scholarly journals Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state

IUCrJ ◽  
2021 ◽  
Vol 8 (6) ◽  
Author(s):  
Nobutaka Numoto ◽  
Yoshiaki Kawano ◽  
Hideo Okumura ◽  
Seiki Baba ◽  
Yoshihiro Fukumori ◽  
...  
Keyword(s):  
Oxygen Saturation ◽  
Structural Changes ◽  
Structural Transition ◽  
Structural Information ◽  
Oxygen Binding ◽  
Oxygen Dissociation ◽  
Two State Model ◽  
Prosthetic Groups ◽  
Temperature Factors

Cooperative oxygen binding of hemoglobin (Hb) has been studied for over half a century as a representative example of the allostericity of proteins. The most important problem remaining to be solved is the lack of structural information on the intermediates between the oxygenated and deoxygenated forms. In order to characterize the intermediate structures, it is necessary to obtain intermediate-state crystals, determine their oxygen saturations and then determine the oxygen saturations of each of their constituent subunits, all of which are challenging issues even now. Here, intermediate forms of the 400 kDa giant Hb from the tubeworm Oligobrachia mashikoi are reported. To overcome the above problems without any artificial modifications to the protein or prosthetic groups, intermediate crystals of the giant Hb were prepared from fully oxygenated crystals by a soaking method. The oxygen saturation of the crystals was measured by in situ observation with a microspectrophotometer using thin plate crystals processed by an ultraviolet laser to avoid saturation of absorption. The oxygen saturation of each subunit was determined by occupancy refinement of the bound oxygen based on ambient temperature factors. The obtained structures reveal the detailed relationship between the structural transition and oxygen dissociation. The dimer subassembly of the giant Hb shows strong correlation with the local structural changes at the heme pockets. Although some local ternary-structural changes occur in the early stages of the structural transition, the associated global ternary-structural and quaternary-structural changes might arise at about 50% oxygen saturation. The models based on coarse snapshots of the allosteric transition support the conventional two-state model of Hbs and provide the missing pieces of the intermediate structures that are required for full understanding of the allosteric nature of Hbs in detail.

scholarly journals Partial oxygen-dissociation of crystalline giant hemoglobin

2014 ◽  
Vol 70 (a1) ◽  
pp. C474-C474 ◽  
Author(s):  
Nobutaka Numoto ◽  
Taro Nakagawa ◽  
Akiko Kita ◽  
Nobutoshi Ito ◽  
Yoshihiro Fukumori ◽  
...  
Keyword(s):  
Structural Changes ◽  
Quaternary Structure ◽  
Oxygen Binding ◽  
Nitrogen Gas ◽  
Soaking Time ◽  
Allosteric Mechanism ◽  
Oxygen Dissociation ◽  
Intermediate States ◽  
Complete Dissociation ◽  
Partial Oxygen

Allosteric oxygen-binding of hemoglobin (Hb) has been widely discussed based on the quaternary structural changes elucidated by the crystal structures of the oxygenated and deoxygenated states. However, it remains to be determined the structure of intermediate states between the oxy and deoxy forms without any artificial modification of the Hb molecule. A tubeworm, Lamellibrachia satsuma has extracellular giant hemoglobins with a molecular mass of about 400 and 3,600 kDa. Recently, we have determined the crystal structure of the 400 kDa Hb (V2Hb) in the oxy state, and then we successfully obtained the deoxygenated crystals of V2Hb from oxy crystals by the soaking methods [1]. These findings encourage us to initiate structural studies for the intermediate states between the oxy and deoxy forms of V2Hb, which should provide a more accurate understanding of the allosteric mechanism of Hbs. The deoxy crystals of V2Hb were obtained from oxy crystals through the soaking in a solution containing 50 mM sodium hydrosulfite, and incubated for a few minutes. We tested various soaking times from 3 s to 180 s and then immediately flash-frozen under a nitrogen gas stream. The obtained structures reveal that in the case of the soaking time was longer than 10 s, the electron densities of the oxygen molecules at some heme pockets (oxygen binding sites) were very week or disappeared. These `intermediate' structures show almost the same quaternary structure as that of the oxy structure. This fact suggests that quaternary rearrangement of V2Hb might arise just before a complete dissociation of all the oxygen molecules from all the subunits.

