scholarly journals “In Silico” Characterization of 3-Phytase A and 3-Phytase B from Aspergillus niger

2017 ◽  
Vol 2017 ◽  
pp. 1-23 ◽  
Author(s):  
Doris C. Niño-Gómez ◽  
Claudia M. Rivera-Hoyos ◽  
Edwin D. Morales-Álvarez ◽  
Edgar A. Reyes-Montaño ◽  
Nury E. Vargas-Alejo ◽  
...  
Keyword(s):  
Aspergillus Niger ◽  
Phytic Acid ◽  
Aqueous Media ◽  
Alpha Helix ◽  
Proton Donor ◽  
Van Der Waals Interactions ◽  
Beta Sheet ◽  
Instability Index ◽  
Bioinformatic Tools ◽  
Helix 12

Phytases are used for feeding monogastric animals, because they hydrolyze phytic acid generating inorganic phosphate. Aspergillus niger 3-phytase A (PDB: 3K4Q) and 3-phytase B (PDB: 1QFX) were characterized using bioinformatic tools. Results showed that both enzymes have highly conserved catalytic pockets, supporting their classification as histidine acid phosphatases. 2D structures consist of 43% alpha-helix, 12% beta-sheet, and 45% others and 38% alpha-helix, 12% beta-sheet, and 50% others, respectively, and pI 4.94 and 4.60, aliphatic index 72.25 and 70.26 and average hydrophobicity of −0,304 and −0.330, respectively, suggesting aqueous media interaction. Glycosylation and glycation sites allowed detecting zones that can affect folding and biological activity, suggesting fragmentation. Docking showed that H59 and H63 act as nucleophiles and that D339 and D319 are proton donor residues. MW of 3K4Q (48.84 kDa) and 1QFX (50.78 kDa) is similar; 1QFX forms homodimers which will originate homotetramers with several catalytic center accessible to the ligand. 3K4Q is less stable (instability index 45.41) than 1QFX (instability index 33.66), but the estimated lifespan for 3K4Q is superior. Van der Waals interactions generate hydrogen bonds between the active center and O2 or H of the phytic acid phosphate groups, providing greater stability to these temporal molecular interactions.

Biphasic effects of alcohols on the phase transition of poly(L-lysine) between .alpha.-helix and .beta.-sheet conformations

Biochemistry ◽  
1992 ◽  
Vol 31 (25) ◽  
pp. 5728-5733 ◽  
Author(s):  
Akira Shibata ◽  
Miharu Yamamoto ◽  
Takuya Yamashita ◽  
Jang Shing Chiou ◽  
Hiroshi Kamaya ◽  
...  
Keyword(s):  
Phase Transition ◽  
Alpha Helix ◽  
Beta Sheet

scholarly journals Hydrolysis of Phytic Acid in Brown-Rice Bread by Aspergillus niger Phytase

2005 ◽  
Vol 58 (5) ◽  
pp. 267-272 ◽  
Author(s):  
Akiko Matsuo ◽  
Kenji Sato ◽  
Yasushi Nakamura ◽  
Kozo Ohtsuki
Keyword(s):  
Aspergillus Niger ◽  
Phytic Acid ◽  
Brown Rice ◽  
Hydrolysis Of ◽  
Aspergillus Niger Phytase

Alpha-Helix Self-Assembly of Oligopeptides Originated From Beta-Sheet Keratin

2012 ◽  
Vol 213 (24) ◽  
pp. 2628-2638 ◽  
Author(s):  
Qianjie Zhang ◽  
Bernd M. Liebeck ◽  
Kelu Yan ◽  
Dan E. Demco ◽  
Andrea Körner ◽  
...  
Keyword(s):  
Self Assembly ◽  
Alpha Helix ◽  
Beta Sheet

scholarly journals Multiple native-like conformations trapped via self-association-induced hydrophobic collapse of the 33-residue β-sheet domain from platelet factor 4

1995 ◽  
Vol 306 (2) ◽  
pp. 407-419 ◽  
Author(s):  
E Ilyina ◽  
K H Mayo
Keyword(s):  
Electrostatic Interactions ◽  
Nuclear Overhauser Effect ◽  
Alpha Helix ◽  
Platelet Factor 4 ◽  
Random Coil ◽  
Beta Sheet ◽  
Platelet Factor ◽  
Hydrophobic Collapse ◽  
Low Dielectric ◽  
Self Association

