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We report a systematic combinatorial exploration of affinity enhancement of antibodies by insertions and deletions (InDels). Transposon-based introduction of InDels via the method TRIAD (transposition-based random insertion and deletion mutagenesis) was used to generate large libraries with random in-frame InDels across the entire single-chain variable fragment gene that were further recombined and screened by ribosome display. Knowledge of potential insertion points from TRIAD libraries formed the basis of exploration of length and sequence diversity of novel insertions by insertional-scanning mutagenesis (InScaM). An overall 256-fold affinity improvement of an anti-IL-13 antibody BAK1 as a result of InDel mutagenesis and combination with known point mutations validates this approach, and suggests that the results of this InDel mutagenesis and conventional exploration of point mutations can synergize to generate antibodies with higher affinity.

We report the first systematic combinatorial exploration of affinity enhancement of antibodies by insertions and deletions (InDels). Transposon-based introduction of InDels via the method TRIAD was used to generate large libraries with random in-frame InDels across the entire scFv gene that were further recombined and screened by ribosome display. Knowledge of potential insertion points from TRIAD libraries formed the basis of exploration of length and sequence diversity of novel insertions by insertional-scanning mutagenesis (ISM). An overall 256-fold affinity improvement of an anti-IL-13 antibody BAK1 as a result of InDel mutagenesis and combination with known point mutations validates this approach and suggests that the results of this InDel approach and conventional exploration of point mutations can synergize to generate antibodies with higher affinity.SignificanceInsertion/deletion (InDel) mutations play key roles in genome and protein evolution. Despite their prominence in evolutionary history, the potential of InDels for changing function in protein engineering by directed evolution remains unexplored. Instead point mutagenesis is widely used. Here we create antibody libraries containing InDels and demonstrate that affinity maturation can be achieved in this way, establishing an alternative to the point mutation strategies employed in all previous in vitro selections. These InDels mirror the observation of considerable length variation in loops of natural antibodies originating from the same germline genes and be combined with point mutations, making both natural sources of functional innovation available for artificial evolution in the test tube.

Purpose An investigation was carried out into the effect of three image registration techniques on the diagnostic image quality of contrast-enhanced magnetic resonance angiography (CE-MRA) images. Methods Whole-body CE-MRA data from the lower legs of 27 patients recruited onto a study of asymptomatic atherosclerosis were processed using three deformable image registration algorithms. The resultant diagnostic image quality was evaluated qualitatively in a clinical evaluation by four expert observers, and quantitatively by measuring contrast-to-noise ratios and volumes of blood vessels, and assessing the techniques' ability to correct for varying degrees of motion. Results The first registration algorithm (‘AIR’) introduced significant stenosis-mimicking artefacts into the blood vessels' appearance, observed both qualitatively (clinical evaluation) and quantitatively (vessel volume measurements). The two other algorithms (‘Slicer’ and ‘SEMI’), based on the normalised mutual information (NMI) concept and designed specifically to deal with variations in signal intensity as found in contrast-enhanced image data, did not suffer from this serious issue but were rather found to significantly improve the diagnostic image quality both qualitatively and quantitatively, and demonstrated a significantly improved ability to deal with the common problem of patient motion. Conclusions This work highlights both the significant benefits to be gained through the use of suitable registration algorithms and the deleterious effects of an inappropriate choice of algorithm for contrast-enhanced MRI data. The maximum benefit was found in the lower legs, where the small arterial vessel diameters and propensity for leg movement during image acquisitions posed considerable problems in making accurate diagnoses from the un-registered images.

Discovery of new catalysts for demanding aqueous reactions is challenging. Here, we describe methodology for selection of catalytic phages by taking advantage of localized assembly of the product of the catalytic reaction that is screened for. A phage display library covering 10(9) unique dodecapeptide sequences is incubated with nonassembling precursors. Phages which are able to catalyze formation of the self-assembling reaction product (via amide condensation) acquire an aggregate of reaction product, enabling separation by centrifugation. The thus selected phages can be amplified by infection of Escherichia coli. These phages are shown to catalyze amide condensation and hydrolysis. Kinetic analysis shows a minor role for substrate binding. The approach enables discovery and mass-production of biocatalytic phages.

Antibodies are an important class of therapeutics that have significant clinical impact for the treatment of severe diseases. Computational tools to support antibody drug discovery have been developing at an increasing rate over the last decade and typically rely upon a predetermined co-crystal structure of the antibody bound to the antigen for structural predictions. Here, we show an example of successful in silico affinity maturation of a hybridoma derived antibody, AB1, using just a homology model of the antibody fragment variable region and a protein-protein docking model of the AB1 antibody bound to the antigen, murine CCL20 (muCCL20). In silico affinity maturation, together with alanine scanning, has allowed us to fine-tune the protein-protein docking model to subsequently enable the identification of two single-point mutations that increase the affinity of AB1 for muCCL20. To our knowledge, this is one of the first examples of the use of homology modelling and protein docking for affinity maturation and represents an approach that can be widely deployed., Author summary The role of computational techniques in therapeutic protein development is multifaceted and includes structure prediction (homology modelling), interface identification (docking), and mutational energy change calculation. Success has been reported in the areas of protein structure prediction and interface prediction (see competition results such as Critical Assessment of Structure Prediction [CASP] and Critical Assessment of Predicted Interactions [CAPRI]), but perhaps one of the greatest challenges is the translation of in silico derived binding energy changes upon mutation into affinity matured antibody variants. In these applications, it is important to choose the correct structural models, or approximations, that make sense across all aspects of in silico protein design. The challenges are compounded when no antibody-antigen co-crystal structure is available and there is a high degree of uncertainty around the protein-protein interface. Although the field is arguably far from its goal of precisely correlating computational predictions with experimental data, we show that even in the absence of a co-crystal structure, it is possible to identify modest affinity-improving mutations by using in silico mutagenesis in combination with homology modelling, protein docking, and simple experimental checkpoints.

