Three-in-one chromatography-free purification, tag removal, and site-specific modification of recombinant fusion proteins using sortase A and elastin-like polypeptides

Enzyme purification and sustained enzyme activity for pharmaceutical biocatalysis by fusion with phase-separating intrinsically disordered protein

In recent decades, biocatalysis has emerged as an important alternative to chemical catalysis in pharmaceutical manufacturing. Biocatalysis is attractive because enzymatic cascades can synthesize complex molecules with incredible selectivity, yield, and in an environmentally benign manner. Enzymes for pharmaceutical biocatalysis are typically used in their unpurified state, since it is time-consuming and cost-prohibitive to purify enzymes using conventional chromatographic processes at scale. However, impurities present in crude enzyme preparations can consume substrate, generate unwanted byproducts, as well as make the isolation of desired products more cumbersome. Hence, a facile, nonchromatographic purification method would greatly benefit pharmaceutical biocatalysis. To address this issue, here we have captured enzymes into membraneless compartments by fusing enzymes with an intrinsically disordered protein region, the RGG domain from LAF-1. The RGG domain can undergo liquid-liquid phase separation, forming liquid condensates triggered by changes in temperature or salt concentration. By centrifuging these liquid condensates, we have successfully purified enzyme-RGG fusions, resulting in significantly enhanced purity compared to cell lysate. Furthermore, we performed enzymatic reactions utilizing purified fusion proteins to assay enzyme activity. Results from the enzyme assays indicate that enzyme-RGG fusions purified by the centrifugation method retain enzymatic activity, with greatly reduced background activity compared to crude enzyme preparations. Our work focused on three different enzymes-a kinase, a phosphorylase, and an ATP-dependent ligase. The kinase and phosphorylase are components of the biocatalytic cascade for manufacturing molnupiravir, and we demonstrated facile co-purification of these two enzymes by co-phase separation. To conclude, enzyme capture by RGG tagging promises to overcome difficulties in bioseparations and biocatalysis for pharmaceutical synthesis.

Transcription-Factor-Induced Aggregation of Biomimetic Oligonucleotide-b-Protein Micelles

Polymeric micelles and especially those based on natural diblocks are of particular interest due to their advantageous properties in terms of molecular recognition, biocompatibility, and biodegradability. We herein report a facile and straightforward synthesis of thermoresponsive elastin-like polypeptide (ELP) and oligonucleotide (ON) diblock bioconjugates, ON-b-ELP, through copper-catalyzed azide-alkyne cycloaddition. The resulting thermosensitive diblock copolymer self-assembles above its critical micelle temperature (CMT ∼30 °C) to form colloidally stable micelles of ∼50 nm diameter. The ON-b-ELP micelles hybridize with an ON complementary strand and maintain their size and stability. Next, we describe the capacity of these micelles to bind proteins, creating more complex structures using the classic biotin-streptavidin pairing and the specific recognition between a transcription factor protein and the ON strand. In both instances, the micelles are intact, form larger structures, and retain their sensitivity to temperature.

Emerging opportunities in bioconjugates of Elastin-like polypeptides with synthetic or natural polymers

Nature is an everlasting source of inspiration for chemical and polymer scientists seeking to develop ever more innovative materials with greater performances. Natural structural proteins are particularly scrutinized to design biomimetic materials. Often characterized by repeat peptide sequences, that together interact by inter- and intramolecular interactions and form a 3D skeleton, they contribute to the mechanical properties of individual cells, tissues, organs, and whole organisms. (Numata, K. Polymer Journal 2020, 52, 1043-1056) Among them elastin, and its main repeat sequences, have been a source of intense studies for more than 50 years resulting in the specific research field dedicated to elastin-like polypeptides (ELPs). These are currently widely investigated in different applications, namely protein purification, tissue engineering, and drug delivery, and some technologies based on ELPs are currently explored by several start-up companies. In the present review, we have summarized pioneering contributions on ELPs, progress made in their genetic engineering, and understanding of their thermal behavior and self-assembly properties. Considered as intrinsically disordered protein polymers, we have finally focused on the works where ELPs have been conjugated to other synthetic macromolecules as covalent hybrid, statistical, graft, or block copolymers, highlighting the huge opportunities that have still not been explored so far.

