Nanohole-based surface plasmon resonance instruments with improved spectral resolution quantify a broad range of antibody-ligand binding kinetics

We demonstrate an affordable low-noise surface plasmon resonance (SPR) instrument based on extraordinary optical transmission (EOT) in metallic nanohole arrays and quantify a broad range of antibody-ligand binding kinetics with equilibrium dissociation constants ranging from 200 pM to 40 nM. This nanohole-based SPR instrument is straightforward to construct, align, and operate, since it is built around a standard microscope and a portable fiber-optic spectrometer. The measured refractive index resolution of this platform is 3.1 × 10(-6) without on-chip cooling, which is among the lowest reported for SPR sensors based on EOT. This is accomplished via rapid full-spectrum acquisition in 10 ms followed by frame averaging of the EOT spectra, which is made possible by the production of template-stripped gold nanohole arrays with homogeneous optical properties over centimeter-sized areas. Sequential SPR measurements are performed using a 12-channel microfluidic flow cell after optimizing surface modification protocols and antibody injection conditions to minimize mass-transport artifacts. The immobilization of a model ligand, the protective antigen of anthrax on the gold surface, is monitored in real-time with a signal-to-noise ratio of ~860. Subsequently, real-time binding kinetic curves were measured quantitatively between the antigen and a panel of small, 25 kDa single-chain antibodies at concentrations down to 1 nM. These results indicate that nanohole-based SPR instruments have potential for quantitative antibody screening and as a general-purpose platform for integrating SPR sensors with other bioanalytical tools.

Crystallization chaperone strategies for membrane proteins

From G protein-coupled receptors to ion channels, membrane proteins represent over half of known drug targets. Yet, structure-based drug discovery is hampered by the dearth of available three-dimensional models for this large category of proteins. Other than efforts to improve membrane protein expression and stability, current strategies to improve the ability of membrane proteins to crystallize involve examining many orthologs and DNA constructs, testing the effects of different detergents for purification and crystallization, creating a lipidic environment during crystallization, and cocrystallizing with covalent or non-covalent soluble protein chaperones with an intrinsic high propensity to crystallize. In this review, we focus on this last category, highlighting successes of crystallization chaperones in membrane protein structure determination and recent developments in crystal chaperone engineering, including molecular display to enhance chaperone crystallizability, and end with a novel generic approach in development to target any membrane protein of interest.

Conversion of scFv peptide-binding specificity for crystal chaperone development

In spite of advances in protein expression and purification over the last decade, many proteins remain recalcitrant to structure determination by X-ray crystallography. One emerging tactic to obtain high-quality protein crystals for structure determination, particularly in the case of membrane proteins, involves co-crystallization with a protein-specific antibody fragment. Here, we report the development of new recombinant single-chain antibody fragments (scFv) capable of binding a specific epitope that can be introduced into internal loops of client proteins. The previously crystallized hexa-histidine-specific 3D5 scFv antibody was modified in the complementary determining region and by random mutagenesis, in conjunction with phage display, to yield scFvs with new biochemical characteristics and binding specificity. Selected variants include those specific for the hexa-histidine peptide with increased expression, solubility (up to 16.6 mg/ml) and sub-micromolar affinity, and those with new specificity for the EE hexa-peptide (EYMPME) and nanomolar affinity. Complexes of one such chaperone with model proteins harboring either an internal or a terminal EE tag were isolated by gel filtration. The 3.1 Å resolution structure of this chaperone reveals a binding surface complementary to the EE peptide and a ∼52 Å channel in the crystal lattice. Notably, in spite of 85% sequence identity, and nearly identical crystallization conditions, the engineered scFv crystallizes in a different space group than the parent 3D5 scFv, and utilizes two new crystal contacts. These engineered scFvs represent a new class of chaperones that may eliminate the need for de novo identification of candidate chaperones from large antibody libraries.

