HYDROPHOBIC FREE-ENERGY EIGENFUNCTIONS OF PORE, CHANNEL, AND TRANSPORTER PROTEINS CONTAIN BETA-BURST PATTERNS

Hydropathy plots are often used in place of missing physical data to m odel transmembrane proteins that are difficult to crystallize. The seq uential maxima of their graphs approximate the number and locations of transmembrane segments, but potentially useful additional information about sequential hydrophobic variation is lost in this smoothing proc edure. To explore a broader range of hydrophobic variations without lo ss of the transmembrane segment-relevant sequential maxima, we utilize a sequence of linear decompositions and transformations of the n-leng th hydrophobic free energy sequences, H-i,H- i = 1...n, of proteins. C onstructions of hydrophobic free energy eigenfunctions, psi(1), from M -lagged, M x M autocovariance matrices, C-M, were followed by their al l-poles, maximum entropy power spectral, S-omega(psi(1)), and Mexican Hat wavelet, W (a, b)(psi(1)), transformations. These procedures yield ed graphs indicative of inverse frequencies, omega(-1), and sequence l ocations of hydrophobic modes suggestive of secondary and superseconda ry protein structures. The graphs of these computations discriminated between Greek Key, Jelly Role, and Up and Down categories of antiparal lel p-barrel proteins. With these methods, examples of porins, connexi ns, hexose transporters, nuclear membrane proteins, and potassium but not sodium channels appear to belong to the Up and Down antiparallel b eta-barrel variety.