A guide to designing photocontrol in proteins: methods, strategies and applications

Light is essential for various biochemical processes in all domains of life. In its presence certain proteins inside a cell are excited, which either stimulates or inhibits subsequent cellular processes. The artificial photocontrol of specifically proteins is of growing interest for the investigation of scientific questions on the organismal, cellular and molecular level as well as for the development of medicinal drugs or biocatalytic tools. For the targeted design of photocontrol in proteins, three major methods have been developed over the last decades, which employ either chemical engineering of small-molecule photosensitive effectors (photopharmacology), incorporation of photoactive non-canonical amino acids by genetic code expansion (photoxenoprotein engineering), or fusion with photoreactive biological modules (hybrid protein optogenetics). This review compares the different methods as well as their strategies and current applications for the light-regulation of proteins and provides background information useful for the implementation of each technique.

Protein Phase Separation Arising from Intrinsic Disorder: First-Principles to Bespoke Applications

The phase separation of biomolecules has become the focus of intense research in the past decade, with a growing body of research implicating this phenomenon in essentially all biological functions, including but not limited to homeostasis, stress responses, gene regulation, cell differentiation, and disease. Excellent reviews have been published previously on the underlying physical basis of liquid-liquid phase separation (LLPS) of biological molecules (Nat. Phys. 2015, 11, 899-904) and LLPS as it occurs natively in physiology and disease (Science 2017, 357, eaaf4382; Biochemistry 2018, 57, 2479-2487; Chem. Rev. 2014, 114, 6844-6879). Here, we review how the theoretical physical basis of LLPS has been used to better understand the behavior of biomolecules that undergo LLPS in natural systems and how this understanding has also led to the development of novel synthetic systems that exhibit biomolecular phase separation, and technologies that exploit these phenomena. In part 1 of this Review, we explore the theory behind the phase separation of biomolecules and synthetic macromolecules and introduce a few notable phase-separating biomolecules. In part 2, we cover experimental and computational methods used to study phase-separating proteins and how these techniques have uncovered the mechanisms underlying phase separation in physiology and disease. Finally, in part 3, we cover the development and applications of engineered phase-separating polypeptides, ranging from control of their self-assembly to create defined supramolecular architectures to reprogramming biological processes using engineered IDPs that exhibit LLPS.

Short intrinsically disordered polypeptide-oligonucleotide conjugates for programmed self-assembly of nanospheres with temperature-dependent size controllability

A series of short intrinsically disordered polypeptide conjugated oligonucleotides (IDPOCs) were rationally developed and assembled into well-defined nanospheres. The nanospheres exhibited excellent reversible thermoresponsive regulation of their contraction and expansion. Furthermore, the nanospheres showed biocompatibility, drug encapsulation and effective cellular uptake.

Nanoscopic Dynamics Dictate the Phase Separation Behavior of Intrinsically Disordered Proteins

Many intrinsically disordered proteins (IDPs) in nature may undergo liquid-liquid phase separation to assemble membraneless organelles with varied liquid-like properties and stability/dynamics. While solubility changes underlie these properties, little is known about hydration dynamics in phase-separating IDPs. Here, by studying IDP polymers of similar composition but distinct liquid-like dynamics and stability upon separation, namely, thermal hysteresis, we probe at a nanoscopic level hydration/dehydration dynamics in IDPs as they reversibly switch between phase separation states. Using continuous-wave electron paramagnetic resonance (CW EPR) spectroscopy, we observe distinct backbone and amino acid side-chain hydration dynamics in these IDPs. This nanoscopic view reveals that side-chain rehydration creates a dynamic water shield around the main-chain backbone that effectively and counterintuitively prevents water penetration and governs IDP solubility. We find that the strength of this superficial water shell is a sequence feature of IDPs that encodes for the stability of their phase-separated assemblies. Our findings expose and offer an initial understanding of how the complexity of nanoscopic water-IDP interactions dictate their rich phase separation behavior.

Elastin-Like Polypeptides for Biomedical Applications

Elastin-like polypeptides (ELPs) are stimulus-responsive biopolymers derived from human elastin. Their unique properties—including lower critical solution temperature phase behavior and minimal immunogenicity—make them attractive materials for a variety of biomedical applications. ELPs also benefit from recombinant synthesis and genetically encoded design; these enable control over the molecular weight and precise incorporation of peptides and pharmacological agents into the sequence. Because their size and sequence are defined, ELPs benefit from exquisite control over their structure and function, qualities that cannot be matched by synthetic polymers. As such, ELPs have been engineered to assemble into unique architectures and display bioactive agents for a variety of applications. This review discusses the design and representative biomedical applications of ELPs, focusing primarily on their use in tissue engineering and drug delivery.

