Site-specific photocoupling of pBpa mutated scFv antibodies for use in affinity proteomics.

Recombinant antibody libraries can provide a source of renewable and high-performing binders tailored for use in affinity proteomics. In this context, the process of generating site-specific 1:1 tagging/functionalization and/or orientated surface immobilization of antibodies has, however, proved to be challenging. Hence, novel ways of generating such engineered antibodies for use in affinity proteomics could have a major impact on array performance. In this study, we have further tailored the design of human recombinant scFv antibodies for site-specific photocoupling through the use of an unnatural amino acid (UAA) and the Dock'n'Flash technology. In more detail, we have generated the 2nd generation of scFvs carrying the photoreactive UAA p-benzoyl-l-phenylalanine (pBpa). Based on key properties, such as expression levels, activity, and affinity, a preferred choice of site for pBpa, located in the beginning of the C-terminal affinity-tag, was for the first time pin-pointed. Further, the results showed that pBpa mutated antibody could be site-specifically photocoupled to free and surface immobilized ß-cyclodextrin (an affinity ligand to pBpa). This paves the way for use of scFv antibodies, engineered for site-specific photochemical-based tagging, functionalization, and orientated surface immobilization, in affinity proteomics.

Synthesis and surface grafting of a ß-cyclodextrin dimer facilitating cooperative inclusion of 2,6-ANS.

A novel ß-cyclodextrin (ß-CD) dimer was synthesized and surface-grafted by click chemistry onto azide-functionalized quartz surfaces in order to introduce the cooperative features of the ß-CD dimer to solid surfaces. Using NMR and fluorescence spectroscopy, it is shown that the free ß-CD dimer forms a 1:1 complex with the fluorescent guest molecule, 2-anilinonaphthalene-6-sulfonic acid (otherwise known not to form 1:2 complexes with parent ß-CD), with an apparent association constant of 7300 M(-1). Further, it is shown using total internal reflection fluorescence spectroscopy that the inclusion of the fluorescent guest into both cavities of the ß-CD dimer is maintained when grafted onto a solid surface.

Nonfouling tunable ßCD dextran polymer films for protein applications.

Polymeric ß-cyclodextrin (ßCD) films tunable with respect to thickness and ßCD content were prepared in order to develop a suitable platform, allowing for inclusion of nonpolar guest molecules in the ßCD cavity, while suppressing nonspecific protein adsorption. The ßCD films were synthesized from linear ßCD dextran polymers, and grafted onto silicon oxide surfaces by "click" chemistry. Topographic and morphological characteristics are controllable by reaction conditions and polymer type, with average film heights from 2.5 to 12.5 nm. Reversible introduction of electrostatic charges in the ßCD dextran by complex formation with 1-adamantanecarboxylic acid prior to surface grafting resulted in a thinner and denser film, presumably by decompaction of the polymers. Total internal reflection fluorescence spectroscopy (TIRF) was employed to evaluate the accessibility of ßCD cavities to the fluorescent probe 2-anilinonaphthalene-6-sulfonic acid. Only a minor fraction of the ßCD cavities was accessible in the thicker and less dense films; however, accessibility was largely improved with increased ionic strength using NaCl up to 1 M. Antifouling properties of the ßCD dextran polymer films were assessed by TIRF real-time monitoring, using bovine serum albumin as a model protein, and showed a 5- to 10-fold reduction in nonspecific adsorption as compared to a bare quartz surface with the degree of reduction reflecting film thickness and interfacial polymer density.

Formation of nanoparticles by cooperative inclusion between (S)-camptothecin-modified dextrans and ß-cyclodextrin polymers.

Novel (S)-camptothecin-dextran polymers were obtained by "click" grafting of azide-modified (S)-camptothecin and alkyne-modified dextrans. Two series based on 10 kDa and 70 kDa dextrans were prepared with a degree of substitution of (S)-camptothecin between 3.1 and 10.2%. The binding properties with ß-cyclodextrin and ß-cyclodextrin polymers were measured by isothermal titration calorimetry and fluorescence spectroscopy, showing no binding with ß-cyclodextrin but high binding with ß-cyclodextrin polymers. In aqueous solution nanoparticles were formed from association between the (S)-camptothecin-dextran polymers and the ß-cyclodextrin polymers.

Molecular design of recombinant scFv antibodies for site-specific photocoupling to ß-cyclodextrin in solution and onto solid support.

