scholarly journals Tethering-induced destabilization and ATP-binding for tandem RRM domains of ALS-causing TDP-43 and hnRNPA1

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mei Dang ◽  
Yifan Li ◽  
Jianxing Song
Keyword(s):  
Conformational Dynamics ◽  
Md Simulations ◽  
Atp Binding ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Nucleic Acid Binding ◽  
General Role ◽  
Nmr Characterization ◽  
Lateral Sclerosis

AbstractTDP-43 and hnRNPA1 contain tandemly-tethered RNA-recognition-motif (RRM) domains, which not only functionally bind an array of nucleic acids, but also participate in aggregation/fibrillation, a pathological hallmark of various human diseases including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), alzheimer's disease (AD) and Multisystem proteinopathy (MSP). Here, by DSF, NMR and MD simulations we systematically characterized stability, ATP-binding and conformational dynamics of TDP-43 and hnRNPA1 RRM domains in both tethered and isolated forms. The results reveal three key findings: (1) upon tethering TDP-43 RRM domains become dramatically coupled and destabilized with Tm reduced to only 49 °C. (2) ATP specifically binds TDP-43 and hnRNPA1 RRM domains, in which ATP occupies the similar pockets within the conserved nucleic-acid-binding surfaces, with the affinity slightly higher to the tethered than isolated forms. (3) MD simulations indicate that the tethered RRM domains of TDP-43 and hnRNPA1 have higher conformational dynamics than the isolated forms. Two RRM domains become coupled as shown by NMR characterization and analysis of inter-domain correlation motions. The study explains the long-standing puzzle that the tethered TDP-43 RRM1–RRM2 is particularly prone to aggregation/fibrillation, and underscores the general role of ATP in inhibiting aggregation/fibrillation of RRM-containing proteins. The results also rationalize the observation that the risk of aggregation-causing diseases increases with aging.

scholarly journals Stabilization and ATP-binding for tandem RRM domains of ALS-causing TDP-43 and hnRNPA1

2020 ◽  
Author(s):  
Mei Dang ◽  
Yifan Li ◽  
Jianxing Song
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Conformational Dynamics ◽  
Md Simulations ◽  
Human Diseases ◽  
Atp Binding ◽  
Nucleic Acid Binding ◽  
General Role ◽  
Nmr Characterization

AbstractTDP-43 and hnRNPA1 contain tandemly-tethered RRM domains, which not only functionally bind an array of nucleic acids, but also participate in aggregation/fibrillation, a pathological hallmark of various human diseases including ALS, FTD, AD and MSP. Here, by DSF, NMR and MD simulations we systematically characterized stability, ATP-binding and conformational dynamics of TDP-43 and hnRNPA1 RRM domains in both tethered and isolated forms. The results reveal three key findings: 1) very unexpectedly, upon tethering TDP-43 RRM domains become dramatically coupled and destabilized with Tm reduced to only 49 °C. 2) ATP specifically binds TDP-43 and hnRNPA1 RRM domains, in which ATP occupies the similar pockets within the conserved nucleic-acid-binding surfaces, with the affinity higher to the tethered than isolated forms. 3) MD simulations indicate that the tethered RRM domains of TDP-43 and hnRNPA1 have higher conformational dynamics than the isolated forms. Two RRM domains become coupled as shown by NMR characterization and analysis of inter-domain correlation motions. The study explains the long-standing puzzle that the tethered TDP-43 RRM1-RRM2 is particularly prone to aggregation/fibrillation, and underscores the general role of ATP in inhibiting aggregation/fibrillation of RRM-containing proteins. The results also rationalize the observation that the risk of aggregation-causing diseases increases with aging.

scholarly journals Arginine-enriched mixed-charge domains provide cohesion for nuclear speckle condensation