Characterization of a key neutralizing epitope on pertussis toxin recognized by monoclonal antibody 1B7

Despite more than five decades of research and vaccination, infection by Bordetella pertussis remains a serious disease with no specific treatments or validated correlates of protective immunity. Of the numerous monoclonal antibodies binding pertussis toxin (PTx) that have been produced and characterized, murine IgG2a monoclonal antibody 1B7 is uniquely neutralizing in all in vitro assays and in vivo murine models of infection. 1B7 binds an epitope on the enzymatically active S1 subunit of PTx (PTx-S1) with some linear elements, but previous work with S1 scanning peptides, phage-displayed peptide libraries, and S1 truncation/deletion variants was unable to more precisely define the epitope. Using computational docking algorithms, alanine scanning mutagenesis, and surface plasmon resonance, we characterize the epitope bound by 1B7 on PTx-S1 in molecular detail and define energetically important interactions between residues at the interface. Six residues on PTx-S1 and six residues on 1B7 were identified that, when altered to alanine, resulted in variants with significantly reduced affinity for the native partner. Using this information, a model of the 1B7-S1 interaction was developed, indicating a predominantly conformational epitope located on the base of S1 near S4. The location of this epitope is consistent with previous data and is shown to be conserved across several naturally occurring strain variants, including PTx-S1A, -B (Tohama-I), -D, and -E (18-323) in addition to the catalytically inactive 9K/129G variant. This highly neutralizing but poorly immunogenic epitope may represent an important target for next-generation vaccine development, identification of immune correlates, and passive immunization strategies for pertussis.

Surface plasmon resonance for high-throughput ligand screening of membrane-bound proteins

Technologies based on surface plasmon resonance (SPR) have allowed rapid, label-free characterization of protein-protein and protein-small molecule interactions. SPR has become the gold standard in industrial and academic settings, in which the interaction between a pair of soluble binding partners is characterized in detail or a library of molecules is screened for binding against a single soluble protein. In spite of these successes, SPR is only beginning to be adapted to the needs of membrane-bound proteins which are difficult to study in situ but represent promising targets for drug and biomarker development. Existing technologies, such as BIAcoreTM, have been adapted for membrane protein analysis by building supported lipid layers or capturing lipid vesicles on existing chips. Newer technologies, still in development, will allow membrane proteins to be presented in native or near-native formats. These include SPR nanopore arrays, in which lipid bilayers containing membrane proteins stably span small pores that are addressable from both sides of the bilayer. Here, we discuss current SPR instrumentation and the potential for SPR nanopore arrays to enable quantitative, high-throughput screening of G protein coupled receptor ligands and applications in basic cellular biology.

A strategic framework for responding to coral bleaching events in a changing climate

The frequency and severity of mass coral bleaching events are predicted to increase as sea temperatures continue to warm under a global regime of rising ocean temperatures. Bleaching events can be disastrous for coral reef ecosystems and, given the number of other stressors to reefs that result from human activities, there is widespread concern about their future. This article provides a strategic framework from the Great Barrier Reef to prepare for and respond to mass bleaching events. The framework presented has two main inter-related components: an early warning system and assessment and monitoring. Both include the need to proactively and consistently communicate information on environmental conditions and the level of bleaching severity to senior decision-makers, stakeholders, and the public. Managers, being the most timely and credible source of information on bleaching events, can facilitate the implementation of strategies that can give reefs the best chance to recover from bleaching and to withstand future disturbances. The proposed framework is readily transferable to other coral reef regions, and can easily be adapted by managers to local financial, technical, and human resources.

