Proteins-Structure Function and Bioinformatics最新文献

The effect of the presence of the BAF-binding LEM-domain and LaminA Ig-fold on the stability of the BAF dimer was studied qualitatively using non-equilibrium pull simulations and quantitatively through the calculation of the potential of mean force profile along BAF-BAF separation distance. We find that hydrophobicity plays a significant role in stabilizing the BAF dimer when LEM-domain and LaminA are bound. The role of LEM-domain and LaminA in stabilizing the BAF dimer is explored by quantifying the strength of interaction between them, which are critical components of the nuclear lamina.

Serine acetyltransferase (CysE) is a member of the left-handed β-helix family of acetyltransferases that catalyze the rate limiting step in de novo cysteine biosynthesis. There are two isoforms of CysE that differ in length, with the shorter isoform lacking approximately 76 amino acids at the N-terminus of the protein from the serine acetyltransferase (SATase) domain. Here, we analyze the distribution and diversity of CysE isoforms across the bacterial kingdom. The isoforms can be classified into two discrete groups, with the truncated isoform prevalent in Gram-positive bacteria and the full-length isoform prevalent in Proteobacteria. Moreover, we demonstrate that the truncation is discrete with the loss of four N-terminal α-helices conserved for the truncated isoform. Using predictive modeling, we show that this truncation likely weakens the CysE trimer interface, potentially resulting in a trimeric assembly instead of the canonical CysE hexamer. This expands our understanding of CysE enzymes and their distribution across bacterial species, an important consideration given the increasing interest in targeting CysE enzymes for potential antimicrobials.

Glutathione S-transferase P1 (GSTP1) plays a crucial role in detoxifying cytotoxic agents and contributes to cancer chemoresistance. Due to its key role in tumor progression and its impact on treatment efficacy, GSTP1 has emerged as a promising therapeutic target for anticancer therapies. Ethacrynic acid (EA) is a known GSTP1 inhibitor; however, the specific molecular mechanisms behind its inhibitory action remain unclear. To clarify the effects of EA and its glutathione conjugate (EA-GSH) on the GSTP1 dimer, we conducted a comparative molecular dynamics (MD) study of four enzymatic states: apo (unbound), holo (GSH-bound), the GSTP1-EA and GSTP1-EA-GSH complexes, to analyze both interchain and ligand-enzyme interactions. Our results showed that GSTP1 flexibility depends on the movement of the α2 helix, which appears essential for accommodating substrates. Ligand binding made the enzyme more rigid, and EA disrupted dynamic coordination within the dimer by altering secondary-structure elements, potentially impairing enzymatic activity. Additionally, EA influenced dimerization by reducing binding energy at the dimer interface, possibly interfering with GSTP1's nonenzymatic role in apoptosis signaling. Energy analysis demonstrated that while GSH conjugation enhanced EA's binding affinity through favorable electrostatic interactions, it also imposed a significant energetic penalty due to increased solvent exposure. These findings highlight the need to optimize the lipophilic/hydrophilic balance of future GSTP1 inhibitors to match the physicochemical properties of the binding pocket. Overall, this study offers a deeper understanding of the molecular mechanisms behind GSTP1 inhibition and provides a structural basis for designing targeted therapies to overcome cancer chemoresistance.

Given the critical importance of preventing protein aggregation in neurodegenerative diseases, aggregation prediction tools are essential. Amyloid predictors would facilitate the understanding and exploitation of the amyloid state of proteins, providing an alternative to costly and slow laboratory tests. In recent years, hexapeptides have become a model for studying amyloid formation. Hexapeptides can also be used to identify aggregation-prone regions in proteins, particularly those involved in amyloid formation. While numerous computational methods using sophisticated feature sets and architectures have been developed for classifying hexapeptides and predicting amyloidogenic regions in proteins, predictive performance remains limited; for instance, BAP achieves only 84% accuracy. Here, we designed a novel feature selection method for hexapeptides, resulting in an easy to interpret four-feature representation called the AmyloPick model. A classifier based on this representation outperforms existing state-of-the-art methods. When extended to detect aggregation-prone regions (APRs) in full proteins, it performs comparably to established tools. A key contribution of this study is the statistical methodology that enables a rigorous performance assessment and direct comparison with other classifiers. This is particularly important because differing methodologies in the literature often hinder the comparability of the proposed methods. Our AmyloPick classifier significantly outperformed the state-of-the-art Budapest Amyloid Predictor (BAP) across all metrics, particularly in adjusted geometric mean (AGM) (0.7808 vs. 0.7649 for BAP) and accuracy (0.8089 vs. 0.7955 for BAP). For APR identification, APR-AmyloPick was comparable to ANuPP overall but significantly outperformed it in the ${\mathrm{SOV}}_{\text{Non}-\mathrm{APR}}$ metric. We have also developed a web server for the AmyloPick classifier.

