scholarly journals An ice-binding protein from an Arctic grass, Leymus mollis

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 648
Author(s):  
Todd L. Sformo ◽  
James A. Raymond
Keyword(s):  
Amino Acid ◽  
Gene Sequence ◽  
3D Structure ◽  
Ice Recrystallization ◽  
Freeze Thaw ◽  
Ice Binding ◽  
Ice Binding Protein ◽  
Probable Presence ◽  
Cold Hardy ◽  
Leymus Mollis

Several cold-hardy grasses have been shown to have ice-binding proteins (IBPs) that protect against freeze-thaw injury. Here, we looked for IBP activity in an Alaskan coastal grass that had not previously been examined, Leymus mollis (Pooidae). Rhizome tissue had strong ice-structuring and ice recrystallization inhibiting (IRI) activities, indicating the probable presence of IBPs. The gene sequence of an IBP was obtained. The sequence encoded a 118-amino acid IRI domain that contained eight repeats. A 3D structure of the IRI domain was predicted from the structure of the IRI domain of the perennial ryegrass Lolium perenne. The predicted structure appeared to have the same eight beta-roll coils found in the L. perenne IBP.

scholarly journals An ice-binding protein from an Arctic population of American dunegrass, Leymus mollis

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 648
Author(s):  
Todd L. Sformo ◽  
James A. Raymond
Keyword(s):  
Amino Acid ◽  
Gene Sequence ◽  
3D Structure ◽  
Ice Recrystallization ◽  
Freeze Thaw ◽  
Ice Binding ◽  
Ice Binding Protein ◽  
Probable Presence ◽  
Cold Hardy ◽  
Leymus Mollis

Several cold-hardy grasses have been shown to have ice-binding proteins (IBPs) that protect against freeze-thaw injury. Here, we looked for IBP activity in an Alaskan coastal grass, Leymus mollis (Pooidae), that had not previously been examined. Rhizome tissue had strong ice-structuring and ice recrystallization inhibiting (IRI) activities, indicating the probable presence of IBPs. The gene sequence of an IBP was obtained. The sequence encoded a 118-amino acid IRI domain composed of eight repeats and that was 80% identical to the IRI domain of the IBP of perennial ryegrass Lolium perenne. The predicted 3D structure of the IRI domain had eight beta-roll coils like those in L. perenne IBP

scholarly journals Protection of Alcohol Dehydrogenase against Freeze–Thaw Stress by Ice-Binding Proteins Is Proportional to Their Ice Recrystallization Inhibition Property

Marine Drugs ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. 638
Author(s):  
Young Hoon Lee ◽  
Kitae Kim ◽  
Jun Hyuck Lee ◽  
Hak Jun Kim
Keyword(s):  
Alcohol Dehydrogenase ◽  
Binding Proteins ◽  
Residual Activity ◽  
Fluorescence Emission ◽  
Fluorescence Emission Spectra ◽  
Ice Recrystallization Inhibition ◽  
Ice Recrystallization ◽  
Freeze Thaw ◽  
Ice Binding ◽  
Recrystallization Inhibition

Ice-binding proteins (IBPs) have ice recrystallization inhibition (IRI) activity. IRI property has been extensively utilized for the cryopreservation of different types of cells and tissues. Recent reports demonstrated that IRI can also play a significant role in protecting proteins from freezing damage during freeze–thaw cycles. In this study, we hypothesized that the protective capability of IBPs on proteins against freeze–thaw damage is proportional to their IRI activity. Hence we used two IBPs: one with higher IRI activity (LeIBP) and the other with lower activity (FfIBP). Yeast alcohol dehydrogenase (ADH) was used as a freeze-labile model protein. IBPs and ADH were mixed, frozen at −20 °C, and thawed repeatedly. The structure of ADH was assessed using fluorescence emission spectra probed by 1-anilinonaphthalene-8-sulfonate over the repeated freeze–thaw cycles. The activity was monitored at 340 nm spectrophotometrically. Fluorescence data and activity clearly indicated that ADH without IBP was freeze-labile. However, ADH maintained about 70% residual activity after five repeated cycles at a minimal concentration of 0.1 mg mL-1 of high IRI-active LeIBP, but only 50% activity at 4 mg mL−1 of low active FfIBP. These results showed that the protection of proteins from freeze–thaw stress by IBPs is proportional to their IRI activity.