Non-chromatographic purification of thermostable endoglucanase from Thermotoga maritima by fusion with a hydrophobic elastin-like polypeptide

Endoglucanase EG12B from Thermotoga maritima is a thermophilic cellulase that has great potential for industrial applications. Here, to enable the selective purification of EG12B in a simple and efficient manner, an elastin-like polypeptide (ELP), which acts as a thermally responsive polypeptide, was fused with EG12B to enable its inverse phase transition cycling (ITC). A small gene library comprising ELPs from ELP₅ to ELP₅₀ was constructed using recursive directional ligation by plasmid reconstruction. ELP₅₀ was added to the C-terminus of EG12B as a fusion tag to obtain the expression vector pET28-EG12B-ELP₅₀, which was transformed into Escherichia coli BL21 (DE3) to enable the expression of fusion protein via IPTG induction. Gray scanning analysis revealed that the EG12B-ELP₅₀ expression level was up to about 35% of the total cellular proteins. After three rounds of ITC, 8.14 mg of EG12B-ELP₅₀ was obtained from 500-mL lysogeny broth culture medium. The recovery rate and purification fold of EG12B-ELP₅₀ purified by ITC reached 78.1% and 11.8, respectively. The cellulase activity assay showed that EG12B-ELP₅₀ had a better thermostability, higher optimal temperature, and longer half-life than those of free EG12B. Overall, our results suggested that ELP₅₀ could be used as a favorable fusion tag, providing a rapid, simple, and inexpensive strategy for non-chromatographic target-protein purification.

Natural Occurring and Engineered Enzymes for Peptide Ligation and Cyclization

The renaissance of peptides as prospective therapeutics has fostered the development of novel strategies for their synthesis and modification. In this context, besides the development of new chemical peptide ligation approaches, especially the use of enzymes as a versatile tool has gained increased attention. Nowadays, due to their inherent properties such as excellent regio- and chemoselectivity, enzymes represent invaluable instruments in both academic and industrial laboratories. This mini-review focuses on natural- and engineered peptide ligases that can form a new peptide (amide) bond between the C-terminal carboxy and N-terminal amino group of a peptide and/or protein. The pro's and cons of several enzyme classes such as Sortases, Asparaginyl Endoproteases, Trypsin related enzymes and as a central focus subtilisin-derived variants are summarized. Most recent developments with regards to ligation and cyclization are highlighted.

Using Tools from Optogenetics to Create Light-Responsive Biomaterials: LOVTRAP-PEG Hydrogels for Dynamic Peptide Immobilization

Hydrogel materials have become a versatile platform for in vitro cell culture due to their ability to simulate many aspects of native tissues. However, precise spatiotemporal presentation of peptides and other biomolecules has remained challenging. Here we report the use of light-sensing proteins (LSPs), more commonly used in optogenetics research, as light-activated reversible binding sites within synthetic poly(ethylene glycol) (PEG) hydrogels. We used LOVTRAP, a two component LSP system consisting of LOV2, a protein domain that can cycle reversibly between "light" and "dark" conformations in response to blue light, and a z-affibody, Zdark (Zdk), that binds the dark state of LOV2, to spatiotemporally control the presentation of a recombinant protein within PEG hydrogels. By immobilizing LOV2 within PEG gels, we were able to capture a recombinant fluorescent protein (used as a model biomolecule) containing a Zdk domain, and then release the Zdk fusion protein using blue light. Zdk was removed from LOV2-containing PEG gels using focused blue light, resulting in a 30% reduction of fluorescence compared to unexposed regions of the gel. Additionally, the reversible binding capability of LOVTRAP was observed in our system, enabling our LOV2 gels to capture and release Zdk at least three times. By adding a Zdk domain to a recombinant peptide or protein, dynamic, spatially constrained displays of non-diffusing ligands within a PEG gel could feasibly be achieved using LOV2.

Broadening the scope of sortagging

Sortases are enzymes occurring in the cell wall of Gram-positive bacteria. Sortase A (SrtA), the best studied sortase class, plays a key role in anchoring surface proteins with the recognition sequence LPXTG covalently to oligoglycine units of the bacterial cell wall. This unique transpeptidase activity renders SrtA attractive for various purposes and motivated researchers to study multiple in vivo and in vitro ligations in the last decades. This ligation technique is known as sortase-mediated ligation (SML) or sortagging and developed to a frequently used method in basic research. The advantages are manifold: extremely high substrate specificity, simple access to substrates and enzyme, robust nature and easy handling of sortase A. In addition to the ligation of two proteins or peptides, early studies already included at least one artificial (peptide equipped) substrate into sortagging reactions - which demonstrates the versatility and broad applicability of SML. Thus, SML is not only a biology-related technique, but has found prominence as a major interdisciplinary research tool. In this review, we provide an overview about the use of sortase A in interdisciplinary research, mainly for protein modification, synthesis of protein-polymer conjugates and immobilization of proteins on surfaces.

