Biomolecular interaction analysis: affinity biosensor technologies for functional analysis of proteins

Modification of Cysteine-Substituted Antibodies Using Enzymatic Oxidative Coupling Reactions

Cysteines are routinely used as site-specific handles to synthesize antibody-drug conjugates for targeted immunotherapy applications. Michael additions between thiols and maleimides are some of the most common methods for modifying cysteines, but these functional groups can be difficult to prepare on scale, and the resulting linkages have been shown to be reversible under some physiological conditions. Here, we show that the enzyme tyrosinase, which oxidizes conveniently accessed phenols to afford reactive ortho-quinone intermediates, can be used to attach phenolic cargo to cysteines engineered on antibody surfaces. The resulting linkages between the thiols and ortho-quinones are shown to be more resistant than maleimides to reversion under physiological conditions. Using this approach, we construct antibody conjugates bearing cytotoxic payloads, which exhibit targeted cell killing, and further demonstrate this method for the attachment of a variety of cargo to antibodies, including fluorophores and oligonucleotides.

Evaluation of Galectin Binding by Surface Plasmon Resonance

Surface plasmon resonance (SPR) instruments, like the BIAcore 3000, are useful for studying the binding between macromolecules in real time. The high sensitivity and low sample consumption in the Biacore enables the measurement of rapid kinetics and low affinities characteristics of many biological interactions. This chapter describes the affinity measurement of Galectins-1, -2 and -3 and their glycoside ligands using this approach.

Secondary modification of oxidatively-modified proline N-termini for the construction of complex bioconjugates

A convenient two-step method is reported for the ligation of alkoxyamine- or hydrazine-bearing cargo to proline N-termini. Using this approach, bifunctional proline N-terminal bioconjugates are constructed and proline N-terminal proteins are immobilized.

Evaluation of galectin binding by surface plasmon resonance

Surface Plasmon Resonance (SPR) instruments, like the BIAcore 3000, are useful for studying the binding between macromolecules in real time. The high sensitivity and low sample consumption in the BIAcore enables the measurement of rapid kinetics and low affinities characteristic of many biological interactions. This chapter describes the affinity measurement of Galectins-1, -2, and -3 and their glycoside ligands using this approach.

Disruption of integrin-fibronectin complexes by allosteric but not ligand-mimetic inhibitors

Failure of Arg-Gly-Asp (RGD)-based inhibitors to reverse integrin-ligand binding has been reported, but the prevalence of this phenomenon among integrin heterodimers is currently unknown. In the present study we have investigated the interaction of four different RGD-binding integrins (α5β1, αVβ1, αVβ3 and αVβ6) with fibronectin (FN) using surface plasmon resonance. The ability of inhibitors to reverse ligand binding was assessed by their capacity to increase the dissociation rate of pre-formed integrin-FN complexes. For all four receptors we showed that RGD-based inhibitors (such as cilengitide) were completely unable to increase the dissociation rate. Formation of the non-reversible state occurred very rapidly and did not rely on the time-dependent formation of a high-affinity state of the integrin, or the integrin leg regions. In contrast with RGD-based inhibitors, Ca2+ (but not Mg2+) was able to greatly increase the dissociation rate of integrin-FN complexes, with a half-maximal response at ~0.4 mM Ca2+ for αVβ3-FN. The effect of Ca2+ was overcome by co-addition of Mn2+, but not Mg2+. A stimulatory anti-β1 monoclonal antibody (mAb) abrogated the effect of Ca2+ on α5β1-FN complexes; conversely, a function-blocking mAb mimicked the effect of Ca2+. These results imply that Ca2+ acts allosterically, probably through binding to the adjacent metal-ion-dependent adhesion site (ADMIDAS), and that the α1 helix in the β subunit I domain is the key element affected by allosteric modulators. The data suggest an explanation for the limited clinical efficacy of RGD-based integrin antagonists, and we propose that allosteric antagonists could prove to be of greater therapeutic benefit.