The ability to design and tailor-make antibodies to meet the biophysical demands required by the vast range of current and future antibody-based applications within biotechnology and biomedicine will be essential. In this proof-of-concept study, we have for the first time tailored human recombinant scFv antibodies for site-specific photocoupling through the use of an unnatural amino acid (UAA) and the dock'n'flash technology. In more detail, we have successfully explored the possibility to expand the genetic code of E. coli and introduced the photoreactive UAA p-benzoyl-L-phenylalanine (pBpa), and showed that the mutated scFv antibody could be expressed in E. coli with retained structural and functional properties, as well as binding affinity. The pBpa group was then used for affinity capture of the mutated antibody by ß-cyclodextrin (ß-CD), which provided the hydrogen atoms to be abstracted in the subsequent photocoupling process upon irradiation at 365nm. The results showed that the pBpa mutated antibody could be site-specifically photocoupled to free and surface (array) immobilized ß-CD. Taken together, this paves the way for novel means of tailoring recombinant scFv antibodies for site-specific photochemical-based tagging, functionalization and immobilization in numerous applications.

Direct site-directed photocoupling of proteins onto surfaces coated with beta-cyclodextrins.

A method called Dock'n'Flash was developed to offer site-specific capture and direct UVA-induced photocoupling of recombinant proteins. The method involves the tagging of recombinant proteins with photoreactive p-benzoyl-L-phenylalanine (pBpa) by genetic engineering. The photoreactive pBpa tag is used for affinity capture of the recombinant protein by beta-cyclodextrin (beta-CD), which provides hydrogen atoms to be abstracted in the photocoupling process. To exemplify the method, a recombinant, folded, and active N27pBpa mutant of cutinase from Fusarium solani pisi was produced in E. coli. Insertion of pBpa was verified by matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectroscopy. A molecular dynamic simulation, with water as solvent, showed high solvent accessibility of the pBpa benzophenone group in N27pBpa-cutinase mutant. The formation of an inclusion complex between the benzophenone group of N27pBpa-cutinase and beta-CD was shown, and an apparent K(d) of 1.65 mM was determined using (1)H NMR. Photocoupling of beta-CD to N27pBpa-cutinase in a 1:1 ratio, upon UVA irradiation at 360 +/- 20 nm, was shown by MALDI-TOF mass spectroscopy. UVA photoimmobilization of N27pBpa-cutinase on quartz slides coated with beta-CD was achieved from liquid or dry films by total internal reflection fluorescence (TIRF). The Dock'n'Flash method offers a solution for direct photocoupling and patterning of recombinant proteins onto surfaces with site-specific attachment.

Immobilizing biomolecules near the diffraction limit.

Our group has previously shown that biomolecules containing disulfide bridges in close proximity to aromatic residues can be immobilized, through covalent bonds, onto thiol derivatized surfaces upon UV excitation of the aromatic residue(s). We have also previously shown that our new technology can be used to print arrays of biomolecules and to immobilize biomolecules according to any specific pattern on a planar substrates with micrometer scale resolution. In this paper we show that we can immobilize proteins according to diffraction patterns of UV light. We also show that the feature size of the immobilized patterns can be as small as the diffraction limit for the excitation light, and that the immobilized patterns correspond to the diffraction pattern used to generate it. The flexibility of this new technology will in principle make it possible to create any pattern of biomolecules onto a substrate, which can be generated by a UV diffraction pattern. Such patterns can have sub-micron feature sizes and could therefore be of great relevance for present and future nanotechnological applications.

Backbone and sidechain 1H, 13C and 15N resonance assignments of the human brain-type fatty acid binding protein (FABP7) in its apo form and the holo forms binding to DHA, oleic acid, linoleic acid and elaidic acid.

In this manuscript, we present the backbone and side chain assignments of human brain-type fatty acid binding protein, also known as FABP7, in its apo form and in four different holo forms, bound to DHA, oleic acid, linoleic acid and elaidic acid.

Printing novel molecular architectures with micrometer resolution using light.

In this paper we present a new photonic technology and demonstrate that it allows for precise immobilisation of proteins to sensor surfaces. The new technology secures spatially controlled molecular immobilisation since the immobilisation of each molecule to a support surface can be limited to the focal point of the UV laser beam, with dimensions as small as a few micrometers. We have demonstrated that we are not limited to immobilising molecules according to conventional patterns like microarrays. We can immobilise molecules on a surface with any arbitrary pattern. The different illumination/immobilisation setups presented expand the capabilities and usefulness of the new technology, since immobilisation can both be achieved with a laser system and with an affordable Xenon lamp setup. Of extreme relevance to the success of this technology is the precise knowledge of photon flux, energy flux, total number of photons per area, fluency and peak intensity. The expected resolution, taken into account the size of the focused laser beam, the precision of translation stage, and the scanner resolution of our laser scanner is in good agreement with the experimental resolution obtained. The flexibility of this new technology allows creating any patterns/ structures of molecules, with micrometer resolution, thus being of relevance for present and future nanotechnological applications.

Light-induced immobilisation of biomolecules as an attractive alternative to microdroplet dispensing-based arraying technologies.

