Relating Protein Structure and Function Through a Bijection and Its Implications on Protein Structure Prediction

Proteins are studied by measuring different properties, typically the chemical structure and biochemical activity. Given that these measurements are done on the same protein molecule, they must be related. Despite the fact that this relationship exists, the mathematical nature of this relationship has remained elusive to our understanding, and is not commonly considered in the so called “structure-function relationship problem of proteins” (Punta & Ofran, 2008). While this is a fundamental problem in biochemistry and biology, that is, to establish a procedure that allows scientists to reliably relate protein structure and protein activity, the likelihood to succeed in this enterprise depends on our ability to understand the mere nature of this relationship. The possibility to effectively relate structure and activity has motivated years of research in different areas in biology, including biophysics, molecular biology, biochemistry, bioinformatics, and computational biology, among others. Although great advances have been achieved from these different areas of expertise, the question remains unsolved. That is, there is no general procedure that may have proven to effectively relate protein structure and activity. However, recent results in the prediction of protein three-dimensional structure (from now on referred simply as 3D structure) are addressing this problem with a fresh look, revealing a new aspect of this relationship that may explain why this particular problem has remained elusive. The present work reviews the general concepts being used to predict protein 3D structure with emphasis on the contribution of these methods to unravel the structureactivity relationship of proteins.