A surface plasmon resonance-based solution affinity assay for heparan sulfate-binding proteins

A surface plasmon resonance-based solution affinity assay is described for measuring the Kd of binding of heparin/heparan sulfate-binding proteins with a variety of ligands. The assay involves the passage of a pre-equilibrated solution of protein and ligand over a sensor chip onto which heparin has been immobilised. Heparin sensor chips prepared by four different methods, including biotin–streptavidin affinity capture and direct covalent attachment to the chip surface, were successfully used in the assay and gave similar Kd values. The assay is applicable to a wide variety of heparin/HS-binding proteins of diverse structure and function (e.g., FGF-1, FGF-2, VEGF, IL-8, MCP-2, ATIII, PF4) and to ligands of varying molecular weight and degree of sulfation (e.g., heparin, PI-88, sucrose octasulfate, naphthalene trisulfonate) and is thus well suited for the rapid screening of ligands in drug discovery applications.

A study of water binding, mobility and dehydration in contact lens hydrogels using NMR

Hydrogel polymers are used for the manufacture of soft (or disposable) contact lenses worldwide today, but have a tendency to dehydrate on the eye. In vitro methods that can probe the potential for a given hydrogel polymer to dehydrate in vivo are much sought after. Nuclear magnetic resonance (NMR) has been shown to be effective in characterising water mobility and binding in similar systems (Barbieri, Quaglia et al., 1998, Larsen, Huff et al., 1990, Peschier, Bouwstra et al., 1993), predominantly through measurement of the spin-lattice relaxation time (T1), the spinspin relaxation time (T2) and the water diffusion coefficient (D). The aim of this work was to use NMR to quantify the molecular behaviour of water in a series of commercially available contact lens hydrogels, and relate these measurements to the binding and mobility of the water, and ultimately the potential for the hydrogel to dehydrate. As a preliminary study, in vitro evaporation rates were measured for a set of commercial contact lens hydrogels. Following this, comprehensive measurement of the temperature and water content dependencies of T1, T2 and D was performed for a series of commercial hydrogels that spanned the spectrum of equilibrium water content (EWC) and common compositions of contact lenses that are manufactured today. To quantify material differences, the data were then modelled based on theory that had been used for similar systems in the literature (Walker, Balmer et al., 1989, Hills, Takacs et al., 1989). The differences were related to differences in water binding and mobility. The evaporative results suggested that the EWC of the material was important in determining a material's potential to dehydrate in this way. Similarly, the NMR water self-diffusion coefficient was also found to be largely (if not wholly) determined by the WC. A specific binding model confirmed that the we was the dominant factor in determining the diffusive behaviour, but also suggested that subtle differences existed between the materials used, based on their equilibrium we (EWC). However, an alternative modified free volume model suggested that only the current water content of the material was important in determining the diffusive behaviour, and not the equilibrium water content. It was shown that T2 relaxation was dominated by chemical exchange between water and exchangeable polymer protons for materials that contained exchangeable polymer protons. The data was analysed using a proton exchange model, and the results were again reasonably correlated with EWC. Specifically, it was found that the average water mobility increased with increasing EWe approaching that of free water. The T1 relaxation was also shown to be reasonably well described by the same model. The main conclusion that can be drawn from this work is that the hydrogel EWe is an important parameter, which largely determines the behaviour of water in the gel. Higher EWe results in a hydrogel with water that behaves more like bulk water on average, or is less strongly 'bound' on average, compared with a lower EWe material. Based on the set of materials used, significant differences due to composition (for materials of the same or similar water content) could not be found. Similar studies could be used in the future to highlight hydrogels that deviate significantly from this 'average' behaviour, and may therefore have the least/greatest potential to dehydrate on the eye.

Multiple human single-stranded DNA binding proteins function in genome maintenance : structural, biochemical and functional analysis

DNA exists predominantly in a duplex form that is preserved via specific base pairing. This base pairing affords a considerable degree of protection against chemical or physical damage and preserves coding potential. However, there are many situations, e.g. during DNA damage and programmed cellular processes such as DNA replication and transcription, in which the DNA duplex is separated into two singlestranded DNA (ssDNA) strands. This ssDNA is vulnerable to attack by nucleases, binding by inappropriate proteins and chemical attack. It is very important to control the generation of ssDNA and protect it when it forms, and for this reason all cellular organisms and many viruses encode a ssDNA binding protein (SSB). All known SSBs use an oligosaccharide/oligonucleotide binding (OB)-fold domain for DNA binding. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating strand-exchange proteins and helicases, and mediation of protein–protein interactions. Recently two additional human SSBs have been identified that are more closely related to bacterial and archaeal SSBs. Prior to this it was believed that replication protein A, RPA, was the only human equivalent of bacterial SSB. RPA is thought to be required for most aspects of DNA metabolism including DNA replication, recombination and repair. This review will discuss in further detail the biological pathways in which human SSBs function.

