The fold of human aquaporin 1

The fold of human aquaporin 1 is determined from cryo-electron microscopic data at 4.5 Angstrom resolution. The monomeric structure consists of two tr ansmembrane triple helices arranged around a pseudo-2-fold axis connected b y a long flexible extracellular loop. Each triplet contains between its sec ond and third helix a functional loop containing the highly conserved finge rprint NPA motif. These functional loops are assumed to fold inwards betwee n the two triplets, thereby forming the heart of the water channel. The hel ix topology was determined from the directionality pattern of each of the s ix transmembrane helices with respect to the membrane, together with constr aints defined by the sequence and atomic force microscopy data. The directi onality of the helices was determined by collecting the best-fitting orient ations resulting from a search through the three-dimensional experimental m ap for a large number of alpha-helical fragments. Tests on cryo-electron cr ystallographic bacteriorhodopsin data suggest that our method is generally applicable to determine the topology of helical proteins for which only med ium-resolution electron microscopy data are available. (C) 2000 Academic Pr ess.