scholarly journals Synergistic SHAPE/Single-Molecule Deconvolution of RNA Conformation under Physiological Conditions

2018 ◽  
Vol 114 (8) ◽  
pp. 1762-1775 ◽  
Author(s):  
Mario Vieweger ◽  
David J. Nesbitt
2019 ◽  
Author(s):  
Hamilton Lee ◽  
Jenica Lumata ◽  
Michael A. Luzuriaga ◽  
Candace Benjamin ◽  
Olivia Brohlin ◽  
...  

<div><div><div><p>Many contrast agents for magnetic resonance imaging are based on gadolinium, however side effects limit their use in some patients. Organic radical contrast agents (ORCAs) are potential alternatives, but are reduced rapidly in physiological conditions and have low relaxivities as single molecule contrast agents. Herein, we use a supramolecular strategy where cucurbit[8]uril binds with nanomolar affinities to ORCAs and protects them against biological reductants to create a stable radical in vivo. We further over came the weak contrast by conjugating this complex on the surface of a self-assembled biomacromolecule derived from the tobacco mosaic virus.</p></div></div></div>


2019 ◽  
Author(s):  
Pilar Gutierrez-Escribano ◽  
Matthew D. Newton ◽  
Aida Llauró ◽  
Jonas Huber ◽  
Loredana Tanasie ◽  
...  

AbstractEssential processes such as accurate chromosome segregation, regulation of gene expression and DNA repair rely on protein-mediated DNA tethering. Sister chromatid cohesion requires the SMC complex cohesin to act as a protein linker that holds replicated chromatids together (1, 2). The molecular mechanism by which cohesins hold sister chromatids has remained controversial. Here, we used a single molecule approach to visualise the activity of cohesin complexes as they hold DNA molecules. We describe a DNA bridging activity that requires ATP and is conserved from yeast to human cohesin. We show that cohesin can form two distinct classes of bridges at physiological conditions, a “permanent bridge” able to resists high force (over 80pN) and a “reversible bridge” that breaks at lower forces (5-40pN). Both classes of bridges require Scc2/Scc4 in addition to ATP. We demonstrate that bridge formation requires physical proximity of the DNA segments to be tethered and show that “permanent” cohesin bridges can move between two DNA molecules but cannot be removed from DNA when they occur in cis. This suggests that separate physical compartments in cohesin molecules are involved in the bridge. Finally, we show that cohesin tetramers, unlike condensin, cannot compact linear DNA molecules against low force, demonstrating that the core activity of cohesin tetramers is bridging DNA rather than compacting it. Our findings carry important implications for the understanding of the basic mechanisms behind cohesin-dependent establishment of sister chromatid cohesion and chromosome architecture.


Author(s):  
Kristina Cechova ◽  
Chenyang Lan ◽  
Matus Macik ◽  
Nicolas P. F. Barthes ◽  
Manfred Jung ◽  
...  

AbstractOpioid receptors (ORs) have been observed as homo- and heterodimers, but it is unclear if the dimers are stable under physiological conditions, and whether monomers or dimers comprise the predominant fraction in a cell. Here, we use three live-cell imaging approaches to assess dimerization of ORs at expression levels that are 10–100 × smaller than in classical biochemical assays. At membrane densities around 25/µm2, a split-GFP assay reveals that κOR dimerizes, while µOR and δOR stay monomeric. At receptor densities < 5/µm2, single-molecule imaging showed no κOR dimers, supporting the concept that dimer formation depends on receptor membrane density. To directly observe the transition from monomers to dimers, we used a single-molecule assay to assess membrane protein interactions at densities up to 100 × higher than conventional single-molecule imaging. We observe that κOR is monomeric at densities < 10/µm2 and forms dimers at densities that are considered physiological. In contrast, µOR and δOR stay monomeric even at the highest densities covered by our approach. The observation of long-lasting co-localization of red and green κOR spots suggests that it is a specific effect based on OR dimerization and not an artefact of coincidental encounters.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 91-91
Author(s):  
William Planer ◽  
Zhiwei Chen ◽  
Mathivanan Chinnaraj ◽  
Xiaobing Zuo ◽  
Vittorio Pengo ◽  
...  

