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CreateGlycanSequonMover

Table of Contents

Reference

Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design Jared Adolf-Bryfogle, J. W Labonte, J. C Kraft, M. Shapavolov, S. Raemisch, T. Lutteke, F. Dimaio, C. D Bahl, J. Pallesen, N. P King, J. J Gray, D. W Kulp, W. R Schief bioRxiv 2021.09.27.462000; https://doi.org/10.1101/2021.09.27.462000

Details

Autogenerated Tag Syntax Documentation:

Author: Jared Adolf-Bryfogle (jadolfbr@gmail.com) @brief Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation as well as other positions that have been shown to influence the glycosylation chemistry.

@details Creates the glycan sequence motif around (and including) the potential glycosylation site. If the site could not be created due to the position being too close to the beginning or end of the sequence, Will set the mover status to fail, do not retry.

Creates an N-Linked Sequence Motif by default using the non-enhanced motif. This can be changed in options.

References and author information for the CreateGlycanSequonMover mover:

CreateGlycanSequonMover Mover's author(s): Jared Adolf-Bryfogle, The Scripps Research Institute, La Jolla, CA [jadolfbr@gmail.com]

<CreateGlycanSequonMover name="(&string;)"
        basic_enhanced_n_sequon="(false &bool;)" c_linked_NxC="(false &bool;)"
        c_linked_WxxW="(false &bool;)" c_linked_WSTxC="(false &bool;)"
        positions_as_start_of_sequon="(false &bool;)"
        design_x_positions="(false &bool;)" pack_neighbors="(true &bool;)"
        design_neighbors="(false &bool;)" neighbor_distance="(6.0 &real;)"
        pack_rounds="(5 &non_negative_integer;)" residue_selector="(&string;)"
        scorefxn="(&string;)" />

  • basic_enhanced_n_sequon: Set to use the enhanced sequon which has been shown to result in higher rates of glycosylation. REFERENCES: Enhanced Aromatic Sequons Increase Oligosaccharyltransferase Glycosylation Efficiency and Glycan Homogeneity Murray et al., 2015, Chemistry and Biology 22, 1052 1062 http://dx.doi.org/10.1016/j.chembiol.2015.06.017

    Residues Comprising the Enhanced Aromatic Sequon Influence Protein N-Glycosylation Efficiency Yen-Wen Huang, J. Am. Chem. Soc. 2017, 139, 12947 12955 DOI: 10.1021/jacs.7b03868

    If this is in beginning or end of protein and could not be created, will set fail do not retry mover status.

  • c_linked_NxC: Design in a c-linked sequon using NxC as the motif (Glycosylation at the N)
  • c_linked_WxxW: Design in a c-linked sequon using WxxW as the motif (Glycosylation at the first W)
  • c_linked_WSTxC: Design in a c-linked sequon using WSTxC as the motif (Glycosylation at W)
  • positions_as_start_of_sequon: Instead of having each position be the glycosylation position, have each position be the start of the sequon. This just makes using ResidueSelectors with this class a bit easier if needed. Only really applies to enhanced motifs
  • design_x_positions: Design any X position (which can be ANY reside, instead of keeping it as the input residue type in the pose.
  • pack_neighbors: Should we pack the neighboring residues to the motif during design?
  • design_neighbors: Should we design the neighboring residues to the motif during design?
  • neighbor_distance: Packing distance to neighbors?
  • pack_rounds: Number of rounds to run packing/design.
  • residue_selector: Set a number of positions using a residue selector. The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.
  • scorefxn: Name of score function to use

See Also