Tuberculosis kills millions worldwide. Drug-resistance demands exploring new targets against this illness. Methionyl-tRNA synthetase (MetRS) is a crucial target in Mycobacterium tuberculosis (Mtb) that participates in the initiation and elongation of translation and represents a protein of evolutionary interest. To elucidate the structure-function relationships of MetRS, we performed detailed sequence analyses and molecular dynamics simulations of Mtb MetRS in the substrate-bound (methionine and ATP) and intermediate (methionyl-AMP) states, for both the wild-type and three single-mutant forms (H21A, K54A, and E130A). Eight systems (two wild-type and six mutants) were simulated for 36 μs. Differential dynamics and binding effects of the substrate versus intermediate states were identified, along with the molecular reasons for the loss of activity in mutants. The wild-type substrate state was more stable than the intermediate state. In contrast, the mutants were more unstable in the substrate state but incorporated stability into the intermediate state protein. These findings suggest that methionyl-AMP, being a reaction intermediate, exhibits a short residence time at the protein's active site, while the substrate state shows a longer residence time of methionine and ATP. The increased instability of mutants in the substrate state indicates disruption of the pyrophosphate-ATP exchange by altering substrate-protein interactions. Once the intermediate is formed, the mutations have minimal or no effect. These observations are consistent with experimental data. In brief, our study finds the molecular basis for the distinct substrate and intermediate recognition by Mtb MetRS and establishes a mechanism for the loss of activity in the mutants.

Structural divergence varies among protein residues, yet this variation has been largely overlooked compared with the well-studied case of sequence rate variation. Here we show that, in families of functionally conserved homologous enzymes, structural divergence increases with both residue flexibility and distance from the active site. Although these properties are correlated, modeling reveals that the pattern arises from two independent types of evolutionary constraints: non-functional and functional. The balance between these constraints varies widely across enzyme families, from non-functional to functional dominance. As functional constraints strengthen, structural divergence patterns are reshaped, becoming increasingly distinct from flexibility patterns and breaking the commonly assumed correspondence between evolutionary and dynamical structural ensembles. Active sites are more structurally conserved than average, but this conservation stems not only from functional constraints. Because active sites typically lie in rigid regions where non-functional constraints are high, both constraint types contribute comparably on average, with dominance shifting from one to the other depending on active-site rigidity. Together, these findings revise two long-standing assumptions: that evolutionary structural variation universally mirrors protein dynamics and that active-site conservation reflects functional requirements alone. Both depend on the balance between non-functional and functional constraints that shape enzyme structural evolution.

Since CASP13, experimentalists have been encouraged to provide their cryo-EM data along with the derived atomic models to the CASP organizers to aid assessment. In CASP16, 38 cryo-EM datasets were provided for assessment, which represented most cryo-EM targets. The corresponding targets typically comprised a single derived atomic structure; however, that model may be only one of several valid conformations. Flexibility often manifests as low-resolution regions in a cryo-EM reconstruction, particularly in RNA but often also in protein complexes. We show that local resolution in the reconstruction correlates well with the root-mean-square fluctuations (RMSF) of residues of accurate CASP predictions. The correlation between the local resolution and pLDDT was less clear, especially when mobile domains were present. When the resolution allowed, assessment of features such as sidechains, using our variant of SMOC with local fragment alignment, indicated that even high-quality predictions have room for improvement; on the other hand, some predictions fitted the density better in specific regions, indicating modeling discrepancies in the target. In one extreme case, a submitted target had regions of low-resolution that limited unambiguous model building. In such cases, part of the target structure is essentially a prediction itself, with implications for the assessment. Experimental data remain essential for model-free assessment of predictions and offer unique analyses such as comparisons to local resolution and thus flexibility.

