Tracking ligand-migration pathways of carbonmonoxy myoglobin in crystals at cryogenic temperatures

2010 ◽  
Vol 66 (2) ◽  
pp. 220-228 ◽  
Author(s):  
Ayana Tomita ◽  
Tokushi Sato ◽  
Shunsuke Nozawa ◽  
Shin-ya Koshihara ◽  
Shin-ichi Adachi
Keyword(s):  
Structural Changes ◽  
Continuous Wave ◽  
Cryogenic Temperatures ◽  
Amino Acid Residues ◽  
Migration Pathway ◽  
Laser Pumping ◽  
Ligand Migration ◽  
Migration Dynamics ◽  
Carbonmonoxy Myoglobin ◽  
Migration Pathways

In order to explore the ligand-migration dynamics in myoglobin induced by photodissociation, cryogenic X-ray crystallographic investigations of carbonmonoxy myoglobin crystals illuminated by continuous wave and pulsed lasers at 1–15 kHz repetition rate have been carried out. Here it is shown that this novel method, extended pulsed-laser pumping of carbonmonoxy myoglobin, promotes ligand migration in the protein matrix by crossing the glass transition temperature repeatedly, and enables the visualization of the migration pathway of the photodissociated ligands in native Mb at cryogenic temperatures. It has revealed that the migration of the CO molecule into each cavity induces structural changes of the amino-acid residues around the cavity which result in the expansion of the cavity. The sequential motion of the ligand and the cavity suggests a self-opening mechanism of the ligand-migration channel arising by induced fit.

scholarly journals Slow ligand migration dynamics in carbonmonoxy myoglobin at cryogenic temperature

2008 ◽  
Vol 64 (a1) ◽  
pp. C358-C358
Author(s):  
A. Tomita ◽  
T. Sato ◽  
K. Ichiyanagi ◽  
S. Nozawa ◽  
H. Ichikawa ◽  
...  
Keyword(s):  
Cryogenic Temperature ◽  
Ligand Migration ◽  
Migration Dynamics ◽  
Carbonmonoxy Myoglobin

scholarly journals Paracellular and Transcellular Leukocytes Diapedesis Are Divergent but Interconnected Evolutionary Events

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 254
Author(s):  
Michel-Edwar Mickael ◽  
Norwin Kubick ◽  
Pavel Klimovich ◽  
Patrick Henckell Flournoy ◽  
Irmina Bieńkowska ◽  
...  
Keyword(s):  
Immune Cell ◽  
Critical Role ◽  
Cellular Polarity ◽  
Endothelial Layer ◽  
Trichoplax Adhaerens ◽  
Migration Pathway ◽  
Two Systems ◽  
Sequence Reconstruction ◽  
Rhoa Protein ◽  
Migration Pathways

Infiltration of the endothelial layer of the blood-brain barrier by leukocytes plays a critical role in health and disease. When passing through the endothelial layer during the diapedesis process lymphocytes can either follow a paracellular route or a transcellular one. There is a debate whether these two processes constitute one mechanism, or they form two evolutionary distinct migration pathways. We used artificial intelligence, phylogenetic analysis, HH search, ancestor sequence reconstruction to investigate further this intriguing question. We found that the two systems share several ancient components, such as RhoA protein that plays a critical role in controlling actin movement in both mechanisms. However, some of the key components differ between these two transmigration processes. CAV1 genes emerged during Trichoplax adhaerens, and it was only reported in transcellular process. Paracellular process is dependent on PECAM1. PECAM1 emerged from FASL5 during Zebrafish divergence. Lastly, both systems employ late divergent genes such as ICAM1 and VECAM1. Taken together, our results suggest that these two systems constitute two different mechanical sensing mechanisms of immune cell infiltrations of the brain, yet these two systems are connected. We postulate that the mechanical properties of the cellular polarity is the main driving force determining the migration pathway. Our analysis indicates that both systems coevolved with immune cells, evolving to a higher level of complexity in association with the evolution of the immune system.

scholarly journals Brown Spiders’ Phospholipases-D with Potential Therapeutic Applications: Functional Assessment of Mutant Isoforms

