org.biopax.paxtools.model.level3

Interface Catalysis

All Superinterfaces:

BioPAXElement, Cloneable, Control, Entity, Interaction, Level3Element, Named, Observable, Process, Serializable, XReferrable

All Known Implementing Classes:

CatalysisImpl

public interface Catalysis
extends Control

Definition: A control interaction in which a physical entity (a catalyst) increases the rate of a conversion interaction by lowering its activation energy. Instances of this class describe a pairing between a catalyzing entity and a catalyzed conversion. Rationale: Catalysis, theoretically, is always bidirectional since it acts by lowering the activation energy. Physiologically, however, it can have a direction because of the concentration of the participants. For example, the oxidative decarboxylation catalyzed by Isocitrate dehydrogenase always happens in one direction under physiological conditions since the produced carbon dioxide is constantly removed from the system. Usage: A separate catalysis instance should be created for each different conversion that a physicalEntity may catalyze and for each different physicalEntity that may catalyze a conversion. For example, a bifunctional enzyme that catalyzes two different biochemical reactions would be linked to each of those biochemical reactions by two separate instances of the catalysis class. Also, catalysis reactions from multiple different organisms could be linked to the same generic biochemical reaction (a biochemical reaction is generic if it only includes small molecules). Generally, the enzyme catalyzing a conversion is known and the use of this class is obvious, however, in the cases where a catalyzed reaction is known to occur but the enzyme is not known, a catalysis instance can be created without a controller specified. Synonyms: facilitation, acceleration. Examples: The catalysis of a biochemical reaction by an enzyme, the enabling of a transport interaction by a membrane pore complex, and the facilitation of a complex assembly by a scaffold protein. Hexokinase -> (The "Glucose + ATP -> Glucose-6-phosphate +ADP" reaction). A plasma membrane Na+/K+ ATPase is an active transporter (antiport pump) using the energy of ATP to pump Na+ out of the cell and K+ in. Na+ from cytoplasm to extracellular space would be described in a transport instance. K+ from extracellular space to cytoplasm would be described in a transport instance. The ATPase pump would be stored in a catalysis instance controlling each of the above transport instances. A biochemical reaction that does not occur by itself under physiological conditions, but has been observed to occur in the presence of cell extract, likely via one or more unknown enzymes present in the extract, would be stored in the CONTROLLED property, with the CONTROLLER property empty.

Field Summary

Fields inherited from interface org.biopax.paxtools.model.BioPAXElement

UNKNOWN_DOUBLE, UNKNOWN_FLOAT, UNKNOWN_INT

Method Summary

Modifier and Type	Method and Description
void	addCofactor(PhysicalEntity cofactor) Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
CatalysisDirectionType	getCatalysisDirection() This property represents the direction of this catalysis under all physiological conditions if there is one.
Set<PhysicalEntity>	getCofactor() Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
void	removeCofactor(PhysicalEntity cofactor) Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme.
void	setCatalysisDirection(CatalysisDirectionType catalysisDirection) This property represents the direction of this catalysis under all physiological conditions if there is one.

Methods inherited from interface org.biopax.paxtools.model.level3.Control

addControlled, addController, getControlled, getController, getControlType, removeControlled, removeController, setControlType

Methods inherited from interface org.biopax.paxtools.model.level3.Interaction

addInteractionType, addParticipant, getInteractionType, getParticipant, removeInteractionType, removeParticipant

Methods inherited from interface org.biopax.paxtools.model.level3.Process

getControlledOf, getPathwayComponentOf, getStepProcessOf

Methods inherited from interface org.biopax.paxtools.model.level3.Entity

addAvailability, addDataSource, getAvailability, getDataSource, getParticipantOf, removeAvailability, removeDataSource

Methods inherited from interface org.biopax.paxtools.model.level3.Observable

addEvidence, getEvidence, removeEvidence

Methods inherited from interface org.biopax.paxtools.model.level3.Named

addName, getDisplayName, getName, getStandardName, removeName, setDisplayName, setName, setStandardName

Methods inherited from interface org.biopax.paxtools.model.level3.XReferrable

addXref, getXref, removeXref

Methods inherited from interface org.biopax.paxtools.model.level3.Level3Element

addComment, getComment, removeComment

Methods inherited from interface org.biopax.paxtools.model.BioPAXElement

equivalenceCode, getAnnotations, getModelInterface, getRDFId, isEquivalent

Method Detail

getCofactor

Set<PhysicalEntity> getCofactor()

Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. This is a suproperty of participants.

Returns:

cofactor(s) or coenzyme(s) required for catalysis of the conversion

addCofactor

void addCofactor(PhysicalEntity cofactor)

Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. This is a suproperty of participants.

Parameters:

cofactor - cofactor(s) or coenzyme(s) required for catalysis of the conversion

removeCofactor

void removeCofactor(PhysicalEntity cofactor)

Any cofactor(s) or coenzyme(s) required for catalysis of the conversion by the enzyme. This is a suproperty of participants.

Parameters:

cofactor - cofactor(s) or coenzyme(s) required for catalysis of the conversion

getCatalysisDirection

CatalysisDirectionType getCatalysisDirection()

This property represents the direction of this catalysis under all physiological conditions if there is one. Note that chemically a catalyst will increase the rate of the reaction in both directions. In biology, however, there are cases where the enzyme is expressed only when the controlled bidirectional conversion is on one side of the chemical equilibrium. olled bidirectional conversion is on one side of the chemical equilibrium. For example E.Coli's lac operon ensures that lacZ gene is only synthesized when there is enough lactose in the medium. If that is the case and the controller, under biological conditions, is always catalyzing the conversion in one direction then this fact can be captured using this property. If the enzyme is active for both directions, or the conversion is not bidirectional, this property should be left empty.

Returns:

direction of this catalysis under all physiological conditions if there is one

setCatalysisDirection

void setCatalysisDirection(CatalysisDirectionType catalysisDirection)

This property represents the direction of this catalysis under all physiological conditions if there is one. Note that chemically a catalyst will increase the rate of the reaction in both directions. In biology, however, there are cases where the enzyme is expressed only when the controlled bidirectional conversion is on one side of the chemical equilibrium. olled bidirectional conversion is on one side of the chemical equilibrium. For example E.Coli's lac operon ensures that lacZ gene is only synthesized when there is enough lactose in the medium. If that is the case and the controller, under biological conditions, is always catalyzing the conversion in one direction then this fact can be captured using this property. If the enzyme is active for both directions, or the conversion is not bidirectional, this property should be left empty.

Parameters:

catalysisDirection - direction of this catalysis under all physiological conditions if there is one