org.biopax.paxtools.model.level2
Interface catalysis
- All Superinterfaces:
- BioPAXElement, java.lang.Cloneable, control, entity, interaction, InteractionParticipant, Level2Element, pathwayComponent, physicalInteraction, process, java.io.Serializable, XReferrable
public interface catalysis
- extends control
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.
Comment: 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. In the cases where a catalyzed reaction is known to occur
but the enzyme is not known, a catalysis instance should be created without a
controller specified (i.e. the CONTROLLER property should remain empty).
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.
| Methods inherited from interface org.biopax.paxtools.model.level2.entity |
addAVAILABILITY, addDATA_SOURCE, addSYNONYMS, getAVAILABILITY, getDATA_SOURCE, getNAME, getSHORT_NAME, getSYNONYMS, removeAVAILABILITY, removeDATA_SOURCE, removeSYNONYMS, setAVAILABILITY, setDATA_SOURCE, setNAME, setSHORT_NAME, setSYNONYMS |
addCOFACTOR
void addCOFACTOR(physicalEntityParticipant COFACTOR)
removeCOFACTOR
void removeCOFACTOR(physicalEntityParticipant COFACTOR)
setCOFACTOR
void setCOFACTOR(java.util.Set<physicalEntityParticipant> COFACTOR)
getCOFACTOR
java.util.Set<physicalEntityParticipant> getCOFACTOR()
getDIRECTION
Direction getDIRECTION()
setDIRECTION
void setDIRECTION(Direction DIRECTION)
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