Similar Amino Acid Compositions Research Articles

An internal loop region is responsible for inherent target specificity of bacterial Cold-shock proteins.

Cold shock proteins (Csps), of around 70 amino acids, share a protein fold for the cold shock domain (CSD) that contains RNA binding motifs, RNP1 and RNP2, and constitute one family of bacterial RNA-binding proteins. Despite similar amino acid composition, Csps have been shown to individually possess inherent specific functions. Here we identify the molecular differences in Csps that allow selective recognition of RNA targets. Using chimeras and mutants of Escherichia coli CspD and CspA, we demonstrate that Lys43-Ala44 in an internal loop of CspD and the N-terminal portion with Lys4 of CspA are important for determining their target specificities. Pull-down assays suggest these distinct specificities reflect differences in the ability to act on the target RNAs rather than differences in binding to the RNA targets. A phylogenetic tree constructed from 1,573 Csps reveals that the Csps containing Lys-Ala in the loop form a monophyletic clade, and the members in this clade are shown to have target specificities similar to E. coli CspD. The phylogenetic tree also finds a small cluster of Csps containing Lys-Glu in the loop, and these exhibit different specificity than E. coli CspD. Examination of this difference suggests a role of the loop of CspD type proteins in recognition of specific targets. Additionally, each identified type of Csp shows a different distribution pattern among bacteria. Our findings provide a basis for subclassification of Csps based on target RNA specificity, which will be useful for understanding of the functional specialization of Csps.

A Deep Mining Strategy for Peptide Rapid Identification in Lactobacillus reuteri Based on LC-MS/MS Integrated with FBMN and De Novo Sequencing.

Lactobacillus reuteri (L. reuteri) is widely recognized as a probiotic that produces prebiotics. However, studies on bioactive peptides or amino acid (AA) derivatives produced by L. reuteri are still lacking, whereas many bioactive peptides and AA derivatives have been found in other Lactobacillus species. In addition, rapid identification of peptides is challenged by the large amount of data and is limited by the coverage of protein databases. In this study, we performed a rapid and thorough profile of peptides in L. reuteri incorporating Global Natural Products Social Molecular Networking (GNPS) platform database searching, de novo sequencing, and deep mining, based on feature-based molecular networking (FBMN). According to FBMN, it was found that peptides containing identical or similar AA compositions were grouped into the same clusters, especially cyclic dipeptides (CDPs). Therefore, the grouping characteristics of clusters, differences in precursor ions, and characteristic fragment ions were utilized for the mining of deeply unknown compounds. Through this strategy, a total of 192 compounds, including 184 peptides, were rapidly identified. Among them, 53 CDPs, including four novel ones, were found for the first time in L. reuteri. Then, one of the novel CDPs, cyclo(5-OMe-Glu-4-OH-Pro), was isolated and characterized, which was consistent with the identification results. Moreover, some of the identified peptides exhibited considerable interactions with seven anti-inflammatory-related target proteins through molecular docking. According to the binding energies of peptides with different AA consistencies, it was considered that the existence of unnatural AAs in CDPs might contribute to their anti-inflammatory activity. These results provide a valuable strategy for the rapid identification of peptides, including CDPs. This study also reveals the substance basis for the potential anti-inflammatory effects exerted by L. reuteri.

Spatio-temporal expression patterns of glycine-rich beta proteins and cysteine-rich beta proteins in setae development of Gekko japonicus