Structure-based characterization and antifreeze properties of a hyperactive ice-binding protein from the Antarctic bacteriumFlavobacterium frigorisPS1

2014 ◽  
Vol 70 (4) ◽  
pp. 1061-1073 ◽  
Author(s):  
Hackwon Do ◽  
Soon-Jong Kim ◽  
Hak Jun Kim ◽  
Jun Hyuck Lee
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Disulfide Bond ◽  
Binding Protein ◽  
Size Exclusion ◽  
Sequence Alignments ◽  
Ice Binding ◽  
Ice Binding Protein ◽  
Binding Residues ◽  
The Antarctic

Ice-binding proteins (IBPs) inhibit ice growth through direct interaction with ice crystals to permit the survival of polar organisms in extremely cold environments. FfIBP is an ice-binding protein encoded by the Antarctic bacteriumFlavobacterium frigorisPS1. The X-ray crystal structure of FfIBP was determined to 2.1 Å resolution to gain insight into its ice-binding mechanism. The refined structure of FfIBP shows an intramolecular disulfide bond, and analytical ultracentrifugation and analytical size-exclusion chromatography show that it behaves as a monomer in solution. Sequence alignments and structural comparisons of IBPs allowed two groups of IBPs to be defined, depending on sequence differences between the α2 and α4 loop regions and the presence of the disulfide bond. Although FfIBP closely resemblesLeucosporidium(recently re-classified asGlaciozyma) IBP (LeIBP) in its amino-acid sequence, the thermal hysteresis (TH) activity of FfIBP appears to be tenfold higher than that of LeIBP. A comparison of the FfIBP and LeIBP structures reveals that FfIBP has different ice-binding residues as well as a greater surface area in the ice-binding site. Notably, the ice-binding site of FfIBP is composed of a T-A/G-X-T/N motif, which is similar to the ice-binding residues of hyperactive antifreeze proteins. Thus, it is proposed that the difference in TH activity between FfIBP and LeIBP may arise from the amino-acid composition of the ice-binding site, which correlates with differences in affinity and surface complementarity to the ice crystal. In conclusion, this study provides a molecular basis for understanding the antifreeze mechanism of FfIBP and provides new insights into the reasons for the higher TH activity of FfIBP compared with LeIBP.

scholarly journals S-Acylation of Proteins of Coronavirus and Influenza Virus: Conservation of Acylation Sites in Animal Viruses and DHHC Acyltransferases in Their Animal Reservoirs

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 669
Author(s):  
Dina A. Abdulrahman ◽  
Xiaorong Meng ◽  
Michael Veit
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Ion Channels ◽  
Substrate Specificity ◽  
Influenza A ◽  
3D Structure ◽  
Viral Fitness ◽  
Amino Acid Substitutions ◽  
Essential Function ◽  
Animal Reservoirs

Recent pandemics of zoonotic origin were caused by members of coronavirus (CoV) and influenza A (Flu A) viruses. Their glycoproteins (S in CoV, HA in Flu A) and ion channels (E in CoV, M2 in Flu A) are S-acylated. We show that viruses of all genera and from all hosts contain clusters of acylated cysteines in HA, S and E, consistent with the essential function of the modification. In contrast, some Flu viruses lost the acylated cysteine in M2 during evolution, suggesting that it does not affect viral fitness. Members of the DHHC family catalyze palmitoylation. Twenty-three DHHCs exist in humans, but the number varies between vertebrates. SARS-CoV-2 and Flu A proteins are acylated by an overlapping set of DHHCs in human cells. We show that these DHHC genes also exist in other virus hosts. Localization of amino acid substitutions in the 3D structure of DHHCs provided no evidence that their activity or substrate specificity is disturbed. We speculate that newly emerged CoVs or Flu viruses also depend on S-acylation for replication and will use the human DHHCs for that purpose. This feature makes these DHHCs attractive targets for pan-antiviral drugs.

scholarly journals Whole-genome sequencing of the endemic Antarctic fungus Antarctomyces pellizariae reveals an ice-binding protein, a scarce set of secondary metabolites gene clusters and provides insights on Thelebolales phylogeny

Genomics ◽  
2020 ◽  
Vol 112 (5) ◽  
pp. 2915-2921 ◽  
Author(s):  
Thiago Mafra Batista ◽  
Heron Oliveira Hilario ◽  
Gabriel Antônio Mendes de Brito ◽  
Rennan Garcias Moreira ◽  
Carolina Furtado ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Binding Protein ◽  
Protein A ◽  
Gene Clusters ◽  
Whole Genome ◽  
Ice Binding ◽  
Ice Binding Protein

scholarly journals d-alanine: d-alanine ligase of Escherichia coli. Expression, purification and inhibitory studies on the cloned enzyme

1992 ◽  
Vol 282 (3) ◽  
pp. 747-752 ◽  
Author(s):  
O A M al-Bar ◽  
C D O'Connor ◽  
I G Giles ◽  
M Akhtar
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Gene Sequence ◽  
Phosphinic Acid ◽  
Mature Protein ◽  
Bamhi Fragment ◽  
E Coli ◽  
Escherichia Coli Expression ◽  
Slow Binding Inhibitor

