Bjarni Asgeirsson - Academia.edu (original) (raw)

Papers by Bjarni Asgeirsson

The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment... more The electrostatic profile of consecutive Cβ atoms applied to protein structure quality assessment [v3; ref status: indexed,

F1000Research, Nov 4, 2014

Immune response suppression is crucial for viral invasion. The protein VP24 is pivotal in achievi... more Immune response suppression is crucial for viral invasion. The protein VP24 is pivotal in achieving this in Ebola, although interestingly the mechanism of immune suppression is different in the closely related Marburg virus. Here, we illustrate that a possible molecular basis for this diffrence emanates from two alpha helical structures (α5 and α6) in VP24 involved in binding human karyopherin (KPNA) (PDBid:4U2X), wherein the Ebola and Marburg viruses have distinctly different charged properties in α5. α6 is absent in Marburg, and has a different hydrophobic moment in the Reston Ebola (REBOV) species, which is surprisingly non-pathogenic in humans. Based on the hypothesis that REBOV is not immunosuppressive, which is in turn is due to its inability to bind KPNA, we show by docking KPNA to the REBOV VP24 that the single amino acid substitution R140S is responsible for this difference between REBOV and Zaire Ebola strains. Such a scenario of getting a virulent REBOV through a single mutation is particularly worrisome, since the REBOV, once found only in monkeys, has been recently detected in pigs. We also reiterate the potential of using these helices as potential epitopes for generating protective antibodies against Ebola.

This document is a WHAT_CHECK-report that holds the findings of the WHAT IF program during the an... more This document is a WHAT_CHECK-report that holds the findings of the WHAT IF program during the analysis of a PDB-file. Each rep orted fact has an assigned severity, one of: error : Items marked as errors are considered seve re problems requiring immediate attention. warning: Either less severe problems or uncommon st ructural features. These still need special attention. note : Statistical values, plots, or other verbos e results of tests and analyses that have been performed. If alternate conformations are present, only the fi rst is evaluated. Hydrogen atoms are only included if explicitly requested, an d even then they are not used in all checks. The software functions less wel l for non-canonical amino acids and exotic ligands than for the 20 canonical residues and canonical nucleic acids. Some remarks regarding the output: Residues/atoms in tables are normally given in a fe w parts:

Springer eBooks, 1991

A mixture of psychrophilic proteolytic enzymes, called Cryotin, has been prepared from a neutral ... more A mixture of psychrophilic proteolytic enzymes, called Cryotin, has been prepared from a neutral extract of pyloric caeca from Atlantic cod Gadus morhua. This proteinase mixture has many unique characteristics. The proteinases, studied so far, are more active at low temperatures, when compared to their mammalian counterparts. They are also unusually thermo-labile as well as acid labile. Cryotin has been shown to contain trypsin, chymototrypsin, elastase and a collogenolytic enzyme, as well as other proteolytic and peptidolytic activities, but it is practically devoid of lipase, amylase and nuclease activities.

FEBS Open Bio, Dec 21, 2018

Biochemistry, Sep 7, 2017

The effect of ionic strength on enzyme activity and stability varies considerably between enzymes... more The effect of ionic strength on enzyme activity and stability varies considerably between enzymes. Ionic strength is known to affect the catalytic activity of some alkaline phosphatases (AP), such as the E. coli AP, but how ions affect APs is debated. Here, we studied the effect of various ions on a cold-adapted AP from Vibrio splendidus (VAP). Previously, we have found that the active form of VAP is extremely unstable at low ionic strength. Here we showed that NaCl increased both activity and stability of VAP, and that the effect was pH dependent in the range of 7-10. The activity profile as a function of pH formed two maxima, indicating a possible conformational change. Bringing the pH from the neutral to the alkaline range was accompanied by a large increase in both Ki for inorganic phosphate (product inhibition) and KM for pnitrophenyl phosphate. The activity transitions observed as the pH was varied correlated with structural changes as monitored by tryptophan fluorescence. Thermal and urea induced inactivation was shown neither to be accompanied by dissociation of the active site metal ions nor dimer dissociation. This would suggest that the inactivation involved subtle changes in active site conformation. Furthermore, VAP dimer equilibrium was studied for the first time and shown to highly favor dimerization which was dependent on pH and NaCl concentration. Taken together, the data support a model where anions bind to some specific acceptor in the active site of VAP, resulting in great stabilization and catalytic rate enhancement, presumably through a different mechanism.

