Tags:
Life sciences,
Bioinformatics,
ELIXIR Oslo,
Protein structure
Publications
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Ølnes, Åsa Schawlann; Teigen, Marianne; Lærdahl, Jon Kristen; Leren, Trond Paul; Strøm, Thea Bismo & Bjune, Katrine
(2023).
Variants in the CETP gene affect levels of HDL cholesterol by reducing the amount, and not the specific lipid transfer activity, of secreted CETP.
PLOS ONE.
ISSN 1932-6203.
18(12).
doi:
10.1371/journal.pone.0294764.
Full text in Research Archive
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Backe, Paul Hoff; Lærdahl, Jon Kristen; Kittelsen, Lene Svendsen; Dalhus, Bjørn; Mørkrid, Lars & Bjørås, Magnar
(2020).
Structural basis for substrate and product recognition in human phosphoglucomutase-1 (PGM1) isoform 2, a member of the α-D-phosphohexomutase superfamily.
Scientific Reports.
ISSN 2045-2322.
10(1).
doi:
10.1038/s41598-020-62548-0.
Full text in Research Archive
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Lie-Jensen, Anette; Ivanauskiene, Kristina; Malerød, Lene; Jain, Ashish; Tan, Kia Wee & Lærdahl, Jon Kristen
[Show all 9 contributors for this article]
(2019).
Centralspindlin Recruits ALIX to the Midbody during Cytokinetic Abscission in Drosophila via a Mechanism Analogous to Virus Budding.
Current Biology.
ISSN 0960-9822.
29(20),
p. 3538–3548.e7.
doi:
10.1016/j.cub.2019.09.025.
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Vinje, Terje; Lærdahl, Jon Kristen; Bjune, Katrine; Leren, Trond Paul & Strøm, Thea Bismo
(2019).
Characterization of the mechanisms by which missense mutations in the lysosomal acid lipase gene disrupt enzymatic activity .
Human Molecular Genetics.
ISSN 0964-6906.
28(18),
p. 3043–3052.
doi:
10.1093/hmg/ddz114.
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Strøm, Thea Bismo; Lærdahl, Jon Kristen & Leren, Trond Paul
(2017).
Mutations affecting the transmembrane domain of the LDL receptor: Impact of charged residues on the membrane insertion.
Human Molecular Genetics.
ISSN 0964-6906.
26(9),
p. 1634–1642.
doi:
10.1093/hmg/ddx068.
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Strøm, Thea Bismo; Lærdahl, Jon Kristen & Leren, Trond Paul
(2015).
Mutation p.L799R in the LDLR, which affects the transmembrane domain of the LDLR, prevents membrane insertion and causes secretion of the mutant LDLR.
Human Molecular Genetics.
ISSN 0964-6906.
24(20),
p. 5836–5844.
doi:
10.1093/hmg/ddv304.
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Strøm, Thea Bismo; Tveten, Kristian; Lærdahl, Jon Kristen & Leren, Trond Paul
(2014).
Mutation G805R in the transmembrane domain of the LDL receptor gene causes familial hypercholesterolemia by inducing ectodomain cleavage of the LDL receptor in the endoplasmic reticulum.
FEBS Open Bio.
ISSN 2211-5463.
4,
p. 321–327.
doi:
10.1016/j.fob.2014.03.007.
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Zegeye, Ephrem Debebe; Balasingham, Seetha ; Lærdahl, Jon Kristen; Homberset, Håvard; Kristiansen, Per Eugen & Tønjum, Tone
(2014).
Effects of conserved residues and naturally occurring mutations on Mycobacterium tuberculosis RecG helicase activity.
Microbiology (Reading).
ISSN 1350-0872.
160(1),
p. 217–227.
doi:
10.1099/mic.0.072140-0.