Aggregation of biopharmaceuticals in human plasma and human serum: implications for drug research and development

Analytical methods based on light microscopy, 90° light-scattering and surface plasmon resonance (SPR) allowed the characterization of aggregation that can occur when antibodies are mixed with human plasma. Light microscopy showed that aggregates formed when human plasma was mixed with 5% dextrose solutions of Herceptin^® (trastuzumab) or Avastin^® (bevacizumab) but not Remicade^® (infliximab). The aggregates in the plasma-Herceptin^®-5% dextrose solution were globular, size range 0.5–9 μm, with a mean diameter of 4 μm. The aggregates in the plasma-Avastin^®-5% dextrose samples had a mean size of 2 μm. No aggregation was observed when 0.9% NaCl solutions of Herceptin^®, Avastin^® and Remicade^® were mixed with human plasma. 90° light-scattering measurements showed that aggregates were still present 2.5 h after mixing Herceptin^® or Avastin^® with 5% dextrose-plasma solution. A SPR method was utilized to qualitatively describe the extent of interactions of surface-bound antibodies with undiluted human serum. Increased binding was observed in the case of Erbitux^® (cetuximab), whereas no binding was measured for Humira^® (adalimumab). The binding of sera components to 13 monoclonal antibodies was measured and correlated with known serum binding properties of the antibodies. The data presented in this paper provide analytical methods to study the intrinsic and buffer-dependent aggregation tendencies of therapeutic proteins when mixed with human plasma and serum.

Processing of DNA double-stranded breaks and intermediates of recombination and repair by Saccharomyces cerevisiae Mre11 and its stimulation by Rad50, Xrs2, and Sae2 proteins

Saccharomyces cerevisiae RAD50, MRE11, and XRS2 genes are essential for telomere length maintenance, cell cycle checkpoint signaling, meiotic recombination, and DNA double-stranded break (DSB) repair via nonhomologous end joining and homologous recombination. The DSB repair pathways that draw upon Mre11-Rad50-Xrs2 subunits are complex, so their mechanistic features remain poorly understood. Moreover, the molecular basis of DSB end resection in yeast mre11-nuclease deficient mutants and Mre11 nuclease-independent activation of ATM in mammals remains unknown and adds a new dimension to many unanswered questions about the mechanism of DSB repair. Here, we demonstrate that S. cerevisiae Mre11 (ScMre11) exhibits higher binding affinity for single- over double-stranded DNA and intermediates of recombination and repair and catalyzes robust unwinding of substrates possessing a 3' single-stranded DNA overhang but not of 5' overhangs or blunt-ended DNA fragments. Additional evidence disclosed that ScMre11 nuclease activity is dispensable for its DNA binding and unwinding activity, thus uncovering the molecular basis underlying DSB end processing in mre11 nuclease deficient mutants. Significantly, Rad50, Xrs2, and Sae2 potentiate the DNA unwinding activity of Mre11, thus underscoring functional interaction among the components of DSB end repair machinery. Our results also show that ScMre11 by itself binds to DSB ends, then promotes end bridging of duplex DNA, and directly interacts with Sae2. We discuss the implications of these results in the context of an alternative mechanism for DSB end processing and the generation of single-stranded DNA for DNA repair and homologous recombination.

Studying protein-protein affinity and immobilized ligand-protein affinity interactions using MS-based methods

This review discusses the most important current methods employing mass spectrometry (MS) analysis for the study of protein affinity interactions. The methods are discussed in depth with particular reference to MS-based approaches for analyzing protein-protein and protein-immobilized ligand interactions, analyzed either directly or indirectly. First, we introduce MS methods for the study of intact protein complexes in the gas phase. Next, pull-down methods for affinity-based analysis of protein-protein and protein-immobilized ligand interactions are discussed. Presently, this field of research is often called interactomics or interaction proteomics. A slightly different approach that will be discussed, chemical proteomics, allows one to analyze selectivity profiles of ligands for multiple drug targets and off-targets. Additionally, of particular interest is the use of surface plasmon resonance technologies coupled with MS for the study of protein interactions. The review addresses the principle of each of the methods with a focus on recent developments and the applicability to lead compound generation in drug discovery as well as the elucidation of protein interactions involved in cellular processes. The review focuses on the analysis of bioaffinity interactions of proteins with other proteins and with ligands, where the proteins are considered as the bioactives analyzed by MS.

