Mapping the Intramolecular Communications among Different Glutamate Dehydrogenase States Using Molecular Dynamics

Insights into the interactions of RWP-RK and their targets: Role of serine and its conservation across species

The RWP-RK domain is a key DNA-binding domain found in all NIN (Nodule Inception)/NLP (NIN-like proteins) and RKD (RWP-RK Domain Containing) transcription factors (TFs). The RWP-RK domain in NINs/NLPs contains a highly evolutionarily conserved sequence, RWPSRK, while in RKDs, the fourth serine (S) amino acid is substituted with either tyrosine (Y) or histidine (H). To regulate autoregulation of nodulation, the RWP-RK domain of NIN TF binds to the promoter region of CLE peptides but not RKDs. Therefore, investigating the protein-DNA interaction from a structural perspective is essential to understand the evolutionary significance of the serine (S) residue of the RWP-RK domain. Herein, we have modelled both the wild type (WT) and the variant RWP-RK domains containing substitutions like glutamic acid (E), tyrosine (Y), and histidine (H) and docked them with the modelled pCLE13 cis-element. Our docking results revealed that a helix-turn-helix (HTH) motif of the RWP-RK domain interacts with pCLE13. The WT HTH-DNA complex exhibited the most negative binding free energy, indicating a strong interaction, particularly hydrogen bonds acting between them. Simulation analysis of WT and variant models provided deeper insights into protein-DNA binding dynamics. The hydrogen bond occupancy percentage indicated that the fourth serine (S) residue is vital for maintaining a significant percentage of hydrogen bonds with DNA. The variants substituting this conserved serine (S) residue displayed energetic frustration upon binding to DNA and lost correlation among their residues. Overall, it suggested that serine (S) residue of the RWP-RK domain of all NINs/NLPs is crucial for appropriate protein-DNA interaction, which might be required for their biological relevance.

Spatiotemporal expression patterns and RNA interference efficiency of key diapause genes in Lymantria dispar-Investigating the heritability of RNA interference effects for pest biocontrol

The spongy moth (Lymantria dispar Linnaeus), a major quarantine pest, relies on diapause as a key survival strategy. This study examined the temporal and spatial expression of four diapause-associated genes, LdGCLC, LdGLUD1_2, LdIDH1, and LdIDH2. Using fluorescence in situ hybridization and qPCR, their expression was analyzed across developmental stages and tissues. Additionally, RNA interference (RNAi) via microinjection and immersion was employed to systematically silence these genes. The results revealed that (1) all four genes were expressed in the brain; (2) dsRNA microinjection reduced target gene expression in larvae, with FISH showing a decrease in fluorescence intensity; (3) immersing eggs in dsRNA solution significantly lowered target gene expression, diapause hormone and ecdysone levels, along with a notable reduction in hatchability; (4) pre-immersion eggs in 4.4 M HCl at room temperature for 5 min before bacterial immersion significantly enhanced RNAi efficiency; and (5) maternal dsRNA microinjection decreased target gene expression, diapause hormone and ecdysone levels in offspring eggs, confirming transgenerational RNAi. These findings underscore RNAi's potential for heritable gene silencing in pest control.

Conformational flexibility associated with remote residues regulates the kinetic properties of glutamate dehydrogenase

Glutamate dehydrogenase (GDH) is a pivotal metabolic enzyme in all living organisms, and some of the GDHs exhibit substrate-dependent homotropic cooperativity. However, the mode of allosteric communication during the homotropic effect in GDHs remains poorly understood. In this study, we examined two homologous GDHs, Aspergillus niger GDH (AnGDH) and Aspergillus terreus GDH (AtGDH), with differing substrate utilization kinetics to uncover the factors driving their distinct behavior. We report the crystal structures and first-ever cryo-EM structures of apo- AtGDH and AnGDH that captured arrays of conformational ensembles. A wider mouth opening (~ 21 Å) is observed for the cooperative AnGDH as compared to the non-cooperative AtGDH (~17 Å) in their apo states. A network of interactions related to the substitutions in Domain II influence structural flexibility in these GDHs. Remarkably, we have identified a distant substitution (R246 to S) in Domain II, as a part of this network, which can impact the mouth opening and converts non-cooperative AtGDH into a cooperative enzyme. Our study demonstrates that remote residues can influence structural and kinetic properties in homologous GDHs.