BackgroundSetae on the pad lamellae of the Japanese gecko Gekko japonicus (Schlegel, 1836), a vital epidermal derivative, are primarily composed of cornified beta-proteins (CBPs) and play a pivotal role in adhesion and climbing. The amino acid composition of CBPs might be a determining factor influencing their functional properties. However, the molecular mechanisms governed by CBP genes with diverse amino acid compositions in setae development remain unexplored.ResultsBased on RNA-seq analyses, this study confirmed that all G. japonicus CBPs (GjCBPs) are involved in setae formation. Cysteine-rich CBPs encoding genes (ge-cprp-17 to ge-cprp-26) and glycine-rich CBPs encoding genes (ge-gprp-17 to ge-gprp-22) were haphazardly selected, with quantitative real-time PCR revealing their expression patterns in embryonic pad lamellae and dorsal epidermis. It is inferred that glycine-rich CBPs are integral to the formation of both dorsal scales and lamellar setae, cysteine-rich CBPs are primarily associated with setae development. Additionally, fluorescence in situ hybridization revealed spatiotemporal differences in the expression of a glycine-rich CBP encoding gene (ge-gprp-19) and a cysteine-rich CBP encoding gene (ge-cprp-17) during dorsal scales and/or lamellar development.ConclusionsAll 66 CBPs are involved in the formation of setae. Glycine-rich CBPs hold a significant role in the development of dorsal scales and lamellar setae, whereas most cysteine-rich CBPs appear to be essential components of G. japonicus setae. Even GjCBPs with similar amino acid compositions may play diverse functions. The clear spatio-temporal expression differences between the glycine-rich and cysteine-rich CBP encoding genes during epidermal scale and/or setae formation were observed. Embryonic developmental stages 39 to 42 emerged as crucial phases for setae development. These findings lay the groundwork for deeper investigation into the function of GjCBPs in the development of G. japonicus setae.

Protein from tiger nut meal extracted by deep eutectic solvent and alkali-soluble acid precipitation: A comparative study on structure, function, and nutrition

Protein from tiger nut meal (TNP) performance high nutritional value. This study optimized the extraction parameters for TNP (DES-TNP) using deep eutectic solvent, with HBD: HBA = 5:1, Liquid: Solid = 11:1, and the moisture content was 15 %. A comprehensive comparison was conducted with the protein extracted using alkali-soluble acid precipitation (ASAE-TNP). DES-TNP demonstrated significantly higher purity (76.21 ± 2.59 %) than ASAE-TNP (67.48 ± 1.11 %). Density functional theory confirmed the successful synthesis of DES and its strong interaction with TNP. Moreover, DES-TNP and ASAE-TNP were different in structure (microscopic, secondary, and tertiary) and molecular weight distribution. The discrepancy contributed to the different functional properties, DES-TNP exhibiting better solubility, emulsification and foaming properties at pH13 compared to ASAE-TNP. For nutritional properties, DES-TNP and ASAE-TNP exhibited similar amino acid composition and digestibility, but the total amino acid content of DES-TNP was higher. This study presented a novel method for the extraction and comprehensive utilization of TNP.

Effect of molecular weight distributions on the gelation rate and other physicochemical properties of bovine bone gelatin (Type B)

The physicochemical properties of bovine bone gelatins (Type B) including amino acid and subunit compositions, gelation rate, Bloom values, viscosity, dynamic storage modulus (G’), gelling and melting temperature were investigated comparatively on the basis of molecular weight distributions (MWD). The MWD of gelatin was divided into three segments: >1000 kDa (H), 130 kDa–1000 kDa (M), and <130 kDa (L) for quantitative description and analysis. Results showed similar amino acid compositions for gelatins across different MWD. Gelatins with similar Bloom values exhibited different MWD, whose gelation rate increased with increasing segment H content and decreasing segment M and L content. Viscosity of gelatin was positively correlated with segment H content, and their gelling and melting temperature exhibited little difference. The present study suggests that increasing segment H content or decreasing segment M and L content in gelatin samples can increase the gelation rate and viscosity, making it suitable for 3D food printing.

