Protein Chain Research Articles

Unusual substructure conformations observed in crystal structures of a dicistrovirus RNA-dependent RNA polymerase suggest contribution of the N-terminal extension in proper folding

The Dicistroviridae is a virus family that includes many insect pathogens. These viruses contain a positive-sense RNA genome that is replicated by the virally encoded RNA-dependent RNA polymerase (RdRP) also named 3Dpol. Compared with the Picornaviridae RdRPs such as poliovirus (PV) 3Dpol, the Dicistroviridae representative Israeli acute paralysis virus (IAPV) 3Dpol has an additional N-terminal extension (NE) region that is about 40-residue in length. To date, both the structure and catalytic mechanism of the Dicistroviridae RdRP have remain elusive. Here we reported crystal structures of two truncated forms of IAPV 3Dpol, namely Δ85 and Δ40, both missing the NE region, and the 3Dpol protein in these structures exhibited three conformational states. The palm and thumb domains of these IAPV 3Dpol structures are largely consistent with those of the PV 3Dpol structures. However, in all structures, the RdRP fingers domain is partially disordered, while different conformations of RdRP substructures and interactions between them are also present. In particular, a large-scale conformational change occurred in the motif B-middle finger region in one protein chain of the Δ40 structure, while a previously documented alternative conformation of motif A was observed in all IAPV structures. These experimental data on one hand show intrinsic conformational variances of RdRP substructures, and on the other hand suggest possible contribution of the NE region in proper RdRP folding in IAPV.

Protein posttranslational modifications in health and diseases: Functions, regulatory mechanisms, and therapeutic implications.

Protein posttranslational modifications (PTMs) refer to the breaking or generation of covalent bonds on the backbones or amino acid side chains of proteins and expand the diversity of proteins, which provides the basis for the emergence of organismal complexity. To date, more than 650 types of protein modifications, such as the most well-known phosphorylation, ubiquitination, glycosylation, methylation, SUMOylation, short-chain and long-chain acylation modifications, redox modifications, and irreversible modifications, have been described, and the inventory is still increasing. By changing the protein conformation, localization, activity, stability, charges, and interactions with other biomolecules, PTMs ultimately alter the phenotypes and biological processes of cells. The homeostasis of protein modifications is important to human health. Abnormal PTMs may cause changes in protein properties and loss of protein functions, which are closely related to the occurrence and development of various diseases. In this review, we systematically introduce the characteristics, regulatory mechanisms, and functions of various PTMs in health and diseases. In addition, the therapeutic prospects in various diseases by targeting PTMs and associated regulatory enzymes are also summarized. This work will deepen the understanding of protein modifications in health and diseases and promote the discovery of diagnostic and prognostic markers and drug targets for diseases.

Protein-Protein Interaction Sites Prediction Using Batch Normalization Based CNNs and Oversampling Method Borderline-SMOTE.

The recognition of protein-protein interaction sites (PPIs) is beneficial for the interpretation of protein functions and the development of new drugs. Traditional biological experiments to identify PPI sites are expensive and inefficient, leading to the generation of various computational methods to predict PPIs. However, the accurate prediction of PPI sites remains a big challenge due to the existence of the sample imbalance issue. In this work, we design a novel model that combines convolutional neural networks (CNNs) with Batch Normalization to predict PPI sites, and employ an oversampling technique Borderline-SMOTE to address the sample imbalance issue. In particular, to better characterize the amino acid residues on the protein chains, we employ a sliding window approach for feature extraction of target residues and their contextual residues. We verify the effectiveness of our method by comparing our method with the existing state-of-the-art schemes. The performance validations of our method on three public datasets achieve accuracies of 88.6%, 89.9%, and 86.7%, respectively, all showing improved accuracies compared with the existing schemes. Moreover, the ablation experiment results suggest that Batch Normalization can greatly improve the generalization and the prediction stability of our model.

