scholarly journals Prediction of Geraniol Bond Mode in Aspergillus niger Linalool Dehydratase – Isomerase

2019 ◽  
Vol 24 (2) ◽  
pp. 133
Author(s):  
Yelfi Anwar ◽  
Andrianopsyah Mas Jaya Putra ◽  
Elvina Dhiaul Iftitah ◽  
Partomuan Simanjuntak ◽  
Shirly Kumala
Keyword(s):  
Amino Acid ◽  
Aspergillus Niger ◽  
Liquid Culture ◽  
Antioxidant Activities ◽  
Comparative Modeling ◽  
Binding Mode ◽  
Aroma Compound ◽  
Rearrangement Reaction ◽  
Hydrophobic Bond ◽  
Aroma Chemical

Geraniol is a very valuable aroma chemical and has commonly been used in fragrances and aroma compound. Geraniol biotransformation by Aspergillus niger has been studied. The main bioconversion products obtained from geraniol and liquid culture of A. niger are linalool and alpha-terpineol. Linalool plays a major role in anti-inflammatory, antibacterial and antioxidant activities. This study aims to know the interaction of geraniol in Aspergillus niger enzyme with docking molecular. Comparative modeling of Aspergillus niger enzyme was conducted by means of one of the crystal structure of Linalool Dehydratase – Idomerase (LDI) as a template. The best model of this comparative modeling was then used in docking molecular to investigate geraniol binding mode inactive site enzyme of Aspergillus niger. Inactive site enzyme of Aspergillus niger, geraniol is located with hydrophobic and hydrogen bonds: Amino acid – the amino acids are Asn 105, Arg 96, Lys 112 inactive site - OH with hydrogen bond, Arg 97 inactive site – CH3 with hydrophobic bond and Leu54 inactive site – CH3 with the hydrophobic bond. The distances among pharmacophore respectively are 3,603 A, 6,768 A, and 7,345A. It has higher score (ΔGbind: -3.4 kcal/mol) compared to linalool (ΔGbind: -3.6 kcal/mol). Virtual tethering of linalool with LDI Aspergillus niger enzyme in amino acid Leu120 and Glu118 had been done. The pharmacophore is - OH and methyl C8 group. The distances among pharmacophore respectively are 5,835 Å, 2,52 Å, and 5,32 Å. Virtual tethering of LDI Aspergillus niger enzyme with geraniol has a higher score (ΔGbind: -3.4 kcal/mol) compared to linalool (ΔGbind: -3.6 kcal/mol). It shows that interaction between linalool and LDI Aspergillus niger enzyme is easier to occur than the interaction between geraniol and LDI Aspergillus niger enzyme, geraniol reaction to linalool that occurs is rearrangement reaction.

scholarly journals Specificity of the HIV-1 Protease on Substrates Representing the Cleavage Site in the Proximal Zinc-Finger of HIV-1 Nucleocapsid Protein

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1092
Author(s):  
János András Mótyán ◽  
Márió Miczi ◽  
Stephen Oroszlan ◽  
József Tőzsér
Keyword(s):  
Amino Acid ◽  
Zinc Finger ◽  
Cleavage Site ◽  
Potential Role ◽  
Binding Mode ◽  
Interaction Energies ◽  
Vitro Assay ◽  
Hiv 1

To explore the sequence context-dependent nature of the human immunodeficiency virus type 1 (HIV-1) protease’s specificity and to provide a rationale for viral mutagenesis to study the potential role of the nucleocapsid (NC) processing in HIV-1 replication, synthetic oligopeptide substrates representing the wild-type and modified versions of the proximal cleavage site of HIV-1 NC were assayed as substrates of the HIV-1 protease (PR). The S1′ substrate binding site of HIV-1 PR was studied by an in vitro assay using KIVKCF↓NCGK decapeptides having amino acid substitutions of N17 residue of the cleavage site of the first zinc-finger domain, and in silico calculations were also performed to investigate amino acid preferences of S1′ site. Second site substitutions have also been designed to produce “revertant” substrates and convert a non-hydrolysable sequence (having glycine in place of N17) to a substrate. The specificity constants obtained for peptides containing non-charged P1′ substitutions correlated well with the residue volume, while the correlation with the calculated interaction energies showed the importance of hydrophobicity: interaction energies with polar residues were related to substantially lower specificity constants. Cleavable “revertants” showed one residue shift of cleavage position due to an alternative productive binding mode, and surprisingly, a double cleavage of a substrate was also observed. The results revealed the importance of alternative binding possibilities of substrates into the HIV-1 PR. The introduction of the “revertant” mutations into infectious virus clones may provide further insights into the potential role of NC processing in the early phase of the viral life-cycle.

