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1.
Combinatorial libraries of de novo amino acid sequences can provide a rich source of diversity for the discovery of novel proteins with interesting and important activities. Randomly generated sequences, however, rarely fold into well-ordered proteinlike structures. To enhance the quality of a library, features of rational design must be used to focus sequence diversity into those regions of sequence space that are most likely to yield folded structures. This review describes how focused libraries can be constructed by designing the binary pattern of polar and nonpolar amino acids to favor proteins that contain abundant secondary structure, while simultaneously burying hydrophobic side chains and exposing hydrophilic side chains to solvent. The "binary code" for protein design was used to construct several libraries of de novo proteins, including both alpha-helical and beta-sheet structures. The recently determined solution structure of a binary patterned four-helix bundle is well ordered, thereby demonstrating that sequences that have neither been selected by evolution (in vivo or in vitro) nor designed by computer can form nativelike proteins. Examples are presented demonstrating how binary patterned libraries have successfully produced well-ordered structures, cofactor binding, catalytic activity, self-assembled monolayers, amyloid-like nanofibrils, and protein-based biomaterials. 相似文献
2.
ABSTRACT: BACKGROUND: Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consensus assembly is valuable both as a single linear representation of the population and, as a backbone on which intra-host variants can be accurately mapped. The availability of consensus assemblies and robustly mapped variants are crucial to the genetic study of viral disease progression, transmission dynamics, and viral evolution. Existing de novo assembly techniques fail to robustly assemble ultra-deep sequence data from genetically heterogeneous populations such as viruses into full-length genomes due to the presence of extensive genetic variability, contaminants, and variable sequence coverage. RESULTS: We present VICUNA, a de novo assembly algorithm suitable for generating consensus assemblies from genetically heterogeneous populations. We demonstrate its effectiveness on Dengue, Human Immunodeficiency and West Nile viral populations, representing a range of intra-host diversity. Compared to state-of-the-art assemblers designed for haploid or diploid systems, VICUNA recovers full-length consensus and captures insertion/deletion polymorphisms in diverse samples. Final assemblies maintain a high base calling accuracy. VICUNA program is publicly available at: http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/viral-genomics-analysis-software CONCLUSIONS: We developed VICUNA, a publicly available software tool, that enables consensus assembly of ultra-deep sequence derived from diverse viral populations. While VICUNA was developed for the analysis of viral populations, its application to other heterogeneous sequence data sets such as metagenomic or tumor cell population samples may prove beneficial in these fields of research. 相似文献
3.
We previously reported the design of a library of de novo amino acid sequences targeted to fold into four-helix bundles. The design of these sequences was based on a "binary code" strategy, in which the patterning of polar and nonpolar amino acids is specified explicitly, but the exact identities of the side chains is varied extensively (Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH, 1993, Science 262:1680-1685). Because of this variability, the resulting collection of amino acid sequences may include de novo proteins capable of binding biologically important cofactors. To probe for such binding, the de novo sequences were screened for their ability to bind the heme cofactor. Among an initial collection of 30 binary code sequences, 15 are shown to bind heme and form bright red complexes. Characterization of several of these de novo heme proteins demonstrated that their absorption spectra and resonance Raman spectra resemble those of natural cytochromes. Because the design of these sequences is based on global features of polar/ nonpolar patterning, the finding that half of them bind heme highlights the power of the binary code strategy, and demonstrates that isolating de novo heme proteins does not require explicit design of the cofactor binding site. Because bound heme plays a key role in the functions of many natural proteins, these results suggest that binary code sequences may serve as initial prototypes for the development of large collections of functionally active de novo proteins. 相似文献
4.
A new in silico method has been developed that automatically identifies peptide sequences that can bind to targets of known three‐dimensional structure. The method is potentially faster and more economical than traditional methods of raising antibodies by means of hybridomas or biopanning technology. The current algorithm creates an initial peptide library that is either completely random or that is constrained by the user. This library represents only a small fraction of possible sequence space and the peptides are created with a specified torsional geometry. The library is used as input to any number of available molecular docking programs and the library is docked and scored. The final rank ordering is then used to create a new library by constraining that library to the sequence conservation pattern deduced from the top N‐scoring peptides in the first round. Successive rounds of screening, scoring, and new library creation ultimately results in the system converging to a final solution set of peptides. To test the method, a family of novel peptides that can bind to, and inhibit the enzyme Deoxyribonuclease I has been discovered. The peptides inhibit the enzyme either alone or when placed into a protein backbone structure as has been confirmed experimentally. Proteins 2009. © 2009 Wiley‐Liss, Inc. 相似文献
5.
We constructed a single-chain Fv antibody library that permits human complementarity-determining region (CDR) gene fragments of any germline to be incorporated combinatorially into the appropriate positions of the variable-region frameworks VH-DP47 and VL-DPL3. A library of 2 x 109 independent transformants was screened against haptens, peptides, carbohydrates, and proteins, and the selected antibody fragments exhibited dissociation constants in the subnanomolar range. The antibody genes in this library were built on a single master framework into which diverse CDRs were allowed to recombine. These CDRs were sampled from in vivo-processed gene sequences, thus potentially optimizing the levels of correctly folded and functional molecules, and resulting in a molecule exhibiting a lower computed immunogenicity compared to naive immunoglobulins. Using the modularized assembly process to incorporate foreign sequences into an immunoglobulin scaffold, it is possible to vary as many as six CDRs at the same time, creating genetic and functional variation in antibody molecules. 相似文献
6.
Foxp3-expressing regulatory T cells (Treg) play an essential role in maintaining tolerance to self antigens and are generated under physiological conditions when developing T cells encounter antigens expressed by thymic epithelial cells. We have addressed the possibility that Treg can be exploited to prevent or even suppress ongoing immune responses to foreign antigens. To this end, one must develop methods that permit the de novo generation of Treg specific for foreign antigens in peripheral lymphoid tissue. This report describes the methodology of generating Treg by delivering minute doses of peptide contained in fusion Abs directed against the DEC-205 endocytic receptor on steady-state dendritic cells. The process, from cloning and production of fusion Abs to antigen-specific Treg induction in vivo, takes approximately 2 months. The results show that delivery of T-cell receptor agonist ligands under subimmunogenic conditions represents a suitable approach for converting naive T cells into Treg. 相似文献
7.
A completely synthetic gene library encoding the variable light (VL) immunoglobulin domains has been constructed in vitro. The library was constructed by assembling a set of six oligodeoxyribonucleotides (oligos) using the polymerase chain reaction (PCR). Three out of the six overlapping oligonucleotides were synthesized with randomized complementarity determining regions (CDR) with the codon pattern, (NNS) n, where N is any of the four nucleotides (nt) and n is the number of codons with variation in the CDR. The framework regions, taken from the D1.3 anti-lysozyme antibody (Ab), were kept intact. Overlapping regions of approx. 20 nt, together with two additional flanking primers carrying the desired restriction sites, allowed the construction of a library in one single PCR reaction. The VL library was cloned into the phage display vector pEXmide3, and ten randomly picked clones were sequenced. These sequences exhibited complete diversity in all the three CDR and the codons for five canonical amino acid (aa) residues were kept intact and identified. Seven clones contained the full-length gene for the VL domain while deletions were observed in three clones. The restricted use of nt at the third position successfully avoided the stop codons TGA and TAA, whereas the stop codon TAG is read as Gln in an amber suppressor strain. We call this synthetic Ab diversity Domain Library, and it represents an example of syntheticlibraries with extensive, multiple randomized sequences. The use of Domain Libraries opens up the possibility for design in Ab engineering, e.g., additional CDR regions can be added or their length varied. Furthermore, the use of synthetic gene libraries, constructed with the Domain Library strategy, is not limited to the construction of synthetic Ab fragments, but can be used in the design of other types of proteins. 相似文献
8.
