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Summary The generation of a library of variant genes is a prerequisite of directed evolution, a powerful tool for biomolecular engineering. As the number of all possible sequences often far exceeds the diversity of a practical library, methods that allow efficient library diversification in living cells are essential for in vivo directed evolution technologies to effectively sample the sequence space and allow hits to emerge. While traditional whole-genome mutagenesis often results in toxicity and the emergence of “cheater” mutations, recent developments that exploit the targeting and editing abilities of genome editors to facilitate in vivo library diversification have allowed for precise mutagenesis focused on specific genes of interest, higher mutational density, and reduced the occurrence of cheater mutations. This minireview summarizes recent advances in genome editor-directed in vivo library diversification and provides an outlook on their future applications in chemical biology.

Chromatin adopts different configurations that are regulated by reversible covalent modifications, referred to as epigenetic marks. Epigenetic inhibitors have been approved for clinical use to restore epigenetic aberrations that result in silencing of tumor-suppressor genes, oncogene addictions, and enhancement of immune responses. However, these drugs suffer from major limitations, such as a lack of locus selectivity and potential toxicities. Technological advances have opened a new era of precision molecular medicine to reprogram cellular physiology. The locus-specificity of CRISPR/dCas9/12a to manipulate the epigenome is rapidly becoming a highly promising strategy for personalized medicine. This review focuses on new state-of-the-art epigenome editing approaches to modify the epigenome of neoplasms and other disease models towards a more ‘normal-like state’, having characteristics of normal tissue counterparts. We highlight biomolecular engineering methodologies to assemble, regulate, and deliver multiple epigenetic effectors that maximize the longevity of the therapeutic effect, and we discuss limitations of the platforms such as targeting efficiency and intracellular delivery for future clinical applications.

Summary Bispecific antibodies (Bispecifics) demonstrate exceptional clinical potential to address some of the most complex diseases. However, Bispecific production in a single cell often requires the correct pairing of multiple polypeptide chains for desired assembly. This is a considerable hurdle that hinders the development of many immunoglobulin G (IgG)-like bispecific formats. Our approach focuses on the rational engineering of charged residues to facilitate the chain pairing of distinct heavy chains (HC). Here, we deploy structure-guided protein design to engineer charge pair mutations (CPMs) placed in the CH3-CH3′ interface of the fragment crystallizable (Fc) region of an antibody (Ab) to correctly steer heavy chain pairing. When used in combination with our stable effector functionless 2 (SEFL2.2) technology, we observed high pairing efficiency without significant losses in expression yields. Furthermore, we investigate the relationship between CPMs and the sequence diversity in the parental antibodies, proposing a rational strategy to deploy these engineering technologies., Graphical abstract, Highlights • Crystal structures unveil molecular basis of SEFL2.2 and CPM technologies • Next gen structure-guided design of CPMs to steer HC-HC pairing • Top CPMs show high pairing efficiency and optimal expression and stability • Balancing CPM charge distribution minimizes impact of sequence diversity, Biochemistry; Bioengineering; Biomolecular engineering; Structural biology

Summary Mitochondrial biogenesis is a cell response to external stimuli which is generally believed to suppress apoptosis. However, during the process of apoptosis, whether mitochondrial biogenesis occurs in the early stage of the apoptotic cells remains unclear. To address this question, we constructed the COX8-EGFP-ACTIN-mCherry HeLa cells with recombinant fluorescent proteins respectively tagged on the nucleus and mitochondria and monitored the mitochondrial changes in the living cells exposed to gamma-ray radiation. Besides in situ detection of mitochondrial fluorescence changes, we also examined the cell viability, nuclear DNA damage, reactive oxygen species (ROS), mitochondrial superoxide, citrate synthase activity, ATP, cytoplasmic and mitochondrial calcium, mitochondrial mass, mitochondrial morphology, and protein expression related to mitochondrial biogenesis, as well as the apoptosis biomarkers. As a result, we confirmed that significant mitochondrial biogenesis took place preceding the radiation-induced apoptosis, and it was closely correlated with the apoptotic cells at late stage. The involved mechanism was also discussed., Graphical abstract, Highlights • Dual fluorescence approach was used for in situ observation of living cell processes • Radiation-induced effects of mitochondrial biogenesis and apoptosis were observed • Relationship between mitochondrial biogenesis and apoptosis was revisited • Assessing early mitochondrial biogenesis is critical for predicting later fate of cells, Biochemistry methods; Biomolecular engineering; Cell biology

Diseases are caused by mutations in DNA sequences. DNA tends to form double-helix structures but in more recent times, it has been found that it can also form non-canonical structures in response to changes in the environment around it. Japanese researchers have now unearthed some exciting findings about the chain reaction that results, potentially leading to diseases such as cancer. Associate Professor Hisae Tateishi-Karimata and Professor Naoki Sugimoto are based at the Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University in Japan, and are collaborating on important work to better understand the complex inner workings of cells in disease. An area of focus for this research is the elucidation of mechanisms of diseases caused by non-canonical structures of DNA and regulation for DNA function.

One of the central themes of biomolecular engineering is the challenge of exploiting the properties of biological materials. Part of this challenge has been uncovering and harnessing properties of biological components that only emerge following their ordered self-assembly. One biomolecular building block that has received significant interest in the past decade is the M13 bacteriophage. There have been a number of recent attempts to trigger the ordered assembly of M13 bacteriophage into multivirion structures, relying on the innate tendency of M13 to form liquid crystals at high concentrations. These, in general, yield planar two-dimensional materials. Presented here is the production of multivirion assemblies of M13 bacteriophage via the chemical modification of its surface by the covalent attachment of the xanthene-based dye tetramethylrhodamine (TMR) isothiocyanate (TRITC). We show that TMR induces the formation of three-dimensional aster-like assemblies of M13 by providing "adhesive" action between bacteriophage particles through the formation of H-aggregates (face-to-face stacking of dye molecules). We also show that the H-aggregation of TMR is greatly enhanced by covalent attachment to M13 and is enhanced further still upon the ordered self-assembly of M13, leading to the suggestion that M13 could be used to promote the self-assembly of dyes that form J-aggregates, a desirable arrangement of fluorescent dye, which has interesting optical properties and potential applications in the fields of medicine and light harvesting technology.

