Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins

Liquid-liquid Phase Separation in Aging: Novel Insights in the Pathogenesis and Therapeutics

The intricate organization of distinct cellular compartments is paramount for the maintenance of normal biological functions and the orchestration of complex biochemical reactions. These compartments, whether membrane-bound organelles or membraneless structures like Cajal bodies and RNA transport granules, play crucial roles in cellular function. Liquid-liquid phase separation (LLPS) serves as a reversible process that elucidates the genesis of membranelles structures through the self-assembly of biomolecules. LLPS has been implicated in a myriad of physiological and pathological processes, encompassing immune response and tumor genesis. But the association between LLPS and aging has not been clearly clarified. A recent advancement in the realm of aging research involves the introduction of a new edition outlining the twelve hallmarks of aging, categorized into three distinct groups. By delving into the role and mechanism of LLPS in the formation of membraneless structures at a molecular level, this review encapsulates an exploration of the interaction between LLPS and these aging hallmarks, aiming to offer novel perspectives of the intricate mechanisms underlying the aging process and deeper insights into aging therapeutics.

MNDA, a PYHIN factor involved in transcriptional regulation and apoptosis control in leukocytes

Inflammation control is critical during the innate immune response. Such response is triggered by the detection of molecules originating from pathogens or damaged host cells by pattern-recognition receptors (PRRs). PRRs subsequently initiate intra-cellular signalling through different pathways, resulting in i) the production of inflammatory cytokines, including type I interferon (IFN), and ii) the initiation of a cascade of events that promote both immediate host responses as well as adaptive immune responses. All human PYRIN and HIN-200 domains (PYHIN) protein family members were initially proposed to be PRRs, although this view has been challenged by reports that revealed their impact on other cellular mechanisms. Of relevance here, the human PYHIN factor myeloid nuclear differentiation antigen (MNDA) has recently been shown to directly control the transcription of genes encoding factors that regulate programmed cell death and inflammation. While MNDA is mainly found in the nucleus of leukocytes of both myeloid (neutrophils and monocytes) and lymphoid (B-cell) origin, its subcellular localization has been shown to be modulated in response to genotoxic agents that induce apoptosis and by bacterial constituents, mediators of inflammation. Prior studies have noted the importance of MNDA as a marker for certain forms of lymphoma, and as a clinical prognostic factor for hematopoietic diseases characterized by defective regulation of apoptosis. Abnormal expression of MNDA has also been associated with altered levels of cytokines and other inflammatory mediators. Refining our comprehension of the regulatory mechanisms governing the expression of MNDA and other PYHIN proteins, as well as enhancing our definition of their molecular functions, could significantly influence the management and treatment strategies of numerous human diseases. Here, we review the current state of knowledge regarding PYHIN proteins and their role in innate and adaptive immune responses. Emphasis will be placed on the regulation, function, and relevance of MNDA expression in the control of gene transcription and RNA stability during cell death and inflammation.

Developing Community Resources for Nucleic Acid Structures

In this review, we describe the creation of the Nucleic Acid Database (NDB) at Rutgers University and how it became a testbed for the current infrastructure of the RCSB Protein Data Bank. We describe some of the special features of the NDB and how it has been used to enable research. Plans for the next phase as the Nucleic Acid Knowledgebase (NAKB) are summarized.

In vitro evolution reveals non-cationic protein-RNA interaction mediated by metal ions

RNA–peptide/protein interactions have been of utmost importance to life since its earliest forms, reaching even before the last universal common ancestor (LUCA). However, the ancient molecular mechanisms behind this key biological interaction remain enigmatic because extant RNA–protein interactions rely heavily on positively charged and aromatic amino acids that were absent (or heavily under-represented) in the early pre-LUCA evolutionary period. Here, an RNA-binding variant of the ribosomal uL11 C-terminal domain was selected from an approximately 10¹⁰ library of partially randomized sequences, all composed of ten prebiotically plausible canonical amino acids. The selected variant binds to the cognate RNA with a similar overall affinity although it is less structured in the unbound form than the wild-type protein domain. The variant complex association and dissociation are both slower than for the wild-type, implying different mechanistic processes involved. The profile of the wild-type and mutant complex stabilities along with molecular dynamics simulations uncovers qualitative differences in the interaction modes. In the absence of positively charged and aromatic residues, the mutant uL11 domain uses ion bridging (K⁺/Mg²⁺) interactions between the RNA sugar-phosphate backbone and glutamic acid residues as an alternative source of stabilization. This study presents experimental support to provide a new perspective on how early protein–RNA interactions evolved, where the lack of aromatic/basic residues may have been compensated by acidic residues plus metal ions.

