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Classical hydrogen bonds have, for many decades, been the dominant non‐covalent interaction in the toolbox that chemists and chemical engineers have used to design and control the structures of compounds and molecular assemblies as novel materials. Recently, a set of non‐classical non‐covalent (NC−NC) interactions have emerged that exploit the properties of the Group IV, V, VI, and VII elements of the periodic table (the tetrel, pnictogen, chalcogen, and halogen bonds, respectively). Our research group has been characterizing the prevalence, geometric constraints, and structure‐function relationship specifically of the halogen bond in biological systems. We have been particularly interested in exploiting the biological halogen bonds (or BXBs) to control the structures, stabilities, and activities of biomolecules, including the DNA Holliday junction and enzymes. In this review, we first provide a set of criteria for how to determine whether BXBs or any other NC−NC interactions would have biological relevance. We then navigate the trail of studies that had led us from an initial, very biological question to our current point in the journey to establish BXBs as a tool for biomolecular engineering. Finally, we close with a perspective on future directions for this line of research. [ABSTRACT FROM AUTHOR]

The majority of clinically approved therapeutics target membrane proteins (MPs), highlighting the need for tools to study this important category of proteins. To overcome limitations with recombinant MP expression, whole cell screening techniques have been developed that present MPs in their native conformations. Whereas many such platforms utilize adherent cells, here we introduce a novel suspension cell‐based platform termed "biofloating" that enables quantitative analysis of interactions between proteins displayed on yeast and MPs expressed on mammalian cells, without need for genetic fusions. We characterize and optimize biofloating and illustrate its sensitivity advantage compared to an adherent cell‐based platform (biopanning). We further demonstrate the utility of suspension cell‐based approaches by iterating rounds of magnetic‐activated cell sorting selections against MP‐expressing mammalian cells to enrich for a specific binder within a yeast‐displayed antibody library. Overall, biofloating represents a promising new technology that can be readily integrated into protein discovery and development workflows. [ABSTRACT FROM AUTHOR]

Glucose solutions are commonly heated before use in medical and biotech applications to maintain cleanliness, however the resulting degradants can be toxic. This study examines two approaches to evaluating the heat degradants resulting from holding a 40% glucose solution at 55°C for 5 weeks: first, chemical changes to the solution were identified and quantified via analytical testing, and second the toxicity of the heat‐degraded 40% glucose solution was evaluated empirically by using it as a feed stock for a fed‐batch CHO‐cell‐based protein therapeutic manufacturing process. Colorimetric analysis quantified a color change during heating, and liquid chromatography assays measured an increase in the concentrations of two unknown degradants along with the commonly identified glucose impurity 5‐hydroxymethylfurfural (5‐HMF). Solution pH decreased over time, corresponding with an increase in formic acid concentration as measured via GC–MS. Despite this, cell culture toxicity was not observed, and protein productivity and product quality were maintained. [ABSTRACT FROM AUTHOR]

Today's Biochemical Engineer may contribute to advances in a wide range of technical areas. The recent Biochemical and Molecular Engineering XXI conference focused on "The Next Generation of Biochemical and Molecular Engineering: The role of emerging technologies in tomorrow's products and processes". On the basis of topical discussions at this conference, this perspective synthesizes one vision on where investment in research areas is needed for biotechnology to continue contributing to some of the world's grand challenges. [ABSTRACT FROM AUTHOR]

Keywords: biomolecular engineering; early detection; molecular biomedicine; molecular diagnosis; prognosis EN biomolecular engineering early detection molecular biomedicine molecular diagnosis prognosis 1 4 4 05/27/20 20200601 NES 200601 Introduction For the past nine years, Royan Institute (Tehran, Iran) has held annual international summer schools to educate and promote key basic and applied concepts regarding stem cells, cancer, personalized medicine, tissue engineering, and developmental biology. The speakers discussed genome-editing technologies, gene- and RNA interference (RNAi) therapies, cancer vaccines, and molecular diagnosis via biomarkers and biosensors. Overall, the summer school highlighted how combination of molecular diagnosis and molecular therapy can provide higher success rates in disease treatment in the near future. Viral and Non-Viral Gene Therapy Piter Bosma explained that gene therapy, that is, delivering genetic material to treat diseases, is accomplished through non-viral or viral delivery systems. [Extracted from the article]

