scholarly journals High-resolution structure of an α-spectrin SH3-domain mutant with a redesigned hydrophobic core

2010 ◽  
Vol 66 (9) ◽  
pp. 1023-1027 ◽  
Author(s):  
Ana Cámara-Artigas ◽  
Monserrat Andújar-Sánchez ◽  
Emilia Ortiz-Salmerón ◽  
Celia Cuadri ◽  
Eva S. Cobos ◽  
...  
Keyword(s):  
Structural Information ◽  
Sh3 Domain ◽  
Hydrophobic Core ◽  
Orthorhombic Space Group ◽  
Cell Parameters ◽  
High Resolution Structure ◽  
Model Protein ◽  
Distal Loop ◽  
Modular Domain ◽  
The Stability

The α-spectrin SH3 domain (Spc-SH3) is a small modular domain which has been broadly used as a model protein in folding studies and these studies have sometimes been supported by structural information obtained from the coordinates of Spc-SH3 mutants. The structure of B5/D48G, a multiple mutant designed to improve the hydrophobic core and as a consequence the protein stability, has been solved at 1 Å resolution. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 24.79,b= 37.23,c= 62.95 Å. This mutant also bears a D48G substitution in the distal loop and this mutation has also been reported to increase the stability of the protein by itself. The structure of the B5/D48G mutant shows a highly packed hydrophobic core and a more ordered distal loop compared with previous Spc-SH3 structures.

scholarly journals Cloning, expression, crystallization and preliminary X-ray crystallographic analysis of a human condensin SMC2 hinge domain with short coiled coils

2010 ◽  
Vol 66 (9) ◽  
pp. 1067-1070 ◽  
Author(s):  
Kazuki Kawahara ◽  
Shota Nakamura ◽  
Yasuhiro Katsu ◽  
Daisuke Motooka ◽  
Yuki Hosokawa ◽  
...  
Keyword(s):  
Structural Information ◽  
Critical Role ◽  
Crystallographic Analysis ◽  
Coiled Coils ◽  
Orthorhombic Space Group ◽  
Electron Microscopic ◽  
Space Group ◽  
Cell Parameters ◽  
Microscopic Studies ◽  
Hinge Domain

In higher eukaryotes, the condensin complex, which mainly consists of two structural maintenance of chromosomes (SMC) subunits, SMC2 (CAP-E) and SMC4 (CAP-C), plays a critical role in the formation of higher order chromosome structures during mitosis. Biochemical and electron-microscopic studies have revealed that the SMC2 and SMC4 subunits dimerize through the interaction of their hinge domains, forming a characteristic V-shaped heterodimer. However, the details of their function are still not fully understood owing to a lack of structural information at the atomic level. In this study, the human SMC2 hinge domain with short coiled coils was cloned, expressed, purified and crystallized in the orthorhombic space groupC222 in native and SeMet-derivatized forms. Because of the poor diffraction properties of these crystals, the mutant Leu68→SeMet was designed and crystallized in order to obtain the experimental phases. The SeMet-derivatized crystals of the mutant belonged to space groupP3212, with unit-cell parametersa=b= 128.8,c = 91.4 Å. The diffraction data obtained from a crystal that diffracted to 2.4 Å resolution were suitable for SAD phasing.

scholarly journals Expression, purification, crystallization and preliminary X-ray diffraction analysis of the dihydroorotase domain of human CAD

2012 ◽  
Vol 68 (11) ◽  
pp. 1341-1345 ◽  
Author(s):  
Nada Lallous ◽  
Araceli Grande-García ◽  
Rafael Molina ◽  
Santiago Ramón-Maiques
Keyword(s):  
De Novo ◽  
Structural Information ◽  
Protein Molecule ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Data Set ◽  
X Ray ◽  
Cell Parameters ◽  
Small Crystals ◽  
Crystallization Experiments