Many investigators, observing an apparent dilution in the plasma specific activity (SA) of apolipoprotein B-100 (apoB) in low density lipoprotein (LDL) as compared with that in very low density lipoprotein (VLDL) after injection of radiolabeled VLDL, have formulated kinetic hypotheses incorporating the concept of de novo production of LDL to explain their data in humans and other mammals. These hypotheses, with rare exception, do not account for the kinetic heterogeneity known to exist in the apoB of human VLDL on the basis of size and in the apoB of rabbit VLDL on the basis of size and presence of apolipoprotein E. When a logical analysis of such kinetic heterogeneity of apoB in plasma VLDL is performed, it becomes clear that the apparent dilution of the SA of apoB in LDL relative to that in VLDL can be explained without the requirement for de novo production of LDL. Although this alternative hypothesis, incorporating the concept of kinetic heterogeneity of apoB in VLDL, does not exclude the process of de novo production of LDL, which so many investigators have invoked to explain their data, it does raise a question as to the existence of such a process since an alternative hypothesis can explain such data just as well. Clearly, more experimental data on the kinetic heterogeneity of human and other mammalian VLDL are needed before a reasonable choice can be made between these two hypotheses. 相似文献
9.
BackgroundSpecific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA) in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background. ResultsThrough genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-κB reporter cells expressing Toll like receptor (TLR)-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-α after stimulation with the WTA mutants as compared to the wild-type. ConclusionsThe study presented here correlates structural differences in WTA to their functional characteristics, thereby providing important information aiding to improve our understanding of molecular host-microbe interactions and probiotic functionality. 相似文献
10.
The oxidized kaurene (Ox-Kau) compounds are the core structures of many important diterpenoids with biological activities and economical values. However, easy access to diverse Ox-Kau products is still limited by low natural abundance, and large-scale manufacture remain challenging due to lack of proper heterologous production. To achieve an abundant source alternative to natural extracts, we here report a highly effective Escherichia coli-based platform for the de novo production of multiple Ox-Kau molecules from simple carbon source. Pathway optimization in prokaryotic cells through modification of transmembrane CYP450 oxidases, cytochrome b5 co-expression and AlphaFold-based protein engineering improved a 50-fold yield of steviol (1.07 g L −1), a key intermediate in the kaurenoid biosynthesis. Combinatorial biosynthetic strategy further led to a series of oxidized derivatives (20–600 mg L −1) with rich oxygenated functional groups on C3, C7, C16 and C19 previously hard to be introduced. Our engineered strains not only laid a foundation for realizing the industrial fermentation of gram-scale ent-kaurene diterpenoids, but also provided a reliable platform for characterization and utilization of kaurene-modifying oxidases, which may generate naturally rare or unnatural ent-kaurenoids with potential bioactivity. 相似文献
11.
De novo sequencing of a full-length monoclonal antibody raised against OX40 ligand is described. Using a combination of overlapping complementary proteolytic and chemical digestions, with analysis by mass spectrometry and Edman degradation, both the heavy and light chains were fully sequenced. Particular attention was paid to those modifications that could be susceptible to degradation in the complementarity determining region and Fc region. An overview of the protocol is described, and suggestions for improvements to aid in such sequencing projects in the future are discussed. 相似文献
12.
Methods for the analysis of chromatin immunoprecipitation sequencing (ChIP-seq) data start by aligning the short reads to a reference genome. While often successful, they are not appropriate for cases where a reference genome is not available. Here we develop methods for de novo analysis of ChIP-seq data. Our methods combine de novo assembly with statistical tests enabling motif discovery without the use of a reference genome. We validate the performance of our method using human and mouse data. Analysis of fly data indicates that our method outperforms alignment based methods that utilize closely related species. Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0756-4) contains supplementary material, which is available to authorized users. 相似文献
13.
The challenging field of de novo enzyme design is beginning to produce exciting results. The application of powerful computational methods to functional protein design has recently succeeded at engineering target activities. In addition, efforts in directed evolution continue to expand the transformations that can be accomplished by existing enzymes. The engineering of completely novel catalytic activity requires traversing inactive sequence space in a fitness landscape, a feat that is better suited to computational design. Optimizing activity, which can include subtle alterations in backbone conformation and protein motion, is better suited to directed evolution, which is highly effective at scaling fitness landscapes towards maxima. Improved rational design efforts coupled with directed evolution should dramatically improve the scope of de novo enzyme design. 相似文献
14.