The recent recognition that halogen bonding (XB) plays important roles in the recognition and assembly of biological molecules has led to new approaches in medicinal chemistry and biomolecular engineering. When designing XBs into strategies for rational drug design or into a biomolecule to affect its structure and function, we must consider the relationship between this interaction and the more ubiquitous hydrogen bond (HB). In this review, we explore these relationships by asking whether and how XBs can replace, compete against or behave independently of HBs in various biological systems. The complex relationships between the two interactions inform us of the challenges we face in fully utilizing XBs to control the affinity and recognition of inhibitors against their therapeutic targets, and to control the structure and function of proteins, nucleic acids and other biomolecular scaffolds. [ABSTRACT FROM AUTHOR]

ABSTRACT The N-acylhomoserine lactone (AHL) receptor SpnR is a LuxR family protein that acts as a negative regulator of AHL-dependent quorum sensing (QS). SpnR binds to DNA in Serratia marcescens AS-1 via the spn box; however, the binding affinity of SpnR with the nucleotides on the spn box has not yet been investigated. In this study, we used an spn-box-modified sensor electrode, and quartz crystal microbalance analysis demonstrated a drastic reduction of the uptake of SpnR. The nucleotides G5 and C16 at the AHL-receptor complex-binding site are conserved in Gram-negative bacteria, including the lux box in Vibrio fischeri, the tra box in Agrobacterium tumefaciens, and the spn box in S. marcescens. Indeed, the affinity of SpnR to DNA was reduced to 8% by G5C substitution of the spn box. The affinity of SpnR tagged with maltose-binding protein to the immobilized gene promoter was reduced in the order of C16G and G5C substitutions, which corresponded with previous reports on the lux box. These results suggest that formation of hydrogen bonds at amino acid residues containing guanine at position 5 on a lux-box-like promoter universally contributes to the stability of the receptor complex, whose interaction initiates a sequential QS process in the LuxR family. Biotechnol. Bioeng. 2016;113: 2513-2517. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Engineering materials using supramolecular principles enables generalizable and modular platforms that have tunable chemical, mechanical, and biological properties. Applying this bottom-up, molecular engineering-based approach to therapeutic design affords unmatched control of emergent properties and functionalities. In preparing responsive materials for biomedical applications, the dynamic character of typical supramolecular interactions facilitates systems that can more rapidly sense and respond to specific stimuli through a fundamental change in material properties or characteristics, as compared to cases where covalent bonds must be overcome. Several supramolecular motifs have been evaluated toward the preparation of 'smart' materials capable of sensing and responding to stimuli. Triggers of interest in designing materials for therapeutic use include applied external fields, environmental changes, biological actuators, applied mechanical loading, and modulation of relative binding affinities. In addition, multistimuli-responsive routes can be realized that capture combinations of triggers for increased functionality. In sum, supramolecular engineering offers a highly functional strategy to prepare responsive materials. Future development and refinement of these approaches will improve precision in material formation and responsiveness, seek dynamic reciprocity in interactions with living biological systems, and improve spatiotemporal sensing of disease for better therapeutic deployment. [ABSTRACT FROM AUTHOR]

Collagen-based biomedical materials have developed into important, clinically effective materials used in a range of devices that have gained wide acceptance. These devices come with collagen in various formats, including those based on stabilized natural tissues, those that are based on extracted and purified collagens, and designed composite, biosynthetic materials. Further knowledge on the structure and function of collagens has led to on-going developments and improvements. Among these developments has been the production of recombinant collagen materials that are well defined and are disease free. Most recently, a group of bacterial, non-animal collagens has emerged that may provide an excellent, novel source of collagen for use in biomaterials and other applications. These newer collagens are discussed in detail. They can be modified to direct their function, and they can be fabricated into various formats, including films and sponges, while solutions can also be adapted for use in surface coating technologies. © 2015 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 104B: 665-675, 2016. [ABSTRACT FROM AUTHOR]