Microfluidic Channels on Nanopatterned Substrates: Monitoring Protein Binding to Lipid Bilayers with Surface-Enhanced Raman Spectroscopy

We used Surface Enhanced Raman Spectroscopy (SERS) to detect binding events between streptavidin and biotinylated lipid bilayers. The binding events took place at the surface between microfluidic channels and anodized aluminum oxide (AAO) with the latter serving as substrates. The bilayers were incorporated in the substrate pores. It was revealed that non-bound molecules were easily washed away and that large suspended cells (Salmonella enterica) are less likely to interfere with the monitoring process: when focusing to the lower surface of the channel, one may resolve mostly the bound molecules.

Dissociation constant measurement using combination tapered fiber-optic biosensor (CTFOB) dip-probes

The document reports a novel method of measuring dissociation constant (k(D)) of antibody-antigen interaction using evanescent wave based combination tapered fiber-optic biosensor (CTFOB) dip-probes. The method was demonstrated by measuring the dissociation constant of human Interleukin-6 (IL-6) and anti-IL-6 interaction. Sandwich immunoassay was used to generate fluorescence signal proportional to antigen-antibody conjugate pairs. A portable CCD based spectrometer setup was used to record spectral profile of the fluorescence signal. The measured value of dissociation constant k(D) for IL-6 and capture anti-IL-6 (clone MQ2-13A5) antibodies at room temperature is588 ±19 pM .

High density scaffolding of functional polymer brushes: surface initiated atom transfer radical polymerization of active esters

In this Article, we describe a method for the polymerization of active esters based on N-hydroxysuccinimide 4-vinyl benzoate (NHS4VB) using surface initiated atom transfer radical polymerization (SI-ATRP). Poly(NHS4VB) brushes have high grafting density and a uniform and smooth morphology, and film thickness increases linearly with reaction time. Block copolymer brushes with 2-hydroxyethyl acrylate, tert-butyl acrylate, and styrene were synthesized from surface bound poly(NHS4VB) macroinitiators. The active ester brushes show rapid and quantitative conversion under aminolysis conditions with primary amines, which was studied using grazing incidence attenuated total reflection Fourier transform infrared (GATR-FTIR) and UV-vis spectroscopy. UV-vis was also used to quantify the amount of reactive groups in polymer brush layers of differing thickness. Functionalization of the active ester pendant groups with chromophores containing primary amines showed a linear correlation between the amount of chromophore incorporated into the brush layer and brush thickness. Grafting densities as high as 25.7 nmol/cm(2) were observed for a 50 nm brush. Block copolymer brushes with buried active ester functional moieties also undergo quantitative conversion with primary amines as confirmed by GATR-FTIR. We discuss the potential of activated ester brushes as universal scaffolds for sensor and microarray surfaces, where the twofold control of functionalizable active ester polymer and block copolymers provides well-ordered, tunable microenvironments.

High-affinity immobilization of proteins using biotin- and GST-based coupling strategies

Surface plasmon resonance (SPR) is a highly sensitive method for the detection of molecular interactions. One interacting partner is immobilized on the sensor chip surface while the other is injected across the sensor surface. This chapter focuses on high-affinity immobilization of protein substrates for affinity and kinetic analyses using biotin/streptavidin interaction and GST/anti-GST-antibody interaction.