Degumming and characterization of Bombyx mori and non-mulberry silks from Saturniidae silkworms

In this study, cocoons and degummed silk samples of Bombyx mori and twenty Saturniidae species of the genera Actias, Attacus, Argema, Antheraea, Caligula, Callosamia, Cricula, Epiphora, Hyalophora, Loepa, Samia and Saturnia are studied to gain an insight into their morphology, chemical composition and physical structure. For this purpose, silk samples are characterized by optical microscopy and FTIR spectroscopy in attenuated total reflection mode (ATR-FTIR spectroscopy). Furthermore, degummed silk samples are analyzed for their amino acid (AA) composition by GC-FID. In the course of method development, various degumming methods are tested using alkalis, citric acid, enzymes and detergents. A mixture of 0.1% sodium carbonate and 2.5% ethylenediamine proves to be an effective agent for degumming Saturniidae and B. mori cocoons. After hydrolysis of the fibroin filaments with 6 N hydrochloric acid and derivatization with propyl chloroformate, fifteen AAs are identified and qualified. This method shows a satisfactory overall analytical performance with an average recovery rate of 95% at the medium concentration level. The chemical composition of the different silks was considered comparatively. Within a genus, the analyses usually show a high degree of similarity in AA composition and the resulting structural indices, whereas differences are found between genera.

Ultraviolet Resonance Raman Spectra of Serum Albumins.

The ultraviolet resonance Raman (UVRR) spectra of the two proteins bovine serum albumin (BSA) and human serum albumin (HSA) in an aqueous solution are compared with the aim to distinguish between them based on their very similar amino acid composition and structure and to obtain signals from tryptophan that has only very few residues. Comparison of the protein spectra with solutions of tryptophan, tyrosine, and phenylalanine in comparative ratios as in the two proteins shows that at an excitation wavelength of 220 nm, the spectra are dominated by the strong resonant contribution from these three amino acids. While the strong enhancement of two and one single tryptophan residue in BSA and HSA, respectively, results in pronounced bands assigned to fundamental vibrations of tryptophan, its weaker overtones and combination bands do not play a major role in the spectral range above 1800 cm-1. There, the protein spectra clearly reveal the signals of overtones and combination bands of phenylalanine and tyrosine. Assignments of spectral features in the range of Raman shifts from 3800 to 5100 cm-1 to combinations comprising fundamentals and overtones of tyrosine were supported by spectra of amino acid mixtures that contain deuterated tyrosine. The information in the high-frequency region of the UVRR spectra could provide information that is complementary to near-infrared absorption spectroscopy of the proteins.

Structural characteristics of a low molecular weight velvet antler protein and the anti-tumor activity on S180 tumor-bearing mice

Velvet antler is a traditional Chinese medicine with various pharmacological values, which is an important raw material for traditional Chinese medicinal wine. Nevertheless, the chemical compositions and bioactivities of velvet antler residue used for making medicinal wine are rarely reported, leading to a waste of resources. In this study, a velvet antler protein (VA-pro) was extracted from velvet antler residue by simulating the gastrointestinal digestion, and its composition, structural characteristics and in vivo anti-tumor activities were determined and investigated. VA-pro possessed high purity with a relatively low molecular weight as 22.589 kDa under HPLC, one- and two-dimensional electrophoresis, and it contained high contents of Pro, Gly, Glu and Ala. Besides, the secondary structure of VA-pro was dominated by β-turn and β-sheet, and VA-pro possessed similar protein sequence, isoelectric point and amino acid compositions to hypothetical protein G4228_020061. The in vivo results substantiated that VA-pro could improve the body weights and immune organ indices, increase the expressions of sera cytokines and regulate the distributions of T and B lymphocytes subsets in peripheral blood of S180 tumor-bearing mice. Furthermore, VA-pro could effectively inhibit solid S180 tumors growth by inducing S phase cell cycle arrest mediated through mitochondria. To summarize, our study provided theoretical support that VA-pro had the potential to be used as an immunopotentiator in immunocompromised or cancer-bearing hosts.