The alkyne functionality has attracted much interest due to its diverse chemical and biological applications. We recently elucidated an acyl carrier protein (ACP)-dependent alkyne biosynthetic pathway, however, little is known about ACP interactions with the alkyne biosynthetic enzymes, an acyl-ACP ligase (JamA) and a membrane-bound bi-functional desaturase/acetylenase (JamB). Here, we showed that JamB has a more stringent interaction with ACP than JamA. In addition, site directed mutagenesis of a non-cognate ACP significantly improved its compatibility with JamB, suggesting a possible electrostatic interaction at the ACP-JamB interface. Finally, error-prone PCR and screening of a second non-cognate ACP identified hot spots on the ACP that are important for interacting with JamB and yielded mutants which were better recognized by JamB. Our data thus not only provide insights into the ACP interactions in alkyne biosynthesis, but it also potentially aids in future combinatorial biosynthesis of alkyne-tagged metabolites for chemical and biological applications.Topical HeadingBiomolecular Engineering, Bioengineering, Biochemicals, Biofuels, and Food

Synthetic biologists have applied biomolecular engineering approaches toward the goal of novel biological devices and have shown progress in diverse areas of medicine and biotechnology. Especially promising is the application of synthetic biological devices towards a novel class of molecular diagnostics. As an example, a de-novo-designed riboregulator called toehold switch, with its programmability and compatibility with field-deployable devices showed promising in vitro applications for viral RNA detection such as Zika and Corona viruses. However, the in vivo application of high-performance RNA sensors remains challenging due to the secondary structure of long mRNA species. Here, we introduced ‘Helper RNAs’ that can enhance the functionality of toehold switch sensors by mitigating the effect of secondary structures around a target site. By employing the helper RNAs, previously reported mCherry mRNA sensor showed improved fold-changes in vivo. To further generalize the Helper RNA approaches, we employed automatic design pipeline for toehold sensors that target the essential genes within the pks island, an important target of biomedical research in connection with colorectal cancer. The toehold switch sensors showed fold-changes upon the expression of full-length mRNAs that apparently depended sensitively on the identity of the gene as well as the predicted local structure within the target region of the mRNA. Still, the helper RNAs could improve the performance of toehold switch sensors in many instances, with up to 10-fold improvement over no helper cases. These results suggest that the helper RNA approaches can further assist the design of functional RNA devices in vivo with the aid of the streamlined automatic design software developed here. Further, our solutions for screening and stabilizing single-stranded region of mRNA may find use in other in vivo mRNA-sensing applications such as cas13 crRNA design, transcriptome engineering, and trans-cleaving ribozymes.

International audience; ERK1/2 involvement in cell death remains unclear, although many studies have demonstrated the importance of ERK1/2 dynamics in determining cellular re- sponses. To untangle how ERK1/2 contributes to two cell death programs, we investigated ERK1/2 signaling dynamics during hFasL-induced apoptosis and TNF-induced necroptosis in L929 cells. We observed that ERK1/2 inhibition sensi- tizes cells to apoptosis while delaying necroptosis. By monitoring ERK1/2 activity by live-cell imaging using an improved ERK1/2 biosensor (EKAR4.0), we reported differential ERK1/2 signaling dynamics between cell survival, apoptosis, and nec- roptosis. We also decrypted a temporally shifted amplitude- and frequency-modu- lated (AM/FM) ERK1/2 activity profile in necroptosis versus apoptosis. ERK1/2 inhibition, which disrupted ERK1/2 signaling dynamics, prevented TNF and IL-6 gene expression increase during TNF-induced necroptosis. Using an inducible cell line for activated MLKL, the final executioner of necroptosis, we showed ERK1/2 and its distinctive necroptotic ERK1/2 activity dynamics to be positioned downstream of MLKL.

Molecular hydrogen is a promising currency in the future energy economy due to the uncertain availability of finite fossil fuel resources and environmental effects from their combustion. It also has important uses in the production of fertilizers and platform chemicals as well as in upgrading conventional fuels. Conventional methods for producing molecular hydrogen from natural gas produce carbon dioxide and use a finite resource as feedstock. However, these issues can be overcome by using light energy from the Sun combined with microorganisms and their molecular machinery capable of photosynthesis. In the presence of light, the proteins involved in photosynthesis coupled with appropriate catalysts in higher plants, algae, and cyanobacteria can produce molecular hydrogen, and optimization via genetic modifications and biomolecular engineering further improves production rates. In this review, we will discuss techniques that have been utilized to improve rates of hydrogen production in biological systems based on the protein machinery of photosynthesis coupled with appropriate catalysts. We will also suggest areas for improvement and future directions for work in the field.

We used the molecular modeling program Rosetta to identify clusters of amino acid substitutions in antibody fragments (scFvs and scAbs) that improve global protein stability and resistance to thermal deactivation. Using this methodology, we increased the melting temperature (T(m)) and resistance to heat treatment of an antibody fragment that binds to the Clostridium botulinum hemagglutinin protein (anti-HA33). Two designed antibody fragment variants with two amino acid replacement clusters, designed to stabilize local regions, were shown to have both higher T(m) compared to the parental scFv and importantly, to retain full antigen binding activity after 2 hours of incubation at 70 °C. The crystal structure of one thermostabilized scFv variants was solved at 1.6 Å and shown to be in close agreement with the RosettaAntibody model prediction.