Isolation and Structural Characterization of Antioxidant Peptides from Degreased Apricot Seed Kernels

2018 ◽  
Vol 101 (5) ◽  
pp. 1661-1663 ◽  
Author(s):  
Haisheng Zhang ◽  
Jing Xue ◽  
Huanxia Zhao ◽  
Xinshuai Zhao ◽  
Huanhuan Xue ◽  
...  
Keyword(s):  
Amino Acid ◽  
Antioxidant Activities ◽  
Gel Filtration ◽  
Reversed Phase ◽  
Amino Acid Sequences ◽  
Seed Kernel ◽  
Antioxidant Peptides ◽  
Food Preservatives ◽  
Isolation And Purification ◽  
Rp Hplc

Abstract Background: The composition and sequence of amino acids have a prominent influence on the antioxidant activities of peptides. Objective: A series of isolation and purification experiments was conducted to explore the amino acid sequence of antioxidant peptides, which led to its antioxidation causes. Methods: The degreased apricot seed kernels were hydrolyzed by compound proteases of alkaline protease and flavor protease (3:2, u/u) to prepare apricot seed kernel hydrolysates (ASKH). ASKH were separated into ASKH-A and ASKH-B by dialysis bag. ASKH-B (MW < 3.5 kDa) was further separated into fractions by Sephadex G-25 and G-15 gel-filtration chromatography. Reversed-phase HPLC (RP-HPLC) was performed to separate fraction B4b into two antioxidant peptides (peptide B4b-4 and B4b-6). Results: The amino acid sequences were Val-Leu-Tyr-Ile-Trp and Ser-Val-Pro-Tyr-Glu, respectively. Conclusions: The results suggested that ASKH antioxidant peptides may have potential utility as healthy ingredients and as food preservatives due to their antioxidant activity. Highlights: Materials with regional characteristics were selected to explore, and hydrolysates were identified by RP-HPLC and matrix-assisted laser desorption ionization-time-of-flight-MS to obtain amino acid sequences.

scholarly journals Diverse Mechanisms of Antimicrobial Activities of Lactoferrins, Lactoferricins, and Other Lactoferrin-Derived Peptides

2021 ◽  
Vol 22 (20) ◽  
pp. 11264
Author(s):  
Špela Gruden ◽  
Nataša Poklar Ulrih
Keyword(s):  
Antimicrobial Activity ◽  
Amino Acid ◽  
Amino Acid Composition ◽  
Molecular Level ◽  
Antioxidant Activities ◽  
Antimicrobial Activities ◽  
Iron Binding ◽  
Primary Focus ◽  
Binding Glycoprotein

Lactoferrins are an iron-binding glycoprotein that have important protective roles in the mammalian body through their numerous functions, which include antimicrobial, antitumor, anti-inflammatory, immunomodulatory, and antioxidant activities. Among these, their antimicrobial activity has been the most studied, although the mechanism behind antimicrobial activities remains to be elucidated. Thirty years ago, the first lactoferrin-derived peptide was isolated and showed higher antimicrobial activity than the native lactoferrin lactoferricin. Since then, numerous studies have investigated the antimicrobial potencies of lactoferrins, lactoferricins, and other lactoferrin-derived peptides to better understand their antimicrobial activities at the molecular level. This review defines the current antibacterial, antiviral, antifungal, and antiparasitic activities of lactoferrins, lactoferricins, and lactoferrin-derived peptides. The primary focus is on their different mechanisms of activity against bacteria, viruses, fungi, and parasites. The role of their structure, amino-acid composition, conformation, charge, hydrophobicity, and other factors that affect their mechanisms of antimicrobial activity are also reviewed.

scholarly journals Photoaffinity labelling of cyanomethaemoglobin with derivatives of tryptophan and 5-bromotryptophan

