Abstract
BackgroundIt had long been thought that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions. However, subsequent research has shown that there are many proteins without specific 3D-structures under physiological conditions, so-called intrinsically disordered proteins (IDPs). This study presents a new technique for predicting intrinsically disordered regions in a protein, based on our average distance map (ADM) technique. The ADM technique was developed to predict compact regions or structural domains in a protein. In a protein containing partially disordered regions, a domain region is likely to be ordered, thus it is unlikely that a disordered region would be part of any domain. Therefore, the ADM technique is expected to also predict a disordered region between domains.ResultsThe results of our new technique are comparable to the top three performing techniques in the community-wide CASP10 experiment. We further discuss the case of p53, a tumor-suppressor protein, which is the most significant protein among cell cycle regulatory proteins. This protein exhibits a disordered character as a monomer but an ordered character when two p53s form a dimer.ConclusionOur technique can predict the location of an intrinsically disordered region in a protein with an accuracy comparable to the best techniques proposed so far. Furthermore, it can also predict a core region of IDPs forming definite 3D structures through interactions, such as dimerization. The technique in our study may also serve as a means of predicting a disordered region which would become an ordered structure when binding to another protein.
Highlights
It had long been thought that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions
The present study proposes a new technique for predicting intrinsically disordered region (IDR) from their sequence based on a map derived from the inter-residue average distance statistics, an average distance map (ADM)
In the present study, we introduced a new technique for predicting IDRs by means of maps based on inter-residue average distance statistics, average distance maps (ADM)
Summary
It had long been thought that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions. Subsequent research has shown that there are many proteins without specific 3D-structures under physiological conditions, so-called intrinsically disordered proteins (IDPs). The ADM technique was developed to predict compact regions or structural domains in a protein. Anfinsen’s discovery [1] that a protein exhibits its specific function through its own specific 3D-structure under physiological conditions dominated protein research for many years. Proteins without specific 3D-structure under physiological conditions, known as intrinsically disordered proteins (IDPs), were later recognized [2, 3]. Dunker et al were the first to apply bioinformatics techniques to the study of IDPs [4] by developing a. An example is cyclic-AMP response element-binding protein (CREB) This protein contains a partially disordered region which becomes ordered upon (2019) 19:3 interaction with its co-activator, CREB-binding protein (CBP), thereby permiting its function
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