Unraveling folding pathways of dynamic DNA quadruplexes

G-quadruplexes (G4s) are non-B form DNA structures containing genomic regions rich in guanine that sometimes fold into and often act as transcriptional regulators. They are frequently located at regulatory sites including promoters, replication origins and telomeres11. Understanding their folding pathways, while important to a fundamental understanding of form and function, has been challenging. G4 quadruplex folding pathways are distinct from not only proteins but also duplex RNA and DNA12. Previous work characterizing folding pathways using FRET, CD or stopped-flow absorbance suggested a complex, multi-step pathway. Researchers from the University of Louisville, some of whom are frequent BioCAT users, performed continuous-flow mixing time-resolved SAXS experiments to directly structurally characterize, for the first time, early steps in the G4 quadruplex folding pathway.

G4 formation is primarily driven by hydrogen bonding, ion coordination and nucleotide pi-stacking and their resulting structures are stabilized (or destabilized) by a combination of factors including pH, temperature, ionic strength and loop length. Unlike proteins or most duplex nucleic acids, common chaotropic agents such as urea or Guanidinium hydrochloride are not effective at unfolding G-quadruplexes. As such, preliminary equilibrium circular dichroism studies of the systems of interest, two human telomere hybrid structures, were used to identify effective denaturation conditions …

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A role for titin in residual force enhancement in skeletal muscle

Mechanism of RFE. Configuration of sarcomeric proteins during (A) IsoS, (B) IsoL, and (C) IsoR indicating isometric contractions and short length, long length and after an active stretch respectively. In passive muscle, titin-thin filament interactions are weak so that myofilaments do not show significant strain during passive stretch. During contraction, the titin-thin filament interaction becomes stronger, so that during an eccentric contraction, titin is extended, producing elevated titin-based force and explaining the mechanical and structural signatures in IsoR. Increased titin-based force contributes to RFE by decreasing smaller lattice spacing and increased thick filament stiffness, leading to increased force production and force transmission, respectively.

Residual force enhancement (RFE) is a property of skeletal muscle where more force is produced after an active stretch than if it were simply activated at the longer length. This property is important for jumping, locomotive, and stabilizing movements of the body. The molecular mechanism underlying RFE is not well understood.

In muscle, the protein titin connects myofilaments and has been shown to have many roles in sarcomere stability and modulating contraction. The authors of this study investigated titin’s function during contraction using small-angle X-ray diffraction of untreated WT mouse skeletal muscle and muscle where 50 …

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Role of titin in the pathophysiology of diaphragm weakness during mechanical ventilation

ICU patient diaphragm produces less titin based passive tension increasing interfilament lattice spacing (d10) and reducing calcium sensitivity.

Diaphragm unloading during mechanical ventilation is an important clinical problem. The diaphragm is the main muscle of respiration and contracts during each breath, thereby changing the anatomic configurations of the chest wall so that air flows into the lungs. Increased diaphragm loading is associated with diaphragm fiber contractile dysfunction, atrophy and injury. Whereas these effects of increased loading on the diaphragm take months or years to develop, the effects of decreased loading, as occurs when ICU patients are mechanically ventilated, occur extremely rapidly, within hours. For ICU patients with respiratory failure this mechanical ventilation is considered a life-saving supportive therapy. However, mechanical ventilation, with its attendant diaphragm muscle inactivity, can cause rapid diaphragmatic weakness, leading to difficulties in discontinuing this ventilatory support (i.e. weaning failure). Weaning failure is a major clinical problem; it is encountered in >30% of mechanically ventilated ICU patients, it consumes ~40% of all ICU resources, and, importantly, patients experiencing weaning failure are at much higher risk for death due to pneumonia and airway trauma. These issues came to the fore with the large numbers of mechanically ventilated …

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How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins

Temperature-controlled SEX-SAXS capabilities at BioCAT were the main tool used in these studies.

