Change search
Refine search result
1 - 5 of 5
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Mark, Pekka
    et al.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Baumann, Martin J.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Eklöf, Jens M.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Gullfot, Fredrika
    KTH, School of Biotechnology (BIO), Glycoscience.
    Michel, Gurvan
    Kallas, Åsa M.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Teeri, Tuula T.
    KTH, School of Biotechnology (BIO), Glycoscience.
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Czjzek, Mirjam
    Analysis of nasturtium TmNXG1 complexes by crystallography and molecular dynamics provides detailed insight into substrate recognition by family GH16 xyloglucan endo-transglycosylases and endo-hydrolases2009In: Proteins: Structure, Function, and Bioinformatics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 75, no 4, p. 820-836Article in journal (Refereed)
    Abstract [en]

    Reorganization and degradation of the wall crosslinking and seed storage polysaccharide xyloglucan by glycoside hydrolase family 16 (GH16) endo-transglycosylases and hydrolases are crucial to the growth of the majority of land plants, affecting processes as diverse as germination, morphogenesis, and fruit ripening. A high-resolution, three-dimensional structure of a nasturtium (Tropaeolum majus) endo-xyloglucanase loop mutant, TmNXG1-Delta YNIIG, with an ohgosaccharide product bound in the negative active-site subsites, has been solved by X-ray crystallography. Comparison of this novel complex to that of the strict xyloglucan endotransglycosylase PttXET16-34 from hybrid aspen (Populus tremula x tremuloides), previously solved with a xylogluco-oligosaccharide bound in the positive subsites, highlighted key protein structures that affect the disparate catalytic activities displayed by these closely related enzymes. Combination of these "partial" active-site complexes through molecular dynamics simulations in water allowed modeling of wild-type TmNXG1, TmNXG1-Delta YNIIG, and wild-type PttXET16-34 in complex with a xyloglucan octadecasaccharide spanning the entire catalytic cleft. A comprehensive analysis of these full-length complexes underscored the importance of various loops lining the active site. Subtle differences leading to a tighter hydrogen bonding pattern on the negative (glycosyl donor) binding subsites, together with loop flexibility on the positive (glycosyl acceptor) binding subsites appear to favor hydrolysis over transglycosylation in GH16 xyloglucan-active enzymes.

  • 2.
    Mark, Pekka
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Qiong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Czjzek, Mirjam
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucan endo-transglycosylase2011In: Molecular Simulation, ISSN 0892-7022, E-ISSN 1029-0435, Vol. 37, no 12, p. 1001-1013Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 have been performed and analysed with respect to structure, dynamics, flexibility and ligand interactions. Notably, the charge state of the so-called 'helper residue' aspartate 87 (Asp87), which lies between the catalytic nucleophile [glutamate 85 (Glu85)] and general acid/base (Glu89) residues on the same beta strand, had a significant effect on PttXET16-34 active site structure. When Asp87 was deprotonated, electrostatic repulsion forced the nucleophile away from C1 of the sugar ring in subsite - 1 and the proton-donating ability of Glu89 was also weakened due to the formation of a hydrogen bond with Asp87, whereas the protonation of Asp87 resulted in the formation of a hydrogen bond with the catalytic nucleophile and correct positioning of the catalytic machinery. The results suggest that catalysis in glycoside hydrolase family 16, and by extension clan GH-B enzymes, is optimal when the catalytic nucleophile is deprotonated for nucleophilic attack on the substrate, whereas the 'helper residue' and general acid/base residue are both in their conjugate acid forms to align the nucleophile and deliver a proton to the departing sugar, respectively.

  • 3.
    Mark, Pekka
    et al.
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhang, Qiong
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Czjzek, Mirjam
    Brumer, Harry
    KTH, School of Biotechnology (BIO), Glycoscience.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Molecular dynamics simulations of a branched tetradecasaccharide substrate in the active site of a xyloglucan endo-transglycosylaseIn: Molecular Simulation, ISSN 0892-7022, E-ISSN 1029-0435Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics (MD) simulations of the tetradecasaccharide XXXGXXXG in complex with the hybrid aspen xyloglucan endo-transglycosylase PttXET16-34 have been performed and analyzed with respect to structure, dynamics, flexibility and ligand interactions. Notably, the charge state of the so-called “helper residue” Asp87, which lies between the catalytic nucleophile (Glu85) and general acid/base (Glu89) residues on the same beta strand, had a significant effect on PttXET16-34 active site structure. When Asp87 was deprotonated, electrostatic repulsion forced the nucleophile Glu85 away from C-1 of the sugar ring in subsite -1 and the electrophile Glu89 was also weakened due to the formation of a hydrogen bond to Asp87, whereas the protonation of Asp87 resulted in the formation of a hydrogen bond with the catalytic nucleophile and correct positioning of the catalytic machinery. The results suggest that catalysis in glycoside hydrolase family 16, and by extension clan GH-B enzymes, is optimal when the catalytic nucleophile is deprotonated for nucleophilic attack on the substrate, while the “helper residue” and general acid/base residue are both in their conjugate-acid forms to align the nucleophile and deliver a proton to the departing sugar, respectively.

  • 4. Rundgren, Henrik
    et al.
    Mark, Pekka
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Laaksonen, Aatto
    Molecular dynamics simulations of conserved Hox protein hexapeptides - II. Folded structures in water solution2007In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 805, no 1-3, p. 61-70Article in journal (Refereed)
    Abstract [en]

    MD simulations of Hox protein N-terminal hexapeptides TFDWMK (Hox B1) and LFPWMR (Hox B8) are performed in water solution and complemented with simulations where the aromatic residues phenylalanine (F) and tryptophan (W) are successively replaced by alanine (A). Results from this study give support that different hexapeptides can form similar folded structures in water, stabilized mainly by internal hydrogen bonding where the arrangement of the aromatic side chains together with the methionine (M) side chain forming a hydrophobic core covers and protects the internal hydrogen bonds from water. Replacement of the aromatic side chains with Alanine did not lead to unfolding, but rather the hexapeptides were slightly changing their conformations where the Methionine side chain together with the peptide backbone protected the internal hydrogen bonds and the hexapeptides remain folded. Our results give support that these hexapeptides are able to remain folded to some extent even without the aromatic side chains.

  • 5. Rundgren, Henrik
    et al.
    Mark, Pekka
    KTH, School of Biotechnology (BIO), Theoretical Chemistry (closed 20110512).
    Laaksonen, Aatto
    Molecular dynamics simulations of conserved Hox protein hexapeptides. I. Folding behavior in water solution2007In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 810, no 1-3, p. 113-120Article in journal (Refereed)
    Abstract [en]

    Molecular dynamics simulations of hexapeptides TFDWMK and LFPWMR; the highly conserved regions of Hox proteins Hox B1 and Hox B8, respectively, are carried out starting from extended structures to investigate their conformational space in water solution. In addition, we have studied TADWMK and TADAMK, where the aromatic residues Phenylalanine and Tryptophan were successively substituted for Alanine to investigate effects from the presence/absence of aromatic amino acids and interactions between them to folding behavior. The backbone of the hexapeptides in all simulations folds to a similar conformation found in experimental studies in solution. Intramolecular, hydrophobically driven interactions between the aromatic residues and internal hydrogen bonds are found to stabilize the conformations.

1 - 5 of 5
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf