scholarly journals Comparative structure of the lateral pedal defensive glands of three species of Siphonaria (Gastropoda: Basommatophora)

2009 ◽  
Vol 75 (4) ◽  
pp. 371-380 ◽  
Author(s):  
S. C. Pinchuck ◽  
A. N. Hodgson
Keyword(s):  
Defensive Glands ◽  
Comparative Structure

The Deaths of King and Kindred (Agis 16.6–17.5, 17.9–18.3; 19.5–21.1)

2018 ◽  
Author(s):  
G. O. Hutchinson
Keyword(s):  
Comparative Structure

A catastrophe in Hellenistic Sparta is portrayed in rhythmic passages that contrast with each other. The comparisons involved in and between both are intricate, within a particularly complex comparative structure, where two Spartan kings, Agis and Cleomenes, are compared with two Roman nobiles, Ti. and C. Gracchus. The king Cleombrotus is compared with Agis and with his own wife; Agis’ death is made part of a structure in which the most important figure is his mother. The accounts gain more force from rhetoric, multiple characterization, and perversion of legality and the constitution. Rhythm creates a powerful narrative; if the source is Phylarchus, the source is unrhythmic. The passages have been underestimated through scorn for Pylarchus and under-appreciation of Plutarch’s rhythmic writing.

scholarly journals Structural design principles for specific ultra-high affinity interactions between colicins/pyocins and immunity proteins

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Avital Shushan ◽  
Mickey Kosloff
Keyword(s):  
Protein Interactions ◽  
Structural Elements ◽  
Protein Protein Interactions ◽  
Immunity Protein ◽  
Rational Engineering ◽  
High Affinity ◽  
Comparative Structure ◽  
Polar Interactions ◽  
Exquisite Specificity

AbstractThe interactions of the antibiotic proteins colicins/pyocins with immunity proteins is a seminal model system for studying protein–protein interactions and specificity. Yet, a precise and quantitative determination of which structural elements and residues determine their binding affinity and specificity is still lacking. Here, we used comparative structure-based energy calculations to map residues that substantially contribute to interactions across native and engineered complexes of colicins/pyocins and immunity proteins. We show that the immunity protein α1–α2 motif is a unique structurally-dissimilar element that restricts interaction specificity towards all colicins/pyocins, in both engineered and native complexes. This motif combines with a diverse and extensive array of electrostatic/polar interactions that enable the exquisite specificity that characterizes these interactions while achieving ultra-high affinity. Surprisingly, the divergence of these contributing colicin residues is reciprocal to residue conservation in immunity proteins. The structurally-dissimilar immunity protein α1–α2 motif is recognized by divergent colicins similarly, while the conserved immunity protein α3 helix interacts with diverse colicin residues. Electrostatics thus plays a key role in setting interaction specificity across all colicins and immunity proteins. Our analysis and resulting residue-level maps illuminate the molecular basis for these protein–protein interactions, with implications for drug development and rational engineering of these interfaces.

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.

scholarly journals VI. On the comparative structure of the brain in rodents

1882 ◽  
Vol 33 (216-219) ◽  
pp. 15-21
Keyword(s):  
Olfactory Organ ◽  
Cortical Surface ◽  
Complex Relationship ◽  
Comparative Structure ◽  
The Subject ◽  
The Brain

I have endeavoured in this abstract to summarise the results of my recent researches into the minute structure of the brain in the smaller Rodents. The pig and sheep, which were the subjects of my former memoir, possess a highly developed olfactory apparatus conjoined to a well convoluted cortical surface; but in the smaller animals now under consideration the surface of the hemispheres is almost perfectly smooth, while the olfactory organ, from its comparative size and complex relationship, has an important part to play in the architecture of the brain. Animals possessing the latter type of cerebrum have been classed together as the Osmatic Lissencéphales, in contradistinction to those which were the subject of my former enquiries, the Osmatic Gyren-céphales. My researches into the structure of the brain of prominent members of the former group, viz., the rabbit and rat, may be considered under two heads:— ( a .) The histology of the complete cortical envelope.

Modeling to support physicochemical enhancement techniques

2021 ◽  
pp. 79-90
Author(s):  
Т. A. Pospelova
Keyword(s):  
Enhanced Oil Recovery ◽  
Oil Recovery ◽  
Oil And Gas ◽  
Chemical Modeling ◽  
Comparative Structure ◽  
Water Cut ◽  
Physical And Chemical ◽  
Oil And Gas Companies ◽  
The Impact ◽  
Selection Of