One of the limitations of the use of phage antibody libraries in high throughput selections is the production of sufficient phage antibody library at the appropriate quality. Here, we successfully adapt a bioreactor-based protocol for the production of phage peptide libraries to the production of phage antibody libraries. The titers obtained in the stirred-tank bioreactor are 4 to 5 times higher than in a standard shake flask procedure, and the quality of the phage antibody library produced is indistinguishable to that produced using standard procedures as assessed by Western blotting and functional selections. Availability of this protocol will facilitate the use of phage antibody libraries in high-throughput scale selections. 相似文献
15.
One of the limitations of the use of phage antibody libraries in high throughput selections is the production of sufficient phage antibody library at the appropriate quality. Here, we successfully adapt a bioreactor-based protocol for the production of phage peptide libraries to the production of phage antibody libraries. The titers obtained in the stirred-tank bioreactor are 4 to 5 times higher than in a standard shake flask procedure, and the quality of the phage antibody library produced is indistinguishable to that produced using standard procedures as assessed by Western blotting and functional selections. Availability of this protocol will facilitate the use of phage antibody libraries in high-throughput scale selections. 相似文献
16.
The de novo production of the fungal metabolite, (+)-aristolochene by sporulated surface cultures of Penicillium roqueforti is reported for the first time. The biosynthesis of fungal volatiles by various sporulated surface cultures was monitored by solid phase micro-extraction (SPME). When comparing malt extract agar with sabouraud dextrose agar, the highest yield of the fungal metabolite (0.04 mg/ml of culture) was obtained with the latter medium. The biosynthesis of (+)-aristolochene showed a maximum during the fourth day after inoculation. 相似文献
17.
Prions are responsible for a heterogeneous group of fatal neurodegenerative diseases. They can manifest as infectious, sporadic or genetic disorders involving posttranslational modifications of the cellular prion protein (PrP C). Prions (PrP Sc) are characterized by their infectious property and intrinsic ability to convert the physiological PrP C into the pathological form, acting as a template. The “protein-only” hypothesis, postulated by Stanley B. Prusiner, implies the possibility to generate de novo prions in vivo and in vitro. Here we will describe major milestones towards proving this hypothesis, taking into account physiological environment/s, biochemical properties and interactors of the PrP C. 相似文献
18.
Prions are responsible for a heterogeneous group of fatal neurodegenerative diseases. They can be sporadic, genetic, or infectious disorders involving post-translational modifications of the cellular prion protein (PrP C). Prions (PrP Sc) are characterized by their infectious property and intrinsic ability to convert the physiological PrP C into the pathological form, acting as a template. The “protein-only” hypothesis, postulated by Stanley B. Prusiner, implies the possibility to generate de novo prions in vivo and in vitro. Here we describe major milestones towards proving this hypothesis, taking into account physiological environment/s, biochemical properties and interactors of the PrP C.Key words: prion protein (PrP), prions, amyloid, recombinant prion protein, transgenic mouse, protein misfolding cyclic amplification (PMCA), synthethic prionPrions are responsible for a heterogeneous group of fatal neurodegenerative diseases ( They can be sporadic, genetic or infectious disorders involving post-translational modifications of the cellular prion protein (PrP C). 2 Prions are characterized by their infectious properties and by their intrinsic ability to encipher distinct biochemical properties through their secondary, tertiary and quaternary protein structures. In particular, the transmission of the disease is due to the ability of a prion to convert the physiological PrP C into the pathological form (PrP Sc), acting as a template. 3 The two isoforms of PrP appear to be different in terms of protein structures, as revealed by optical spectroscopy experiments such as Fourier-transform infrared and circular dichroism. 