The diversity of molecular interactions involving intrinsically disordered proteins: A molecular modeling perspective

Weighted families of contact maps to characterize conformational ensembles of (highly-)flexible proteins

MOTIVATION

Characterizing the structure of flexible proteins, particularly within the realm of intrinsic disorder, presents a formidable challenge due to their high conformational variability. Currently, their structural representation relies on (possibly large) conformational ensembles derived from a combination of experimental and computational methods. The detailed structural analysis of these ensembles is a difficult task, for which existing tools have limited effectiveness.

RESULTS

This study proposes an innovative extension of the concept of contact maps to the ensemble framework, incorporating the intrinsic probabilistic nature of disordered proteins. Within this framework, a conformational ensemble is characterized through a weighted family of contact maps. To achieve this, conformations are first described using a refined definition of contact that appropriately accounts for the geometry of the inter-residue interactions and the sequence context. Representative structural features of the ensemble naturally emerge from the subsequent clustering of the resulting contact-based descriptors. Importantly, transiently populated structural features are readily identified within large ensembles. The performance of the method is illustrated by several use cases and compared with other existing approaches, highlighting its superiority in capturing relevant structural features of highly flexible proteins.

AVAILABILITY AND IMPLEMENTATION

An open-source implementation of the method is provided together with an easy-to-use Jupyter notebook, available at https://gitlab.laas.fr/moma/WARIO.

Unraveling the assembly mechanism of SADS-CoV virus nucleocapsid protein: insights from RNA binding, dimerization, and epitope diversity profiling

The swine acute diarrhea syndrome coronavirus (SADS-CoV) has caused significant disruptions in porcine breeding and raised concerns about potential human infection. The nucleocapsid (N) protein of SADS-CoV plays a vital role in viral assembly and replication, but its structure and functions remain poorly understood. This study utilized biochemistry, X-ray crystallography, and immunization techniques to investigate the N protein's structure and function in SADS-CoV. Our findings revealed distinct domains within the N protein, including an RNA-binding domain, two disordered domains, and a dimerization domain. Through biochemical assays, we confirmed that the N-terminal domain functions as an RNA-binding domain, and the C-terminal domain is involved in dimerization, with the crystal structure analysis providing visual evidence of dimer formation. Immunization experiments demonstrated that the disordered domain 2 elicited a significant antibody response. These identified domains and their interactions are crucial for viral assembly. This comprehensive understanding of the N protein in SADS-CoV enhances our knowledge of its assembly and replication mechanisms, enabling the development of targeted interventions and therapeutic strategies.

IMPORTANCE

SADS-CoV is a porcine coronavirus that originated from a bat HKU2-related coronavirus. It causes devastating swine diseases and poses a high risk of spillover to humans. The coronavirus N protein, as the most abundant viral protein in infected cells, likely plays a key role in viral assembly and replication. However, the structure and function of this protein remain unclear. Therefore, this study employed a combination of biochemistry and X-ray crystallography to uncover distinct structural domains in the N protein, including RNA-binding domains, two disordered domains, and dimerization domains. Additionally, we made the novel discovery that the disordered domain elicited a significant antibody response. These findings provide new insights into the structure and functions of the SADS-CoV N protein, which have important implications for future studies on SADS-CoV diagnosis, as well as the development of vaccines and anti-viral drugs.

Characterization of Intrinsically Disordered Proteins in Healthy and Diseased States by Nuclear Magnetic Resonance

INTRODUCTION

Intrinsically Disordered Proteins (IDPs) are active in different cellular procedures like ordered assembly of chromatin and ribosomes, interaction with membrane, protein, and ligand binding, molecular recognition, binding, and transportation via nuclear pores, microfilaments and microtubules process and disassembly, protein functions, RNA chaperone, and nucleic acid binding, modulation of the central dogma, cell cycle, and other cellular activities, post-translational qualification and substitute splicing, and flexible entropic linker and management of signaling pathways.

METHODS

The intrinsic disorder is a precise structural characteristic that permits IDPs/IDPRs to be involved in both one-to-many and many-to-one signaling. IDPs/IDPRs also exert some dynamical and structural ordering, being much less constrained in their activities than folded proteins. Nuclear magnetic resonance (NMR) spectroscopy is a major technique for the characterization of IDPs, and it can be used for dynamic and structural studies of IDPs.

RESULTS AND CONCLUSION

This review was carried out to discuss intrinsically disordered proteins and their different goals, as well as the importance and effectiveness of NMR in characterizing intrinsically disordered proteins in healthy and diseased states.