Metal-chelating activity of soy and pea protein hydrolysates obtained after different enzymatic treatments from protein isolates

Soy and pea proteins are two rich sources of essential amino acids. The hydrolysis of these proteins reveals functional and bioactive properties of the produced small peptide mixtures. In our study, we employed the hydrolysis of soy and pea protein isolates with the endopeptidases Alcalase® and Protamex®, used alone or followed by the exopeptidase Flavourzyme®. The sequential enzyme treatments were the most efficient regarding the degree of hydrolysis. Then, soy and pea protein hydrolysates (SPHs and PPHs, respectively) were ultrafiltrated in order to select peptides of molecular weight ≤ 1 kDa. Whatever the protein source or the hydrolysis treatment, the hydrolysates showed similar molecular weight distributions and amino acid compositions. In addition, all the ultrafiltrated hydrolysates possess metal-chelating activities, as determined by UV-spectrophotometry and Surface Plasmon Resonance (SPR). However, the SPR data revealed better chelating affinities in SPHs and PPHs when produced by sequential enzymatic treatment.

Identification and transcriptional profile of Culex quinquefasciatus Say (Diptera: Culicidae) lipophorin in different stages.

Lipophorin is a major hemolymph lipoprotein found in insects with a molecular native mass of 700 kDa. In mosquitoes,two different types of apolipoproteins are characterized, apolipophorin-I (ApoLp-I, ~250 kDa) and apolipophorin-II (ApoLp-II, ~80 kDa). This concentration depends on the stage of development and the age of the insects. Lipophorins are best studied in mosquitoes of the genus Aedes and Anopheles. In this study, we analyze the lipophorin sequence and show the lipophorin purification of the Culexquinquefasciatus and the transcriptional profile of the lipophorin gene in different life cycle stages. Similar amino acid composition and molecular weights are founded in three mosquitoes species lipophorins amino acid sequence. The two subunits of purified lipophorin (Apo I and Apo II) showed molecular masses of approximately 248 and 93 kDa, like that found in other mosquitoes. A gradual increase in the lipophorin expression gene was obtained during the previtellogenic period and after feeding we obtained peak expression at 24 h after feeding. With our results, we conclude that C. quinquefasciatusprotein sequence has the same characteristics as those observed in other mosquitoes and that the expression of its apolipophorins is induced by blood feeding.

Reevaluation of dietary condensed tannins on growth, antioxidant and immune response and muscle quality of Chinese seabass (Lateolabrax maculatus)

Chinese seabass (Lateolabtax maculatus) is a popular carnivorous fish that is widely cultured in China in recent years. Previous studies suggested that low dose of CT enhanced antioxidant and immune response, but high dose of CT inhibited growth and induced tissue damage of fish. Meanwhile, information regarding effects of CT on muscle quality of L. maculatus is limited. A 63-day feeding trial was performed to assess the effects of dietary CT on growth, antioxidant and immune response and muscle quality of L. maculatus. Four diets were formulated to contain 0 g/kg of CT (G1), 1 g/kg of CT (G2), 2 g/kg of CT (G3), and 2 g/kg of CT plus 4 g/kg of polyethylene glycol (PEG) (G4, as positive control). PEG specifically binds with CT to neutralize CT activity. Fish were randomly distributed into 16 tanks with 4 tanks per diet and 40 fish per tank, and were fed to apparent satiation twice daily during the feeding trial. Results indicated that dietary CT at the concentration of 1 g/kg did not alter (P > 0.05) growth and feed utilization of L. maculatus. Fish fed G3 had lower (P < 0.05) final body weight, weight gain rate, thermal growth coefficient and feed intake than those of fish fed G1, G2 and G4. Fish fed G3 had lower (P < 0.05) total feed intake than those fed other diets in the 1, 2, 3, 4 and 5 week of the feeding trial. As compared with G1, serum catalase and superoxide dismutase activities were higher (P < 0.05) in G2, lower (P < 0.05) in G3, and similar (P > 0.05) in G4. Serum lysozyme activity and immune globulin M concentration were higher (P < 0.05) in G2 and G3 than those in G1 and G4. Muscle fiber density was increased (P < 0.05) as dietary CT increasing from 0 to 2 g/kg, but was similar (P > 0.05) between G1 and G4. Muscle water loss rate of post thawing was higher (P < 0.05) in G2 and G3 than that in G1 and G4, but was similar (P > 0.05) between G1 and G4 as well as G2 and G3. All fish had similar (P > 0.05) muscle amino acid compositions. Fish fed G3 had lower (P < 0.05) mRNA relative expressions of GH, IGF-1, Myf5, MyoD and Pax7 than those of fish fed other diets. The mRNA relative expressions of GH, IGF-1, Myf5, MyoD and Pax7 were similar (P > 0.05) among G1, G2 and G4. All fish had similar (P > 0.05) RNA relative expressions of IGF-2, MyoG and Mstn2 among groups. In summary, inclusion of 1 g/kg CT in L. maculatus diets did not alter growth but enhanced serum antioxidant and immune response, whereas 2 g/kg of CT declined feed intake and growth, decreased antioxidant enzyme activities but enhanced immune response of fish. Supplementation of CT increased muscle fiber density, decreased muscle water holding capacity but did not affect muscle amino acid compositions of L. maculatus. Dietary CT at the concentration of 2 g/kg down-regulated the majority of muscle growth-related genes expression, which may account for the decreased growth performance of L. maculatus.