Biomedicines ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 320
Author(s):  
Thaís Pereira da Silva ◽  
Fernando Jacomini de Castro ◽  
Larissa Vuitika ◽  
Nayanne Louise Costacurta Polli ◽  
Bruno César Antunes ◽  
...  
Keyword(s):  
Structural Changes ◽  
Capillary Permeability ◽  
Structural Data ◽  
Histopathological Analysis ◽  
Amino Acid Residues ◽  
Wild Type ◽  
Antigenic Properties ◽  
Harmful Effects

Phospholipases-D (PLDs) found in Loxosceles spiders’ venoms are responsible for the dermonecrosis triggered by envenomation. PLDs can also induce other local and systemic effects, such as massive inflammatory response, edema, and hemolysis. Recombinant PLDs reproduce all of the deleterious effects induced by Loxosceles whole venoms. Herein, wild type and mutant PLDs of two species involved in accidents—L. gaucho and L. laeta—were recombinantly expressed and characterized. The mutations are related to amino acid residues relevant for catalysis (H12-H47), magnesium ion coordination (E32-D34) and binding to phospholipid substrates (Y228 and Y228-Y229-W230). Circular dichroism and structural data demonstrated that the mutant isoforms did not undergo significant structural changes. Immunoassays showed that mutant PLDs exhibit conserved epitopes and kept their antigenic properties despite the mutations. Both in vitro (sphingomyelinase activity and hemolysis) and in vivo (capillary permeability, dermonecrotic activity, and histopathological analysis) assays showed that the PLDs with mutations H12-H47, E32-D34, and Y228-Y229-W230 displayed only residual activities. Results indicate that these mutant toxins are suitable for use as antigens to obtain neutralizing antisera with enhanced properties since they will be based on the most deleterious toxins in the venom and without causing severe harmful effects to the animals in which these sera are produced.

scholarly journals Structural Aspects of Remelting of the AZ91 Magnesium Alloy Surface Layer

2016 ◽  
Vol 16 (1) ◽  
pp. 13-18
Author(s):  
J. Iwaszko ◽  
M. Strzelecka
Keyword(s):  
Surface Layer ◽  
Magnesium Alloy ◽  
Structural Changes ◽  
Continuous Wave ◽  
Sample Surface ◽  
Alloy Surface ◽  
Az91 Alloy ◽  
Az91 Magnesium Alloy ◽  
Az91 Magnesium ◽  
Alloy Surface Layer

Abstract In this study, modification of the AZ91 magnesium alloy surface layer with a CO2 continuous wave operation laser has been taken on. The extent and character of structural changes generated in the surface layer of the material was being assessed on the basis of both macro- and microscopy investigations, and the EDX analysis. Considerable changes in the structure of the AZ91 alloy surface layer and the morphology of phases have been found. The remelting processing was accompanied by a strong refinement of the structure and a more uniform distribution of individual phases. The conducted investigations showed that the remelting zone dimensions are a result of the process parameters, and that they can be controlled by an appropriate combination of basic remelting parameters, i.e. the laser power, the distance from the sample surface, and the scanning rate. The investigations and the obtained results revealed the possibility of an effective modification of the AZ91 magnesium alloy surface layer in the process of remelting carried out with a CO2 laser beam.

scholarly journals Following Ligand Migration Pathways from Picoseconds to Milliseconds in Type II Truncated Hemoglobin from Thermobifida fusca

PLoS ONE ◽  
2012 ◽  
Vol 7 (7) ◽  
pp. e39884 ◽  
Author(s):  
Agnese Marcelli ◽  
Stefania Abbruzzetti ◽  
Juan Pablo Bustamante ◽  
Alessandro Feis ◽  
Alessandra Bonamore ◽  
...  
Keyword(s):  
Thermobifida Fusca ◽  
Type Ii ◽  
Truncated Hemoglobin ◽  
Ligand Migration ◽  
Migration Pathways

Structural Changes in Confined Lysozyme

2009 ◽  
Vol 131 (7) ◽  
Author(s):  
Eduardo Reátegui ◽  
Alptekin Aksan
Keyword(s):  
Fourier Transform ◽  
Infrared Spectroscopy ◽  
Structural Changes ◽  
Heat Denaturation ◽  
Cryogenic Temperatures ◽  
Key Factors ◽  
Denaturation Temperature ◽  
Novel Technologies ◽  
Factors Influencing ◽  
The Matrix