Show summary
RecG is a helicase that is conserved in nearly all bacterial species. The prototypical Escherichia coli RecG promotes regression of stalled replication forks, participates in DNA recombination and DNA repair, and prevents aberrant replication. Mycobacterium tuberculosis RecG (RecGMtb) is a DNA-dependent ATPase that unwinds a variety of DNA substrates, although its preferred substrate is a Holliday junction. Here, we performed site-directed mutagenesis of selected residues in the wedge domain and motifs Q, I, Ib and VI of RecGMtb. Three of the 10 substitution mutations engineered were detected previously as naturally occurring SNPs in the gene encoding RecGMtb. Alanine substitution mutations at residues Q292, F286, K321 and R627 abolished the RecGMtb unwinding activity, whilst RecGMtb F99A, P285S and T408A mutants exhibited ~25-50 % lower unwinding activity than WT. We also found that RecGMtb bound ATP in the absence of a DNA cofactor.
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Ellinghaus, David; Folseraas, Trine; Holm, Kristian; Ellinghaus, Eva; Melum, Espen & Balschun, Tobias
[Show all 37 contributors for this article]
(2013).
Genome-wide association analysis in Primary sclerosing cholangitis and ulcerative colitis identifies risk loci at GPR35 and TCF4.
Hepatology.
ISSN 0270-9139.
58(3),
p. 1074–1083.
doi:
10.1002/hep.25977.
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Fladeby, Cathrine; Vik, Erik Sebastian; Lærdahl, Jon Kristen; Neurauter, Christine Gran; Heggelund, Julie Elisabeth & Thorgaard, Eirik
[Show all 10 contributors for this article]
(2012).
The Human Homolog of Escherichia coli Endonuclease V Is a Nucleolar Protein with Affinity for Branched DNA Structures.
PLOS ONE.
ISSN 1932-6203.
7(11).
doi:
10.1371/journal.pone.0047466.
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Zegeye, Ephrem Debebe; Balasingham, Seetha ; Lærdahl, Jon Kristen; Homberset, Håvard & Tønjum, Tone
(2012).
Mycobacterium tuberculosis RecG binds and unwinds model DNA substrates with a preference for Holliday junctions.
Microbiology (Reading).
ISSN 1350-0872.
158(Pt 8),
p. 1982–1993.
doi:
10.1099/mic.0.058693-0.
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Korvald, Hanne; Falnes, Pål; Lærdahl, Jon Kristen; Bjørås, Magnar & Alseth, Ingrun
(2012).
The Schizosaccharomyces pombe AlkB homolog Abh1 exhibits AP lyase activity but no demethylase activity.
DNA Repair.
ISSN 1568-7864.
11(5),
p. 453–462.
doi:
10.1016/j.dnarep.2012.01.014.
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Tveten, Kristian; Holla, Øystein Lunde; Cameron, Jamie; Strøm, Thea Bismo; Berge, Knut Erik & Lærdahl, Jon Kristen
[Show all 7 contributors for this article]
(2012).
Interaction between the ligand-binding domain of the LDL receptor and the C-terminal domain of PCSK9 is required for PCSK9 to remain bound to the LDL receptor during endosomal acidification.
Human Molecular Genetics.
ISSN 0964-6906.
21(6),
p. 1402–1409.
doi:
10.1093/hmg/ddr578.
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Korvald, Hanne; Moe, Anne Margrethe Mølstad; Cederkvist, Fritjof Henning; Thiede, Bernd; Lærdahl, Jon Kristen & Bjørås, Magnar
[Show all 7 contributors for this article]
(2011).
Schizosaccharomyces pombe Ofd2 Is a Nuclear 2-Oxoglutarate and Iron Dependent Dioxygenase Interacting with Histones.
PLOS ONE.
ISSN 1932-6203.
6(9).
doi:
10.1371/journal.pone.0025188.
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Melum, Espen; Franke, Andre; Schramm, Christoph; Weismüller, Tobias J.; Gotthardt, Daniel & Offner, Felix A.
[Show all 43 contributors for this article]
(2011).
Genome-wide association analysis in primary sclerosing cholangitis identifies two non-HLA susceptibility loci.
Nature Genetics.
ISSN 1061-4036.
43(1),
p. 17–19.
doi:
10.1038/ng.728.
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Cameron, Jamie; Holla, Øystein Lunde; Lærdahl, Jon Kristen; Kulseth, Mari Ann; Berge, Knut Erik & Leren, Trond Paul
(2009).
Mutation S462P in the PCSK9 gene reduces secretion of mutant PCSK9 without affecting the autocatalytic cleavage.
Atherosclerosis.
ISSN 0021-9150.