Physical and functional interaction of the archaeal single-stranded DNA-binding protein SSB with RNA polymerase

Archaeal transcription utilizes a complex multisubunit RNA polymerase and the basal transcription factors TBP and TF(II)B, closely resembling its eukaryal counterpart. We have uncovered a tight physical and functional interaction between RNA polymerase and the single-stranded DNA-binding protein SSB in Sulfolobus solfataricus. SSB stimulates transcription from promoters in vitro under TBP-limiting conditions and supports transcription in the absence of TBP. SSB also rescues transcription from repression by reconstituted chromatin. We demonstrate the potential for promoter melting by SSB, suggesting a plausible basis for the stimulation of transcription. This stimulation requires both the single-stranded DNA-binding domain and the acidic C-terminal tail of the SSB. The tail forms a stable interaction with RNA polymerase. These data reveal an unexpected role for single-stranded DNA-binding proteins in transcription in archaea.

Single-stranded DNA-binding protein hSSB1 is critical for genomic stability

Single-strand DNA (ssDNA)-binding proteins (SSBs) are ubiquitous and essential for a wide variety of DNA metabolic processes, including DNA replication, recombination, DNA damage detection and repair1. SSBs have multiple roles in binding and sequestering ssDNA, detecting DNA damage, stimulating nucleases, helicases and strand-exchange proteins, activating transcription and mediating protein–protein interactions. In eukaryotes, the major SSB, replication protein A (RPA), is a heterotrimer1. Here we describe a second human SSB (hSSB1), with a domain organization closer to the archaeal SSB than to RPA. Ataxia telangiectasia mutated (ATM) kinase phosphorylates hSSB1 in response to DNA double-strand breaks (DSBs). This phosphorylation event is required for DNA damage-induced stabilization of hSSB1. Upon induction of DNA damage, hSSB1 accumulates in the nucleus and forms distinct foci independent of cell-cycle phase. These foci co-localize with other known repair proteins. In contrast to RPA, hSSB1 does not localize to replication foci in S-phase cells and hSSB1 deficiency does not influence S-phase progression. Depletion of hSSB1 abrogates the cellular response to DSBs, including activation of ATM and phosphorylation of ATM targets after ionizing radiation. Cells deficient in hSSB1 exhibit increased radiosensitivity, defective checkpoint activation and enhanced genomic instability coupled with a diminished capacity for DNA repair. These findings establish that hSSB1 influences diverse endpoints in the cellular DNA damage response.

Do we have a legally binding contract?

Legal advisers are often called upon to advise whether informal correspondence between clients may give rise to a binding contract. The decision of Mullins J in Teviot Downs Estate Pty Ltd v MTAA Superannuation Fund (Flagstone Creek and Spring Mountain Park) Property Pty Ltd [2003] QSC 403 provides general guidance as to matters that may be relevant when faced with this thorny issue.

Homodimerization controls the fibroblast growth factor 9 subfamily's receptor binding and heparan sulfate-dependent diffusion in the extracellular matrix

Uncontrolled fibroblast growth factor (FGF) signaling can lead to human diseases, necessitating multiple layers of self-regulatory control mechanisms to keep its activity in check. Herein, we demonstrate that FGF9 and FGF20 ligands undergo a reversible homodimerization, occluding their key receptor binding sites. To test the role of dimerization in ligand autoinhibition, we introduced structure-based mutations into the dimer interfaces of FGF9 and FGF20. The mutations weakened the ability of the ligands to dimerize, effectively increasing the concentrations of monomeric ligands capable of binding and activating their cognate FGF receptor in vitro and in living cells. Interestingly, the monomeric ligands exhibit reduced heparin binding, resulting in their increased radii of heparan sulfate-dependent diffusion and biologic action, as evidenced by the wider dilation area of ex vivo lung cultures in response to implanted mutant FGF9-loaded beads. Hence, our data demonstrate that homodimerization autoregulates FGF9 and FGF20's receptor binding and concentration gradients in the extracellular matrix. Our study is the first to implicate ligand dimerization as an autoregulatory mechanism for growth factor bioactivity and sets the stage for engineering modified FGF9 subfamily ligands, with desired activity for use in both basic and translational research.