In silico designing of therapeutic protein enriched with branched-chain amino acids for the dietary treatment of chronic liver disease

Homology Modeling, Molecular Dynamics Simulation, and Prediction of Bovine TLR2 Heterodimerization

Toll-like receptor 2 (TLR2) is a major membrane-bound receptor with ligand and species specificity that activates the host immune response. Heterodimerization of TLR2 with TLR1 (TLR2/1) or TLR6 (TLR2/6), triggered by ligand binding, is essential to initiating the signaling pathway. Bovine TLR2 (bTLR2) heterodimerization has not been defined yet compared with human and mouse TLR2s (hTLR2 and mTLR2). The aim of the present study was to model bovine TLRs (TLRs 1, 2 and 6) and create the heterodimeric forms of the bovine TLR2 using molecular dynamics (MD) simulations. We compared the intermolecular interactions in bTLR2/1-PAM3 and bTLR2/6-PAM2 with the hTLR2 and mTLR2 complexes through docking simulations and subsequent MD analyses. The present computational findings showed that bTLR2 dimerization could have a biological function and activate the immune response, similar to hTLR2 and mTLR2. Agonists and antagonists that are designed for hTLR2 and mTLR2 can target bTLR2. However, the experimental approaches to comparing the functional immune response of TLR2 across species were missing in the present study. This computational study provides a structural analysis of the bTLR2 interaction with bTLR1 and bTLR6 in the presence of an agonist/antagonist and reveals the three-dimensional structure of bTLR2 dimerization. The present findings could guide future experimental studies targeting bTLR2 with different ligands and lipopeptides.

Hypoglycemic Effect of Hydrophobic BCAA Peptides Is Associated with Altered PI3K/Akt Protein Expression

The hypoglycemic activities of the hydrophobic branched-chain amino acid (BCAA) peptides from seabuckthorn seed protein were preliminarily characterized in type 2 diabetic db/db mice. Four novel BCAA peptides (18.27 ± 0.26% (w/w): Leu/Ile-Pro-Glu-Asp-Pro, Asp-Leu/Ile-Val-Gly-Glu, Leu/Ile-Pro, and Leu/Ile-Pro-Leu/Ile) were identified in seabuckthorn seed protein. The protein content in seabuckthorn seed protein hydrolysate, obtained using 80% ethanol, was 78.8 ± 1.4% (w/w). Animal experiments revealed that oral administration of BCAA peptides (all four) significantly reversed the diabetic symptoms. Compared to the db/db group (control), body weight and insulin resistance were ameliorated after treatment with BCAA peptides (0.5, 1.0, 2.0 mg/(g d)). Also, the treatment remarkably reduced the fasting blood glucose (FBG) levels by upregulation of glucose transporter 4 (GULT4). Moreover, BCAA peptides significantly increased the muscle glycogen content (22.6 ± 0.9 nmol/mg) via the downregulation of protein kinase B (AKT) and glycogen synthase kinase-3β (GSK-3β) while increasing the activity of glycogen synthase (GS). BCAA peptides also significantly upregulated the protein levels of phosphatidylinositol 3-kinase (PI3K). We show that BCAA peptides alleviated insulin resistance associated with altered PI3K/Akt protein expression in the skeletal muscle of db/db mice.

Characterization of in silico modeled synthetic protein enriched with branched-chain amino acids expressed in Pichia pastoris

We have designed earlier the 3-dimensional structure of protein enriched with 56% branched-chain amino acids (BCAA) based on an α-helical coiled-coil structure. The chemically synthesized DNA (BCAA51 gene) was expressed in Pichia pastoris and confirmed by SDS-PAGE and western blot analysis. In the present study, the purified recombinant protein was characterized using circular dichroism and data revealed that the secondary structure contained 53.5% α-helix, 3.2% β-strand, and 43.3% turns, which is in concurrence with the overall structure predicted by in silico modeling. The LC-ESI-MS/MS spectra revealed that three peptide masses showed similarity to peptides like EQLTK, LEIVIR, and ILDK, of the modeled BCAA51 protein with the sequence coverage of ~16% from N-terminal region. The N-terminal sequence of the first seven amino acid residues (EQLTKLE) was exactly matching with the in silico designed protein. In vitro digestibility of the protein using SGF and SIF showed the disappearance of ~11 kDa band and appearance of low molecular weight peptides, which indicated that the protein was easily digestible and non-allergenic, which is the overall objective of this study. Further in vivo digestibility and toxicology studies are required to conclusively utilize this protein as a supplement for the treatment of chronic liver diseases.

