Functional roles of intrinsic disorder in CRISPR-associated protein Cas9

Lighting up Nobel Prize-winning studies with protein intrinsic disorder

Intrinsically disordered proteins and regions (IDPs and IDRs) and their importance in biology are becoming increasingly recognized in biology, biochemistry, molecular biology and chemistry textbooks, as well as in current protein science and structural biology curricula. We argue that the sequence → dynamic conformational ensemble → function principle is of equal importance as the classical sequence → structure → function paradigm. To highlight this point, we describe the IDPs and/or IDRs behind the discoveries associated with 17 Nobel Prizes, 11 in Physiology or Medicine and 6 in Chemistry. The Nobel Laureates themselves did not always mention that the proteins underlying the phenomena investigated in their award-winning studies are in fact IDPs or contain IDRs. In several cases, IDP- or IDR-based molecular functions have been elucidated, while in other instances, it is recognized that the respective protein(s) contain IDRs, but the specific IDR-based molecular functions have yet to be determined. To highlight the importance of IDPs and IDRs as general principle in biology, we present here illustrative examples of IDPs/IDRs in Nobel Prize-winning mechanisms and processes.

Investigating the disordered regions (MoRFs, SLiMs and LCRs) and functions of mimicry proteins/peptides in silico

Microbial mimicry of the host proteins/peptides can elicit host auto-reactive T- or B-cells resulting in autoimmune disease(s). Since intrinsically disordered protein regions (IDPRs) are involved in several host cell signaling and PPI networks, molecular mimicry of the IDPRs can help the pathogens in substituting their own proteins in the host cell-signaling and PPI networks and, ultimately hijacking the host cellular machinery. Thus, the present study was conducted to discern the structural disorder and intrinsically disordered protein regions (IDPRs) like, molecular recognition features (MoRFs), short linear motifs (SLiMs), and low complexity regions (LCRs) in the experimentally verified mimicry proteins and peptides (mimitopes) of bacteria, viruses and host. Also, functional characteristics of the mimicry proteins were studied in silico. Our results indicated that 78% of the bacterial host mimicry proteins and 45% of the bacterial host mimitopes were moderately/highly disordered while, 73% of the viral host mimicry proteins and 31% of the viral host mimitopes were moderately/highly disordered. Among the pathogens, 27% of the bacterial mimicry proteins and 13% of the bacterial mimitopes were moderately/highly disordered while, 53% of the viral mimicry proteins and 21% of the viral mimitopes were moderately/highly disordered. Though IDPR were frequent in host, bacterial and viral mimicry proteins, only a few mimitopes overlapped with the IDPRs like, MoRFs, SLiMs and LCRs. This suggests that most of the microbes cannot use molecular mimicry to modulate the host PPIs and hijack the host cell machinery. Functional analyses indicated that most of the pathogens exhibited mimicry with the host proteins involved in ion binding and signaling pathways. This is the first report on the disordered regions and functional aspects of experimentally proven host and microbial mimicry proteins.

Functions of intrinsic disorder in proteins involved in DNA demethylation during pre-implantation embryonic development

DNA demethylation is involved in many biological processes during pre-implantation embryonic development in mammals. To date, the complicated mechanism of DNA demethylation is still not fully understood. Ten-eleven translocation family (TET3, TET1 and TET2), thymine DNA glycosylase (TDG) and DNA methyltransferase 1 (DNMT1) are considered the major protein enzymes of DNA demethylation in pre-implantation embryos. TET3, TET1, TET2, TDG, and DNMT1 contain abundant levels of intrinsically disordered protein regions (IDPRs), which contribute to increasing the functional diversity of proteins. Thus we tried to explore the complicated DNA demethylation in pre-implantation embryos from the intrinsic disorder perspective. These five biological macromolecules all have DNA demethylation-related functional domains. They can work together to fulfill DNA demethylation in pre-implantation embryos through complex protein-protein interaction networks. Intrinsic disorder analysis results showed these proteins were partial intrinsically disordered proteins. Many identifiable disorder-based DNA-binding sites, protein-binding sites and post-translational modification sites located in the intrinsically disordered regions, and DNA demethylation deficiency point mutations in the IDPRs could significantly change the local disorder propensity of these proteins. To the best of our knowledge, this work provides a new viewpoint for studying the mechanism of DNA methylation reprogramming during mammalian pre-implantation embryonic development.

Direct AFM Visualization of the Nanoscale Dynamics of Biomolecular Complexes

High-speed AFM (HS-AFM) is an advanced technique with numerous applications in biology, particularly in molecular biophysics. Developed as a time-lapse AFM technique for direct imaging fully hydrated biological molecules, HS-AFM is currently capable of visualizing the dynamics of biological molecules and their complexes at a video-data acquisition rate. Spatial resolution at the nanometer level is another important characteristic of HS-AFM. This review focuses on examples of primarily protein-DNA complexes to illustrate the high temporal and spatial resolution capabilities of HS-AFM that have resulted in novel models and/or the functional mechanisms of these biological systems.