Tackling Covid-19 using disordered-to-order transition of residues in the spike protein upon angiotensin-converting enzyme 2 binding

The 2019-novel coronavirus also known as severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) is a common threat to animals and humans, and is responsible for the human SARS pandemic in 2019 to 2021. The infection of SARS-CoV-2 in humans involves a viral surface glycoprotein named as spike proteins, which bind to the human angiotensin-converting enzyme 2 (ACE2) proteins. Particularly, the receptor binding domains (RBDs) mediate the interaction and contain several disordered regions, which help in the binding. Investigations on the influence of disordered residues/regions in stability and binding of spike protein with ACE2 help to understand the disease pathogenesis, which has not yet been studied. In this study, we have used molecular-dynamics simulations to characterize the structural changes in disordered regions of the spike protein that result from ACE2 binding. We observed that the disordered regions undergo disorder-to-order transition (DOT) upon binding with ACE2, and the DOT residues are located at functionally important regions of RBD. Although the RBD is having rigid structure, DOT residues make conformational rearrangements for the spike protein to attach with ACE2. The binding is strengthened via hydrophilic and aromatic amino acids mainly present in the DOTs. The positively correlated motions of the DOT residues with its nearby residues also explain the binding profile of RBD with ACE2, and the residues are observed to be contributing more favorable binding energies for the spike-ACE2 complex formation. This study emphasizes that intrinsically disordered residues in the RBD of spike protein may provide insights into its etiology and be useful for drug and vaccine discovery.

Understanding disorder-to-order transitions in protein-RNA complexes using molecular dynamics simulations

Intrinsically disordered regions (IDRs) in proteins are characterized by their flexibilities and low complexity regions, which lack unique 3 D structures in solution. IDRs play a significant role in signaling, regulation, and binding multiple partners, including DNA, RNA, and proteins. Although various experiments have shown the role of disordered regions in binding with RNA, a detailed computational analysis is required to understand their binding and recognition mechanism. In this work, we performed molecular dynamics simulations of 10 protein-RNA complexes to understand the binding governed by intrinsically disordered regions. The simulation results show that most of the disordered regions are important for RNA-binding and have a transition from disordered-to-ordered conformation upon binding, which often contribute significantly towards the binding affinity. Interestingly, most of the disordered residues are present at the interface or located as a linker between two regions having similar movements. The DOT regions are overlaped or flanked with experimentally reported functionally important residues in the recognition of protein-RNA complexes. This study provides additional insights for understanding the role and recognition mechanism of disordered regions in protein-RNA complexes.Communicated by Ramaswamy H. Sarma.

Unusual RNA binding of FUS RRM studied by molecular dynamics simulation and enhanced sampling method

Amyotrophic lateral sclerosis (ALS) and frontotemporal lobe degeneration (FTLD) are two inter-related intractable diseases of motor neuron degeneration. Fused in sarcoma (FUS) is found in cytoplasmic accumulation of ALS and FTLD patients, which readily link the protein with the diseases. The RNA recognition motif (RRM) of FUS has the canonical α-β folds along with an unusual lysine-rich loop (KK-loop) between α1 and β2. This KK-loop is highly conserved among FET family proteins. Another contrasting feature of FUS RRM is the absence of critical binding residues, which are otherwise highly conserved in canonical RRMs. These residues in FUS RRM are Thr286, Glu336, Thr338, and Ser367, which are substitutions of lysine, phenylalanine, phenylalanine, and lysine, respectively, in other RRMs. Considering the importance of FUS in RNA regulation and metabolism, and its implication in ALS and FTLD, it is important to elucidate the underlying molecular mechanism of RNA recognition. In this study, we have performed molecular dynamics simulation with enhanced sampling to understand the conformational dynamics of noncanonical FUS RRM and its binding with RNA. We studied two sets of mutations: one with alanine mutation of KK-loop and another with KK-loop mutations along with critical binding residues mutated back to their canonical form. We find that concerted movement of KK-loop and loop between β2 and β3 facilitates the folding of the partner RNA, indicating an induced-fit mechanism of RNA binding. Flexibility of the RRM is highly restricted upon mutating the lysine residues of the KK-loop, resulting in weaker binding with the RNA. Our results also suggest that absence of the canonical residues in FUS RRM along with the KK-loop is equally important in regulating its binding dynamics. This study provides a significant structural insight into the binding of FUS RRM with its cognate RNA, which may further help in designing potential drugs targeting noncanonical RNA recognition.