Understanding the driving forces behind stability of denatured state ensembles (DSE’s) and intrinsically disordered proteins (IDP’s) is central to a number of unresolved questions in bimolecular thermodynamics regarding protein folding pathways and foldability, thermodynamic stability, aggregation and misfolding. Researchers at the University of Chicago and Notre Dame used temperature-controlled size-exclusion chromatography-coupled SAXS (SEC-SAXS) and NMR to examine how temperature and solvent ionic strength influences the solution structure(s) of the N-terminal domain of pertactin (PNt). PNt is a valuable model system from a fundamental biophysical point of view, as the full-length 539-residue pertactin folds into a parallel β-helix but the 334 N-terminal residues do not and instead behave as a highly expanded, intrinsically disordered chain.

In this work, the authors used temperature-series SEC-SAXS experiments performed at BioCAT, with temperatures ranging from 4 to 60 degrees C, to show that PNt displays a mild, temperature-dependent contraction (as measured by Rg value). Glycine-rich low hydrophobicity model systems (as proxies for protein backbones alone) did not display an analogous trend, showing the specific importance of side chain interactions. Increasing the ionic strength of the …

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Titin-Based Force Modulates Cardiac Thick and Thin Filaments

Molecular changes to cardiac sarcomeres after 50% titin cleavage. A. Schematic of a half sarcomere with myosin heads shown in ON (green) and off (gray) states and TEV protease recognition site (scissors). B. X-ray diffraction pattern of permeabilized TC papillary muscle. C-H. Changes in diffraction features with changes in SL before and after protease treatment.

The Frank-Starling Law of the Heart states that the heart’s stroke volume increases with greater preload due to increased venous return, allowing the heart to adapt to varying circulatory demands. At the molecular level, increasing preload increases sarcomere length (SL), which alters structures within the sarcomere that are correlated to increased calcium sensitivity upon activation. The titin protein, spanning the half-sarcomere acts as a spring in the I-band, applies a SL-dependent passive force on the myosin containing thick filaments changing its structure and functional properties. Altered titin-based forces play a crucial role in the etiology of many cardiomyopathies; however, the disease state obscures titin’s role, impeding therapeutic solutions.

The authors studied titin’s specific role using the titin cleavage (TC) mouse model, where a tobacco-etch virus protease (TEVP) recognition site is inserted into distal I-band titin and allows for rapid, specific cleavage …

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Myosin-binding protein C regulates the sarcomere lattice and stabilizes the OFF states of myosin heads

Muscle contraction is produced via the interaction of myofilaments and is regulated so that muscle performance matches demand. Myosin-binding protein C (MyBP-C) is a long and flexible protein that is tightly bound to the thick filament at its C-terminal end (MyBP-CC8C10), but may be loosely bound at its middle- and N-terminal end (MyBP-CC1C7) to myosin heads and/or the thin filament. MyBP-C is thought to control muscle contraction via the regulation of myosin motors, as mutations lead to debilitating disease. Thick filament based regulatory mechanisms involve either sequestering myosin head into an inactive ordered off state close to the thick filament backbone or releasing them so that they can interact with actin. Strain in the thick filaments, either from a few active heads or passively generated by stretching titin, is presumed to act as a trigger to release inactive heads. While MyBP-C has been presumed to play a role(s) in thick filament activation, details of these mechanisms have been lacking. Here the authors used combination of mechanics and small-angle X-ray diffraction to study the effects of immediate and selective removal of the MyBP-CC1C7 domains of fast MyBP-C on sarcomere structure and function in permeabilized skeletal muscle …

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Structural insights into the formation of repulsive netrin guidance complexes

Negative stain electron microscopy and SAXS results demonstrated the UNC-6–heparin–UNC-5 complexes have stable, ordered architectures.

Netrins are a conserved class of proteins involved in synaptic connectivity of the nervous system in bilaterian animals. They act as secreted guidance cues, with the unique ability to exert repulsive and attractive responses on growing axons. They are also known to be involved in cell proliferation, migration and differentiation, and are therefore targets for treating cancer and insulin resistance. During axon growth and cell migration, the presence of the receptor Uncoordinated-5 (UNC-5) on target cells results in repulsion. However, the exact mechanism involved in the induction of repulsive forces has been relatively unknown due to the lack of biochemical and structural information about these systems. Researchers at the University of Chicago and Stanford University, in collaboration with BioCAT staff, showed that UNC-5 is a heparin-binding protein, determined its structure bound to a heparin fragment, and could modulate UNC-5–heparin affinity using a directed evolution platform or structure-based rational design.

