Water is an active matrix of life for cell and molecular biology

Abstract

Szent-Győrgi called water the "matrix of life" and claimed that there was no life without it. This statement is true, as far as we know, on our planet, but it is not clear whether it must hold throughout the cosmos. To evaluate that question requires a close consideration of the many varied and subtle roles that water plays in living cells-a consideration that must be free of both an assumed essentialism that gives water an almost mystical life-giving agency and a traditional tendency to see it as a merely passive solvent. Water is a participant in the "life of the cell," and here I describe some of the features of that active agency. Water's value for molecular biology comes from both the structural and dynamic characteristics of its status as a complex, structured liquid as well as its nature as a polar, protic, and amphoteric reagent. Any discussion of water as life's matrix must, however, begin with an acknowledgment that our understanding of it as both a liquid and a solvent is still incomplete.

Keywords: hydration; hydrophobic effect; protein chemistry; solvation chemistry; water.

Fig. 1.

The hierarchy of timescales for motions of proteins and their hydration environment. HB, hydrogen bond. Reproduced from ref. with permission from AIP Publishing.

Fig. 2.

Water reorientational decay times seen in simulations of (Left) native and (Right) misfolded bovine α-lactalbumin. Reproduced from ref. with permission, copyright 2016 American Chemical Society.

Fig. 3.

(A) The hydration halo of PSII. (B) The same with protein chains shown only in light gray for clarity. (C) Water molecules (W) attached to the Mn–Ca complex. (D) A water channel within PSII that ferries protons to the bulk aqueous phase. Reproduced from ref. with permission from Macmillan Publishers Ltd: Nature, copyright 2011.

Fig. 4.

Water-assisted excision of a damaged adenine in DNA by MutY. (Left) The mispaired adenine is extruded into a cavity. (Right) The catalytic site contains five water molecules. Proton transfer from E43 to N₇ is mediated by W1, supported by neighboring structured water molecules. Reproduced from ref. with permission, copyright 2012 American Chemical Society.

Fig. 5.

(A) The network of some 400 interior waters in the antifreeze protein Maxi, with hydrogen bonds indicated by dotted lines. (B) Cross-section showing part of the water network rich in five-membered clathrate-like rings. Reproduced from ref. with permission from AAAS.