Comparison of a Resonant Mirror Biosensor (IAsys) and a Quartz Crystal Microbalance (QCM) for the Study on Interaction between Paeoniae Radix 801 and Endothelin-1

A resonant mirror biosensor, IAsys, and a quartz crystal microbalance (QCM) are known independently as surface sensitive analytical devices capable of label-free and in situ bioassays. In this study, an IAsys and a QCM are employed for a new study on the action mechanism of Paeoniae Radix 801 (P. radix 801) by detecting the specific interaction between P. radix 801 and endothelin-1 (ET-1). In the experiments, ET-1 was immobilized on the surfaces of the IAsys cuvette and the QCM substrate by surface modification techniques, and then P. radix 801 solution was contacted to the cuvette and the substrate, separately. Then, the binding and interaction process between P. radix 801 and ET-1 was monitored by IAsys and QCM, respectively. The experimental results showed that P. radix 801 binds ET-1 specifically. The IAsys and QCM response curves to the ET-1 immobilization and P. radix 801 binding are similar in reaction process, but different in binding profiles, reflecting different resonation principles. Although both IAsys and QCM could detect the interaction of P. radix 801 and ET-1 with high reproducibility and reliability through optimization of the ET-1 coating, the reproducibility and reliability obtained by IAsys are better than those obtained by QCM, since the QCM frequency is more sensitive to temperature fluctuations, atmospheric changes and mechanical disturbances. However, IAsys and QCM are generally potent and reliable tools to study the interaction of P. radix 801 and ET-1, and can conclusively be applied to the action mechanism of P. radix 801.

Analysis of interactions of signaling proteins with phage-displayed ligands by fluorescence correlation spectroscopy

Fluorescent correlation spectroscopy (FCS) was used to measure binding affinities of ligands to ligates that are expressed by phage-display technology. Using this method we have quantified the binding of the 14-3-3 signaling protein to artificial peptide ligand. As a ligand we used the R18 artificial peptide expressed as a fusion in the cpIII coat protein that is present in 3 to 5 copies in an M13 phage. Comparisons of binding affinities were made with free R18 ligands using FCS. The result showed a relatively high binding affinity for the phage-displayed R18 peptide compared with binding to free fluorescently labeled R18. Quantification was supported by titration of the phage numbers using atomic force microscopy (AFM). AFM was shown to accurately determine phage numbers in solution as a good alternative for electron microscopy. It was shown to give reliable data that correlated perfectly with those of the viable phage numbers determined by classical bacterial infection studies. In conclusion, a very fast and sensitive method for the selection of new peptide ligands or ligates based on a quantitative assay in solution has been developed.

Biosensor-surface plasmon resonance methods for quantitative analysis of biomolecular interactions

The surface plasmon resonance (SPR) biosensor method has emerged as a very flexible and powerful approach for detecting a wide diversity of biomolecular interactions. SPR monitors molecular interactions in real time and provides significant advantages over optical or calorimetric methods for systems with strong binding and low spectroscopic signals or reaction heats. The SPR method simultaneously provides kinetic and equilibrium characterization of the interactions of biomolecules. Such information is essential for development of a full understanding of molecular recognition as well as for areas such as the design of receptor-targeted therapeutics. This article presents basic, practical procedures for conducting SPR experiments. Initial preparation of the SPR instrument, sensor chips, and samples are described. This is followed by suggestions for experimental design, data analysis, and presentation. Steady-state and kinetic studies of some small molecule-DNA complexes are used to illustrate the capability of this technique. Examples of the agreement between biosensor-SPR and solution studies are presented.

An RNA aptamer that recognizes a specific conformation of the protein calsenilin

The generation of molecules that selectively recognize specific conformations of a protein is an important component of the elucidation protein function. We have used SELEX (Systematic Evolution of Ligands by EXponential enrichment) technology to produce aptamers that bind in a conformationally selective manner to calsenilin, which involved in Ca(2+)-mediated apoptotic signaling. Since the conformations of calsenilin are quite different in the presence and absence of Ca(2+), aptamers were selected against the dimeric protein both under calcium-bound and calcium-free conditions. We have found that aptamer-12 selectively binds to the dimeric form of the protein in the presence of calcium ion, while the binding of aptamer-2 does not discriminate between the Ca(2+) bound and unbound protein. Data obtained from biochemical and biophysical experiments suggest that a dominant conformation of calcium-bound calsenilin exists in one dominant conformation and that one aptamer can be generated to recognize this conformation. In addition, observation made in this effort that aptamers selected against the two different conformations of calsenilin have different characteristics suggest that aptamers can serve as a plausible tool for recognizing various conformations of proteins, even those caused by interactions with small molecules or ions such as Ca(2+).

