Combination of engineering the substrate and Ca2+ binding domains of heparinase I to improve the catalytic activity

Heparinase I (EC 4.2.2.7), is an enzyme that cleaves heparin, showing great potential for eco-friendly production of low molecular weight heparin (LMWH). However, owing to its poor catalytic activity and thermal stability, the industrial application of heparinase I has been severely hindered. To improve the catalytic activity, we proposed to engineer both the substrate and Ca2+ binding domains of heparinase I. Several heparinases I from different organisms were selected for multiple sequence alignment and molecular docking to screen the key residues in the binding domain. Nine single-point mutations were selected to enhance the catalytic activity of heparinase I. Among them, T250D was the most highly active one, whereas mutations around Ca2+ binding domain yielded two active mutants. Mutant D152S/R244K/T250D with significantly increased catalytic activity was obtained by combined mutation. The catalytic efficiency of the mutant was 118,875.8 min-1·µM-1, which was improved 5.26 times. Molecular modeling revealed that the improved activity and stability of the mutants were probably attributed to the formation of new hydrogen bonds. The highly active mutant had great potential applications in industry and the strategy could be used to improve the performance of other enzymes.

Binding domain on CD22 molecules contributing to the biological activity of T cell-engaging bispecific antibodies

CD22, as the B-cell malignancies antigen, has been targeted for immunotherapies through CAR-T cells, antibody-drug conjugates (ADCs) and immunotoxins via interaction of antibodies with binding domains on the receptor. We hypothesized that avidity and binding domain of antibody to target cells may have significant impact on the biological function in tumor immunotherapy, and T cell-engaging bispecific antibody (TCB) targeting CD22 could be used in the therapy of hematologic malignancies. So, to address the question, we utilized the information of six previously reported CD22 mAbs to generate CD22-TCBs with different avidity to different domains on CD22 protein. We found that the avidity of CD22-TCBs to protein was not consistent with the avidity to target cells, indicating that TCBs had different binding mode to the protein and cells. In vitro results indicated that CD22-TCBs mediated cytotoxicity depended on the avidity of antibodies to target cells rather than to protein. Moreover, distal binding domain of the antigen contributed to the avidity and biological activity of IgG-[L]-scfv-like CD22-TCBs. The T cells' proliferation, activation, cytotoxicity as well as cytokine release were compared, and G5/44 BsAb was selected for further in vivo assessment in anti-tumor activity. In vivo results demonstrated that CD22-TCB (G5/44 BsAb) significantly inhibited the tumors growth in mice. All these data suggested that CD22-TCBs could be developed as a promising candidate for B-cell malignancies therapy through optimizing the design with avidity and binding domain to CD22 target in consideration.

The CDR3 region as the major driver of TREM-1 interaction with its ligands, an in silico characterization

The triggering receptor expressed on myeloid cells-1 (TREM-1) is a pattern recognition receptor heavily investigated in infectious and non-infectious diseases. Because of its role in amplifying inflammation, TREM-1 has been explored as a diagnostic/prognostic biomarker. Further, as the receptor has been implicated in the pathophysiology of several diseases, therapies aiming at modulating its activity represent a promising strategy to constrain uncontrolled inflammatory or infectious diseases. Despite this, several aspects concerning its interaction with ligands and activation process, remain unclear. Although many molecules have been suggested as TREM-1 ligands, only five have been confirmed to interact with the receptor: actin, eCIRP, HMGB1, Hsp70 and PGLYRP1. However, the domains involved in the interaction between the receptor and these proteins are not clarified yet. Therefore, here we used in silico approaches to investigate the putative binding domains in the receptor, using hot spots analysis, molecular docking and molecular dynamics simulations between TREM-1 and its five known ligands. Our results indicated the complementarity-determining regions (CDRs) of the receptor as the main mediators of antigen recognition, especially the CDR3 loop. We believe that our study could be used as structural basis for the elucidation of TREM-1's recognition process, and may be useful for prospective in silico and biological investigations exploring the receptor in different contexts.

Truncated affinity-improved aptamers for 17β-estradiol determination by AuNPs-based colorimetric aptasensor

17β-estradiol (E2) residues could enrich in organisms via food chain and lead to harmful biological effects for human body. To ascertain the binding domain of original E2 aptamer (E00) with long-sequence (76-mer), we developed novel truncated aptamers from E00, through rationally designed truncation by intercepting a single ring or a combination of rings (containing hairpin loop, interior loop or multiloop) at different sites and retaining appropriate double helix regions. Through comparison, 15-mer E09 presented improved affinity and higher specificity, indicating the hairpin loop near to 3' end of E00 served on the binding domain to E2. E09 was used for gold nanoparticles (AuNPs)-based colorimetric determination of E2, achieved the detection limit of 0.02 μg/mL. The truncated aptamer (only 15-mer) first proposed in this study has great application potential in E2 determination, and this work provides proof-of-concept study for truncation of other long-sequence aptamers.