Abstract 501: Endothelin-1 Expression Is Dependent On The Stability Of Endothelial Glycocalyx Heparan Sulfate

Introduction: Endothelin-1 (ET-1) is a vasoconstrictor produced by the vascular endothelium [1]. It binds to endothelial B receptor(ETB) on the endothelial cells(EC) [2]. Increased ET-1 has been observed in the EC of patients with moderate to severe hypertension [3]. Studies suggest that the EC cytoskeletal disruptions could mediate its production[4,5,6]. ETB is a plasma membrane bound receptor present in the EC surface with EC glycocalyx (GCX) [7,8]. GCX is flow sensitive and consists of several transmembrane solid core proteins [10,11,12]. Linked to the core protein chains include heperan sulfate (HS) [12]. GCX HS and ETB are located in the surface of the EC and are both flow sensitive. We hypothesize that the shear stress induced upregulation of the GCX HS could lead to expression of ETB which will trigger the release of ET1. Methods: Human Lung Microvascular Endothelial cells (HLMVEC) were cultured until 70-80% confluence. To mimic disease progression the GCX were degraded with Heparinase III which targets the HS component of the GCX. Immunostaining was used to determine the expression of GCX HS, ETB and ET-1. Results: Data revealed that the degradation of GCX HS resulted in the significant decrease in the expression of ETB. Conversely, the removal of GCX HS caused a significant increase in the expression of ET-1. Discussion: The preliminary results from, immunostaining reveals a potential co-participation of GCX HS and ETB in the expression of ET-1.

The monomeric archaeal primase from Nanoarchaeum equitans harbours the features of heterodimeric archaeoeukaryotic primases and primes sequence-specifically.

The marine thermophilic archaeon Nanoarchaeum equitans possesses a monomeric primase encompassing the conserved domains of the small catalytic and the large regulatory subunits of archaeoeukaryotic heterodimeric primases in one protein chain. The recombinant protein primes on templates containing a triplet with a central thymidine, thus displaying a pronounced sequence specificity typically observed with bacterial type primases only. The N. equitans primase (NEQ395) is a highly active primase enzyme synthesizing short RNA primers. Termination occurs preferentially at about nine nucleotides, as determined by HPLC analysis and confirmed with mass spectrometry. Possibly, the compact monomeric primase NEQ395 represents the minimal archaeoeukaryotic primase and could serve as a functional and structural model of the heterodimeric archaeoeukaryotic primases, whose study is hindered by engagement in protein assemblies and rather low activity.

Serum Glial Fibrillary Acidic Protein compared with Neurofilament Light Chain as Biomarker for Multiple Sclerosis Disease Progression (P5-3.016)

Serum Glial Fibrillary Acidic Protein compared with Neurofilament Light Chain as Biomarker for Multiple Sclerosis Disease Progression (P5-3.016)

Tough, waterproof, and mildew-resistant fully biobased soybean protein adhesives enhanced by furfuryl alcohol with dynamic covalent linkages

The adhesives formulated from soy protein (SP) exhibit desirable dry bonding strength needed to eradicate over-reliance on unsustainable petroleum-based formaldehyde adhesives. However, the adhesive full industrial adoption is limited by its inherent poor water resistance, short shelf-life, and proneness to mildew. This study explored a feasible, versatile, green, and sustainable strategy to engineer superior SP-based adhesives using furfuryl alcohol (FA) and 2,5-diamino-1,4-benzenedithiol hydrochloride (DBH). FA/DBH was conjugated via the carbodiimide-mediated addition of DBH under a light-proof condition. The acidity was controlled by NaOH, creating a mildly acidic medium for FA/DBH to develop a strong crosslinked network. The FA and DBH were hybridized by an amide bond, with subsequent SP integration via dynamic covalent linkages and amide bonds. The synergistic interactions between FA/DBH hybrid and the protein chains remarkably enhanced the adhesive properties. Consequently, the added FA/DBH hybrid (6 wt% of SP) achieved high dry and wet shear strengths of 2.38 and 1.43 MPa (plywood), which were 63 % and 200 % higher than the unmodified soy protein adhesive (USPA), respectively. In addition, the constructed organic network improved the adhesive thermal stability, mildew resistance, and shelf-life. Therefore, this sustainable, versatile, and green approach could serve as an alternative crosslinking pathway for developing highly competitive SP-based adhesives.

Myoglobin and Hemoglobin: Discoloration, Lipid Oxidation, and Solvent Access to the Heme Pocket