Progress towards recombinant anti-infective antibodies

The global market for monoclonal antibody therapeutics reached a total of $11.2 billion in 2004, with an impressive 42% growth rate over the previous five years and is expected to reach approximately $34 billion by 2010. Coupled with this growth are stream-lined product development, production scale-up and regulatory approval processes for the highly conserved antibody structure. While only one of the 21 current FDA-approved antibodies, and one of the 38 products in advanced clinical trials target infectious diseases, there is increasing academic, government and commercial interest in this area. Synagis, an antibody neutralizing respiratory syncitial virus (RSV), garnered impressive sales of $1.1 billion in 2006 in spite of its high cost and undocumented effects on viral titres in human patients. The success of anti-RSV passive immunization has motivated the continued development of anti-infectives to treat a number of other infectious diseases, including those mediated by viruses, toxins and bacterial/ fungal cells. Concurrently, advances in antibody technology suggest that cocktails of several monoclonal antibodies with unique epitope specificity or single monoclonal antibodies with broad serotype specificity may be the most successful format. Recent patents and patent applications in these areas will be discussed as predictors of future anti-infective therapeutics.

Modeling the structure of mAb 14B7 bound to the anthrax protective antigen

The anthrax protective antigen (PA) is a key component of the tripartite anthrax toxin. Monoclonal antibody (mAb) 14B7 and its engineered, affinity-matured variants have been shown to be effective in blocking PA binding to cellular receptors and mitigating anthrax toxicity. Here, we perform computational structural modeling of the mAb 14B7-PA interaction. Our objectives are to determine the structure of the 14B7-PA complex, to deduce a structural explanation for the affinity maturation from the docking models, and to study the effect of inaccuracies in the antibody homology model on docking. We used the RosettaDock program to dock PA with the mAb 14B7 crystal structure or homology model. Our simulations generate two distinct binding orientations consistent with experimental residue mutations that diminish 14B7-PA binding. Furthermore, the models suggest new site-directed mutations to positively identify one of these two solutions as the correct 14B7-PA docking orientation. The models indicate that PA regions 648-660 and 712-720 may be important for 14B7 binding in addition to the known PA epitope, and the binding interfaces are similar to that seen in the PA complex with cellular receptor CMG2. Antibody residues involved in affinity maturation do not contact the antigen in the docking models, suggesting that affinity maturation in the 14B7 family does not result from direct enhancements of antibody-antigen contacts. Docking the homology model produces low-resolution representations of the crystal structure docking orientations, but homology model docking is frustrated by antibody H3 loop conformation errors. This work demonstrates the usefulness and limitations of computational structure prediction for the development of antibody therapeutics, and reemphasizes the need for flexible backbone docking algorithms to achieve high-resolution docking using homology models.

Microarrays in infection and immunity

Over the past decade, microarrays have revolutionized the scientific world as dramatically as the internet has changed everyday life. From the initial applications of DNA microarrays to uncover gene expression patterns that are diagnostic and prognostic of cancer, understanding the interplay between immune responses and disease has been a prime application of this technology. More recent efforts have moved beyond genetic analysis to functional analysis of the molecules involved, including identification of immunodominant antigens and peptides as well as the role of post-translational glycosylation. Here, we focus on recent applications of microarray technology in understanding the detailed chemical biology of immune responses to disease in an effort to guide development of vaccines and other protective therapies.

Protection against anthrax toxin by recombinant antibody fragments correlates with antigen affinity

The tripartite toxin produced by Bacillus anthracis is the key determinant in the etiology of anthrax. We have engineered a panel of toxin-neutralizing antibodies, including single-chain variable fragments (scFvs) and scFvs fused to a human constant kappa domain (scAbs), that bind to the protective antigen subunit of the toxin with equilibrium dissociation constants (K(d)) between 63 nM and 0.25 nM. The entire antibody panel showed high serum, thermal, and denaturant stability. In vitro, post-challenge protection of macrophages from the action of the holotoxin correlated with the K(d) of the scFv variants. Strong correlations among antibody construct affinity, serum half-life, and protection were also observed in a rat model of toxin challenge. High-affinity toxin-neutralizing antibodies may be of therapeutic value for alleviating the symptoms of anthrax toxin in infected individuals and for medium-term prophylaxis to infection.

