An intein-based genetic selection allows the construction of a high-quality library of binary patterned de novo protein sequences

Combinatorial libraries of synthetic DNA are increasingly being used to identify and evolve proteins with novel folds and functions. An effective strategy for maximizing the diversity of these libraries relies on the assembly of large genes from smaller fragments of synthetic DNA. To optimize library assembly and screening, it is desirable to remove from the synthetic libraries any sequences that contain unintended frameshifts or stop codons. Although genetic selection systems can be used to accomplish this task, the tendency of individual segments to yield misfolded or aggregated products can decrease the effectiveness of these selections. Furthermore, individual protein domains may misfold when removed from their native context. We report the development and characterization of an in vivo system to preselect sequences that encode uninterrupted gene segments regardless of the foldedness of the encoded polypeptide. In this system, the inserted synthetic gene segment is separated from an intein/thymidylate synthase (TS) reporter domain by a polyasparagine linker, thereby permitting the TS reporter to fold and function independently of the folding and function of the segment-encoded polypeptide. TS-deficient Escherichia coli host cells survive on selective medium only if the insert is uninterrupted and in-frame, thereby allowing selection and amplification of desired sequences. We demonstrate that this system can be used as a highly effective preselection tool for the production of large, diverse and high-quality libraries of de novo protein sequences.     

Incorporating Synthetic Oligonucleotides via Gene Reassembly (ISOR): a versatile tool for generating targeted libraries

The directed evolution of proteins has benefited greatly from site-specific methods of diversification such as saturation mutagenesis. These techniques target diversity to a number of chosen positions that are usually non-contiguous in the protein's primary structure. However, the number of targeted positions can be large, thus leading to impractically large library size, wherein almost all library variants are inactive and the likelihood of selecting desirable properties is extremely small. We describe a versatile combinatorial method for the partial diversification of large sets of residues. Our library oligonucleotides comprise randomized codons that are flanked by wild-type sequences. Adding these oligonucleotides to an assembly PCR of wild-type gene fragments incorporates the randomized cassettes, at their target sites, into the reassembled gene. Varying the oligonucleotides concentration resulted in library variants that carry a different average number of mutated positions that comprise a random subset of the entire set of diversified codons. This method, dubbed Incorporating Synthetic Oligos via Gene Reassembly (ISOR), was used to create libraries of a cytosine-C5 methyltransferase wherein 45 individual positions were randomized. One library, containing an average of 5.6 mutated residues per gene, was selected, and mutants with wild-type-like activities isolated. We also created libraries of serum paraoxonase PON1 harboring insertions and deletions (indels) in various areas surrounding the active site. Screening these libraries yielded a range of mutants with altered substrate specificities and indicated that certain regions of this enzyme have a surprisingly high tolerance to indels.     

A Single-Framework Synthetic Antibody Library Containing a Combination of Canonical and Variable Complementarity-Determining Regions

Synthetic antibody libraries have been used to generate antibodies with favorable biophysical and pharmacological properties. Here, we describe the design, construction, and validation of a phage-displayed antigen-binding fragment (Fab) library built on a modified trastuzumab framework with four fixed and two diversified complementarity-determining regions (CDRs). CDRs L1, L2, H1, and H2 were fixed to preserve the most commonly observed “canonical” CDR conformation preferred by the modified trastuzumab Fab framework. The library diversity was engineered within CDRs L3 and H3 by use of custom-designed trinucleotide phosphoramidite mixes and biased towards human antibody CDR sequences. The library contained ≈7.6 billion unique Fabs, and >95 % of the library correctly encoded both diversified CDR sequences. We used this library to conduct selections against the human epidermal growth factor receptor-3 extracellular domain (HER3-ECD) and compared the CDR diversity of the naïve library and the anti-HER3 selection pool by use of next-generation sequencing. The most commonly observed CDR combination isolated, named Her3-3, was overexpressed and purified in Fab and immunoglobulin G (IgG) formats. Fab HER3-3 bound to HER3-ECD with a K_D value of 2.14 nm and recognized cell-surface HER3. Although HER3-3 IgG bound to cell-surface HER3, it did not inhibit the proliferation of HER3-positive cells. Near-infrared imaging showed that Fab HER3-3 selectively accumulated in a murine HER3-postive xenograft, thus providing a lead for the development of HER3 imaging probes.     

Highly Diverse Protein Library Based on the Ubiquitous (β/α)8 Enzyme Fold Yields Well‐Structured Proteins through in Vitro Folding Selection

Proper protein folding is a prerequisite for protein stability and enzymatic activity. Although directed evolution can be a powerful tool to investigate enzymatic function and to isolate novel activities, well‐designed libraries of folded proteins are essential. In vitro selection methods are particularly capable of searching for enzymatic activities in libraries of trillions of protein variants, yet high‐quality libraries of well‐folded enzymes with such high diversity are lacking. We describe the construction and detailed characterization of a folding‐enriched protein library based on the ubiquitous (β/α)₈ barrel fold, which is found in five of the six enzyme classes. We introduced seven randomized loops on the catalytic face of the monomeric, thermostable (β/α)₈ barrel of glycerophosphodiester phosphodiesterase (GDPD) from Thermotoga maritima. We employed in vitro folding selection based on protease digestion to enrich intermediate libraries containing three to four randomized loops for folded variants, and then combined them to assemble the final library (10¹⁴ DNA sequences). The resulting library was analyzed by using the in vitro protease assay and an in vivo GFP‐folding assay; it contains ～10¹² soluble monomeric protein variants. We isolated six library members and demonstrated that these proteins are soluble, monomeric and show (β/α)₈‐barrel fold‐like secondary and tertiary structure. The quality of the folding‐enriched library improved up to 50‐fold compared to a control library that was assembled without the folding selection. To the best of our knowledge, this work is the first example of combining the ultra‐high throughput mRNA display method with selection for folding. The resulting (β/α)₈ barrel libraries provide a valuable starting point to study the unique catalytic capabilities of the (β/α)₈ fold, and to isolate novel enzymes.     

Exploiting bias in a non-immune human antibody library to predict antigenicity

Non-immune human antibody fragment libraries have generated antigen-binding proteins useful as prospective research, imaging, diagnostic and therapeutic agents. However, because the generation of such libraries relies on cloning antibody sequences from the circulating immune repertoire rather than truly na?ve, germline sequences, their composition may reflect the deletion of autoreactive sequences, making them less suited for isolating binding clones to human antigens, but perhaps useful in applications where an in vitro handle on representative circulating antibody diversity is desired. Here we demonstrate that a large non-immune human scFv library is relatively depleted of sequences capable of recognizing human antigens as compared with orthologs antigens. Additionally, because this non-na?ve, non-immune library may capture a representative section of antibody diversity, we explore its possible utility in conducting early pre-screens to predict the antigenicity of prospective therapeutics and find a correlation between the clinical immunogenicity of a small panel of protein therapeutics with their propensity for interacting with the library.     

Deep Sequencing of a Systematic Peptide Library Reveals Conformationally-Constrained Protein Interface Peptides that Disrupt a Protein-Protein Interaction

Disrupting protein-protein interactions is difficult due to the large and flat interaction surfaces of the binding partners. The BLIP and BLIP-II proteins are unrelated in sequence and structure and yet each potently inhibit β-lactamases. High-throughput oligonucleotide synthesis was used to construct a 12,470-member library containing overlapping linear and cyclic peptides ranging in size from 6 to 21 amino acids that scan through the sequences of BLIP and BLIP-II. Phage display affinity selections and deep sequencing revealed that, despite the differences in interaction surfaces with β-lactamases, rapid enrichment of consensus peptide regions originating from both BLIP and BLIP-II contact residues in the binding interface occurred. BLIP and BLIP-II peptides that were enriched by affinity selection were shown to bind β-lactamases and disrupt the BLIP/β-lactamase interaction. The results suggest that peptides that bind at and disrupt PPI interfaces can be identified through systematic peptide library construction, affinity selection, and deep sequencing.     