Conversion of the heme iron in myoglobin (Mb) and hemoglobin (Hb) from Fe2+ to Fe3+ is a critical step that causes quality deterioration—such as discoloration and generation of oxidative species, including dissociated heme, that oxidize lipids and proteins—in muscle foods. Increased solvent access to the heme pocket has been proposed to cause oxidation of the heme iron and decrease heme affinity for the globin, although empirical results are lacking. This review introduces plasma-induced modification of biomolecules (PLIMB) as an approach to modify amino acids of Mb and Hb and thereby assess solvent access to the heme pocket. After PLIMB, liquid chromatography tandem mass spectrometry peptide analysis and a user-friendly, software platform are used to quantify modified amino acid side chains of the heme proteins. Our findings indicate that PLIMB➔liquid chromatography-tandem mass spectrometry provides a platform to measure solvent access to portions of the heme pocket environment. Evaluation of PLIMB under additional conditions(e.g., different pH values) can differentiate the role of solvent access to the heme pocket relative to the“outer-sphere”mechanism of heme protein oxidation and the ability of hydrogen bonding to stabilize heme within metHb. Some aspects of heme protein-mediated lipid oxidation that occur at low O2partial pressures are discussed in relationship to solvent access to the heme pocket. Other approaches to study mechanisms of discoloration and lipid oxidation related to Mb/Hb oxidation and heme loss from metHb are also discussed.

Increased trypsin resilience in aqueous-acetonitrile environment when immobilized on glyoxyl-agarose may improve its applicability

Although trypsin is a protease naturally applicable in many processes, it is still possible to increase its efficiency and forms of use. Processes that increase their resilience to different conditions in the reaction medium can expand and/or refine their range of applications. Its performance in the presence of organic solvents, such as acetonitrile (ACN), has been indicated as a promising way to increase the efficiency of digestion processes, such as in sample treatment for MALDI-MS peptide mapping. The maintenance of the activity of trypsin immobilized on glyoxyl-agarose was herein demonstrated in different temperature and ACN ranges. Compared to the soluble, the immobilized enzyme was able to remain active above 50% ACN, where the soluble trypsin showed no activity. Although low, it was still possible to detect about 7% activity at 70% ACN when immobilized form was used. With 7.5% of ACN, the soluble enzyme has already shown loss of activity. The same only occurred with immobilized trypsin at 20% or more. Although the immobilized enzyme may have lower specific activity compared to the soluble one, as confirmed by the determined kinetic parameters, its possibility of reuse was confirmed, with no loss of activity for 5 cycles at 0% and 5% ACN. Added to this is the simplicity that the reaction can be interrupted, through the removal of the enzyme from the medium. What could prevent its own protein chain from contaminating the final product. With these characteristics added, trypsin in its immobilized form presents itself as a promising biocatalyst.

Charge migration of ferrocene-labeled peptide self-assembled monolayers at various interfaces: The roles of peptide composition

Understanding charge migration across peptide chain of proteins is important for both biology and biomolecular electronics. Despite experimental and theoretical researches showing that the charge migration in wet electrochemistry and on solid state are interrelated, there are still limited insights about this interrelation. Here, taken ferrocene-labeled peptide self-assembled monolayers on the Au substrate as a model, the relation between the charge migration on solid state (charge transport, CTp) and in wet electrochemistry (charge transfer, CT) was investigated. By characterizing the current density from solid state molecular junctions and the electron transfer rate (kET) from electrochemical measurement in solution, we found that the ability of peptides to transmit charge was more sensitive to peptide's length on solid state than that in wet electrochemistry, comparing to the reported alkane and peptide nucleic acid oligomers. In addition, changing peptide compositions, such as doping phenylalanine (F) or aspartic acid (D) into the initial glycine (G) peptide backbone, made a different consequence for charge migration: the kET in wet electrochemistry was F > G ≈ D, while the CTp rate on solid state was G ≈ F > D. Our findings provide further insights into the comprehension of relations between charge migration and peptide structures.

Ethanolic Extract of Duea Ching Fruit: Extraction, Characterization and Its Effect on the Properties and Storage Stability of Sardine Surimi Gel.

The quality of surimi gel can be improved using protein cross-linkers, especially from plant extracts. Apart from the presence of phenolic compounds, Duea ching fruit is rich in calcium, which can activate indigenous transglutaminase or form the salt bridge between protein chains. Its extract can serve as a potential additive for surimi. The effect of different media for the extraction of Duea ching was studied and the use of the extract in sardine surimi gel was also investigated. The Duea ching fruit extract (DCE) was prepared using distilled water and ethanol (EtOH) at varying concentrations. The DCE prepared using 60% EtOH (DCE-60) had the highest antioxidant activity and total phenolic content. When DCE-60 (0-0.125%; w/w) was added to the sardine surimi gel, the breaking force (BF), deformation (DF) and water holding capacity (WHC) of the gel upsurged and the highest values were attained with the 0.05% DCE-60 addition (p < 0.05). However, the whiteness of the gel decreased when DCE-60 levels were augmented. The gel containing 0.05% DCE-60, namely D60-0.05, showed a denser network and had a higher overall likeness score than the control. When the D60-0.05 gel was packed in air, under vacuum or modified atmospheric packaging and stored at 4 °C, BF, DF, WHC and whiteness gradually decreased throughout 12 days of storage. However, the D60-0.05 gel sample showed lower deterioration than the control, regardless of the packaging. Moreover, the gel packaged under vacuum conditions showed the lowest reduction in properties throughout the storage than those packaged with another two conditions. Thus, the incorporation of 0.05% DCE-60 could improve the properties of sardine surimi gel and the deterioration of the resulting gel was retarded when stored at 4 °C under vacuum packaging conditions.