2019 ◽  
Author(s):  
Jamie A. Greig ◽  
Tu Anh Nguyen ◽  
Michelle Lee ◽  
Alex S. Holehouse ◽  
Ammon E. Posey ◽  
...  
Keyword(s):  
Low Complexity ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Nuclear Speckle ◽  
Net Charge ◽  
Intrinsically Disordered ◽  
Recognition Motif ◽  
Condensate Formation ◽  
Dynamic Material Properties

AbstractLow-complexity protein domains promote the formation of various biomolecular condensates. However, in many cases, the precise sequence features governing condensate formation and identity remain unclear. Here, we investigate the role of intrinsically disordered mixed-charge domains (MCDs) in nuclear speckle condensation. Proteins composed exclusively of arginine/aspartic-acid dipeptide repeats undergo length-dependent condensation and speckle incorporation. Substituting arginine with lysine in synthetic and natural speckle-associated MCDs abolishes these activities, identifying a key role for multivalent contacts through arginine’s guanidinium ion. MCDs can synergise with a speckle-associated RNA recognition motif to promote speckle specificity and residence. MCD behaviour is tuneable through net-charge: increasing negative charge abolishes condensation and speckle incorporation. By contrast, increasing positive charge through arginine leads to enhanced condensation, speckle enlargement, decreased splicing factor mobility, and defective mRNA export. Together, these results identify key sequence determinants of MCD-promoted speckle condensation, and link the speckle’s dynamic material properties with function in mRNA processing.

ATP-binding cassette transporters and neurodegenerative diseases

2021 ◽  
Author(s):  
Jared S. Katzeff ◽  
Woojin Scott Kim
Keyword(s):  
Neurodegenerative Diseases ◽  
Abc Transporters ◽  
Brain Diseases ◽  
Atp Binding ◽  
Future Directions ◽  
Diverse Range ◽  
The Brain ◽  
Lateral Sclerosis ◽  
Atp Binding Cassette

Abstract ATP-binding cassette (ABC) transporters are one of the largest groups of transporter families in humans. ABC transporters mediate the translocation of a diverse range of substrates across cellular membranes, including amino acids, nucleosides, lipids, sugars and xenobiotics. Neurodegenerative diseases are a group of brain diseases that detrimentally affect neurons and other brain cells and are usually associated with deposits of pathogenic proteins in the brain. Major neurodegenerative diseases include Alzheimer’s disease, Parkinson’s disease and amyotrophic lateral sclerosis. ABC transporters are highly expressed in the brain and have been implicated in a number of pathological processes underlying neurodegenerative diseases. This review outlines the current understanding of the role of ABC transporters in neurodegenerative diseases, focusing on some of the most important pathways, and also suggests future directions for research in this field.

scholarly journals Essential Loop Dynamics Modulates Catalytic Activity in α-Chymotrypsin

2021 ◽  
Author(s):  
Pritam Biswas ◽  
Uttam Pal ◽  
Aniruddha Adhikari ◽  
Susmita Mondal ◽  
Ria Ghosh ◽  
...  
Keyword(s):  
Catalytic Activity ◽  
Md Simulation ◽  
Conformational Dynamics ◽  
Principal Component ◽  
Catalytic Efficiency ◽  
Md Simulations ◽  
Essential Dynamics ◽  
Loop Dynamics ◽  
Loop Regions

Conformational dynamics of macromolecules including enzymes are essential for their function. The present work reports the role of essential dynamics in alpha-chymotrypsin (CHT) which correlates with its catalytic activity. Detailed optical spectroscopy and classical molecular dynamics (MD) simulation were used to study thermal stability, catalytic activity and dynamical flexibility of the enzyme. The study of the enzyme kinetics reveals an optimum catalytic efficiency at 308K. Polarization gated fluorescence anisotropy with 8-anilino-1-napthelene sulfonate (ANS) have indicated increasing flexibility of the enzyme with an increase in temperature. Examination of the structure of CHT reveal the presence of five loop regions (LRs) around the catalytic S1 pocket. MD simulations have indicated that flexibility increases concurrently with temperature which decreases beyond optimum temperature. Principal component analysis (PCA) of the eigenvectors manifests essential dynamics and gatekeeping role of the five LRs surrounding the catalytic pocket which controls the enzyme activity.