Materials with novel and enhanced functionalities can be obtained by modifying cellulose with a range of biomolecules. This functionalization can deliver tailored cellulose-based materials with enhanced physical and chemical properties and control of biological interactions that match specific applications. One of the foundations for the success of such biomaterials is to efficiently control the capacity to combine relevant biomolecules into cellulose materials in such a way that the desired functionality is attained. In this context, our main goal was to develop bi-functional biomolecular constructs for the precise modification of cellulose hydrogels with bioactive molecules of interest. The main idea was to use biomolecular engineering techniques to generate and purify different recombinant fusions of carbohydrate binding modules (CBMs) with significant biological entities. Specifically, CBM-based fusions were designed to enable the bridging of proteins or oligonucleotides with cellulose hydrogels. The work focused on constructs that combine a family 3 CBM derived from the cellulosomal-scaffolding protein A from Clostridium thermocellum (CBM3) with the following: (i) an N-terminal green fluorescent protein (GFP) domain (GFP-CBM3); (ii) a double Z domain that recognizes IgG antibodies; and (iii) a C-terminal cysteine (CBM3C). The ability of the CBM fusions to bind and/or anchor their counterparts onto the surface of cellulose hydrogels was evaluated with pull-down assays. Capture of GFP-CBM3 by cellulose was first demonstrated qualitatively by fluorescence microscopy. The binding of the fusion proteins, the capture of antibodies (by ZZ-CBM3), and the grafting of an oligonucleotide (to CBM3C) were successfully demonstrated. The bioactive cellulose platform described here enables the precise anchoring of different biomolecules onto cellulose hydrogels and could contribute significatively to the development of advanced medical diagnostic sensors or specialized biomaterials, among others.

Antibodies are vital for human health because of their ability to function as nature’s drugs by protecting the body from infection. In recent decades, antibodies have been used as pharmaceutics for targeted therapy in patients with cancer, autoimmune diseases, and cardiovascular diseases. Capturing the dynamic structure of antibodies and characterizing antibody fluctuation is critical for gaining a deeper understanding of their structural characteristics and for improving drug development. Current techniques for studying three-dimensional (3D) structural heterogeneity and variability of proteins have limitations in ascertaining the dynamic structural behavior of antibodies and antibody-antigen complexes. Here, we review current techniques used to study antibody structures with a focus on the recently developed individual-particle electron tomography (IPET) technique. IPET, as a particle-by-particle methodology for 3D structural characterization, has shown advantages in studying structural variety and conformational changes of antibodies, providing direct imaging data for biomolecular engineering to improve development and clinical application of synthetic antibodies.

Cellular reprogramming using cocktails of transcription factors (TFs) affirms the epigenetic and developmental plasticity of mammalian cells. It demonstrates the ability of TFs to 'read' genetic information and to rewire regulatory networks in different cellular contexts. Silenced chromatin is not an impediment to the genome engagement by ectopically expressed TFs. Reprogramming TFs have been identified in diverse structural families that lack shared domains or sequence motifs. Interestingly, the reprogramming activity of non-redundant paralogous TFs can be switched with a few point mutations. These findings revealed that the sequence-function relationships influencing reprogramming are tied to subtle features directing genome wide binding. Therefore, endogenous reprogramming TFs are amenable to directed biomolecular engineering that opens up new avenues to optimize cell fate conversions.

Control over the functionality of interfaces through biomolecular engineering is a central tool for nanoscale technology as well as many current applications of biology. In this work we designed fusion proteins that combined the surface adhesion and interfacial activity of a hydrophobin-protein together with the high affinity biotin-binding capability of an avidin-protein. We found that an overall architecture that was based on a circularly permuted version of avidin, dual-chain avidin, and hydrophobin gave a highly functional combination. The protein was produced in the filamentous fungus Trichoderma reesei and was efficiently purified using an aqueous two-phase partitioning procedure. The surface adhesive properties were widely different compared to wild-type avidin. Functional characterization showed that the protein assembled on hydrophobic surfaces as a thin layer even at very low concentrations and efficiently bound a biotinylated compound. The work shows how the challenge of creating a fusion protein with proteins that form multimers can be solved by structural design and how protein self-assembly can be used to efficiently functionalize interfaces.

Fungi are a prolific source of bioactive compounds, some of which have been developed as essential medicines and life-enhancing drugs. Genome sequencing has revealed that fungi have the potential to produce considerably more natural products (NPs) than are typically observed in the laboratory. Recently, there have been significant advances in the identification, understanding, and engineering of fungal biosynthetic gene clusters (BGCs). This review briefly describes examples of the engineering of fungal NP biosynthesis at the global, pathway, and enzyme level using in vivo and in vitro approaches and refers to the range and scale of heterologous expression systems available, developments in combinatorial biosynthesis, progress in understanding how fungal BGCs are regulated, and the applications of these novel biosynthetic enzymes as biocatalysts.

Biomolecular engineering enables synthesis of improved proteins through synergistic fusion of modules from unrelated biomolecules. Modularization of peptide antigen from an unrelated pathogen for presentation on a modular virus-like particle (VLP) represents a new and promising approach to synthesize safe and efficacious vaccines. Addressing a key knowledge gap in modular VLP engineering, this study investigates the underlying fundamentals affecting the ability of induced antibodies to recognize the native pathogen. Specifically, this quality of immune response is correlated to the peptide antigen module structure. We modularized a helical peptide antigen element, helix 190 (H190) from the influenza hemagglutinin (HA) receptor binding region, for presentation on murine polyomavirus VLP, using two strategies aimed to promote H190 helicity on the VLP. In the first strategy, H190 was flanked by GCN4 structure-promoting elements within the antigen module; in the second, dual H190 copies were arrayed as tandem repeats in the module. Molecular dynamics simulation predicted that tandem repeat arraying would minimize secondary structural deviation of modularized H190 from its native conformation. In vivo testing supported this finding, showing that although both modularization strategies conferred high H190-specific immunogenicity, tandem repeat arraying of H190 led to a strikingly higher immune response quality, as measured by ability to generate antibodies recognizing a recombinant HA domain and split influenza virion. These findings provide new insights into the rational engineering of VLP vaccines, and could ultimately enable safe and efficacious vaccine design as an alternative to conventional approaches necessitating pathogen cultivation.