Abstract 1161: Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function

Abstract The Warburg effect, aerobic glycolysis, is a hallmark feature of cancer cells grown in culture. However, the relative roles of glycolysis and respiratory metabolism in supporting in vivo tumor growth and processes such as tumor dissemination and metastatic growth remain poorly understood, particularly on a systems level. Using a CRISPRi mini-library enriched for mitochondrial ribosomal protein and respiratory chain genes in multiple human lung cancer cell lines we analyzed in vivo metabolic requirements in xenograft tumors grown in distinct anatomic contexts. While knockdown of mitochondrial ribosomal protein and respiratory chain genes (mito-respiratory genes) has little impact on growth in vitro, tumor cells depend heavily on these genes when grown in vivo as either flank or primary orthotopic lung tumor xenografts. In contrast, respiratory function is comparatively dispensable for metastatic tumor growth. RNA-Seq and metabolomics analysis of tumor cells expressing individual sgRNAs against mito-respiratory genes indicate overexpression of glycolytic genes and increased sensitivity of glycolytic inhibition compared to control when grown in vitro, but when grown in vivo as primary tumors these cells downregulate glycolytic mechanisms. Metabolic shifts associated with silencing mito-respiratory genes can be detected in vivo with metabolic imaging. These studies demonstrate that discrete perturbations of mitochondrial respiratory chain function impact in vivo tumor growth in a context-specific manner with differential impacts on primary and metastatic tumors. Citation Format: Neal K. Bennett, Hiroki J. Nakaoka, Danny Laurent, Ross Okimoto, Yoshitaka Sei, Andrew E. Horvai, Trever G. Bivona, Georgios Batsios, Pavithra Viswanath, Johanna ten Hoeve, Thomas G. Graeber, Ken Nakamura, Jean L. Nakamura. Primary and metastatic tumors exhibit systems-level differences in dependence on mitochondrial respiratory function [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1161.

Promising Bioactivity of Vitamin B1-Au Nanocluster: Structure, Enhanced Antioxidant Behavior, and Serum Protein Interaction.

In the current work, we first present a simple synthesis method for the preparation of novel Vitamin-B1-stabilized few-atomic gold nanoclusters with few atomic layers. The formed nanostructure contains ca. eight Au atoms and shows intensive blue emissions at 450 nm. The absolute quantum yield is 3%. The average lifetime is in the nanosecond range and three main components are separated and assigned to the metal-metal and ligand-metal charge transfers. Based on the structural characterization, the formed clusters contain Au in zero oxidation state, and Vitamin B1 stabilizes the metal cores via the coordination of pyrimidine-N. The antioxidant property of the Au nanoclusters is more prominent than that of the pure Vitamin B1, which is confirmed by two different colorimetric assays. For the investigation into their potential bioactivity, interactions with bovine serum albumin were carried out and quantified. The determined stoichiometry indicates a self-catalyzed binding, which is almost the same value based on the fluorometric and calorimetric measurements. The calculated thermodynamic parameters verify the spontaneous bond of the clusters along the protein chain by hydrogen bonds and electrostatic interactions.

RNA-NRD: a non-redundant RNA structural dataset for benchmarking and functional analysis.

The significance of RNA functions and their role in evolution and disease control have remarkably increased the research scope in the field of RNA science. Though the availability of RNA structure data in PBD has been growing tremendously, maintaining their quality and integrity has become the greater challenge. Since the data available in PDB are results of different independent research, they might contain redundancy. As a result, there remains a possibility of data bias for both protein and RNA chains. Quite a few studies have been conducted to remove the redundancy of protein structures by introducing high-quality representatives. However, the amount of research done to remove the redundancy of RNA structures is still very low. To remove RNA chain redundancy in PDB, we have introduced RNA-NRD, a non-redundant dataset of RNA chains based on sequence and 3D structural similarity. We compared RNA-NRD with the existing non-redundant RNA structure dataset RS-RNA and showed that it has better-formed clusters of redundant RNA chains with lower average RMSD and higher average PSI, thus improving the overall quality of the dataset.

Serum glial fibrillary acidic protein and neurofilament light chain as biomarkers of retinal neurodysfunction in early diabetic retinopathy: results of the EUROCONDOR study.

Neurodegeneration and glial activation are primary events in the pathogenesis of diabetic retinopathy. Serum glial fibrillary acidic protein (GFAP) and neurofilament light chain (NfL) are biomarkers of underlying neuroinflammatory and neurodegenerative disease processes. The aim of the present study was to assess the usefulness of these serum biomarkers for the identification and monitoring of retinal neurodysfunction in subjects with type 2 diabetes. A case-control study was designed including 38 patients from the placebo arm of the EUROCONDOR clinical trial: 19 with and 19 without retinal neurodysfunction assessed by multifocal electroretinography. GFAP and NfL were measuredby Simoa. Serum levels of GFAP and NfL directly correlated with age (r = 0.37, p = 0.023 and r = 0.54, p < 0.001, respectively). In addition, a direct correlation between GFAP and NfL was observed (r = 0.495, p = 0.002). Serum levels of GFAPwere significantly higher at baseline in those subjects in whom neurodysfunction progressed after the 2years of follow-up (139.1 ± 52.5pg/mL vs. 100.2 ± 54.6pg/mL; p = 0.04). GFAP could be a useful serumbiomarker for retinal neurodysfunction. Monitoring retinal neurodysfunction using blood samples would be of benefit in clinical decision-making. However, further research is needed to validate this result as well as to establish the best cutoff values.

Heat-Treated Lysozyme Hydrochloride: A Study on Its Structural Modifications and Anti-SARS-CoV-2 Activity.

Lysozyme (E.C. 3.2.1.17), an about 14 kDa protein and pI 11, widely spread in nature, is present in humans mainly in milk, saliva, and intestinal mucus as a part of innate defense mechanisms. It is endowed with antimicrobial activity due to its action as an N-acetylmuramidase, cleaving the 1-4β glycosidic linkage in the peptidoglycan layer of Gram-positive bacteria. This antimicrobial activity is exerted only against a limited number of Gram-negative bacteria. Different action mechanisms are proposed to explain its activity against Gram-negative bacteria, viruses, and fungi. The antiviral activity prompted the study of a possible application of lysozyme in the treatment of SARS-CoV-2 infections. Among the different sources of lysozyme, the chicken egg albumen was chosen, being the richest source of this protein (c-type lysozyme, 129 amino acids). Interestingly, the activity of lysozyme hydrochloride against SARS-CoV-2 was related to the heating (to about 100 °C) of this molecule. A chemical-physical characterization was required to investigate the possible modifications of native lysozyme hydrochloride by heat treatment. The FTIR analysis of the two preparations of lysozyme hydrochloride showed appreciable differences in the secondary structure of the two protein chains. HPLC and NMR analyses, as well as the enzymatic activity determination, did not show significant modifications.

GFAP and NfL increase during neurotoxicity from high baseline levels in pediatric CD19-CAR T-cell patients.

There is a need for biomarkers to predict and measure the severity of immune effector cell-associated neurotoxicity syndrome (ICANS). Glial fibrillary acidic protein (GFAP) and neurofilament light chain (NfL) are well-validated biomarkers of astroglial and neuronal injury, respectively. We hypothesized that pretreatment GFAP and NfL levels can predict the risk of subsequent ICANS and that increases in GFAP and NfL levels during treatment reflect ICANS severity. We measured cerebrospinal fluid GFAP (cGFAP) and NfL (cNfL) along with serum NfL (sNfL) levels at pretreatment and day 7 to 10 after chimeric antigen receptor (CAR) T-cell infusion in 3 pediatric cohorts treated with CD19- or CD19/CD22-directed CAR T cells. cGFAP and cNfL levels increased during grade ≥1 ICANS in patients treated with CD19-directed CAR T cells but not in those who received CD19/CD22-directed CAR T cells. The sNfL levels did not increase during ICANS. Prelymphodepletion cGFAP, cNfL, and sNfL levels were not predictive of subsequent ICANS. Elevated baseline cGFAP levels were associated with a history of transplantation. Patients with prior central nervous system (CNS) radiation had higher cNfL levels, and elevated baseline sNfL levels were associated with a history of peripheral neuropathy. Thus, cGFAP and cNfL may be useful biomarkers for measuring the severity of CNS injury during ICANS in children. Elevated baseline levels of cGFAP, cNfL, and sNfL likely reflect the cumulative injury to the central and peripheral nervous systems from prior treatment. However, levels of any of the 3 biomarkers before CAR T-cell infusion did not predict the risk of ICANS.

Scalable Manufacturing of Environmentally Stable All-Solid-State Plant Protein-Based Supercapacitors with Optimal Balance of Capacitive Performance and Mechanically Robust.

The development of advanced biomaterial with mechanically robust and high energy density is critical for flexible electronics, such as batteries and supercapacitors. Plant proteins are ideal candidates for making flexible electronics due to their renewable and eco-friendly natures. However, due to the weak intermolecular interactions and abundant hydrophilic groups of protein chains, the mechanical properties of protein-based materials, especially in bulk materials, are largely constrained, which hinders their performance in practical applications. Here, a green and scalable method is shown for the fabrication of advanced film biomaterials with high mechanical strength (36.3MPa), toughness (21.25MJm-3 ), and extraordinary fatigue-resistance (213000 times) by incorporating tailor-made core-double-shell structured nanoparticles. Subsequently, the film biomaterials combine to construct an ordered, dense bulk material by stacking-up and hot-pressing techniques. Surprisingly, the solid-state supercapacitor based on compacted bulk material shows an ultrahigh energy density of 25.8Whkg-1 , which is much higher than those previously reported advanced materials. Notably, the bulk material also demonstrates long-term cycling stability, which can be maintained under ambient condition or immersed in H2 SO4 electrolyte for more than 120 days. Thus, this research improves the competitiveness of protein-based materials for real-world applications such as flexible electronics and solid-state supercapacitors.

Dynamic Association of ESCRT-II Proteins with ESCRT-I and ESCRT-III Complexes during Phagocytosis of Entamoeba histolytica.

By their active movement and voraux phagocytosis, the trophozoites of Entamoeba histolytica constitute an excellent system to investigate the dynamics of the Endosomal Sorting Complex Required for Transport (ESCRT) protein interactions through phagocytosis. Here, we studied the proteins forming the E. histolytica ESCRT-II complex and their relationship with other phagocytosis-involved molecules. Bioinformatics analysis predicted that EhVps22, EhVps25, and EhVps36 are E. histolytica bona fide orthologues of the ESCRT-II protein families. Recombinant proteins and specific antibodies revealed that ESCRT-II proteins interact with each other, with other ESCRT proteins, and phagocytosis-involved molecules, such as the adhesin (EhADH). Laser confocal microscopy, pull-down assays, and mass spectrometry analysis disclosed that during phagocytosis, ESCRT-II accompanies the red blood cells (RBCs) from their attachment to the trophozoites until their arrival to multivesicular bodies (MVBs), changing their interactive patterns according to the time and place of the process. Knocked-down trophozoites in the Ehvps25 gene presented a 50% lower rate of phagocytosis than the controls and lower efficiency to adhere RBCs. In conclusion, ESCRT-II interacts with other molecules during prey contact and conduction throughout the phagocytic channel and trophozoites membranous system. ESCRT-II proteins are members of the protein chain during vesicle trafficking and are fundamental for the continuity and efficiency of phagocytosis.

Population-based heteropolymer design to mimic protein mixtures

Biological fluids, the most complex blends, have compositions that constantly vary and cannot be molecularly defined1. Despite these uncertainties, proteins fluctuate, fold, function and evolve as programmed2–4. We propose that in addition to the known monomeric sequence requirements, protein sequences encode multi-pair interactions at the segmental level to navigate random encounters5,6; synthetic heteropolymers capable of emulating such interactions can replicate how proteins behave in biological fluids individually and collectively. Here, we extracted the chemical characteristics and sequential arrangement along a protein chain at the segmental level from natural protein libraries and used the information to design heteropolymer ensembles as mixtures of disordered, partially folded and folded proteins. For each heteropolymer ensemble, the level of segmental similarity to that of natural proteins determines its ability to replicate many functions of biological fluids including assisting protein folding during translation, preserving the viability of fetal bovine serum without refrigeration, enhancing the thermal stability of proteins and behaving like synthetic cytosol under biologically relevant conditions. Molecular studies further translated protein sequence information at the segmental level into intermolecular interactions with a defined range, degree of diversity and temporal and spatial availability. This framework provides valuable guiding principles to synthetically realize protein properties, engineer bio/abiotic hybrid materials and, ultimately, realize matter-to-life transformations.