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. More...

#include <CreateGlycanSequonMover.hh>

Inheritance diagram for protocols::carbohydrates::CreateGlycanSequonMover:

[legend]

Public Member Functions
	CreateGlycanSequonMover ()
	Constructors ///. More...

	CreateGlycanSequonMover (core::select::residue_selector::ResidueSelectorCOP selector)

	CreateGlycanSequonMover (CreateGlycanSequonMover const &src)
	Copy constructor (not needed unless you need deep copies) More...

	~CreateGlycanSequonMover () override
	Destructor (important for properly forward-declaring smart-pointer members) More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

void	set_glycosylation_position (core::Size position, core::pose::Pose const &pose)
	Set the target glycosylation position for which the sequence motif will be created around. If this is in beginning or end of protein and could not be created, will set fail do not retry mover status. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Set a number of positions using a residue selector. The positions are where glycosylation is intended to occur. More...

void	set_positions_as_start_of_sequon (bool positions_as_start)
	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. More...

void	set_use_basic_enhanced_n_linked_sequon (bool enhanced)
	Set to use the enhanced sequon which has been shown to result in higher rates of glycosylation and slightly lower complex types as the glycan site. (Aromatics at n+2) More...

void	set_glycan_sequon_type (GlycanSequon sequon)
	Set any sequon type. More...

void	set_score_function (core::scoring::ScoreFunctionCOP scorefxn)

void	set_design_x_positions (bool const design_x_positions)
	If there is an X in the motif, should we design it or leave it alone. Default is to leave it alone. More...

void	set_pack_rounds (core::Size pack_rounds)
	Number of rounds to run packing/design. Default is 5. More...

void	set_pack_neighbors (bool const pack_neighbors)
	Should we pack neighbors of the motif? Default is True. More...

void	set_design_neighbors (bool const design_neighbors)
	Should we design neighbors of the motif? Default is False. More...

void	set_pack_distance (core::Real const pack_distance)
	Set the neighbor detection distance for any packing/design of neighbors. More...

void	show (std::ostream &output=std::cout) const override
	Show the contents of the Mover. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Rosetta Scripts Support ///. More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Attributes
std::map< GlycanSequon, std::string >	sequons_

core::select::residue_selector::ResidueSelectorCOP	selector_ = nullptr

GlycanSequon	sequon_type_ = n_linked_typical

bool	positions_as_start_of_sequon_ = false

bool	design_x_positions_ = false

calc_taskop_movers::CreateSequenceMotifMoverOP	motif_mover_

bool	pack_neighbors_ = true

bool	design_neighbors_ = false

core::Real	pack_distance_ = 6.0

core::Size	pack_rounds_ = 5

core::scoring::ScoreFunctionCOP	scorefxn_ = nullptr

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

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.

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.

Constructor & Destructor Documentation

protocols::carbohydrates::CreateGlycanSequonMover::CreateGlycanSequonMover ( )

Constructors ///.

Default constructor

References protocols::carbohydrates::create_sequons(), motif_mover_, and sequons_.

protocols::carbohydrates::CreateGlycanSequonMover::CreateGlycanSequonMover ( core::select::residue_selector::ResidueSelectorCOP selector )

References protocols::carbohydrates::create_sequons(), motif_mover_, sequons_, and set_residue_selector().

protocols::carbohydrates::CreateGlycanSequonMover::CreateGlycanSequonMover ( CreateGlycanSequonMover const & src )

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References protocols::carbohydrates::create_sequons(), motif_mover_, scorefxn_, selector_, and sequons_.

protocols::carbohydrates::CreateGlycanSequonMover::~CreateGlycanSequonMover ( )

override

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

void protocols::carbohydrates::CreateGlycanSequonMover::apply ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Apply the mover.

Apply the mover

If the sequon could not be created (for example the length of the sequon is longer than the protein/etc. It will set mover_failed_do_not retry. It is your responsiblity to catch this and do whatever you wish with it.

Implements protocols::moves::Mover.

References design_neighbors_, design_x_positions_, motif_mover_, protocols::carbohydrates::n_linked_basic_enhanced, protocols::carbohydrates::n_linked_best_enhanced, pack_distance_, pack_neighbors_, pack_rounds_, positions_as_start_of_sequon_, scorefxn_, selector_, sequon_type_, sequons_, core::id::to_string(), core::pose::Pose::total_residue(), and protocols::TR().

protocols::moves::MoverOP protocols::carbohydrates::CreateGlycanSequonMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::carbohydrates::CreateGlycanSequonMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::carbohydrates::CreateGlycanSequonMover::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::carbohydrates::CreateGlycanSequonMover::mover_name ( )

static

Referenced by get_name(), protocols::carbohydrates::CreateGlycanSequonMoverCreator::keyname(), provide_citation_info(), and provide_xml_schema().

void protocols::carbohydrates::CreateGlycanSequonMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References protocols::carbohydrates::c_linked_NxC, protocols::carbohydrates::c_linked_WSTxC, protocols::carbohydrates::c_linked_WxxW, design_neighbors_, protocols::carbohydrates::n_linked_basic_enhanced, protocols::carbohydrates::n_linked_typical, pack_distance_, pack_neighbors_, pack_rounds_, core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), sequon_type_, set_design_neighbors(), set_design_x_positions(), set_pack_distance(), set_pack_neighbors(), set_pack_rounds(), set_residue_selector(), and set_score_function().

void protocols::carbohydrates::CreateGlycanSequonMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References mover_name().

void protocols::carbohydrates::CreateGlycanSequonMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_get_score_function_name(), core::select::residue_selector::attributes_for_parse_residue_selector_default_option_name(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::carbohydrates::CreateGlycanSequonMoverCreator::provide_xml_schema().

void protocols::carbohydrates::CreateGlycanSequonMover::set_design_neighbors ( bool const design_neighbors )

Should we design neighbors of the motif? Default is False.