The ability to synthesize, characterize, and manipulate DNA forms the foundation of a range of advanced disciplines including genomics, molecular biology, and biomolecular engineering. In particular for the latter field, DNA has proven useful as a structural or functional component in nanoscale self-assembled structures, antisense therapeutics, microarray diagnostics, and biosensors. Such applications frequently require DNA to be modified and conjugated to other macromolecules, including proteins, polymers, or fatty acids, in order to equip the system with properties required for a particular application. However, conjugation of DNA to large molecular components using classical chemistries often suffers from suboptimal yields. Here, we report the use of terminal deoxynucleotidyl transferase (TdT) for direct enzymatic ligation of native DNA to nucleotide triphosphates coupled to proteins and other large macromolecules. We demonstrate facile synthesis routes for a range of NTP-activated macromolecules and subsequent ligation to the 3' hydroxyl group of oligodeoxynucleotides using TdT. The reaction is highly specific and proceeds rapidly and essentially to completion at micromolar concentrations. As a proof of principle, parallelly labeled oligonucleotides were used to produce nanopatterned DNA origami structures, demonstrating rapid and versatile incorporation of non-DNA components into DNA nanoarchitectures.

Natural products are complex small molecules produced by an array of organisms and which humans have put to diverse uses, including as pesticides, antibiotics, and anticancer agents. While a wide range has already been uncovered it is clear that there are many more potential biosynthetic pathways for which the products have never been studied. Using the tools of synthetic biology allows us to manipulate these pathways and produce the desired compounds. The genes involved can also be transferred into other organisms which can be more easily manipulated. Recent advances in understanding these complex systems have also informed the targeted manipulation of biosynthetic pathways to produce specific modifications of the final natural product. In the future it may be possible, rather than relying on chemical synthesis, to design and build artificial pathways to synthesize completely new compounds as desired.

Proteins are the key biomolecules in almost all the physiological and pathological processes that are occurring in the cell. Functionality of proteins is related to its conformation, which is ultimately dictated by their unique amino acid sequence. In the current chapter, a brief overview will be provided on the nature of amino acids, structural characteristics and functional versatility of proteins. A glimpse on various interactions present in stabilizing the protein fold and the methods for unraveling their atomic level structures are also discussed. Finally, we present the role of engineered synthetic proteins for the welfare of humanity with huge potential in research and industrial sectors including biotechnological and biomedical fields under the emerging concepts of biomolecular/protein engineering.

Erratum Erratum to ‘‘Pharmacophore modeling strategies for the development of novel nonsteroidal inhibitors of human aromatase (CYP19)” [Bioorg. Med. Chem. Lett. 20 (2010) 3050] Yagmur Muftuoglu , Gabriela Mustata b,* Departments of Biophysics and Chemical Biomolecular Engineering, Johns Hopkins University, Baltmore, MD 21218, United States Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, United States

A promising alternative to replace the current egg- or cell culture-based technology for vaccine production from live viruses is virus-like particle (VLP) technology based on a microbial platform. VLPs are macromolecular assemblies of viral capsid proteins, which have been shown to tolerate insertion of antigen modules via genetic recombinant technology, yielding modular VLPs. Many studies on modular VLPs presume that when a peptide antigen element is taken out from the intact proteins and then modularised on VLPs, it is unable to fold into its native structure. However, until now, presentation of a peptide antigen element on a VLP and the impact of the display strategy to present the antigen element on the quality of the resulting antibodies (i.e. the ability of the antibodies to recognise the intact protein) are not fully understood. This thesis aims to understand the underlying fundamentals regarding modularisation of peptide antigen elements on VLPs for induction of high-quality antibodies. A hypervariable receptor-binding domain, Helix 190 (H190), from the hemagglutinin protein of influenza A virus was used as a model for modularisation on VLPs from murine polyomavirus (MuPyV) VP1 protein. Four major findings are presented. Firstly, two display strategies, i.e. arraying of H190 in tandem repeats and the use of helix promoter elements, were shown to display H190 in its immunogenic form equally. However, modularisation using tandem repeat display induced antibodies of a higher quality than modularisation using helix promoter elements. Secondly, the quality of antibodies induced by the tandem repeat display bearing two copies of H190 was optimum, thus no significant improvement was observed following the use of adjuvant or increasing the copy number of H190. Additionally, the increase in the copy number of H190 was shown to reduce the assembly capability and solubility of modular VP1 in an environment that was optimised for wild-type VP1. Thirdly, this thesis shows the novel finding in the use of flanking ionic elements to stabilise VLP precursors, termed as capsomeres, bearing two copies of H190 containing a hydrophobic stretch, which caused aggregation. Fourthly, the first steps towards obtaining the atomic crystal structure of presented H190 on a modular protein were performed, i.e. a mild and satisfactory laboratory process was developed to achieve high-purity modular VP1 capsomeres, unattainable using previously established expression and purification process of wild-type MuPyV VP1. This thesis shows a step forward towards understanding the presentation of a peptide antigen element on a VLP that enables induction of highquality antibodies, and towards VLP engineering to manipulate the aggregation and solubility of modular VP1. VLP technology based on a microbial platform presented here is a potentially safe and effective alternative vaccine candidate that targets a hypervariable peptide antigen element. The speed of the microbial platform allows a rapid response to the hypervariability of the peptide antigen element, which otherwise may be unachievable using the egg- and cell culture-based technologies.

