scholarly journals TopMatch-web: pairwise matching of large assemblies of protein and nucleic acid chains in 3D

2020 ◽  
Vol 48 (W1) ◽  
pp. W31-W35 ◽  
Author(s):  
Markus Wiederstein ◽  
Manfred J Sippl
Keyword(s):  
Nucleic Acid ◽  
High Performance ◽  
Three Dimensional ◽  
Biological Molecules ◽  
Dimensional Structure ◽  
Complex Structures ◽  
Single Session ◽  
Molecular Assemblies ◽  
Mitochondrial Ribosomes ◽  
Structural Alignments

Abstract Frequently, the complete functional units of biological molecules are assemblies of protein and nucleic acid chains. Stunning examples are the complex structures of ribosomes. Here, we present TopMatch-web, a computational tool for the study of the three-dimensional structure, function and evolution of such molecules. The unique feature of TopMatch is its ability to match the protein as well as nucleic acid chains of complete molecular assemblies simultaneously. The resulting structural alignments are visualized instantly using the high-performance molecular viewer NGL. We use the mitochondrial ribosomes of human and yeast as an example to demonstrate the capabilities of TopMatch-web. The service responds immediately, enabling the interactive study of many pairwise alignments of large molecular assemblies in a single session. TopMatch-web is freely accessible at https://topmatch.services.came.sbg.ac.at.

Crystal structure of the hinge domain of Smchd1 reveals its dimerization mode and nucleic acid–binding residues

2020 ◽  
Vol 13 (636) ◽  
pp. eaaz5599 ◽  
Author(s):  
Kelan Chen ◽  
Richard W. Birkinshaw ◽  
Alexandra D. Gurzau ◽  
Iromi Wanigasuriya ◽  
Ruoyun Wang ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Muscular Dystrophy ◽  
Three Dimensional ◽  
Underlying Mechanism ◽  
Structural Features ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Dimensional Structure ◽  
Nucleic Acid Binding ◽  
X Ray Crystallography ◽  
Hinge Domain

Structural maintenance of chromosomes flexible hinge domain containing 1 (SMCHD1) is an epigenetic regulator in which polymorphisms cause the human developmental disorder, Bosma arhinia micropthalmia syndrome, and the degenerative disease, facioscapulohumeral muscular dystrophy. SMCHD1 is considered a noncanonical SMC family member because its hinge domain is C-terminal, because it homodimerizes rather than heterodimerizes, and because SMCHD1 contains a GHKL-type, rather than an ABC-type ATPase domain at its N terminus. The hinge domain has been previously implicated in chromatin association; however, the underlying mechanism involved and the basis for SMCHD1 homodimerization are unclear. Here, we used x-ray crystallography to solve the three-dimensional structure of the Smchd1 hinge domain. Together with structure-guided mutagenesis, we defined structural features of the hinge domain that participated in homodimerization and nucleic acid binding, and we identified a functional hotspot required for chromatin localization in cells. This structure provides a template for interpreting the mechanism by which patient polymorphisms within the SMCHD1 hinge domain could compromise function and lead to facioscapulohumeral muscular dystrophy.

Hepatocyte Aggregate Culture Technique for Bioreactors in Hybrid Liver Support Systems

1993 ◽  
Vol 16 (12) ◽  
pp. 843-846 ◽  
Author(s):  
J.C. Gerlach ◽  
K. Klöppel ◽  
C. MÜller ◽  
N. Schnoy ◽  
M.D. Smith ◽  
...  
Keyword(s):  
High Performance ◽  
Large Scale ◽  
Support Systems ◽  
Three Dimensional ◽  
Culture Technique ◽  
Dimensional Structure ◽  
Cell Aggregates ◽  
Liver Support ◽  
Aggregate Culture

Utilizing a modified culture technique for hepatocytes, a high performance suspension culture is possible in which hepatocytes spontaneously form cell aggregates. The aggregates of 20-100 cells have been histologically confirmed to hold a three-dimensional structure, they show a long-term external metabolism and a survival time comparable with standard adhesion cultures. This technique has several advantages in the construction of large scale bioreactors for hybrid liver support systems.

scholarly journals DUF3380 Domain from a Salmonella Phage Endolysin Shows PotentN-Acetylmuramidase Activity