Computational Analysis of IDH1, IDH2, and TP53 Mutations in Low-Grade Gliomas Including Oligodendrogliomas and Astrocytomas

Introduction:

The emergence of new omics approaches, such as genomic algorithms to identify tumor mutations and molecular modeling tools to predict the three-dimensional structure of proteins, has facilitated the understanding of the dynamic mechanisms involved in the pathogenesis of low-grade gliomas including oligodendrogliomas and astrocytomas.

Methods:

In this study, we targeted known mutations involved in low-grade gliomas, starting with the sequencing of genomic regions encompassing exon 4 of isocitrate dehydrogenase 1 (IDH1) and isocitrate dehydrogenase 2 (IDH2) and the four exons (5-6 and 7-8) of TP53 from 32 samples, followed by computational analysis to study the impact of these mutations on the structure and function of 3 proteins IDH1, IDH2, and p53.

Results:

We obtain a mutation that has an effect on the catalytic site of the protein IDH1 as R132H and on the catalytic site of the protein IDH2 as R172M. Other mutations at p53 have been identified as K305N, which is a pathogenic mutation; R175 H, which is a benign mutation; and R158G, which disrupts the structural conformation of the tumor suppressor protein.

Conclusion:

In low-grade gliomas, mutations in IDH1, IDH2, and TP53 may be the key to tumor progression because they have an effect on the function of the protein such as mutations R132H in IDH1 and R172M in IDH2, which change the function of the enzyme alpha-ketoglutarate, or R158G in TP53, which affects the structure of the generated protein, thus their importance in understanding gliomagenesis and for more accurate diagnosis complementary to the anatomical pathology tests.

Cloning and expression of in silico modeled protein enriched with branched chain amino acids in Pichia pastoris

We have earlier in silico designed the 3-dimensional structure of a protein enriched with branched chain amino acids (BCAA, 56.4%), having only α-helical coiled-coil structure. Here, homology modeling was used to improve the in silico designed protein model. The secondary and tertiary structures of improved protein model were predicted, and validated using various online bioinformatics tools. The amino acid sequence of the final predicted Protein Model-51 was EQLTKLEIVIRVLKLLKLIGGLVSLVEWVLTALVTLLGDKVLDDILTDVIMLVKKIL DKVIGIVYVLAILALILSEVLDILWLLEKLVEILEGHHHHHH. The amino acid sequence of the protein model was reverse translated to DNA sequence and codons were optimized using codon optimization tool. The chemically synthesized BCAA51 gene was cloned to pPICZαC vector, and transformed into DH5α E. coli strain. After successful transformation, the protein was expressed in P. pastoris system by inducing with 0.5% methanol, every 24 h for up to 144 h. The expressed protein was purified by His Select Nickel affinity chromatography with an yield of 1.412 mg/L. The recombinant protein was confirmed by SDS-PAGE and western blot analysis, which showed a clear band at the expected molecular weight of ~11 kDa. Thus, here we have shown that the in silico designed protein is successfully cloned and expressed in P. pastoris.

Improvement, cloning, and expression of an in silico designed protein enriched with large neutral amino acids in Pichia pastoris for possible application in phenylketonuria

Phenylketonuria (PKU) is an inborn disease caused by defective phenylalanine hydroxylase, which consequently results in the accumulation of phenylalanine in the brain leading to further complications. One of the promising approaches in dietary treatment is the supplementation of large neutral amino acid (LNAA). The LNAA compete with phenylalanine for the common L-type LNAA transporter across the blood-brain barrier, and decrease phenylalanine levels in the brain. In this study, the earlier LNAA-enriched protein model was improved (Protein Model-66) and validated in silico. The reverse translated and codon-optimized synthetic LNAA66 gene was cloned into pPICZαC and expressed in Pichia pastoris. The expressed protein was purified by His Select affinity chromatography. SDS-PAGE and Western blotting analysis showed a band at an expected molecular weight of 12 kDa, confirming the expression of the modeled protein. To our knowledge, this is the first report showing the cloning and expression of an in silico designed LNAA-enriched protein. PRACTICAL APPLICATIONS: One of the promising dietary treatment of phenylketonuria (PKU) is the supplementation of large neutral amino acid (LNAA), wherein high levels of LNAA compete with phenylalanine for the same L-type LNAA transporter, and consequently decrease phenylalanine accumulation in the brain, thereby decreasing neurological complications. For the first time, here, we are showing that an in silico designed and validated Protein Model-66, rich in LNAA, can be successfully cloned and expressed in Pichia pastoris. The complete biochemical and structural characterization of this protein will give a clear insight into its potential application for PKU treatment. The protein can be potentially used as a supplement to treat PKU to those who are non-adherent to the restricted, non-palatable, and expensive diet. Furthermore, this novel and effective strategy of in silico designing, cloning and expression can be exploited to develop proteins for various applications of industrial, food, medical, and academic relevance.