Microbial transglutaminase (MTG), a robust enzyme developed initially for the manipulation of edible proteins in the food industry, has now been widely recognized as a practical protein-modifying reagent in the range of biotechnological applications. In this chapter, we introduce the potential use of MTG through our basic studies on the design of novel glutamine (Gln) donor substrates for lysine (Lys)-specific protein modification. Based on the core structure of a conventional transglutaminase substrate, benzyloxycarbonyl-L-glutaminylglycine (Z-QG), new Gln-donor substrates have been developed for the conjugation of recombinant proteins with different functionalities. The first target site for the substrate engineering was the C-terminal carboxylic group of Z-QG, which is feasibly labeled with functional moieties. For the preparation of protein-nucleic acid conjugates with novel molecular architecture, a new nucleotidyl substrate, Z-QG-(d)UTP, was created. We have also explored substitution of the N-terminal protecting group (Z) with fluorophores and biotin, and found that MTG accepts diverse functional groups at the N-terminus by inserting a short linker, leading to an increase in the utility of MTG in site-specific modification of functional proteins. Our results demonstrated how the design of (small) Gln-donor substrates of MTG can expand the scope of enzymatic manipulation in biomolecular engineering.

Antibodies are important molecules in many research fields, where they play a key role in various assays. Antibody labeling is therefore of great importance. Currently, most labeling techniques take advantage of certain amino acid side chains that commonly appear throughout proteins. This makes it hard to control the position and exact degree of labeling of each antibody. Hence, labeling of the antibody may affect the antibody-binding site. This paper presents a novel protein domain based on the IgG-binding domain C2 of streptococcal protein G, containing the unnatural amino acid BPA, that can cross-link other molecules. This novel domain can, with improved efficiency compared to previously reported similar domains, site-specifically cross-link to IgG at the Fc region. An efficient method for simultaneous in vivo incorporation of BPA and specific biotinylation in a flask cultivation of Escherichia coli is described. In comparison to a traditionally labeled antibody sample, the C2-labeled counterpart proved to have a higher proportion of functional antibodies when immobilized on a solid surface and the same limit of detection in an ELISA. This method of labeling is, due to its efficiency and simplicity, of high interest for all antibody-based assays where it is important that labeling does not interfere with the antibody-binding site.

The advances in high throughput screening technology for discovery of target molecules and the accumulation of functional genomics and proteomics data at an ever-accelerating rate will enable us to design and discover novel biomolecules and proteins on a rational basis in diverse areas of pharmaceutical, agricultural, industrial, and environmental applications. The biomolecular engineering will no doubt become one of the most important scientific disciplines in that it will enable us to comprehensively analyze gene expression patterns in both normal and diseased cells and to discover many new biologically active molecules rationally and systematically. As an applied molecular evolution technology, DNA shuffling will play a key role in biomolecular engineering. In contrast to the point mutation techniques, DNA shuffling exchanges large functional domains of sequences to search for the best candidate molecule, thus mimicking and accelerating the process of sexual recombination in the evolution of life. The phage-display system of combinatorial peptide libraries will be extensively exploited to design and create many more novel proteins, due to the relative ease of screening and identifying desirable proteins. Its application will be extended further into the science of protein–receptor or protein–ligand interactions. The bioinformatics including EST-based or SAGE-tag-based functional genomics and proteomics will continue to advance rapidly. Its biological knowledge base will expand the scope of biomolecular engineering, and the impact of well-coordinated biomolecular engineering research will be very significant on our understanding of gene expression, upregulation and downregulation, and posttranslational protein processing in healthy and diseased cells. The bioinformatics for genome and proteome analysis will contribute substantially toward ever more accelerated advances in pharmaceutical industry. When the functional genomics database, EST and SAGE techniques, microarray technique, and proteome analysis by 2-dimensional gel electrophoresis or capillary electrophoresis are all put to good use, the biomolecular engineering research will yield new drug discoveries, improved therapies, and new or significantly improved bioprocesses. With the advances in biomolecular engineering, the rate of finding new high-value peptides or proteins including antibodies, vaccines, enzymes, and therapeutic peptides will continue to be accelerated. The targets for rational design of biomolecules will be very broad, diverse, and complex, but many application goals can be achieved through the expansion of knowledge base on biomolecules of interest and their roles and functions in cells and tissues. In the near future, more therapeutic drugs and high-value biomolecules will be designed and produced for the treatment or prevention of not-so-easily-cured diseases such as cancers, genetic diseases, age-related diseases, and other metabolic diseases. Also anticipated are many more industrial enzymes that will be engineered to confer desirable properties for the process improvement and manufacturing of many high-value biomolecular products. Many more new metabolites including novel antibiotics that are active against resistant strains will be also produced by recombinant organisms having de novo engineered biosynthetic pathway enzyme systems. The biomolecular engineering era is here and a great deal of benefits can be derived from this field of scientific research for many years to come if we are willing to put it to good use.

