scholarly journals Structural Contour Map of the Iota Carbonic Anhydrase from the Diatom Thalassiosira pseudonana Using a Multiprong Approach

2021 ◽  
Vol 22 (16) ◽  
pp. 8723
Author(s):  
Erik L. Jensen ◽  
Véronique Receveur-Brechot ◽  
Mohand Hachemane ◽  
Laura Wils ◽  
Pascale Barbier ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Experimental Data ◽  
Protein Kinase ◽  
Three Dimensional ◽  
Thalassiosira Pseudonana ◽  
Marine Diatom ◽  
Carbonic Anhydrases ◽  
Contour Map ◽  
Biophysical Techniques ◽  
High Flexibility

Carbonic anhydrases (CAs) are a family of ubiquitous enzymes that catalyze the interconversion of CO2 and HCO3−. The “iota” class (ι-CA) was first found in the marine diatom Thalassiosira pseudonana (tpι-CA) and is widespread among photosynthetic microalgae and prokaryotes. The ι-CA has a domain COG4875 (or COG4337) that can be repeated from one to several times and resembles a calcium–calmodulin protein kinase II association domain (CaMKII-AD). The crystal structure of this domain in the ι-CA from a cyanobacterium and a chlorarachniophyte has been recently determined. However, the three-dimensional organization of the four domain-containing tpι-CA is unknown. Using biophysical techniques and 3-D modeling, we show that the homotetrameric tpι-CA in solution has a flat “drone-like” shape with a core formed by the association of the first two domains of each monomer, and four protruding arms formed by domains 3 and 4. We also observe that the short linker between domains 3 and 4 in each monomer confers high flexibility, allowing for different conformations to be adopted. We propose the possible 3-D structure of a truncated tpι-CA containing fewer domain repeats using experimental data and discuss the implications of this atypical shape on the activity and metal coordination of the ι-CA.

Localization of putative carbonic anhydrases in the marine diatom, Thalassiosira pseudonana

2014 ◽  
Vol 121 (2-3) ◽  
pp. 235-249 ◽  
Author(s):  
Mio Samukawa ◽  
Chen Shen ◽  
Brian M. Hopkinson ◽  
Yusuke Matsuda
Keyword(s):  
Thalassiosira Pseudonana ◽  
Marine Diatom ◽  
Carbonic Anhydrases

Crystal Structure Analysis

2010 ◽  
Author(s):  
Jenny Pickworth Glusker ◽  
Kenneth N. Trueblood
Keyword(s):  
Crystal Structure ◽  
Experimental Data ◽  
Structure Analysis ◽  
Crystalline State ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
X Rays ◽  
Diffraction Patterns ◽  
The Many ◽  
Types Of Information

This book aims to explain how and why the detailed three-dimensional architecture of molecules can be determined by an analysis of the diffraction patterns obtained when X rays or neutrons are scattered by the atoms in single crystals. Part 1 deals with the nature of the crystalline state, diffraction generally, and diffraction by crystals in particular, and, briefly, the experimental procedures that are used. Part II examines the problem of converting the experimentally obtained data into a model of the atomic arrangement that scattered these beams. Part III is concerned with the techniques for refining the approximate structure to the degree warranted by the experimental data. It also describes the many types of information that can be learned by modern crystal structure analysis. There is a glossary of terms used and several appendixes to which most of the mathematical details have been relegated.