The Influence of Short Motifs on the Anticancer Activity of HB43 Peptide.

Despite the remarkable similarity in amino acid composition, many anticancer peptides (ACPs) display significant differences in terms of activity. This strongly suggests that particular relative dispositions of amino acids (motifs) play a role in the interaction with their biological target, which is often the cell membrane. To better verify this hypothesis, we intentionally modify HB43, an ACP active against a wide variety of cancers. Sequence alignment of related ACPs by ADAPTABLE web server highlighted the conserved motifs that could be at the origin of the activity. In this study, we show that changing the order of amino acids in such motifs results in a significant loss of activity against colon and breast cancer cell lines. On the contrary, amino acid substitution in key motifs may reinforce or weaken the activity, even when the alteration does not perturb the amphipathicity of the helix formed by HB43 on liposomes mimicking their surface. NMR and MD simulations with different membrane models (micelles, bicelles, and vesicles) indicate that the activity reflects the insertion capability in cancer-mimicking serine-exposing membranes, supported by the insertion of N-terminal phenylalanine in the FAK motif and the anchoring to the carboxylate of phosphatidylserine by means of arginine side chains.

A TCR mimic monoclonal antibody reactive with the "public" phospho-neoantigen pIRS2/HLA-A*02:01 complex.

Phosphopeptides derived from dysregulated protein phosphorylation in cancer cells can be processed and presented by MHC class I and class II molecules and, therefore, represent an untapped class of tumor-specific antigens that could be used as widely expressed “public” cancer neoantigens (NeoAgs). We generated a TCR mimic (TCRm) mAb, 6B1, specific for a phosphopeptide derived from insulin receptor substrate 2 (pIRS2) presented by HLA-A*02:01. The pIRS2 epitope’s presentation by HLA-A*02:01 was confirmed by mass spectrometry. The TCRm 6B1 specifically bound to pIRS2/HLA-A2 complex on tumor cell lines that expressed pIRS2 in the context of HLA-A*02:01. Bispecific mAbs engaging CD3 of T cells were able to kill tumor cell lines in a pIRS2- and HLA-A*02:01–restricted manner. Structure modeling shows a prerequisite for an arginine or lysine at the first position to bind mAb. Therefore, 6B1 could recognize phosphopeptides derived from various phosphorylated proteins with similar amino acid compositions. This raised the possibility that a TCRm specific for the pIRS2/HLA-A2 complex could target a range of phosphopeptides presented by HLA-A*02:01 in various tumor cells. This is the first TCRm mAb to our knowledge targeting a phosphopeptide/MHC class I complex; the potential of this class of agents for clinical applications warrants further investigation.

Neutralizing Monoclonal Antibody, mAb 10D8, Is an Effective Detoxicant against Abrin-a Both In Vitro and In Vivo.