Recent progress in enzymatic protein labelling techniques and their applications

Protein-based conjugates are valuable constructs for a variety of applications. Conjugation of proteins to fluorophores is commonly used to study their cellular localization and the protein-protein interactions. Modification of therapeutic proteins with either polymers or cytotoxic moieties greatly enhances their pharmacokinetics or potency. To label a protein of interest, conventional direct chemical reaction with the side-chains of native amino acids often yields heterogeneously modified products. This renders their characterization complicated, requires difficult separation steps and may impact protein function. Although modification can also be achieved via the insertion of unnatural amino acids bearing bioorthogonal functional groups, these methods can have lower protein expression yields, limiting large scale production. As a site-specific modification method, enzymatic protein labelling is highly efficient and robust under mild reaction conditions. Significant progress has been made over the last five years in modifying proteins using enzymatic methods for numerous applications, including the creation of clinically relevant conjugates with polymers, cytotoxins or imaging agents, fluorescent or affinity probes to study complex protein interaction networks, and protein-linked materials for biosensing. This review summarizes developments in enzymatic protein labelling over the last five years for a panel of ten enzymes, including sortase A, subtiligase, microbial transglutaminase, farnesyltransferase, N-myristoyltransferase, phosphopantetheinyl transferases, tubulin tyrosin ligase, lipoic acid ligase, biotin ligase and formylglycine generating enzyme.

Incorporation of macrophages into engineered skeletal muscle enables enhanced muscle regeneration

Adult skeletal muscle has a robust capacity for self-repair, owing to synergies between muscle satellite cells and the immune system. In vitro models of muscle self-repair would facilitate the basic understanding of muscle regeneration and the screening of therapies for muscle disease. Here, we show that the incorporation of macrophages into muscle tissues engineered from adult-rat myogenic cells enables near-complete structural and functional repair after cardiotoxic injury in vitro. First, we show that-in contrast with injured neonatal-derived engineered muscle-adult-derived engineered muscle fails to properly self-repair after injury, even when treated with pro-regenerative cytokines. We then show that rat bone-marrow-derived macrophages or human blood-derived macrophages resident within the in vitro engineered tissues stimulate muscle satellite cell-mediated myogenesis while significantly limiting myofibre apoptosis and degeneration. Moreover, bone-marrow-derived macrophages within engineered tissues implanted in a mouse dorsal window-chamber model augmented blood vessel ingrowth, cell survival, muscle regeneration and contractile function.

Bioorthogonal Elastin-like Polypeptide Scaffolds for Immunoassay Enhancement

Artificial multiprotein complexes are sought after reagents for biomolecular engineering. A current limiting factor is the paucity of molecular scaffolds which allow for site-specific multicomponent assembly. Here, we address this limitation by synthesizing bioorthogonal elastin-like polypeptide (ELP) scaffolds containing periodic noncanonical l-azidohomoalanine amino acids in the guest residue position. The nine azide ELP guest residues served as conjugation sites for site-specific modification with dibenzocyclooctyne (DBCO)-functionalized single-domain antibodies (SdAbs) through strain-promoted alkyne-azide cycloaddition (SPAAC). Sortase A and ybbR tags at the C- and N-termini of the ELP scaffold provided two additional sites for derivatization with small molecules and peptides by Sortase A and 4'-phosphopantetheinyl transferase (Sfp), respectively. These functional groups are chemically bioorthogonal, mutually compatible, and highly efficient, thereby enabling synthesis of multi-antibody ELP complexes in a one-pot reaction. We demonstrate application of this material for enhancing the performance of sandwich immunoassays of the recombinant protein mCherry. In undiluted human plasma, surfaces modified with multi-antibody ELP complexes showed between 2.3- and 14.3-fold improvement in sensitivity and ∼30-40% lower limits of detection as compared with nonspecifically adsorbed antibodies. Dual-labeled multi-antibody ELP complexes were further used for cytometric labeling and analysis of live eukaryotic cells. These results demonstrate how multiple antibodies complexed onto bioorthogonal protein-based polymers can be used to enhance immunospecific binding interactions through multivalency effects.

