Structure and Dynamics of N-Glycosylated Human Ribonuclease 1

Deglycosylation significantly affects the activity, stability and appropriate folding of recombinant Aspergillus niger α-L-rhamnosidase expressed in Pichia pastoris

Glycosylation plays a critical role in regulating activity, stability, and correct folding of enzymes. In this study, recombinant Aspergillus niger α-L-rhamnosidase (r-Rha1) was employed to explore the impact of glycosylation in Pichia pastoris on the enzymatic properties and protein folding. β-elimination reaction and deglycosylase treatment assays demonstrated that r-Rha1 undergoes primarily N-glycosylation. The deglycosylated r-Rha1 was prepared in two ways: treating with Endoglycosidase F1 after expression (referred to as r-Rha1-vitro), or inhibiting intracellular glycosylation using tunicamycin (referred to as r-Rha1-vivo). Deglycosylation resulted in a 0.22-fold decrease in activity for r-Rha1-vitro and due to its slower turnover rate, r-Rha1-vivo showed a 0.73-fold decrease in activity. r-Rha1-vitro maintained the similar optimal temperature as r-Rha1, r-Rha1-vivo displayed a 10 °C lower optimal temperature. Compared to the decreased extent of r-Rha1-vitro in t1/2 at 55 °C, 60 °C, and 65 °C and Tm, chemical interferent deglycosylation in vivo showed a more profound impact on r-Rha1. Analyses based on circular dichroism, fluorescence spectroscopy, and differential scanning calorimetry revealed significant changes in the structure and thermodynamic stability of r-Rha1-vivo, accounting for its marked decline in activity and stability. The significant and unpredictable structure changes of r-Rha1-vivo proved the essential role of glycosylation for appropriate folding in P. pastoris.

Molecular Modeling of Glycosylated Catalytic Domain of Human Carbonic Anhydrase IX

Glycans exhibit significant structural diversity due to the flexibility of glycosidic bonds linking their constituent monosaccharides and the formation of numerous hydrogen bonds. The present work searches a simulated ensemble of glycan chain conformations attached to the catalytic domain of N-glycosylated human carbonic anhydrase IX (HCA IX-c) to identify conformations pointed away or back-folded toward the protein surface guided by different amino acid residues. A series of classical molecular dynamics (MD) simulation studies for a total of 30 μs followed by accelerated MD simulations for a total of 2 μs have been performed using two different force fields to capture varying degrees of fluctuations of both glycan chain and HCA IX. From the underlying free energy profile and kinetics derived using hidden Markov state model, several stable glycan orientations are identified that extend away from the protein surface and convert among each other with rate constants of the order 107-1010 S-1. Most importantly, we have identified a rare glycan conformation which reaches close to a catalytically important amino acid residue, Glu-106. We further enlist the protein residues that couple such less frequent event of the glycan chain back-folding toward the surface of the protein.

Beyond microtubules: The cellular environment at the endoplasmic reticulum attracts proteins to the nucleus, enabling nuclear transport

All proteins are translated in the cytoplasm, yet many, including transcription factors, play vital roles in the nucleus. While previous research has concentrated on molecular motors for the transport of these proteins to the nucleus, recent observations reveal perinuclear accumulation even in the absence of an energy source, hinting at alternative mechanisms. Here, we propose that structural properties of the cellular environment, specifically the endoplasmic reticulum (ER), can promote molecular transport to the perinucleus without requiring additional energy expenditure. Specifically, physical interaction between proteins and the ER impedes their diffusion and leads to their accumulation near the nucleus. This result explains why larger proteins, more frequently interacting with the ER membrane, tend to accumulate at the perinucleus. Interestingly, such diffusion in a heterogeneous environment follows Chapman's law rather than the popular Fick's law. Our findings suggest a novel protein transport mechanism arising solely from characteristics of the intracellular environment.

Glycosylation Contributes to Thermostability and Proteolytic Resistance of rFIP-nha (Nectria haematococca)

Glycosylation is an important post-translational modification of proteins, contributing to protein function, stability and subcellular localization. Fungal immunomodulatory proteins (FIPs) are a group of small proteins with notable immunomodulatory activity, some of which are glycoproteins. In this study, the impact of glycosylation on the bioactivity and biochemical characteristics of FIP-nha (from Nectria haematococca) is described. Three rFIP-nha glycan mutants (N5A, N39A, N5+39A) were constructed and expressed in Pichia pastoris to study the functionality of the specific N-glycosylation on amino acid N5 and N39. Their protein characteristics, structure, stability and activity were tested. WT and mutants all formed tetramers, with no obvious difference in crystal structures. Their melting temperatures were 82.2 °C (WT), 81.4 °C (N5A), 80.7 °C (N39A) and 80.1 °C (N5+39A), indicating that glycosylation improves thermostability of rFIP-nha. Digestion assays showed that glycosylation on either site improved pepsin resistance, while 39N-glycosylation was important for trypsin resistance. Based on the 3D structure and analysis of enzyme cleavage sites, we conclude that glycosylation might interfere with hydrolysis via increasing steric hindrance. WT and mutants exerted similar bioactivity on tumor cell metabolism and red blood cells hemagglutination. Taken together, these findings indicate that glycosylation of FIP-nha impacts its thermostability and digestion resistance.

