scholarly journals Direct Evidence of Effect of Glycerol on Hydration and Helix-to-Sheet Transition of Myoglobin

2018 ◽  
Author(s):  
M. Hirai ◽  
S. Ajito ◽  
M. Sugiyama ◽  
H. Iwase ◽  
S.-I. Takata ◽  
...  
Keyword(s):  
Neutron Scattering ◽  
Tertiary Structure ◽  
Hydration Shell ◽  
Scattering Data ◽  
Variation Method ◽  
Protein Surface ◽  
X Ray ◽  
X Ray Scattering ◽  
Structural Levels ◽  
Ray Scattering

AbstractBy using wide-angle X-ray scattering (WAXS), small-angle neutron scattering, and theoretical scattering function simulation, we have clarified the effect of glycerol on both the thermal structure transition and the hydration-shell of myoglobin. At the glycerol concentration, ≤ ∼40 % v/v, the decreasing tendency in the maximum dimension and the radius of gyration was observed by X-ray scattering. The neutron scattering result using the inverse contrast variation method directly shows the preservation of the hydration-shell density at the concentration ≤ ∼40 % v/v. This phenomenon is reasonably explained by the preferential exclusion of glycerol from the protein surface to preserve the hydration shell, as suggested by the previous studies. While, at the concentration, ≥ 50 % v/v, the opposite tendency was observed. It suggests the preferential solvation (partial preferential penetration or replacement of glycerol into or with hydration-shell water surrounding the protein surface) occurs at the higher concentration. The observed WAXS scattering data covers the distinct hierarchical structural levels of myoglobin structure ranging from the tertiary structure to the secondary one. Therefore, we have clarified the effect of glycerol on the thermal structural stability myoglobin at different hierarchical structural levels separately. Against the temperature rise, the structural transition temperatures for all hierarchical structural levels were elevated. Especially, the tertiary structure of myoglobin was more stabilized compared with the internal-structure and the helix-to-cross transition. It suggests that the protective action of glycerol on protein structures essentially results from the preservation of the preferential hydration-shell of proteins.

scholarly journals Modelling of the serine-proteinase fold by X-ray and neutron scattering and sedimentation analyses: occurrence of the fold in factor D of the complement system

1993 ◽  
Vol 295 (1) ◽  
pp. 87-99 ◽  
Author(s):  
S J Perkins ◽  
K F Smith ◽  
J M Kilpatrick ◽  
J E Volanakis ◽  
R B Sim
Keyword(s):  
Neutron Scattering ◽  
Sedimentation Coefficient ◽  
Serine Proteinase ◽  
Scattering Data ◽  
Multidomain Proteins ◽  
X Ray ◽  
Trypsinogen Activation ◽  
X Ray Scattering ◽  
Monomeric Proteins ◽  
Ray Scattering

Solution scattering is a powerful means of determining the overall arrangement of domains in the multidomain proteins of complement. the serine-proteinase domain is central to all proteolytic events during complement activation. As models of this domain, bovine beta-trypsin, trypsinogen, alpha-chymotrypsin and chymotrypsinogen A were studied by neutron and X-ray synchrotron solution scattering. At pH 7, all the X-ray and neutron M(r) values corresponded to monomeric proteins. The X-ray radii of gyration, RG, of beta-trypsin, trypsinogen, alpha-chymotrypsin and chymotrypsinogen A (measured in positive solute-solvent contrasts) were 1.59 nm, 1.78 nm, 1.71 nm and 1.76 nm (+/- 0.05-0.11 nm) in that order. Neutron contrast variation showed that the RG at infinite contrast, RC, for these four proteins were 1.57 nm, 1.70 nm, 1.67 nm and 1.78 nm (+/- 0.03 nm) in that same order. The radial inhomogeneity of neutron-scattering density, alpha, was positive at (5-13) x 10(-5), and corresponds to the preponderance of hydrophilic residues near the protein surface. On trypsinogen activation, a small reduction in the RG value of 0.13 +/- 0.07 nm was just detectable, while the RG of chymotrypsinogen A was unchanged after activation. The RC and alpha values of the four proteins can be calculated by using crystallographic co-ordinates. The reduced RG of beta-trypsin relative to trypsinogen was explained in terms of the removal of the extended N-terminal hexapeptide of trypsinogen. The full X-ray and neutron-scattering curves in positive and negative contrasts agreed well with scattering curves calculated from crystallographic coordinates to a nominal structural resolution of 4.5 nm, provided that the internal structure was considered in neutron modelling, and that the hydration was considered in X-ray modelling. Sedimentation-coefficient data also provide information on the disposition of domains in multidomain proteins. It was found that the hydrated X-ray sphere model could be directly utilized to calculate sedimentation coefficients. X-ray scattering on factor D showed from its RG of 1.78 nm that this is monomeric and very similar in structure to beta-trypsin. The X-ray-scattering curve of factor D was readily modelled using the beta-trypsin crystal structure after allowance for sequence changes. The success of these modellings provides a basis for the constrained modelling of solution scattering data for the multidomain proteins of complement.