Electrophoresis mobility shift assay and biosensor used in studying the interaction between bleomycin A5 and DNA

DNA is the potential target of numerous drugs utilized widely in clinical cancer therapy. Here we employed bleomycin A5, with its deactivated form as contrast, to investigate the interaction between small pharmaceutical and DNA. Electrophoresis mobility shift assay (EMSA) which is a common technique used in studying specific interactions between DNA and proteins is applied in visualizing the binding of bleomycin A5 with DNA intuitively. More accurate association equilibrium constant for native and deactivated bleomycin A5 to DNA achieved on biosensor IAsys AUTO+ is 1.25x10(4) and 1.3x10(3) M(-1), respectively. With combination of EMSA and biosensor, a qualitative and quantitative method is described, which can be extended to studying the binding of most small molecules with targeting DNA and serves as a powerful tool in designing and screening for novel drugs.

Biosensor-surface plasmon resonance: Quantitative analysis of small molecule–nucleic acid interactions

Surface plasmon resonance (SPR)-biosensor techniques directly provide essential information for the study and characterization of small molecule-nucleic acid interactions, and the use of these methods is steadily increasing. The method is label-free and monitors the interactions in real time. Both dynamic and steady-state information can be obtained for a wide range of reaction rates and binding affinities. This article presents the basics of the SPR technique, provides suggestions for experimental design, and illustrates data processing and analysis of results. A specific example of the interaction of a well-known minor groove binding agent, netropsin, with DNA is evaluated by both kinetic and steady-state SPR methods. Three different experiments are used to illustrate different approaches and analysis methods. The three sets of results show the reproducibility of the binding constants and agreement from both steady-state and kinetic analyses. These experiments also show that reliable kinetic information can be obtained, even with difficult systems, if the experimental conditions are optimized to minimize mass transport effects. Limitations of the biosensor-SPR technique are also discussed to provide an awareness of the care needed to conduct a successful experiment.

Direct measurement of VDAC-actin interaction by surface plasmon resonance

VDAC--a mitochondrial channel involved in the control of aerobic metabolism and apoptosis--interacts in vitro and in vivo with a wide repertoire of proteins including cytoskeletal elements. A functional interaction between actin and Neurospora crassa VDAC was reported, excluding other VDAC isoforms. From a recent genome-wide screen of the VDAC interactome, we found that human actin is a putative ligand of yeast VDAC. Since such interaction may have broader implications for various mitochondrial processes, we probed it with Surface Plasmon Resonance (SPR) technology using purified yeast VDAC (YVDAC) and rabbit muscle G-actin (RGA). We show that RGA binds to immobilized YVDAC in a reversible and dose-dependent manner with saturating kinetics and an apparent K(D) of 50 microg/ml (1.2 microM actin). BSA does not bind VDAC regardless of the concentrations. Alternatively, VDAC binds similarly to immobilized RGA but without saturating kinetics. VDAC being known to interact with itself, this latter interaction was directly measured to interpret the RGA signals. VDAC could bind to VDAC without saturating kinetics as expected if higher order binding occurred, and could account for maximally 66% of the non-saturating behavior of VDAC binding onto RGA. Hence, actin-VDAC interactions are not a species-specific oddity and may be a more general phenomenon, the role of which ought to be further investigated.