Native platelet factor 4 (PF4) (70 residues) has a hydrophobic three-stranded anti-parallel beta-sheet domain on to which is folded an amphipathic C-terminal alpha-helix and an aperiodic N-terminal domain. The 33-amino acid beta-sheet domain from PF4 (residues 23-55) has been synthesized and studied by c.d. and n.m.r. At 10 degrees C and low concentration, peptide 23-55 appears to exist in aqueous solution in a random-coil distribution of highly flexible conformational states. Some preferred conformation, however, is observed, particularly within a relatively stable chain reversal from Leu-45 to Arg-49. As the peptide concentration and/or temperature is increased, a new conformational state(s) appears and intensifies as slowly exchanging (600 MHz 1H-n.m.r. chemical-shift time scale) random-coil resonances disappear. Hill plots of the concentration-dependence indicated mostly tetramer formation as found in native PF4. Although apparent resonance linewidths in aggregate state(s) are of the order of 100 Hz, sequence-specific assignments for most resonances could be made. N.m.r./nuclear Overhauser effect structural analysis indicates the formation of multiple native-like anti-parallel beta-sheet conformations, kinetically trapped via subunit-association-induced hydrophobic collapse and stabilized by low-dielectric electrostatic interactions among/between Gly-28 and Lys-50 in opposing subunits. Results are discussed in terms of protein folding.

scholarly journals The oxygen isotope composition of phosphate released from phytic acid by the activity of wheat and <i>Aspergillus niger</i> phytase

2015 ◽  
Vol 12 (13) ◽  
pp. 4175-4184 ◽  
Author(s):  
C. von Sperber ◽  
F. Tamburini ◽  
B. Brunner ◽  
S. M. Bernasconi ◽  
E. Frossard
Keyword(s):  
Aspergillus Niger ◽  
Oxygen Isotope ◽  
Phytic Acid ◽  
Wheat Germ ◽  
Isotope Composition ◽  
Isotopic Fractionation ◽  
Oxygen Isotope Composition ◽  
Acid Phosphatases ◽  
Enzymatic Assays ◽  
Hydrolysis Of

Abstract. Phosphorus (P) is an essential nutrient for living organisms. Under P-limiting conditions plants and microorganisms can exude extracellular phosphatases that release inorganic phosphate (Pi) from organic phosphorus compounds (Porg). Phytic acid (myo-inositol hexakisphosphate, IP6) is an important form of Porg in many soils. The enzymatic hydrolysis of IP6 by phytase yields available Pi and less phosphorylated inositol derivates as products. The hydrolysis of organic P compounds by phosphatases leaves an isotopic imprint on the oxygen isotope composition (δ18O) of released Pi, which might be used to trace P in the environment. This study aims at determining the effect of phytase on the oxygen isotope composition of released Pi. For this purpose, enzymatic assays with histidine acid phytases from wheat and Aspergillus niger were prepared using IP6, adenosine 5'-monophosphate (AMP) and glycerophosphate (GPO4) as substrates. For a comparison to the δ18O of Pi released by other extracellular enzymes, enzymatic assays with acid phosphatases from potato and wheat germ with IP6 as a substrate were prepared. During the hydrolysis of IP6 by phytase, four of the six Pi were released, and one oxygen atom from water was incorporated into each Pi. This incorporation of oxygen from water into Pi was subject to an apparent inverse isotopic fractionation (&amp;varepsilon; ~ 6 to 10 ‰), which was similar to that imparted by acid phosphatase from potato during the hydrolysis of IP6 (&amp;varepsilon; ~ 7 ‰), where less than three Pi were released. The incorporation of oxygen from water into Pi during the hydrolysis of AMP and GPO4 by phytase yielded a normal isotopic fractionation (&amp;varepsilon; ~ −12 ‰), similar to values reported for acid phosphatases from potato and wheat germ. We attribute this similarity in &amp;varepsilon; to the same amino acid sequence motif (RHGXRXP) at the active site of these enzymes, which leads to similar reaction mechanisms. We suggest that the striking substrate dependency of the isotopic fractionation could be attributed to a difference in the δ18O values of the C–O–P bridging and non-bridging oxygen atoms in organic phosphate compounds.

scholarly journals Generating Bona Fide Mammalian Prions with Internal Deletions

2016 ◽  
Vol 90 (15) ◽  
pp. 6963-6975 ◽  
Author(s):  
Carola Munoz-Montesino ◽  
Christina Sizun ◽  
Mohammed Moudjou ◽  
Laetitia Herzog ◽  
Fabienne Reine ◽  
...  
Keyword(s):  
De Novo ◽  
Alpha Helix ◽  
Transmissible Spongiform Encephalopathies ◽  
Specific Information ◽  
Beta Sheet ◽  
Internal Deletion ◽  
C Terminus ◽  
Parkinson’S Diseases ◽  
Bona Fide ◽  
Mammalian Prions