High-Throughput Sequencing of Phage Display Libraries Reveals Parasitic Enrichment of Indel Mutants Caused by Amplification Bias

The combination of phage display technology with high-throughput sequencing enables in-depth analysis of library diversity and selection-driven dynamics. We applied short-read sequencing of the mutagenized region on focused display libraries of two homologous nucleic acid modification eraser proteins—AlkB and FTO—biopanned against methylated DNA. This revealed enriched genotypes with small indels and concomitant doubtful amino acid motifs within the FTO library. Nanopore sequencing of the entire display vector showed additional enrichment of large deletions overlooked by region-specific sequencing, and further impacted the interpretation of the obtained amino acid motifs. We could attribute enrichment of these corrupted clones to amplification bias due to arduous FTO display slowing down host cell growth as well as phage production. This amplification bias appeared to be stronger than affinity-based target selection. Recommendations are provided for proper sequence analysis of phage display data, which can improve motive discovery in libraries of proteins that are difficult to display.     

A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile

Antibody discovery by phage display consists of two phases, i.e., the binding phase and the amplification phase. Ideally, the selection process is dominated by the former, and all the retrieved clones are amplified equally during the latter. In reality, the amplification efficiency of antibody fragments varies widely among different sequences and, after a few rounds of phage display panning, the output repertoire often includes rapidly amplified sequences with low or no binding activity, significantly diminishing the efficiency of antibody isolation. In this work, a novel synthetic single-chain variable fragment (scFv) library with complementarity-determining region (CDR) diversities aimed at improved amplification efficiency was designed and constructed. A previously reported synthetic scFv library with low, non-combinatorial CDR diversities was panned against protein A superantigen, and the library repertoires before and after the panning were analyzed by next generation sequencing. The enrichment or depletion patterns of CDR sequences after panning served as the basis for the design of the new library. Especially for CDR-H3 with a higher and more random diversity, a machine learning method was applied to predict potential fast-amplified sequences among a simulated sequence repertoire. In a direct comparison with the previous generation library, the new library performed better against a panel of antigens in terms of the number of binders isolated, the number of unique sequences, and/or the speed of binder enrichment. Our results suggest that the amplification-centric design of sequence diversity is a valid strategy for the construction of highly functional phage display antibody libraries.     

Construction of Synthetic Nanobody Library in Mammalian Cells by dsDNA-Based Strategies**

A nanobody is an antibody fragment consisting of a single monomeric variable antigen-binding domain. Mammalian cells are ideal platforms for identifying nanobodies targeting hard-to-display transmembrane proteins and nanobodies that function as modulators of cellular phenotypes. However, the introduction of a high-diversity nanobody library into mammalian cells is challenging. We have developed two novel methods for constructing a nanobody library in mammalian cells. Complementarity-determining region (CDR) random sequences were first incorporated into upstream and downstream dsDNAs by PCR. In the first method, named dsDNA-HR, upstream and downstream dsDNAs containing an identical overlapping sequence were co-transfected into cultured mammalian cells for intracellular homologous recombination that resulted in the formation of an intact nanobody library expression cassette. In the second method, named in vitro ligation, we generated full-length nanobody expression dsDNAs via ligation of restriction digested upstream and downstream dsDNAs. The obtained full-length dsDNAs were transfected into mammalian cells for nanobody library expression. Using both methods, we generated over a million unique nanobody sequences, as revealed by high-throughput sequencing. Single-cell sequencing was employed to resolve the diversity of the dsDNA-HR nanobody library. We also identified a small molecule, Nocodazole, which could enhance the efficacy of dsDNA-HR.     