Pharmacophore-based identification and in Silico characterization of microbial metabolites as potential modulators of Wnt signaling pathway in colorectal cancer therapy

Aberrant activation of the Wnt/β-catenin signaling pathway, primarily driven by APC mutation and AXIN degradation via Tankyrase, contributes significantly to colorectal cancer (CRC) progression and metastasis. The accumulation of β-catenin, resulting from the dysregulated ubiquitination, underscores the need for alternative therapeutic strategies targeting Tankyrase and β-catenin. This present study explores microbial metabolites as a source of novel anti-cancer agents, leveraging their unique bioactivity and structural diversity, often exhibiting superior target specificity and lower toxicity than synthetic drugs. Through a computational drug discovery pipeline, a large library of 27641 microbial metabolites was initially screened based on multiple drug-likeliness criteria, resulting in the selection of 2527 compounds. Among the screened compounds, an integrated computational workflow comprising molecular docking, molecular dynamic simulations (MDS), MM/PBSA analysis, and Principal component analysis (PCA) identified Terreustoxin I (T1) as a potential Tankyrase inhibitor. In contrast, compound 10- phenyl-[12]-cytochalasin Z16 (B1) demonstrated a strong binding affinity within the β-catenin active site. Under physiological conditions, these lead compounds were evaluated for conformational stability, binding efficacy, and dynamic behavior. Additionally, ADMET profiling, physiochemical properties, and bioactivity score predictions confirmed the identified compounds' pharmacokinetic suitability and reduced toxicity profile. In silico, cytotoxicity predictions showed significant activity against SW480 and HCT90 colorectal cell lines, with additional anti-neoplastic and anti-leukemic properties, strengthening their candidacy as effective anti-cancer agents. These findings provide a foundation for further experimental validation and development of novel CRC therapies with improved safety and efficacy potential.

Phosphorylation at the D56 residue of MtrA in Mycobacterium tuberculosis enhances its DNA binding affinity by modulating inter-domain interaction

The response regulator, MtrA, plays a major role in adaptation to the host environment, cell division, replication, and dormancy activation of Mycobacterium tuberculosis (Mtb). The phosphorylation of the response regulator MtrA alters the downstream activity, typically involving changes in DNA binding activity. However, there is a substantial knowledge gap in understanding the phosphorylation-mediated structural changes in MtrA. Additionally, the active conformation of the protein has yet to be determined. Therefore, in this study, we have investigated the phosphorylation-induced conformational changes of MtrA using all-atom molecular dynamics simulations under various phosphorylation conditions. The results from this study demonstrate that the phosphorylation at D56 (pD56-MtrA) increases the compactness of the MtrA protein by stabilizing the inter-domain interaction between the regulatory domain and DNA binding domain. Notably, the higher occupancy H-bond (over 95 %) between Arg200-Asn100 in case of the pD56-MtrA condition, which is otherwise absent in the non-phosphorylated (uMtrA) condition, suggests the importance of this interaction in the active conformation of the protein. The dynamic cross-correlation analysis reveals that phosphorylation (especially pD56-MtrA) reduces the anti-correlated motions and increases correlated motions between different domains. Moreover, the higher DNA binding affinity of pD56-MtrA compared to uMtrA supported by molecular docking and MD simulation followed by MMPBSA analysis suggests that pD56-MtrA is the possible active conformation of the MtrA protein. Overall, this investigation elucidates the key structural changes in MtrA under different phosphorylated conditions, which might help in designing novel therapeutics against tuberculosis.

Unveiling local and global conformational changes and allosteric communications in SOD1 systems using molecular dynamics simulation and network analyses

BACKGROUND

Amyotrophic lateral sclerosis (ALS) is a serious neurodegenerative disorder affecting nerve cells in the brain and spinal cord that is caused by mutations in the superoxide dismutase 1 (SOD1) enzyme. ALS-related mutations cause misfolding, dimerisation instability, and increased formation of aggregates. The underlying allosteric mechanisms, however, remain obscure as far as details of their fundamental atomistic structure are concerned. Hence, this gap in knowledge limits the development of novel SOD1 inhibitors and the understanding of how disease-associated mutations in distal sites affect enzyme activity.

METHODS

We combined microsecond-scale based unbiased molecular dynamics (MD) simulation with network analysis to elucidate the local and global conformational changes and allosteric communications in SOD1 Apo (unmetallated form), Holo, Apo_CallA (mutant and unmetallated form), and Holo_CallA (mutant form) systems. To identify hotspot residues involved in SOD1 signalling and allosteric communications, we performed network centrality, community network, and path analyses.

RESULTS

Structural analyses showed that unmetallated SOD1 systems and cysteine mutations displayed large structural variations in the catalytic sites, affecting structural stability. Inter- and intra H-bond analyses identified several important residues crucial for maintaining interfacial stability, structural stability, and enzyme catalysis. Dynamic motion analysis demonstrated more balanced atomic displacement and highly correlated motions in the Holo system. The rationale for structural disparity observed in the disulfide bond formation and R143 configuration in Apo and Holo systems were elucidated using distance and dihedral probability distribution analyses.

CONCLUSION

Our study highlights the efficiency of combining extensive MD simulations with network analyses to unravel the features of protein allostery.

