betty Belknap ◽  
Maicon Landim-Vieira ◽  
Howard D. White ◽  
...  
Keyword(s):  
Cardiac Muscle ◽  
Binding Sites ◽  
Short Range ◽  
Bound States ◽  
Thin Filament ◽  
Narrow Range ◽  
The Other ◽  
Thin Filaments ◽  
Troponin Complex ◽  
Myosin Binding

Every heartbeat relies on cyclical interactions between myosin thick and actin thin filaments orchestrated by rising and falling Ca2+ levels. Thin filaments are comprised of two actin strands, each harboring equally separated troponin complexes, which bind Ca2+ to move tropomyosin cables away from the myosin binding sites and, thus, activate systolic contraction. Recently, structures of thin filaments obtained at low (pCa ∼9) or high (pCa ∼3) Ca2+ levels revealed the transition between the Ca2+-free and Ca2+-bound states. However, in working cardiac muscle, Ca2+ levels fluctuate at intermediate values between pCa ∼6 and pCa ∼7. The structure of the thin filament at physiological Ca2+ levels is unknown. We used cryoelectron microscopy and statistical analysis to reveal the structure of the cardiac thin filament at systolic pCa = 5.8. We show that the two strands of the thin filament consist of a mixture of regulatory units, which are composed of Ca2+-free, Ca2+-bound, or mixed (e.g., Ca2+ free on one side and Ca2+ bound on the other side) troponin complexes. We traced troponin complex conformations along and across individual thin filaments to directly determine the structural composition of the cardiac native thin filament at systolic Ca2+ levels. We demonstrate that the two thin filament strands are activated stochastically with short-range cooperativity evident only on one of the two strands. Our findings suggest a mechanism by which cardiac muscle is regulated by narrow range Ca2+ fluctuations.

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