scholarly journals A DNA structural alphabet provides new insight into DNA flexibility

2018 ◽  
Vol 74 (1) ◽  
pp. 52-64 ◽  
Author(s):  
Bohdan Schneider ◽  
Paulína Božíková ◽  
Iva Nečasová ◽  
Petr Čech ◽  
Daniel Svozil ◽  
...  
Keyword(s):  
Biological Function ◽  
Graphical Representation ◽  
Structural Alphabet ◽  
Dna Structures ◽  
Binding Partners ◽  
Validation Score ◽  
Fibre Diffraction ◽  
Interactive 3D ◽  
Automated Protocol ◽  
Insight Into

DNA is a structurally plastic molecule, and its biological function is enabled by adaptation to its binding partners. To identify the DNA structural polymorphisms that are possible in such adaptations, the dinucleotide structures of 60 000 DNA steps from sequentially nonredundant crystal structures were classified and an automated protocol assigning 44 distinct structural (conformational) classes called NtC (for Nucleotide Conformers) was developed. To further facilitate understanding of the DNA structure, the NtC were assembled into the DNA structural alphabet CANA (Conformational Alphabet of Nucleic Acids) and the projection of CANA onto the graphical representation of the molecular structure was proposed. The NtC classification was used to define a validation score called confal, which quantifies the conformity between an analyzed structure and the geometries of NtC. NtC and CANA assignment were applied to analyze the structural properties of typical DNA structures such as Dickerson–Drew dodecamers, guanine quadruplexes and structural models based on fibre diffraction. NtC, CANA and confal assignment, which is accessible at the website https://dnatco.org, allows the quantitative assessment and validation of DNA structures and their subsequent analysis by means of pseudo-sequence alignment. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:Acta_Cryst_D:2.

scholarly journals Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy

2020 ◽  
Vol 21 (8) ◽  
pp. 2673 ◽  
Author(s):  
Kwang-Im Oh ◽  
Jinwoo Kim ◽  
Chin-Ju Park ◽  
Joon-Hwa Lee
Keyword(s):  
Nmr Spectroscopy ◽  
Biological Function ◽  
Conformational Exchange ◽  
Biological Processes ◽  
Dynamic Characterization ◽  
Dynamic Features ◽  
Dna Structures ◽  
Left Handed ◽  
G Quadruplex ◽  
Insight Into

The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.

AN ANALYSIS OF THE THZ FREQUENCY SIGNATURES IN THE CELLULAR COMPONENTS OF BIOLOGICAL AGENTS

2007 ◽  
Vol 17 (02) ◽  
pp. 225-237 ◽  
Author(s):  
ALEXEI BYKHOVSKI ◽  
TATIANA GLOBUS ◽  
TATYANA KHROMOVA ◽  
BORIS GELMONT ◽  
DWIGHT WOOLARD
Keyword(s):  
Molecular Structure ◽  
Structural Similarity ◽  
Md Simulations ◽  
Detection Capability ◽  
Dna Structures ◽  
E Coli ◽  
Cellular Components ◽  
First Time ◽  
Insight Into ◽  
Specific Contribution

The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of E. coli was simulated and the associated THz signature was derived theoretically. The tRNA that binds amino acid tyrosine (tRNAtyr) was studied. Here, the molecular structure was optimized using the potential energy minimization and molecular dynamical (MD) simulations. Solvation effects (water molecules) were also included explicitly in the MD simulations. To verify that realistic molecular signatures were simulated, a parallel experimental study of tRNAs of E. coli was also conducted. Two very similar molecules, valine and tyrosine tRNA were investigated experimentally. Samples were prepared in the form of water solutions with the concentrations in the range 0.01-1 mg/ml. A strong correlation of the measured THz signatures associated with valine tRNA and tyrosine tRNA was observed. These findings are consistent with the structural similarity of the two tRNAs. The calculated THz signature of the tyrosine tRNA of E. coli reproduces many features of our measured spectra, and, therefore, provides valuable new insights into bio-agent detection.

The evolutionarily conserved MOS4-associated complex

2011 ◽  
Vol 6 (5) ◽  
pp. 776-784 ◽  
Author(s):  
Kaeli Johnson ◽  
Oliver Dong ◽  
Xin Li
Keyword(s):  
Biological Function ◽  
Plant Immunity ◽  
Biological Processes ◽  
Future Studies ◽  
Time Control ◽  
Core Member ◽  
Evolutionarily Conserved ◽  
Core Components ◽  
Flowering Time Control ◽  
Insight Into