Asn57 N-glycosylation promotes the degradation of hemicellulose by β-1,3-1,4-glucanase from Rhizopus homothallicus

N-glycosylation alters the properties of different enzymes in different ways. Rhizopus homothallicus was first described as an environmental isolate from desert soil in Guatemala. A new gene encoding glucanase RhGlu16B was identified in R. homothallicus. It had high specific activity (9673 U/mg) when barley glucan was used as a substrate, and β-glucan is hemicellulose that is abundant in nature. RhGlu16B has only one N-glycosylation site in its Ala55-Gly64 loop. It was found that N-glycosylation increased its T_m value and catalytic efficiency by 5.1 °C and 59%, respectively. Adding N-glycosylation to the same region of GH16 family glucanases TlGlu16A (from Talaromyces leycettanus) increased its thermostability and catalytic efficiency by 6.4 °C and 38%, respectively. In a verification experiment using GH16 family glucanases BisGlu16B (from Bisporus) in which N-glycosylation was removed, N-glycosylation also appeared to promote thermostability and catalytic efficiency. N-glycosylation reduced the overall root mean square deviation of the enzyme structure, creating rigidity and increasing overall thermostability. This study provided a reference for the molecular modification of GH16 family glucanases and guided the utilization of β-glucan in hemicellulose.

Enhancing the Thermostability of Phytase to Boiling Point by Evolution-Guided Design

The good thermostability of enzymes is an important basis for their wide application in industry. In this study, the phytase APPA from Yersinia intermedia was designed by evolution-guided design. Through the collection of homologous sequences in the NCBI database, we obtained a sequence set composed of 5,569 sequences, counted the number and locations of motif N-X-T/S, and selected the sites with high frequency in evolution as candidate sites for experiments. Based on the principle that N-glycosylation modification sites are located on the protein surface, 13 mutants were designed to optimize the number and location of N-glycosylation sites. Through experimental verification, 7 single mutants with improved thermostability were obtained. The best mutant, M14, with equal catalytic efficiency as the wild-type was obtained through combined mutation. The half-life (t_1/2) value of mutant M14 was improved from 3.32 min at 65°C to 25 min of at 100°C, allowing it to withstand boiling water treatment, retaining approximately 75% initial activity after a 10-min incubation at 100°C. Differential scanning calorimetry analysis revealed that while the mutants' thermodynamic stability was nearly unchanged, their kinetic stability was greatly improved, and the combined mutant exhibited strong refolding ability. The results of a in vitro digestibility test indicated that the application effect of mutant M14 was about 4.5 times that of wild-type APPA, laying a foundation for its industrial application. IMPORTANCE Due to the harsh reaction conditions of industrial production, the relative instability of enzymes limits their application in industrial production, such as for food, pharmaceuticals, and feed. For example, the pelleting process of feed includes a brief high temperature (80 to 85°C), which requires the enzyme to have excellent thermostability. Therefore, a simple and effective method to improve the thermostability of enzymes has important practical value. In this study, we make full use of the existing homologous sequences (5,569) in the database to statistically analyze the existence frequency of N-X-T/S motifs in this large sequence space to design the phytase APPA with improved thermostability and a high hit rate (~50%). We obtained the best combination mutant, M14, that can tolerate boiling water treatment and greatly improved its kinetic stability without damaging its specific activity. Simultaneously, we proved that its performance improvement is due to its enhanced refolding ability, which comes from N-glycan modification rather than amino acid replacement. Our results provide a feasible and effective method for the modification of enzyme thermostability.

Emerging biological functions of ribonuclease 1 and angiogenin

Pancreatic-type ribonucleases (ptRNases) are a large family of vertebrate-specific secretory endoribonucleases. These enzymes catalyze the degradation of many RNA substrates and thereby mediate a variety of biological functions. Though the homology of ptRNases has informed biochemical characterization and evolutionary analyses, the understanding of their biological roles is incomplete. Here, we review the functions of two ptRNases: RNase 1 and angiogenin. RNase 1, which is an abundant ptRNase with high catalytic activity, has newly discovered roles in inflammation and blood coagulation. Angiogenin, which promotes neovascularization, is now known to play roles in the progression of cancer and amyotrophic lateral sclerosis, as well as in the cellular stress response. Ongoing work is illuminating the biology of these and other ptRNases.

Human ribonuclease 1 serves as a secretory ligand of ephrin A4 receptor and induces breast tumor initiation

Human ribonuclease 1 (hRNase 1) is critical to extracellular RNA clearance and innate immunity to achieve homeostasis and host defense; however, whether it plays a role in cancer remains elusive. Here, we demonstrate that hRNase 1, independently of its ribonucleolytic activity, enriches the stem-like cell population and enhances the tumor-initiating ability of breast cancer cells. Specifically, secretory hRNase 1 binds to and activates the tyrosine kinase receptor ephrin A4 (EphA4) signaling to promote breast tumor initiation in an autocrine/paracrine manner, which is distinct from the classical EphA4-ephrin juxtacrine signaling through contact-dependent cell-cell communication. In addition, analysis of human breast tumor tissue microarrays reveals a positive correlation between hRNase 1, EphA4 activation, and stem cell marker CD133. Notably, high hRNase 1 level in plasma samples is positively associated with EphA4 activation in tumor tissues from breast cancer patients, highlighting the pathological relevance of the hRNase 1-EphA4 axis in breast cancer. The discovery of hRNase 1 as a secretory ligand of EphA4 that enhances breast cancer stemness suggests a potential treatment strategy by inactivating the hRNase 1-EphA4 axis.