scholarly journals SAXSDom: Modeling multi-domain protein structures using small-angle X-ray scattering data

2019 ◽  
Author(s):  
Jie Hou ◽  
Badri Adhikari ◽  
John J. Tanner ◽  
Jianlin Cheng
Keyword(s):  
Homology Modeling ◽  
Small Angle ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Scattering Data ◽  
Multidomain Proteins ◽  
X Ray ◽  
X Ray Scattering ◽  
Domain Protein ◽  
Ray Scattering

AbstractMany proteins are composed of several domains that pack together into a complex tertiary structure. Some multidomain proteins can be challenging for protein structure modeling, particularly those for which templates can be found for the domains but not for the entire sequence. In such cases, homology modeling can generate high quality models of the domains but not for the assembled protein. Small-angle X-ray scattering (SAXS) reports on the solution structural properties of proteins and has the potential for guiding homology modeling of multidomain proteins. In this work, we describe a novel multi-domain protein assembly modeling method, SAXSDom, that integrates experimental knowledge from SAXS profiles with probabilistic Input-Output Hidden Markov model (IOHMM). Four scoring functions to account for the energetic contribution of SAXS restraints for domain assembly were developed and tested. The method was evaluated on multi-domain proteins from two public datasets. Based on the results, the accuracy of domain assembly was improved for 40 out of 46 CASP multi-domain proteins in terms of RMSD and TM-score when SAXS information was used. Our method also achieved higher accuracy for at least 45 out of 73 multi-domain proteins according to RMSD and TM-score metrics in the AIDA dataset. The results demonstrate that SAXS data can provide useful information to improve the accuracy of domain-domain assembly. The source code and tool packages are available at http://github.com/multicom-toolbox/SAXSDom.

scholarly journals Structure of aqueous sodium acetate solutions by X-Ray scattering and density functional theory

2020 ◽  
Vol 92 (10) ◽  
pp. 1627-1641
Author(s):  
Guangguo Wang ◽  
Yongquan Zhou ◽  
He Lin ◽  
Zhuanfang Jing ◽  
Hongyan Liu ◽  
...  
Keyword(s):  
Sodium Acetate ◽  
Density Functional ◽  
Hydration Shell ◽  
Ion Pair ◽  
Water Molecules ◽  
Sodium Acetate Solution ◽  
Acetate Solution ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

AbstractThe structure of aq. sodium acetate solution (CH3COONa, NaOAc) was studied by X-ray scattering and density function theory (DFT). For the first hydrated layer of Na+, coordination number (CN) between Na+ and O(W, I) decreases from 5.02 ± 0.85 at 0.976 mol/L to 3.62 ± 1.21 at 4.453 mol/L. The hydration of carbonyl oxygen (OC) and hydroxyl oxygen (OOC) of CH3COO− were investigated separately and the OC shows a stronger hydration bonds comparing with OOC. With concentrations increasing, the hydration shell structures of CH3COO− are not affected by the presence of large number of ions, each CH3COO− group binds about 6.23 ± 2.01 to 7.35 ± 1.73 water molecules, which indicates a relatively strong interaction between CH3COO− and water molecules. The larger uncertainty of the CN of Na+ and OC(OOC) reflects the relative looseness of Na-OC and Na-OOC ion pairs in aq. NaOAc solutions, even at the highest concentration (4.453 mol/L), suggesting the lack of contact ion pair (CIP) formation. In aq. NaOAc solutions, the so called “structure breaking” property of Na+ and CH3COO− become effective only for the second hydration sphere of bulk water. The DFT calculations of CH3COONa (H2O)n=5–7 clusters suggest that the solvent-shared ion pair (SIP) structures appear at n = 6 and become dominant at n = 7, which is well consistent with the result from X-ray scattering.

scholarly journals Global Small-Angle X-ray Scattering Data Analysis of Triacylglycerols in the Molten State (Part I)

2018 ◽  
Vol 122 (45) ◽  
pp. 10320-10329 ◽  
Author(s):  
Amin Sadeghpour ◽  
Marjorie Ladd Parada ◽  
Josélio Vieira ◽  
Megan Povey ◽  
Michael Rappolt
Keyword(s):  
Data Analysis ◽  
Small Angle ◽  
Scattering Data ◽  
Molten State ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering

Reconstruction of viruses from solution x-ray scattering data

1995 ◽  
Author(s):  
Yibin Zheng ◽  
Peter C. Doerschuk ◽  
John E. Johnson
Keyword(s):  
Scattering Data ◽  
X Ray ◽  
X Ray Scattering ◽  
Ray Scattering
Sign in / Sign up

Export Citation Format

Share Document