Optimizing the surface plasmon resonance/mass spectrometry interface for functional proteomics applications: How to avoid and utilize nonspecific adsorption

A great challenge in functional or interaction proteomics is to map protein networks and establish a functional relationship between expressed proteins and their effects on cellular processes. These cellular processes can be studied by characterizing binding partners to a "bait" protein against a complex background of other molecules present in cells, tissues, or biological fluids. This so-called ligand fishing process can be performed by combining surface plasmon resonance biosensors with MS. This combination generates a unique and automated method to quantify and characterize biomolecular interactions, and identify the interaction partners. A general problem in chip-based affinity separation systems is the large surface-to-volume ratio of the fluidic system. Extreme care, therefore, is required to avoid nonspecific adsorption, resulting in losses of the target protein and carry-over during the affinity purification process, which may lead to unwanted signals in the final MS analysis and a reduction in sensitivity. In this study, carry-over of protein and low-molecular weight substances has been investigated systematically and cleaning strategies are presented. Furthermore, it is demonstrated that by the introduction of colloidal particles as a capturing and transporting agent, the recovery yield of the affinity-purified ligand could be improved nearly twofold.

Surface plasmon optical studies of carboxymethyl dextran brushes versus networks

The conformational changes of carboxymethyl dextran (CMD) substrates induced by variations in pH and ionic strength were studied using surface plasmon field-enhanced fluorescence spectroscopy (SPFS). A typical response was an increase in swelling upon increasing the pH and decreasing the ionic strength. Furthermore, the effects of the surface charge and cross-link density of the CMD on the degree of stimulus responses were investigated. The swelling/collapse ratio decreased with decreasing carboxyl group surface concentration and increasing cross-link density.

Nanotechnologies in proteomics

Progress in proteomic researches is largely determined by development and implementation of new methods for the revelation and identification of proteins in biological material in a wide concentration range (from 10(-3) M to single molecules). The most perspective approaches to address this problem involve (i) nanotechnological physicochemical procedures for the separation of multicomponent protein mixtures; among these of particular interest are biospecific nanotechnological procedures for selection of proteins from multicomponent protein mixtures with their subsequent concentration on solid support; (ii) identification and counting of single molecules by use of molecular detectors. The prototypes of biospecific nanotechnological procedures, based on the capture of ligand biomolecules by biomolecules of immobilized ligate and the concentration of the captured ligands on appropriate surfaces, are well known; these are affinity chromatography, magnetic biobeads technology, different biosensor methods, etc. Here, we review the most promising nanotechnological approaches for selection of proteins and kinetic characterization of their complexes based on these biospecific methods with subsequent MS/MS identification of proteins and protein complexes. Two major groups of methods for the analysis and identification of individual molecules and their complexes by use of molecular detectors will be reviewed: scanning probe microscopy (SPM) (including atomic-force microscopy) and cryomassdetector technology.

Reactive Thin Polymer Films as Platforms for the Immobilization of Biomolecules

Spin-coated thin films of poly(N-hydroxysuccinimidyl methacrylate) (PNHSMA) on oxidized silicon and gold surfaces were investigated as reactive layers for obtaining platforms for biomolecule immobilization with high molecular loading. The surface reactivity of PNHSMA films in coupling reactions with various primary amines, including amine-terminated poly(ethylene glycol) (PEG-NH2) and fluoresceinamine, was determined by Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), fluorescence microscopy, and ellipsometry measurements, respectively. The rate constants of PEG-NH2 attachment on the PNHSMA films were found to be significantly increased compared to the coupling on self-assembled monolayers (SAMs) of 11,11'-dithiobis(N-hydroxysuccinimidylundecanoate) (NHS-C10) on gold under the same conditions. More significantly, the PEG loading observed was about 3 times higher for the polymer thin films. These data indicate that the coupling reactions are not limited to the very surface of the polymer films, but proceed into the near-surface regions of the films. PNHSMA films were shown to be stable in contact with aqueous buffer; the swelling analysis, as performed by atomic force microscopy (AFM), indicated a film thickness independent swelling of approximately 2 nm. An increased loading was also observed by surface plasmon resonance for the covalent immobilization of amino-functionalized probe DNA. Hybridization of fluorescently labeled target DNA was successfully detected by fluorescence microscopy and surface plasmon resonance enhanced fluorescence spectroscopy (SPFS), thereby demonstrating that thin films of PNHSMA comprise an attractive and simple platform for the immobilization of biomolecules with high densities.

