Comprehensive study of the interaction between Puerariae Radix flavonoids and DNA: From theoretical simulation to structural analysis to functional analysis

2020 ◽  
Vol 231 ◽  
pp. 118109 ◽  
Author(s):  
Xu Chen ◽  
Ziyu He ◽  
Xianyong Wu ◽  
Dongsheng Mao ◽  
Chang Feng ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Structural Analysis ◽  
Theoretical Simulation ◽  
Puerariae Radix ◽  
Comprehensive Study

scholarly journals Identification of fidelity-governing factors in human recombinases DMC1 and RAD51 from cryo-EM structures

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Shih-Chi Luo ◽  
Hsin-Yi Yeh ◽  
Wei-Hsuan Lan ◽  
Yi-Min Wu ◽  
Cheng-Han Yang ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Structural Analysis ◽  
Md Simulation ◽  
Structural Basis ◽  
High Fidelity ◽  
Dna Dynamics ◽  
Genomic Integrity ◽  
Mismatched Dna ◽  
Dna Backbone ◽  
Loop 2

AbstractBoth high-fidelity and mismatch-tolerant recombination, catalyzed by RAD51 and DMC1 recombinases, respectively, are indispensable for genomic integrity. Here, we use cryo-EM, MD simulation and functional analysis to elucidate the structural basis for the mismatch tolerance of DMC1. Structural analysis of DMC1 presynaptic and postsynaptic complexes suggested that the lineage-specific Loop 1 Gln244 (Met243 in RAD51) may help stabilize DNA backbone, whereas Loop 2 Pro274 and Gly275 (Val273/Asp274 in RAD51) may provide an open “triplet gate” for mismatch tolerance. In support, DMC1-Q244M displayed marked increase in DNA dynamics, leading to unobservable DNA map. MD simulation showed highly dispersive mismatched DNA ensemble in RAD51 but well-converged DNA in DMC1 and RAD51-V273P/D274G. Replacing Loop 1 or Loop 2 residues in DMC1 with RAD51 counterparts enhanced DMC1 fidelity, while reciprocal mutations in RAD51 attenuated its fidelity. Our results show that three Loop 1/Loop 2 residues jointly enact contrasting fidelities of DNA recombinases.

Construction and Structural Analysis of Tethered Lipid Bilayer Containing Photosynthetic Antenna Proteins for Functional Analysis

2011 ◽  
Vol 12 (7) ◽  
pp. 2850-2858 ◽  
Author(s):  
Ayumi Sumino ◽  
Takehisa Dewa ◽  
Toshikazu Takeuchi ◽  
Ryuta Sugiura ◽  
Nobuaki Sasaki ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Structural Analysis ◽  
Lipid Bilayer ◽  
Antenna Proteins ◽  
Photosynthetic Antenna

scholarly journals Isolation, sequencing, and functional analysis of the TATA-less murine ATPase II promoter and structural analysis of the ATPase II gene

2007 ◽  
Vol 1769 (1) ◽  
pp. 61-75 ◽  
Author(s):  
Tomasz Sobocki ◽  
Farah Jayman ◽  
Malgorzata B. Sobocka ◽  
Jonathan D. Marmur ◽  
Probal Banerjee
Keyword(s):  
Functional Analysis ◽  
Structural Analysis ◽  
Atpase Ii

History and future of shotgun glycomics

2019 ◽  
Vol 47 (1) ◽  
pp. 1-11 ◽  
Author(s):  
David F. Smith ◽  
Richard D. Cummings ◽  
Xuezheng Song
Keyword(s):  
Signal Transduction ◽  
Functional Analysis ◽  
Structural Analysis ◽  
Cellular Adhesion ◽  
Intercellular Signaling ◽  
Animal Cells ◽  
Natural Sources ◽  
Biologically Relevant ◽  
Glycan Microarray ◽  
Detailed Structural Analysis

Abstract Glycans in polysaccharides and glycoconjugates of the hydrophilic exterior of all animal cells participate in signal transduction, cellular adhesion, intercellular signaling, and sites for binding of pathogens largely through protein–glycan interactions. Microarrays of defined glycans have been used to study the binding specificities of biologically relevant glycan-binding proteins (GBP), but such arrays are limited by their lack of diversity or relevance to the GBP being investigated. Shotgun glycan microarrays are made up of structurally undefined glycans that were released from natural sources, labeled with bifunctional reagents so that they can be monitored during their purification using multidimensional chromatographic procedures, stored as a tagged glycan library (TGL) and subsequently printed onto microarrays at equal molar concentrations. The shotgun glycan microarray is then interrogated with a biologically relevant GBP and the corresponding glycan ligands can be retrieved from the TGL for detailed structural analysis and further functional analysis. Shotgun glycomics extended the defined glycan microarray to a discovery platform that supports functional glycomic analyses and may provide a useful process for ultimately defining the human glycome.