ABSTRACTMammalian prions are PrP proteins with altered structures causing transmissible fatal neurodegenerative diseases. They are self-perpetuating through formation of beta-sheet-rich assemblies that seed conformational change of cellular PrP. Pathological PrP usually forms an insoluble protease-resistant core exhibiting beta-sheet structures but no more alpha-helical content, loosing the three alpha-helices contained in the correctly folded PrP. The lack of a high-resolution prion structure makes it difficult to understand the dynamics of conversion and to identify elements of the protein involved in this process. To determine whether completeness of residues within the protease-resistant domain is required for prions, we performed serial deletions in the helix H2 C terminus of ovine PrP, since this region has previously shown some tolerance to sequence changes without preventing prion replication. Deletions of either four or five residues essentially preserved the overall PrP structure and mutant PrP expressed in RK13 cells were efficiently converted into bona fide prions upon challenge by three different prion strains. Remarkably, deletions in PrP facilitated the replication of two strains that otherwise do not replicate in this cellular context. Prions with internal deletion were self-propagating andde novoinfectious for naive homologous and wild-type PrP-expressing cells. Moreover, they caused transmissible spongiform encephalopathies in mice, with similar biochemical signatures and neuropathologies other than the original strains. Prion convertibility and transfer of strain-specific information are thus preserved despite shortening of an alpha-helix in PrP and removal of residues within prions. These findings provide new insights into sequence/structure/infectivity relationship for prions.IMPORTANCEPrions are misfolded PrP proteins that convert the normal protein into a replicate of their own abnormal form. They are responsible for invariably fatal neurodegenerative disorders. Other aggregation-prone proteins appear to have a prion-like mode of expansion in brains, such as in Alzheimer's or Parkinson's diseases. To date, the resolution of prion structure remains elusive. Thus, to genetically define the landscape of regions critical for prion conversion, we tested the effect of short deletions. We found that, surprisingly, removal of a portion of PrP, the C terminus of alpha-helix H2, did not hamper prion formation but generated infectious agents with an internal deletion that showed characteristics essentially similar to those of original infecting strains. Thus, we demonstrate that completeness of the residues inside prions is not necessary for maintaining infectivity and the main strain-specific information, while reporting one of the few if not the only bona fide prions with an internal deletion.

scholarly journals Conversion of alpha-helices into beta-sheets features in the formation of the scrapie prion proteins

1993 ◽  
Vol 90 (23) ◽  
pp. 10962-10966 ◽  
Author(s):  
K M Pan ◽  
M Baldwin ◽  
J Nguyen ◽  
M Gasset ◽  
A Serban ◽  
...  
Keyword(s):  
Chemical Modification ◽  
Prion Protein ◽  
Conformational Transition ◽  
Prion Proteins ◽  
Limited Proteolysis ◽  
Alpha Helix ◽  
Beta Sheets ◽  
Cellular Prion Protein ◽  
Beta Sheet ◽  
Alpha Helices

Prions are composed largely, if not entirely, of prion protein (PrPSc in the case of scrapie). Although the formation of PrPSc from the cellular prion protein (PrPC) is a post-translational process, no candidate chemical modification was identified, suggesting that a conformational change features in PrPSc synthesis. To assess this possibility, we purified both PrPC and PrPSc by using nondenaturing procedures and determined the secondary structure of each. Fourier-transform infrared (FTIR) spectroscopy demonstrated that PrPC has a high alpha-helix content (42%) and no beta-sheet (3%), findings that were confirmed by circular dichroism measurements. In contrast, the beta-sheet content of PrPSc was 43% and the alpha-helix 30% as measured by FTIR. As determined in earlier studies, N-terminally truncated PrPSc derived by limited proteolysis, designated PrP 27-30, has an even higher beta-sheet content (54%) and a lower alpha-helix content (21%). Neither PrPC nor PrPSc formed aggregates detectable by electron microscopy, while PrP 27-30 polymerized into rod-shaped amyloids. While the foregoing findings argue that the conversion of alpha-helices into beta-sheets underlies the formation of PrPSc, we cannot eliminate the possibility that an undetected chemical modification of a small fraction of PrPSc initiates this process. Since PrPSc seems to be the only component of the "infectious" prion particle, it is likely that this conformational transition is a fundamental event in the propagation of prions.

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