scholarly journals Graph Clustering Based on Structural Similarity of Fragments

2006 ◽  
pp. 97-114 ◽  
Author(s):  
Tetsuya Yoshida ◽  
Ryosuke Shoda ◽  
Hiroshi Motoda
Keyword(s):  
Structural Similarity ◽  
Graph Clustering

Graph clustering using k-Neighbourhood Attribute Structural similarity

2016 ◽  
Vol 47 ◽  
pp. 216-223 ◽  
Author(s):  
M. Parimala Boobalan ◽  
Daphne Lopez ◽  
X.Z. Gao
Keyword(s):  
Structural Similarity ◽  
Graph Clustering

Virus-Like Particles in a Human Breast Cancer: Structural Similarity to Previously Reported Particles

1973 ◽  
Vol 31 ◽  
pp. 378-379
Author(s):  
G. Kasnic ◽  
S. E. Stewart ◽  
C. Urbanski
Keyword(s):  
Breast Cancer ◽  
Biological Activity ◽  
Human Breast Cancer ◽  
Osteogenic Sarcoma ◽  
Human Tumor ◽  
Structural Similarity ◽  
Cell Tumor ◽  
Human Breast ◽  
Human Tumor Cell ◽  
Type Particle

We have reported the maturation of an intracisternal A-type particle in murine plasma cell tumor cultures and three human tumor cell cultures (rhabdomyosarcoma, lung adenocarcinoma, and osteogenic sarcoma) after IUDR-DMSO activation. In all of these studies the A-type particle seems to develop into a form with an electron dense nucleoid, presumably mature, which is also intracisternal. A similar intracisternal A-type particle has been described in leukemic guinea pigs. Although no biological activity has yet been demonstrated for these particles, on morphologic grounds, and by the manner in which they develop within the cell, they may represent members of the same family of viruses.

Structural similarity of ribosomes from E. coli and A. salina

1978 ◽  
Vol 36 (2) ◽  
pp. 242-243
Author(s):  
M. Boublik ◽  
R.M. Wydro ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Ribosomal Proteins ◽  
Direct Evidence ◽  
Structural Similarity ◽  
Carbon Support ◽  
Artemia Salina ◽  
Uranyl Acetate ◽  
Biological Assays ◽  
E Coli ◽  
And Function ◽  
Fine Carbon

Ribosomes are ribonucleoprotein particles necessary for processing the genetic information of mRNA into proteins. Analogy in composition and function of ribosomes from diverse species, established by biochemical and biological assays, implies their structural similarity. Direct evidence obtained by electron microscopy seems to be of increasing relevance in understanding the structure of ribosomes and the mechanism of their role in protein synthesis.The extent of the structural homology between prokaryotic and eukaryotic ribosomes has been studied on ribosomes of Escherichia coli (E.c.) and Artemia salina (A.s.). Despite the established differences in size and in the amount and proportion of ribosomal proteins and RNAs both types of ribosomes show an overall similarity. The monosomes (stained with 0.5% aqueous uranyl acetate and deposited on a fine carbon support) appear in the electron micrographs as round particles with a diameter of approximately 225Å for the 70S E.c. (Fig. 1) and 260Å for the 80S A.s. monosome (Fig. 2).

Role of the Small (40S) Subunits in the Structure of the Interface of Eukaryotic Ribosomes

1980 ◽  
Vol 38 ◽  
pp. 548-549
Author(s):  
M. Boublik ◽  
N. Robakis ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Structural Similarity ◽  
High Resolution Electron Microscopy ◽  
Peptide Bond ◽  
Uranyl Acetate ◽  
Mutual Orientation ◽  
Mutual Position ◽  
Peptide Bond Formation ◽  
Resolution Electron ◽  
Direct Technique ◽  
Structural Details

Ribosomes are ribonucleoprotein particles which process the genetic information coded in mRNA into protein synthesis. The analogy in function and composition of ribosomes from various sources, both prokaryotic and eukaryo-tic, imply a structural similarity. At present, high resolution electron microscopy is the most direct technique with a potential to resolve the extent of the structural homology of ribosomal particles at a macromolecular level. The structure of ribosomes is highly complex as a result of the large number of their constituents. In general, 80S eukaryotic monosomes consist of two uneven subunits - large (60S) and small (40S) - accomodating four different RNAs and approximately 80 different proteins. Mutual orientation of both subunits on the monosome is of particular interest because it determines the interface, the supposed site of interactions of ribosomes with other macro-molecules involved in peptide bond formation. Since entrapping of the contrasting solution (0.5% aqueous uranyl acetate) obscures all structural details in the interface, information on its architecture is limited to an indirect reconstruction based on the established 3-D structure of both sub-units and their mutual position after association.