Molecular Docking of Intrinsically Disordered Proteins: Challenges and Strategies

Intrinsically disordered proteins (IDPs) are a novel class of proteins that have established a significant importance and attention within a very short period of time. These proteins are essentially characterized by their inherent structural disorder, encoded mainly by their amino acid sequences. The profound abundance of IDPs and intrinsically disordered regions (IDRs) in the biological world delineates their deep-rooted functionality. IDPs and IDRs convey such extensive functionality through their unique dynamic nature, which enables them to carry out huge number of multifaceted biomolecular interactions and make them "interaction hub" of the cellular systems. Additionally, with such widespread functions, their misfunctioning is also intimately associated with multiple diseases. Thus, understanding the dynamic heterogeneity of various IDPs along with their interactions with respective binding partners is an important field with immense potentials in biomolecular research. In this context, molecular docking-based computational approaches have proven to be remarkable in case of ordered proteins. Molecular docking methods essentially model the biomolecular interactions in both structural and energetic terms and use this information to characterize the putative interactions between the two participant molecules. However, direct applications of the conventional docking methods to study IDPs are largely limited by their structural heterogeneity and demands for unique IDP-centric strategies. Thus, in this chapter, we have presented an overview of current methodologies for successful docking operations involving IDPs and IDRs. These specialized methods majorly include the ensemble-based and fragment-based approaches with their own benefits and limitations. More recently, artificial intelligence and machine learning-assisted approaches are also used to significantly reduce the complexity and computational burden associated with various docking applications. Thus, this chapter aims to provide a comprehensive summary of major challenges and recent advancements of molecular docking approaches in the IDP field for their better utilization and greater applicability.Asp (D).

Short Linear Motifs in Colorectal Cancer Interactome and Tumorigenesis

Colorectal tumorigenesis is driven by alterations in genes and proteins responsible for cancer initiation, progression, and invasion. This multistage process is based on a dense network of protein-protein interactions (PPIs) that become dysregulated as a result of changes in various cell signaling effectors. PPIs in signaling and regulatory networks are known to be mediated by short linear motifs (SLiMs), which are conserved contiguous regions of 3-10 amino acids within interacting protein domains. SLiMs are the minimum sequences required for modulating cellular PPI networks. Thus, several in silico approaches have been developed to predict and analyze SLiM-mediated PPIs. In this review, we focus on emerging evidence supporting a crucial role for SLiMs in driver pathways that are disrupted in colorectal cancer (CRC) tumorigenesis and related PPI network alterations. As a result, SLiMs, along with short peptides, are attracting the interest of researchers to devise small molecules amenable to be used as novel anti-CRC targeted therapies. Overall, the characterization of SLiMs mediating crucial PPIs in CRC may foster the development of more specific combined pharmacological approaches.

Intrinsically Disordered Proteins: An Overview

Many proteins and protein segments cannot attain a single stable three-dimensional structure under physiological conditions; instead, they adopt multiple interconverting conformational states. Such intrinsically disordered proteins or protein segments are highly abundant across proteomes, and are involved in various effector functions. This review focuses on different aspects of disordered proteins and disordered protein regions, which form the basis of the so-called "Disorder-function paradigm" of proteins. Additionally, various experimental approaches and computational tools used for characterizing disordered regions in proteins are discussed. Finally, the role of disordered proteins in diseases and their utility as potential drug targets are explored.

APE1 assembles biomolecular condensates to promote the ATR-Chk1 DNA damage response in nucleolus

Multifunctional protein APE1/APEX1/HAP1/Ref-1 (designated as APE1) plays important roles in nuclease-mediated DNA repair and redox regulation in transcription. However, it is unclear how APE1 regulates the DNA damage response (DDR) pathways. Here we show that siRNA-mediated APE1-knockdown or APE1 inhibitor treatment attenuates the ATR–Chk1 DDR under stress conditions in multiple immortalized cell lines. Congruently, APE1 overexpression (APE1-OE) activates the ATR DDR under unperturbed conditions, which is independent of APE1 nuclease and redox functions. Structural and functional analysis reveals a direct requirement of the extreme N-terminal motif within APE1 in the assembly of distinct biomolecular condensates in vitro and DNA/RNA-independent activation of the ATR DDR. Overexpressed APE1 co-localizes with nucleolar NPM1 and assembles biomolecular condensates in nucleoli in cancer but not non-malignant cells, which recruits ATR and activator molecules TopBP1 and ETAA1. APE1 protein can directly activate ATR to phosphorylate its substrate Chk1 in in vitro kinase assays. W119R mutant of APE1 is deficient in nucleolar condensation, and is incapable of activating nucleolar ATR DDR in cells and ATR kinase in vitro. APE1-OE-induced nucleolar ATR DDR activation leads to compromised ribosomal RNA transcription and reduced cell viability. Taken together, we propose distinct mechanisms by which APE1 regulates ATR DDR pathways.