AbstractRecent work in plant immunity has shown that MOS4, a known intermediate in R protein mediated resistance, is a core member of the nuclear MOS4-associated complex (MAC). This complex is highly conserved in eukaryotes, as orthologous complexes known as the CDC5L-SNEVPrp19-Pso4 complex and the Nineteen complex (NTC) were previously identified in human and yeast, respectively. The involvement of these complexes in pre-mRNA splicing and spliceosome assembly suggests that the MAC probably has a similar function in plants. Double mutants of any two MAC components are lethal, whereas single mutants of the MAC core components mos4, Atcdc5, mac3, and prl1 are all viable and display pleiotropic defects. This suggests that while the MAC is required for some essential biological function such as splicing, individual MAC components are not crucial for complex functionality and likely have regulatory roles in other biological processes such as plant immunity and flowering time control. Future studies on MAC components in Arabidopsis will provide further insight into the regulatory mechanisms of the MAC on specific biological processes.

Application of Screw Theory to Rigid Body Dynamics

1992 ◽  
Vol 114 (2) ◽  
pp. 262-269 ◽  
Author(s):  
G. R. Pennock ◽  
B. A. Oncu
Keyword(s):  
Rigid Body ◽  
Euler Equation ◽  
Computer Aided Design ◽  
Graphical Representation ◽  
Screw Theory ◽  
Rigid Body Dynamics ◽  
The Body ◽  
Dynamic State ◽  
Disk Rolling ◽  
Insight Into

This paper applies screw theory to the dynamic analysis of a rigid body in general spatial motion. Particular emphasis is placed upon the geometric interpretation of the velocity screw, the momentum screw, and the force screw which provide valuable physical insight into the dynamic behavior of the rigid body. The geometric relation between the velocity screw and the momentum screw is discussed in some detail. The paper shows that the dual angle between the two screws provides insight into the kinetics of the rigid body. The dynamic state of motion of the body is then described by a dual vector equation, referred to as the dual Euler equation. The paper shows that the geometric equivalent of the dual Euler equation is a spatial triangle which can be used as a graphical method of solution, or as a check, of the analytical formulation. The concepts introduced in this paper are illustrated by the well-known example of a thin, homogeneous, circular disk rolling without slipping on a flat horizontal surface. With the widespread use of computer graphics and computer-aided design, the geometric approach presented here will prove useful in the graphical representation of the dynamics of a rigid body.

An analytical tool for understanding the properties and behaviour of variable charge soils

Soil Research ◽  
2007 ◽  
Vol 45 (2) ◽  
pp. 83 ◽  
Author(s):  
G. P. Gillman
Keyword(s):  
Surface Charge ◽  
Large Scale ◽  
Graphical Representation ◽  
Resource Assessment ◽  
Ideal Condition ◽  
Soil Resource ◽  
Variable Charge ◽  
Ph Range ◽  
Soil Resource Assessment ◽  
Insight Into

Routine analyses for soil cation exchange properties usually give only limited insight into the properties and management of soils containing significant amounts of variable charge. In this paper a procedure for determining a soil Charge Fingerprint is fully described, a model developed from simplified theory to underpin the methodology is discussed, and examples of the usefulness of the approach are given. Operationally defined cation and anion exchange capacities (CEC and AEC) are determined over an appropriate pH range (pH 4 to pH 6 is suggested) using Ca and Cl as the index cations. At low pH, Ca does not always fully saturate the CEC, so that it is necessary to distinguish a Basic CEC (Ca ads.) from the Total CEC (Ca + Al ads.). The graphical representation of CECT, CECB, and AEC v. pH constitutes the Charge Fingerprint. Though not intended as a routine instrument, its determination on key samples in a characterisation exercise places routinely determined basic and acidic cations in context. Examples are given of large scale characterisation studies that link soils from different continents having similar surface charge characteristics; of the assessment of the success or otherwise of producing permanent positive charge in synthetically prepared Ti-substituted goethites; and of the evaluation of the effect of adding crushed basic rock amendment on the surface charge properties of a variable charge soil. The formulation of a Depreciation Index, which classifies soils in terms of their departure in basic cation content from an arbitrarily defined ‘ideal’ condition, is suggested for use in soil resource assessment.

scholarly journals MicroRNAs expression profile in CCR6+ regulatory T cells

2014 ◽  
Author(s):  
Juanjuan Zhao ◽  
Yongju Li ◽  
Yan Hu ◽  
Chao Chen ◽  
Ya Zhou ◽  
...  
Keyword(s):  
T Cells ◽  
Regulatory T Cells ◽  
Signaling Pathways ◽  
Expression Profile ◽  
Immune Cells ◽  
Potential Role ◽  
Biological Function ◽  
Fold Change ◽  
Insight Into