A novel all helix fold of the AP180 amino-terminal domain for phosphoinositide binding and clathrin assembly in synaptic vesicle endocytosis

Clathrin-mediated endocytosis plays a major role in retrieving synaptic vesicles from the plasma membrane following exocytosis. This endocytic process requires AP180 (or a homolog), which promotes the assembly and restricts the size of clathrin-coated vesicles. The highly conserved 33 kDa amino-terminal domain of AP180 plays a critical role in binding to phosphoinositides and in regulating the clathrin assembly activity of AP180. The crystal structure of the amino-terminal domain reported herein reveals a novel fold consisting of a large double layer of sheets of ten alpha helices and a unique site for binding phosphoinositides. The finding that the clathrin-box motif is mostly buried and lies in a helix indicates a different site and mechanism for binding of the domain to clathrins than previously assumed.

CD44 expression in the developing and growing rat intervertebral disc

CD44 has been identified at the time of extracellular matrix formation and expansion in several sites of the developing embryo (Wheatley et al. [1993] Development 119:295-306). The nucleus pulposus, consisting of a hydrated extracellular matrix tissue at birth, not previously closely analyzed, was examined for expression of CD44 in the developing and aging rat intervertebral disc. CD44 was identified solely on notochordal cells from the first onset of intervertebral disc formation (day 15 embryo) through the loss of notochordal cells from the nucleus pulposus (12-24 months of age). No CD44 expression was found in the notochordal cells prior to disc formation or in any cells other than the notochordal cells in the annulus fibrosus or nucleus pulposus of the intervertebral disc. Using reverse transcriptase-polymerase chain reaction methodology, the single 365 amino acid CD44 standard, CD44s, open reading frame was amplified from notochordal cells isolated from the nucleus pulposus. Western blot analysis of a cultured nucleus pulposus notochordal cells total protein extract identified a single CD44 species devoid of chondroitin sulfate with a mass of approximately 85 kDa, characteristic of CD44s. Cell surface detection for CD44 was co-localized with hyaluronan and proteoglycans at first appearance of disc formation in the nucleus pulposus.

Effects of 2 weeks hypergravity on the composition of the intervertebral disc

BACKGROUND

The effects of loading on connective tissues similar to the intervertebral disk have primarily been studied using articular cartilage organ culture in vitro techniques. The effects of in vivo loading on the intervertebral disk are less well documented.

METHODS

The lumbar annuli of rats centrifuged at 2G for 2 wk were compared with those of similar rats kept under analogous conditions at 1G. The studies involved the water, hydroxyproline (collagen), and uronic acid (proteoglycan, PG) content of the L4-5 and L5-6 annuli. Comparisons were also made between the 2G animals and the previous Cosmos 2044 spaceflight animals at 0G.

RESULTS

The water content of annuli did not differ between the control and 2G annuli; however, the PG content of the tissue was decreased in the 2G animals and the collagen content slightly increased, resulting in an increased collagen-PG ratio in the 2G animals. When the annuli were immersed in water for 2 h, more PG leached from the annuli of the 2G animals than the control animals, suggesting an alteration in the nature of the PG population comprising the annuli. Interestingly, the direction of changes in the 2G annuli was identical to that of the previous Cosmos 2044 0G animals when they were compared with their respective controls. Therefore, directly opposite experimental conditions (2G and 0G) produced similar results.

CONCLUSION

Previous studies regarding PG synthesis and content in cartilaginous tissues suggest alterations in intratissue pH and hydration to be among the factors involved in controlling the PG population. If the observed changes are permanent, they may affect the integrity of the intervertebral disk although it is likely they are totally reversible on return to 1G after an interim period, providing injuries are avoided.