Background. Antiphospholipid antibodies (aPL) recognizing an epitope comprising residues R39-R43 in the N-terminal domain, Domain I (DI), of beta-2 glycoprotein I (b2GPI) are considered among the most pathogenic in patients with Antiphospholipid Syndrome (APS). How such autoantibodies engage b2GPI at the molecular level remains incompletely understood. Aim. To better understand how pathogenic anti-DI antibodies engage b2GPI at the molecular level. Results. Under physiological conditions, b2GPI is believed to adopt a closed conformation featuring an intramolecular interaction between DI and DV with amino acids R39 and R43 in DI being masked by DV. This conformation is therefore predicted to be immunologically inert, incapable of reacting against pathogenic anti-DI antibodies. Once bound to the membranes, however, b2GPI is believed to undergo a dramatic conformational change which liberates DI to the solvent. To get a better grasp of the molecular flexibility of b2GPI under conditions relevant to physiology, we expressed and purified fully-glycosylated human recombinant b2GPI (hr-b2GPI) from HEK293 cells at high yield and purity suitable for structural biology and biophysical studies. After native purification, we found that the recombinant protein bound to heparin and negatively charged phospholipids with affinities comparable to those obtained for b2GPI that was purified from plasma using the perchloric acid method (p-b2GPI); hr-b2GPI also displayed similar reactivity against anti-b2GPI immunoglobulin G antibodies that were isolated from 5 APS patients. Surprisingly, hr-b2GPI and p-b2GPI were structurally similar, too. The X-ray crystal structures of hr-b2GPI and p-b2GPI solved at 2.6 and 2.4 Å resolution were superimposable documenting a J-shaped elongated conformation of the molecule in which DI was located &gt; 90 Å away from the C-terminal DV. Both structures were characterized by 22 oxidized cysteine residues forming 11 disulfide bonds, 4 N-glycosylations, and an intact yet flexible phospholipid-binding loop in DV. Since crystallization occurred at high salt concentrations, validation of the crystal structure of hr-b2GPI in solution was obtained by single-molecule Förster Resonance Energy Transfer (smFRET) and small-angle X-ray scattering (SAXS), while surface plasmon resonance (SPR) was used to probe the binding of a recently developed monoclonal anti-DI antibody, i.e., MBBS, to hr-b2GPI and p-b2GPI in solution. In keeping with the X-ray structural data, donor and acceptor fluorophores incorporated at positions 13/312 in DI and DV and 112/312 in DII and DV reported no measurable energy transfer whereas probes located at positions 13/112 in DI and DII displayed very high energy transfer. Likewise, the scattering profiles of the recombinant and plasma purified proteins returned similar hydrodynamic radii characteristic of elongated, flexible protein structures, and not circular. Notably, both hr-b2GPI and p-b2GPI in the elongated conformation were capable of interacting with MBBS without the need of phospholipids, even though addition of negatively charged phospholipids decreased the apparent dissociation affinity constant due to a reduction of the dissociation rate constant and a remarkable time-dependent accumulation of b2GPI onto the lipid surface, suggestive of a phospholipid-induced oligomerization mechanism. Conclusions. This study demonstrates that human b2GPI can adopt an elongated conformation in solution that is primed for phospholipid, heparin, and autoantibodies binding with DI constitutively exposed to the solvent. The fact that phospholipid-bound b2GPI is a better antigen for anti-DI autoantibody under physiological conditions as compared to the elongated form in solution can be explained by the relatively low affinity and bivalency of such autoantibodies that likely recognize a peptide motif pattern rather than a specific sequence of residues. Whether other context-dependent conformational changes occur after binding of the protein to the lipid surface, thus facilitating aPL binding, remain to be established. Since our studies failed to detect the closed form of b2GPI previously documented by electron and atomic force microscopy studies, it is possible that this conformation may arise from chemical and/or posttranslational modifications that occur in vivo while the protein circulates in the plasma. Disclosures No relevant conflicts of interest to declare.


Author(s):  
Liang Ma ◽  
Meixiang Xu ◽  
Andres F. Oberhauser

The activity of proteins and their complexes often involves the conversion of chemical energy (stored or supplied) into mechanical work through conformational changes. Mechanical forces are also crucial for the regulation of the structure and function of cells and tissues. Thus, the shape of eukaryotic cells is the result of cycles of mechano-sensing, mechano-transduction, and mechano-response. Recently developed single-molecule atomic force microscopy (AFM) techniques can be used to manipulate single molecules, both in real time and under physiological conditions, and are ideally suited to directly quantify the forces involved in both intra- and intermolecular protein interactions. In combination with molecular biology and computer simulations, these techniques have been applied to characterize the unfolding and refolding reactions in a variety of proteins, such as titin (an elastic mechano-sensing protein found in muscle) and polycystin-1 (PC1, a mechanosensor found in the kidney).