TFE-induced local unfolding and fibrillation of SOD1: bridging the experiment and simulation studies

2018 ◽  
Vol 475 (10) ◽  
pp. 1701-1719 ◽  
Author(s):  
Vijay Kumar ◽  
Amresh Prakash ◽  
Preeti Pandey ◽  
Andrew M. Lynn ◽  
Md. Imtaiyaz Hassan
Keyword(s):  
Conformational Dynamics ◽  
Dynamics Simulation ◽  
Helical Content ◽  
Partial Unfolding ◽  
Local Unfolding ◽  
Partially Unfolded ◽  
Β Sheet ◽  
Shed Light ◽  
Lateral Sclerosis

Misfolding and aggregation of Cu, Zn Superoxide dismutase (SOD1) is involved in the neurodegenerative disease, amyotrophic lateral sclerosis. Many studies have shown that metal-depleted, monomeric form of SOD1 displays substantial local unfolding dynamics and is the precursor for aggregation. Here, we have studied the structure and dynamics of different apo monomeric SOD1 variants associated with unfolding and aggregation in aqueous trifluoroethanol (TFE) through experiments and simulation. TFE induces partially unfolded β-sheet-rich extended conformations in these SOD1 variants, which subsequently develops aggregates with fibril-like characteristics. Fibrillation was achieved more easily in disulfide-reduced monomeric SOD1 when compared with wild-type and mutant monomeric SOD1. At higher concentrations of TFE, a native-like structure with the increase in α-helical content was observed. The molecular dynamics simulation results illustrate distinct structural dynamics for different regions of SOD1 variants and show uniform local unfolding of β-strands. The strands protected by the zinc-binding and electrostatic loops were found to unfold first in 20% (v/v) TFE, leading to a partial unfolding of β-strands 4, 5, and 6 which are prone to aggregation. Our results thus shed light on the role of local unfolding and conformational dynamics in SOD1 misfolding and aggregation.

scholarly journals In silico investigation of Aedes aegypti male-determining factor (NIX): RNA recognition motif-3, structural model and selective nucleic acid binding mode

2020 ◽  
Author(s):  
Monika A. Coronado ◽  
Danilo S. Olivier ◽  
Kelly C. Borsatto ◽  
Marcos S. Amaral ◽  
Raghuvir K. Arni ◽  
...  
Keyword(s):  
Aedes Aegypti ◽  
Structural Model ◽  
Early Stage ◽  
Control Strategies ◽  
Homology Model ◽  
Binding Mode ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Nucleic Acid Binding ◽  
Target Rna

AbstractMosquito borne viruses and their corresponding human infections have a fast growing impact on worldwide public health systems; in particular, Aedes aegypti and Aedes albopictus are transmitting these viruses. Only female mosquitoes bite and spread diseases. Male development in A. aegypti is initiated by male determining factors. These factors are potential candidates for the implementation of vector control strategies. Where at an early stage in gender development female mosquitoes are converted into harmless males. Among these factors, a novel gene, NIX, has been identified that shares moderate identity with transformer-2, one of the key sex-determination genes in Drosophila melanogaster. Hall et al. 2015 described two RNA recognition motifs (RRMs) in the NIX sequence, but a UniProt database search showed that A. aegypti NIX contains three RNA RRM. A homology model of NIX_RRM-3 was generated to investigate the interaction with RNA using molecular dynamics simulations. The sequence AGACGU was the most interesting result. During the binding process A1, G2 and G5 adopt an unusual syn conformation. The results let assume that the C-terminus of NIX_RRM-3 is involved in the recognition process of the target RNA motif (e.g. AG) and controls the interaction between target RNA and A. aegypti NIX.