A question they needed to answer was whether the heparin + UNC-6–mediated UNC-5 oligomers are an ordered and well-defined molecular species or (ii) whether these oligomers …

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Myosin in autoinhibited off state(s), stabilized by mavacamten, can be recruited in response to inotropic interventions

A) Representative X-ray diffraction patterns from permeabilized porcine myocardium under relaxing conditions (pCa 8, Top) and activating conditions (pCa 4.5) with (Bottom Right) and without (Bottom Left) mavacamten in the absence of active force (treated with 100 μM MYK-7660). (B-E) Changes in diffraction signatures of off to on transitions in the myosin heads, as a function of calcium concentration, showing that Ca2+ induced structural changes in the thick filament were blunted but not eliminated by the presence of mavacamten.

Mavacamten is the first myosin-targeted small-molecule therapy approved by the Food and Drug Administration to treat obstructive hypertrophic cardiomyopathy by attenuating excessive myocardial sarcomere activity. Mavacamten regulates cardiac function at the sarcomere level by selectively but reversibly inhibiting the enzymatic activity of myosin. It shifts myosin toward ordered off states close to the thick filament backbone making them unavailable for binding to actin and generating force. It is necessary, however for the heart to adjust its output to ensure sufficient cardiac output, especially during increased physiological demands. It was unknown whether mavacamten stabilized heads could still be recruited by the usual physiological inotropic mechanisms for the patient to be able to adapt to changing demands on their hearts …

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The structural OFF and ON states of myosin can be decoupled from the biochemical super- and disordered-relaxed states

X-ray diffraction patterns from permeabilized porcine myocardium in relaxing solution in the presence and absence of myosin activators. A) X-ray diffraction patterns from relaxed muscle in the absence (left panel) and presence (right panel) of 10 µM OM. B) X-ray diffraction patterns from relaxed muscle in the absence (left panel) and presence (right panel) of 50 µM piperine (PIP). Equatorial intensity ratio (I1,1/I1,0) at different concentrations of OM C) and piperine D). Myosin heads move radially closer to actin as OM and piperine concentration increases as expected for myosin activators that promote off to on transitions in the myosin heads. These are under conditions where there is no observed changes in SRX/DRX ratios.

Myosin-based thick-filament regulation is now known to be critical for muscle contraction with myosin dysregulation found in hypertrophic and dilated cardiomyopathies but many details of thick filament regulation remain to be discovered. Myosin ATPase assays have demonstrated that under relaxed conditions, myosin may reside either in a high-energy-consuming disordered-relaxed (DRX) state available for binding actin to generate force or in an energy-sparing super-relaxed (SRX) state unavailable for actin binding. X-ray diffraction studies have shown that the majority of myosin heads are in a …

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Insights Into Unusual Morphologies of Lipid Nanoparticle Encapsulations

The success of mRNA-based COVID-19 vaccines has brought increased attention to lipid nanoparticles (LNPs) as an RNA therapeutic delivery method. One of the main challenges of LNPs as a delivery method remains the significant percentage of unloaded LNPs in most (if not all) RNA-LNP formulations, highlighting a need for better characterization of their formation, composition and morphology. While there have been a number of recent advances in understanding the formation and structure of LNPs, studies exploring the influence of non-mRNA RNAs on LNP morphology remain limited. Of particular interest is the delivery of self-amplifying mRNA (SAM), which has the potential to both significantly lower dosage as well extend the antigen expression lifetime in the body. However, given that SAM molecules are typically significantly larger than conventional nonreplicating mRNA, and that larger nucleic acids are known to promote the formation of significant populations of empty LNPs, further work is needed to better understand the formation, composition and morphology of LNPs in order to better inform LNPs as a delivery system for promising therapeutic strategies that rely on larger nucleic acids.

Researchers from ORNL, NIST and the GSK Center for Vaccine research characterized the morphology of LNPs encapsulating SAMs using …

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