References design_neighbors_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_design_x_positions ( bool const design_x_positions )

If there is an X in the motif, should we design it or leave it alone. Default is to leave it alone.

References design_x_positions_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_glycan_sequon_type ( GlycanSequon sequon )

Set any sequon type.

References sequon_type_.

void protocols::carbohydrates::CreateGlycanSequonMover::set_glycosylation_position	(	core::Size	position,
		core::pose::Pose const &	pose
	)

Set the target glycosylation position for which the sequence motif will be created around. If this is in beginning or end of protein and could not be created, will set fail do not retry mover status.

Mover Methods ///.

References selector_, and core::pose::Pose::size().

void protocols::carbohydrates::CreateGlycanSequonMover::set_pack_distance ( core::Real const pack_distance )

Set the neighbor detection distance for any packing/design of neighbors.

References pack_distance_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_pack_neighbors ( bool const pack_neighbors )

Should we pack neighbors of the motif? Default is True.

References pack_neighbors_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_pack_rounds ( core::Size pack_rounds )

Number of rounds to run packing/design. Default is 5.

References pack_rounds_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_positions_as_start_of_sequon ( bool positions_as_start )

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.

This only effects the basic_enhanced and best_enhanced sequons!

References positions_as_start_of_sequon_.

void protocols::carbohydrates::CreateGlycanSequonMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Set a number of positions using a residue selector. The positions are where glycosylation is intended to occur.

References selector_.

Referenced by CreateGlycanSequonMover(), and parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_score_function ( core::scoring::ScoreFunctionCOP scorefxn )

References scorefxn_.

Referenced by parse_my_tag().

void protocols::carbohydrates::CreateGlycanSequonMover::set_use_basic_enhanced_n_linked_sequon ( bool enhanced )

Set to use the enhanced sequon which has been shown to result in higher rates of glycosylation and slightly lower complex types as the glycan site. (Aromatics at n+2)

DEFAULT: False

REFS: "Enhanced Aromatic Sequons Increase Oligosaccharyltransferase Glycosylation Efficiency and Glycan Homogeneity" Murray et al., 2015, Chemistry & 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

References protocols::carbohydrates::n_linked_basic_enhanced, protocols::carbohydrates::n_linked_typical, and sequon_type_.

void protocols::carbohydrates::CreateGlycanSequonMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::carbohydrates::operator<<().

Member Data Documentation

bool protocols::carbohydrates::CreateGlycanSequonMover::design_neighbors_ = false

private

Referenced by apply(), parse_my_tag(), and set_design_neighbors().

bool protocols::carbohydrates::CreateGlycanSequonMover::design_x_positions_ = false

private

Referenced by apply(), and set_design_x_positions().

calc_taskop_movers::CreateSequenceMotifMoverOP protocols::carbohydrates::CreateGlycanSequonMover::motif_mover_

private

Referenced by apply(), and CreateGlycanSequonMover().

core::Real protocols::carbohydrates::CreateGlycanSequonMover::pack_distance_ = 6.0

private

Referenced by apply(), parse_my_tag(), and set_pack_distance().

bool protocols::carbohydrates::CreateGlycanSequonMover::pack_neighbors_ = true

private

Referenced by apply(), parse_my_tag(), and set_pack_neighbors().

core::Size protocols::carbohydrates::CreateGlycanSequonMover::pack_rounds_ = 5

private

Referenced by apply(), parse_my_tag(), and set_pack_rounds().

bool protocols::carbohydrates::CreateGlycanSequonMover::positions_as_start_of_sequon_ = false

private

Referenced by apply(), and set_positions_as_start_of_sequon().

core::scoring::ScoreFunctionCOP protocols::carbohydrates::CreateGlycanSequonMover::scorefxn_ = nullptr

private

Referenced by apply(), CreateGlycanSequonMover(), and set_score_function().

core::select::residue_selector::ResidueSelectorCOP protocols::carbohydrates::CreateGlycanSequonMover::selector_ = nullptr

private

Referenced by apply(), CreateGlycanSequonMover(), set_glycosylation_position(), and set_residue_selector().

GlycanSequon protocols::carbohydrates::CreateGlycanSequonMover::sequon_type_ = n_linked_typical

private

Referenced by apply(), parse_my_tag(), set_glycan_sequon_type(), and set_use_basic_enhanced_n_linked_sequon().

std::map< GlycanSequon, std::string > protocols::carbohydrates::CreateGlycanSequonMover::sequons_

private

Referenced by apply(), and CreateGlycanSequonMover().

The documentation for this class was generated from the following files:

src/protocols/carbohydrates/CreateGlycanSequonMover.hh
src/protocols/carbohydrates/CreateGlycanSequonMover.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation