scholarly journals De novo design of self-assembling helical protein filaments

Science ◽  
2018 ◽  
Vol 362 (6415) ◽  
pp. 705-709 ◽  
Author(s):  
Hao Shen ◽  
Jorge A. Fallas ◽  
Eric Lynch ◽  
William Sheffler ◽  
Bradley Parry ◽  
...  

We describe a general computational approach to designing self-assembling helical filaments from monomeric proteins and use this approach to design proteins that assemble into micrometer-scale filaments with a wide range of geometries in vivo and in vitro. Cryo–electron microscopy structures of six designs are close to the computational design models. The filament building blocks are idealized repeat proteins, and thus the diameter of the filaments can be systematically tuned by varying the number of repeat units. The assembly and disassembly of the filaments can be controlled by engineered anchor and capping units built from monomers lacking one of the interaction surfaces. The ability to generate dynamic, highly ordered structures that span micrometers from protein monomers opens up possibilities for the fabrication of new multiscale metamaterials.

2021 ◽  
Author(s):  
Koya Sakuma ◽  
Naohiro Kobayashi ◽  
Toshihiko Sugiki ◽  
Toshio Nagashima ◽  
Toshimichi Fujiwara ◽  
...  

A wide range of de novo protein structure designs have been achieved, but the complexity of naturally occurring protein structures is still far beyond these designs. To expand the diversity and complexity of de novo designed protein structures, we sought to develop a method for designing 'difficult-to-describe' α-helical protein structures composed of irregularly aligned α-helices, such as globins. Backbone structure libraries consisting of a myriad of α-helical structures with 5- or 6- helices were generated by combining 18 helix-loop-helix motifs and canonical α-helices, and five distinct topologies were selected for de novo design. The designs were found to be monomeric with high thermal stability in solution and fold into the target topologies with atomic accuracy. This study demonstrated that complicated α-helical proteins are created using typical building blocks. The method we developed would enable us to explore the universe of protein structures for designing novel functional proteins.


2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
Patricia Bolanos-Palmieri ◽  
Ahmed Kotb ◽  
Heiko Schenk ◽  
Heike Bähre ◽  
Patricia Schroder ◽  
...  

Abstract Background and Aims Tryptophan catabolism is carried out by the enzymes of the kynurenine pathway leading to the de novo synthesis of NAD and the production of a series of bioactive metabolites. Kynurenine 3-Monooxigenase (KMO) is a key component of this pathway and it is one of the enzymes responsible for the degradation of kynurenine. The kynurenine metabolites participate in various cellular processes, so systemic dysregulation of tryptophan metabolism, marked by increased kynurenine in the circulation, has been linked to the onset and severity of a wide range of pathologies, such as chronic kidney disease and associated co-morbidities. Since the enzymes of the kynurenine pathway are expressed in the kidney and the metabolites are cleared in the urine, we aim to describe the effects of changes in tryptophan catabolism on glomerular cells, both in vitro and in vivo. Method Modulation of KMO expression or enzymatic function was performed in a transgenic zebrafish line that allows for the monitoring of a fluorescently labelled protein in the circulation as an indicator for proteinuria. Morpholinos targeting three enzymes of the kynurenine pathway were injected into fish embryos, leading to a knockdown of Afmid, Kmo and Kynu. Additionally, dechorionated larvae were treated with a Kmo inhibitor administered via the embryo rearing media, starting at 48hpf. In all cases at 96hpf, circulating fluorescent protein levels were determined, larval phenotype was scored based on the severity of the edema, and samples were collected for metabolite analysis or fixed and prepared for imaging. Since the kynurenine pathway results in the de novo production of NAD, and the enzyme KMO is located in the outer mitochondrial membrane, cultured murine parietal epithelial cells as well as immortalized human and mouse podocytes were incubated with a KMO inhibitor. Changes in NAD+ and NADH, as well as alterations in the mitochondrial membrane polarization were assessed. Additionally, the oxygen consumption rate was measured in order to determine if KMO inhibition leads to changes in the bioenergetics parameters of glomerular cells in vitro. Results The modification of Afmid, Kmo and Kynu expression levels by morpholino mediated knockdown or inhibition of Kmo lead to the accumulation of upstream kynurenine metabolites in the treated larvae, as was confirmed by mass spectrometry analysis. Following our previous results, alteration of the kynurenine pathway led to the development of yolk sac edema, pericardial effusion and loss of protein from the circulation, accompanied by an enlargement of the Bowman’s space and changes in nephrin expression in the glomerulus of the treated larvae. Under cell culture conditions, KMO inhibition in immortalized podocytes led to a reduction in cell size and focal adhesion proteins (podocalyxin). The NAD+/NADH ratio as well as mitochondrial membrane polarity were also altered. Additionally, changes in spare respiratory capacity, coupling efficiency and proton leak suggest that alterations in the kynurenine pathway might impair the cell’s ability to adapt its bioenergetic profile in response to stress. Conclusion Taken together these results suggest that the modulation of tryptophan catabolism through the kynurenine pathway may contribute to maintaining the structural integrity of glomerular cytoskeleton as well a flexible energy metabolism in podocytes. Moreover, the results from our in vivo model also suggest that imbalances in kynurenine metabolites might ultimately impact the function of the glomerular filtration barrier.


