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Items: 1 to 50 of 53

1.

QresFEP: An Automated Protocol for Free Energy Calculations of Protein Mutations in Q.

Jespers W, Isaksen GV, Andberg TAH, Vasile S, van Veen A, Åqvist J, Brandsdal BO, Gutiérrez-de-Terán H.

J Chem Theory Comput. 2019 Sep 4. doi: 10.1021/acs.jctc.9b00538. [Epub ahead of print]

PMID:
31436990
2.

Catalytic Adaptation of Psychrophilic Elastase.

Sočan J, Kazemi M, Isaksen GV, Brandsdal BO, Åqvist J.

Biochemistry. 2018 May 22;57(20):2984-2993. doi: 10.1021/acs.biochem.8b00078. Epub 2018 May 10.

PMID:
29726678
3.

A comparative study of cold- and warm-adapted Endonucleases A using sequence analyses and molecular dynamics simulations.

Michetti D, Brandsdal BO, Bon D, Isaksen GV, Tiberti M, Papaleo E.

PLoS One. 2017 Feb 13;12(2):e0169586. doi: 10.1371/journal.pone.0169586. eCollection 2017.

4.

Entropy and Enzyme Catalysis.

Åqvist J, Kazemi M, Isaksen GV, Brandsdal BO.

Acc Chem Res. 2017 Feb 21;50(2):199-207. doi: 10.1021/acs.accounts.6b00321. Epub 2017 Feb 7.

5.

Thermodynamics of the Purine Nucleoside Phosphorylase Reaction Revealed by Computer Simulations.

Isaksen GV, Åqvist J, Brandsdal BO.

Biochemistry. 2017 Jan 10;56(1):306-312. doi: 10.1021/acs.biochem.6b00967. Epub 2016 Dec 27.

PMID:
27976868
6.

Probing the ATP-Binding Pocket of Protein Kinase DYRK1A with Benzothiazole Fragment Molecules.

Rothweiler U, Stensen W, Brandsdal BO, Isaksson J, Leeson FA, Engh RA, Svendsen JS.

J Med Chem. 2016 Nov 10;59(21):9814-9824. Epub 2016 Oct 21.

PMID:
27736065
7.

Enzyme surface rigidity tunes the temperature dependence of catalytic rates.

Isaksen GV, Åqvist J, Brandsdal BO.

Proc Natl Acad Sci U S A. 2016 Jul 12;113(28):7822-7. doi: 10.1073/pnas.1605237113. Epub 2016 Jun 27.

8.

Computer Simulations Reveal Substrate Specificity of Glycosidic Bond Cleavage in Native and Mutant Human Purine Nucleoside Phosphorylase.

Isaksen GV, Hopmann KH, Åqvist J, Brandsdal BO.

Biochemistry. 2016 Apr 12;55(14):2153-62. doi: 10.1021/acs.biochem.5b01347. Epub 2016 Mar 29.

PMID:
26985580
9.

Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems.

Isaksen GV, Andberg TA, Åqvist J, Brandsdal BO.

J Mol Graph Model. 2015 Jul;60:15-23. doi: 10.1016/j.jmgm.2015.05.007. Epub 2015 May 21.

PMID:
26080356
10.

Stem cell regulation: Implications when differentiated cells regulate symmetric stem cell division.

Høyem MR, Måløy F, Jakobsen P, Brandsdal BO.

J Theor Biol. 2015 Sep 7;380:203-19. doi: 10.1016/j.jtbi.2015.05.009. Epub 2015 May 19.

11.

Protein surface softness is the origin of enzyme cold-adaptation of trypsin.

Isaksen GV, Åqvist J, Brandsdal BO.

PLoS Comput Biol. 2014 Aug 28;10(8):e1003813. doi: 10.1371/journal.pcbi.1003813. eCollection 2014 Aug.

12.

Anticancer potency of small linear and cyclic tetrapeptides and pharmacokinetic investigations of peptide binding to human serum albumin.

Sivertsen A, Tørfoss V, Isaksson J, Ausbacher D, Anderssen T, Brandsdal BO, Havelkova M, Skjørholm AE, Strøm MB.