203(1),
p. 161–165.
doi:
10.1016/j.atherosclerosis.2008.10.007.
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Nordlund, Marianne Sparby; Warren, David; Lærdahl, Jon Kristen & Paus, Elisabeth
(2009).
Studies on Multiple Forms of proGRP in Serum from Small Cell Lung Cancer Patients.
Tumour Biology.
ISSN 1010-4283.
30(5-6),
p. 265–275.
doi:
10.1159/000258135.
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Hayes, Ben J.; Lærdahl, Jon Kristen; Lien, Sigbjørn; Moen, T; Berg, P & Hindar, Kjetil
[Show all 10 contributors for this article]
(2007).
An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences.
Aquaculture.
ISSN 0044-8486.
265,
p. 82–90.
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Klungland, Arne; Lærdahl, Jon Kristen & Rognes, Torbjørn
(2007).
OGG1: From Structural Analysis to the Knockout Mouse.
In Evans, Mark D. & Cooke, Marcus S. (Ed.),
Oxidative Damage to Nucleic Acids.
Springer Science+Business Media B.V..
ISSN 9780387729732.
p. 67–80.
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Adjoubei, Alexei Alexeevich; Lærdahl, Jon Kristen & Vlasova, AV
(2006).
preAssemble: a tool for automatic sequencer trace data processing.
BMC Bioinformatics.
ISSN 1471-2105.
7.
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Lærdahl, Jon Kristen; Civcir, Pervin U.; Bache-Andreassen, Lihn & Uggerud, Einar
(2006).
Nucleophilic identity substitution reactions. The reaction between hydrogen fluoride and protonated alkyl fluorides.
Organic and biomolecular chemistry.
ISSN 1477-0520.
4,
p. 135–141.
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Hagen-Larsen, Heidi; Lærdahl, Jon Kristen; Panitz, Frank; Adzhubei, Alexei A & Høyheim, Bjørn
(2005).
An EST-based approach for identifying genes expressed in the intestine and gills of pre-smolt Atlantic salmon (Salmo salar).
BMC Genomics.
ISSN 1471-2164.
6,
p. 171–171.
doi:
10.1186/1471-2164-6-171.
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Schwerdtfeger, P; Kuhn, A; Bast, R; Lærdahl, Jon Kristen; Faglioni, F & Lazzeretti, P
(2004).
The vibrational spectrum of camphor from ab initio and density functional theory and parity violation in the C-C*-CO bending mode.
Chemical Physics Letters.
ISSN 0009-2614.
383,
p. 496–501.
Show summary
The C-C*-CO bending mode in camphor (C* denotes a chiral carbon) as originally investigated for parity violation effects by Arimondo et al. [Opt. Commun. 23 (1977) 369] lies in the CO2 laser frequency range with the most intense transition at 1045 cm-1. The vibrational spectrum of camphor is, therefore, reinvestigated by ab initio and d. functional calcns. and compared with exptl. results. This provides the basis for a local mode anal. which reveals that the C-C*-CO bending mode has only minute parity violation contributions (<10-5 Hz) to vibrational transitions far below the current detection limit of high resoln. spectroscopy.
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Lærdahl, Jon Kristen & Uggerud, Einar
(2003).
Nucleophilic identity substitution reactions. The reaction between water and protonated alcohols.
Organic and biomolecular chemistry.
ISSN 1477-0520.
1(16),
p. 2935–2942.
Show summary
The potential energy surfaces for the reaction between H2O and the protonated alcs. MeOH2+, EtOH2+, PriOH2+, and ButOH2+ have been explored by means of high level ab initio theor. methods. Both nucleophilic substitution (SN2) and elimination (E2) pathways have been investigated. Front side (SNF) and the familiar back side (SNB) Walden inversion attack of the nucleophile have been found to be competing for the H2O-ButOH2+ system. In contradiction with the customary relationship between so-called "steric effects" and barrier heights-more alkyl-substituted SN2 reaction centers have higher SN2 reaction barriers-the SN2 reaction barriers are found to be Et > Me > Pri > But. This result is in excellent agreement with available exptl. data.
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Lærdahl, Jon Kristen; Bache-Andreassen, Lihn & Uggerud, Einar
(2003).