2010 ◽  
Vol 76 (18) ◽  
pp. 6257-6265 ◽  
Author(s):  
Vikas Yadav ◽  
Bruce J. Paniliatis ◽  
Hai Shi ◽  
Kyongbum Lee ◽  
Peggy Cebe ◽  
...  

ABSTRACT Despite excellent biocompatibility and mechanical properties, the poor in vitro and in vivo degradability of cellulose has limited its biomedical and biomass conversion applications. To address this issue, we report a metabolic engineering-based approach to the rational redesign of cellular metabolites to introduce N-acetylglucosamine (GlcNAc) residues into cellulosic biopolymers during de novo synthesis from Gluconacetobacter xylinus. The cellulose produced from these engineered cells (modified bacterial cellulose [MBC]) was evaluated and compared with cellulose produced from normal cells (bacterial cellulose [BC]). High GlcNAc content and lower crystallinity in MBC compared to BC make this a multifunctional bioengineered polymer susceptible to lysozyme, an enzyme widespread in the human body, and to rapid hydrolysis by cellulase, an enzyme commonly used in biomass conversion. Degradability in vivo was demonstrated in subcutaneous implants in mice, where modified cellulose was completely degraded within 20 days. We provide a new route toward the production of a family of tailorable modified cellulosic biopolymers that overcome the longstanding limitation associated with the poor degradability of cellulose for a wide range of potential applications.


2018 ◽  
Vol 15 (141) ◽  
pp. 20180021 ◽  
Author(s):  
Joshua A. Mancini ◽  
Molly Sheehan ◽  
Goutham Kodali ◽  
Brian Y. Chow ◽  
Donald A. Bryant ◽  
...  

Bilins are linear tetrapyrrole chromophores with a wide range of visible and near-visible light absorption and emission properties. These properties are tuned upon binding to natural proteins and exploited in photosynthetic light-harvesting and non-photosynthetic light-sensitive signalling. These pigmented proteins are now being manipulated to develop fluorescent experimental tools. To engineer the optical properties of bound bilins for specific applications more flexibly, we have used first principles of protein folding to design novel, stable and highly adaptable bilin-binding four-α-helix bundle protein frames, called maquettes, and explored the minimal requirements underlying covalent bilin ligation and conformational restriction responsible for the strong and variable absorption, fluorescence and excitation energy transfer of these proteins. Biliverdin, phycocyanobilin and phycoerythrobilin bind covalently to maquette Cys in vitro . A blue-shifted tripyrrole formed from maquette-bound phycocyanobilin displays a quantum yield of 26%. Although unrelated in fold and sequence to natural phycobiliproteins, bilin lyases nevertheless interact with maquettes during co-expression in Escherichia coli to improve the efficiency of bilin binding and influence bilin structure. Bilins bind in vitro and in vivo to Cys residues placed in loops, towards the amino end or in the middle of helices but bind poorly at the carboxyl end of helices. Bilin-binding efficiency and fluorescence yield are improved by Arg and Asp residues adjacent to the ligating Cys on the same helix and by His residues on adjacent helices.