Proteins and enzymes can be encapsulated in nanoporous gels to develop novel technologies for biosensing, biocatalysis, and biosynthesis. When encapsulated, certain macromolecules retain high levels of activity and functionality and are more resistant to denaturation when exposed to extremes of pH and temperature. We have utilized intrinsic fluorescence and Fourier transform infrared spectroscopy to determine the structural transitions of encapsulated lysozyme in the range of −120°C<T<100°C. At cryogenic temperatures encapsulated lysozyme did not show cold denaturation, instead became more structured. However, at high temperatures, the onset of heat denaturation of confined lysozyme was reduced by 15°C when compared with lysozyme in solution. Altered dynamics of the solvent and pore size distribution of the nanopores in the matrix appear to be key factors influencing the decrease in the denaturation temperature.

Vacancy Migration Barrier Energetics and Pathways in Silica

1998 ◽  
Vol 538 ◽  
Author(s):  
L. R. Corrales ◽  
R.M. Van Ginhoven ◽  
J. Song ◽  
H. Jónsson
Keyword(s):  
Point Defect ◽  
Defect Formation ◽  
Vacancy Defect ◽  
Elastic Band ◽  
Simulation Methodology ◽  
Defect Migration ◽  
Migration Pathway ◽  
Empirical Potentials ◽  
Band Method ◽  
Migration Pathways

AbstractA study of vacancy defect migration pathways and energetics in a-quartz is carried out using an empirical simulation methodology that is coupled with the nudged elastic band method. Results from this study indicate that the migration pathway for migration is between adjacent sites. We anticipate the results will guide modifications to empirical potentials for use in the study of point defect formation of more complex systems.

scholarly journals Improving Hydride Conductivity in Layered Perovskites via Crystal Engineering

2020 ◽  
Author(s):  
Harry W. T. Morgan ◽  
Harry J. Stroud ◽  
Neil Allan
Keyword(s):  
Crystal Engineering ◽  
Density Functional ◽  
Rational Design ◽  
Ionic Mobility ◽  
Theory Approach ◽  
Ion Migration ◽  
Energy Applications ◽  
Migration Pathway ◽  
Migration Pathways ◽  
Layered Perovskites

Hydride ion conduction in layered perovskites is of great interest for sustainable-energy applications. In this report we study Ba2ScHO3, a recently synthesized oxyhydride with an unusual anion ordering, using a multifaceted density functional theory approach involving both transition state calculations and molecular dynamics simulations. Beyond simply identifying the key ion migration pathways, we perform detailed analysis of transition states and identify key interactions which drive trends in ionic mobility. Our key findings are that ionic mobility is, remarkably, independent of hydride-oxide disorder, the dominant migration pathway changes under pressure, and a reduction in A-site cation size accelerates hydride diffusion. Local structural flexibility along migration pathways is understood in terms of dimensionality and ionic size, and we thus identify crystal engineering principles for rational design of ion conductors. On the basis of our new insights into these materials, we predict that Sr2ScHO3 will show improved conductivity over existing analogues.

A large anisotropic plasticity of L-leucinium hydrogen maleate preserved at cryogenic temperatures

2019 ◽  
Vol 75 (2) ◽  
pp. 143-151 ◽  
Author(s):  
S. G. Arkhipov ◽  
E. A. Losev ◽  
T. T. Nguyen ◽  
D. A. Rychkov ◽  
E. V. Boldyreva
Keyword(s):  
Organic Compound ◽  
Structural Changes ◽  
Cryogenic Temperatures ◽  
Ambient Conditions ◽  
Anisotropic Plasticity ◽  
Temperature Range ◽  
Cryogenic Conditions

L-Leucinium hydrogen maleate crystals are very plastic at ambient conditions. Here it is shown that this plasticity is preserved at least down to 77 K. The structural changes in the temperature range 293–100 K were followed in order to rationalize the large anisotropic plasticity in this compound. To the best of our knowledge, this is the first reported example of an organic compound remaining so plastic at cryogenic conditions.

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