Structural evolution of protein-biofilms: Simulations and experiments

Schmitt, Yvonne; Hähl, Hendrik; Gilow, Christoph; Mantz, Hubert; Jacobs, Karin; Leidinger, O.; Bellion, M.; Santen, Ludger

doi:10.1063/1.3488672

Cited by 21 publications

(28 citation statements)

References 115 publications

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“…By offsetting deactivation of the solid support due to consumption of probes, the alignment could contribute to the near constancy in rate of hybridization observed during stage II. Interestingly, in protein adsorption, stage II like behavior has been attributed to conformational changes in which the occupied area per protein decreases as coverage increases; 56 this is analogous to the duplex reorientation mechanism proposed here.…”

Section: Resultssupporting

confidence: 56%

“…Our inspection of published hybridization traces reveals that such behavior can also arise in hybridization to PNA probes (especially at lower ionic strengths) 53-54 and, at times, to DNA probes, 26,55 as well as in protein adsorption. 56 At even longer times, stage III in Fig. 2D, the hybridization rate again starts to decrease with S D in a protracted approach to equilibrium.…”

Section: Resultsmentioning

confidence: 87%

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Kinetic Mechanisms in Morpholino–DNA Surface Hybridization

et al. 2011

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Morpholinos (MOs) are DNA analogues whose uncharged nature can bring fundamental advantages to surface hybridization technologies such as DNA microarrays, by using MOs as the immobilized, or “probe”, species. Advancement of MO-based diagnostics, however, is challenged by limited understanding of the surface organization of MO molecules and of how this organization impacts hybridization kinetics and thermodynamics. The present study focuses on hybridization kinetics between monolayers of MO probes and DNA targets as a function of the instantaneous extent of hybridization (i.e. duplex coverage), total probe coverage, and ionic strength. Intriguingly, these experiments reveal distinct kinetic stages, none of which are consistent with Langmuir kinetics. The initial stage, in which duplex coverage remains relatively sparse, indicates confluence of two effects: blockage of target access to unhybridized probes by previously formed duplexes, and deactivation of the solid support due to consumption of probe molecules. This interpretation is consistent with a surface organization in which unhybridized MO probes localize near the solid support, underneath a layer of MO-DNA duplexes. As duplex coverage builds, provided saturation is not reached first, the initial stage can transition to an unusual regime characterized by near independence of hybridization rate on duplex coverage, followed by a prolonged approach to equilibrium. The possible origins of these more complex latter behaviors are discussed. Comparison with published data for DNA and peptide nucleic acid (PNA) probes is carried out to look for universal trends in kinetics. This comparison reveals qualitative similarities when comparable surface organization of probes is expected. In addition, MO monolayers are found capable of a broad range of reactivities that span reported values for PNA and DNA probes.

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Section: Resultssupporting

confidence: 56%

Section: Resultsmentioning

confidence: 87%

Kinetic Mechanisms in Morpholino–DNA Surface Hybridization

et al. 2011

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“…Given the growing importance of biotechnologies which depend on a detailed understanding of the nature of protein film formation, 23 we believe this type of simulation has an important role to play in future research. We have demonstrated that it is possible to gain insight into the earliest stages of protein aggregation at a surface, and believe the same approach will provide essential guidance to a wide range of technologically relevant systems.…”

Section: Discussionmentioning

confidence: 99%

Multiprotein Interactions during Surface Adsorption: a Molecular Dynamics Study of Lysozyme Aggregation at a Charged Solid Surface

Kubiak-Ossowska

Mulheran

2011

J. Phys. Chem. B

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Multiprotein adsorption of hen egg white lysozyme at a model charged ionic surface is studied using fully atomistic molecular dynamics simulations. Simulations with two, three, and five proteins, in various orientations with respect the surface, are performed over a 100 ns time scale. Mutated proteins with point mutations at the major (Arg128 and Arg125) and minor (Arg68) surface adsorption sites are also studied. The 100 ns time scale used is sufficient to observe protein translations, rotations, adsorption, and aggregation. Two competing processes of particular interest are observed, namely surface adsorption and protein–protein aggregation. At low protein concentration, the proteins first adsorb in isolation and can then reorientate on the surface to aggregate. At high concentration, the proteins aggregate in the solution and then adsorb in nonspecific ways. This work demonstrates the role of protein concentration in adsorption, indicates the residues involved in both types of interaction (protein–protein and protein–surface), and gives an insight into processes to be considered in the development of new functionalized material systems.

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“…Hydrophobicity to the silica surfaces for applications like protein immobilization [13,14] can be imparted by functionalising them via hydrophobic carbon chain. Octadecyltrichlorosilane (OTS) and octadecyltrimethoxysilane (OTMS) are widely used alkylsilane for synthesising hydrophobic surfaces with 18 carbon atom hydrocarbon chain present between terminal and head group [15][16][17].…”

Section: Introductionmentioning

confidence: 99%