Abrin is a types II ribosome-inactivating protein (RIP) isolated from Abrus precatorious seeds, which comprises a catalytically active A chain and a lectin-like B chain linked by a disulfide bond. Four isotoxins of abrin have been reported with similar amino-acid composition but different cytotoxicity, of which abrin-a is the most potent toxin. High lethality and easy availability make abrin a potential bioterrorism agent. However, there are no antidotes available for managing abrin poisoning, and treatment is only symptomatic. Currently, neutralizing antibodies remain the most effective therapy against biotoxin poisoning. In this study, we prepared, identified, and acquired a high-affinity neutralizing monoclonal antibody (mAb) 10D8 with a potent pre- and post-exposure protective effect against cytotoxicity and animal toxicity induced by abrin-a or abrin crude extract. The mAb 10D8 could rescue the mouse injected intraperitoneally with a 25 × LD50 dose of abrin-a from lethality and prevent tissue damages. Results indicated that 10D8 does not prevent the binding and internalization of abrin-a to cells but inhibits the enzymatic activity of abrin-a and reduces protein synthesis inhibition of cells. The high affinity, good specificity, and potent antitoxic efficiency of 10D8 make it a promising candidate for therapeutic antibodies against abrin.

Expression of the Antimicrobial Peptide Piscidin 1 and Neuropeptides in Fish Gill and Skin: A Potential Participation in Neuro-Immune Interaction.

Antimicrobial peptides (AMPs) are found widespread in nature and possess antimicrobial and immunomodulatory activities. Due to their multifunctional properties, these peptides are a focus of growing body of interest and have been characterized in several fish species. Due to their similarities in amino-acid composition and amphipathic design, it has been suggested that neuropeptides may be directly involved in the innate immune response against pathogen intruders. In this review, we report the molecular characterization of the fish-specific AMP piscidin1, the production of an antibody raised against this peptide and the immunohistochemical identification of this peptide and enkephalins in the neuroepithelial cells (NECs) in the gill of several teleost fish species living in different habitats. In spite of the abundant literature on Piscidin1, the biological role of this peptide in fish visceral organs remains poorly explored, as well as the role of the neuropeptides in neuroimmune interaction in fish. The NECs, by their role as sensors of hypoxia changes in the external environments, in combination with their endocrine nature and secretion of immunomodulatory substances would influence various types of immune cells that contain piscidin, such as mast cells and eosinophils, both showing interaction with the nervous system. The discovery of piscidins in the gill and skin, their diversity and their role in the regulation of immune response will lead to better selection of these immunomodulatory molecules as drug targets to retain antimicrobial barrier function and for aquaculture therapy in the future.

The Clonotypic BCR IG of CLL Patients Contain Predicted T-Cell Class I Epitopes with Shared Structural Properties