J Pept Sci. 2014 Apr;20(4):279-91.

PMID:
24677781
13.

Synthetic cationic antimicrobial peptides bind with their hydrophobic parts to drug site II of human serum albumin.

Sivertsen A, Isaksson J, Leiros HK, Svenson J, Svendsen JS, Brandsdal BO.

BMC Struct Biol. 2014 Jan 23;14:4. doi: 10.1186/1472-6807-14-4.

14.

Short cationic antimicrobial peptides bind to human alpha-1 acid glycoprotein with no implications for the in vitro bioactivity.

Sivertsen A, Brandsdal BO, Svendsen JS, Andersen JH, Svenson J.

J Mol Recognit. 2013 Oct;26(10):461-9. doi: 10.1002/jmr.2288.

PMID:
23996488
15.

A polarizable embedding DFT study of one-photon absorption in fluorescent proteins.

Beerepoot MT, Steindal AH, Kongsted J, Brandsdal BO, Frediani L, Ruud K, Olsen JM.

Phys Chem Chem Phys. 2013 Apr 7;15(13):4735-43. doi: 10.1039/c3cp44659j.

PMID:
23426505
16.

Improved anticancer potency by head-to-tail cyclization of short cationic anticancer peptides containing a lipophilic β(2,2) -amino acid.

Tørfoss V, Isaksson J, Ausbacher D, Brandsdal BO, Flaten GE, Anderssen T, Cavalcanti-Jacobsen Cde A, Havelkova M, Nguyen LT, Vogel HJ, Strøm MB.

J Pept Sci. 2012 Oct;18(10):609-19. doi: 10.1002/psc.2441. Epub 2012 Aug 30.

PMID:
22933412
17.

Targeting the S1 and S3 subsite of trypsin with unnatural cationic amino acids generates antimicrobial peptides with potential for oral administration.

Karstad R, Isaksen G, Wynendaele E, Guttormsen Y, De Spiegeleer B, Brandsdal BO, Svendsen JS, Svenson J.

J Med Chem. 2012 Jul 26;55(14):6294-305. doi: 10.1021/jm3002058. Epub 2012 Jul 11.

PMID:
22720778
18.

Crystal structure of the mobile metallo-β-lactamase AIM-1 from Pseudomonas aeruginosa: insights into antibiotic binding and the role of Gln157.

Leiros HK, Borra PS, Brandsdal BO, Edvardsen KS, Spencer J, Walsh TR, Samuelsen O.

Antimicrob Agents Chemother. 2012 Aug;56(8):4341-53. doi: 10.1128/AAC.00448-12. Epub 2012 Jun 4.

19.

Synthesis of anticancer heptapeptides containing a unique lipophilic β(2,2) -amino acid building block.

Tørfoss V, Ausbacher D, Cavalcanti-Jacobsen Cde A, Hansen T, Brandsdal BO, Havelkova M, Strøm MB.

J Pept Sci. 2012 Mar;18(3):170-6. doi: 10.1002/psc.1434. Epub 2012 Jan 16.

PMID:
22249949
20.

A synthetic antimicrobial peptidomimetic (LTX 109): stereochemical impact on membrane disruption.

Isaksson J, Brandsdal BO, Engqvist M, Flaten GE, Svendsen JS, Stensen W.

J Med Chem. 2011 Aug 25;54(16):5786-95. doi: 10.1021/jm200450h. Epub 2011 Jul 26.

PMID:
21732630
21.

Unnatural amino acid side chains as S1, S1', and S2' probes yield cationic antimicrobial peptides with stability toward chymotryptic degradation.

Karstad R, Isaksen G, Brandsdal BO, Svendsen JS, Svenson J.

J Med Chem. 2010 Aug 12;53(15):5558-66. doi: 10.1021/jm1006337.

PMID:
20608742
22.

Near native-state conformational landscape of psychrophilic and mesophilic enzymes: probing the folding funnel model.

Mereghetti P, Riccardi L, Brandsdal BO, Fantucci P, De Gioia L, Papaleo E.