Sortase A: A Model for Transpeptidation and Its Biological Applications

Molecular biologists and chemists alike have long sought to modify proteins with substituents that cannot be installed by standard or even advanced genetic approaches. We here describe the use of transpeptidases to achieve these goals. Living systems encode a variety of transpeptidases and peptide ligases that allow for the enzyme-catalyzed formation of peptide bonds, and protein engineers have used directed evolution to enhance these enzymes for biological applications. We focus primarily on the transpeptidase sortase A, which has become popular over the past few years for its ability to perform a remarkably wide variety of protein modifications, both in vitro and in living cells.

Fusion of fibroblast growth factor 21 to a thermally responsive biopolymer forms an injectable depot with sustained anti-diabetic action

Fibroblast growth factor 21 (FGF21) is under investigation as a type 2 diabetes protein drug, but its efficacy is impeded by rapid in vivo clearance and by costly production methods. To improve the protein's therapeutic utility, we recombinantly expressed FGF21 as a fusion with an elastin-like polypeptide (ELP), a peptide polymer that exhibits reversible thermal phase behavior. Below a critical temperature, ELPs exist as miscible unimers, while above, they associate into a coacervate. The thermal responsiveness of ELPs is retained upon fusion to proteins, which has notable consequences for the production and in vivo delivery of FGF21. First, the ELP acts as a solubility enhancer during E. coli expression, yielding active fusion protein from the soluble cell lysate fraction and eliminating the protein refolding steps that are required for purification of FGF21 from inclusion bodies. Second, the ELP's phase transition behavior is exploited for facile chromatography-free purification of the ELP-FGF21 fusion. Third, the composition and molecular weight of the ELP are designed such that the ELP-FGF21 fusion undergoes a phase transition triggered solely by body heat, resulting in an immiscible viscous phase upon subcutaneous (s.c.) injection and thereby creating an injectable depot. Indeed, a single s.c. injection of ELP-FGF21 affords up to five days of sustained glycemic control in ob/ob mice. The ELP fusion partner massively streamlines production and purification of FGF21, while providing a controlled release method for delivery that reduces the frequency of injection, thereby enhancing the pharmacological properties of FGF21 as a protein drug to treat metabolic disease.

Sortase-Mediated Ligation of Purely Artificial Building Blocks

Sortase A (SrtA) from Staphylococcus aureus has been often used for ligating a protein with other natural or synthetic compounds in recent years. Here we show that SrtA-mediated ligation (SML) is universally applicable for the linkage of two purely artificial building blocks. Silica nanoparticles (NPs), poly(ethylene glycol) and poly(N-isopropyl acrylamide) are chosen as synthetic building blocks. As a proof of concept, NP–polymer, NP–NP, and polymer–polymer structures are formed by SrtA catalysis. Therefore, the building blocks are equipped with the recognition sequence needed for SrtA reaction—the conserved peptide LPETG—and a pentaglycine motif. The successful formation of the reaction products is shown by means of transmission electron microscopy (TEM), matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-ToF MS), and dynamic light scattering (DLS). The sortase catalyzed linkage of artificial building blocks sets the stage for the development of a new approach to link synthetic structures in cases where their synthesis by established chemical methods is complicated.

Enrichment of high affinity subclasses and glycoforms from serum-derived IgG using FcγRs as affinity ligands

As antibodies continue to gain predominance in drug discovery and development pipelines, efforts to control and optimize their activity in vivo have matured to incorporate sophisticated abilities to manipulate engagement of specific Fc binding partners. Such efforts to promote diverse functional outcomes include modulating IgG-Fc affinity for FcγRs to alternatively potentiate or reduce effector functions, such as antibody-dependent cellular cytotoxicity and phagocytosis. While a number of natural and engineered Fc features capable of eliciting variable effector functions have been demonstrated in vitro and in vivo, elucidation of these important functional relationships has taken significant effort through use of diverse genetic, cellular and enzymatic techniques. As an orthogonal approach, we demonstrate use of FcγR as chromatographic affinity ligands to enrich and therefore simultaneously identify favored binding species from a complex mixture of serum-derived pooled polycloncal human IgG, a load material that contains the natural repertoire of Fc variants and post-translational modifications. The FcγR-enriched IgG was characterized for subclass and glycoform composition and the impact of this bioseparation step on antibody activity was measured in cell-based effector function assays including Natural Killer cell activation and monocyte phagocytosis. This work demonstrates a tractable means to rapidly distinguish complex functional relationships between two or more interacting biological agents by leveraging affinity chromatography followed by secondary analysis with high-resolution biophysical and functional assays and emphasizes a platform capable of surveying diverse natural post-translational modifications that may not be easily produced with high purity or easily accessible with recombinant expression techniques.

