Cunning Simplicity of a Stoichiometry Driven Protein Folding Thesis

Structural disorder originates beyond narrow stoichiometric margins of amino acids in naturally occurring folded proteins

Rigorous analyses of Euclidean distances between non-peptide bonded residues in structures of several thousand naturally occurring folded proteins yielded a surprising "margin of life" for percentage occurrence of individual amino acids in naturally occurring folded proteins. On one hand, the concept of "margin of life", referring to lower than expected variances in average stoichiometric occurrences of individual amino acids in folded proteins, remains unchallenged since its discovery a decade ago. On the other hand, within this past decade there has been a strong emergence of a gradual paradigm shift in biology, from sequence-structure-function in proteins to sequence-disorder-function, fuelled by discoveries on functional implications of intrinsically disordered proteins (primary sequences that do not form stable structures). Thus the applicability of "margin of life" to peptide-bonded residues in all known natural proteins, adopting stable structures vis-à-vis intrinsically disordered needs to be explored. Therefore in this work, we analyze compositions of the complete naturally occurring primary sequence space (over 560000 sequences) after dividing it into mutually exclusive subsets of structured and intrinsically disordered proteins along with a subset without any structural information. While finding that occurrence of different peptides (up to pentapeptides) is a direct consequence of the relative occurrences of their constituting residues in folded proteins, we report that structural disorder in natural proteins originates beyond the narrow stoichiometric margins of amino acids found in structured proteins.Communicated by Ramaswamy H. Sarma.

Amino acid composition analysis of human secondary transport proteins and implications for reliable membrane topology prediction

Secondary transporters in humans are a large group of proteins that transport a wide range of ions, metals, organic and inorganic solutes involved in energy transduction, control of membrane potential and osmotic balance, metabolic processes and in the absorption or efflux of drugs and xenobiotics. They are also emerging as important targets for development of new drugs and as target sites for drug delivery to specific organs or tissues. We have performed amino acid composition (AAC) and phylogenetic analyses and membrane topology predictions for 336 human secondary transport proteins and used the results to confirm protein classification and to look for trends and correlations with structural domains and specific substrates and/or function. Some proteins showed statistically high contents of individual amino acids or of groups of amino acids with similar physicochemical properties. One recurring trend was a correlation between high contents of charged and/or polar residues with misleading results in predictions of membrane topology, which was especially prevalent in Mitochondrial Carrier family proteins. We demonstrate how charged or polar residues located in the middle of transmembrane helices can interfere with their identification by membrane topology tools resulting in missed helices in the prediction. Comparison of AAC in the human proteins with that in 235 secondary transport proteins from Escherichia coli revealed similar overall trends along with differences in average contents for some individual amino acids and groups of similar amino acids that are presumed to result from a greater number of functions and complexity in the higher organism.