scholarly journals A Computational Approach to Investigate TDP-43 RNA-Recognition Motif 2 C-Terminal Fragments Aggregation in Amyotrophic Lateral Sclerosis

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1905
Author(s):  
Greta Grassmann ◽  
Mattia Miotto ◽  
Lorenzo Di Rienzo ◽  
Federico Salaris ◽  
Beatrice Silvestri ◽  
...  
Keyword(s):  
Amyotrophic Lateral Sclerosis ◽  
Md Simulations ◽  
Molecular Surface ◽  
Rna Recognition Motif ◽  
Large Set ◽  
Aggregation Process ◽  
Cytoplasmic Inclusions ◽  
Shape Complementarity ◽  
The Brain ◽  
Lateral Sclerosis

Many of the molecular mechanisms underlying the pathological aggregation of proteins observed in neurodegenerative diseases are still not fully understood. Among the aggregate-associated diseases, Amyotrophic Lateral Sclerosis (ALS) is of relevant importance. In fact, although understanding the processes that cause the disease is still an open challenge, its relationship with protein aggregation is widely known. In particular, human TDP-43, an RNA/DNA binding protein, is a major component of the pathological cytoplasmic inclusions observed in ALS patients. Indeed, the deposition of the phosphorylated full-length TDP-43 in spinal cord cells has been widely studied. Moreover, it has also been shown that the brain cortex presents an accumulation of phosphorylated C-terminal fragments (CTFs). Even if it is debated whether the aggregation of CTFs represents a primary cause of ALS, it is a hallmark of TDP-43 related neurodegeneration in the brain. Here, we investigate the CTFs aggregation process, providing a computational model of interaction based on the evaluation of shape complementarity at the molecular interfaces. To this end, extensive Molecular Dynamics (MD) simulations were conducted for different types of protein fragments, with the aim of exploring the equilibrium conformations. Adopting a newly developed approach based on Zernike polynomials, able to find complementary regions in the molecular surface, we sampled a large set of solvent-exposed portions of CTFs structures as obtained from MD simulations. Our analysis proposes and assesses a set of possible association mechanisms between the CTFs, which could drive the aggregation process of the CTFs. To further evaluate the structural details of such associations, we perform molecular docking and additional MD simulations to propose possible complexes and assess their stability, focusing on complexes whose interacting regions are both characterized by a high shape complementarity and involve β3 and β5 strands at their interfaces.

scholarly journals An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2

2020 ◽  
Vol 117 (13) ◽  
pp. 7140-7149 ◽  
Author(s):  
Hyun-Seo Kang ◽  
Carolina Sánchez-Rico ◽  
Stefanie Ebersberger ◽  
F. X. Reymond Sutandy ◽  
Anke Busch ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Intramolecular Interaction ◽  
Intramolecular Interactions ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Rna Motifs ◽  
Intrinsically Disordered ◽  
Molecular Features

The recognition of cis-regulatory RNA motifs in human transcripts by RNA binding proteins (RBPs) is essential for gene regulation. The molecular features that determine RBP specificity are often poorly understood. Here, we combined NMR structural biology with high-throughput iCLIP approaches to identify a regulatory mechanism for U2AF2 RNA recognition. We found that the intrinsically disordered linker region connecting the two RNA recognition motif (RRM) domains of U2AF2 mediates autoinhibitory intramolecular interactions to reduce nonproductive binding to weak Py-tract RNAs. This proofreading favors binding of U2AF2 at stronger Py-tracts, as required to define 3′ splice sites at early stages of spliceosome assembly. Mutations that impair the linker autoinhibition enhance the affinity for weak Py-tracts result in promiscuous binding of U2AF2 along mRNAs and impact on splicing fidelity. Our findings highlight an important role of intrinsically disordered linkers to modulate RNA interactions of multidomain RBPs.

Sign in / Sign up

Export Citation Format

Share Document