scholarly journals HU multimerization shift controls nucleoid compaction

2016 ◽  
Vol 2 (7) ◽  
pp. e1600650 ◽  
Author(s):  
Michal Hammel ◽  
Dhar Amlanjyoti ◽  
Francis E. Reyes ◽  
Jian-Hua Chen ◽  
Rochelle Parpana ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Molecular Mechanisms ◽  
Bacterial Chromosome ◽  
Binding Modes ◽  
Dna Complexes ◽  
X Ray ◽  
X Ray Scattering ◽  
Nucleoid Structure ◽  
Ray Scattering

Molecular mechanisms controlling functional bacterial chromosome (nucleoid) compaction and organization are surprisingly enigmatic but partly depend on conserved, histone-like proteins HUαα and HUαβ and their interactions that span the nanoscale and mesoscale from protein-DNA complexes to the bacterial chromosome and nucleoid structure. We determined the crystal structures of these chromosome-associated proteins in complex with native duplex DNA. Distinct DNA binding modes of HUαα and HUαβ elucidate fundamental features of bacterial chromosome packing that regulate gene transcription. By combining crystal structures with solution x-ray scattering results, we determined architectures of HU-DNA nucleoproteins in solution under near-physiological conditions. These macromolecular conformations and interactions result in contraction at the cellular level based on in vivo imaging of native unlabeled nucleoid by soft x-ray tomography upon HUβ and ectopic HUα38 expression. Structural characterization of charge-altered HUαα-DNA complexes reveals an HU molecular switch that is suitable for condensing nucleoid and reprogramming noninvasiveEscherichia coliinto an invasive form. Collective findings suggest that shifts between networking and cooperative and noncooperative DNA-dependent HU multimerization control DNA compaction and supercoiling independently of cellular topoisomerase activity. By integrating x-ray crystal structures, x-ray scattering, mutational tests, and x-ray imaging that span from protein-DNA complexes to the bacterial chromosome and nucleoid structure, we show that defined dynamic HU interaction networks can promote nucleoid reorganization and transcriptional regulation as efficient general microbial mechanisms to help synchronize genetic responses to cell cycle, changing environments, and pathogenesis.

scholarly journals A hypothesis to reconcile the physical and chemical unfolding of proteins

2015 ◽  
Vol 112 (21) ◽  
pp. E2775-E2784 ◽  
Author(s):  
Guilherme A. P. de Oliveira ◽  
Jerson L. Silva
Keyword(s):  
Molecular Mechanisms ◽  
Chemical Shifts ◽  
Mechanistic Model ◽  
Solvent System ◽  
Threshold Concentration ◽  
Moniliophthora Perniciosa ◽  
X Ray ◽  
X Ray Scattering ◽  
Physical And Chemical ◽  
Ray Scattering

High pressure (HP) or urea is commonly used to disturb folding species. Pressure favors the reversible unfolding of proteins by causing changes in the volumetric properties of the protein–solvent system. However, no mechanistic model has fully elucidated the effects of urea on structure unfolding, even though protein–urea interactions are considered to be crucial. Here, we provide NMR spectroscopy and 3D reconstructions from X-ray scattering to develop the “push-and-pull” hypothesis, which helps to explain the initial mechanism of chemical unfolding in light of the physical events triggered by HP. In studying MpNep2 from Moniliophthora perniciosa, we tracked two cooperative units using HP-NMR as MpNep2 moved uphill in the energy landscape; this process contrasts with the overall structural unfolding that occurs upon reaching a threshold concentration of urea. At subdenaturing concentrations of urea, we were able to trap a state in which urea is preferentially bound to the protein (as determined by NMR intensities and chemical shifts); this state is still folded and not additionally exposed to solvent [fluorescence and small-angle X-ray scattering (SAXS)]. This state has a higher susceptibility to pressure denaturation (lower p1/2 and larger ΔVu); thus, urea and HP share concomitant effects of urea binding and pulling and water-inducing pushing, respectively. These observations explain the differences between the molecular mechanisms that control the physical and chemical unfolding of proteins, thus opening up new possibilities for the study of protein folding and providing an interpretation of the nature of cooperativity in the folding and unfolding processes.

