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General Life Science Research

Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5
S. Lee, Y. C. Tsai, R. Mattera, W. J. Smith, M. S. Kostelansky, A. M. Weissman, J. S. Bonifacino and J. H. Hurley
Nat Struct Mol Biol 13: 264-71 (2006)
Affinity analysis of point mutated proteins is used to complement crystallographic data on interactions between (1) the zinc finger domain and an adjacent helix on an exchange factor, Rabex-5, and (2) ubiquitin. Biacore T100 data are crucial in defining how both domains on Rabex-5 are necessary for recognition of ubiquitin and subsequent ligase activity.
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High-throughput kinase assay based on surface plasmon resonance suitable for native protein substrates
H. Takeda, A. Fukumoto, A. Miura, N. Goshima and N. Nomura
Anal Biochem 357: 262-71 (2006)
A high-throughput assay for screening kinase activity. Tyrosine phosphorylation is performed in a microtiter plate, after which the substrate is captured with an antibody on a sensor surface and phosphotyrosine (pTyr) is detected by injecting an anti-pTyr antibody in solution over the surface. Multiple sample processing of 1000 samples per day and high-quality data sampling.
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Selective recognition of synthetic lysine and meso diaminopimelic acid-type peptidoglycan fragments by human peptidoglycan recognition protein-Ialpha and -S
S. Kumar, A. Roychowdhury, B. Ember, Q. Wang, R. Guan, R. A. Mariuzza and G. J. Boons
J Biol Chem 280: 37005-12 (2005)
On the interaction between a receptor and multiple small peptidoglycan constructs.  This paper provides an excellent example of the conclusions on function that can be drawn from Biacore data. 
Link to abstract
Ca2+/calmodulin transfers the membrane-proximal lipid-binding domain of the v-SNARE synaptobrevin from cis to trans bilayers
L. De Haro, G. Ferracci, S. Opi, C. Iborra, S. Quetglas, R. Miquelis, C. Leveque and M. Seagar
Proc Natl Acad Sci U S A 101: 1578-1583 (2004)

On integral membrane proteins in neurons. Authors demonstrate that the interaction of calmodulin with the vesicle-associated membrane protein 2 (VAMP 2) is involved in Ca-dependent exocytosis.

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Real time analysis of intact organelles using surface plasmon resonance
G. Ferracci, M. Seagar, C. Joel, R. Miquelis and C. Leveque
Anal Biochem 334: 367-75 (2004)

On the direct capture of synaptic vesicles from neurons as a means to study synapse-specific membrane proteins on a sensor surface. The paper is rich in experimental detail and the method is proposed as a general approach to differential proteomics, or the use of organelles as markers or pharmacological targets.

Link to abstract
Quantitative high-throughput analysis of transcription factor binding specificities
J. Linnell, R. Mott, S. Field, D. P. Kwiatkowski, J. Ragoussis and I. A. Udalova
Nucleic Acids Res 32: e44 (2004)

A high-throughput approach to quantify DNA-protein interactions, which can aid the identification of functional genetic polymorphisms. Biacore experiments support microarray data based on fluorescent reading. The method was tested on two distinct transcription factors. Biacore’s experimental conditions and data analysis are well described.

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The IL-10R2 binding hot spot on IL-22 is located on the N-terminal helix and is dependent on N-linked glycosylation
N. J. Logsdon, B. C. Jones, J. C. Allman, L. Izotova, B. Schwartz, S. Pestka and M. R. Walter
J Mol Biol 342: 503-14 (2004)

Thorough mutation and glycosylation analysis of the interaction of IL22 with sIL22R1 and sIL10R2, revealing the need of a glycosylated asparagine residue in the binding-site. The paper is almost exclusively based on well-performed Biacore measurements, ranging from simple interaction analysis to on-chip enzymatic reactions. Highly recommended to all scientists interested in mutation analysis.

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Kinetics and binding sites for interaction of the prefoldin with a group II chaperonin: contiguous non-native substrate and chaperonin binding sites in the archaeal prefoldin
M. Okochi, T. Nomura, T. Zako, T. Arakawa, R. Iizuka, H. Ueda, T. Funatsu, M. Leroux and M. Yohda
J Biol Chem 279: 31788-95 (2004)
On the interaction between prefoldins and group II chaperonins.  This is shown to be important in protein folding, assembly, transport, and degradation.  Contains an excellent explanation of the assay and analysis.
Link to abstract
Binding interactions of Escherichia coli with globotetraosylceramide (globoside) using a surface plasmon resonance biosensor
M. R. Pourshafie, B. I. Marklund and S. Ohlson
J Microbiol Methods 58: 313-20 (2004)
On the adhesion mechanisms used by E. coli. Sensor Chip L1 was found to be ideal for globoside absorption – providing a stable, reproducible surface, which could quantifiably detect live or fixed bacteria. Assay was also specific for E. coli & authors suggest this would be a good tool for developing inhibitors of bacterial attachment to cells.
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Membrane association, electrostatic sequestration, and cytotoxicity of Gly-Leu-rich peptide orthologs with differing functions
D. Vanhoye, F. Bruston, S. El Amri, A. Ladram, M. Amiche and P. Nicolas
Biochemistry 43: 8391-409 (2004)

Detailed study on the power of Biacore kinetic analysis to rationally deduce the mechanisms by which cationic peptides bind and disrupt bacterial membranes, leading to cell death. The peptides are potentially therapeutic in humans: the task is to find those that are bactericidal but non-toxic to eukaryotic cells. The authors achieve this by constructing and immobilizing prokaryotic-like and eukaryotic-like membranes on a sensor surface and observing peptide binding patterns.