The formation of bimolecular complexes of HOOOH and the HOOOﰀ radical with sulfuric acid (H2SO4– HOOOH, H2SO4–HOOOﰀ) has been investigated by using DFT (B3LYP/6-311++G(3df,3pd)) and CCSD(T)- F12 methods. For the first time the structures and the binding energies (BEs) for the various isomeric hydrogen-bonded complexes have been reported. The results reveal an unusually stable H2SO4–HOOOH eight-membered ring structure with two relatively strong hydrogen bonds, and with a calculated BE (CCSD(T)-F12) of 12.7 kcal molﰁ1. This is equivalent to the BE in the H2SO4–HOOH complex investigated at the same theoretical level. The complexation of HOOOﰀ with H2SO4 stabilizes this metastable polyoxide intermediate by about 10.0 kcal molﰁ1.

We report on-demand formation of emulsions stabilised by interfacial nanoscale networks. These are formed through biocatalytic dephosphorylation and self-assembly of Fmoc(9-fluorenylmethoxycarbonyl)-dipeptide amphiphiles in aqueous/organic mixtures. This is achieved by using alkaline phosphatase which transforms surfactant-like phosphorylated precursors into self-assembling aromatic peptide amphiphiles (Fmoc-tyrosine-leucine, Fmoc-YL) that form nanofibrous networks. In biphasic organic/aqueous systems, these networks form preferentially at the interface thus providing a means of emulsion stabilisation. We demonstrate on-demand emulsification by enzyme addition, even after storage of the biphasic mixture for several weeks. Experimental (Fluorescence, FTIR spectroscopy, fluorescence microscopy, electron microscopy, atomic force microscopy) and computational techniques (atomistic molecular dynamics) are used\ud to characterise the interfacial self-assembly process.

The surprising transformation of the saturated diamine (iPr)NHCH(2)CH(2)NH(iPr) to the unsaturated diazaethene [(iPr)NCH═CHN(iPr)](2-) via the synergic mixture nBuM, (tBu)(2)Zn and TMEDA (where M = Li, Na; TMEDA = N,N,N',N'-tetramethylethylenediamine) has been investigated by multinuclear NMR spectroscopic studies and DFT calculations. Several pertinent intermediary and related compounds (TMEDA)Li[(iPr)NCH(2)CH(2)NH(iPr)]Zn(tBu)(2) (3), (TMEDA)Li[(iPr)NCH(2)CH(2)CH(2)N(iPr)]Zn(tBu) (5), {(THF)Li[(iPr)NCH(2)CH(2)N(iPr)]Zn(tBu)}(2) (6), and {(TMEDA)Na[(iPr)NCH(2)CH(2)N(iPr)]Zn(tBu)}(2) (11), characterized by single-crystal X-ray diffraction, are discussed in relation to their role in the formation of (TMEDA)M[(iPr)NCH═CHN(iPr)]Zn(tBu) (M = Li, 1; Na, 10). In addition, the dilithio zincate molecular hydride [(TMEDA)Li](2)[(iPr)NCH(2)CH(2)N(iPr)]Zn(tBu)H 7 has been synthesized from the reaction of (TMEDA)Li[(iPr)NCH(2)CH(2)NH(iPr)]Zn(tBu)(2)3 with nBuLi(TMEDA) and also characterized by both X-ray crystallographic and NMR spectroscopic studies. The retention of the Li-H bond of 7 in solution was confirmed by (7)Li-(1)H HSQC experiments. Also, the (7)Li NMR spectrum of 7 in C(6)D(6) solution allowed for the rare observation of a scalar (1)J(Li-H) coupling constant of 13.3 Hz. Possible mechanisms for the transformation from diamine to diazaethene, a process involving the formal breakage of four bonds, have been determined computationally using density functional theory. The dominant mechanism, starting from (TMEDA)Li[(iPr)NCH(2)CH(2)N(iPr)]Zn(tBu) (4), involves the formation of a hydride intermediate and leads directly to the observed diazaethene product. In addition the existence of 7 in equilibrium with 4 through the dynamic association and dissociation of a (TMEDA)LiH ligand, also provides a secondary mechanism for the formation of the diazaethene. The two reaction pathways (i.e., starting from 4 or 7) are quite distinct and provide excellent examples in which the two distinct metals in the system are able to interact synergically to catalyze this otherwise challenging transformation.

Protein binding to surfaces is an important phenomenon in biology and in modern technological applications. Extensive experimental and theoretical research has been focused in recent years on revealing the factors that govern binding affinity to surfaces. Theoretical studies mainly focus on examining the contribution of the individual amino acids or, alternatively, the binding potential energies of the full peptide, which are unable to capture entropic contributions and neglect the dynamic nature of the system. We present here a methodology that involves the combination of nonequilibrium dynamics simulations with strategic mutation of polar residues to reveal the different factors governing the binding free energy of a peptide to a surface. Using a gold-binding peptide as an example, we show that relative binding free energies are a consequence of the balance between strong interactions of the peptide with the surface and the ability for the bulk solvent to stabilize the peptide.