Niclosamide-conjugated polypeptide nanoparticles inhibit Wnt signaling and colon cancer growth

Abnormal Wnt activity is a major mechanism responsible for many diseases, including cancer. Previously, we reported that the anthelmintic drug Niclosamide (NIC) inhibits Wnt/β-catenin signaling and suppresses colon cancer cell growth. Although the pharmacokinetic properties of NIC are appropriate for use as an anthelmintic agent, its low solubility, low bioavailability and low systemic exposure limit its usefulness in treating systemic diseases. To overcome these limitations, we conjugated NIC to recombinant chimeric polypeptides (CPs), and the CP-NIC conjugate spontaneously self-assembled into sub-100 nm near-monodisperse nanoparticles. CP-NIC nanoparticles delivered intravenously act as a pro-drug of NIC to dramatically increase exposure of NIC compared to dosing with free NIC. CP-NIC improved anti-tumor activity compared to NIC in a xenograft model of human colon cancer. Because NIC has multiple biological activities, CP-NIC could be used for treatment of multiple diseases, including cancer, bacterial and viral infection, type II diabetes, NASH and NAFLD.

From Composition to Cure: A Systems Engineering Approach to Anticancer Drug Carriers

The molecular complexity and heterogeneity of cancer has led to a persistent, and as yet unsolved, challenge to develop cures for this disease. The pharmaceutical industry focuses the bulk of its efforts on the development of new drugs, but an alternative approach is to improve the delivery of existing drugs with drug carriers that can manipulate when, where, and how a drug exerts its therapeutic effect. For the treatment of solid tumors, systemically delivered drug carriers face significant challenges that are imposed by the pathophysiological barriers that lie between their site of administration and their site of therapeutic action in the tumor. Furthermore, drug carriers face additional challenges in their translation from preclinical validation to clinical approval and adoption. Addressing this diverse network of challenges requires a systems engineering approach for the rational design of optimized carriers that have a realistic prospect for translation from the laboratory to the patient.

High-molecular-weight poly(Gly-Val-Gly-Val-Pro) synthesis through microwave irradiation

In this study, we synthesized a polypeptide from its pentapeptide unit using microwave irradiation. Effective methods for polypeptide synthesis from unit peptides have not been reported. Here, we used a key elastin peptide, H-GlyValGlyValPro-OH (GVGVP), as the monomer peptide. It is difficult to obtain poly(Gly-Val-Gly-Val-Pro) (poly(GVGVP)) from the pentapeptide unit of elastin, GVGVP, via polycondensation. Poly(GVGVP) prepared from genetically recombinant Escherichia coli is a well-known temperature-sensitive polypeptide, and this temperature sensitivity is known as the lower critical solution temperature. When microwave irradiation was performed in the presence of various additives, the pentapeptide (GVGVP) polycondensation reaction proceeded smoothly, resulting in a product with a high molecular weight in a relatively good yield. The reaction conditions, like microwave irradiation, coupling agents, and solvents, were optimized to increase the reaction efficiency. The product exhibited a molecular weight greater than Mr 7000. Further, the product could be synthesized on a gram scale. The synthesized polypeptide exhibited a temperature sensitivity that was similar to that of poly(GVGVP) prepared from genetically recombinant E. coli. Therefore, this technique offers a facile and quick approach to prepare polypeptides in large amounts. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Recent advances in sortase-catalyzed ligation methodology

The transpeptidation reaction catalyzed by bacterial sortases continues to see increasing use in the construction of novel protein derivatives. In addition to growth in the number of applications that rely on sortase, this field has also seen methodology improvements that enhance reaction performance and scope. In this opinion, we present an overview of key developments in the practice and implementation of sortase-based strategies, including applications relevant to structural biology. Topics include the use of engineered sortases to increase reaction rates, the use of redesigned acyl donors and acceptors to mitigate reaction reversibility, and strategies for expanding the range of substrates that are compatible with a sortase-based approach.

Looking at the carcinogenicity of human insulin analogues via the intrinsic disorder prism

Therapeutic insulin, in its native and biosynthetic forms as well as several currently available insulin analogues, continues to be the protein of most interest to researchers. From the time of its discovery to the development of modern insulin analogues, this important therapeutic protein has passed through several stages and product generations. Beside the well-known link between diabetes and cancer risk, the currently used therapeutic insulin analogues raised serious concerns due to their potential roles in cancer initiation and/or progression. It is possible that structural variations in some of the insulin analogues are responsible for the appearance of new oncogenic species with high binding affinity to the insulin-like growth factor 1 (IGF1) receptor. The question we are trying to answer in this work is: are there any specific features of the distribution of intrinsic disorder propensity within the amino acid sequences of insulin analogues that may provide an explanation for the carcinogenicity of the altered insulin protein?

Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-assembly in nature and in man-made material systems. Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level.

Engineering structure and function using thermoresponsive biopolymers

Self-assembly enables exquisite control at the smallest scale and generates order among macromolecular-building blocks that remain too small to be manipulated individually. Environmental cues, such as heating, can trigger the organization of these materials from individual molecules to multipartixcle assemblies with a variety of compositions and functions. Synthetic as well as biological polymers have been engineered for these purposes; however, biological strategies can offer unparalleled control over the composition of these macromolecular-building blocks. Biologic polymers are macromolecules composed of monomeric units that can be precisely tailored at the genetic level; furthermore, they can often utilize endogenous biodegradation pathways, which may enhance their potential clinical applications. DNA (nucleotides), polysaccharides (carbohydrates), and proteins (amino acids) have all been engineered to self-assemble into nanostructures in response to a change in temperature. This focus article reviews the growing body of literature exploring temperature-dependent nano-assembly of these biological macromolecules, summarizes some of their physical properties, and discusses future directions.

A noncanonical function of sortase enables site-specific conjugation of small molecules to lysine residues in proteins

We provide the first demonstration that isopeptide ligation, a noncanonical activity of the enzyme sortase A, can be used to modify recombinant proteins. This reaction was used in vitro to conjugate small molecules to a peptide, an engineered targeting protein, and a full-length monoclonal antibody with an exquisite level of control over the site of conjugation. Attachment to the protein substrate occurred exclusively through isopeptide bonds at a lysine ε-amino group within a specific amino acid sequence. This reaction allows more than one molecule to be site-specifically conjugated to a protein at internal sites, thereby overcoming significant limitations of the canonical native peptide ligation reaction catalyzed by sortase A. Our method provides a unique chemical ligation procedure that is orthogonal to existing methods, supplying a new method to site-specifically modify lysine residues that will be a valuable addition to the protein conjugation toolbox.

Flow-based enzymatic ligation by sortase A

Sortase-mediated ligation (sortagging) is a versatile, powerful strategy for protein modification. Because the sortase reaction reaches equilibrium, a large excess of polyglycine nucleophile is often employed to drive the reaction forward and suppress sortase-mediated side reactions. A flow-based sortagging platform employing immobilized sortase A within a microreactor was developed that permits efficient sortagging at low nucleophile concentrations. The platform was tested with several reaction partners and used to generate a protein bioconjugate inaccessible by solution-phase batch sortagging.

Applications of elastin-like polypeptides in drug delivery

Elastin-like polypeptides (ELPs) are biopolymers inspired by human elastin. Their lower critical solution temperature phase transition behavior and biocompatibility make them useful materials for stimulus-responsive applications in biological environments. Due to their genetically encoded design and recombinant synthesis, the sequence and size of ELPs can be exactly defined. These design parameters control the structure and function of the ELP with a precision that is unmatched by synthetic polymers. Due to these attributes, ELPs have been used extensively for drug delivery in a variety of different embodiments-as soluble macromolecular carriers, self-assembled nanoparticles, cross-linked microparticles, or thermally coacervated depots. These ELP systems have been used to deliver biologic therapeutics, radionuclides, and small molecule drugs to a variety of anatomical sites for the treatment of diseases including cancer, type 2 diabetes, osteoarthritis, and neuroinflammation.

Sortagging: a robust and efficient chemoenzymatic ligation strategy

Bioorthogonal, chemoselective ligation methods are an essential part of the tools utilized to investigate biochemical pathways. Specifically enzymatic approaches are valuable methods in this context due to the inherent specificity of the deployed enzymes and the mild conditions of the modification reactions. One of the most common strategies is based on the transpeptidation catalyzed by sortase A derived from Staphylococcus aureus. The procedure is well established and a wide variety of applications have been published to date. Here, implementations of sortase A, which range from protein labeling using fluorescence dyes and the preparation of cyclic proteins to the modification of entire cells, are summarized. Furthermore, there is a focus on the optimization approaches established to solve the drawbacks of sortase-mediated transpeptidation.