scholarly journals Dynamic characterization of structural changes in vapochromic compounds by pair distribution function

2017 ◽  
Vol 32 (S1) ◽  
pp. S118-S122
Author(s):  
R. Caliandro ◽  
B. D. Belviso ◽  
C. Cuocci ◽  
S. Fuertes ◽  
V. Sicilia ◽  
...  
Keyword(s):  
Distribution Function ◽  
Pair Distribution Function ◽  
Structural Changes ◽  
Structural Information ◽  
Powder Samples ◽  
Anionic Complexes ◽  
Overlapping Peaks ◽  
Vapochromic Behavior

Two examples of anionic complexes having vapochromic behavior are investigated: [K(H2O)][Pt(ppy)(CN)2] “Pt(ppy)” and [K(H2O)][Pt(bzq)(CN)2] “Pt(bzq)”, where ppy = 2-phenylpyridinate and bzq = 7,8-benzoquinolate. These monohydrate-potassium salts exhibit a change in color from purple to yellow [Pt(ppy)] and from red to yellow [Pt(bzq)] upon heating to 110 °C, and they transform back into the original color upon absorption of water molecules from the environment. Available only in the form of polycrystalline samples, no structural information on such compounds is accessible, due to highly overlapping peaks in powder diffraction profiles. We use in situ Pair Distribution Function measurements on powder samples to investigate the dynamics of the structural changes induced by temperature variations. By means of a multivariate approach, we were able to extract dynamic structural information from collected profiles without using prior knowledge on the static crystal structure of the compounds. The critical temperature and the characteristics of the vapochromic transition have been identified, as well as the main structural changes causing it.

scholarly journals Mechanism of silica–lysozyme composite formation unravelled by in situ fast SAXS

2019 ◽  
Vol 10 ◽  
pp. 182-197 ◽  
Author(s):  
Tomasz M Stawski ◽  
Daniela B van den Heuvel ◽  
Rogier Besselink ◽  
Dominique J Tobler ◽  
Liane G Benning
Keyword(s):  
Structural Changes ◽  
Structural Information ◽  
Aqueous Media ◽  
Inorganic Nanoparticles ◽  
Interparticle Interactions ◽  
Aggregation Processes ◽  
Composite Formation ◽  
Quantitative Understanding ◽  
Inherent Nature

A quantitative understanding of aggregation mechanisms leading to the formation of composites of inorganic nanoparticles (NPs) and proteins in aqueous media is of paramount interest for colloid chemistry. In particular, the interactions between silica (SiO2) NPs and lysozyme (LZM) have attracted attention, because LZM is well-known to adsorb strongly to silica NPs, while at the same time preserving its enzymatic activity. The inherent nature of the aggregation processes leading to NP–LZM composites involves structural changes at length scales from few to at least hundreds of nanometres but also time scales much smaller than one second. To unravel these we used in situ synchrotron-based small-angle X-ray scattering (SAXS) and followed the subtle interparticle interactions in solution at a time resolution of 50 ms/frame (20 fps). We show that if the size of silica NPs (ca. 5 nm diameter) is matched by the dimensions of LZM, the evolving scattering patterns contain a unique structure-factor contribution originating from the presence of LZM. We developed a scattering model and applied it to analyse this structure function, which allowed us to extract structural information on the deformation of lysozyme molecules during aggregation, as well as to derive the mechanisms of composite formation.

scholarly journals Fast operando X-ray pair distribution function using the DRIX electrochemical cell

2020 ◽  
Vol 27 (5) ◽  
pp. 1190-1199
Author(s):  
Maria Diaz-Lopez ◽  
Geoffrey L. Cutts ◽  
Phoebe K. Allan ◽  
Dean S. Keeble ◽  
Allan Ross ◽  
...  
Keyword(s):  
Distribution Function ◽  
Pair Distribution Function ◽  
Structural Changes ◽  
Structural Information ◽  
Scattering Data ◽  
Cell Design ◽  
Total Scattering ◽  
X Ray ◽  
Electrochemical Cycling