Targeted therapies have revolutionized the treatment of chronic lymphocytic leukemia (CLL) with remarkable overall response rates. Against that, however, CLL remains incurable, indicating a need for novel strategies towards disease control and eventual eradication, including reinvigoration of anti-tumor immune responses. T cells in CLL display an oligoclonal profile and appear selected by restricted antigens, with recent evidence suggesting that the selecting epitopes may lie within the clonotypic B-cell receptor immunoglobulins (BcR IG). Should this prove to be the case, such neoepitopes could be exploited as idiotypic targets for cellular therapy or for peptide vaccine design, aiming to augment response to current treatments.Here we performed ad hoc prediction of putative T-cell class I neoepitopes contained within the clonotypic BcR IGs of CLL patients, with an intended bias towards major stereotyped CLL subsets. We selected 27 patients to represent the full spectrum of CLL: (i) with mutated IGHV genes (M-CLL, n=5), (ii) with unmutated IGHV genes (U-CLL, n=5), (iii) assigned to major stereotyped subsets (subset #1, n=7; subset #2, n=5; subset #4, n=5). RT-PCR was performed for the heavy (H) and the light (K/L) IG chains using subgroup-specific Leader primers for the IGHV/IGK/LV gene and universal primers annealing to the constant domain (IGHG, IGHM, IGKC, IGLC), in order to produce the full-length V-(D)-J gene rearrangement sequence, plus the start of the constant domain. PCR products were subjected to direct double-strand Sanger sequencing with a quality-optimized protocol. The amino acid sequences were subsequently parsed in peptides and subjected to NetMHCpan. The rank score was calculated, considering the 4-digit HLA-A and -B typing for each individual patient. High- and medium-binding peptides (rank score <2%) were selected. Exact matches to germline and/or proteome databases were excluded.Overall, 1,007 predicted neoepitopes were identified. All patients had predicted CD8 + T-cell epitopes within the clonotypic BcR IG, either in the heavy chain (26/27 pts, n=632 epitopes) or the light chain (26/27 pts, n=375 epitopes). The majority of the peptides resulted from somatic hypermutations (SHMs) across the IGHV gene outside the complementarity-determining region 3 (CDR3; n=538, 53.4%). With the exception of few peptides located within the FR4 region (n=11, 0.1%), the remaining (n=458, 45.5%) involved (at least part of) the CDR3, which is particularly relevant given its small length (9-27 aa) within the full sequence (331-660 aa). There was no statistically significant difference in the rank score of peptides involving the CDR3 vs. all others. Peptide clustering assigned most of the predicted neoepitopes (970/1007, 96.3%) in 54 clusters of similar length and amino acid composition. Also, it revealed similar or identical predicted neoepitopes among different patients (30 clusters of two, 10 clusters of three, 8 clusters of four, 4 clusters of five, 1 cluster of six and 1 cluster of eight). Importantly, these clusters involved: (i) shared CDR3 patterns in patients assigned to the same stereotyped subset, but also (ii) subset-specific recurrent SHMs across the rearranged IGHV gene, e.g. G-to-E SHM at position 28 in the VH CDR1 of subset #4, a recurrent SHM in this subset. Also of note, the two most highly populated clusters involved peptides within the VL CDR3, and were biased towards specific subsets; the cluster of eight patients contained 4 patients assigned to subset #1 and the cluster of six patients included 4 patients assigned to subset #2.In conclusion, in silico prediction identified a significant number of putative T-cell class I neoepitopes contained within the clonotypic BcR IG of CLL patients. The majority of these neoepitopes can be assigned to clusters based on amino acid similarity and are shared among different patients. Many of them culminate from subset-specific (‘stereotyped‘) CDR3 patterns or recurrent SHMs, suggesting that the targeted SHM which shapes the CLL BcR IG repertoire may produce immunogenic CD8 + T-cell epitopes. Their actual immunogenicity has to be tested in ex vivo studies, currently underway by our group. DisclosuresAnagnostopoulos: Abbvie: Other: clinical trials; Sanofi: Other: clinical trials ; Ocopeptides: Other: clinical trials ; GSK: Other: clinical trials; Incyte: Other: clinical trials ; Takeda: Other: clinical trials ; Amgen: Other: clinical trials ; Janssen: Other: clinical trials; novartis: Other: clinical trials; Celgene: Other: clinical trials; Roche: Other: clinical trials; Astellas: Other: clinical trials . Chatzidimitriou: Abbvie: Honoraria, Research Funding; Janssen: Honoraria, Research Funding.

Effects of fishmeal replacement with eight protein sources on growth performance, blood biochemistry and stress resistance in Opsariichthys bidens

Nine experimental diets were formulated to study the effects of fishmeal replacement on Opsariichthys bidens. Weight gain rate, protein efficiency rate and apparent digestibility coefficient of fish in fishmeal (FM), maggot meal (MM) and soybean meal (SM) groups were significantly the highest. There was no significant difference in intestinal amylase activity between FM and SM groups. Principal component analysis showed that SM group and wild fish (WF) individual had similar essential amino acid compositions in muscle. The lowest value of serum malondialdehyde and the highest value of total antioxidant capacity were found in SM group, but fish in MM group did the opposite. Fish in MM group had the higher whole-body lipid, serum triglycerides, glucose, complement C3, C4 and immunoglobulin contents and lysozyme activity. After ammonia exposure, cumulative mortality of fish in FM and SM groups was significantly the lowest. Liver carbamyl phosphate synthetase activity of fish in FM group was significantly the highest, but the highest values of glutamine synthetase and glutamate dehydrogenase were found in SM group. This study suggests that fishmeal replacement with soybean meal is acceptable, and muscle amino acid compositions of fish in SM group were more similar to wild individual.