Spatial and temporal expression of CD44 isoforms in the developing and growing joints of the rat limb

Hyaluronan is an integral component of proteoglycan-rich extracellular matrices such as hyaline cartilage. Hyaluronan is commonly found in embryonic tissue and is important in the formation of hydrated matrices that allow cellular expansion and migration. Cell surface hyaluronan-binding proteins such as CD44 are presumed to be important in the cellular interactions with hyaluronan in both of these processes. The primary aim of this study was to document the spatial and temporal expressions of CD44 isoforms during the development and growth of the diarthrodial joints of rat limbs. With use of in situ hybridization and immunohistochemistry, the CD44s isoform is selectively identified as localized to a single cell layer on opposing sides of the joint at the first appearance of joint cavitation (on the 18th day of gestation). After joint formation in the neonate, the expression of the CD44s isoform in the cells at the joint surface is lost. These findings suggest that the CD44s isoform has a role in the development of the diarthrodial joint, presumably through interaction with hyaluronan.

Rhizoremediation of trichloroethylene by a recombinant, root-colonizing Pseudomonas fluorescens strain expressing toluene ortho-monooxygenase constitutively

Trichloroethylene (TCE) was removed from soils by using a wheat rhizosphere established by coating seeds with a recombinant, TCE-degrading Pseudomonas fluorescens strain that expresses the tomA+ (toluene o-monooxygenase) genes from Burkholderia cepacia PR1(23)(TOM23C). A transposon integration vector was used to insert tomA+ into the chromosome of P. fluorescens 2-79, producing a stable strain that expressed constitutively the monooxygenase at a level of 1.1 nmol/min.mg of protein (initial TCE concentration, 10 microM, assuming that all of the TCE was in the liquid) for more than 280 cell generations (36 days). We also constructed a salicylate-inducible P. fluorescens strain that degraded TCE at an initial rate of 2.6 nmol/min.mg of protein in the presence of 10 microM TCE [cf. B. cepacia G4 PR1(23) (TOM23C), which degraded TCE at an initial rate of 2.5 nmol/min.mg of protein]. A constitutive strain, P. fluorescens 2-79TOM, grew (maximum specific growth rate, 0.78 h-1) and colonized wheat (3 x 10(6) CFU/cm of root) as well as wild-type P. fluorescens 2-79 (maximum specific growth rate, 0.77 h-1; level of colonization, 4 x 10(6) CFU/cm of root). Rhizoremediation of TCE was demonstrated by using microcosms containing the constitutive monooxygenase-expressing microorganism, soil, and wheat. These closed microcosms degraded an average of 63% of the initial TCE in 4 days (20.6 nmol of TCE/day.plant), compared to the 9% of the initial TCE removed by negative controls consisting of microcosms containing wild-type P. fluorescens 2-79-inoculated wheat, uninoculated wheat, or sterile soil.

Morphological and biochemical effects of strenuous exercise on immature long bones

To determine the effects of intense exercise on the growth of long bones in immature animals, young male white leghorn chickens were run five days per week starting at four weeks of age on motor-driven treadmills. Work intensity was determined on the basis of maximal oxygen consumption (VO2 max) with the exercise intensity maintained at 70-80 percent VO2 max. Young animals ran continuously for 30 minutes, older animals 45 to 60 minutes each day. Runners and controls (10 animals per group) were sacrificed at 8, 12, 14 and 20 weeks of age. The lengths of the femurs and tibiotarsus were significantly stunted at 8-, 12- and 14 weeks in the runners but had nearly recovered at 20 weeks of age. Both bones also demonstrated significantly decreased total cross-sectional areas in 8-, 12- and 14 week-old runners as well as decreased cortical cross-sectional areas. The tibiotarsus also remained significantly smaller in the 20-week-old runners, but the femur had recovered in terms of radial growth. Intermolecular pyridinoline collagen crosslinks were identical in amount in the two groups with the femur collagen significantly less cross-linked than the tibiotarsus. The delayed growth of the exercised avian young bone is consistent with data obtained from children and young mammalian models. The osteogenic response to exercise that produces an increased bone mass in adult tissue appears either suppressed or overcome in young avian bone indicating that it may be erroneous to assume that data obtained from adult tissue are also applicable to young growing bone.