Classroom-Based Strategies to Incorporate Hypothesis Testing in Functional Behavior Assessments

2017 ◽  
Vol 26 (2) ◽  
pp. 48-56 ◽  
Author(s):  
Blair P. Lloyd ◽  
Emily S. Weaver ◽  
Johanna L. Staubitz
Keyword(s):  
Functional Analysis ◽  
Structural Analysis ◽  
Hypothesis Testing ◽  
Classroom Environment ◽  
Challenging Behavior ◽  
Advantages And Disadvantages ◽  
Functional Behavior ◽  
Testing Strategies ◽  
Functional Behavior Assessments

When results of descriptive functional behavior assessments are unclear, hypothesis testing can help school teams understand how the classroom environment affects a student’s challenging behavior. This article describes two hypothesis testing strategies that can be used in classroom settings: structural analysis and functional analysis. For each strategy, we (a) review relevant examples from the literature, (b) identify advantages and disadvantages, and (c) offer recommendations for when and how to use them.

MODELING AND ANALYZING THE METABOLISM OF RIBOFLAVIN PRODUCTION USING PETRI NETS

2009 ◽  
Vol 17 (03) ◽  
pp. 479-490 ◽  
Author(s):  
D.-W. DING ◽  
L. N. LI
Keyword(s):  
Functional Analysis ◽  
Bacillus Subtilis ◽  
Structural Analysis ◽  
Petri Nets ◽  
In Silico ◽  
Visual Representation ◽  
Riboflavin Production ◽  
Biochemical Pathways ◽  
Functional Capabilities ◽  
Analysis Methods

A number of recent studies have focused on structural and functional analysis and simulation of biochemical pathways, and it suggested that these structure-oriented analysis methods could be greatly helpful for the understanding of the metabolism. Among several structural analysis methods, Petri nets analysis (PNA) has a visual representation that facilitates users' comprehension and thus is employed in this study. The main results in the present paper are: (1) an in silico model of the metabolism of riboflavin production in bacillus subtilis based on PNA; and (2) a study with structural analysis. The obtained invariants are analyzed and classified based on their structural and functional capabilities.

scholarly journals Tricalcium silicate Ca3SiO5, the major component of anhydrous Portland cement: on the conservation of distances and directions and their relationship to the structural elements

2003 ◽  
Vol 218 (1) ◽  
Author(s):  
M.- N. de Noirfontaine ◽  
F. Dunstetter ◽  
M. Courtial ◽  
G. Gasecki ◽  
M. Signes-Frehel
Keyword(s):  
Phase Diagram ◽  
Structural Analysis ◽  
Portland Cement ◽  
Tricalcium Silicate ◽  
Structural Elements ◽  
Complex Phase ◽  
New Ideas ◽  
Comprehensive Study

AbstractTricalcium silicate, the major component of Portland cement exhibits a complex phase diagram, surprisingly still not completely understood. In this letter, new results are highlighted including a comprehensive study of the superstructure relationship between the polymorphs, and new ideas about the structural analysis. The organisation of the silicate skeleton can be described in terms of 1-D or 2-D elements, from which arise new hypotheses about the cohesion and the chemical origin of the observed superstructures.

scholarly journals Verification of the Saccharina japonica Translocon Tic20 and its Localization in the Chloroplast Membrane in Diatoms

2019 ◽  
Vol 20 (16) ◽  
pp. 4000 ◽  
Author(s):  
Zhihang Chen ◽  
Xiuliang Wang ◽  
Shuang Li ◽  
Jianting Yao ◽  
Zhanru Shao ◽  
...  
Keyword(s):  
Functional Analysis ◽  
Structural Analysis ◽  
Phaeodactylum Tricornutum ◽  
Protein Transport ◽  
Saccharina Japonica ◽  
Structural Domain ◽  
Helix Loop Helix ◽  
Topological Features ◽  
Ef Hand ◽  
Chloroplast Stroma

Tic20 is an important translocon protein that plays a role in protein transport in the chloroplast. The sequence of Tic20 was determined in the lower brown alga Saccharina japonica. Structural analysis of SjTic20 revealed a noncanonical structure consisting of an N-terminal non-cyanobacterium-originated EF-hand domain (a helix-loop-helix structural domain) and a C-terminal cyanobacterium-originated Tic20 domain. Subcellular localization and transmembrane analysis indicated that SjTic20 featured an “M”-type Nin-Cin-terminal orientation, with four transmembrane domains in the innermost membrane of the chloroplast in the microalga Phaeodactylum tricornutum, and the EF-hand domain was entirely extruded into the chloroplast stroma. Our study provides information on the structure, localization, and topological features of SjTic20, and further functional analysis of SjTic20 in S. japonica is needed.

Structure, Function and Nonsense: A Guide to the Perplexed

1979 ◽  
Vol 9 (3) ◽  
pp. 205-208 ◽  
Author(s):  
Harris B. Peck
Keyword(s):  
Functional Analysis ◽  
Structural Analysis ◽  
Structure Function ◽  
Systems Theory ◽  
Therapy Group ◽  
General Systems Theory ◽  
Psychoanalytic Therapy ◽  
General Systems ◽  
Historical Developments ◽  
Practical Implications

TA therapists disagree about the distinctions between structural and functional analysis. Structural commonly refers to (1) historical developments, (2) intrapsychic or internal transactions, (3) the internal organization of such components or some combination of the above. Berne's own progression from descriptive (functional) analysis to structural analysis parallels his increasing use of the therapy group for work he had previously conducted in one to one psychoanalytic therapy. Concepts from general systems theory may be employed to clarify the theoretical distinctions between structural and functional analysis as well as their practical implications for psychotherapy and TA.

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