J Phys Chem B. 2010 Jun 10;114(22):7609-19. doi: 10.1021/jp911523h.

PMID:
20518574
23.

Experimental and computational characterization of the ferric uptake regulator from Aliivibrio salmonicida (Vibrio salmonicida).

Pedersen HL, Ahmad R, Riise EK, Leiros HK, Hauglid S, Espelid S, Brandsdal BO, Leiros I, Willassen NP, Haugen P.

J Microbiol. 2010 Apr;48(2):174-83. doi: 10.1007/s12275-010-9199-5. Epub 2010 May 1.

PMID:
20437149
24.

Thermodynamics and structure of a salmon cold active goose-type lysozyme.

Kyomuhendo P, Myrnes B, Brandsdal BO, Smalås AO, Nilsen IW, Helland R.

Comp Biochem Physiol B Biochem Mol Biol. 2010 Aug;156(4):254-63. doi: 10.1016/j.cbpb.2010.04.002. Epub 2010 Apr 14.

PMID:
20398783
25.

Biophysical characterization and mutational analysis of the antibiotic resistance protein NimA from Deinococcus radiodurans.

Leiros HK, Brandsdal BO, McSweeney SM.

Biochim Biophys Acta. 2010 Apr;1804(4):967-76. doi: 10.1016/j.bbapap.2010.01.010. Epub 2010 Jan 21.

PMID:
20096385
26.

Altered activity and physicochemical properties of short cationic antimicrobial peptides by incorporation of arginine analogues.

Svenson J, Karstad R, Flaten GE, Brandsdal BO, Brandl M, Svendsen JS.

Mol Pharm. 2009 May-Jun;6(3):996-1005. doi: 10.1021/mp900057k.

PMID:
19341291
27.

Ferric uptake regulator protein: binding free energy calculations and per-residue free energy decomposition.

Ahmad R, Brandsdal BO, Michaud-Soret I, Willassen NP.

Proteins. 2009 May 1;75(2):373-86. doi: 10.1002/prot.22247.

PMID:
18831042
28.

Cold adaptation of enzyme reaction rates.

Bjelic S, Brandsdal BO, Aqvist J.

Biochemistry. 2008 Sep 23;47(38):10049-57. doi: 10.1021/bi801177k. Epub 2008 Aug 30.

PMID:
18759500
29.

Structural evidence for lack of inhibition of fish goose-type lysozymes by a bacterial inhibitor of lysozyme.

Kyomuhendo P, Nilsen IW, Brandsdal BO, Smalås AO.

J Mol Model. 2008 Sep;14(9):777-88. doi: 10.1007/s00894-008-0317-9. Epub 2008 May 20.

PMID:
18491152
30.

Effects of salt on the kinetics and thermodynamic stability of endonuclease I from Vibrio salmonicida and Vibrio cholerae.

Niiranen L, Altermark B, Brandsdal BO, Leiros HK, Helland R, Smalås AO, Willassen NP.

FEBS J. 2008 Apr;275(7):1593-605. doi: 10.1111/j.1742-4658.2008.06317.x. Epub 2008 Feb 27.

31.

Antimicrobial peptides with stability toward tryptic degradation.

Svenson J, Stensen W, Brandsdal BO, Haug BE, Monrad J, Svendsen JS.

Biochemistry. 2008 Mar 25;47(12):3777-88. doi: 10.1021/bi7019904. Epub 2008 Feb 29.

PMID:
18307313
32.

Electrostatic interactions play an essential role in DNA repair and cold-adaptation of uracil DNA glycosylase.

Olufsen M, Smalås AO, Brandsdal BO.

J Mol Model. 2008 Mar;14(3):201-13. doi: 10.1007/s00894-007-0261-0. Epub 2008 Jan 15.

PMID:
18196298
33.

Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase.

Olufsen M, Papaleo E, Smalås AO, Brandsdal BO.

Proteins. 2008 May 15;71(3):1219-30.

PMID:
18004790
34.

Albumin binding of short cationic antimicrobial micropeptides and its influence on the in vitro bactericidal effect.

Svenson J, Brandsdal BO, Stensen W, Svendsen JS.