Comparative Biochemistry and Physiology B, 2010

Lipid rafts are glycosphingolipid/cholesterol-enriched membrane microdomains that have been exten... more Lipid rafts are glycosphingolipid/cholesterol-enriched membrane microdomains that have been extensively studied during the past two decades. Our aim was to isolate and perform biochemical characterization of lipid rafts from the intestinal brush border membrane (BBM) of Atlantic cod (Gadus morhua) to confirm their existence in a cold-water species and compare their characteristics with lipid rafts from other species in terms of lipid and protein content. To validate the isolation process, we assayed marker enzymes for subcellular organelles, including alkaline phosphatase (AP) and leucine aminopeptidase (LAP), both well-known marker enzymes for BBM and lipid rafts. All biochemical methods showed enrichment of AP in both the BBM and lipid raft fractions. Proteomic studies were performed by MALDI-TOF mass spectrometry using trypsin digested SDS-PAGE samples. Various proteins were associated with the cod intestinal lipid raft preparation such as aminopeptidase-N, prohibitin, and beta-actin. Lipid analysis with (31)P NMR and thin layer chromatography on BBMs and lipid rafts samples gave higher content of sphingomyelin than previously reported in the BBM and lower content of phosphatidylcholine. Furthermore, sphingomyelin was highly dominant in the lipid rafts together with cholesterol. The existence of lipid rafts containing previously reported lipid raft characteristics from the cod intestine has, therefore, been confirmed in a ray-finned fish for the first time to the best of our knowledge.

Biochemistry, Oct 4, 2022

Enzyme stability and function can be affected by various environmental factors, such as temperatu... more Enzyme stability and function can be affected by various environmental factors, such as temperature, pH and ionic strength. Enzymes that are located outside the relatively unchanging environment of the cytosol, such as those residing in the periplasmic space of bacteria or extracellularly secreted, are challenged by more fluctuations in the aqueous medium. Bacterial alkaline phosphatases (APs) are generally affected by ionic strength of the medium, but this varies substantially between species. An AP from the marine bacterium Vibrio splendidus (VAP) shows

FEBS Open Bio, Dec 2, 2020

Molecular and Cellular Endocrinology, Mar 1, 1984

ABSTRACT

F1000Research, Jun 16, 2015

The therapeutic potential of α-helical anti-microbial peptides (AH-AMP) to combat pathogens is fa... more The therapeutic potential of α-helical anti-microbial peptides (AH-AMP) to combat pathogens is fast gaining prominence. Based on recently published open access software for characterizing α-helical peptides (PAGAL), we elucidate a search methodology (SCALPEL) that leverages the massive structural data pre-existing in the PDB database to obtain AH-AMPs belonging to the host proteome. We provide in vitro validation of SCALPEL on plant pathogens (Xylella fastidiosa, Xanthomonas arboricola and Liberibacter crescens) by identifying AH-AMPs that mirror the function and properties of cecropin B, a wellstudied AH-AMP. The identified peptides include a linear AH-AMP present within the existing structure of phosphoenolpyruvate carboxylase (PPC20), and an AH-AMP mimicing the properties of the two α-helices of cecropin B from chitinase (CHITI25). The minimum inhibitory concentration of these peptides are comparable to that of cecropin B, while anionic peptides used as control failed to show any inhibitory effect on these pathogens. Substitute therapies in place of conventional chemotherapies using membrane permeabilizing peptides like these might also prove effective to target cancer cells. The use of native structures from the same organism could possibly ensure that administration of such peptides will be better tolerated and not elicit an adverse immune response. We suggest a similar Open Peer Review Approval Status 1 2 3 version 2 (revision)