Using a PCR-Based Method To Analyze and Model Large,Heterogeneous Populations of DNA

The study of populations of large size and high diversity is limited by the capability of collecting data. Moreover, for a pool of individuals, each associated with a unique characteristic feature, as the pool size grows, the possible interactions increase exponentially and quickly go beyond the limit of computation and experimental studies. Herein, the design of DNA libraries with various diversity is reported. By using a facile analytical method based on real-time PCR, the diversity of a pool of DNA can be evaluated to allow extraordinarily high heterogenicity (e.g., >1 trillion). It is demonstrated that these DNA libraries can be used to model heterogeneous populations; these libraries exhibit functions such as self-protection, suitability for biased expansion, and the possibility to evolve into amorphous structures. The method has shown the remarkable power of parallel computing with DNA, since it can resemble an analogue computer and be applied in selection-based biotechnology methods, such as DNA-encoded chemical libraries. As a chemical approach to solve problems traditionally for genetic and statistical analysis, the method provides a quick and cost-efficient evaluation of library diversity for intermediate steps through a selection process.     

Affinity proteins and their generation

Engineered affinity proteins have, together with antibodies and antibody derivatives, become indispensable tools in many areas of life science and with an increasing number of applications. The need for high‐throughput methods for generation of these different affinity proteins is evident. Today, combinatorial protein engineering is the most successful strategy to generate novel affinity proteins of non‐immunoglobulin origin. In this approach, high‐complexity combinatorial libraries are constructed from which affinity proteins are isolated using appropriate selection methods, thus circumventing the need for detailed knowledge of the protein structure and the binding mechanism that is necessary in more rational approaches. Since the introduction of the phage display technology, several alternative selection systems have been developed for this purpose. This review presents briefly some of the more commonly used affinity proteins, and gives an overview of the different methods and challenges related to the generation of library diversity and the selection methods available for the isolation of affinity proteins with desired properties. Copyright © 2012 Society of Chemical Industry     

Enzyme-like proteins from an unselected library of designed amino acid sequences

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. However, since arbitrary sequences rarely fold into well ordered protein-like structures, randomly generated libraries will yield functional proteins only very rarely. To enhance the likelihood of finding functional de novo proteins, we use binary patterning of polar and non-polar amino acids to design focused libraries of sequences that are predisposed to fold into ordered structures. Proteins isolated from binary patterned libraries have been shown previously to fold into well ordered and native-like three-dimensional structures. To probe the potential of such libraries to also yield proteins with enzyme-like activity, we measured the esterase activity of S-824, a de novo binary patterned protein whose alpha-helical three-dimensional structure was reported recently. Protein S-824 displayed a rate enhancement (k(cat)/k(uncat)) of 8700. The observed activity is similar to, or better than, that observed for several esterases designed previously using rational design or automated computational methods. Moreover, the observed activity rivals those of the first catalytic antibodies. To assess whether the activity of S-824 is representative of other proteins in binary patterned libraries, we measured the esterase activity of six additional proteins from two libraries. These libraries were 'na?ve' in that they were neither designed to bind substrate, nor subjected to high throughput screens for activity. All six of the additional proteins displayed esterase activity significantly above background. These findings demonstrate that novel proteins with enzyme-like properties are surprisingly common in focused libraries designed by binary patterning. Moreover, the activity of these unselected proteins provides a reference state for the levels of activity that have been obtained by selection and/or computational design.     

Flow-Seq Evaluation of Translation Driven by a Set of Natural Escherichia coli 5′-UTR of Variable Length

Flow-seq is a method that combines fluorescently activated cell sorting and next-generation sequencing to deduce a large amount of data about translation efficiency from a single experiment. Here, we constructed a library of fluorescent protein-based reporters preceded by a set of 648 natural 5′-untranslated regions (5′-UTRs) of Escherichia coli genes. Usually, Flow-seq libraries are constructed using uniform-length sequence elements, in contrast to natural situations, where functional elements are of heterogenous lengths. Here, we demonstrated that a 5′-UTR library of variable length could be created and analyzed with Flow-seq. In line with previous Flow-seq experiments with randomized 5′-UTRs, we observed the influence of an RNA secondary structure and Shine–Dalgarno sequences on translation efficiency; however, the variability of these parameters for natural 5′-UTRs in our library was smaller in comparison with randomized libraries. In line with this, we only observed a 30-fold difference in translation efficiency between the best and worst bins sorted with this factor. The results correlated with those obtained with ribosome profiling.     