The effects of space flight on the composition of the intervertebral disc

The lumbar annuli of rats flown on a COSMOS space flight were compared with those of three control groups and a ground antigravity tail suspension model. The wet and dry weights of the space flight annuli were significantly smaller than the three control groups. In addition, the collagen-to-proteoglycan ratio was significantly greater in the flight group due to a proportional increase in collagen and a decrease in proteoglycan. Finally, it appears microgravity may have altered the nature of the proteoglycan population as more proteoglycans leached from the annuli of flight animals than control animals when immersed in water.

Anatomy of the oblique retinacular ligament of the index finger

The available literature includes conflicting descriptions of the anatomy and function of the oblique retinacular ligament. We have studied this ligament in the index finger to better define its presence, configuration, points of attachment, length, and relationship to the proximal interphalangeal joint axis. Twenty fresh frozen index fingers were dissected. Five additional specimens were decalcified, mounted, sectioned transversely at 1 mm intervals and studied under the microscope. An oblique retinacular ligament was identified on the radial side of the index finger in 95% and on the ulnar side in 90% of the specimens. The radial oblique retinacular ligament was usually longer and more developed than the ulnar oblique retinacular ligament. Proximally, the ligament arose from the middle third of the proximal phalanx and the A-2 pulley whereas, distally, it inserted into the lateral extensor band with a fan-shaped expansion centered 4 to 6 mm distal to the proximal interphalangeal joint line. In 70% of the specimens, the oblique retinacular ligament was supplemented by a contribution from the proximal cruciform pulley (C-1). Histologic cross sections also confirmed the presence of the oblique retinacular ligament but not the supplemental contribution arising from the C-1 pulley. The relationship of the oblique retinacular ligament to the proximal interphalangeal joint axis is dependent on the proximal interphalangeal joint position; the ligament lies palmar to the proximal interphalangeal joint axis only when the proximal interphalangeal joint is flexed.

Effects of microgravity on the composition of the intervertebral disk

The lumbar annuli of rats flown on COSMOS 2044 were compared with those of three control groups and a tail-suspension experimental model. The wet and dry weights of the annuli were significantly smaller (P less than 0.05) in the flight group than in three control groups. The collagen-to-proteoglycan ratio was significantly greater (P less than 0.001) in the flight group than in the three control groups, but there were no detectable changes in the relative proportions of type I and II collagen or in the number of pyridinoline cross-links. When the annuli were immersed in water for 2 h, more proteoglycans (P less than 0.001) leached from the annuli of flown rats than from the tissue of control animals, suggesting abnormal or smaller proteoglycans. Safranin-O indicated a normal spatial distribution of the proteoglycans within the annulus. Tail suspension did not affect the size of the annuli, but more proteoglycans (P less than 0.05) leached from the tissue of suspended animals than from the normal annuli. The reasons for smaller disks and the abnormal ratio between the fibrous collagenous network and the proteoglycan gel in the flight group are unknown at this time. It is, however, probable that these changes may affect the biomechanical functions of the annulus, although they may be temporary and totally reversible if injuries are avoided in the interim period.

A microvascular anastomotic device: Part II. A histologic study in arteries and veins

This study analyzes the histology associated with the polyethylene ring-pin device. The device was placed in 20 rabbit femoral arteries and 20 femoral veins. Specimens were harvested at 24-hour and 3-week postoperative intervals and were analyzed using light, scanning electron, and transmission electron microscopy. Generally, the reparative process in the arteries and veins was similar. In 24-hour artery and vein specimens, the endothelial cells were absent, the media tapered within the device, but smooth muscle cells (SMC) remained partially viable. In 3-week specimens, the device junction was well healed and reendothelialized. Subintimal hyperplasia was present, the internal elastic lamina was not reconstituted, and the SMCs were partially viable. Small vascular channels formed at the device junction, and small venous valves were noted near the device. Macrophages lined the margins of the device. The early reparative process proceeds favorably, by histologic criteria, after vessel repair with the polyethylene ring-pin device.