De novo protein design by an energy function based on series expansion in distance and orientation dependence.

Despite many successes, de novo protein design is not yet a solved problem as its success rate remains low. The low success rate is largely because we do not yet have an accurate energy function for describing the solvent-mediated interaction between amino acid residues in a protein chain. Previous studies showed that an energy function based on series expansions with its parameters optimized for side-chain and loop conformations can lead to one of the most accurate methods for side chain (OSCAR) and loop prediction (LEAP). Following the same strategy, we developed an energy function based on series expansions with the parameters optimized in four separate stages (recovering single-residue types without and with orientation dependence, selecting loop decoys and maintaining the composition of amino acids). We tested the energy function for de novo design by using Monte Carlo simulated annealing. The method for protein design (OSCAR-Design) is found to be as accurate as OSCAR and LEAP for side-chain and loop prediction, respectively. In de novo design, it can recover native residue types ranging from 38% to 43% depending on test sets, conserve hydrophobic/hydrophilic residues at ∼75%, and yield the overall similarity in amino acid compositions at more than 90%. These performance measures are all statistically significantly better than several protein design programs compared. Moreover, the largest hydrophobic patch areas in designed proteins are near or smaller than those in native proteins. Thus, an energy function based on series expansion can be made useful for protein design. The Linux executable version is freely available for academic users at http://zhouyq-lab.szbl.ac.cn/resources/.

The proline-rich myticalins from Mytilus galloprovincialis display a membrane-permeabilizing antimicrobial mode of action

Bivalve mollusks are continuously exposed to potentially pathogenic microorganisms living in the marine environment. Not surprisingly, these filter-feeders developed a robust innate immunity to protect themselves, which includes a broad panel of antimicrobial peptides. Among these, myticalins represent a recently discovered family of linear cationic peptides expressed in the gills of Mytilus galloprovincialis. Even though myticalins and insect and mammalian proline-rich antimicrobial peptides (PrAMPs) share a similar amino acid composition, we here show that none of the tested mussel peptides use a non-lytic mode of action relying on the bacterial transporter SbmA. On the other hand, all the tested myticalins perturbed and permeabilized the membranes of E. coli BW25113, as shown by flow-cytometry and atomic force microscopy. Circular dichroism spectra revealed that most myticalins did not adopt recognizable secondary structures in the presence of amphipathic environments, such as biological membranes. To explore possible uses of myticalins for biotech, we assessed their biocompatibility with a human cell line. Non-negligible cytotoxic effects displayed by myticalins indicate that their optimization would be required before their further use as lead compounds in the development of new antibiotics.

Pilot-scale biorefining of Scenedesmus obliquus for the production of lipids and proteins

The whole process of algae farming and biomass biorefining was evaluated on a pilot scale for the production of protein concentrate for poultry feeding and crude lipids. Scenedesmus obliquus was produced in open raceway ponds, and the cells were disrupted under low-pressure homogenization operating at 150 bar. Lipids were efficiently extracted using a hybrid multistage process based on a wet extraction using hexane and ethyl acetate, followed by dry extractions using hexane. The protein concentrate containing 43.1% of total proteins was recovered at low centrifugation of 400g and submitted to a desolventization process to remove residual hexane. The protein concentrate showed a similar composition of essential amino acids in comparison to soybean which is the main protein source used in feed formulation. Aspartic acid and glutamic acid were the main amino acids observed in the microalgal protein concentrate. As a feed supplement for broilers, the protein concentrate-based feed showed equal ingestion of the control, but the latter showed lower energy efficiency. The processing of 168 kg of wet biomass (14.8 kg on a dry weight basis) resulted in a production of 1.3 kg of crude lipids and 12.6 kg of protein concentrate, which corresponded to 93.7% of the total dry biomass.