C-Terminal Tag Location Hampers in Vitro Profiling of OGT Peptide Substrates by mRNA Display

O-GlcNAc transferase (OGT) is the only enzyme that catalyzes the post-translational modification of proteins at Ser/Thr with a single β-N-acetylglucosamine (O-GlcNAcylation). Its activity has been associated with chronic diseases such as cancer, diabetes and neurodegenerative disease. Although numerous OGT substrates have been identified, its accepted substrate scope can still be refined. We report here an attempt to better define the peptide-recognition requirements of the OGT active site by using mRNA display, taking advantage of its extremely high throughput to assess the substrate potential of a library of all possible nonamer peptides. An antibody-based selection process is described here that is able to enrich an OGT substrate peptide from such a library, but with poor absolute recovery. Following four rounds of selection for O-GlcNAcylated peptides, sequencing revealed 14 peptides containing Ser/Thr, but these were shown by luminescence-coupled assays and peptide microarray not to be OGT substrates. By contrast, subsequent testing of an N-terminal tag approach showed exemplary recovery. Our approach demonstrates the power of genetically encoded libraries for selection of peptide substrates, even from a very low initial starting abundance and under suboptimal conditions, and emphasizes the need to consider the binding biases of antibodies and both C- and N-terminal tags in profiling peptide substrates by high-throughput display.     

Selection of an active enzyme by phage display on the basis of the enzyme's catalytic activity in vivo

We have developed a novel phage display method based on catalytic activity for the in vivo selection of an enzyme. To confirm the validity of our method and to demonstrate its potential utility, we used biotin protein ligase (BPL) from Escherichia coli as a model enzyme. We were able to demonstrate the potential value of our method by selective enrichment for the birA gene, which encodes BPL, in a mixed library. The presented method for in vivo selection should allow selection of various enzymes that catalyze modification of peptides or proteins, such as protein ligase, acetylase, kinase, phosphatase, ubiquitinase, and protease (including caspase). The method should be useful in efforts to analyze mechanisms of signal transduction, to find unidentified enzymes encoded by cDNA libraries, and to exploit artificial enzymes.     

User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries

Directed evolution of proteins depends on the production ofmolecular diversity by random mutagenesis. While a number ofmethods have been developed for introducing this diversity,the best ways to sample it are not always clear. Here we usedsimple statistics to analyse completeness and diversity in randomizedlibraries generated by oligonucleotide-directed mutagenesis,error-prone polymerase chain reaction (epPCR) and in vitro recombinationof highly homologous sequences. For oligonucleotide-directedmutagenesis, we derive equations to estimate how complete agiven library is expected to be and also to predict the sizeof library required to give a fixed probability of being 100%complete. We describe the statistical bases for computer programswhich estimate the number of distinct variants represented inepPCR and shuffled libraries, dubbed PEDEL and DRIVeR, respectively.These programs allow the user to calculate (rather than guess)the diversity represented in a given library and also provideempirical guidelines for maximizing this diversity. PEDEL andDRIVeR are available at www.bio.cam.ac.uk/     