During the next decade or so, there will be significant and impressive advances in biomolecular engineering, especially in our understanding of the biological roles of various biomolecules inside the cell. The advances in high throughput screening technology for discovery of target molecules and the accumulation of functional genomics and proteomics data at accelerating rates will enable us to design and discover novel biomolecules and proteins on a rational basis in diverse areas of pharmaceutical, agricultural, industrial, and environmental applications. As an applied molecular evolution technology, DNA shuffling will play a key role in biomolecular engineering. In contrast to the point mutation techniques, DNA shuffling exchanges large functional domains of sequences to search for the best candidate molecule, thus mimicking and accelerating the process of sexual recombination in the evolution of life. The phage-display system of combinatorial peptide libraries will be extensively exploited to design and create many novel proteins, as a result of the relative ease of screening and identifying desirable proteins. Even though this system has so far been employed mainly in screening the combinatorial antibody libraries, its application will be extended further into the science of protein-receptor or protein-ligand interactions. The bioinformatics for genome and proteome analyses will contribute substantially toward ever more accelerated advances in the pharmaceutical industry. Biomolecular engineering will no doubt become one of the most important scientific disciplines, because it will enable systematic and comprehensive analyses of gene expression patterns in both normal and diseased cells, as well as the discovery of many new high-value molecules. When the functional genomics database, EST and SAGE techniques, microarray technique, and proteome analysis by 2-dimensional gel electrophoresis or capillary electrophoresis in combination with mass spectrometer are all put to good use, biomolecular engineering research will yield new drug discoveries, improved therapies, and significantly improved or new bioprocess technology. With the advances in biomolecular engineering, the rate of finding new high-value peptides or proteins, including antibodies, vaccines, enzymes, and therapeutic peptides, will continue to accelerate. The targets for the rational design of biomolecules will be broad, diverse, and complex, but many application goals can be achieved through the expansion of knowledge based on biomolecules and their roles and functions in cells and tissues. Some engineered biomolecules, including humanized Mab's, have already entered the clinical trials for therapeutic uses. Early results of the trials and their efficacy are positive and encouraging. Among them, Herceptin, a humanized Mab for breast cancer treatment, became the first drug designed by a biomolecular engineering approach and was approved by the FDA. Soon, new therapeutic drugs and high-value biomolecules will be designed and produced by biomolecular engineering for the treatment or prevention of not-so-easily cured diseases such as cancers, genetic diseases, age-related diseases, and other metabolic diseases. Many more industrial enzymes, which will be engineered to confer desirable properties for the process improvement and manufacturing of high-value biomolecular products at a lower production cost, are also anticipated. New metabolites, including novel antibiotics that are active against resistant strains, will also be produced soon by recombinant organisms having de novo engineered biosynthetic pathway enzyme systems. The biomolecular engineering era is here, and many of benefits will be derived from this field of scientific research for years to come if we are willing to put it to good use.

Biomolecular engineering is a technology to create novel structures of high-value biomolecules for use in medicine and industry, through the directed alteration of proteins and/or biologically active molecules in living cells to produce a novel biometabolites as well as engineered protein itself. For the development of new drugs by biomolecular engineering, desired biomolecules have to be rationally designed based on their structure-stability/structure-activity relationship, and then screened through well-established mutation and selection program. Over the past decade, there has been significant progress in mutation and selection methodology; DNA shuffling technology mimicking natural evolution for artificial DNA recombination and phage-displayed combinatorial peptide library for rapid selection of proteins expressed from mutated genes. Bioinformatic tools including functional genomics and proteomics have been also developed for the ready access to the information related to the protein-function and genome-protein, leading to the design and identification of new drug targets. Throughout the use of an enormous amount of bioinformatic databases, many protein/peptide drugs and biometabolite molecules have been designed. The candidates of new drugs are monoclonal antibodies, vaccines, enzymes, antibiotics, therapeutic peptides, and so on. Two humanized monoclonal antibodies approved by FDA became the first line of drugs designed by biomolecular engineering approach. They are Herceptin and Synagis, for the treatment of breast cancer and pediatric respiratory syncytial viral infection, respectively. Many more newly engineered biomolecules are under developing for medicinal application. Some clinical trials for therapeutic applications are now in progress, and very positive results are already anticipated.

Genetically modified (GM) technique, one of the modern biomolecular engineering technologies, has been deemed as profitable strategy to fight against global starvation. Yet rapid and reliable analytical method is deficient to evaluate the quality and potential risk of such resulting GM products. We herein present a biomolecular analytical system constructed with distinct biochemical activities to expedite the computational detection of genetically modified organisms (GMOs). The computational mechanism provides an alternative to the complex procedures commonly involved in the screening of GMOs. Given that the bioanalytical system is capable of processing promoter, coding and species genes, affirmative interpretations succeed to identify specified GM event in terms of both electrochemical and optical fashions. The biomolecular computational assay exhibits detection capability of genetically modified DNA below sub-nanomolar level and is found interference-free by abundant coexistence of non-GM DNA. This bioanalytical system, furthermore, sophisticates in array fashion operating multiplex screening against variable GM events. Such a biomolecular computational assay and biosensor holds great promise for rapid, cost-effective, and high-fidelity screening of GMO.

Genetic and biomolecular engineering are two of the leading disciplines in biotechnology that have lead to great advancements in protein engineering. Applications of analytical bioluminescence, such as genetic reporter assays, optical in vivo imaging, and cell viability assays can often be improved by enhancing wild-type bioluminescent systems. The ability to rationally or randomly modify proteins has expanded their employment in various bioanalytical applications. Specifically, a wide range of bioluminescent proteins and photoproteins have been engineered that can be utilized in many detection and diagnostic applications. Herein, we focus on the improvements of two of the most commonly studied photoproteins, aequorin and obelin, and their uses in a variety of bioanalytical applications. Techniques such as random mutagenesis, site-directed mutagenesis, bioluminescence resonance energy transfer, and the incorporation of coelenterazine analogues are discussed as ways that have expanded the palette of these designer proteins by altering their emission wavelengths and/or half-lifes. Strategic amino acid substitutions and insertions have been also used to improve luciferase stability in high temperature, extreme pH, and harsh chemical environments, and to customize their kinetic properties and bioluminescence colors. As researchers advance engineering techniques to expand the array of photoproteins, luciferases from fireflies, click beetles, marine organisms and bacteria, their use in bioanalytical applications will continue to grow and it is envisioned that photoproteins and bioluminescent proteins will become as diverse as their fluorescence counterparts.