CAD is a 243 kDa eukaryotic multifunctional polypeptide that catalyzes the first three reactions ofde novopyrimidine biosynthesis: glutamine-dependentcarbamyl phosphate synthetase,aspartate transcarbamylase anddihydroorotase (DHO). In prokaryotes, these activities are associated with monofunctional proteins, for which crystal structures are available. However, there is no detailed structural information on the full-length CAD protein or any of its functional domains apart from that it associates to form a homohexamer of ∼1.5 MDa. Here, the expression, purification and crystallization of the DHO domain of human CAD are reported. The DHO domain forms homodimers in solution. Crystallization experiments yielded small crystals that were suitable for X-ray diffraction studies. A diffraction data set was collected to 1.75 Å resolution using synchrotron radiation at the SLS, Villigen, Switzerland. The crystals belonged to the orthorhombic space groupC2221, with unit-cell parametersa= 82.1,b= 159.3,c= 61.5 Å. The Matthews coefficient calculation suggested the presence of one protein molecule per asymmetric unit, with a solvent content of 48%.

scholarly journals Major conformational changes in the structure of lysozyme obtained from a crystal with a very low solvent content

2019 ◽  
Vol 75 (11) ◽  
pp. 687-696
Author(s):  
M. Carmen Salinas-Garcia ◽  
Marina Plaza-Garrido ◽  
Daniel Alba-Elena ◽  
Ana Camara-Artigas
Keyword(s):  
Conformational Changes ◽  
Crystal Form ◽  
Catalytic Site ◽  
Side Chain ◽  
Hydrophobic Core ◽  
Orthorhombic Space Group ◽  
Solvent Content ◽  
Cell Parameters ◽  
Saccharide Binding ◽  
Α Helix

A new crystal form of lysozyme with a very low solvent content (26.35%) has been obtained in the orthorhombic space group P212121 (with unit-cell parameters a = 30.04, b = 51.68, c = 61.53 Å). The lysozyme structure obtained from these crystals does not show the typical overall fold. Instead, major conformational changes take place in some elements of the secondary structure and in the hydrophobic core of the protein. At the end of the central α-helix (α2), Glu35 is usually buried in the catalytic site and shows an abnormally high pK a value, which is key to the activity of the enzyme. The high pK a value of this glutamate residue is favoured by the hydrophobic environment, particularly by its neighbour Trp108, which is important for structural stability and saccharide binding. In this new structure, Trp108 shows a 90° rotation of its side chain, which results in the rearrangement of the hydrophobic core. Conformational changes also result in the exposure of Glu35 to the solvent, which impairs the catalytic site by increasing the distance between Glu35 and Asp52 and lowering the pK a value of the glutamate. Altogether, this new lysozyme structure reveals major conformational changes in the hydrophobic core and catalytic site that might play a role in the folding and bactericidal function of the protein.

scholarly journals A proposed carbon-utilization and virulence protein A, CuvA (Rv1422), from Mycobacterium tuberculosis H37Rv: crystallization, X-ray diffraction analysis and ligand binding

2020 ◽  
Vol 76 (7) ◽  
pp. 314-319
Author(s):  
Yoon Chae Jeong ◽  
Ki Seog Lee
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Environmental Changes ◽  
Structural Information ◽  
Critical Role ◽  
Nutrient Utilization ◽  
Diffusion Method ◽  
Uridine Diphosphate ◽  
Carbon Utilization ◽  
Orthorhombic Space Group ◽  
Cell Parameters

Mycobacterium tuberculosis possesses the ability to undergo physiological adaptations in order to persist during the prolonged course of infection despite the active immune response of the host and in order to overcome multiple environmental changes. Previous studies have proposed that M. tuberculosis CuvA (Rv1422; MtCuvA) might play a critical role in the adaptation of the bacterium to environmental changes, such as nutrient utilization and alteration of the growth rate. However, the detailed function of MtCuvA still remains unclear owing to a lack of structural information. To better understand its role in host adaptation, MtCuvA was purified to homogeneity and was crystallized for the first time using the hanging-drop vapor-diffusion method. The crystal of MtCuvA diffracted to a resolution of 2.1 Å and belonged to the orthorhombic space group P212121, with unit-cell parameters a = 47.27, b = 170.93, c = 178.10 Å. The calculated Matthews coefficient (V M) was 2.4 Å3 Da−1, with a solvent content of 48.02%, and thus four molecules appeared to be present in the asymmetric unit. Moreover, it is reported that MtCuvA can bind to the cell-wall precursor components uridine diphosphate (UDP)-glucose and UDP-N-acetylglucosamine.