In situ electrochemical cycling combined with total scattering measurements can provide valuable structural information on crystalline, semi-crystalline and amorphous phases present during (dis)charging of batteries. In situ measurements are particularly challenging for total scattering experiments due to the requirement for low, constant and reproducible backgrounds. Poor cell design can introduce artefacts into the total scattering data or cause inhomogeneous electrochemical cycling, leading to poor data quality or misleading results. This work presents a new cell design optimized to provide good electrochemical performance while performing bulk multi-scale characterizations based on total scattering and pair distribution function methods, and with potential for techniques such as X-ray Raman spectroscopy. As an example, the structural changes of a nanostructured high-capacity cathode with a disordered rock-salt structure and composition Li4Mn2O5 are demonstrated. The results show that there is no contribution to the recorded signal from other cell components, and a very low and consistent contribution from the cell background.

scholarly journals A graph-based algorithm for detecting rigid domains in protein structures

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Truong Khanh Linh Dang ◽  
Thach Nguyen ◽  
Michael Habeck ◽  
Mehmet Gültas ◽  
Stephan Waack
Keyword(s):  
Structural Changes ◽  
Viterbi Algorithm ◽  
Structural Information ◽  
Line Graph ◽  
Clustering Algorithms ◽  
Protein Structures ◽  
Alternative Methods ◽  
Structural Transitions ◽  
Tuning Parameters ◽  
Conformational Ensembles

Abstract Background Conformational transitions are implicated in the biological function of many proteins. Structural changes in proteins can be described approximately as the relative movement of rigid domains against each other. Despite previous efforts, there is a need to develop new domain segmentation algorithms that are capable of analysing the entire structure database efficiently and do not require the choice of protein-dependent tuning parameters such as the number of rigid domains. Results We develop a graph-based method for detecting rigid domains in proteins. Structural information from multiple conformational states is represented by a graph whose nodes correspond to amino acids. Graph clustering algorithms allow us to reduce the graph and run the Viterbi algorithm on the associated line graph to obtain a segmentation of the input structures into rigid domains. In contrast to many alternative methods, our approach does not require knowledge about the number of rigid domains. Moreover, we identified default values for the algorithmic parameters that are suitable for a large number of conformational ensembles. We test our algorithm on examples from the DynDom database and illustrate our method on various challenging systems whose structural transitions have been studied extensively. Conclusions The results strongly suggest that our graph-based algorithm forms a novel framework to characterize structural transitions in proteins via detecting their rigid domains. The web server is available at http://azifi.tz.agrar.uni-goettingen.de/webservice/.

Roughened gold electrode for in situ SERS analysis of structural changes accompanying the doping process of polyaniline in acidic aqueous media

2021 ◽  
Vol 882 ◽  
pp. 115034
Author(s):  
A. El Guerraf ◽  
M. Bouabdallaoui ◽  
Z. Aouzal ◽  
S. Ben Jadi ◽  
N.K. Bakirhan ◽  
...  
Keyword(s):  
Gold Electrode ◽  
Structural Changes ◽  
Aqueous Media

Effect of Age on Oxygen-Binding in Normal Human Subjects

1976 ◽  
Vol 51 (2) ◽  
pp. 185-188
Author(s):  
P. M. Tweeddale ◽  
R. J. E. Leggett ◽  
D. C. Flenley
Keyword(s):  
Oxygen Saturation ◽  
Oxygen Tension ◽  
Inorganic Phosphate ◽  
Human Subjects ◽  
Oxygen Binding ◽  
Corpuscular Haemoglobin ◽  
Positive Correlation ◽  
Normal Human ◽  
Mean Corpuscular Haemoglobin ◽  
Effect Of Age

1. Oxygen-binding, plasma and intra-erythrocytic pH, and haemoglobin, 2,3-diphosphoglycerate and inorganic phosphate concentrations were measured in sixty-two healthy non-smokers aged between 18 and 89 years. 2. P50 (oxygen tension at 50% oxygen saturation) expressed at plasma pH 7·40 and Pco2 5·33 kPa showed a positive correlation with age. 3. This correlation of P50 with age was closer when P50 was expressed at a constant intra-erythrocytic pH 7·20. On average P50 at intra-erythrocytic pH 7·20 increased from 3·59 kPa at 20 years to 3·96 kPa at 90 years of age. 4. 2,3-Diphosphoglycerate, inorganic phosphate, haemoglobin and mean corpuscular haemoglobin concentrations did not correlate with P50 or with age.

scholarly journals High temperature structural study of decagonal Al-Cu-Rh quasicrystal.

