There are three subtypes of vertebrate inositol 1,4,5-trisphosphate receptor (IP 3 R), a Ca 2+ -release channel on the ER membrane-IP 3 R1, IP 3 R2, and IP 3 R3-each of which has a distinctive role in disease development. To determine the subtype-specific IP 3 -binding mechanism, we compared the thermodynamics, thermal stability, and conformational dynamics between the N-terminal regions of IP 3 R1 (IP 3 R1-NT) and IP 3 R3 (IP 3 R3-NT) by performing circular dichroism (CD), isothermal titration calorimetry (ITC), and hydrogen-deuterium exchange mass spectrometry (HDX-MS). Previously determined crystal structures of IP 3 R1-NT and HDX-MS results from this study revealed that both IP 3 R1 and IP 3 R3 adopt a similar IP 3 -binding mechanism. However, several regions, including the α- and β-interfaces, of IP 3 R1-NT and IP 3 R3-NT show significantly different conformational dynamics upon IP 3 binding, which may explain the different IP 3 -binding affinities between the subtypes. The importance of the interfaces for subtype-specific IP 3 binding is also supported by the different dynamic conformations of the two subtypes in the apo-states. Furthermore, IP 3 R1-NT and IP 3 R3-NT show different IP 3 -binding affinities and thermal stabilities, but share similar thermodynamic properties for IP 3 binding. These results collectively provide new insights into the mechanism underlying IP 3 binding to IP 3 Rs and the subtype-specific regulatory mechanism.