Nucleophilic identity substitution reactions. The reaction between ammonia and protonated amines.
Organic and biomolecular chemistry.
ISSN 1477-0520.
1(16),
p. 2943–2950.
Show summary
The gas phase reactions between NH3 and the protonated amines MeNH3+, EtNH3+, PriNH3+, and ButNH3+ have been studied by high level ab initio methods. Mass spectrometric expts. yielded no significant reaction products; this result being consistent with the calcd. reaction barriers. The potential energy profiles for both nucleophilic substitution (SN2) and elimination (E2) pathways have been investigated. Both back side Walden inversion (SNB) and front side (SNF) nucleophilic reaction profiles have been generated. The SNB reaction barriers are found to be higher for the more alkyl substituted reaction centers. Reaction barrier trends have been analyzed and compared with the results of a similar study of the H2O-ROH2+ system (R = Me, Et, Pri, and But).
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Heiberg, Hanne; Gropen, Odd; Lærdahl, Jon Kristen; Swang, Ole & Wahlgren, Ulf
(2003).
The performance of density functional theory for LnF (Ln = Nd, Eu, Gd, Yb) and YbH.
Theoretical Chemistry Accounts.
ISSN 1432-881X.
110(3),
p. 118–125.
Show summary
Different d. functional theory (DFT) functionals have been evaluated by studying geometries and bond strengths of YbH, YbF, EuF, GdF, and NdF and compared with accurate CCSD(T) results and, when available, expt. The agreement between the CCSD(T) results and expt., when available, is good. The agreement is also good between bond strengths calcd. at the DFT level using relativistic effective core potentials and the CCSD(T) results. However, the all-electron ADF calcns. systematically overestimate binding energies. The geometries obtained by both the all-electron and the effective-core-potential-based DFT calcns. are generally in good agreement with the CCSD(T) results.
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Wesendrup, Ralf; Lærdahl, Jon Kristen; Compton, Robert N. & Schwerdtfeger, Peter
(2003).
Biomolecular Homochirality and Electroweak Interactions. I. The Yamagata Hypothesis.
Journal of Physical Chemistry A.
ISSN 1089-5639.
107(34),
p. 6668–6673.
Show summary
In 1966, Y. Yamagata proposed that neutral weak currents between electrons and nucleons could be responsible for specific biomol. homochirality in life. The authors critically evaluate this hypothesis by applying relativistic parity nonconserving calcns. for amino acids. The results reveal no clear evidence that the naturally occurring L-amino acids are stabilized by parity violation effects.
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Schwerdtfeger, Peter; Lærdahl, Jon Kristen & Chardonnet, Christian
(2002).
Calculation of parity-violation effects for the C-F stretching mode of chiral methyl fluorides.
Physical Review A. Atomic, Molecular, and Optical Physics (PRA).
ISSN 1050-2947.
65(4),
p. 042508/1–042508/7.
Show summary
Relativistic four-component electronic structure calcns. including the
nuclear spin-independent parity-odd (P-odd) electroweak neutral current are
presented for the study of the breaking of mirror symmetry in the
vibrational structure of chiral mols. The structures of all four chiral
CFXYZ compds. (X,Y,Z = H,Cl,Br,I) were optimized by coupled cluster
techniques with a subsequent normal-mode anal. Vibrational wave functions
for the C-F stretching mode along the normal coordinate were produced
numerically from calcd. coupled cluster potential-energy curves that yield
the following left-right parity-violating differences in frequency for the
C-F stretching fundamental transitions: 1.7 mHz for CHFClBr, 11.6 mHz for
CFClBrI, 23.7 mHz for CHFClI, and 50.8 mHz for CHFBrI. In order to measure
these differences in the spectra of the two enantiomers of these chiral
mols., a two orders of magnitude improvement in the resoln. of current
precision optical spectroscopy is required.
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Lim, Ivan S.; Lærdahl, Jon Kristen & Schwerdtfeger, Peter
(2002).
Fully relativistic coupled-cluster static dipole polarizabilities of the positively charged alkali ions from Li+ to 119+.
Journal of Chemical Physics.
ISSN 0021-9606.
116(1),
p. 172–178.
