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- Jabak, Adam A., et al.
(författare)
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Effect of Chirality on the Elastic Properties of the DNA-Threading Binuclear Ruthenium Complex
- 2020
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 118:3, Supplement 1, s. 617a-
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Konferensbidrag (refereegranskat)abstract
- Transition metal-based small molecules have been promising candidates for cancer treatments. A certain type of these molecules falls into a category known as threading intercalators, that have a dumbbell shape with a flat intercalating section in between bulky side chains. In order to bind to DNA, they must thread one of their bulky side chains through the DNA base pairs. The ruthenium-based molecule, ΛΛ-[μ-bidppz(phen)4Ru2]4+ (ΛΛ-P for short), is a transition metal-based threading intercalator. We use optical tweezers to study the interactions of ΛΛ-P with DNA to compare it with the previously studied ΔΔ-P, a complex that has the same chemical components but an opposite chirality. In these studies, we use the optical tweezers to trap a single DNA molecule and stretch it in the presence of various concentrations of ΛΛ-P. The DNA stretches obtained at saturated concentrations of ΛΛ-P at various forces allows us to obtain the effective elastic properties of the DNA-ΛΛ-P complex. This allows us to compare these properties to the previously studied ΔΔ-P complex to determine whether chirality has an effect. This type of comparison may lead us towards a better understanding of the role chirality has towards DNA binding.
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| 4. |
- Ambrosetti, Elena, et al.
(författare)
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A DNA-nanoassembly-based approach to map membrane protein nanoenvironments
- 2020
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Ingår i: Nature Nanotechnology. - Stockholm : Karolinska Institutet, Dept of Medical Biochemistry and Biophysics. - 1748-3387 .- 1748-3395. ; 120:3, s. 273A-274A
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Tidskriftsartikel (refereegranskat)abstract
- Most proteins at the plasma membrane are not uniformly distributed but localize to dynamic domains of nanoscale dimensions. To investigate their functional relevance, there is a need for methods that enable comprehensive analysis of the compositions and spatial organizations of membrane protein nanodomains in cell populations. Here we describe the development of a non-microscopy based method for ensemble analysis of membrane protein nanodomains. The method, termed NANOscale DEciphEring of membrane Protein nanodomains (NanoDeep), is based on the use of DNA nanoassemblies to translate membrane protein organization information into a DNA sequencing readout. Using NanoDeep, we characterised the nanoenvironments of Her2, a membrane receptor of critical relevance in cancer. Importantly, we were able to modulate by design the inventory of proteins analysed by NanoDeep. NanoDeep has the potential to provide new insights into the roles of the composition and spatial organization of protein nanoenvironments in the regulation of membrane protein function.
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| 6. |
- Baker, Joseph, et al.
(författare)
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Unveiling the Contributions of Secondary Structure and Disulfide Bonds for Bacterial Adhesion Pili Extension using a Multiscale Approach
- 2021
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Bacterial adhesion pili are essential virulence factors for many pathogenic Escherichia coli, including bacteria that cause urinary tract infections (UPEC) and diarrheal diseases (ETEC). To sustain adhesion under forces similar to those in the fluid environments of the urinary tract and gastrointestinal tract, these pili (also called fimbriae) can extend to over seven times their original length. Both UPEC and ETEC can uncoil their quaternary structure under pulling force and re-coil to their helical form when the force is reduced, as observed using optical tweezers. However, after extension to a linear polymer UPEC undergo an additional reversible conformational change, that is not seen in ETEC. The mechanism for this conformational change in UPEC is not known. Therefore, to obtain a comprehensive picture of pilus extension we have taken a synergistic approach that combines optical tweezer experiments, structural data from cryo-EM, and steered molecular dynamics simulations to investigate the response of pilin subunits to force.Our multi-faceted approach provides novel molecular-scale insights into the structural changes that occur in UPEC and ETEC pili under pulling forces. We find that the conformational change observed in UPEC pili in optical tweezer experiments is correlated with the presence of an alpha helix. In addition, structural analysis and steered molecular dynamics simulations show that there is a disulfide bond that provides additional stability of UPEC pilin subunits that is not observed in ETEC pilins, which lack cysteine residues. Together, these results suggest that the mechanism of extension of bacterial adhesion pili is related to their environmental niche, and the magnitude of fluid forces in the urinary tract versus the GI tract.
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