Crystal Structure Analysis of Cu-Zr Alloys by Convergent Beam Diffraction

1981 ◽  
Vol 39 ◽  
pp. 354-355
Author(s):  
A. F. Marshall ◽  
J. W. Steeds ◽  
D. Bouchet ◽  
S. L. Shinde ◽  
R. G. Walmsley
Keyword(s):  
Crystal Structure ◽  
Point Group ◽  
Intermetallic Phase ◽  
Three Dimensional ◽  
Crystal Structure Analysis ◽  
Ion Milling ◽  
Composition And Structure ◽  
Unit Cells ◽  
Sputter Deposited ◽  
Convergent Beam

Convergent beam electron diffraction is a powerful technique for determining the crystal structure of a material in TEM. In this paper we have applied it to the study of the intermetallic phases in the Cu-rich end of the Cu-Zr system. These phases are highly ordered. Their composition and structure has been previously studied by microprobe and x-ray diffraction with sometimes conflicting results.The crystalline phases were obtained by annealing amorphous sputter-deposited Cu-Zr. Specimens were thinned for TEM by ion milling and observed in a Philips EM 400. Due to the large unit cells involved, a small convergence angle of diffraction was used; however, the three-dimensional lattice and symmetry information of convergent beam microdiffraction patterns is still present. The results are as follows:1) 21 at% Zr in Cu: annealed at 500°C for 5 hours. An intermetallic phase, Cu3.6Zr (21.7% Zr), space group P6/m has been proposed near this composition (2). The major phase of our annealed material was hexagonal with a point group determined as 6/m.

scholarly journals Crystal structure of K[Hg(SCN)3] – a redetermination

2014 ◽  
Vol 70 (9) ◽  
pp. i46-i46 ◽  
Author(s):  
Matthias Weil ◽  
Thomas Häusler
Keyword(s):  
Crystal Structure ◽  
Room Temperature ◽  
Three Dimensional ◽  
Lattice Parameters ◽  
Bond Lengths ◽  
Dimensional Network ◽  
Anisotropic Displacement Parameters ◽  
Precision And Accuracy ◽  
Standard Deviations ◽  
Atomic Coordinates

The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium trithiocyanatomercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952).Zh. Fiz. Khim.26, 469–478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg—S bond lengths of 2.3954 (11), 2.4481 (8) and 2.7653 (6) Å in comparison with values of 2.24, 2.43 and 2.77 Å. All atoms in the crystal structure are located on mirror planes. The Hg2+cation is surrounded by four S atoms in a seesaw shape [S—Hg—S angles range from 94.65 (2) to 154.06 (3)°]. The HgS4polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting1∞[HgS2/1S2/2] chains are also part of SCN−anions that link these chains with the K+cations into a three-dimensional network. The K—N bond lengths of the distorted KN7polyhedra lie between 2.926 (2) and 3.051 (3) Å.

scholarly journals An investigation of polyhedral deformation in two mixed-metal diarsenates: SrZnAs2O7and BaCuAs2O7

2015 ◽  
Vol 71 (4) ◽  
pp. 330-337 ◽  
Author(s):  
Sabina Kovač ◽  
Ljiljana Karanović ◽  
Tamara Đorđević
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
General Formula ◽  
Three Dimensional ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Open Framework ◽  
Geometrical Characteristics ◽  
Barium Copper

Two isostructural diarsenates, SrZnAs2O7(strontium zinc diarsenate), (I), and BaCuAs2O7[barium copper(II) diarsenate], (II), have been synthesized under hydrothermal conditions and characterized by single-crystal X-ray diffraction. The three-dimensional open-framework crystal structure consists of corner-sharingM2O5(M2 = Zn or Cu) square pyramids and diarsenate (As2O7) groups. Each As2O7group shares its five corners with five differentM2O5square pyramids. The resulting framework delimits two types of tunnels aligned parallel to the [010] and [100] directions where the large divalent nine-coordinatedM1 (M1 = Sr or Ba) cations are located. The geometrical characteristics of theM1O9,M2O5and As2O7groups of known isostructural diarsenates, adopting the general formulaM1IIM2IIAs2O7(M1II= Sr, Ba, Pb;M2II= Mg, Co, Cu, Zn) and crystallizing in the space groupP21/n, are presented and discussed.

