A new perspective on analysis of helix-helix packing preferences in globular proteins.
For many years, statistical analysis of protein databanks has led to the belief that the steric compatibility of helix interfaces may be the source of observed preferences for particular angles between neighboring helices. Several elegant models describing how side chains on helices can interdigitate without steric clashes were able to account quite reasonably for the observed distributions. However, it was later recognized that the 'bare' measured angle distribution should be corrected to avoid statistical bias.12 Disappointingly, the rescaled distributions dramatically lost their similarity with theoretical predictions, casting doubts on the validity of the geometrical assumptions and models. In this article, we elucidate a few points concerning the proper choice of a random reference distribution. In particular we demonstrate the need for corrections induced by unavoidable uncertainties in determining whether two helices are in face-to-face contact or not and their relative orientations. By using this new rescaling, we show that 'true' packing angle preferences are well described by regular packing models, thus proving that preferential angles between contacting helices do exist.
Trovato
Antonio
A
INFM-Dipartimento di Fisica G. Galilei, Università di Padova, Via Marzolo 8, 35131 Padova, Italy. trovato@pd.infn.it
Seno
Flavio
F
D008958:Models, Molecular; D015394:Molecular Structure; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry
D011506:Proteins