Description of the quaternary structure of tetrameric proteins. Forms that show either right-handed or left-handed symmetry at the subunit level

Abstract

A method is described for comparing the shapes of tetrameric proteins whose three-dimensional structure is known. The centres of mass of single subunits are calculated as Cartesian co-ordinates with respect to their three dyad axes. The axes are allocated on the basis of the extent of the intersubunit contacts that they relate. This results in the division of proteins into two classes called right-handed and left-handed. A second division, which also contains right-handed and left-handed forms, is made according to the distances between the centres of mass of the subunits measured across the two axes with the most extensive contacts. Two other parameters have been calculated from the coordinates; they are named "aplanarity" and "twist". The eight tetramers so far investigated are discussed. One, lactate dehydrogenase, cannot be treated in this way. Among the others, right-handed structures (according to both definitions) are found to be commoner; most have low twist; all are of fairly high aplanarity except phosphoglycerate mutase. Prealbumin is exceptional, being left-handed in both ways and of high twist; it has a figure-of-eight structure with the centres of mass lying in one plane. The changes in the quaternary structure of haemoglobin are also presented by using this approach; on deoxygenation the aplanarity and the twist decrease.