F1000Research, Jan 27, 2015

Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into ... more Ebola, considered till recently as a rare and endemic disease, has dramatically transformed into a potentially global humanitarian crisis. The genome of Ebola, a member of the Filoviridae family, encodes seven proteins. Based on the recently implemented software (PAGAL) for analyzing the hydrophobicity and amphipathicity properties of alpha helices (AH) in proteins, we characterize the helices in the Ebola proteome. We demonstrate that AHs with characteristically unique features are involved in critical interactions with the host proteins. For example, the Ebola virus membrane fusion subunit, GP2, from the envelope glycoprotein ectodomain has an AH with a large hydrophobic moment. The neutralizing antibody (KZ52) derived from a human survivor of the 1995 Kikwit outbreak recognizes a protein epitope on this AH, emphasizing the critical nature of this secondary structure in the virulence of the Ebola virus. Our method ensures a comprehensive list of such `hotspots'. These helices probably are or can be the target of molecules designed to inhibit AH mediated protein-protein interactions. Further, by comparing the AHs in proteins of the related Marburg viruses, we are able to elicit subtle changes in the proteins that might render them ineffective to previously successful drugs. Such differences are difficult to identify by a simple sequence or structural alignment. Thus, analyzing AHs in the small Ebola proteome can aid rational design aimed at countering the `largest Ebola epidemic, affecting multiple countries in West Africa' ().

Biochemistry and Biophysics Reports, 2020

Background: Para-nitrophenyl phosphate, the common substrate for alkaline phosphatase (AP), is av... more Background: Para-nitrophenyl phosphate, the common substrate for alkaline phosphatase (AP), is available as a cyclohexylamine salt. Here, we report that cyclohexylamine is a non-competitive inhibitor of APs. Methods: Cyclohexylamine inhibited four different APs. Co-crystallization with the cold-active Vibrio AP (VAP) was performed and the structure solved. Results: Inhibition of VAP fitted a non-competitive kinetic model (K m unchanged, V max reduced) with IC 50 45.3 mM at the pH optimum 9.8, not sensitive to 0.5 M NaCl, and IC 50 27.9 mM at pH 8.0, where the addition of 0.5 M NaCl altered the inhibition to the level observed at pH 9.8. APs from E. coli and calf intestines were less sensitive to cyclohexylamine, whereas an Antarctic bacterial AP was similar to VAP in this respect. X-ray crystallography at 2.3 Å showed two binding sites, one in the active site channel and another at the surface close to dimer interface. Antarctic bacterial AP and VAP have Trp274 in common in their active-sites, that takes part in binding cyclohexylamine. VAP variants W274A, W274K, and W274H gave IC 50 values of 179 mM, 188 mM and 187 mM, respectively, at pH 9.8. Conclusions: The binding of cyclohexylamine in locations at the dimeric interface and/or in the active site of APs may delay product release or reduce the rate of catalytic step(s) involving conformational changes and intersubunit communications. General significance: Cyclohexylamine is a common chemical in industries and used as a counterion in substrates for alkaline phosphatase, a clinically important and common enzyme in the biosphere.

Directed evolution induces tributyrin hydrolysis in a virulence factor of using a duplicated gene... more Directed evolution induces tributyrin hydrolysis in a virulence factor of using a duplicated gene as a template Xylella fastidiosa

ABSTRACTEnzyme stability and function can be affected by various environmental factors, such as t... more ABSTRACTEnzyme stability and function can be affected by various environmental factors, such as temperature, pH and ionic strength. Enzymes that are located outside the relatively unchanging environment of the cytosol, such as those residing in the periplasmic space of bacteria or extracellularly secreted, are challenged by more fluctuations in the aqueous medium. Bacterial alkaline phosphatases (APs) are generally affected by ionic strength of the medium, but this varies substantially between species. An AP from the marine bacterium Vibrio splendidus (VAP) shows complex pH-dependent activation and stabilization in the 0 – 1.0 M range of halogen salts and has been hypothesized to specifically bind chloride anions. Here, using X-ray crystallography and anomalous scattering, we have located two chloride binding sites in the structure of VAP, one in the active site and another one at a peripheral site. Further characterization of the binding sites using site-directed mutagenesis and sm...

$Research paper thumbnail of 2.2 Å resolution anomalous diffraction data of Vibrio alkaline phosphatase, crystallised in 1.0 M NaCl$

2.20 Å resolution anomalous diffraction dataset for <em>Vibrio</em> alkaline phosphat... more 2.20 Å resolution anomalous diffraction dataset for <em>Vibrio</em> alkaline phosphatase, crystallised in 1.0 M NaCl. Data were collected with an X-ray energy of 6 keV at the P14 beamline at the DESY-PETRA III synchrotron in Hamburg, Germany. This dataset was used to estimate the location of chloride ions bound to the enzyme. "NaClAnon.hkl" is the final non-merged anomalous reflection file from data processing in XDS and XSCALE.