scholarly journals RNA fragment assembly with experimental restraints

2021 ◽  
Author(s):  
Grzegorz Chojnowski ◽  
Rafał Zaborowski ◽  
Marcin Magnus ◽  
Janusz M. Bujnicki
Keyword(s):  
Web Service ◽  
Structural Studies ◽  
Recent Application ◽  
Automated Assembly ◽  
Saxs Data ◽  
Viral Rnas ◽  
Fragment Assembly ◽  
X Ray ◽  
X Ray Scattering ◽  
Rna Fragments

ABSTRACTWe present RNA Masonry, a computer program and a web service for a fully automated assembly of RNA fragments into geometrically plausible models fulfilling user-provided secondary structure constraints and restraints on tertiary contacts and Small Angle X-ray Scattering (SAXS) data. We illustrate the method description with its recent application to structural studies of viral RNAs with SAXS restraints. The program web server is available at http://iimcb.genesilico.pl/[email protected]

Structural refinement by restrained molecular-dynamics algorithm with small-angle X-ray scattering constraints for a biomolecule

2004 ◽  
Vol 37 (1) ◽  
pp. 103-109 ◽  
Author(s):  
Masaki Kojima ◽  
Alexander A. Timchenko ◽  
Junichi Higo ◽  
Kazuki Ito ◽  
Hiroshi Kihara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Small Angle ◽  
Protein Structures ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Saxs Curve ◽  
Restrained Molecular Dynamics ◽  
Ray Scattering

A new algorithm to refine protein structures in solution from small-angle X-ray scattering (SAXS) data was developed based on restrained molecular dynamics (MD). In the method, the sum of squared differences between calculated and observed SAXS intensities was used as a constraint energy function, and the calculation was started from given atomic coordinates, such as those of the crystal. In order to reduce the contribution of the hydration effect to the deviation from the experimental (objective) curve during the dynamics, and purely as an estimate of the efficiency of the algorithm, the calculation was first performed assuming the SAXS curve corresponding to the crystal structure as the objective curve. Next, the calculation was carried out with `real' experimental data, which yielded a structure that satisfied the experimental SAXS curve well. The SAXS data for ribonuclease T1, a single-chain globular protein, were used for the calculation, along with its crystal structure. The results showed that the present algorithm was very effective in the refinement and adjustment of the initial structure so that it could satisfy the objective SAXS data.

scholarly journals Structural Analysis of the Partially Disordered Protein EspK from Mycobacterium tuberculosis

Crystals ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 18
Author(s):  
Abril Gijsbers ◽  
Nuria Sánchez-Puig ◽  
Ye Gao ◽  
Peter J. Peters ◽  
Raimond B. G. Ravelli ◽  
...  
Keyword(s):  
Host Response ◽  
Limited Proteolysis ◽  
Maximal Dimension ◽  
Globular Domain ◽  
Saxs Data ◽  
X Ray ◽  
Disordered Protein ◽  
X Ray Scattering ◽  
C Terminus ◽  
New Treatments

For centuries, tuberculosis has been a worldwide burden for human health, and gaps in our understanding of its pathogenesis have hampered the development of new treatments. ESX-1 is a complex machinery responsible for the secretion of virulence factors that manipulate the host response. Despite the importance of these secreted proteins for pathogenicity, only a few of them have been structurally and functionally characterised. Here, we describe a structural study of the ESX-secretion associated protein K (EspK), a 74 kDa protein known to be essential for the secretion of other substrates and the cytolytic effects of ESX-1. Small-Angle X-ray Scattering (SAXS) data show that EspK is a long molecule with a maximal dimension of 228 Å. It consists of two independent folded regions at each end of the protein connected by a flexible unstructured region driving the protein to coexist as an ensemble of conformations. Limited proteolysis identified a 26 kDa globular domain at the C-terminus of the protein consisting of a mixture of α-helices and β-strands, as shown by circular dichroism (CD) and SAXS. In contrast, the N-terminal portion is mainly helical with an elongated shape. Sequence conservation suggests that this architecture is preserved amongst the different mycobacteria species, proposing specific roles for the N- and C-terminal domains assisted by the middle flexible linker.