N-glycans are structurally complex carbohydrates commonly found on eukaryotic glycoproteins, where they play essential roles in protein folding, stability, and cellular signaling. Some bacteria have evolved specialized degradation pathways to access N-glycans as nutrient sources, terminating in enzymes that cleave the conserved core Manβ1-4GlcNAc disaccharide. Members of glycoside hydrolase family 5 subfamily 18 (GH5_18) have recently been identified to catalyze this reaction. Here, we report the biochemical and structural characterization of MoGH5_18, which is encoded within a gene cluster consisting of other genes likely involved in N-glycan degradation. Biochemical assays show that MoGH5_18 hydrolyzes Manβ1-4GlcNAc but not Manβ1-4Man, consistent with substrate specificity observed in other GH5_18s. We solved the crystal structure of MoGH5_18 to 1.92 Å resolution, revealing a canonical (β/α) 8 TIM-barrel fold, dimeric architecture, and a conserved active site architecture. These findings demonstrate that MoGH5_18, despite sequence divergence, retains the structural and functional hallmarks of GH5_18 enzymes and further illustrate the power of SSN-guided approaches to uncover conserved enzymatic mechanisms within diverse glycan degradation pathways.

Prenylated flavin mononucleotide (prFMN) is a modified flavin cofactor required by the UbiD family of (de)carboxylase enzymes. While the reduced prFMNH₂ form is produced by the flavin prenyltransferase UbiX, the corresponding two-electron oxidized prFMN^iminium form is required to support UbiD catalysis. Thus, oxidative maturation of prFMNH₂ is required, which can be catalyzed by UbiD. However, heterologous (over)expression of UbiDs frequently leads to the accumulation of the stable but non-active one-electron oxidized purple prFMN^radical species. A dedicated prFMN maturase enzyme (PhdC) from Mycolicibacterium fortuitum was recently identified as capable of catalyzing the oxidative maturation of prFMN^radical to prFMN^iminium, thereby enabling an effective supply of active cofactor to the associated phenazine-1-carboxylate (de)carboxylase PhdA. We report the crystal structure of PhdC in complex with flavin, revealing it is a distant member of the class I HpaC-like family of short-chain dimeric flavin reductases and demonstrate catalytic conversion of the prFMN^radical species to prFMN^iminium in the presence of oxygen or ferricyanide. Co-expression of PhdC or a distant homologue from Priestia megaterium (YclD) with the canonical UbiD from Escherichia coli leads to activation of the latter, similar in effect to co-expression with the prFMNH₂-binding chaperone LpdD. Conserved Glu residues in the PhdC active site suggest catalysis occurs through C1' proton-abstraction coupled oxidation. This study thus provides both structural and mechanistic insight into the function of PhdC, adding to the expanding repertoire of prFMN-binding proteins associated with the widespread UbiDX system.

Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis. The emergence of Mtb's multidrug-resistant and extremely drug-resistant strains has imposed a great challenge for TB treatment. Hence, there is always a demand to explore new targets that may be crucial for the survival and pathogenicity of the bacilli. Oxidoreductases are a class of enzymes that transfer electrons in various biological pathways and reactions, at the expense of cellular NADPH/NADH. Here, we analyzed oxidoreductases from the H37Rv proteome and identified two uncharacterized putative oxidoreductases, Rv1260 and Rv1714. These putative oxidoreductases showed conservation among pathogenic and opportunistic mycobacterial species and were predicted to be virulence factors essential for the pathogen's survival. The 3D structural model and amino acid sequence of one of the oxidoreductases, Rv1260, showed similarities with tetracycline destructase, a flavin-dependent monooxygenase. Thin-layer chromatography and UV-visible spectroscopic experiments confirmed the presence of the FAD molecule in a bound form with the recombinant protein. Fluorescence quenching studies demonstrated a comparatively better affinity of NADPH than NADH with the protein. The protein also displayed efficient binding with chlortetracycline. Molecular dynamics simulations were employed to gain insights into the substrate binding and conformational changes in the protein. Moreover, the importance of the substrate binding region, the C-terminal helix, and the FAD binding cavity, located near the isoalloxazine ring, was highlighted. Overall, the study provides biochemical, biophysical, and mechanistic insights into one of the putative Mtb oxidoreductases. Based on our data, we propose that this protein may perform monooxygenation functions under specific redox conditions and contribute to the redox processes in Mtb.