The present work shows how UV 'light-induced molecular immobilisation' (LIMI) of biomolecules onto thiol reactive surfaces can be used to make biosensors, without the need for traditional microdispensing technologies. Using 'LIMI,' arrays of biomolecules can be created with a high degree of reproducibility. This technology can be used to circumvent the need for often expensive nano/microdispensing technologies. The ultimate size of the immobilised spots is defined by the focal area of the UV beam, which for a diffraction-limited beam can be less than 1 microm in diameter. LIMI has the added benefit that the immobilised molecules will be spatially oriented and covalently bound to the surface. The activity of the sensor molecules is retained. Antibody sensor arrays made using LIMI demonstrated successful antigen binding. In addition, the pattern of immobilised molecules on the surface is not restricted to conventional array formats. The ultimate consequence of the LIMI is that it is possible to write complex protein patterns using bitmaps at high resolution onto substrates. Thus, LIMI of biomolecules provides a new technological platform for biomolecular immobilisation and the potential for replacing present microdispensing arraying technologies.

The interaction of Fusarium solani pisi cutinase with long chain spin label esters.

We here present a study of the interaction between the Fusarium solani pisi cutinase mutant S120A and spin-labeled 4,4-dimethyloxazoline-N-oxyl-(DOXYL)-stearoyl-glycerol substrates in a micellar system. The interaction is detected by NMR measuring changes in chemical shift for 1H and 15N as well as relaxation parameters for backbone 1H (T1) and 15N (T1, T2) atoms as well as for side chain methyl groups 1H (T1). The detected interaction shows a weak binding of cutinase to the lipid micelles. Structural and mobility changes are located inside and around the active site, its flanking loops, and the oxyanion hole, respectively. Relaxation changes in the amino acid pairs Ser 92, Ala 93 and Thr 173, Gly 174 positioned at the edge of each of the active site flanking loops make these residues prime candidates for hinges, allowing for structural rearrangement during substrate binding. The cutinase mutant S120A used carries a 15 amino acid pro-peptide; the significance of this pro-peptide was so far undetermined. We show here that the pro-peptide is affected by the presence of the micellar substrate. Relaxation enhancements indicative of spatial proximity between the DOXYL group in the lipid chain and some hydrophobic residues surrounding the active site could be found.

The peroxidase gene family in plants: a phylogenetic overview.

The 73 class III peroxidase genes in Arabidopsis thaliana were used for surveying the evolutionary relationships among peroxidases in the plant kingdom. In Arabidopsis, the 73 genes were clustered in robust similarity groups. Comparison to peroxidases from other angiosperms showed that the diversity observed in Arabidopsis preceded the radiation of dicots, whereas some clusters were absent from grasses. Grasses contained some unique peroxidase clusters not seen in dicot plants. We found peroxidases in other major groups of land plants but not in algae. This might indicate that the class III peroxidase gene family appeared with the colonization of land by plants. The present survey may be used as a rational basis for further investigating the functional roles of class III peroxidases.

Structural diversity and transcription of class III peroxidases from Arabidopsis thaliana.

Understanding peroxidase function in plants is complicated by the lack of substrate specificity, the high number of genes, their diversity in structure and our limited knowledge of peroxidase gene transcription and translation. In the present study we sequenced expressed sequence tags (ESTs) encoding novel heme-containing class III peroxidases from Arabidopsis thaliana and annotated 73 full-length genes identified in the genome. In total, transcripts of 58 of these genes have now been observed. The expression of individual peroxidase genes was assessed in organ-specific EST libraries and compared to the expression of 33 peroxidase genes which we analyzed in whole plants 3, 6, 15, 35 and 59 days after sowing. Expression was assessed in root, rosette leaf, stem, cauline leaf, flower bud and cell culture tissues using the gene-specific and highly sensitive reverse transcriptase-polymerase chain reaction (RT-PCR). We predicted that 71 genes could yield stable proteins folded similarly to horseradish peroxidase (HRP). The putative mature peroxidases derived from these genes showed 28-94% amino acid sequence identity and were all targeted to the endoplasmic reticulum by N-terminal signal peptides. In 20 peroxidases these signal peptides were followed by various N-terminal extensions of unknown function which are not present in HRP. Ten peroxidases showed a C-terminal extension indicating vacuolar targeting. We found that the majority of peroxidase genes were expressed in root. In total, class III peroxidases accounted for an impressive 2.2% of root ESTs. Rather few peroxidases showed organ specificity. Most importantly, genes expressed constitutively in all organs and genes with a preference for root represented structurally diverse peroxidases (< 70% sequence identity). Furthermore, genes appearing in tandem showed distinct expression profiles. The alignment of 73 Arabidopsis peroxidase sequences provides an easy access to the identification of orthologous peroxidases in other plant species and will provide a common platform for combining knowledge of peroxidase structure and function relationships obtained in various species.