J Med Chem. 2007 Jul 12;50(14):3334-9. Epub 2007 Jun 15.

PMID:
17569519
35.
36.

Optimization of electrostatics as a strategy for cold-adaptation: a case study of cold- and warm-active elastases.

Papaleo E, Olufsen M, De Gioia L, Brandsdal BO.

J Mol Graph Model. 2007 Jul;26(1):93-103. Epub 2006 Sep 30.

PMID:
17084098
37.

Free energy calculations show that acidic P1 variants undergo large pKa shifts upon binding to trypsin.

Brandsdal BO, Smalås AO, Aqvist J.

Proteins. 2006 Aug 15;64(3):740-8.

PMID:
16752417
38.

Inspection of the binding sites of proteinase3 for the design of a highly specific substrate.

Hajjar E, Korkmaz B, Gauthier F, Brandsdal BO, Witko-Sarsat V, Reuter N.

J Med Chem. 2006 Feb 23;49(4):1248-60.

PMID:
16480262
39.

Predicting proteinase specificities from free energy calculations.

Mekonnen SM, Olufsen M, Smalås AO, Brandsdal BO.

J Mol Graph Model. 2006 Oct;25(2):176-85. Epub 2006 Jan 10.

PMID:
16386933
40.

Probing the effect of point mutations at protein-protein interfaces with free energy calculations.

Almlöf M, Aqvist J, Smalås AO, Brandsdal BO.

Biophys J. 2006 Jan 15;90(2):433-42. Epub 2005 Nov 4.

41.

Resolving the energy paradox of chaperone/usher-mediated fibre assembly.

Zavialov AV, Tischenko VM, Fooks LJ, Brandsdal BO, Aqvist J, Zav'yalov VP, Macintyre S, Knight SD.

Biochem J. 2005 Aug 1;389(Pt 3):685-94.

42.

Increased flexibility as a strategy for cold adaptation: a comparative molecular dynamics study of cold- and warm-active uracil DNA glycosylase.

Olufsen M, Smalås AO, Moe E, Brandsdal BO.

J Biol Chem. 2005 May 6;280(18):18042-8. Epub 2005 Mar 3.

43.

Binding affinity prediction with different force fields: examination of the linear interaction energy method.

Almlöf M, Brandsdal BO, Aqvist J.

J Comput Chem. 2004 Jul 30;25(10):1242-54.

PMID:
15139037
44.

The primary structure and specificity determining residues displayed by recombinant salmon antibody domains.

Solem ST, Brandsdal BO, Smalås A, Jørgensen TØ.

Mol Immunol. 2004 Apr;40(18):1347-60.

PMID:
15072853
45.

Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements.

Leiros HK, Brandsdal BO, Andersen OA, Os V, Leiros I, Helland R, Otlewski J, Willassen NP, Smalås AO.

Protein Sci. 2004 Apr;13(4):1056-70.

46.

Free energy calculations and ligand binding.

Brandsdal BO, Osterberg F, Almlöf M, Feierberg I, Luzhkov VB, Aqvist J.

Adv Protein Chem. 2003;66:123-58. Review. No abstract available.

PMID:
14631818
47.

Ligand binding affinities from MD simulations.

Aqvist J, Luzhkov VB, Brandsdal BO.

Acc Chem Res. 2002 Jun;35(6):358-65. Review.

PMID:
12069620
48.

The antibody site in Atlantic salmon; phage display and modeling of scFv with anti-hapten binding ability.

Jørgensen TØ, Solem ST, Espelid S, Warr GW, Brandsdal BO, Smalås A.

Dev Comp Immunol. 2002 Mar;26(2):201-6.

PMID:
11696385
49.

Computational analysis of binding of P1 variants to trypsin.

Brandsdal BO, Aqvist J, Smalås AO.

Protein Sci. 2001 Aug;10(8):1584-95.

50.

Electrostatic effects play a central role in cold adaptation of trypsin.

Brandsdal BO, Smalås AO, Aqvist J.

FEBS Lett. 2001 Jun 15;499(1-2):171-5.

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