A combined NMR and EPR investigation on the effect of the disordered RGG regions in the structure and the activity of the RRM domain of FUS

Structural disorder represents a key feature in the mechanism of action of RNA-binding proteins (RBPs). Recent insights revealed that intrinsically disordered regions (IDRs) linking globular domains modulate their capability to interact with various sequences of RNA, but also regulate aggregation processes, stress-granules formation, and binding to other proteins. The FET protein family, which includes FUS (Fused in Sarcoma), EWG (Ewing Sarcoma) and TAF15 (TATA binding association factor 15) proteins, is a group of RBPs containing three different long IDRs characterized by the presence of RGG motifs. In this study, we present the characterization of a fragment of FUS comprising two RGG regions flanking the RNA Recognition Motif (RRM) alone and in the presence of a stem-loop RNA. From a combination of EPR and NMR spectroscopies, we established that the two RGG regions transiently interact with the RRM itself. These interactions may play a role in the recognition of stem-loop RNA, without a disorder-to-order transition but retaining high dynamics.

Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control

Alternative splicing is a highly sophisticated process, playing a significant role in posttranscriptional gene expression and underlying the diversity and complexity of organisms. Its regulation is multilayered, including an intrinsic role of RNA structural arrangement which undergoes time- and tissue-specific alterations. In this review, we describe the principles of RNA structural arrangement and briefly decipher its cis- and trans-acting cellular modulators which serve as crucial determinants of biological functionality of the RNA structure. Subsequently, we engage in a discussion about the RNA structure-mediated mechanisms of alternative splicing regulation. On one hand, the impairment of formation of optimal RNA structures may have critical consequences for the splicing outcome and further contribute to understanding the pathomechanism of severe disorders. On the other hand, the structural aspects of RNA became significant features taken into consideration in the endeavor of finding potential therapeutic treatments. Both aspects have been addressed by us emphasizing the importance of ongoing studies in both fields.

MNDA controls the expression of MCL-1 and BCL-2 in chronic lymphocytic leukemia cells

The myeloid nuclear differentiation antigen (MNDA) is a stress-induced protein that promotes degradation of the anti-apoptotic factor MCL-1 and apoptosis in myeloid cells. MNDA is also expressed in normal lymphoid cells and in B-cell clones isolated from individuals with chronic lymphocytic leukemia (CLL), a disease characterized by abnormal apoptosis control. We found that MNDA expression levels inversely correlate with the amount of the anti-apoptotic proteins MCL-1 and BCL-2 in human CLL samples. We report that in response to chemotherapeutic agents that induce genotoxic stress, MNDA exits its typical nucleolar localization and accumulates in the nucleoplasm of CLL and lymphoid cells. Then, MNDA binds chromatin at Mcl1 and Bcl2 genes and affects the transcriptional competence of RNA polymerase II. Our data also reveal that MNDA specifically associates with Mcl1 and Bcl2 (pre-) mRNAs and favors their rapid turnover as a prompt response to genotoxic stress. We propose that this rapid dynamic tuning of RNA levels, which leads to the destabilization of Mcl1 and Bcl2 transcripts, represents a post-transcriptional mechanism of apoptosis control in CLL cells. These results provide an explanation of previous clinical data and corroborate the finding that higher MNDA expression levels in CLL are associated with a better clinical course.

Y-Box Binding Proteins in mRNP Assembly, Translation, and Stability Control

Y-box binding proteins (YB proteins) are DNA/RNA-binding proteins belonging to a large family of proteins with the cold shock domain. Functionally, these proteins are known to be the most diverse, although the literature hardly offers any molecular mechanisms governing their activities in the cell, tissue, or the whole organism. This review describes the involvement of YB proteins in RNA-dependent processes, such as mRNA packaging into mRNPs, mRNA translation, and mRNA stabilization. In addition, recent data on the structural peculiarities of YB proteins underlying their interactions with nucleic acids are discussed.