Insights into the biochemical and functional characterization of sortase E transpeptidase of Corynebacterium glutamicum

2019 ◽  
Vol 476 (24) ◽  
pp. 3835-3847 ◽  
Author(s):  
Aliyath Susmitha ◽  
Kesavan Madhavan Nampoothiri ◽  
Harsha Bajaj
Keyword(s):  
Protein Engineering ◽  
Cell Attachment ◽  
Functional Characterization ◽  
Protein Structures ◽  
Structural Similarity ◽  
Surface Proteins ◽  
Sortase A ◽  
Peptide Cleavage ◽  
New Findings

Most Gram-positive bacteria contain a membrane-bound transpeptidase known as sortase which covalently incorporates the surface proteins on to the cell wall. The sortase-displayed protein structures are involved in cell attachment, nutrient uptake and aerial hyphae formation. Among the six classes of sortase (A–F), sortase A of S. aureus is the well-characterized housekeeping enzyme considered as an ideal drug target and a valuable biochemical reagent for protein engineering. Similar to SrtA, class E sortase in GC rich bacteria plays a housekeeping role which is not studied extensively. However, C. glutamicum ATCC 13032, an industrially important organism known for amino acid production, carries a single putative sortase (NCgl2838) gene but neither in vitro peptide cleavage activity nor biochemical characterizations have been investigated. Here, we identified that the gene is having a sortase activity and analyzed its structural similarity with Cd-SrtF. The purified enzyme showed a greater affinity toward LAXTG substrate with a calculated KM of 12 ± 1 µM, one of the highest affinities reported for this class of enzyme. Moreover, site-directed mutation studies were carried to ascertain the structure functional relationship of Cg-SrtE and all these are new findings which will enable us to perceive exciting protein engineering applications with this class of enzyme from a non-pathogenic microbe.

Method application of optimal multi-parameter analysis to assess the distribution of water masses as an example of CTD data of the Barents Sea in summer 2017

2019 ◽  
pp. 38-51
Author(s):  
Valeriy G. Yakubenko ◽  
Anna L. Chultsova
Keyword(s):  
Barents Sea ◽  
Field Measurements ◽  
Structural Similarity ◽  
Water Masses ◽  
Parameter Analysis ◽  
Water Dynamics ◽  
Phosphorus Concentration ◽  
Nitrogen And Phosphorus ◽  
The Barents Sea ◽  
Expert Assessments

Identification of water masses in areas with complex water dynamics is a complex task, which is usually solved by the method of expert assessments. In this paper, it is proposed to use a formal procedure based on the application of the method of optimal multiparametric analysis (OMP analysis). The data of field measurements obtained in the 68th cruise of the R/V “Academician Mstislav Keldysh” in the summer of 2017 in the Barents Sea on the distribution of temperature, salinity, oxygen, silicates, nitrogen, and phosphorus concentration are used as a data for research. A comparison of the results with data on the distribution of water masses in literature based on expert assessments (Oziel et al., 2017), allows us to conclude about their close structural similarity. Some differences are related to spatial and temporal shifts of measurements. This indicates the feasibility of using the OMP analysis technique in oceanological studies to obtain quantitative data on the spatial distribution of different water masses.

The complements in an affine group

2013 ◽  
Vol 50 (2) ◽  
pp. 258-265
Author(s):  
Pál Hegedűs
Keyword(s):  
Permutation Group ◽  
Structural Similarity ◽  
Affine Group ◽  
Permutation Module ◽  
Regular Module ◽  
Brauer Characters

In this paper we analyse the natural permutation module of an affine permutation group. For this the regular module of an elementary Abelian p-group is described in detail. We consider the inequivalent permutation modules coming from nonconjugate complements. We prove their strong structural similarity well exceeding the fact that they have equal Brauer characters.

Pathway Complexity in the Stacking of Imine-linked Macrocycles Related to Two-Dimensional Covalent Organic Frameworks

2019 ◽  
Author(s):  
Shiwei Wang ◽  
Anton Chavez ◽  
Simil Thomas ◽  
Hong Li ◽  
Nathan C. Flanders ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Structural Similarity ◽  
Discrete Models ◽  
Side Chains ◽  
Two Dimensional ◽  
Assembly Process ◽  
Covalent Organic Frameworks ◽  
Electron Systems ◽  
Monomer Structure ◽  
Kinetic Traps

This work reports on the assembly of imine-linked macrocycles that serve as models of two-dimensional covalent organic frameworks (2D COFs). Interlayer interactions play an important role in the formation of 2D COFs, yet the effect of monomer structure on COF formation, crystallinity, and susceptibility to exfoliation are not well understood. For example, monomers with both electron-rich and electron-poor π-electron systems have been proposed to strengthen interlayer inter-actions and improve crystallinity. Here we probe these effects by studying the stacking behavior of imine-linked macrocycles that represent discrete models of 2D COFs. <div><br></div><div>Specifically, macrocycles based on terephthaldehyde (PDA) or 2,5-dimethoxyterephthaldehyde (DMPDA) stack upon cooling molecularly dissolved solutions. Both macrocycles assemble cooperatively with similar ΔHe values of -97 kJ/mol and -101 kJ/mol, respectively, although the DMPDA macrocycle assembly process showed a more straightforward temperature dependence. Circular dichroism spectroscopy performed on macrocycles bearing chiral side chains revealed a helix reversion process for the PDA macrocycles that was not observed for the DMPDA macrocycles. <br></div><div><br></div><div>Given the structural similarity of these monomers, these findings demonstrate that the stacking processes associated with nanotubes derived from these macrocycles, as well as for the corresponding COFs, are complex and susceptible to kinetic traps, casting doubt on the relevance of thermodynamic arguments for improving materials quality. <br></div>

Sign in / Sign up

Export Citation Format

Share Document