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Regulation of PutA-membrane associations by flavin adenine dinucleotide reduction
W. Zhang, Y. Zhou and D. F. Becker
Biochemistry 43: 13165-74 (2004)

On how FAD reduction and substrate binding affect the interaction between the multifunctional flavoprotein, PutA and bacterial membranes. A complex biochemical mechanistic study on bacterial metabolism with Biacore the principal technology used.

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Determining the folding and unfolding rate constants of nucleic acids by biosensor. Application to telomere G-quadruplex
Y. Zhao, Z. Y. Kan, Z. X. Zeng, Y. H. Hao, H. Chen and Z. Tan
J Am Chem Soc 126: 13255-64 (2004)
On the kinetics of DNA folding, especially in the telomere region, in comparison to the kinetics of duplex formation.
Link to abstract

SPR-MS Applications

Screening for enzyme inhibitors by surface plasmon resonance combined with mass spectrometry
J. Borch and P. Roepstorff
Anal Chem 76: 5243-8 (2004)

A screen for enzyme inhibitors, based on SPR-MS, is described, with the sensor surface the focal point for all the reactions.

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Biomolecular interaction analysis and MS
B. Mattei, J. Borch and P. Roepstorff
Anal Chem 76: 19A-25A (2004)

An excellent general review of SPR-MS.

Link to abstract
Integration of Surface Plasmon Resonance with Mass Spectrometry: Automated Ligand Fishing and Sample Preparation for MALDI MS Using a Biacore 3000 Biosensor
A. Zhukov, M. Schurenberg, O. Jansson, D. Areskoug and J. Buijs
J Biomol Tech 15: 112-9 (2004)

Proof-of-principle and reference paper for SPR-MS.  It describes a streamlined procedure that from ligand fishing and recovery to sample preparation for MALDI mass spectrometry including on-target digestion with a model system consisting of calmodulin captured from a crude biological mixture.

Link to abstract

Clinical Research

Surface plasmon resonance for the analysis of beta-amyloid interactions and fibril formation in Alzheimer's disease research
M. I. Aguilar and D. H. Small
Neurotox Res 7: 17-27 (2005)

Review of uses of Biacore to study b-amyloid interactions for Alzheimer’s disease research. Discusses a variety of Biacore assay approaches and details about assay design and the data that was generated from each.

Link to abstract
Affinity-based inhibition of beta-amyloid toxicity
C. W. Cairo, A. Strzelec, R. M. Murphy and L. L. Kiessling
Biochemistry 41: 8620-9 (2002)

Neuroscience. Screening for low molecular weight inhibitors of aggregation and thus toxicity of b-amyloid by affinity analysis. Affinity data shown to correlate seen with cell toxicity data.

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A direct interaction between the survival motor neuron protein and p53 and its relationship to spinal muscular atrophy
Young, P. J.Day, P. M.Zhou, J.Androphy, E. J.Morris, G. E.Lorson, C. L.
J Biol Chem 277: 2852-9 (2002)

Carefully controlled experiments encompassing multicomponent analysis in the field of neuropathology. A clever application in which the authors have used Biacore as a more rapid alternative to immunoprecipitation followed by detection with an antibody to a second molecule.

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Binding Energetics and Thermodynamics

Thermodynamics of the cyclophilin-A/cyclosporin-A interaction: A direct comparison of parameters determined by surface plasmon resonance using Biacore T100 and isothermal titration calorimetry
M. A. Wear and M. D. Walkinshaw
Anal Biochem 359: 285-7 (2006)
A technique comparison in which thermodynamic parameters of the interaction between cyclophilin-A and its natural inhibitor, cyclosporin-A, are calculated using Biacore T100 and isothermal titration calorimetry (ITC). Shows that equilibrium thermodynamic data derived using Biacore T100 are comparable to ITC. The unique application of SPR to transition state thermodynamics and the implications of this for structure based drug discovery are discussed. Finally, Biacore T100 is shown to be much more economic than ITC in terms of reagents consumed (micrograms compared to milligrams).
Link to abstract
Structural, kinetic, and thermodynamic analysis of the binding of the 40 kDa PEG-interferon-alpha2a and its individual positional isomers to the extracellular domain of the receptor IFNAR2
C. Dhalluin, A. Ross, W. Huber, P. Gerber, D. Brugger, B. Gsell and H. Senn
Bioconjug Chem 16: 518-27 (2005)

An excellent paper that explains what thermodynamics can tell us!

Link to abstract