2014 ◽  
Vol 70 (a1) ◽  
pp. C94-C94
Author(s):  
Pawel Kuczera ◽  
Walter Steurer
Keyword(s):  
Structural Changes ◽  
Configurational Entropy ◽  
Lattice Vibrations ◽  
X Ray Diffraction ◽  
Stabilization Mechanism ◽  
X Ray ◽  
Comparative Structure ◽  
The Stability

The structure of d(ecagonal)-Al-Cu-Rh has been studied as a function of temperature by in-situ single-crystal X-ray diffraction in order to contribute to the discussion on energy or entropy stabilization of quasicrystals (QC) [1]. The experiments were performed at 293 K, 1223 K, 1153 K, 1083 K, and 1013 K. A common subset of 1460 unique reflections was used for the comparative structure refinements at each temperature. The results obtained for the HT structure refinements of d-Al-Cu-Rh QC seem to contradict a pure phasonic-entropy-based stabilization mechanism [2] for this QC. The trends observed for the ln func(I(T1 )/I(T2 )) vs.|k⊥ |^2 plots indicate that the best on-average quasiperiodic order exists between 1083 K and 1153 K, however, what that actually means is unclear. It could indicate towards a small phasonic contribution to entropy, but such contribution is not seen in the structure refinements. A rough estimation of the hypothetic phason instability temperature shows that it would be kinetically inaccessible and thus the phase transition to a 12 Å low T structure (at ~800 K) is most likely not phason-driven. Except for the obvious increase in the amplitude of the thermal motion, no other significant structural changes, in particular no sources of additional phason-related configurational entropy, were found. All structures are refined to very similar R-values, which proves that the quality of the refinement at each temperature is the same. This suggests, that concerning the stability factors, some QCs could be similar to other HT complex intermetallic phases. The experimental results clearly show that at least the ~4 Å structure of d-Al-Cu-Rh is a HT phase therefore entropy plays an important role in its stabilisation mechanism lowering the free energy. However, the main source of this entropy is probably not related to phason flips, but rather to lattice vibrations, occupational disorder unrelated to phason flips like split positions along the periodic axis.

Identifying and Evaluating Anomalous Structural Change-based Nodes in Generalized Dynamic Social Networks

2021 ◽  
Vol 15 (4) ◽  
pp. 1-22
Author(s):  
Huan Wang ◽  
Chunming Qiao ◽  
Xuan Guo ◽  
Lei Fang ◽  
Ying Sha ◽  
...  
Keyword(s):  
Social Networks ◽  
Structural Change ◽  
Structural Changes ◽  
Structural Information ◽  
Similarity Index ◽  
Dynamic Social Network ◽  
Dynamic Social Networks ◽  
Micro Level ◽  
Anomaly Analysis ◽  
Similarity Method

Recently, dynamic social network research has attracted a great amount of attention, especially in the area of anomaly analysis that analyzes the anomalous change in the evolution of dynamic social networks. However, most of the current research focused on anomaly analysis of the macro representation of dynamic social networks and failed to analyze the nodes that have anomalous structural changes at a micro level. To identify and evaluate anomalous structural change-based nodes in generalized dynamic social networks that only have limited structural information, this research considers undirected and unweighted graphs and develops a multiple-neighbor superposition similarity method ( ), which mainly consists of a multiple-neighbor range algorithm ( ) and a superposition similarity fluctuation algorithm ( ). introduces observation nodes, characterizes the structural similarities of nodes within multiple-neighbor ranges, and proposes a new multiple-neighbor similarity index on the basis of extensional similarity indices. Subsequently, maximally reflects the structural change of each node, using a new superposition similarity fluctuation index from the perspective of diverse multiple-neighbor similarities. As a result, based on and , not only identifies anomalous structural change-based nodes by detecting the anomalous structural changes of nodes but also evaluates their anomalous degrees by quantifying these changes. Results obtained by comparing with state-of-the-art methods via extensive experiments show that can accurately identify anomalous structural change-based nodes and evaluate their anomalous degrees well.

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