The crystal structure of yeast regulatory subunit reveals key evolutionary insights into Protein Kinase A oligomerization

2021 ◽  
pp. 107732
Author(s):  
Nicolás González Bardeci ◽  
Enzo Tofolón ◽  
Felipe Trajtenberg ◽  
Julio Caramelo ◽  
Nicole Larrieux ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Protein Kinase ◽  
Protein Kinase A ◽  
Regulatory Subunit ◽  
Kinase A

scholarly journals Toxicity of Combinations of Kinase Pathway Inhibitors to Normal Human Cells in a Three-Dimensional Culture

2021 ◽  
pp. 247263032110088
Author(s):  
Pouria Rafsanjani Nejad ◽  
Pradip Shahi Thakuri ◽  
Sunil Singh ◽  
Astha Lamichhane ◽  
Jacob Heiss ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Clinical Trials ◽  
Protein Kinase ◽  
Single Agent ◽  
Three Dimensional ◽  
Drug Combinations ◽  
Toxic Effects ◽  
Combination Drug ◽  
Normal Cells ◽  
Colon Cells

Resistance to single-agent chemotherapy and molecularly targeted drugs prevents sustained efficacy of treatments. To address this challenge, combination drug treatments have been used to improve outcomes for patients. Potential toxicity of combination treatments is a major concern, however, and has led to the failure of several clinical trials in different cancers. The use of cell-based models of normal tissues in preclinical studies enables testing and identifying toxic effects of drug combinations and facilitates an informed decision-making process for advancing the treatments to animal models and clinical trials. Recently, we established that combinations of molecular inhibitors of mitogen-activated protein kinase (MAPK) and phosphatidylinositol-3-kinase–protein kinase B (PI3K/Akt) pathways effectively and synergistically inhibit growth of BRAFmut and KRASmut colorectal tumor spheroids by blocking feedback signaling of downstream kinase pathways. These pathways are important for cell proliferation, however, and their simultaneous inhibition may cause toxicity to normal cells. We used a cellular spheroid model to study toxicities of drug combinations to human bone marrow and colon. Our results indicated that MAPK and PI3K/Akt inhibitors used simultaneously were only moderately toxic to bone marrow cells but significantly more toxic to colon cells. Our molecular analysis of proliferative cell activities and housekeeping proteins further corroborated these results. Overall, our approach to identify toxic effects of combinations of cancer drugs to normal cells in three-dimensional cultures will facilitate more informed treatment selections for subsequent animal studies.

Three-dimensional asymmetric maximum weight lifting prediction considering dynamic joint strength

2021 ◽  
pp. 095441192098703
Author(s):  
Rahid Zaman ◽  
Yujiang Xiang ◽  
Jazmin Cruz ◽  
James Yang
Keyword(s):  
Experimental Data ◽  
Degrees Of Freedom ◽  
Inverse Dynamics ◽  
Three Dimensional ◽  
Optimization Method ◽  
Weight Lifting ◽  
Joint Torque ◽  
Maximum Weight ◽  
Angular Velocities ◽  
Asymmetric Lifting

In this study, the three-dimensional (3D) asymmetric maximum weight lifting is predicted using an inverse-dynamics-based optimization method considering dynamic joint torque limits. The dynamic joint torque limits are functions of joint angles and angular velocities, and imposed on the hip, knee, ankle, wrist, elbow, shoulder, and lumbar spine joints. The 3D model has 40 degrees of freedom (DOFs) including 34 physical revolute joints and 6 global joints. A multi-objective optimization (MOO) problem is solved by simultaneously maximizing box weight and minimizing the sum of joint torque squares. A total of 12 male subjects were recruited to conduct maximum weight box lifting using squat-lifting strategy. Finally, the predicted lifting motion, ground reaction forces, and maximum lifting weight are validated with the experimental data. The prediction results agree well with the experimental data and the model’s predictive capability is demonstrated. This is the first study that uses MOO to predict maximum lifting weight and 3D asymmetric lifting motion while considering dynamic joint torque limits. The proposed method has the potential to prevent individuals’ risk of injury for lifting.

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