1995 ◽  
Vol 308 (1) ◽  
pp. 251-260 ◽  
Author(s):  
M Li ◽  
Z Lin ◽  
M E Johnson
Keyword(s):  
Amino Acid ◽  
Binding Sites ◽  
Tryptic Peptide ◽  
Fast Atom Bombardment ◽  
Binding Mode ◽  
Reversed Phase ◽  
Reversed Phase Hplc ◽  
Photoaffinity Labelling ◽  
Derivatives Of ◽  
Fast Atom Bombardment Ms

Tryptophan and 5-bromotryptophan (5-BrTrp) are relatively potent inhibitors of sickle-haemoglobin polymerization. The binding sites of these compounds to normal and sickle haemoglobin (HBA and HBS) have been suggested, but not firmly established, through the use of spin-labelled derivatives and/or computer modeling. In the present study we approached the problem by utilizing the technique of photoaffinity labelling. The cyanomet forms of HBA and HBS were subjected to photoaffinity labelling with N alpha-(4-azidotetrafluorobenzoyl)tryptophan and N alpha-(1-ethyl-2-diazomalonyl)-5-bromotryptophan respectively. Both irradiated samples of HBA and HBS were denatured, digested with trypsin, and then separated by reversed-phase HPLC. A labelled tryptic peptide was isolated from the photolabelling of HBS with N alpha-(1-ethyl-2-diazomalonyl)-5-bromotryptophan. The peptide was identified to be Val1(alpha)-Lys7(alpha), with the label attached to Val1(alpha), by virtue of amino acid analysis and sequencing, in conjunction with fast-atom-bombardment MS. The binding mode of N alpha-(1-ethyl-2-diazomalonyl)-5-bromotryptophan is proposed and its relevance to the potency of the 5-BrTrp-based anti-sickling agents is discussed.

scholarly journals Assessment of antioxidant properties of membrane ultrafiltration peptides from mungbean meal protein hydrolysates

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5337 ◽  
Author(s):  
Chanikan Sonklin ◽  
Natta Laohakunjit ◽  
Orapin Kerdchoechuen
Keyword(s):  
Molecular Weight ◽  
Amino Acid ◽  
Metal Ion ◽  
Antioxidant Activities ◽  
Radical Scavenging Activity ◽  
Radical Scavenging ◽  
Peptide Chain ◽  
Antioxidant Power ◽  
Meal Protein ◽  
Ferric Reducing Antioxidant Power

Background Bioactive peptides can prevent damage associated with oxidative stress in humans when consumed regularly. Recently, peptides have attracted immense interest because of their beneficial functional properties, safety and little or no side effects when used at high concentration. Most antioxidant peptides are small in size, less than 1 kDa, and contains a high proportion of hydrophobic amino acid. Particularly, tyrosine, leucine, alanine, isoleucine, valine, lysine, phenyalanine, cysteine, methionine and histidine in peptide chain exhibited high antioxidant activity. Mungbean meal protein (MMP) is highly abundant in hydrophobic amino acids. It indicated that MMP might be a good source of antioxidants. Therefore, the objectives were to optimize the conditions used to generate mungbean meal protein hydrolysate (MMPH) with antioxidant activity from bromelain and to investigate the antioxidant activities of different molecular weight (MW) peptide fraction. Methods Response Surface Methodology (RSM) was used for screening of the optimal conditions to produce MMPH. After that MMPH was fractionated using ultrafiltration membranes with different MW distributions. Crude-MMPH and four fractions were investigated for five antioxidant activities: 2,2,1-diphenyl-1-picrylhydrazyl (DPPH), hydroxyl, superoxide, ferric reducing antioxidant power (FRAP) and metal ion chelation activity. Results The optimal condition to produce the MMPH was 15% (w/w) of bromelain and hydrolysis time for 12 h which showed the greatest DPPH and ABTS radical scavenging activity. After mungbean protein from optimal condition was separated based on different molecular weight, the DPPH radical scavenging activity was the highest for the F4 (less than 1 kDa) peptide fraction. Metal ion chelating activity was generally weak, except for the F4 that had a value of 43.94% at a protein concentration of 5 mg/mL. The F4 also exhibited high hydroxyl and superoxide activities (54 and 65.1%), but moderate activity for ferric reducing antioxidant power (0.102 mmole Fe2+/g protein) compared to other peptide fractions and crude-MMPH. Molecular weight and amino acid were the main factors that determined the antioxidant activities of these peptide fractions. Results indicated that F4 had strong antioxidant potentials. Discussion The lowest MW fraction (less than 1 kDa) contributed to the highest DPPH, superoxide, hydroxyl and metal chelation activity because influence of low MW and high content of hydrophobic amino acid in peptide chain. Results from this study indicated that MMPH peptides donate protons to free radicals because they had significantly high DPPH value compared to superoxide, hydroxyl and FRAP, which reactions were electron donation. Moreover, MMPH peptides had the ability to inhibit transition metal ions because of highly abundant glutamic acid and aspartic acid in peptide chain.