Structural studies of carbons by neutron and x-ray scattering

2018 ◽  
Vol 82 (1) ◽  
pp. 016501 ◽  
Author(s):  
Andrzej Burian ◽  
John C Dore ◽  
Karolina Jurkiewicz
Keyword(s):  
Structural Studies ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

scholarly journals Universal nature of collapsibility in the context of protein folding and evolution

2018 ◽  
Author(s):  
D. Thirumalai ◽  
Himadri S. Samanta ◽  
Hiranmay Maity ◽  
Govardhan Reddy
Keyword(s):  
Single Molecule ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Saxs Data ◽  
X Ray ◽  
Model Free ◽  
X Ray Scattering ◽  
Theoretical Predictions ◽  
Helical Proteins ◽  
Universal Nature

AbstractTheory and simulations predicted sometime ago that the sizes of unfolded states of globular proteins should decrease continuously as the denaturant concentration is shifted from a high to a low value. However, small angle X-ray scattering (SAXS) data were used to assert the opposite, while interpretation of single molecule Forster resonance energy transfer experiments (FRET) supported the theoretical predictions. The disagreement between the two experiments is the SAXS-FRET controversy. By harnessing recent advances in SAXS and FRET experiments and setting these findings in the context of a general theory and simulations, we establish that compaction of unfolded states is universal. The theory also predicts that proteins rich in β-sheets are more collapsible than α-helical proteins. Because the extent of compaction is small, experiments have to be accurate and their interpretations should be as model free as possible. Theory also suggests that collapsibility itself could be a physical restriction on the evolution of foldable sequences, and provides a physical basis for the origin of multi-domain proteins.

scholarly journals Plasmodium falciparum Kelch13 and its artemisinin-resistant mutants assemble as hexamers in solution: a SAXS data driven shape restoration study

2021 ◽  
Author(s):  
Nainy Goel ◽  
Kanika Dhiman ◽  
Nidhi Kalidas ◽  
Anwesha Mukhopadhyay ◽  
Ashish ◽  
...  
Keyword(s):  
Artemisinin Resistance ◽  
Resistant Mutant ◽  
Data Driven ◽  
Wild Type ◽  
Saxs Data ◽  
Mutant Proteins ◽  
X Ray ◽  
X Ray Scattering ◽  
Shape Restoration ◽  
Spatial Positioning

AbstractArtemisinin-resistant mutations in PfKelch13 identified worldwide are mostly confined to its BTB/POZ and KRP domains. To date, only two crystal structures of the BTB/POZ-KRP domains as tight dimers are available, which limits structure-based interpretations of its functionality. Our solution Small-Angle X-ray Scattering (SAXS) data driven shape restoration of larger length of protein brought forth that: i) PfKelch13 forms a stable hexamer in P6 symmetry, ii) interactions of the N-termini drive the hexameric assembly, and iii) the six KRP domains project independently in space, forming a cauldron-like architecture. While artemisinin-sensitive mutant A578S packed like the wild-type, hexameric assemblies of dominant artemisinin-resistant mutant proteins R539T and C580Y displayed detectable differences in spatial positioning of their BTB/POZ-KRP domains. Lastly, mapping of mutations known to enable artemisinin resistance explained that most mutations exist mainly in these domains because they are non-detrimental to assembly of mutant PfKelch13 and yet can alter the flux of downstream events essential for susceptibility to artemisinin.

