Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept

Allec, Nicholas; Choi, Mina; Yesupriya, Nikhil; Szychowski, Brian; White, Michael R. H.; Kann, Maricel G.; Garcin, Elsa D.; Daniel, Marie‐Christine; Badano, Aldo

doi:10.1038/srep12085

Cited by 35 publications

(30 citation statements)

References 53 publications

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“…No form of intermolecular interaction, be it attractive, repulsive, hydrophobic etc can ensue outside the region of mutual perturbative influence. The quantification of interactions (which is a function of vectorial motion) between biomolecules is essential for understanding the molecular basis of biological processes (rate of digestion, passive transport etc) [45]. Here there is need to define interaction in the light of Kirkwood-Buff solution theory [46].…”

Section: Usefulness Of Translational Velocitymentioning

confidence: 99%

The State of Proteins not with Standing, Translational Velocity is Vital for their Function

Udema¹,

Onigbinde

2019

AJRB

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Background: Targeting of macromolecules by means of translational diffusion for therapeutic reason is generally of interest. But translational velocity that enables directional delivery of any molecule on target is given less attention. Objectives: The objectives of this research are to: 1) determine the value of the cohesion factor affecting solutes, 2) determine the translational velocity of porcine pancreatic (PPAA) - and human salivary (HSAA) – alpha amylase and ions, 3) rederive the effective kinetic energy (K.E.) of solutes, 4) determine the thermodynamic parameters for a folded to an unfolded transition and 5) give reasons why the velocity of solution components is generally very important. Methods: A theoretical research and experimentation using Bernfeld method. Results and Discussion: The K.E. of solution components as re-derived is « 3kBT / 2 (where kB and T are Boltzmann constant and Kelvin temperature respectively.). The velocities of hydrolysis of the substrate with the sucrose-treated PPAA were generally higher than those of HSAA. The values of conformational entropy change (∆Sconf) for PPAA were generally higher than those of HSAA. Expectedly the values of ∆Sconf were positive. Conclusion: In conclusion, the square root of the cohesion factor is larger than 22.4 exp (+3) 310.15 K / 273.15 K / 18, accounting for the translational velocity (u) in solution being « gas phase velocity (U). The translational diffusion D and u remain respectively, a function of the hydrodynamic radius of the solutes in particular and the magnitude of D; unfolding of proteins decreases the values of the parameters. Overall, unfolding is entropy driven. Without the mobility of solution components at desired velocity directional delivery of small molecules to site of need such as intrinsically disordered proteins etc may remain impossible.

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Section: Usefulness Of Translational Velocitymentioning

confidence: 99%

The State of Proteins not with Standing, Translational Velocity is Vital for their Function

Udema¹,

Onigbinde

2019

AJRB

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“…There are an increasing number of imaging applications for small-angle X-ray scattering (SAXS) using scanning (Gourrier et al, 2007) and tomographic methods (Schroer et al, 2006;Jensen et al, 2011). We have proposed a particular biomedical application that utilizes SAXS molecular imaging of probed protein-protein interactions (Allec et al, 2015). SAXS imaging is a promising alternative tool for in vivo molecular imaging because the coherent scattering provides nanostructural information about a sample without the need for destructive sample preparation techniques.…”

Section: Introductionmentioning

confidence: 99%

“…Well defined SAXS signatures from high-contrast molecular probes, such as gold nanoparticles (GNPs), could be correlated with the presence of biomolecular interactions and provide a higher-specificity option that is able to image protein-protein interactions in vivo in deep tissue. It was demonstrated that GNP signals could be determined even within a complex background such as Escherichia coli lysate (Allec et al, 2015). However, concerns remain regarding the long measurement times and the excessive amount of energy deposited into live samples.…”

Section: Introductionmentioning

confidence: 99%

“…We describe the procedure of converting scattering intensity profiles to cross sections that can be used as inputs to the simulations. After simulation of the SAXS instrument measurement of virtual samples, a previously developed method (Allec et al, 2015) was used to extract from the scattering profiles the required information regarding the fraction of interacting particles in a solution and the size of monomers and dimers.…”

Section: Introductionmentioning

confidence: 99%

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Monte Carlo X-ray transport simulation of small-angle X-ray scattering instruments using measured sample cross sections

et al. 2016

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Small‐angle X‐ray scattering (SAXS) has recently been proposed as a novel noninvasive in vivo molecular imaging technique to characterize molecular interactions deep within the body using high‐contrast probes. This article describes a detailed Monte Carlo X‐ray transport simulation technique that utilizes user‐provided cross sections to describe X‐ray interaction in virtual samples and explore SAXS instrument design choices. The accuracy of the simulation code is validated with sample material cross sections derived from analytical models and empirical measurements of a homogeneous spherical gold nanoparticle (GNP) monomer, a dimer and heterogeneous mixtures of the two in aqueous solution. Analytical and measured scattering profiles from these samples were converted to cross sections using an absolute water standard. Our Monte Carlo estimates of the fraction of dimers from analytically derived and empirically derived cross sections are strongly correlated, with less than 1.5 and 16% error, respectively, to the expected concentration of monomer and dimer species. In addition, a variety of monoenergetic X‐ray beams were simulated to investigate coherent scattering versus radiation dose for a range of sample sizes. For GNP spheres in aqueous solution, the energy range that produces the most coherent scattering at the detector per deposited energy was between 31 and 49 keV for a sample thickness of 1 mm to 10 cm. The method described here for the detailed simulation of SAXS using measured and modeled cross sections will enable instrumentation optimization for in vivo molecular imaging applications.

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“…solvent subtraction and contrast), and molecular modeling. Research involving the SAS method has accelerated in recent years, which includes the characterization of molecular interactions [1] and the development of software for comparing atomistic models with data from SAS [11].…”

mentioning

confidence: 99%

Quantitative biology: from molecular to cellular systems

Stadtländer

2015

Journal of Biological Dynamics

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Small-angle X-ray scattering method to characterize molecular interactions: Proof of concept

Cited by 35 publications

References 53 publications

The State of Proteins not with Standing, Translational Velocity is Vital for their Function

The State of Proteins not with Standing, Translational Velocity is Vital for their Function

Monte Carlo X-ray transport simulation of small-angle X-ray scattering instruments using measured sample cross sections

Quantitative biology: from molecular to cellular systems

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