Two lithium tricyanomethanide compounds: syntheses and single-crystal structure determination of LiK[C(CN)3]2 and Li[C(CN)3]·½ (H3C)2CO

2015 ◽  
Vol 70 (3) ◽  
pp. 191-196 ◽  
Author(s):  
Olaf Reckeweg ◽  
Francis J. DiSalvo
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Single Crystals ◽  
Structure Determination ◽  
Monoclinic Space Group ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Cell Parameters ◽  
New Compounds

AbstractThe new compounds LiK[C(CN)3]2 and Li[C(CN)3]·½ (H3C)2CO were synthesized and their crystal structures were determined. Li[C(CN)3]·½ (H3C)2CO crystallizes in the orthorhombic space group Ima2 (no. 46) with the cell parameters a=794.97(14), b=1165.1(2) and c=1485.4(3) pm, while LiK[C(CN)3]2 adopts the monoclinic space group P21/c (no. 14) with the cell parameters a=1265.7(2), b=1068.0(2) and c=778.36(12) pm and the angle β=95.775(7)°. Single crystals of K[C(CN)3] were also acquired, and the crystal structure was refined more precisely than before corroborating earlier results.

scholarly journals Crystallization and preliminary X-ray analysis of thePlasmodium falciparumapicoplast DNA polymerase

2015 ◽  
Vol 71 (3) ◽  
pp. 333-337 ◽  
Author(s):  
Morgan E. Milton ◽  
Jun-yong Choe ◽  
Richard B. Honzatko ◽  
Scott W. Nelson
Keyword(s):  
Dna Polymerase ◽  
Structural Information ◽  
Klenow Fragment ◽  
X Ray Diffraction ◽  
Dna Polymerase I ◽  
X Ray ◽  
Cell Parameters ◽  
A Genome ◽  
Reported Data ◽  
Polymerase I

Infection by the parasitePlasmodium falciparumis the leading cause of malaria in humans. The parasite has a unique and essential plastid-like organelle called the apicoplast. The apicoplast contains a genome that undergoes replication and repair through the action of a replicative polymerase (apPOL). apPOL has no direct orthologs in mammalian polymerases and is therefore an attractive antimalarial drug target. No structural information exists for apPOL, and the Klenow fragment ofEscherichia coliDNA polymerase I, which is its closest structural homolog, shares only 28% sequence identity. Here, conditions for the crystallization of and preliminary X-ray diffraction data from crystals ofP. falciparumapPOL are reported. Data complete to 3.5 Å resolution were collected from a single crystal (2 × 2 × 5 µm) using a 5 µm beam. The space groupP6522 (unit-cell parametersa=b= 141.8,c= 149.7 Å, α = β = 90, γ = 120°) was confirmed by molecular replacement. Refinement is in progress.

Release Profile of a Model Protein Drug Depending on the Stability of Microspheres Based on Polyelectrolyte Complex

2007 ◽  
Vol 342-343 ◽  
pp. 505-508
Author(s):  
Sung Won Kim ◽  
Yun Sik Nam ◽  
Yeon Jin Min ◽  
Jong Ho Kim ◽  
Kwang Meyong Kim ◽  
...  
Keyword(s):  
Polyelectrolyte Complex ◽  
Coating Layer ◽  
Great Influence ◽  
Release Profile ◽  
Core Material ◽  
Glycol Chitosan ◽  
The Core ◽  
Key Factor ◽  
Model Protein ◽  
The Stability