2016 ◽  
Vol 82 (16) ◽  
pp. 4975-4981 ◽  
Author(s):  
Lorena Rodríguez-Rubio ◽  
Hans Gerstmans ◽  
Simon Thorpe ◽  
Stéphane Mesnage ◽  
Rob Lavigne ◽  
...  
Keyword(s):  
Enzymatic Activity ◽  
Thermal Resistance ◽  
High Performance ◽  
Antimicrobial Agents ◽  
Biochemical Characterization ◽  
Specific Activity ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Gram Negative ◽  
Content Type

ABSTRACTBacteriophage-encoded endolysins are highly diverse enzymes that cleave the bacterial peptidoglycan layer. Current research focuses on their potential applications in medicine, in food conservation, and as biotechnological tools. Despite the wealth of applications relying on the use of endolysin, little is known about the enzymatic properties of these enzymes, especially in the case of endolysins of bacteriophages infecting Gram-negative species. Automated genome annotations therefore remain to be confirmed. Here, we report the biochemical analysis and cleavage site determination of a novelSalmonellabacteriophage endolysin, Gp110, which comprises an uncharacterizeddomain ofunknownfunction (DUF3380; pfam11860) in its C terminus and shows a higher specific activity (34,240 U/μM) than that of 14 previously characterized endolysins active against peptidoglycan from Gram-negative bacteria (corresponding to 1.7- to 364-fold higher activity). Gp110 is a modular endolysin with an optimal pH of enzymatic activity of pH 8 and elevated thermal resistance. Reverse-phase high-performance liquid chromatography (RP-HPLC) analysis coupled to mass spectrometry showed that DUF3380 hasN-acetylmuramidase (lysozyme) activity cleaving the β-(1,4) glycosidic bond betweenN-acetylmuramic acid andN-acetylglucosamine residues. Gp110 is active against directly cross-linked peptidoglycans with various peptide stem compositions, making it an attractive enzyme for developing novel antimicrobial agents.IMPORTANCEWe report the functional and biochemical characterization of theSalmonellaphage endolysin Gp110. This endolysin has a modular structure with an enzymatically active domain and a cell wall binding domain. The enzymatic activity of this endolysin exceeds that of all other endolysins previously characterized using the same methods. A domain of unknown function (DUF3380) is responsible for this high enzymatic activity. We report that DUF3380 hasN-acetylmuramidase activity against directly cross-linked peptidoglycans with various peptide stem compositions. This experimentally verified activity allows better classification and understanding of the enzymatic activities of endolysins, which mostly are inferred by sequence similarities. Three-dimensional structure predictions for Gp110 suggest a fold that is completely different from that of known structures of enzymes with the same peptidoglycan cleavage specificity, making this endolysin quite unique. All of these features, combined with increased thermal resistance, make Gp110 an attractive candidate for engineering novel endolysin-based antibacterials.

Address of the President Lord Blackett, O.M., C.H. at the Anniversary Meeting, 30 November 1970

1971 ◽  
Vol 177 (1046) ◽  
pp. 1-14
Keyword(s):  
Natural Products ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Biological Systems ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Theoretical Knowledge ◽  
Three Dimensional Structure ◽  
Subsequent Determination

Todd has made highly significant contributions to the chemistry of natural products, in particular in relation to compounds which play important roles in biological systems. His researches on vitamins B 1 , E and B 12 were most elegant and have had far-reaching implications, but none more so than his structural and synthetic studies in the nucleic acid field. Here he developed methods for the synthesis of the nucleosides and for their phosphorylation; his work on the way they are combined made possible the subsequent determination of the three-dimensional structure of the nucleic acids thereby providing the basis for much of the exciting activity in the nucleotide field today. Todd’s achievements arise out of a rare combination of theoretical knowledge and outstanding experimental skill, with the most judicious exploitation of modern techniques. His work and his quality as an investigator have been widely recognized by biologists as well as by organic chemists.