Quality control of protein standards for molecular mass determinations by small-angle X-ray scattering

2010 ◽  
Vol 43 (2) ◽  
pp. 237-243 ◽  
Author(s):  
Shuji Akiyama
Keyword(s):  
Quality Control ◽  
Molecular Mass ◽  
Small Angle ◽  
Biological Macromolecules ◽  
Average Deviation ◽  
Saxs Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Standard Quality ◽  
Ray Scattering

Small-angle X-ray scattering (SAXS) is a powerful technique with which to evaluate the size and shape of biological macromolecules in solution. Forward scattering intensity normalized relative to the particle concentration,I(0)/c, is useful as a good measure of molecular mass. A general method for deducing the molecular mass from SAXS data is to determine the ratio ofI(0)/cof a target protein to that of a standard protein with known molecular mass. The accuracy of this interprotein calibration is affected considerably by the monodispersity of the prepared standard, as well as by the precision in estimating its concentration. In the present study, chromatographic fractionation followed by hydrodynamic characterization is proposed as an effective procedure by which to prepare a series of monodispersed protein standards. The estimation of molecular mass within an average deviation of 8% is demonstrated using monodispersed bovine serum albumin as a standard. The present results demonstrate the importance of protein standard quality control in order to take full advantage of interprotein calibration.

scholarly journals Structural Study of the Photo-Mediated Growth of Silver Nanoprisms

Molecules ◽  
2020 ◽  
Vol 25 (22) ◽  
pp. 5413
Author(s):  
Matti Knaapila ◽  
Ulla Vainio ◽  
Sophie E. Canton ◽  
Gunnel Karlsson
Keyword(s):  
Particle Size ◽  
Small Angle ◽  
Volume Ratio ◽  
Direct Methods ◽  
Saxs Data ◽  
Aqueous Dispersions ◽  
X Ray ◽  
Silver Nanoprisms ◽  
X Ray Scattering ◽  
Ag Particles

We present a small-angle X-ray scattering (SAXS) study of the anisotropic photoinduced growth of silver (Ag) nanoprisms in aqueous dispersions. The growth of nearly spherical (<10 nm) Ag particles into large (>40 nm) and thin (<10 nm) triangular nanoprisms induced by 550 nm laser is followed in terms of particle size using indirect and direct methods for irradiation times up to 150 min. During the process, the surface-to-volume ratio of the particles decreased. The SAXS data of the initial solution fit well to the model of polydisperse spheres with pronounced average diameters around 7.4 nm and 10 nm. The data after 45 min irradiation fit well to the model containing approximately the same amount of the initial particles and the end product, the nanoprisms.

scholarly journals Supercritical CO2extraction of porogen phase: An alternative route to nanoporous dielectrics

2004 ◽  
Vol 19 (11) ◽  
pp. 3224-3233 ◽  
Author(s):  
J.A. Lubguban ◽  
S. Gangopadhyay ◽  
B. Lahlouh ◽  
T. Rajagopalan ◽  
N. Biswas ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Selective Extraction ◽  
Porous Structures ◽  
Saxs Data ◽  
3D Images ◽  
X Ray ◽  
X Ray Scattering ◽  
Through Diffusion ◽  
Organosilicate Thin Films ◽  
Poly Propylene

We present a supercritical CO2(SCCO2) process for the preparation of nanoporous organosilicate thin films for ultralow dielectric constant materials. The porous structure was generated by SCCO2extraction of a sacrificial poly(propylene glycol) (PPG) from a nanohybrid film, where the nanoscopic domains of PPG porogen are entrapped within the crosslinked poly(methylsilsesquioxane) (PMSSQ) matrix. As a comparison, porous structures generated by both the usual thermal decomposition (at approximately 450 °C) and by a SCCO2process for 25 and 55 wt% porogen loadings were evaluated. It is found that the SCCO2process is effective in removing the porogen phase at relatively low temperatures (<200 °C) through diffusion of the supercritical fluid into the phase-separated nanohybrids and selective extraction of the porogen phase. Pore morphologies generated from the two methods are compared from representative three-dimensional (3D) images built from small-angle x-ray scattering (SAXS) data.

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