Stability and disintegration of natural polyelectrolyte complex microspheres for protein drugs delivery have been extensively investigated because of their great influence on the drug release patterns. In this study, we tested stability of microspheres with alginate (Alg) core layered by either chitosan (Chi) or glycol chitosan (GChi) by examining release profiles of fluorophorelabeled bovine serum albumin (BSA) and lysozyme (Lys) from the microspheres. While GChi shell was disintegrated quickly, Chi-shell microspheres showed good stability in PBS. Disintegration of the coated layer induced the core material instable. The results indicated that while the charges of the shell material provided additional diffusion barrier against the protein release, the key factor to hold the proteins inside the microspheres was the integrity of the outer coating layer.

Heklaite, KNaSiF6, a new fumarolic mineral from Hekla volcano, Iceland

2010 ◽  
Vol 74 (1) ◽  
pp. 147-157 ◽  
Author(s):  
A. Garavelli ◽  
T. Balić-Žunić ◽  
D. Mitolo ◽  
P. Acquafredda ◽  
E. Leonardsen ◽  
...  
Keyword(s):  
Powder Diffraction ◽  
Quantitative Chemical Analysis ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
Synthetic Compound ◽  
Calculated Density ◽  
X Ray ◽  
Cell Parameters ◽  
Fine Grained ◽  
The Ideal

AbstractHeklaite, with the ideal formula KNaSiF6, was found among fumarolic encrustations collected in 1992 on the Hekla volcano, Iceland. Heklaite forms a fine-grained mass of micron- to sub-micron-sized crystals intimately associated with malladrite, hieratite and ralstonite. The mineral is colourless, transparent, non-fluorescent, has a vitreous lustre and a white streak. The calculated density is 2.69 g cm–3. An SEM-EDS quantitative chemical analysis shows the following range of concentrations (wt.%): Na 11.61–12.74 (average 11.98), K 17.02–18.97 (average 18.29), Si 13.48 –14.17 (average 13.91), F 54.88–56.19 (average 55.66). The empirical chemical formula, calculated on the basis of 9 a.p.f.u., is Na1.07K0.96Si1.01F5.97. X-ray powder diffraction indicates that heklaite is orthorhombic, space group Pnma, with the following unit-cell parameters: a = 9.3387(7) Å, b = 5.5032(4) Å, c = 9.7957(8) Å , V = 503.43(7) Å3, Z = 4. The eight strongest reflections in the powder diffraction pattern [d in Å (I/I0) (hkl)] are: 4.33 (53) (102); 4.26 (56) (111); 3.40 (49) (112); 3.37 (47) (202); 3.34 (100) (211); 2.251 (27) (303); 2.050 (52) (123); 2.016 (29) (321). On the basis of chemical analyses and X-ray data, heklaite corresponds to the synthetic compound KNaSiF6. The name is for the type locality, the Hekla volcano, Iceland.

scholarly journals Crystallization, optimization and preliminary X-ray characterization of a metal-dependent PI-PLC fromStreptomyces antibioticus

2012 ◽  
Vol 68 (11) ◽  
pp. 1378-1386 ◽  
Author(s):  
Michael R. Jackson ◽  
Thomas L. Selby
Keyword(s):  
X Ray Diffraction ◽  
Hanging Drop ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Streptomyces Antibioticus ◽  
Cell Parameters ◽  
Heavy Atoms ◽  
Hanging Drop Method

A recombinant metal-dependent phosphatidylinositol-specific phospholipase C (PI-PLC) fromStreptomyces antibioticushas been crystallized by the hanging-drop method with and without heavy metals. The native crystals belonged to the orthorhombic space groupP222, with unit-cell parametersa= 41.26,b= 51.86,c = 154.78 Å. The X-ray diffraction results showed significant differences in the crystal quality of samples soaked with heavy atoms. Additionally, drop pinning, which increases the surface area of the drops, was also used to improve crystal growth and quality. The combination of heavy-metal soaks and drop pinning was found to be critical for producing high-quality crystals that diffracted to 1.23 Å resolution.

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