Package psidev.psi.mi.jami.model

Interface Allostery<T extends AllostericEffector>

All Superinterfaces:

CooperativeEffect

All Known Implementing Classes:

DefaultAllostery, XmlAllostery, XmlAllostery, XmlAllostery

public interface Allostery<T extends AllostericEffector>
extends CooperativeEffect

The allostery cooperative Effect. Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event

Since:

21/05/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Field Summary

Fields inherited from interface psidev.psi.mi.jami.model.CooperativeEffect

AFFECTED_INTERACTION, AFFECTED_INTERACTION_ID, ALLOSTERIC_DYNAMIC_CHANGE, ALLOSTERIC_DYNAMIC_CHANGE_ID, ALLOSTERIC_EFFECTOR, ALLOSTERIC_EFFECTOR_ID, ALLOSTERIC_K_RESPONSE, ALLOSTERIC_K_RESPONSE_ID, ALLOSTERIC_MOLECULE, ALLOSTERIC_MOLECULE_ID, ALLOSTERIC_PTM, ALLOSTERIC_PTM_ID, ALLOSTERIC_STRUCTURE_CHANE, ALLOSTERIC_STRUCTURE_CHANE_ID, ALLOSTERIC_V_RESPONSE, ALLOSTERIC_V_RESPONSE_ID, ALLOSTERY, ALLOSTERY_ID, ALTERED_PHYSICO_COMPATIBILITY, ALTERED_PHYSICO_COMPATIBILITY_ID, BINDING_HIDING, BINDING_HIDING_ID, COMPOSITE_BINDING, COMPOSITE_BINDING_ID, COOPERATIVE_EFFECT_VALUE, COOPERATIVE_EFFECT_VALUE_ID, EFFECT_OUTCOME, EFFECT_OUTCOME_MI, HETEROTROPIC_ALLOSTERY, HETEROTROPIC_ALLOSTERY_ID, HOMOTROPIC_ALLOSTERY, HOMOTROPIC_ALLOSTERY_ID, NEGATIVE_EFFECT, NEGATIVE_EFFECT_ID, PARTICIPANT_REF, PARTICIPANT_REF_ID, POSITIVE_EFFECT, POSITIVE_EFFECT_ID, PRE_ORGANIZATION, PRE_ORGANIZATION_ID, PREASSEMBLY, PREASSEMBLY_ID

Method Summary

Modifier and Type	Method	Description
T	getAllostericEffector()	The effector that elicits an allosteric response.
CvTerm	getAllostericMechanism()	The process that mediates the allosteric response of a molecule upon allosteric post-translational modification or binding of an allosteric effector.
ModelledEntity	getAllostericMolecule()	A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site.
CvTerm	getAllosteryType()	The allosteric type indicates the chemical relationship between the two ligands whose binding is allosterically coupled.
void	setAllostericEffector(T effector)	Sets the effector that elicits an allosteric response.
void	setAllostericMechanism(CvTerm mechanism)	Sets the allosteric mechanism.
void	setAllostericMolecule(ModelledEntity participant)	Sets the allosteric molecule.
void	setAllosteryType(CvTerm type)	Sets the allostery type.

Methods inherited from interface psidev.psi.mi.jami.model.CooperativeEffect

getAffectedInteractions, getAnnotations, getCooperativityEvidences, getOutCome, getResponse, setOutCome, setResponse

Method Detail

getAllostericMechanism

CvTerm getAllostericMechanism()

The process that mediates the allosteric response of a molecule upon allosteric post-translational modification or binding of an allosteric effector. It is a controlled vocabulary term and can be null if not known. Ex: allosteric change in dynamics, allosteric change in structure, ...

Returns:

the allosteric mechanism

setAllostericMechanism

void setAllostericMechanism(CvTerm mechanism)

Sets the allosteric mechanism.

Parameters:

mechanism - : allosteric mechanism

getAllosteryType

CvTerm getAllosteryType()

The allosteric type indicates the chemical relationship between the two ligands whose binding is allosterically coupled. It is a controlled vocabulary term and can be null if not known. Ex: heterotropic allostery, homotropic allostery

Returns:

the allostery stype

setAllosteryType

void setAllosteryType(CvTerm type)

Sets the allostery type.

Parameters:

type - : allostery type

getAllostericMolecule

ModelledEntity getAllostericMolecule()

A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. It cannot be null.

Returns:

the allosteric molecule

setAllostericMolecule

void setAllostericMolecule(ModelledEntity participant)

Sets the allosteric molecule.

Parameters:

participant - : allosteric molecule (can refer to any participating entity)

Throws:

IllegalArgumentException - when participant is null

getAllostericEffector

T getAllostericEffector()

The effector that elicits an allosteric response. It cannot be null.

Returns:

The effector that elicits an allosteric response (participant or feature).

setAllostericEffector

void setAllostericEffector(T effector)

Sets the effector that elicits an allosteric response.

Parameters:

effector - : the allosteric effector

Throws:

IllegalArgumentException - when effector is null