scholarly journals Relief Role of Lysine Chelated Zinc (Zn) on 6-Week-Old Maize Plants under Tannery Wastewater Irrigation Stress

2020 ◽  
Vol 17 (14) ◽  
pp. 5161
Author(s):  
Rehan Ahmad ◽  
Wajid Ishaque ◽  
Mumtaz Khan ◽  
Umair Ashraf ◽  
Muhammad Atif Riaz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Plant Growth ◽  
Foliar Application ◽  
Antioxidant Activities ◽  
Foliar Spray ◽  
Tannery Wastewater ◽  
Organic Load ◽  
Maize Plants

Tannery wastewater mainly comes from leather industries. It has high organic load, high salinity, and many other pollutants, including chromium (Cr). Tannery wastewater is generally used for crop irrigation in some areas of Pakistan and worldwide, due to the low availability of good quality of irrigation water. As tannery wastewater has many nutrients in it, its lower concentration benefits the plant growth, but at a higher concentration, it damages the plants. Chromium in tannery wastewater accumulates in plants, and causes stress at physiological and biochemical levels. In recent times, the role of micronutrient-amino acid chelated compounds has been found to be helpful in reducing abiotic stress in plants. In our present study, we used lysine chelated zinc (Zn-lys) as foliar application on maize (Zea mays L.), growing in different concentrations of tannery wastewater. Zinc (Zn) is required by plants for growth, and lysine is an essential amino acid. Maize plants were grown in tannery wastewater in four concentrations (0, 25%, 50%, and 100%) and Zn-lys was applied as a foliar spray in three concentrations (0 mM, 12.5 mM, and 25 mM) during plant growth. Plants were cautiously harvested right after 6 weeks of treatment. Foliar spray of Zn-lys on maize increased the biomass and improved the plant growth. Photosynthetic pigments such as total chlorophyll, chlorophyll a, chlorophyll b and contents of carotenoids also increased with Zn-lys application. In contrast to control plants, the hydrogen peroxide (H2O2) contents were increased up to 12%, 50%, and 68% in leaves, as well as 16%, 51% and 89% in roots at 25%, 50%, and 100% tannery water application, respectively, without Zn-lys treatments. Zn-lys significantly reduced the damages caused by oxidative stress in maize plant by decreasing the overproduction of H2O2 and malondialdehyde (MDA) in maize that were produced, due to the application of high amount of tannery wastewater alone. The total free amino acids and soluble protein decreased by 10%, 31% and 64% and 18%, 61% and 122% at 25%, 50% and 100% tannery water treatment. Zn-lys application increased the amino acids production and antioxidant activities in maize plants. Zn contents increased, and Cr contents decreased, in different parts of plants with Zn-lys application. Overall, a high concentration of tannery wastewater adversely affected the plant growth, but the supplementation of Zn-lys assertively affected the plant growth and enhanced the nutritional quality, by enhancing Zn and decreasing Cr levels in plants simultaneously irrigated with tannery wastewater.

High fat diet incorporated with meat proteins changes biomarkers of lipid metabolism, antioxidant activities, and the serum metabolomic profile in Glrx1−/− mice

2020 ◽  
Vol 11 (1) ◽  
pp. 236-252 ◽  
Author(s):  
Muhammad Ijaz Ahmad ◽  
Muhammad Umair Ijaz ◽  
Muzahir Hussain ◽  
Iftikhar Ali Khan ◽  
Noreen Mehmood ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Linoleic Acid ◽  
Bile Acid ◽  
Amino Acid ◽  
High Fat Diet ◽  
Antioxidant Activities ◽  
Glutathione Metabolism ◽  
Metabolomic Profile ◽  
High Fat ◽  
Meat Proteins

High-fat mutton protein diet may alter lipid-, linoleic acid-, amino acid-, bile acid-, sphingolipid-, glycine-, serine- and glutathione-metabolism pathways in Glrx−/− mice whereas HFF diet ameliorated NAFLD by modifying these pathways.

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