Natural selection has created optimal catalysts that exhibit their convincing performance even with a number of sometimes counteracting constraints. Optimal performance of enzyme catalysis does not refer necessarily to maximum reaction rate. Rather, it may involve a compromise between specificity, rate, stability, and other chemical constraints ; in some cases, it may involve aintelligento control of rate and specificity. Because enzymes are capable of catalyzing reactions under mild conditions and with high substrate specificity that often is accompanied by high regioand enantioselectivity, it is not surprising that a continually increasing number of industrial and academic reports concern the use of enzyme catalysts in chemical synthesis as well as in biochemical and biomedical applications. However, the demands of modern synthesis and their commercial application were obviously not targeted during the natural evolution of enzymes. Considering a specific, nonnatural application, any property (or combination of properties) of an enzyme may therefore need to be improved. Of course, scientists desired to mimick nature's powerful concepts for tailoring specific enzymatic properties: Following pioneering experiments for evolving molecules in the test tube, evolutionary engineering of biomolecules was successfully realized with first selections of functional nucleic acids (ribozymes) by using the SELEX (systematic evolution of ligands by exponential enrichment with integrated optimization by non-linear analysis) procedure, 8] and with the development of high-affinity ligands (aptamers) by using similar techniques. Meanwhile, evolutionary engineering, also termed adirected evolutiono, has emerged as a key technology for biomolecular engineering and generated impressive results in the functional adaptation of enzymes to artificial environments. Certainly, evolution in the laboratory does not come to a halt at the optimization of single genes and proteins. Recent results excitingly demonstrate the success of amolecular breedingo of metabolic pathways, and even of complete genomes, and the end is not in sight yet. Directed evolution in the laboratory is highly attractive because its principles are simple and do not require detailed knowledge of structure, function, or mechanism. Essentially like natural evolution, directed evolution comprises the iterative implementation of (1) the generation of a alibraryo of mutated genes, (2) its functional expression, and (3) a sensitive assay to identify individuals showing the desired properties, either by selection or by screening (Figure 1). After each round, the genes of improved variants are deciphered and subsequently serve as parents for another round of optimization. This review covers the most important aspects of directed evolution and summarizes key solutions to problems of optimizing and understanding enzyme function.

Michael J. McLachlan, Ryan P. Sullivan and Huimin Zhao Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA Departments of Chemical and Biomolecular Engineering, and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA

Artificial chemistries are candidates for methodologies that model and design biochemical systems. If artificial chemistries can deal with such systems in beneficial ways, they may facilitate activities in the new area of biomolecular engineering. In order to explore such possibilities, we illustrate four models of biochemical pathways described in our artificial chemistry based on string pattern matching and recombination. The modeled pathways are the replication of DNA, transcription from DNA to mRNA, translation from mRNA to protein, and the oxidation of fatty acids. The descriptions show that the present approach has good modularity and scalability that will be useful for modeling a huge network of pathways. Moreover, we give a procedure to perform reasoning in the artificial chemistry, which checks whether a specified collection of molecules can be generated in a given model, and we demonstrate that it works on a model that describes a natural biochemical pathway.

Biomolecular engineering has many applications in the identification of potentially therapeutic compounds. An important class of these compounds is those that bind and modulate the activity of the human nuclear hormone receptors (NHRs). NHRs are typically made up of clearly defined domains with known function, including one that mediates ligand recognition and NHR activation. Engineered systems that include these ligand-binding domains (LBDs) can be used to identify potential therapeutic ligands that target a given NHR. These methods must couple the binding event to a readily detectable signal, ideally in a high-throughput format. Recent efforts have delivered a variety of new techniques, including those that involve fusions of LBDs to easily assayed reporter proteins. In some cases these systems allow hormone-dependent selectable phenotypes to be generated in non-native hosts, providing potential tools for both isolation and evolution of new therapeutics in vivo. Here we provide an overview and a comparison of many of the available tools in this area, with an emphasis on a novel allosteric hormone-regulated sensor protein that provides ligand-dependent phenotypes in the relatively simple background of Escherichia coli bacterial cells.

With the breakthroughs in biomolecular engineering and synthetic biology, many valuable biologically active compound and commodity chemicals have been successfully manufactured using cell-based approaches in the past decade. However, because of the high complexity of cell metabolism, the identification and optimization of rate-limiting metabolic pathways for improving the product yield is often difficult, which represents a significant and unavoidable barrier of traditional in vivo metabolic engineering. Recently, some in vitro engineering approaches were proposed as alternative strategies to solve this problem. In brief, by reconstituting a biosynthetic pathway in a cell-free environment with the supplement of cofactors and substrates, the performance of each biosynthetic pathway could be evaluated and optimized systematically. Several value-added products, including chemicals, nutraceuticals, and drug precursors, have been biosynthesized as proof-of-concept demonstrations of in vitro metabolic engineering. This mini-review summarizes the recent progresses on the emerging topic of in vitro metabolic engineering and comments on the potential application of cell-free technology to speed up the “design-build-test” cycles of biomanufacturing.