Address of the President Lord Blackett, O.M., C.H. at the Anniversary Meeting, 30 November 1970

1971 ◽  
Vol 321 (1544) ◽  
pp. 1-14
Keyword(s):  
Natural Products ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Biological Systems ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Theoretical Knowledge ◽  
Three Dimensional Structure ◽  
Subsequent Determination

The Copley Medal is awarded to Lord Todd, F. R. S. Todd has made highly significant contributions to the chemistry of natural products, in particular in relation to compounds which play important roles in biological systems. His researches on vitamins B 1 , E and B 12 were most elegant and have had far-reaching implications, but none more so than his structural and synthetic studies in the nucleic acid field. Here he developed methods for the synthesis of the nucleosides and for their phosphorylation; his work on the way they are combined made possible the subsequent determination of the three-dimensional structure of the nucleic acids thereby providing the basis for much of the exciting activity in the nucleotide field today. Todd’s achievements arise out of a rare combination of theoretical knowledge and outstanding experimental skill, with the most judicious exploitation of modern techniques. His work and his quality as an investigator have been widely recognized by biologists as well as by organic chemists.

Vertically aligned VO2(B) nanobelt forest and its three-dimensional structure on oriented graphene for energy storage

2015 ◽  
Vol 3 (20) ◽  
pp. 10787-10794 ◽  
Author(s):  
Guofeng Ren ◽  
Md Nadim Ferdous Hoque ◽  
Xuan Pan ◽  
Juliusz Warzywoda ◽  
Zhaoyang Fan
Keyword(s):  
Energy Storage ◽  
Lithium Ion Batteries ◽  
Forest Structure ◽  
High Performance ◽  
Three Dimensional ◽  
Lithium Ion ◽  
Dimensional Structure ◽  
Two Dimensional ◽  
Three Dimensional Structure ◽  
Vertically Aligned

Assembling two-dimensional graphene and VO2(B) nanomaterials into an ordered three-dimensional forest structure for high performance lithium ion batteries.

Numerical Generation Technology for Three-Dimensional Structure of High-Performance Fiber Bundle

2011 ◽  
Vol 332-334 ◽  
pp. 1024-1027
Author(s):  
Lei Li ◽  
Li Chen ◽  
Jin Chao Li
Keyword(s):  
Fiber Bundle ◽  
High Performance ◽  
Volume Fraction ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Lateral Compression ◽  
Fiber Volume ◽  
Three Dimensional Structure ◽  
High Performance Fiber ◽  
Compression Mechanism

The three-dimensional structure of high-performance fiber bundles are of paramount importance for their study in lateral compression mechanism. Modeling of their true morphologies is still fields of focus research, yet to be exhausted. In this paper, ANSYS were utilized to develop three-dimensional numerical model of fiber bundle on the computer in the way of simulation. This approach is enabled by the finite element packages. It is possible to simulate the true material morphology directly. The key issues of the simulation are to keep fiber volume fraction always a constant value and to ensure no intersection between fibers. This work can simulate the stochastic generation-growth of high-performance fiber bundle and reproduce morphology of fiber bundle on micron scale well and thereby provide reliable information for the study on the lateral compression mechanism in the future.

Effect of Manganese on the Activity of Antibiotic Against Microorganisms

1970 ◽  
Vol 4 (1) ◽  
Author(s):  
S Rahman ◽  
Pinky Karim ◽  
Abu Asad Chowdhury ◽  
Abul Hasnat
Keyword(s):  
Antimicrobial Activity ◽  
Antibacterial Activity ◽  
Nucleic Acid ◽  
Biological System ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Optimum Level ◽  
Bacterial Strains ◽  
Key Words Antibiotics ◽  
Life Threatening

Manganese is an important element in biological system. It is essential for enzymatic activity, maintaining three-dimensional structure of protein, for the synthesis of nucleic acid and protein etc. Deficiency of manganese causes different life threatening diseases. Because of this, the optimum level of manganese must be maintained in all biological system. This experiment, therefore, was designed to evaluate the effect of manganese on the activity of different antibiotics (ciprofloxacin, cephradine, amoxicillin, gentamycin, tetracycline, cloxacillin, nalidixic acid, ceftriaxone, metronidazole and carbenicillin) against different microorganisms. It has been observed that antimicrobial activity of an antibiotic increased significantly with concomitant use of manganese salt ranging from 600-6000 ng per antibiotic disc (P < 0.05). It is revealed from the experiment that manganese increases the activity of antibiotic against bacterial strains. Key words: Antibiotics, Manganese, Antibacterial activity. Dhaka Univ. J. Pharm. Sci. Vol.4(1) 2005 The full text is of this article is available at the Dhaka Univ. J. Pharm. Sci. website

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