2008 ◽  
Vol 67 (2) ◽  
pp. 115-127 ◽  
Author(s):  
James Thorne ◽  
Moray J. Campbell

Over the last 25 years roles have been established for vitamin D receptor (VDR) in influencing cell proliferation and differentiation. For example, murine knock-out approaches have revealed a role for the VDR in controlling mammary gland growth and function. These actions appear widespread, as the enzymes responsible for 1α,25-dihydroxycholecalciferol generation and degradation, and the VDR itself, are all functionally present in a wide range of epithelial and haematopoietic cell types. These findings, combined with epidemiological and functional data, support the concept that local, autocrine and paracrine VDR signalling exerts control over cell-fate decisions in multiple cell types. Furthermore, the recent identification of bile acid lithocholic acid as a VDR ligand underscores the environmental sensing role for the VDR.In vitroandin vivodissection of VDR signalling in cancers (e.g. breast, prostate and colon) supports a role for targeting the VDR in either chemoprevention or chemotherapy settings. As with other potential therapeutics, it has become clear that cancer cells displayde novoand acquired genetic and epigenetic mechanisms of resistance to these actions. Consequently, a range of experimental and clinical options are being developed to bring about more targeted actions, overcome resistance and enhance the efficacy of VDR-centred therapeutics.


2002 ◽  
Vol 22 (3) ◽  
pp. 704-723 ◽  
Author(s):  
Iping G. Lin ◽  
Li Han ◽  
Alexander Taghva ◽  
Laura E. O’Brien ◽  
Chih-Lin Hsieh

ABSTRACT CpG methylation is involved in a wide range of biological processes in vertebrates as well as in plants and fungi. To date, three enzymes, Dnmt1, Dnmt3a, and Dnmt3b, are known to have DNA methyltransferase activity in mouse and human. It has been proposed that de novo methylation observed in early embryos is predominantly carried out by the Dnmt3a and Dnmt3b methyltransferases, while Dntm1 is believed to be responsible for maintaining the established methylation patterns upon replication. Analysis of the sites methylated in vivo using the bisulfite genomic sequencing method confirms the previous finding that some regions of the plasmid are much more methylated by Dnmt3a than other regions on the same plasmid. However, the preferred targets of the enzyme cannot be determined due to the presence of other methylases, DNA binding proteins, and chromatin structure. To discern the DNA targets of Dnmt3a without these compounding factors, sites methylated by Dnmt3a in vitro were analyzed. These analyses revealed that the two cDNA strands have distinctly different methylation patterns. Dnmt3a prefers CpG sites on a strand in which it is flanked by pyrimidines over CpG sites flanked by purines in vitro. These findings indicate that, unlike Dnmt1, Dnmt3a most likely methylates one strand of DNA without concurrent methylation of the CpG site on the complementary strand. These findings also indicate that Dnmt3a may methylate some CpG sites more frequently than others, depending on the sequence context. Methylation of each DNA strand independently and with possible sequence preference is a novel feature among the known DNA methyltransferases.


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Takayuki Miki ◽  
Taichi Nakai ◽  
Masahiro Hashimoto ◽  
Keigo Kajiwara ◽  
Hiroshi Tsutsumi ◽  
...  

AbstractDe novo designed self-assembling peptides (SAPs) are promising building blocks of supramolecular biomaterials, which can fulfill a wide range of applications, such as scaffolds for tissue culture, three-dimensional cell culture, and vaccine adjuvants. Nevertheless, the use of SAPs in intracellular spaces has mostly been unexplored. Here, we report a self-assembling peptide, Y15 (YEYKYEYKYEYKYEY), which readily forms β-sheet structures to facilitate bottom-up synthesis of functional protein assemblies in living cells. Superfolder green fluorescent protein (sfGFP) fused to Y15 assembles into fibrils and is observed as fluorescent puncta in mammalian cells. Y15 self-assembly is validated by fluorescence anisotropy and pull-down assays. By using the Y15 platform, we demonstrate intracellular reconstitution of Nck assembly, a Src-homology 2 and 3 domain-containing adaptor protein. The artificial clusters of Nck induce N-WASP (neural Wiskott-Aldrich syndrome protein)-mediated actin polymerization, and the functional importance of Nck domain valency and density is evaluated.


2021 ◽  
Author(s):  
Qiuke Li ◽  
Jinze Li ◽  
Weikang Yu ◽  
Zhihua Wang ◽  
Jiawei Li ◽  
...  

Abstract BackgroundAcid-tolerant enteric pathogens could evade small intestinal acid barriers, colonizing and infecting the intestinal tract. Whereas broad-spectrum antibiotics are not the best therapeutic strategy because of the disruption of intestinal flora caused by its indiscriminate antimicrobial activity against beneficial and harmful bacteria. So that is what inspired us to combine pH regulation with nanotechnology to develop a pH-triggered site-targeted antimicrobial peptide with entrapping function. ResultsAccording to the features of amino-acid building blocks and the diagonal cation–π interaction principle, a self-assembled peptide (SAP) was designed, and the results showed that changes in pH conditions could trigger the transformation of the microstructure of the nanopeptide, which has great antimicrobial activity against Escherichia coli, Salmonella typhimurium, Listeria monocytogenes, and Bacillus cereus under acidic conditions by disrupting bacterial membrane integrity, and great biocompatibility in vivo and in vitro and high tolerance. Moreover, SAP at high concentrations showed the entrapment property, which plays an important role in phagocytic clearance in the infection forces.ConclusionsOur study revealed the antibacterial activity of a short β-hairpin forming self-assembled peptide and establishes an innovative design strategy for peptide-based nanomaterials and a new treatment strategy for gastrointestinal bacterial infection.