Deciphering the intrinsic dynamics of unphosphorylated IRAK4 kinase bound to type I and type II inhibitors

Interleukin-1 receptor-associated kinase 4 (IRAK4) is a vital protein involved in Toll-like and interleukin-1 receptor signal transduction. Several studies have reported regarding the crystal structure, dynamic properties, and interactions with inhibitors of the phosphorylated form of IRAK4. However, no dynamic properties of inhibitor-bound unphosphorylated IRAK4 have been previously studied. Herein, we report the intrinsic dynamics of unphosphorylated IRAK4 (uIRAK4) bound to type I and type II inhibitors. The corresponding apo and inhibitor-bound forms of uIRAK4 were subjected to three independent simulations of 500 ns (total 1.5 μs) each, and their trajectories were analyzed. The results indicated that all three systems were relatively stable, except for the type II inhibitor-bound form of uIRAK4, which exhibited less compact folding and higher solvent surface area. The intra-hydrogen bonds corroborated the structural deformation of the type-II inhibitor-bound complex, which could be attributed to the long molecular structure of the type-II inhibitor. Moreover, the type II inhibitor bound to uIRAK4 showed higher binding free energy with uIRAK4 than the type I inhibitor. The free energy landscape analysis showed a reorientation of Phe330 side chain from the DFG motif at different metastable states for all the systems. The intra-residual distance between residues Lys213, Glu233, Tyr262, and Phe330 suggests a functional interplay when the inhibitors are bound to uIRAK4, thereby hinting at their crucial role in the inhibition mechanism. Ultimately, the intrinsic dynamics study observed between type I/II inhibitor-bound forms of uIRAK4 may assist in better understanding the enzyme and designing therapeutic compounds.

Amyotrophic lateral sclerosis disease-related mutations disrupt the dimerization of superoxide dismutase 1 - A comparative molecular dynamics simulation study

More than 150 genes are involved in amyotrophic lateral sclerosis (ALS), with superoxide dismutase 1 (SOD1) being one of the most studied. Mutations in SOD1 gene, which encodes the enzyme SOD1 is the second most prevalent and studied cause of familial ALS. SOD1 is a ubiquitous, homodimeric metalloenzyme that forms a critical component of the cellular defense against reactive oxygen species. Several mutations in the SOD1 enzyme cause misfolding, dimerization instability, and increased aggregate formation in ALS. However, there is a lack of information on the dimerization of SOD1 monomers and the mechanistic underpinnings on how the pathogenic mutations disrupt the dimerization mechanism. Here, we presented microsecond-scale molecular dynamics (MD) simulations to unravel how interface-based mutations compromise SOD1 dimerization and provide mechanistic understanding into the corresponding process using WT and three interface-based mutant systems (A4V, T54R, and I113T). Structural stability analysis showed that the mutant systems displayed disparate variations in the catalytic sites which may directly alter the stability and activity of the SOD1 enzyme. Based on the dynamic network analysis and principal component analysis, it has been identified that the mutations weakened the correlated motions along the dimer interface and altered the protein conformational behavior, thus weakening the stability of dimer formation. Moreover, the simulation results identified crucial residues such as G51, D52, G114, I151, and Q153 in establishing the dimerization interaction network, which were weakened or absent in the presence of interfacial mutants. Surface potential analysis on mutant systems also displayed changes in the dimerization potential, thus showing the unfavorable dimer formation. Furthermore, network analysis identified the hotspot residues necessary for SOD1 signal transduction which were surprisingly found in the catalytic sites rather than the anticipated dimerization interface.

Deciphering cell-cell interactions and communication in the tumor microenvironment and unraveling intratumoral genetic heterogeneity via single-cell genomic sequencing

A tumor's heterogeneity has important implications in terms of its clonal origin, progression, stemness, and drug resistance. Therefore, because of its significance in treatment, it is important to understand the gene expression pattern of a single cell, track gene expression or mutation in heterogeneous cells, evaluate the clonal origin of cancer cells, and determine the selective evolution of different subpopulations of cancer cells. Researchers are able to trace a cell's mutation and identify different types of tumor cells by measuring the whole transcriptome with single-cell sequencing (scRNA-seq). This technology provides a better understanding of the molecular mechanisms driving tumor growth than that offered by traditional RNA sequencing methods. In addition, it has revealed changes in the mutations and functions of somatic cells as a tumor evolves; it has also clarified immune cell infiltration and activation. Research on scRNA-seq technology has recently advanced significantly, suggesting new strategies for the treatment of cancer. In short, cancer researchers have become increasingly dependent on scRNA-seq. This paper reviews the development, detection principles, and processes of scRNA-seq technology and their application in tumor research. It also considers potential clinical applications.