Journal of Proteomics & Bioinformatics
Open Access
ISSN: 0974-276X
ISSN: 0974-276X
Here we discuss the development of protein scaling theory, starting from backgrounds in mathematics and statistical mechanics and leading to biomedical applications. Evolution has organized each protein family in different ways, but scaling theory is both simple and effective in providing readily transferable dynamical insights, which are complementary for many proteins represented in the 60 thousand static structures contained in the online Protein Data Base (PDB). Scaling theory is a simplifying magic wand that enables one to search the hundreds of millions of protein articles in the Web of Science and identify those proteins that present new cost-effective methods for early detection and/or treatment of disease through individual protein sequences (personalized medicine). It complements and extends the most popular methods for studying protein evolution, based on amino acid sequence alignments. Applications include evolution of Covid and the abrupt end of the pandemic.
Critical point theory is general and recently it has proved to be the most effective way of describing protein networks that have evolved towards nearly perfect functionality in given environments (self-organized criticality). Evolutionary patterns are governed by common scaling principles, which can be quantified using scales that have been developed bioinformatically by studying thousands of PDB structures. The most effective scale involves hydropathic globular sculpting interactions averaged over length scales centered on membrane domain dimensions.
A central feature of scaling theory is the characteristic length scale associated with a given protein’s functionality. To gain experience with such length scales one should analyze a variety of protein families, as each may have several different critical length scales. Evolution has functioned in such a way that the minimal critical length scale established so far is about nine amino acids, but in some cases it is much larger. Some ingenuity is needed to find this primary length scale, as shown by the examples discussed here. Often a survey of the evolution of the protein suggests a means of determining the critical length scale.
Published Date: 2024-06-03; Received Date: 2024-05-03