Non-chromatographic purification of recombinant elastin-like polypeptides and their fusions with peptides and proteins from Escherichia coli

Elastin-like polypeptides are repetitive biopolymers that exhibit a lower critical solution temperature phase transition behavior, existing as soluble unimers below a characteristic transition temperature and aggregating into micron-scale coacervates above their transition temperature. The design of elastin-like polypeptides at the genetic level permits precise control of their sequence and length, which dictates their thermal properties. Elastin-like polypeptides are used in a variety of applications including biosensing, tissue engineering, and drug delivery, where the transition temperature and biopolymer architecture of the ELP can be tuned for the specific application of interest. Furthermore, the lower critical solution temperature phase transition behavior of elastin-like polypeptides allows their purification by their thermal response, such that their selective coacervation and resolubilization allows the removal of both soluble and insoluble contaminants following expression in Escherichia coli. This approach can be used for the purification of elastin-like polypeptides alone or as a purification tool for peptide or protein fusions where recombinant peptides or proteins genetically appended to elastin-like polypeptide tags can be purified without chromatography. This protocol describes the purification of elastin-like polypeptides and their peptide or protein fusions and discusses basic characterization techniques to assess the thermal behavior of pure elastin-like polypeptide products.

Sorting of LPXTG peptides by archetypal sortase A: role of invariant substrate residues in modulating the enzyme dynamics and conformational signature of a productive substrate

Transpeptidase sortase catalyzes the covalent anchoring of surface proteins to the cell wall in Gram-positive bacteria. Sortase A (SrtA) of Staphylococcus aureus is a prototype enzyme and considered a bona fide drug target because several substrate proteins are virulence-related and implicated in pathogenesis. Besides, SrtA also works as a versatile tool in protein engineering. Surface proteins destined for cell wall anchoring contain a LPXTG sequence located in their C-terminus which serves as a substrate recognition motif for SrtA. Recent studies have implicated substrate-induced conformational dynamics in SrtA. In the present work, we have explored the roles of invariant Leu and Pro residues of the substrate in modulating the enzyme dynamics with a view to understand the selection process of a catalytically competent substrate. Overall results of molecular dynamics simulations and experiments carried out with noncanonical substrates and site-directed mutagenesis reveal that the kinked conformation due to Pro in LPXTG is obligatory for productive binding but does not per se control the enzyme dynamics. The Leu residue of the substrate appears to play the crucial role of an anchor to the beta6-beta7 loop directing the conformational transition of the enzyme from an "open" to a "closed" state subsequent to which the Pro residue facilitates the consummation of binding through predominant engagement of the loop and catalytic motif residues in hydrophobic interactions. Collectively, our study provides insights about specificity, tolerance, and conformational sorting of substrate by SrtA. These results have important implications in designing newer substrates and inhibitors for this multifaceted enzyme.

Irreversible site-specific hydrazinolysis of proteins by use of sortase

Sortase-mediated hydrazinolysis of proteins with hydrazine or its derivatives was developed for the production of recombinant protein hydrazides. This process provides an alternative approach for protein semisynthesis through the use of recombinant protein hydrazides as thioester surrogates. It also provides an alternative method for C-terminal modification of proteins with functional units as well as for the preparation of C-to-C fusion proteins.

Sortase-catalyzed initiator attachment enables high yield growth of a stealth polymer from the C terminus of a protein

Conventional methods for synthesizing protein/peptide-polymer conjugates, as a means to improve the pharmacological properties of therapeutic biomolecules, typically have drawbacks including low yield, non-trivial separation of conjugates from reactants, and lack of site- specificity, which results in heterogeneous products with significantly compromised bioactivity. To address these limitations, the use of sortase A from Staphylococcus aureus is demonstrated to site-specifically attach an initiator solely at the C-terminus of green fluorescent protein (GFP), followed by in situ growth of a stealth polymer, poly(oligo(ethylene glycol) methyl ether methacrylate) by atom transfer radical polymerization (ATRP). Sortase-catalyzed initiator attachment proceeds with high specificity and near-complete (≈95%) product conversion. Subsequent in situ ATRP in aqueous buffer produces 1:1 stoichiometric conjugates with >90% yield, low dispersity, and no denaturation of the protein. This approach introduces a simple and useful method for high yield synthesis of protein/peptide-polymer conjugates.

Designing disorder: Tales of the unexpected tails

Protein tags of various sizes and shapes catalyze progress in biosciences. Well-folded tags can serve to solubilize proteins. Small, unfolded, peptide-like tags have become invaluable tools for protein purification as well as protein-protein interaction studies. Intrinsically Disordered Proteins (IDPs), which lack unique 3D structures, received exponentially increasing attention during the last decade. Recently, large ID tags have been developed to solubilize proteins and to engineer the pharmacological properties of protein and peptide pharmaceuticals. Here, we contrast the complementary benefits and applications of both folded and ID tags based on predictions of ID. Less structure often means more function in a shorter tag.