Role of disordered regions in transferring tyrosine to its cognate tRNA

Aminoacyl tRNA synthetase (AARS) plays an important role in transferring each amino acid to its cognate tRNA. Specifically, tyrosyl tRNA synthetase (TyrRS) is involved in various functions including protection from DNA damage due to oxidative stress, protein synthesis and cell signaling and can be an attractive target for controlling the pathogens by early inhibition of translation. TyrRS has two disordered regions, which lack a stable 3D structure in solution, and are involved in tRNA synthetase catalysis and stability. One of the disordered regions undergoes disorder-to-order transition (DOT) upon complex formation with tRNA whereas the other remains disordered (DR). In this work, we have explored the importance of these disordered regions using molecular dynamics simulations of both free and RNA-complexed states. We observed that the DOT and DR regions of the first subunit acts as a flap and interact with the acceptor arm of the tRNA. The DOT-DR flap closes when tyrosine (TyrRS^Tyr) is present at the active site of the complex and opens in the presence of tyrosine monophosphate (TyrRS^YMP). The DOT and DR regions of the second subunit interact with the anticodon stem as well as D-loop of the tRNA, which might be involved in stabilizing the complex. The anticodon loop of the tRNA binds to the structured region present in the C-terminal of the protein, which is observed to be flexible during simulations. Detailed energy calculations also show that TyrRS^Tyr complex has stronger binding energy between tRNA and protein compared to TyrRS^YMP; on the contrary, the anticodon is strongly bound in TyrRS^YMP. The results obtained in the present study provide additional insights for understanding catalysis and the involvement of disordered regions in Tyr transfer to cognate tRNA.

Sequence-Derived Markers of Drug Targets and Potentially Druggable Human Proteins

Recent research shows that majority of the druggable human proteome is yet to be annotated and explored. Accurate identification of these unexplored druggable proteins would facilitate development, screening, repurposing, and repositioning of drugs, as well as prediction of new drug–protein interactions. We contrast the current drug targets against the datasets of non-druggable and possibly druggable proteins to formulate markers that could be used to identify druggable proteins. We focus on the markers that can be extracted from protein sequences or names/identifiers to ensure that they can be applied across the entire human proteome. These markers quantify key features covered in the past works (topological features of PPIs, cellular functions, and subcellular locations) and several novel factors (intrinsic disorder, residue-level conservation, alternative splicing isoforms, domains, and sequence-derived solvent accessibility). We find that the possibly druggable proteins have significantly higher abundance of alternative splicing isoforms, relatively large number of domains, higher degree of centrality in the protein-protein interaction networks, and lower numbers of conserved and surface residues, when compared with the non-druggable proteins. We show that the current drug targets and possibly druggable proteins share involvement in the catalytic and signaling functions. However, unlike the drug targets, the possibly druggable proteins participate in the metabolic and biosynthesis processes, are enriched in the intrinsic disorder, interact with proteins and nucleic acids, and are localized across the cell. To sum up, we formulate several markers that can help with finding novel druggable human proteins and provide interesting insights into the cellular functions and subcellular locations of the current drug targets and potentially druggable proteins.

Investigating targets for neuropharmacological intervention by molecular dynamics simulations

Medical research has identified over 500 brain disorders. Among these, there are still only very few neuropathologies whose causes are fully understood and, consequently, very few drugs whose mechanism of action is known. No FDA drug has been identified for major neurodegenerative diseases, such as Alzheimer's and Parkinson's. We still lack effective treatments and strategies for modulating progression or even early neurodegenerative disease onset diagnostic tools. A great support toward the highly needed identification of neuroactive drugs comes from computer simulation methods and, in particular, from molecular dynamics (MD). This provides insight into structure-function relationship of a target and predicts structure, dynamics and energetics of ligand/target complexes under biologically relevant conditions like temperature and physiological saline concentration. Here, we present examples of the predictive power of MD for neuroactive ligands/target complexes. This brief survey from our own research shows the usefulness of partnerships between academia and industry, and from joint efforts between experimental and theoretical groups.