Functional protein microarrays: just how functional are they?

Arrays of immobilized proteins have been developed for the discovery and characterization of protein functions ranging from molecular recognition to enzymatic activity. The success of these applications is highly dependent upon the maintenance of protein structure and function while in an immobilized state - a largely untested hypothesis. However, the immobilization of functional proteins is not without precedent. Active enzymes have been successfully immobilized for industrial applications for several decades. Furthermore, a survey of recent protein microarray literature reveals that an even wider range of proteins can maintain 'proper' function while immobilized. These reports help to validate the functionality of so-called functional protein microarrays.

Reflectometric interference spectroscopy combined with MALDI-TOF mass spectrometry to determine quantitative and qualitative binding of mixtures of vancomycin derivatives

This paper describes the combination of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with label free bio-interaction analysis based on reflectometric interference spectroscopy (RIfS). The potential of this concerted approach is demonstrated by measuring the binding properties of different vancomycin-type glycopeptide antibiotic mixtures. Although RIfS is sensitive and does not require use of a label, it cannot determine which components of a mixture have bound to the surface after incubation. Fortunately, each bound species has a unique mass that can, afterwards, be determined by mass spectrometry. Thus, the screening capability of RIfS is combined with the identification capability of mass spectrometry.

Electroimmobilization of proinsulin C-peptide to a quartz crystal microbalance sensor chip for protein affinity purification

Proinsulin C-peptide was electroimmobilized to a quartz crystal microbalance sensor chip, localizing this low-pI peptide for covalent attachment to activated surface carboxyl groups. The resulting chip was used in a continuous flow biosensor to capture anti-C-peptide antibodies, which could subsequently be eluted in 5% formic acid between air bubbles for efficient recovery and mass spectrometric identification. The method is reproducible through repeated cycles, providing affinity purification of proteins under real-time monitoring of the binding and elution processes.

Creating nanoscopic collagen matrices using atomic force microscopy

The atomic force microscope (AFM) is introduced as a biomolecular manipulation machine capable of assembling biological molecules into well-defined molecular structures. Native collagen molecules were mechanically directed into well-defined, two-dimensional templates exhibiting patterns with feature sizes ranging from a few nanometers to several hundreds of micrometers. The resulting nanostructured collagen matrices were only approximately 3-nm thick, exhibited an extreme mechanical stability, and maintained their properties over the time range of several months. Our results directly demonstrate the plasticity of biological assemblies and provide insight into the physical mechanisms by which biological structures may be organized by cells in vivo. These nanoscopic templates may serve as platforms on non-biological surfaces to direct molecular and cellular processes.

