Protein and Chemical Microarrays—Powerful Tools for Proteomics

Xu, Qingchai; Lam, Kit S.

doi:10.1155/s1110724303209220

Cited by 73 publications

(35 citation statements)

References 76 publications

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“…The development of new tools to explore this relationship is an important part of the rapidly expanding fields of proteomics and protein chemistry (10)(11)(12). We have begun to develop a method that is based on a detailed examination of the interactions (which are themselves incompletely understood) between proteins and surfactants, especially those that underlie SDS͞PAGE.…”

mentioning

confidence: 99%

Differentiation of proteins based on characteristic patterns of association and denaturation in solutions of SDS

Gudiksen

Gitlin

Whitesides

2006

Proc. Natl. Acad. Sci. U.S.A.

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This paper shows that proteins display an unexpectedly wide range of behaviors in buffers containing moderate (0.1-10 mM) concentrations of SDS (complete unfolding, formation of stable intermediate states, specific association with SDS, and various kinetic phenomena); capillary electrophoresis provides a convenient method of examining these behaviors. Examination of the dynamics of the response of proteins to SDS offers a way to differentiate and characterize proteins. Based on a survey of 18 different proteins, we demonstrate that proteins differ in the concentrations of SDS at which they denature, in the rates of unfolding in SDS, and in the profiles of the denaturation pathways. We also demonstrate that these differences can be exploited in the analysis of mixtures.capillary electrophoresis ͉ surfactant ͉ intermediates ͉ kinetics T his manuscript surveys the range of electrophoretic behaviors observed for proteins in solutions containing SDS at concentrations below those used in SDS͞PAGE. The aggressive conditions used to prepare proteins for characterization by SDS͞PAGE (1) are designed to produce completely denatured, unfolded aggregates of protein and SDS; less forcing conditions have generally been ignored. Because SDS͞PAGE uses forcing conditions, it has failed to reveal the wealth of information available from systems of protein and SDS: information about the kinetics of denaturation; about previously undetected, stable aggregates of protein and SDS with reasonably well defined stoichiometry; and about intermediates along the pathway to the fully denatured aggregates of protein and SDS.Intermediates in the denaturation of some proteins with SDS have been identified: RNase A (2), cytochrome c that had been denatured in acid (3), BSA (4), and mushroom tyrosinase (5). Many proteins have a ''low'' state, in which the protein binds a few molecules of SDS, and ''high'' state, in which the protein binds one molecule of SDS per two amino acids (6, 7). These studies have concentrated mostly on single proteins or on the similarities between proteins and have not demonstrated or exploited the wide variability in behavior of proteins as they are denatured in SDS.We find that proteins show large differences in the concentrations of SDS and in the rates at which they change conformation and unfold in SDS, in the concentrations of SDS at which intermediates form along the unfolding pathway, and in the number of these intermediates. [We use the term ''rate'' to refer to the kinetics of unfolding of the native protein. With this technique, we can only estimate the time scale for unfolding of a protein at a particular concentration of SDS qualitatively, i.e., estimate whether it is shorter, similar, or longer than the time of the capillary electrophoresis (CE) experiment.] These differences among proteins can be exploited to provide the basis for a method of differentiating (and in some instances separating) proteins and information about the relations between their structure and stabilities. We believe that this procedu...

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confidence: 99%

Differentiation of proteins based on characteristic patterns of association and denaturation in solutions of SDS

Gudiksen

Gitlin

Whitesides

2006

Proc. Natl. Acad. Sci. U.S.A.

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“…A stable attachment of probe molecules is usually achieved by forming covalent bonds to the surface [11,12]. Reactive groups for bond formation can be attached at the end of ( Fig.…”

Section: Molecular Architecturementioning

confidence: 99%

Microarray Technology as a Universal Tool for High-Throughput Analysis of Biological Systems

Sobek¹,

Bartscherer²,

Jacob³

et al. 2006

CCHTS

110

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Over the last years microarray technology has become one of the principal platform technologies for the highthroughput analysis of biological systems. Starting with the construction of first DNA microarrays in the 1990s, microarray technology has flourished in the last years and many different new formats have been developed. Peptide and protein microarrays are now applied for the elucidation of interaction partners, modification sites and enzyme substrates. Antibody microarrays are envisaged to be of high importance for the high-throughput determination of protein abundances in translational profiling approaches. First cell microarrays have been constructed to transform microarray technology from an in vitro technology to an in vivo functional analysis tool. All of these approaches share a common prerequisite: the solid support on which they are generated. The demands on this solid support are thereby as manifold as the applications themselves. This review is aimed to display the recent developments in surface chemistry and derivatization, and to summarize the latest developments in the different application areas of microarray technology.

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“…Functional arrays can be used to study protein properties and interactions [20]. This tool can be used to predict functions based on coexpression after analyzing small molecule and drug-binding properties.…”

Section: Array-based Proteomicsmentioning

confidence: 99%

“…In future, blood tests may be performed by providing fewer drops of blood onto a chip with specific protein markers, providing valuable diagnostic and real-time prognostic information [20]. Advantages of the protein microarray approaches include the ability to use small samples and built-in experimental controls for calibration.…”

Section: Array-based Proteomicsmentioning

confidence: 99%

Automation, parallelism, and robotics for proteomics

et al. 2006

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The speed of the human genome project (Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C. et al., Nature 2001, 409, 860-921) was made possible, in part, by developments in automation of sequencing technologies. Before these technologies, sequencing was a laborious, expensive, and personnel-intensive task. Similarly, automation and robotics are changing the field of proteomics today. Proteomics is defined as the effort to understand and characterize proteins in the categories of structure, function and interaction (Englbrecht, C. C., Facius, A., Comb. Chem. High Throughput Screen. 2005, 8, 705-715). As such, this field nicely lends itself to automation technologies since these methods often require large economies of scale in order to achieve cost and time-saving benefits. This article describes some of the technologies and methods being applied in proteomics in order to facilitate automation within the field as well as in linking proteomicsbased information with other related research areas.

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Protein and Chemical Microarrays—Powerful Tools for Proteomics

Cited by 73 publications

References 76 publications

Differentiation of proteins based on characteristic patterns of association and denaturation in solutions of SDS

Differentiation of proteins based on characteristic patterns of association and denaturation in solutions of SDS

Microarray Technology as a Universal Tool for High-Throughput Analysis of Biological Systems

Automation, parallelism, and robotics for proteomics

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