Show summary
The static dipole polarizabilities of the pos. charged alkali atoms from
Li+ to 119+ (eka-Fr) were obtained from relativistic coupled-cluster theory
using a scalar relativistic Douglas-Kroll Hamiltonian. Spin-orbit coupling
effects were obtained from a fully relativistic four-component
Dirac-Hartree-Fock scheme followed by a second-order many-body perturbation
treatment to account for electron correlation. Electron correlation
effects are found to be small for all ions, but become more sizable as the
nuclear charge increases. Scalar relativistic effects dominate over
electron correlation for Cs+, Fr+, and 119+. Spin-orbit coupling is
non-negligible for the heaviest elements Fr+ and 119+, where they dominate
over both electron correlation and scalar relativistic effects. Breit
interactions obtained for Cs+ and Fr+ can safely be neglected. A
relationship between dipole polarizabilities and second ionization
potentials is established. The use of a basis set limit one-electron
description and a high level treatment of electron correlation and
relativistic effects makes our results the most accurate available for the
stable dipole polarizabilities (1.00 +- 0.04 a.u. for Na+, 5.52 +- 0.04
a.u. for K+, 9.11 +- 0.04 a.u. for Rb+, 15.8 +- 0.1 a.u. for Cs+, 20.4 +-
0.2 a.u. for Fr+, and 32 +- 1 a.u. for 119+).
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Lærdahl, Jon Kristen & Uggerud, Einar
(2002).
Gas Phase Nucleophilic Substitution.
International Journal of Mass Spectrometry.
ISSN 1387-3806.
214(3),
p. 277–314.
Show summary
A review. The literature on gas phase nucleophilic substitution reactions at aliph. carbon has been reviewed. The emphasis has been on journal articles published in the period 1990-2001. The present review outlines our current understanding of concepts such as potential energy surfaces, structure-energy relationships, microsolvation, and dynamical and mechanistic details based on both exptl. and theor. evidence. The accuracy of various theor. schemes for calcg. potential energy surfaces has been assessed. A crit. account on mechanistic concepts used in the literature is given.
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Schwerdtfeger, Peter; Sohnel, Tilo; Pernpointner, Markus; Lærdahl, Jon Kristen & Wagner, Friedrich E.
(2001).
Comparison of ab initio and density functional calculations of electric field gradients: The 57Fe nuclear quadrupole moment from Mossbauer data.
Journal of Chemical Physics.
ISSN 0021-9606.
115(13),
p. 5913–5924.
Show summary
The difficulty in accurate detn. of the nuclear quadrupole moment of the
1st I = 3/2 excited nuclear state of 57Fe from electronic structure calcns.
of the iron elec. field gradient combined with Mossbauer measurements of
the nuclear quadrupole splitting in the isomer shift is addressed by
comparing ab initio with d. functional calcns. for iron pentacarbonyl,
Fe(CO)5, ferrocene, Fe(C5H5)2, and the 5Dg electronic ground states of
FeCl2 and FeBr2. While the ligand field gradient tensor components change
relatively little with the method applied, the iron elec. field gradient is
sensitive to the specific d. functional used. Single ref. many-body
perturbation theory for electron correlation also performs poorly for the
iron elec. field gradient and shows extreme oscillatory behavior with a
change in the order of the perturbation series. Even with larger basis
sets and coupled cluster techniques a precise value for the iron elec.
field gradient could not be detd. from electronic structure calcns. due to
limitations in the theor. procedures. In order to avoid uncertainties in
the measured isomer shift which enters into the nuclear quadrupole coupling
const. the authors detd. the Mossbauer spectrum of Fe(C5H5)2 between temps.
of 4.2 and 295 K. In this range two phase transitions are obsd., but the
quadrupole splitting is not very dependent on the solid state structure in
each phase. Solid state effects for the Fe(CO)5 are detd. by comparing the
iron elec. field gradient of the isolated mol. with the value obtained from
1st principle solid state calcns. at various levels of theory. These
calcns. show that the influence of near neighboring effects to the iron
elec. field gradient is small. Fully relativistic Dirac-Hartree-Fock
calcns. for Fe(CO)5 reveal that relativistic effects for the iron elec.
field gradient are small as well. Fe(CO)5 is therefore an ideal test mol.
for the detn. of an accurate nuclear quadrupole moment from electronic
structure calcns. if combined with an exptl. nuclear quadrupole coupling
const. The best est. for the 57Fe nuclear quadrupole moment is 0.14(2)
barn in reasonable agreement with recent nuclear structure calcns.