Pharmacokinetic aspects of biotechnology products

In recent years, biotechnologically derived peptide and protein-based drugs have developed into mainstream therapeutic agents. Peptide and protein drugs now constitute a substantial portion of the compounds under preclinical and clinical development in the global pharmaceutical industry. Pharmacokinetic and exposure/response evaluations for peptide and protein therapeutics are frequently complicated by their similarity to endogenous peptides and proteins as well as protein nutrients. The first challenge frequently comes from a lack of sophistication in various analytical techniques for the quantification of peptide and protein drugs in biological matrices. However, advancements in bioassays and immunoassays--along with a newer generation of mass spectrometry-based techniques--can often provide capabilities for both efficient and reliable detection. Selection of the most appropriate route of administration for biotech drugs requires comprehensive knowledge of their absorption characteristics beyond physicochemical properties, including chemical and metabolic stability at the absorption site, immunoreactivity, passage through biomembranes, and active uptake and exsorption processes. Various distribution properties dictate whether peptide and protein therapeutics can reach optimum target site exposure to exert the intended pharmacological response. This poses a potential problem, especially for large protein drugs, with their typically limited distribution space. Binding phenomena and receptor-mediated cellular uptake may further complicate this issue. Elimination processes--a critical determinant for the drug's systemic exposure--may follow a combination of numerous pathways, including renal and hepatic metabolism routes as well as generalized proteolysis and receptor-mediated endocytosis. Pharmacokinetic/pharmacodynamic (PK/PD) correlations for peptide and protein-based drugs are frequently convoluted by their close interaction with endogenous substances and physiologic regulatory feedback mechanisms. Extensive use of pharmacokinetic and exposure/response concepts in all phases of drug development has in the past been identified as a crucial factor for the success of a scientifically driven, evidence-based, and thus accelerated drug development process. Thus, PK/PD concepts are likely to continue and expand their role as a fundamental factor in the successful development of biotechnologically derived drug products in the future.

Advances in recombinant antibody microarrays

Antibody microarrays, one emerging class of proteomic technologies, have broad applications in proteome analysis, disease diagnostics and quantitative analysis. Compared to DNA microarrays, protein targets have significantly more complex interactions with their ligands such as antibodies. To introduce antibody microarrays for clinical diagnostics and thus to complement or replace conventional immunoassays, several new developments are addressed. We discuss different microarray surfaces, immobilization techniques, detection systems and advantages and disadvantages of antibody microarrays compared to standard clinical techniques. Currently, the probes with highest specificity, well-characterized binding properties, and the possibility of large-scale production using display libraries are recombinant antibodies.

Protein and antibody microarray technology

Following the age of genomics having sequenced the human genome, interest is shifted towards the function of genes. This new age of proteomics brings about a change of methods to study the properties of gene products on a large scale. Protein separation technologies are now applied to allow high-throughput purification and characterisation of proteins. Two-dimensional-gel electrophoresis (2DE) and mass spectrometry (MS) have become widely used tools in the field of proteomics. At the same time, protein and antibody microarrays have been developed as successor of DNA microarrays to soon allow the proteome-wide screening of protein function in parallel. This review is aimed to introduce this new technology and to highlight its current prospects and limitations.

Surface plasmon resonance spectroscopy: an emerging tool for the study of peptide-membrane interactions

The interactions between peptides and membranes mediate a wide variety of biological processes, and characterization of the molecular details of these interactions is central to our understanding of cellular events such as protein trafficking, cellular signaling and ion-channel formation. A wide variety of biophysical techniques have been combined with the use of model membrane systems to study peptide-membrane interactions, and have provided important information on the relationship between membrane-active peptide structure and their biological function. However, what has generally not been reported is a detailed analysis of the affinity of peptide for different membrane systems, which has largely been due to the difficulty in obtaining this information. To address this issue, surface plasmon resonance (SPR) spectroscopy has recently been applied to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. This article provides an overview of these recent applications that demonstrate the potential of SPR to enhance our molecular understanding of membrane-mediated peptide function.

Surface plasmon resonance spectroscopy in the study of membrane-mediated cell signalling

Peptide-membrane interactions contribute to many important biological processes such as cellular signaling, protein trafficking and ion-channel formation. During receptor-mediated signalling, activated intracellular signalling molecules are often recruited into receptor-induced signaling complexes at the cytoplasmic surface of the cell membrane. Such recruitment can depend upon protein-protein and protein-lipid interactions as well as protein acylation. A wide variety of biophysical techniques have been combined with the use of model membrane systems to study these interactions and have provided important information on the relationship between the structure of these proteins involved in cell signalling and their biological function. More recently, surface plasmon resonance (SPR) spectroscopy has also been applied to the study of biomembrane-based systems using both planar mono- or bilayers or liposomes. This article provides an overview of these recent applications, which demonstrate the potential of SPR to enhance our molecular understanding of membrane-mediated cellular signalling.