The article discusses ways to increase the oil recovery factor in already developed fields, special attention is paid to the methods of enhanced oil recovery. The comparative structure of oil production in Russia in the medium term is given. The experience of oil and gas companies in the application of enhanced oil recovery in the fields is analyzed and the dynamics of the growth in the use of various enhanced oil recovery in Russia is estimated. With an increase in the number of operations in the fields, the requirements for the selection of candidates inevitably increase, therefore, the work focuses on hydrodynamic modeling of physical and chemical modeling, highlights the features and disadvantages of existing simulators. The main dependences for adequate modeling during polymer flooding are given. The calculation with different concentration of polymer solution is presented, which significantly affects the water cut and further reduction of operating costs for the preparation of the produced fluid. The possibility of creating a specialized hydrodynamic simulator for low-volume chemical enhanced oil recovery is considered, since mainly simulators are applicable for chemical waterflooding and the impact is on the formation as a whole.

scholarly journals PDBrenum: a webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences

2021 ◽  
Author(s):  
Bulat Faezov ◽  
Roland L. Dunbrack
Keyword(s):  
Protein Data Bank ◽  
Data Bank ◽  
Post Translational Modifications ◽  
X Ray ◽  
X Ray Crystallography ◽  
Link Type ◽  
Binding Partners ◽  
Cryo Electron Microscopy ◽  
Comparative Structure ◽  
In The Beginning

AbstractThe Protein Data Bank (PDB) was established at Brookhaven National Laboratories in 1971 as an archive for biological macromolecular crystal structures. In the beginning the archive held only seven structures but in early 2021, the database has more than 170,000 structures solved by X-ray crystallography, nuclear magnetic resonance, cryo-electron microscopy, and other methods. Many proteins have been studied under different conditions (e.g., binding partners such as ligands, nucleic acids, or other proteins; mutations and post-translational modifications), thus enabling comparative structure-function studies. However, these studies are made more difficult because authors are allowed by the PDB to number the amino acids in each protein sequence in any manner they wish. This results in the same protein being numbered differently in the available PDB entries. In addition to the coordinates, there are many fields that contain information regarding specific residues in the sequence of each protein in the entry. Here we provide a webserver and Python3 application that fixes the PDB sequence numbering problem by replacing the author numbering with numbering derived from the corresponding UniProt sequences. We obtain this correspondence from the SIFTS database from PDBe. The server and program can take a list of PDB entries and provide renumbered files in mmCIF format and the legacy PDB format for both asymmetric unit files and biological assembly files provided by PDBe. The server can also take a list of UniProt identifiers (“P04637” or “P53_HUMAN”) and return the desired files.AvailabilitySource code is freely available at https://github.com/Faezov/PDBrenum. The webserver is located at: http://dunbrack3.fccc.edu/[email protected] or [email protected].

scholarly journals Comparative characterisation of Plasmodium falciparum Hsp70-1 relative to E. coli DnaK reveals functional specificity of the parasite chaperone

2020 ◽  
Author(s):  
Charity Mekgwa Lebepe ◽  
Pearl Rutendo Matambanadzo ◽  
Xolani Henry Makhoba ◽  
Ikechukwu Achilonu ◽  
Tawanda Zininga ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Molecular Chaperone ◽  
Chimeric Protein ◽  
Cellular Functions ◽  
E Coli ◽  
Adenosylmethionine Decarboxylase ◽  
Comparative Structure ◽  
Functional Features ◽  
Self Association

ABSTRACTHsp70 is one of the most prominent molecular chaperones. Although Hsp70s from various organisms are generally conserved, they exhibit specialised cellular functions. It remains to be fully understood how these highly conserved molecules exhibit specialised functional features. Plasmodium falciparum Hsp70-1 (PfHsp70-1) is a cytosol localised molecular chaperone that is implicated in the cyto-protection and pathogenicity of the malaria parasite. In the current study, we investigated the comparative structure-function features of PfHsp70-1 relative to its homologue, E. coli Hsp70 (DnaK) and a chimeric protein, KPf, that was constituted by the ATPase domain of DnaK and the substrate binding domain (SBD) of PfHsp70-1. Recombinant forms of all the three Hsp70s exhibited similar secondary and tertiary structural fold. We further established that compared to DnaK, both KPf and PfHsp70-1 were more stable to heat stress and exhibited higher basal ATPase activity. A recombinant P. falciparum Hsp40 (PfHsp40) stimulated the ATPase activities of all the three Hsp70s. In addition, both PfHsp70-1 and KPf exhibited preference for asparagine rich peptides as opposed to DnaK. Furthermore, all the three proteins exhibited self-association capabilities in vitro. Recombinant P. falciparum adenosylmethionine decarboxylase (PfAdoMetDC) co-expressed in E. coli with either KPf or PfHsp70-1 was produced as a fully folded product. On the other hand, co-expression of PfAdoMetDC with heterologous DnaK in E. coli did not promote folding of the former. These findings demonstrated that the SBD of PfHsp70-1 regulates several functional features of the protein and that this molecular chaperone is tailored to facilitate folding of plasmodial proteins.

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