4 PrP C contains 40% α-helix and 3% β-sheet, while the pathological isoform, PrP Sc, presents approximately 30% α-helix and 45% β-sheet. 4,5 PrP Sc differs from PrP C because of its altered physical-chemical properties such as insolubility in non-denaturing detergents and proteinases resistance. 2,6,7Table 1The prion diseases Prion disease | Host | Mechanism | iCJD | humans | infection | vCJD | humans | infection | fCJD | humans | genetic: octarepeat insertion, D178N-129V, V180I, T183A, T188K, T188R-129V, E196K, E200K, V203I, R208H, V210I, E211Q, M232R | sCJD | humans | ? | GSS | humans | genetic: octarepeat insertion, P102L-129M, P105-129M, A117V-129V, G131V-129M, Y145*-129M, H197R-129V, F198S-129V, D202N-129V, Q212P, Q217R-129M, M232T | FFI | humans | genetic: D178-129M | Kuru | fore people | infection | sFI | humans | ? | Scrapie | sheep | infection | BSE | cattle | infection | TME | mink | infection | CWD | mule deer, elk | contaminated soils? | FSE | cats | infection | Exotic ungulate encephalopathy | greater kudu, nyala, oryx | infection | Open in a separate windowi, infective form; v, variant; f, familial; s, sporadic; CJD, Creutzfeldt-Jakob disease; GSS, Gerstmann-Straüssler-Sheinker disease; FFI, fatal familial insomnia; sFI, sporadic fatal insomnia; BSE, bovine spongiform encephalopathy; TME, transmissible mink encephalopathy; CWD, chronic wasting disease; FSE, feline spongiform encephalopathy. 73,78The prion conversion occurring in prion diseases seems to involve only conformational changes instead of covalent modifications. However, Mehlhorn et al. demonstrated the importance of a disulfide bond between the two cysteine residues at position 179 and 214 (human (Hu) PrP numbering) to preserve PrP into its physiological form. In the presence of reducing conditions and pH higher than 7, recombinant (rec) PrP tends to assume high β-sheet content and relatively low solubility like PrP Sc. 8 相似文献
19.
Summary Nexus (gap junctions), which are considered to contain cell-to-cell channels, are newly formed in uterine smooth muscle during
parturition or in response to estrogen treatment of virginal animals. A mRNA preparation was isolated from estrogen-dominated
rat myometria and was encapsulated into liposomes. Subsequently the liposomes were fused with cultured cells of a mouse cell
line CL-1D. It is established that these tumor cells normally are neither electrically coupled nor do they contain nexus.
The cells, however, become electrically coupled a few hours after being loaded with the mRNA preparation. This de novo expression
of cell coupling persisted for a little more than 24 hr after a single loading procedure. Freeze-fracture electron microscopy
revealed small nexus-like particle aggregates at the time coupling was present. In control experiments the cells remained
noncoupling when the RNA preparation was pretreated with ribonuclease, when cycloheximide was applied to the cells, or when
liposomes filled with buffer solution only were used. These data suggest that the de novo expression of cell-to-cell coupling
is accomplished by mRNA-induced protein biosynthesis resulting in the formation of cell-to-cell channels.
Presented in the symposium on Molecular Morphological Aspects of Cell-Cell Communication at the 31 st Annual Meeting of the
Tissue Culture Association, St. Louis, Missouri, June 1–5, 1980.
This symposium was supported in part by Contract 263-MD-025754 from the National Cancer Institute and the Fogarty International
Center. 相似文献
20.
Prions are self-replicating proteins that can cause neurodegenerative disorders such as bovine spongiform encephalopathy (also known as mad cow disease). Aberrant conformations of prion proteins accumulate in the central nervous system, causing spongiform changes in the brain and eventually death. Since the inception of the prion hypothesis - which states that misfolded proteins are the infectious agents that cause these diseases - researchers have sought to generate infectious proteins from defined components in the laboratory with varying degrees of success. Here, we discuss several recent studies that have produced an array of novel prion strains in vitro that exhibit increasingly high titres of infectivity. These advances promise unprecedented insight into the structure of prions and the mechanisms by which they originate and propagate. 相似文献
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