旋毛虫新生幼虫DNA结合相关蛋白基因的筛选与分析

目的筛选旋毛虫新生幼虫表达的可与宿主肌细胞染色体DNA结合的相关蛋白基因,寻找旋毛虫侵入及寄生过程中与宿主肌细胞发生结合的相关蛋白,为研究寄生虫与宿主间的信号转导、侵袭及长期寄生机制奠定基础。方法利用噬菌体展示技术构建旋毛虫新生幼虫T7噬菌体展示cDNA文库,用小鼠肌肉染色体DNA对展示文库进行筛选,随机挑选30个阳性克隆,进行PCR鉴定、测序分析和编码蛋白二级结构及翻译后修饰预测。结果旋毛虫新生幼虫T7噬菌体展示cDNA文库的原始文库库容量为2×105pfu,重组率为98%,95%的插入片段长度在250～2000bp之间,扩增后文库滴度为3×1012pfu/ml。对经4轮筛选后的克隆进行PCR鉴定及测序,获得13个基因序列,其中有4个(DN14、DN24、DN9及DN23)为旋毛虫新生幼虫DNA结合相关蛋白基因,分别与旋毛虫未知蛋白及假定ORF11.30、旋毛虫nudix水解酶及血吸虫SJCHGC05997蛋白、秀丽新杆线虫未知蛋白和旋毛虫TGF-β配基具有同源性。经编码蛋白质二级结构及翻译后修饰预测,这4种蛋白可能与旋毛虫包囊形成和寄生虫与宿主间信号转导有关。结论已成功构建了旋毛虫新生幼虫T7噬菌体展示cDNA文库,并利用小鼠肌肉染色体DNA筛选出4个可用于研究旋毛虫包囊形成及与宿主间信号转导机制的候选基因。     

Hidden Markov Models-based system (HMMSPECTR) for detecting structural homologies on the basis of sequential information

HMMSPECTR is a tool for finding putative structural homologsfor proteins with known primary sequences. HMMSPECTR containsfour major components: a data warehouse with the hidden Markovmodels (HMM) and alignment libraries; a search program whichcompares the initial protein sequences with the libraries ofHMMs; a secondary structure prediction and comparison program;and a dominant protein selection program that prepares the setof 10–15 `best' proteins from the chosen HMMs. The datawarehouse contains four libraries of HMMs. The first two librarieswere constructed using different HHM preparation options ofthe HAMMER program. The third library contains parts (`partialHMM') of initial alignments. The fourth library contains trainedHMMs. We tested our program against all of the protein targetsproposed in the CASP4 competition. The data warehouse includedlibraries of structural alignments and HMMs constructed on thebasis of proteins publicly available in the Protein Data Bankbefore the CASP4 meeting. The newest fully automated versionsof HMMSPECTR 1.02 and 1.02ss produced better results than thebest result reported at CASP4 either by r.m.s.d. or by length(or both) in 64% (HMMSPECTR 1.02) and 79% (HMMSPECTR 1.02ss)of the cases. The improvement is most notable for the targetswith complexity 4 (difficult fold recognition cases).     

大容量人源核糖体展示单链抗体文库的构建

目的构建大容量、多样性的人源核糖体展示(Ribosome display,RD)单链抗体(Singe chain Fv segment,scFv)库。方法收集20名健康献血者的新鲜外周血,分离淋巴细胞,提取细胞总RNA;设计兼并引物,利用RT-PCR分别扩增人抗体的VH-linker、Vκ、Vλ及Cκ基因;采用重叠PCR(SOE-PCR)技术,构建VH-linker-Vκ和VH-linker-Vλ-Cκ单链抗体库;将VH-linker-Vκ和VH-linker-Vλ-Cκ等量混合后,与pMD19-T载体连接,并转化感受态E.coli DH5α,对所构建的scFv库进行菌落PCR和测序分析。结果构建的核糖体展示单链抗体库重组率较高,转化产物经菌落PCR鉴定,均可见约1 000 bp的scFv基因片段,库容量为2.06×1013。经分析该抗体库单链抗体序列均完整,内部无终止密码子,可变区序列无一重复,多样性良好,均具有完整的体外核糖体展示框架。结论已成功构建了大容量、多样性好的人源核糖体展示单链抗体库,为进一步筛选高特异性、高亲和力的人源抗体奠定了基础。