Cell factories have been largely exploited for the controlled production of substances of interest for food, pharma and biotech industries. Although human-controlled microbial production and transformation are much older, the cell factory concept was fully established in the 80’s through the intensive public and private investment. Strongly empowered by the then nascent recombinant DNA technologies and supported by the approval of recombinant insulin [1,2], the principle of controlled biological production as a convenient source of difficult-to-obtain molecules (especially those of high added value) deeply penetrated the industrial tissue, soon becoming a widespread platform aiming at cost-effective large-scale production [3]. The first generation cell factories (mainly composed by plain strains of the bacterium Escherichia coli and the yeast Saccharomyces cerevisae) were soon replaced by engineered variants. Resulting from the application of untargeted mutagenesis and phenotypic selection, conventional genetic modification, metabolic engineering, and more recently by systems metabolic engineering that integrates metabolic engineering with systems biology and synthetic biology, new strains having much enhanced performance have been progressively developed [4-19]. In parallel, mammalian and insect cells for the production of high quality proteins, and other microbial species appealing from an industrial point of view due to their unusual physiological traits, have been incorporated to the cell factory family [20,21]. This comprises algae, fungi, psychrophilic bacteria and moss, among others [22-26]. On the other hand, a set of food-grade lactic acid bacteria are under development as emerging platforms in food microbiology but also as a novel source of metabolites and proteins [27-34]. The physiological diversity of the microbial world offers an intricacy of biosynthetic pathways from which novel bio-products, including nano- or micro-structured materials [35-37], offer promises in even more diverse applications. Still, many substances and materials of industrial interest are nowadays produced by chemical synthesis, and the number of (recombinant) proteins approved for therapeutic use hardly reaches 200, a figure much lower than that initially presumed. However, both environmental concerns and medical and industrial needs strongly push towards a fully sustainable bio-production of a larger spectrum of substances. Then, how much limited is the economic feasibility of microbial production? Have the cell factories reached a plateau in their development? Is there more room for further exploitation of the microbial production? Systems metabolic engineering [38,39] offers a set of methodological and strategic tools for the design and optimization of metabolic and gene regulatory networks for the efficient production of chemicals (from pharmaceuticals to bulk chemicals and fuels) and materials (from plastics to high value materials) [5-7,40]. Furthermore, creation of new metabolic pathways and fine tuning of the existing ones have become possible [8,15]. This is already allowing the production of substances so far reluctant to microbial production under industrial requirements and under cost-effective processes, allowing us to overcome limitations of microbial cell factories. In silico genome-scale metabolic modeling and simulation are playing increasingly important roles in system-wide identification of target genes and pathways to be manipulated to enhance production of desired products. Profiling of transcriptome, proteome, metabolome, and/or fluxome is also becoming a routine practice in metabolic engineering for the better understanding of cellular characteristics under given genetic and/or environmental perturbations. Through the system-wide optimized design and development of microbial cell factories, many industrially important chemicals and materials could be efficiently produced. Some example products include, but not limited to, alcohols other than ethanol including propanol, butanol and isobutanol, dicarboxylic acids such as succinic acid, fumaric acid, malic acid and adipic acid, diols such as 1,3-propanediol, 1,2-propanediol, 1,4-butanediol and 2,3-butanediol, diamines such as putrescine and cadaverine, and even polymers including polyhydroxyalkanoates, polylactic acid, spider silk protein, poly-gamma-glutamic acid, and many others [40]. It is expected that increasingly diverse chemicals and materials that are currently produced by petrochemical industry will be produced by employing microbial cell factories. Improving cell factories by systems biotechnology to an industrially relevant level cannot be successfully reached by individual teams alone. A wide range of expertise is needed for the full development of a novel biotechnological process, including microbiology, chemistry, bioinformatics, biochemical engineering, but also agricultural and plant sciences and economics. After a proof of concept has shown the feasibility of a novel approach for cell factory engineering, large consortia or networks of fully skilled teams should take over in collaboration with Biotech companies to accomplish an economically feasible bioprocess. As an early example, the development of bacteria producing 1,3-propanediol from glucose has been well documented, and required the engineering of more than 70 genes, before process development and scale up were reasonably made [41]. Replacing materials which are produced from mineral oil by biobased products requires not only efficient technology but also the assessment of economical and ecological feasibility, as intensely studied for polylactic acid [42]. As the progress of industrial biotechnology did not accomplish the desired speed of development [43] academic researchers have teamed up with industry in publicly funded research centers worldwide. To name a few, the Joint BioEnergy Institute (JBEI) in the San Francisco Bay Area, the Novo Nordisk Foundation Center for Biosustainability (CFB) at the Technical University of Denmark, the Metabolic and Biomolecular Engineering Laboratory (MBEL) of the Korea Advanced Institute of Science and Technology (KAIST), the Dutch Klyuver Centre for Genomics of Industrial Fermentation, or the Austrian Centre of Industrial Biotechnology (ACIB) share the mission to speed up development of industrial bioprocesses by joining forces of different academic disciplines with industrial collaborators.

Rational design and engineering of membrane active peptides remains a largely unsatisfied goal. We have hypothesized that this us due, in part, to the fact that some membrane activities, such as permeabilization, and cell penetrating ability are not dependent on specific amino acid sequences or specific three-dimensional peptide structures. Instead they depend on interfacial activity; the ability of a molecule to partition into in the membrane-water interface and to strain the packing and organization of lipids. We are testing that idea by taking a novel approach to biomolecular engineering and design of membrane-active peptides. Several rational combinatorial peptide libraries containing 10-16,000 members have been screened for water soluble members that either permeabilize phospholipid membranes or translocate without permeabilization. Stringent, two-phase, high-throughput screens were used to identify dozens of unique peptides that had potent membrane permeabilizing activity or cell penetrating activity, but were also highly water soluble. These rare and uniquely active peptides did not always share a particular sequence motif, peptide length or net charge, but always share common compositional features, secondary structure and core hydrophobicity. We suggest that they function by common mechanisms that depends mostly on interfacial activity. We demonstrate here that composition-space peptide libraries coupled with function-based high-throughput screens can lead to the discovery of diverse, soluble, and highly potent interfacially active peptides.