Backgroud: CCR6+ CD4+ regulatory T cells (CCR6+Tregs), a distinct Tregs subset, played an important role in various immune diseases. Recent evidence showed that microRNAs (miRNAs) are vital regulators in the function of immune cells. However, the potential role of miRNAs in the function of CCR6+Tregs remains largely unknown. In this study, we detected the expression profile of miRNAs in CCR6+ Tregs. Materials and Methods: The expression profile of miRNAs as well as genes in CCR6+Tregs or CCR6-Tregs from Balb/c mice were detected by microarray. The signaling pathways were analyzed using Keggs pathway library. Results: We found that there were 58 miRNAs significantly upregulated and 62 downregulated up to 2 fold in CCR6+Tregs compared with CCR6-Tregs. Moreover, 1391 genes were observed with 3 fold change and 20 signaling pathways were enriched using Keggs pathway library. Conclusion: The present data firstly showed CCR6+Tregs expressed specific miRNAs pattern, which provide an insight into the role of miRNAs in the biological function of distinct Tregs subsets.

scholarly journals Linkage Memory in Underivatized Protonated Carbohydrates

2020 ◽  
Author(s):  
Abhigya Mookherjee ◽  
Sanjit S. Uppal ◽  
Taylor A. Murphree ◽  
Miklos Guttman
Keyword(s):  
Mass Spectrometry ◽  
Gas Phase ◽  
Large Scale ◽  
Biological Function ◽  
Hydrogen Deuterium Exchange ◽  
Fragment Ions ◽  
Hydrogen Deuterium ◽  
Structural Insight ◽  
Multiple Conformations ◽  
Insight Into

<p>Carbohydrates are among the most complex class of biomolecules and even subtle variations in their structures are attributed to diverse biological function. Mass spectrometry has been essential for large scale glycomics and glycoproteomics studies, but the gas-phase structures and sometimes anomalous fragmentation properties of carbohydrates present longstanding challenges. Here we investigate the gas-phase properties of a panel of isomeric protonated disaccharides differing in their linkage configurations. Multiple conformations were evident for most of the structures based on their fragment ion abundances by tandem mass spectrometry, their ion mobilities in several gases, and their deuterium uptake kinetics by gas-phase hydrogen deuterium exchange. Most notably, we find that the properties of the Y-ion fragments are characteristically influenced by the precursor carbohydrate’s linkage configuration. This study reveals how protonated carbohydrate fragment ions can retain ‘linkage memory’ that provides structural insight into their intact precursor.</p>

scholarly journals Stabilization of EGLN3 by USP9X Contributes to Antineoplastic Function in Cholangiocarcinoma

2020 ◽  
Author(s):  
Weiqian Chen ◽  
Jingjing Song ◽  
Siyu Liu ◽  
Bufu Tang ◽  
Lin Shen ◽  
...  
Keyword(s):  
Biological Function ◽  
Quantitative Real Time Pcr ◽  
Liver Malignancy ◽  
Apoptosis Pathway ◽  
Efficient Treatment ◽  
Potential Biomarker ◽  
Insight Into ◽  
Silence Gene

Abstract Background: Cholangiocarcinoma represents the second most common primary liver malignancy. The incidence rate has constantly increased over the last decades. Cholangiocarcinoma silent nature limits early diagnosis and prevents efficient treatment. Methods: Immunoblotting and immunohistochemistry were used to assess the expression profiling of USP9X and EGLN3 in cholangiocarcinoma patients. ShRNA was used to silence gene expression. Cell apoptosis, cell cycle, CCK8, clone formation, shRNA interference and xenograft mouse model were used to explore biological function of USP9X and EGLN3. The underlying molecular mechanism of USP9X in cholangiocarcinoma was determined by immunoblotting, co-immunoprecipitation and quantitative real time PCR (qPCR).Results: Here we demonstrated that USP9X is downregulated in cholangiocarcinoma which contributes to tumorigenesis. The expression of USP9X in cholangiocarcinoma inhibited cell proliferation and colony formation in vitro as well as xenograft tumorigenicity in vivo. Clinical data demonstrated that expression levels of USP9X were positively correlated with favorable clinical outcomes. Mechanistic investigations further indicated that USP9X was involved in the deubiquitination of EGLN3, a member of 2-oxoglutarate and iron-dependent dioxygenases. USP9X elicited tumor suppressor role by preventing degradation of EGLN3. Importantly, knockdown of EGLN3 impaired USP9X-mediated suppression of proliferation. USP9X positively regulated the expression level of apoptosis pathway genes KIF1Bβ through EGLN3 thus involved in apoptosis of cholangiocarcinoma. Conclusion: These findings help to understand that USP9X alleviates the malignant potential of cholangiocarcinoma through upregulation of EGLN3. Consequently, we provided novel insight into that USP9X is a potential biomarker or serves as a therapeutic or diagnostic target for cholangiocarcinoma.

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