Joseph P. Zbilut, goals:
Our main objective has been the understanding of biological signals with emphasis on the
amino acid code of proteins which governs their dynamics. Analysis of these signals has
been guided by a recurrence-based approach: proteins are relatively short, nonlinear and
nonstationary, thus precluding the uninformed use of more traditional signal analysis
methods. This strategy seeks to uncover unforeseen "singularities" of hydrophobicity in
proteins and related function. The main steps of this approach are: 1) use of an
hydrophobic code for primary structures; and 2) treatment of the hydrophobicity
distribution along the sequence like a time series, with the corresponding use of nonlinear
signal analysis techniques, in order to underpin fine position-dependent properties of the
hydrophobicity profiles. It is posited that singularities in the code identify important loci
at which proteins may fold correctly vs. aggregate. Moreover, the direction chosen is
dependent upon local factors, or boundary conditions, which force a stochastic
understanding of the process in terms of combinatorial probabilities. This effort has
ramifications for diseases such as “mad cow disease,” and Alzheimer’s. This effort is
sponsored by the Division of Mathematical Sciences (DMS) at the National Science
Foundation and the National Institute of General Medical Sciences (NIGMS) at the
National Institutes of Health (NSF Award No. 0240230)
Colleagues involved in the research include: Charles L. Webber, Jr., Physiology Dept.,
Loyola Univ. Med. Cntr.; Julie C. Mitchell, Univ. of Wisconsin, Madison; Alessandro
Giuliani, Istituto Superiore di Sanita, Rome; Alfredo Colosimo, Dept. of Biochemical
Sciences, Univ. of Rome "La Sapienza"; and Cesare Manetti, Dept. of Chemistry, Univ.
of Rome "La Sapienza".