Water-mediated structural rearrangement establishes active conformation of caspases for apoptosis and inflammation

Abstract

Caspases are cysteine-dependent aspartate-specific proteases that play a crucial role in apoptosis (or programmed cell death) and inflammation. Based on their function, caspases are majorly categorized into apoptotic (initiator/apical and effector/executioner) and inflammatory caspases. Caspases undergo transition from an inactive zymogen to an active caspase to accomplish their function. This transition demands structural rearrangements which are most prominent at the active site loops and are imperative for the catalytic activity of caspases. In effector caspase-3, the structural rearrangement in the active site loop is shown to be facilitated by a set of invariant water (IW) molecules. However, the atomic details involving their role in stabilizing the active conformation have not been reported yet. Moreover, it is not known whether water molecules are essential for the active conformation in all caspases. Thus, in this study, we located IW molecules in initiator, effector, and inflammatory caspases to understand their precise role in rendering the structural arrangement of active caspases. Furthermore, IW molecules involved in anchoring the fragments of the protomer and rendering regulated flaccidity to caspases were identified. Location and identification of IW molecules interacting with amino acid residues involved in establishing the active conformation in the caspases might facilitate the design of potent inhibitors during up-regulated caspase activity in neurodegenerative and immune disorders.

Communicated by Ramaswamy H. Sarma

Keywords:

• Apoptotic caspase
• inflammatory caspase
• invariant water molecules
• molecular dynamics
• protease
• zymogen

Acknowledgments

The authors acknowledge the supercomputer facilities provided by Indian Institute of Technology Guwahati, Assam, India.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

Research fellowships for PG and MC provided by Ministry of Human Resource and Development (MHRD), Government of India is acknowledged.