Combined Small-Angle Neutron and X-Ray Scattering Studies of Polymers

1992 ◽  
Vol 36 ◽  
pp. 355-372
Author(s):  
George D. Wignall
Keyword(s):  
Crystal Structures ◽  
Small Angle ◽  
Polymer Science ◽  
X Ray ◽  
X Ray Scattering ◽  
Made In ◽  
Ray Scattering

Scattering technigues have been employed since the beginnings of polymer science to provide information on the spatial arrangements of macromolecules. The first measurements were made in the 1920s and were concerned primarily with the determination of crystal structures via the Bragg lawnλ = 2dsinθ.

scholarly journals Combining X-ray scattering and spectroscopy as structure resolving tool

2014 ◽  
Vol 70 (a1) ◽  
pp. C1074-C1074
Author(s):  
Sylvio Haas ◽  
Thomás Plivelic ◽  
Cedric Dicko
Keyword(s):  
Molecular Mechanisms ◽  
Basic Research ◽  
Sample Volume ◽  
Complex Behaviour ◽  
X Ray ◽  
Complex Interactions ◽  
X Ray Scattering ◽  
On Line ◽  
Set Up ◽  
Ray Scattering

Modern applications and basic research in medicine, biotechnology and materials are often concerned with hybrid (organic-inorganic) and synergetic systems. In other words, systems that brings enhanced properties and performances. The challenge is now in the understanding of the complex interactions leading to their assembly and operation. Due to their inherent chemical and structural complexities a combination of several techniques is necessary to determine unambiguously the molecular mechanisms of assembly and operation. [1, 2] To address this need, we have implemented a simultaneous measurement platform called SURF [3] that consists of SAXS, UV-Vis, Raman and fluorescence techniques. The SURF platform provides simultaneous measurements on the same sample volume and a multivariate framework to associate the spectroscopic and X-ray scattering information. Convex constraint analysis (CCA) and two dimensional correlation analyses (2DCOS and 2DHCOS) had been introduced to enhance the interpretation and integration of the data from the different techniques producing self-consistent models and resolving complex behaviour details (structure and chemistry). Additional benefits of the SURF are sample quality control and "on line" diagnostics. In this contribution, we illustrate the benefits of the SURF approach on selected examples. Acknowledgements: The SURF set-up has been mainly financial supported by MAX IV laboratory. S. Haas has a postdoctoral grant of MAX IV lab. S Canton and Q. Zhu are acknowledged for fruitful discussions.

The Structural Role of Gangliosides: Insights from X-ray Scattering on Model Membranes

2020 ◽  
Vol 27 (38) ◽  
pp. 6548-6570
Author(s):  
Konstantin Andreev
Keyword(s):  
Cholera Toxin ◽  
Molecular Mechanisms ◽  
Hexagonal Lattice ◽  
Langmuir Monolayers ◽  
Biologically Active ◽  
Adequate Model ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Background: Gangliosides are an essential component of eukaryotic plasma membranes implicated in multiple physiological processes. Little is known about molecular mechanisms underlying the distribution and functions of membrane gangliosides. The overwhelmingly complex organization of glycocalyx impedes the structural analysis on cell surface and the interplay between the lipid components. Advanced X-ray analytical tools applicable to studying biological interfaces call for the simplistic models that mimic ganglioside-enriched cellular membranes. Objective: To summarize the mechanistic evidences of ganglioside interactions with lipid environment and biologically active ligands using high-resolution synchrotron X-ray scattering. Methods: A comprehensive review of studies published over the last decade was done to discuss recent accomplishments and future trends. Results: Langmuir monolayers represent an adequate model system to assess the effect of gangliosides on membrane structure. Grazing incidence X-ray diffraction reveals a condensation effect by gangliosides on zwitterionic phospholipids with the cooperative packing of sialo- and phosphate groups. In turn, the arrangement of negatively charged lipids in ganglioside mixture remains unchanged due to the stretched conformation of carbohydrate moieties. Upon interaction with biological ligands, such as cholera toxin and galectins, the ganglioside redistribution within the ordered regions of monolayer follows distinct mechanistic patterns. The cholera toxin pentamer attached to the oligosaccharide core induces local transition from oblique to the hexagonal lattice resulting in phase coexistence. The incorporation of the A subunit responsible for endocytosis is further promoted by the acidic environment characteristic for endosomal space. X-ray reflectivity shows in-plane orientation of galectin dimers with the spatial mismatch between the lectin binding sites and ganglioside carbohydrates to perturb ceramide alkyl chains. Recent data also demonstrate sialic acid groups to be potential targets for novel peptide mimicking anticancer therapeutics. Conclusion: Coupled with surface X-ray scattering, the membrane mimetic approach allows for better understanding the biological role of gangliosides and their potential applications.

scholarly journals Potential for measurement of the distribution of DNA folds in complex environments using Correlated X-ray Scattering

2016 ◽  
Vol 30 (08) ◽  
pp. 1650117 ◽  
Author(s):  
Gundolf Schenk ◽  
Brad Krajina ◽  
Andrew Spakowitz ◽  
Sebastian Doniach
Keyword(s):  
Metallic Nanoparticles ◽  
Double Helix ◽  
X Rays ◽  
Complex Environments ◽  
Length Scales ◽  
X Ray ◽  
X Ray Scattering ◽  
Dna Double Helix ◽  
Ray Scattering