Rabies virus phosphoprotein P5 binding to BECN1 regulates self-replication by BECN1-mediated autophagy signaling pathway

Background

Rabies virus (RABV) is reported to encode five phosphoproteins (P), which are involved in viral genomic replication, axonal transport, oxidative stress, interferon antagonism, and autophagy induction. However, the functions of the different P proteins are poorly understood.

Methods

Immunofluorescence staining and western blot were performed to detect the autophagy activity, the form of ring-like structure, and the colocalization of BECN1 and P. Co-immunoprecipitation was performed to detect the interaction between P and BECN1. QRT-PCR and TCID₅₀ assay were performed to detect the replication level of RABV. Small interfering RNA was used to detect the autophagy signaling pathway.

Results

We found that P5 attaches to N-terminal residues 1–139 of BECN1 (beclin1) on the BECN1 ring-like structure through amino acid residues 173–222 of P5. Subsequently, we found that P5-induced autophagosomes did not fuse with lysosomes. Becn1 silencing did not recover P5 overexpression-induced promotion of RABV replication. Mechanistically, RABV protein PΔN82 (P5) induced incomplete autophagy via the BECN1-mediated signaling pathway.

Conclusions

Our data indicate that P5 binding to the BECN1 ring benefits RABV replication by inducing BECN1 signaling pathway-dependent incomplete autophagy, which provides a potential target for antiviral drugs against RABV.

Phospho-peptide binding domains in S. cerevisiae model organism

Protein phosphorylation is one of the main mechanisms by which signals are transmitted in eukaryotic cells, and it plays a crucial regulatory role in almost all cellular processes. In yeast, more than half of the proteins are phosphorylated in at least one site, and over 20,000 phosphopeptides have been experimentally verified. However, the functional consequences of these phosphorylation events for most of the identified phosphosites are unknown. A family of protein interaction domains selectively recognises phosphorylated motifs to recruit regulatory proteins and activate signalling pathways. Nine classes of dedicated modules are coded by the yeast genome: 14-3-3, FHA, WD40, BRCT, WW, PBD, and SH2. The recognition specificity relies on a few residues on the target protein and has coevolved with kinase specificity. In the present study, we review the current knowledge concerning yeast phospho-binding domains and their networks. We emphasise the relevance of both positive and negative amino acid selection to orchestrate the highly regulated outcomes of inter- and intra-molecular interactions. Finally, we hypothesise that only a small fraction of yeast phosphorylation events leads to the creation of a docking site on the target molecule, while many have a direct effect on the protein or, as has been proposed, have no function at all.

Regulation of HCN Ion Channels by Non-canonical Cyclic Nucleotides

The hyperpolarization-activated cyclic-nucleotide-modulated (HCN) proteins are cAMP-regulated ion channels that play a key role in nerve impulse transmission and heart rate modulation in neuronal and cardiac cells, respectively. Although they are regulated primarily by cAMP, other cyclic nucleotides such as cGMP, cCMP, and cUMP serve as partial agonists for the HCN2 and HCN4 isoforms. By competing with cAMP for binding, these non-canonical ligands alter ion channel gating, and in turn, modulate the cAMP-dependent activation profiles. The partial activation of non-canonical cyclic nucleotides can be rationalized by either a partial reversal of a two-state inactive/active conformational equilibrium, or by sampling of a third conformational state with partial activity. Furthermore, different mechanisms and degrees of activation have been observed upon binding of non-canonical cyclic nucleotides to HCN2 versus HCN4, suggesting that these ligands control HCN ion channels in an isoform-specific manner. While more work remains to be done to achieve a complete understanding of ion channel modulation by non-canonical cyclic nucleotides, it is already clear that such knowledge will ultimately prove invaluable in achieving a more complete understanding of ion channel signaling in vivo, as well as in the development of therapeutics designed to selectively modulate ion channel gating.