A biotechnological approach for the production of branched chain amino acid containing bioactive peptides to improve human health: A review

Improper nutrition provokes many types of chronic diseases and health problems, which consequently are associated with particularly high costs of treatments. Nowadays, consumer's interest in healthy eating is shifting towards specific foods or food ingredients. As a consequence, bioactive peptides as a promising source of health promoting food additives are currently an intensely debated topic in research. Process design is still on its early stages and is significantly influenced by important preliminary decisions. Thus, parameters like peptide bioactivity within the product, selection of the protein source, enzyme selection for hydrolysis, peptide enrichment method, as well as stability of the peptides within the food matrix and bioavailability are sensitive decision points, which have to be purposefully coordinated, as they are directly linked to amino acid content and structure properties of the peptides. Branched chain amino acids (BCAA) are essential components for humans, possessing various important physiologic functions within the body. Incorporated within peptide sequences, they may induce dual functions, when used as nutraceuticals in functional food, thus preserving the foodstuff and prevent several widespread diseases. Furthermore, there is evidence that consuming this peptide-class can be a nutritional support for elderly people or improve human health to prevent diseases caused by incorrect nutrition. Based on the knowledge about the role of BCAA within various peptide functions, discussed in the review, special attention is given to different approaches for systematic selection of the protein source and enzymes used in hydrolysis, as well as suitable peptide enrichment methods, thereby showing current trends in research.

Late evening snacks with branched-chain amino acids improve the Fischer ratio with patients liver cirrhosis at fasting in the next morning

BACKGROUND & AIMS

A late evening snack (LES) is recommended as a nutritional therapy for liver cirrhosis to minimize early starvation. In patients with liver cirrhosis, the maintenance of the branched-chain amino acid (BCAA) levels is important during muscle synthesis at night. Therefore, we investigated the effects of a LES with BCAAs on the Fischer ratio in patients with liver cirrhosis.

METHODS

This study included 10 outpatients with liver cirrhosis who did not consume a LES. Regarding the patient characteristics, the mean age was 73.1 ± 8.9 years, the male:female ratio was 5:5, and the mean body mass index was 23.3 ± 2.4 kg/m². The etiology was hepatitis C virus in eight patients and alcoholism in two patients. Amino acid levels were measured in all 10 patients at four time points: before LES (control) and 1 month after the administration of each BCAA. The administration levels included 1) LES: BCAA-enriched enteral nutrition (BCAA-EN) containing BCAAs 6.1 g as a LES; 2) GP-no LES: BCAA-enriched granule product (BCAA-GP) containing 4 g BCAAs per pack, two packs per day, and BCAA-EN until dinner containing BCAAs in total 14.1 g per day; and 3) GP-LES: BCAA-GP, two packs per day, and BCAA-EN as a LES containing BCAAs in total 14.1 g per day. The Friedman nonparametric test with a post-hoc Dunn's multiple comparison was used for statistical analyses.

RESULTS

There were no significant changes in body weight and serum albumin levels between the three types of BCAA administration. Valine significantly increased following LES and GP-LES, isoleucine significantly increased following GP-LES, and tyrosine significantly decreased following LES and GP-LES compared with those in the control. There was no significant difference in the leucine and phenylalanine levels among the groups. The Fischer ratio in the LES (2.2 ± 0.8) and GP-LES (2.3 ± 0.8) groups were significantly higher than that in the control (1.8 ± 0.6), but there was no significant difference compared with the Fischer ratio in the GP-no LES (1.8 ± 0.7) group. Furthermore, the Fischer ratio was significantly higher in the GP-LES group than in the GP-no LES group.

CONCLUSION

These results suggested that it is not only the amount of BCAAs, but also LES with BCAAs, which is needed to improve the Fischer ratio at fasting.