A 1.2 kb BamHI fragment from pDK30 [Robinson, Kenan, Sweeney & Donachie (1986) J. Bacteriol. 167, 809-817] was cloned in pDOC55 [O'Connor & Timmis (1987) J. Bacteriol. 169, 4457-4482] to give two constructs, pDOC89 and pDOC87, in which the Escherichia coli D-alanine:D-alanine ligase (EC 6.3.2.4) gene (ddl) was placed under the control of the lac and lambda PL promoters respectively. Both constructs, when used to transform E. coli M72, gave similar levels of expression of the ddl gene. The expressed enzyme was purified to homogeneity and the amino acid sequence of its N-terminal region was found to be consistent with that predicted from the gene sequence, except that the N-terminal methionine was not present in the mature protein. [1(S)-Aminoethyl][(2RS)2-carboxy-1-octyl]phosphinic acid (I), previously shown to bind tightly to Enterococcus faecalis and Salmonella typhimurium D-alanine:D-alanine ligases following phosphorylation Parsons, Patchett, Bull, Schoen, Taub, Davidson, Combs, Springer, Gadebusch, Weissberger, Valiant, Mellin & Busch (1988) J. Med. Chem. 31, 1772-1778; Duncan & Walsh (1988) Biochemistry 27, 3709-3714], was found to be a classical slow-binding inhibitor of the E. coli ligase.

scholarly journals Investigation of major amino acid residues of anti-norfloxacin monoclonal antibodies responsible for binding with fluoroquinolones

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Patamalai Boonserm ◽  
Songchan Puthong ◽  
Thanaporn Wichai ◽  
Sajee Noitang ◽  
Pongsak Khunrae ◽  
...  
Keyword(s):  
Monoclonal Antibodies ◽  
Amino Acid ◽  
3D Structure ◽  
Cross Reactivity ◽  
Enzyme Linked Immunosorbent Assay ◽  
Amino Acid Residues ◽  
Variable Regions ◽  
Complementarity Determining Regions ◽  
Crucial Part ◽  
Major Amino Acid

AbstractIt is important to understand the amino acid residues that govern the properties of the binding between antibodies and ligands. We studied the binding of two anti-norfloxacins, anti-nor 132 and anti-nor 155, and the fluoroquinolones norfloxacin, enrofloxacin, ciprofloxacin, and ofloxacin. Binding cross-reactivities tested by an indirect competitive enzyme-linked immunosorbent assay indicated that anti-nor 132 (22–100%) had a broader range of cross-reactivity than anti-nor 155 (62–100%). These cross-reactivities correlated with variations in the numbers of interacting amino acid residues and their positions. Molecular docking was employed to investigate the molecular interactions between the fluoroquinolones and the monoclonal antibodies. Homology models of the heavy chain and light chain variable regions of each mAb 3D structure were docked with the fluoroquinolones targeting the crucial part of the complementarity-determining regions. The fluoroquinolone binding site of anti-nor 155 was a region of the HCDR3 and LCDR3 loops in which hydrogen bonds were formed with TYR (H:35), ASN (H:101), LYS (H:106), ASN (L:92), and ASN (L:93). These regions were further away in anti-nor 132 and could not contact the fluoroquinolones. Another binding region consisting of HIS (L:38) and ASP (H:100) was found for norfloxacin, enrofloxacin, and ciprofloxacin, whereas only ASP (H:100) was found for ofloxacin.

scholarly journals Neutralizing Epitopes and Residues Mediating the Potential Antigenic Drift of the Hemagglutinin-Esterase Protein of Influenza C Virus

Viruses ◽  
2018 ◽  
Vol 10 (8) ◽  
pp. 417 ◽  
Author(s):  
Yoko Matsuzaki ◽  
Kanetsu Sugawara ◽  
Yuki Furuse ◽  
Yoshitaka Shimotai ◽  
Seiji Hongo ◽  
...  
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Antigenic Site ◽  
Antigenic Drift ◽  
Receptor Binding Site ◽  
Ann Arbor ◽  
Influenza C Virus ◽  
Escape Mutants ◽  
Antigenic Epitopes

We mapped the hemagglutinin-esterase (HE) antigenic epitopes of the influenza C virus on the three-dimensional (3D) structure of the HE glycoprotein using 246 escape mutants that were selected by a panel of nine anti-HE monoclonal antibodies (MAbs), including seven of the C/Ann Arbor/1/50 virus and two of the C/Yamagata/15/2004 virus. The frequency of variant selection in the presence of anti-HE MAbs was very low, with frequencies ranging from 10−4.62 to 10−7.58 for the C/Ann Arbor/1/50 virus and from 10−7.11 to 10−9.25 for the C/Yamagata/15/2004 virus. Sequencing of mutant HE genes revealed 25 amino acid substitutions at 16 positions in three antigenic sites: A-1, A-2, and A-3, and a newly designated Y-1 site. In the 3D structure, the A-1 site was widely located around the receptor-binding site, the A-2 site was near the receptor-destroying enzyme site, and the Y-1 site was located in the loop on the topside of HE. The hemagglutination inhibition reactions of the MAbs with influenza C viruses, circulating between 1947 and 2016, were consistent with the antigenic-site amino acid changes. We also found some amino acid variations in the antigenic site of recently circulating strains with antigenic changes, suggesting that viruses that have the potential to alter antigenicity continue to circulate in humans.

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