In vivo chromosomal behavior is dictated by the organization of genomic DNA at length scales ranging from nanometers to microns. At these disparate scales, the DNA conformation is influenced by a range of proteins that package, twist and disentangle the DNA double helix, leading to a complex hierarchical structure that remains undetermined. Thus, there is a critical need for methods of structural characterization of DNA that can accommodate complex environmental conditions over biologically relevant length scales. Based on multiscale molecular simulations, we report on the possibility of measuring supercoiling in complex environments using angular correlations of scattered X-rays resulting from X-ray free electron laser (xFEL) experiments. We recently demonstrated the observation of structural detail for solutions of randomly oriented metallic nanoparticles [D. Mendez et al., Philos. Trans. R. Soc. B 360 (2014) 20130315]. Here, we argue, based on simulations, that correlated X-ray scattering (CXS) has the potential for measuring the distribution of DNA folds in complex environments, on the scale of a few persistence lengths.

scholarly journals Supramolecular structures of benzyl amine derivate/DNA complexes explored with synchrotron small angle X-ray scattering at SPring-8

2009 ◽  
Vol 184 ◽  
pp. 012008 ◽  
Author(s):  
Mina Sakuragi ◽  
Shouta Kusuki ◽  
Emi Hamada ◽  
Hiroyasu Masunaga ◽  
Hiroki Ogawa ◽  
...  
Keyword(s):  
Small Angle ◽  
Supramolecular Structures ◽  
Dna Complexes ◽  
X Ray ◽  
Benzyl Amine ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals Crystal Structures and Small-angle X-ray Scattering Analysis of UDP-galactopyranose Mutase from the Pathogenic FungusAspergillus fumigatus

2012 ◽  
Vol 287 (12) ◽  
pp. 9041-9051 ◽  
Author(s):  
Richa Dhatwalia ◽  
Harkewal Singh ◽  
Michelle Oppenheimer ◽  
Dale B. Karr ◽  
Jay C. Nix ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Small Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals Revealing the molecular origins of fibrin’s elastomeric properties by in situ X-ray scattering

2019 ◽  
Author(s):  
Bart E. Vos ◽  
Cristina Martinez-Torres ◽  
Federica Burla ◽  
John W. Weisel ◽  
Gijsje H. Koenderink
Keyword(s):  
Molecular Mechanisms ◽  
X Ray ◽  
Packing Structure ◽  
X Ray Scattering ◽  
Fibrin Networks ◽  
Length Increase ◽  
Blood Clots ◽  
Structural Responses ◽  
Ray Scattering

Fibrin is an elastomeric protein forming highly extensible fiber networks that provide the scaffold of blood clots. Here we reveal the molecular mechanisms that explain the large extensibility of fibrin networks by performingin situsmall angle X-ray scattering measurements while applying a shear deformation. We simultaneously measure shear-induced alignment of the fibers and changes in their axially ordered molecular packing structure. We show that fibrin networks exhibit distinct structural responses that set in consecutively as the shear strain is increased. They exhibit an entropic response at small strains (<5%), followed by progressive fiber alignment (>25% strain) and finally changes in the fiber packing structure at high strain (>100%). Stretching reduces the fiber packing order and slightly increases the axial periodicity, indicative of molecular unfolding. However, the axial periodicity changes only by 0.7%, much less than the 80% length increase of the fibers, indicating that fiber elongation mainly stems from uncoiling of the natively disordered αC-peptide linkers that laterally bond the molecules. Upon removal of the load, the network structure returns to the original isotropic state, but the fiber structure becomes more ordered and adopts a smaller packing periodicity compared to the original state. We conclude that the hierarchical packing structure of fibrin fibers, with built-in disorder, makes the fibers extensible and allows for mechanical annealing. Our results provide a basis for interpreting the molecular basis of haemostatic and thrombotic disorders associated with clotting and provide inspiration to design resilient bio-mimicking materials.

scholarly journals Spermine-DNA complexes build up metastable structures. Small-angle X-ray scattering and circular dichroism studies

1979 ◽  
Vol 7 (5) ◽  
pp. 1297-1310 ◽  
Author(s):  
M. Becker ◽  
R. Misselwitz ◽  
Hilde Damaschun ◽  
G. Damaschun ◽  
D. Zirwer
Keyword(s):  
Circular Dichroism ◽  
Small Angle ◽  
Dna Complexes ◽  
X Ray ◽  
X Ray Scattering ◽  
Metastable Structures ◽  
Circular Dichroïsm ◽  
Ray Scattering
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