View all works in Cristin
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Dalhus, Bjørn; Backe, Paul Hoff; Lærdahl, Jon Kristen; Rowe, Alexander D.; Blicher, Pernille & Forstrøm, Rune Johansen
[Show all 8 contributors for this article]
(2015).
Helse Sør-Øst Core Facility for Structural Biology and Bioinformatics.
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Andersen, Pernille Strøm; Backe, Paul Hoff; Lærdahl, Jon Kristen; Rowe, Alexander; Forstrøm, Rune Johansen & Rognes, Torbjørn
[Show all 8 contributors for this article]
(2014).
Helse Sør-Øst Core Facility for Structural Biology and Bioinformatics.
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Lærdahl, Jon Kristen; Nygård, Ståle; Jonassen, Inge; Hovig, Johannes Eivind; Petersen, Kjell & Drabløs, Finn
[Show all 8 contributors for this article]
(2013).
The national technology platform for bioinformatics.
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Zegeye, Ephrem Debebe; Balasingham, Seetha ; Lærdahl, Jon Kristen; Homberset, Håvard & Tønjum, Tone
(2013).
Mycobacterium tuberculosis RecG is a helicase enzyme with broad DNA substrate specificity.
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Balasingham, Seetha ; Zegeye, Ephrem Debebe; Homberset, Håvard; Rossi, Marie; Lærdahl, Jon Kristen & Bohr, Vilhelm A.
[Show all 7 contributors for this article]
(2013).
Unique features of DNA repair helicases in Mycobacterium tuberculosis.
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Balasingham, Seetha ; Zegeye, Ephrem Debebe; Homberset, Håvard; Rossi, Marie; Lærdahl, Jon Kristen & Bohr, Vilhelm A.
[Show all 7 contributors for this article]
(2013).
Unique Features of DNA Helicases in Mycobacterium tuberculosis.
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Zegeye, Ephrem Debebe; Balasingham, Seetha ; Lærdahl, Jon Kristen; Homberset, Håvard & Tønjum, Tone
(2013).
Mycobacterium tuberculosis RecG is a helicase enzyme with broad DNA substrate specificity.
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Zegeye, Ephrem Debebe; Balasingham, Seetha ; Lærdahl, Jon Kristen; Homberset, Håvard & Tønjum, Tone
(2012).
Mycobacterium tuberculosis RecG is a helicase enzyme with diverse DNA substrate affinities.
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Balasingham, Seetha ; Zegeye, Ephrem Debebe; Nilsen, Mariann; Homberset, Håvard; Rossie, Marie & Lærdahl, Jon Kristen
[Show all 8 contributors for this article]
(2012).
Delineating the functions of DNA repair helicases in Mycobacterium tuberculosis.
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Zegeye, Ephrem Debebe; Balasingham, Seetha ; Lærdahl, Jon Kristen; Homberset, Håvard & Tønjum, Tone
(2012).
Mycobacterium tuberculosis RecG is a helicase enzyme with diverse DNA substrate affinities.
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Zegeye, Ephrem Debebe; Balasingham, Seetha ; Lærdahl, Jon Kristen; Backe, Paul Hoff; Dalhus, Bjørn & Tønjum, Tone
(2011).
The M. tuberculosis RecG Enzyme Exhibits Helicase and ATPase Activities.
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Ambur, Ole Herman; Alfsnes, Kristian; Hovland, Eirik; Homberset, Håvard; Lærdahl, Jon Kristen & Frye, Stephan Alfons
[Show all 9 contributors for this article]
(2010).
Mechanisms of neisserial transformation and the evolution of sexual reproduction.
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Ochran, Richard Acquaah; Lærdahl, Jon Kristen; Fernandez, Israel; Frenking, Gernot & Uggerud, Einar
(2008).
The steric effect in SN2 reactions.Is it possible to dissect it from electronic effects?
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Published
Dec. 7, 2011 12:19 PM
- Last modified
Nov. 30, 2022 10:27 AM