Author(s):  
Aleksandar Antanasijevic ◽  
George Ueda ◽  
Philip JM Brouwer ◽  
Jeffrey Copps ◽  
Deli Huang ◽  
...  

AbstractTwo-component, self-assembling nanoparticles represent a versatile platform for multivalent presentation of viral antigens. Nanoparticles of different sizes and geometries can be designed and combined with appropriate antigens to fit the requirements of different immunization strategies. Here, we describe detailed antigenic, structural, and functional characterization of computationally designed tetrahedral, octahedral, and icosahedral nanoparticle immunogens displaying trimeric HIV envelope glycoprotein (Env) ectodomains. Env trimers, based on subtype A (BG505) or consensus group M (ConM) sequences and engineered with SOSIP stabilizing mutations, were fused to the underlying trimeric building block of each nanoparticle. Initial screening yielded one icosahedral and two tetrahedral nanoparticle candidates, capable of presenting twenty or four copies of the Env trimer. A number of analyses, including detailed structural characterization by cryo-EM, demonstrated that the nanoparticle immunogens possessed the intended structural and antigenic properties. Comparing the humoral responses elicited by ConM-SOSIP trimers presented on a two-component tetrahedral nanoparticle to the corresponding soluble protein revealed that multivalent presentation increased the proportion of the overall antibody response directed against autologous neutralizing Ab epitopes present on the ConM-SOSIP trimers.Author SummaryProtein constructs based on soluble ectodomains of HIV glycoprotein (Env) trimers are the basis of many current HIV vaccine platforms. Multivalent antigen display is one strategy applied to improve the immunogenicity of different subunit vaccine candidates. Here, we describe and comprehensively evaluate a library of de novo designed, protein nanoparticles of different geometries for their ability to present trimeric Env antigens. We found three nanoparticle candidates that can stably incorporate model Env trimer on their surface while maintaining its structure and antigenicity. Immunogenicity of the designed nanoparticles is assessed in vitro and in vivo. In addition to introducing a novel set of reagents for multivalent display of Env trimers, this work provides both guiding principles and a detailed experimental roadmap for the generation, characterization, and optimization of Env-presenting, self-assembling nanoparticle immunogens.


2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Qiuke Li ◽  
Jinze Li ◽  
Weikang Yu ◽  
Zhihua Wang ◽  
Jiawei Li ◽  
...  

Abstract Background Acid-tolerant enteric pathogens can evade small intestinal acid barriers, colonize and infect the intestinal tract. However, broad-spectrum antibiotics are not the best therapeutic strategy because of the disruption of intestinal flora caused by its indiscriminate antimicrobial activity against beneficial and harmful bacteria. So that is what inspired us to combine pH regulation with nanotechnology to develop a pH-triggered site-targeted antimicrobial peptide with entrapping function. Results A pH-triggered dual biological functional self-assembled peptide (SAP) was designed according to the features of amino-acid building blocks and the diagonal cation–π interaction principle. The results of characterization experiments showed that changes in pH conditions could trigger microstructural transformation of the nanopeptide from nanospheres to nanofibers. The subsequent antibacterial and toxicity experiments determined that SAP had great antimicrobial activity against Escherichia coli, Salmonella typhimurium, Listeria monocytogenes, and Bacillus cereus above 15.6 μg/mL under acidic conditions by disrupting bacterial membrane integrity, excellent biocompatibility in vitro even at 250 μg/mL and high tolerance in physical environment. Moreover, at peptide concentrations greater than 62.5 μg/mL, SAP showed the entrapment property, which played an important role in phagocytic clearance in infection forces. Meanwhile, the in vivo results revealed that SAP possessed excellent therapeutic effect and good biosafety. Conclusions Our study revealed the antibacterial activity of a short β-hairpin forming self-assembled peptide, and established an innovative design strategy for peptide-based nanomaterials and a new treatment strategy for gastrointestinal bacterial infections. Graphic Abstract


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