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Recognition kinetics of biomolecules at the surface of different-sized spheres.

ABSTRACT: Bead-based assay is widely used in many bioanalytical applications involving the attachment of proteins and other biomolecules to the surface. For further understanding of the formation of a sphere-biomolecule complex and easily optimizing the use of spheres in targeted biological applications, it is necessary to know the kinetics of the binding reaction at sphere/solution interface. In our presented work, a simple fluorescence analysis method was employed to measure the kinetics for the binding of biotin to sphere surface-bound FITC-SA, based on the fact that the fluorescence intensity of FITC was proportionally enhanced by increasing the binding amount of biotin. By monitoring the time-dependent changes of FITC fluorescence, it was found that the binding rate constant of biotin to sphere surface-immobilized FITC-SA was much smaller than that of biotin to freely diffusing FITC-SA. This can be attributed to the decreased encounter frequency of the reaction pair, restricted motion of the attached biomolecule, and the weakened steric accessibility of the binding site. These factors would become more obvious when increasing the size of the sphere upon which the FITC-SA was immobilized. Additionally, the effect of nanoparticles on the diffusion-controlled bimolecular binding reaction was more evident than that on the chemical recognition-controlled binding reaction.

SUBMITTER: Hu J

PROVIDER: S-EPMC4119275 | biostudies-literature | 2014 Jul

REPOSITORIES: biostudies-literature

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Recognition kinetics of biomolecules at the surface of different-sized spheres.

Hu Jun J Wen Cong-Ying CY Zhang Zhi-Ling ZL Xie Min M Xie Hai-Yan HY Pang Dai-Wen DW

Biophysical journal 20140701 1

Bead-based assay is widely used in many bioanalytical applications involving the attachment of proteins and other biomolecules to the surface. For further understanding of the formation of a sphere-biomolecule complex and easily optimizing the use of spheres in targeted biological applications, it is necessary to know the kinetics of the binding reaction at sphere/solution interface. In our presented work, a simple fluorescence analysis method was employed to measure the kinetics for the binding ...[more]

PMID: 24988351

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Project description:BackgroundIn living cells, proteins are in continuous motion and interaction with the surrounding medium and/or other proteins and ligands. These interactions are mediated by protein features such as electrostatic and lipophilic potentials. The availability of protein structures enables the study of their surfaces and surface characteristics, based on atomic contribution. Traditionally, these properties are calculated by physico-chemical programs and visualized as range of colors that vary according to the tool used and imposes the necessity of a legend to decrypt it. The use of color to encode both characteristics makes the simultaneous visualization almost impossible, requiring these features to be visualized in different images. In this work, we describe a novel and intuitive code for the simultaneous visualization of these properties.MethodsRecent advances in 3D animation and rendering software have not yet been exploited for the representation of biomolecules in an intuitive, animated form. For our purpose we use Blender, an open-source, free, cross-platform application used professionally for 3D work. On the basis Blender, we developed BioBlender, dedicated to biological work: elaboration of protein motion with simultaneous visualization of their chemical and physical features. Electrostatic and lipophilic potentials are calculated using physico-chemical software and scripts, organized and accessed through BioBlender interface.ResultsA new visual code is introduced for molecular lipophilic potential: a range of optical features going from smooth-shiny for hydrophobic regions to rough-dull for hydrophilic ones. Electrostatic potential is represented as animated line particles that flow along field lines, proportional to the total charge of the protein.ConclusionsOur system permits visualization of molecular features and, in the case of moving proteins, their continuous perception, calculated for each conformation during motion. Using real world tactile/sight feelings, the nanoscale world of proteins becomes more understandable, familiar to our everyday life, making it easier to introduce "un-seen" phenomena (concepts) such as hydropathy or charges. Moreover, this representation contributes to gain insight into molecular functions by drawing viewer's attention to the most active regions of the protein. The program, available for Windows, Linux and MacOS, can be downloaded freely from the dedicated website http://www.bioblender.eu.

Project description:Salivary scavenger receptor cysteine-rich protein gp340 aggregates streptococci and other bacteria as part of the host innate defense system at mucosal surfaces. In this article, we have investigated the properties of fluid-phase gp340 and hydroxylapatite surface-adsorbed gp340 in aggregation and adherence, respectively, of viridans group streptococci (e.g., Streptococcus gordonii and Streptococcus mutans), non-viridans group streptococci (e.g., Streptococcus pyogenes and Streptococcus suis), and oral Actinomyces. Fluid-phase gp340 and surface-phase gp340 bioforms were differentially recognized by streptococci, which formed three phenotypic groupings according to their modes of interaction with gp340. Group I streptococci were aggregated by and adhered to gp340, and group II streptococci preferentially adhered to surface-bound gp340, while group III streptococci were preferentially aggregated by gp340. Each species of Streptococcus tested was found to contain strains representative of at least two of these gp340 interaction groupings. The gp340 interaction modes I to III and sugar specificities of gp340 binding strains coincided for several species. Many gp340 interactions were sialidase sensitive, and each of the interaction modes (I to III) for S. gordonii was correlated with a variant of sialic acid specificity. Adherence of S. gordonii DL1 (Challis) to surface-bound gp340 was dependent upon expression of the sialic acid binding adhesin Hsa. However, aggregation of cells by fluid-phase gp340 was independent of Hsa and involved SspA and SspB (antigen I/II family) polypeptides. Conversely, both gp340-mediated aggregation and adherence of S. mutans NG8 involved antigen I/II polypeptide. Deletion of the mga virulence regulator gene in S. pyogenes resulted in increased cell aggregation by gp340. These results suggest that salivary gp340 recognizes different bacterial receptors according to whether gp340 is present in the fluid phase or surface bound. This phase-associated differential recognition by gp340 of streptococcal species of different levels of virulence and diverse origins may mediate alternative host responses to commensal or pathogenic bacterial phenotypes.

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Recognition kinetics of biomolecules at the surface of different-sized spheres.

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Recognition kinetics of biomolecules at the surface of different-sized spheres.

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