Communication: Using multiple tethers to stabilize proteins on surfaces

Loong, Brandon K.; Knotts, Thomas A.

doi:10.1063/1.4891971

Cited by 11 publications

(16 citation statements)

References 21 publications

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“…The model is transferable to peptides of any type and has been used to accurately model proteins of many sizes including enzymes and antibodies. 36,38,39,50 The model was parameterized with data at typical biological conditions (e.g., 6 pH 8, [Na] 200 mM) and is not valid far away from such. However, such limitation is of little importance to this work as antibody arrays are used at biological conditions.…”

Section: A Protein and Modelmentioning

confidence: 99%

“…[28][29][30][31][32] Zhuang et al studied the effect of tethering on peptide folding mechanisms, 33 and coarse grain models have also been used to determine the thermodynamic properties of tethered proteins compared to their bulk counterparts. [34][35][36][37][38][39] Another advantage of coarse grain simulations is that they allow the thermodynamically rigorous quantification of protein stability. Determining protein stability on the surface is important because it is related to protein function, [35][36][37][38][39] but in order to quantify protein stability, the free energy of folding must be calculated.…”

Section: Introductionmentioning

confidence: 99%

“…[34][35][36][37][38][39] Another advantage of coarse grain simulations is that they allow the thermodynamically rigorous quantification of protein stability. Determining protein stability on the surface is important because it is related to protein function, [35][36][37][38][39] but in order to quantify protein stability, the free energy of folding must be calculated. Doing this in simulation requires the protein to fold and unfold multiple times.…”

Section: Introductionmentioning

confidence: 99%

“…Previous work with small proteins has shown that the structure immediately around the tether location can be become corrupted. 33,[36][37][38] It is therefore supposed that the farther the tether is placed from the active region, the more stable the active region will be.…”

Section: Introductionmentioning

confidence: 99%

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The effects of tether placement on antibody stability on surfaces

Grawe

Knotts

2017

The Journal of Chemical Physics

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Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. To determine this, 24 tethering locations were selected on the antibody Protein Data Bank (PDB) ID: 1IGT. Replica exchange simulations were run on two different surfaces, one hydrophobic and one hydrophilic, to determine the degree to which these tethering sites stabilize or destabilize the antibody. Results showed that antibodies tethered to hydrophobic surfaces were in general less stable than antibodies tethered to hydrophilic surfaces. Moreover, the stability of the antibody was a function of the tether location on hydrophobic surfaces but not hydrophilic surfaces.

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Section: A Protein and Modelmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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The effects of tether placement on antibody stability on surfaces

Grawe

Knotts

2017

The Journal of Chemical Physics

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“…10,11 As such, molecular simulation has emerged as the primary method used a) Electronic mail: thomas.knotts@byu.edu when studying protein/surface interactions. [12][13][14][15][16] This work uses molecular simulation to determine how tethering an Ab to different types of surfaces in different orientations affects the stability of the molecule. Specifically, two different orientations (flat and upright) and two types of surfaces (hydrophobic and hydrophilic) have been investigated using the IgG Ab 1IGT.…”

Section: Introductionmentioning

confidence: 99%

Communication: Antibody stability and behavior on surfaces

Bush

Knotts

2015

The Journal of Chemical Physics

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Antibody microarrays have the potential to revolutionize molecular detection in scientific, medical, and other biosensor applications, but their current use is limited because of poor reliability. It is hypothesized that one reason for their poor performance results from strong antibody-surface interactions that destabilize the antibody structure and create steric interference for antigen recognition. Using a recently developed coarse-grain protein-surface model that has been parameterized against experimental data, antibody-surface interactions for two antibody orientations on two types of surfaces have been investigated. The results show that regardless of attachment geometry, antibodies tend to collapse onto hydrophobic surfaces and exhibit lower overall stability compared to antibodies on hydrophilic surfaces or in bulk solution. The results provide an unprecedented view into the dynamics of antibodies on surfaces and offer new insights into the poor performance exhibited by current antibody microarrays.

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Interfacial Behaviors of Antimicrobial Peptide Cecropin P1 Immobilized on Different Self-Assembled Monolayers

Wang

Wei

et al. 2015

J. Phys. Chem. C

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Surfaces immobilized with biological molecules such as peptides and proteins are widely used in many important applications including biosensors, medical devices, and food packaging. It was found that the structures of surface-immobilized peptides control their surface properties. In this study, we investigated interfacial behaviors of antimicrobial peptide cecropin P1 (CP1) immobilized onto a maleimide-terminated self-assembled monolayer (Mal SAM) and a mixed SAM (Mal-OH SAM, a mixture of maleimide-terminated SAM and hydroxyl-terminated SAM) surface via C-terminus modified cysteine (CP1c). The surface coverage, secondary structure, orientation, and antimicrobial activity of immobilized CP1c were investigated using surface plasmon resonance (SPR), circular dichroism (CD), sum frequency generation (SFG) vibrational spectroscopy, dynamic contact antimicrobial assay, and coarse grained molecular dynamics (MD) simulations. It was found that the surface coverages of CP1c on the Mal SAM and the mixed Mal-OH SAM are similar. CP1c on Mal SAM possessed a dominant helical structure with a single orientation of ∼32° versus surface normal. CP1c on Mal-OH mixed SAM surface also possessed a dominant helical structure but with multiple orientations. MD simulation results can be correlated to the experimental data: the simulation results indicate a narrow distribution of orientations of CP1c immobilized on Mal SAM, but multiple orientations are sampled on the more hydrophilic Mal-OH SAM. Even though the surface orientations of CP1c immobilized on the two SAM surfaces are different, activity against both Gram-negative and Gram-positive bacteria (Escherichia coli and Staphylococcus aureus) exhibited similar results for CP1c immobilized on both SAM surfaces. We believe that this is because the antimicrobial activity of the surface-immobilized peptides is mainly affected by the electrostatic interactions between the strong basic N-terminal residues and the negatively charged bacteria cell wall/cell membrane.

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Communication: Using multiple tethers to stabilize proteins on surfaces

Cited by 11 publications

References 21 publications

The effects of tether placement on antibody stability on surfaces

The effects of tether placement on antibody stability on surfaces

Communication: Antibody stability and behavior on surfaces

Interfacial Behaviors of Antimicrobial Peptide Cecropin P1 Immobilized on Different Self-Assembled Monolayers

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