ABSTRACT Modularization of a peptide antigen for presentation on a microbially synthesized murine polyomavirus (MuPyV) virus-like particle (VLP) offers a new alternative for rapid and low-cost vaccine delivery at a global scale. In this approach, heterologous modules containing peptide antigenic elements are fused to and displayed on the VLP carrier, allowing enhancement of peptide immunogenicity via ordered and densely repeated presentation of the modules. This study addresses two key engineering questions pertaining to this platform, exploring the effects of (i) pre-existing carrier-specific immunity on modular VLP vaccine effectiveness and (ii) increase in the antigenic element number per VLP on peptide-specific immune response. These effects were studied in a mouse model and with modular MuPyV VLPs presenting a group A streptococcus (GAS) peptide antigen, J8i. The data presented here demonstrate that immunization with a modular VLP could induce high levels of J8i-specific antibodies despite a strong pre-existing anti-carrier immune response. Doubling of the J8i antigenic element number per VLP did not enhance J8i immunogenicity at a constant peptide dose. However, the strategy, when used in conjunction with increased VLP dose, could effectively increase the peptide dose up to 10-fold, leading to a significantly higher J8i-specific antibody titer. This study further supports feasibility of the MuPyV modular VLP vaccine platform by showing that, in the absence of adjuvant, modularized GAS antigenic peptide at a dose as low as 150 ng was sufficient to raise a high level of peptide-specific IgGs indicative of bactericidal activity. Biotechnol. Bioeng. 2013; 110:2343-2351. © 2013 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Translation of nanotherapeutics from preclinical research to clinical application is difficult due to the complex and dynamic interaction space between the nanotherapeutic and the brain environment. To improve translation, increased insight into nanoformulation-brain interactions in preclinical research is necessary. We developed a nanoformulation-brain database and wrote queries to connect the complex physical, chemical, and biological features of neurotherapeutics based on experimental data. We queried the database to select nanoformulations based on specific physical characteristics that enable effective penetration within the brain, including size, polydispersity index, and zeta potential. Additionally, we demonstrate the ability to query the database to return select nanoformulation characteristics, including nanoformulation methodology or methodological variables such as surfactant, polymer, drug loading, and sonication times. Finally, we show the capacity of our database to produce correlations relating nanoparticle formulation parameters to biological outcomes, including nanotherapeutic impact on cell viability in cultured brain slices.

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., Competing Interests: Declaration of Interests JJG is an unpaid board member of the Rosetta Commons. Under institutional participation agreements between the University of Washington, acting on behalf of the Rosetta Commons, Johns Hopkins University may be entitled to a portion of revenue received on licensing Rosetta software including programs described here. As a member of the Scientific Advisory Board of Cyrus Biotechnology, JJG is granted stock options. Cyrus Biotechnology distributes the Rosetta software, which may include methods described in this article.

Many cell behaviors are significantly affected by cell culture geometry, though it remains unclear which geometry from two- to three-dimensional (2D to 3D) culture is appropriate for probing a specific cell function and mimicking native microenvironments. Toward addressing this, we established a 2.5D culture geometry, enabling initial cell spreading while reducing polarization to bridge between 2D and 3D geometries, and examined the responses of wound healing cells, human pulmonary fibroblasts, within it. To achieve this, we used engineered biomimetic hydrogels formed by photopolymerization, creating robust layered hydrogels with spread fibroblasts at the interface. We found that fibroblast responses were similar between 2D and 2.5D culture and different from 3D culture, with some underlying differences in mechanotransduction. These studies established the 2.5D cell culture geometry in conjunction with biomimetic synthetic matrices as a useful tool for investigations of fibroblast activation with relevance to the study of other cell functions and types., Competing Interests: Conflicts of interest The authors have no conflicts of interest to declare.

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.

The combination of cell culture models with microscale technology has fostered emergence of in vitro cell-based microphysiological models, also known as organ-on-a-chip systems. Body-on-a-chip systems, which are multi-organ systems on a chip to mimic physiological relations, enable recapitulation of organ-organ interactions and potentially whole-body response to drugs, as well as serve as models of diseases. Chemical reaction engineering principles can be applied to understanding complex reactions inside the cell or human body, which can be treated as a multi-reactor system. These systems use physiologically-based pharmacokinetic (PBPK) models to guide the development of microscale systems of the body where organs or tissues are represented by living cells or tissues, and integrated into body-on-a-chip systems. Here, we provide a brief overview on the concept of chemical reaction engineering and how its principles can be applied to understanding and predicting the behavior of body-on-a-chip systems.