2016 ◽  
Vol 7 ◽  
pp. 138-148 ◽  
Author(s):  
Vivek S Jadhav ◽  
Dorothea Brüggemann ◽  
Florian Wruck ◽  
Martin Hegner

DNA handles are often used as spacers and linkers in single-molecule experiments to isolate and tether RNAs, proteins, enzymes and ribozymes, amongst other biomolecules, between surface-modified beads for nanomechanical investigations. Custom DNA handles with varying lengths and chemical end-modifications are readily and reliably synthesized en masse, enabling force spectroscopic measurements with well-defined and long-lasting mechanical characteristics under physiological conditions over a large range of applied forces. Although these chemically tagged DNA handles are widely used, their further individual modification with protein receptors is less common and would allow for additional flexibility in grabbing biomolecules for mechanical measurements. In-depth information on reliable protocols for the synthesis of these DNA–protein hybrids and on their mechanical characteristics under varying physiological conditions are lacking in literature. Here, optical tweezers are used to investigate different protein-labelled DNA handles in a microfluidic environment under different physiological conditions. Digoxigenin (DIG)-dsDNA-biotin handles of varying sizes (1000, 3034 and 4056 bp) were conjugated with streptavidin or neutravidin proteins. The DIG-modified ends of these hybrids were bound to surface-modified polystyrene (anti-DIG) beads. Using different physiological buffers, optical force measurements showed consistent mechanical characteristics with long dissociation times. These protein-modified DNA hybrids were also interconnected in situ with other tethered biotinylated DNA molecules. Electron-multiplying CCD (EMCCD) imaging control experiments revealed that quantum dot–streptavidin conjugates at the end of DNA handles remain freely accessible. The experiments presented here demonstrate that handles produced with our protein–DNA labelling procedure are excellent candidates for grasping single molecules exposing tags suitable for molecular recognition in time-critical molecular motor studies.


2019 ◽  
Author(s):  
Hamilton Lee ◽  
Jenica Lumata ◽  
Michael A. Luzuriaga ◽  
Candace Benjamin ◽  
Olivia Brohlin ◽  
...  

<div><div><div><p>Many contrast agents for magnetic resonance imaging are based on gadolinium, however side effects limit their use in some patients. Organic radical contrast agents (ORCAs) are potential alternatives, but are reduced rapidly in physiological conditions and have low relaxivities as single molecule contrast agents. Herein, we use a supramolecular strategy where cucurbit[8]uril binds with nanomolar affinities to ORCAs and protects them against biological reductants to create a stable radical in vivo. We further over came the weak contrast by conjugating this complex on the surface of a self-assembled biomacromolecule derived from the tobacco mosaic virus.</p></div></div></div>


2019 ◽  
Author(s):  
Hamilton Lee ◽  
Jenica Lumata ◽  
Michael A. Luzuriaga ◽  
Candace Benjamin ◽  
Olivia Brohlin ◽  
...  

<div><div><div><p>Many contrast agents for magnetic resonance imaging are based on gadolinium, however side effects limit their use in some patients. Organic radical contrast agents (ORCAs) are potential alternatives, but are reduced rapidly in physiological conditions and have low relaxivities as single molecule contrast agents. Herein, we use a supramolecular strategy where cucurbit[8]uril binds with nanomolar affinities to ORCAs and protects them against biological reductants to create a stable radical in vivo. We further over came the weak contrast by conjugating this complex on the surface of a self-assembled biomacromolecule derived from the tobacco mosaic virus.</p></div></div></div>


2009 ◽  
Vol 37 (4) ◽  
pp. 702-706 ◽  
Author(s):  
Liming Ying

At present, technical hurdles remain in probing biochemical processes in living cells and organisms at nanometre spatial resolution, millisecond time resolution and with high specificity and single-molecule sensitivity. Owing to its unique shape, size and electrical properties, the nanopipette has been used to obtain high-resolution topographic images of live cells under physiological conditions, and to create nanoscale features by controlled delivery of biomolecules. In the present paper, I discuss recent progress in the development of a family of new methods for nanosensing and nanomanipulation using nanopipettes.


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