Identification of the binding domains and key amino acids for the interaction of the transcription factors BmPOUM2 and BmAbd-A in Bombyx mori

The transcription factor BmPOUM2 interacted with another transcription factor BmAbd-A to regulate the expression of the wing cuticle protein gene BmWCP4 in Bombyx mori. In this study, the binding domains and amino acids for the interaction between BmPOUM2 and BmAbd-A were reported. Two isoforms of BmPOUM2 were identified. The short isoform (BmPOUM2-S) lacks a 114-amino acid sequence containing a POU-homeodomain and a nuclear localization signal peptide (NLS), as compared to the full-length isoform (BmPOUM2). Both BmPOUM2 and BmPOUM2-S proteins bound to the BmAbd-A through the POU-specific domain. When the six amino acids (Lys166, Gly173, Gln176, Ser192, Glu200 and Asn208) that are highly conserved in POU family genes were mutated, BmPOUM2 did not bind to BmAbd-A. BmAbd-A interacted with BmPOUM2 by the homeobox domain or the LCR2 (low complexity region) domain. When seven amino acids (Phe156/248, His158/250, Ala175/263, Cys180/265, Glu190/268, Trp196/274 and Val214/289) that are shared in the homeobox and LCR2 domains were mutated, BmAbd-A did not bind to BmPOUM2. Overexpression of either BmPOUM2 or BmAbd-A or both increased the activity of BmWCP4 promoter in CHO cells. ChIP assay and EMSA showed that BmAbd-A protein bound to the Hox cis-regulatory element in the BmWCP4 promoter, while the BmPOUM2 bound to the nearby POU CRE. A model for the interaction and action of BmPOUM2 and BmAbd-A in regulation of the BmWCP4 expression is proposed.

A chimeric protein composed of the binding domains of Clostridium perfringens phospholipase C and Trueperella pyogenes pyolysin induces partial immunoprotection in a mouse model

Trueperella pyogenes and Clostridium perfringens are two kinds of conditional pathogens frequently associated with wound infections and succeeding lethal complications in various economic livestock. Pyolysin (PLO) and phospholipase C (PLC) are the key virulence factors of these two pathogens, respectively. In our study, a chimeric protein called rPC-PD4, which is composed of the binding regions of PLO and PLC, was synthesized. The toxicity of rPC-PD4 was evaluated. Results revealed that rPC-PD4 is a safe chimeric molecule that can be used to develop vaccines. Immunizing BALB/c mice with rPC-PD4 induced high titers of serum antibodies that could efficiently neutralize the hemolytic activity of recombinant PLO and PLC. After the challenge with T. pyogenes or C. perfringens was performed through the intraperitoneal route, we observed that rPC-PD4 immunization could provide partial immunoprotection and reduce lung, intestine, and liver tissue damage to mice. This work demonstrated the efficacy of the rationally designed rPC-PD4 chimeric protein as a potential vaccine candidate against C. perfringens and T. pyogenes.

Cyclosporin A inhibits hepatitis B and hepatitis D virus entry by cyclophilin-independent interference with the NTCP receptor

BACKGROUND & AIMS

Chronic hepatitis B and hepatitis D are global health problems caused by the human hepatitis B and hepatitis D virus. The myristoylated preS1 domain of the large envelope protein mediates specific binding to hepatocytes by sodium taurocholate co-transporting polypeptide (NTCP). NTCP is a bile salt transporter known to be inhibited by cyclosporin A. This study aimed to characterize the effect of cyclosporin A on HBV/HDV infection.

METHODS

HepaRG cells, primary human hepatocytes, and susceptible NTCP-expressing hepatoma cell lines were applied for infection experiments. The mode of action of cyclosporin A was studied by comparing the effect of different inhibitors, cyclophilin A/B/C-silenced cell lines as well as NTCP variants and mutants. Bile salt transporter and HBV receptor functions were investigated by taurocholate uptake and quantification of HBVpreS binding.

RESULTS

Cyclosporin A inhibited hepatitis B and D virus infections during and--less pronounced--prior to virus inoculation. Binding of HBVpreS to NTCP was blocked by cyclosporin A concentrations at 8 μM. An NTCP variant deficient in HBVpreS binding but competent for bile salt transport showed resistance to cyclosporin A. Silencing of cyclophilins A/B/C did not abrogate transporter and receptor inhibition. In contrast, tacrolimus, a cyclophilin-independent calcineurin inhibitor, was inactive.

CONCLUSIONS

HBV and HDV entry via sodium taurocholate co-transporting polypeptide is inhibited by cyclosporin A. The interaction between the drug and the viral receptor is direct and overlaps with a functional binding site of the preS1 domain, which mediates viral entry.