Modeling Protein-Protein and Protein-DNA Docking

2008 ◽  
pp. 601-650 ◽  
Author(s):  
Andreas Hildebrandt ◽  
Oliver Kohlbacher ◽  
Hans-Peter Lenhof
Keyword(s):  
Dna Docking

scholarly journals tagPAINT: covalent labelling of genetically encoded protein tags for DNA-PAINT imaging

2019 ◽  
Vol 6 (12) ◽  
pp. 191268
Author(s):  
Daniel J. Nieves ◽  
Geva Hilzenrat ◽  
Jason Tran ◽  
Zhengmin Yang ◽  
Hugh H. MacRae ◽  
...  
Keyword(s):  
Single Molecule ◽  
Quantitative Imaging ◽  
Cell Receptor ◽  
Great Promise ◽  
Immune Synapse ◽  
Localization Microscopy ◽  
Receptor Signalling ◽  
Protein Tags ◽  
Dna Docking ◽  
Single Molecule Localization Microscopy

Recently, DNA-PAINT single-molecule localization microscopy (SMLM) has shown great promise for quantitative imaging; however, labelling strategies thus far have relied on multivalent and affinity-based approaches. Here, the covalent labelling of expressed protein tags (SNAP tag and Halo tag) with single DNA-docking strands and application of SMLM via DNA-PAINT is demonstrated. tagPAINT is then used for T-cell receptor signalling proteins at the immune synapse as a proof of principle.

scholarly journals Synthesis and amide imidic prototropic tautomerization in thiophene-2-carbohydrazide: XRD, DFT/HSA-computation, DNA-docking, TG and isoconversional kinetics via FWO and KAS models

RSC Advances ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 2037-2048 ◽  
Author(s):  
Nabil Al-Zaqri ◽  
Tamer Khatib ◽  
Ali Alsalme ◽  
Fahad A. Alharthi ◽  
Abdelkader Zarrouk ◽  
...  
Keyword(s):  
Microwave Radiation ◽  
Small Molecule ◽  
Isoconversional Kinetics ◽  
Dna Docking

Thiophene-2-carbohydrazide as a novel small-molecule amide tautomer has been synthesized with an acceptable yield under microwave radiation (MW) conditions.

Radicalic cleavage pathway and DNA docking studies of novel chemotherapic platinum agent of 5,6-di-2-ithienyl-2,3-dihydropyrazine

Polyhedron ◽  
2019 ◽  
Vol 170 ◽  
pp. 25-33
Author(s):  
Rabia El Hag ◽  
Mohamed Musbah Abdusalam ◽  
Ceyda Acilan ◽  
Hakan Kayı ◽  
Şeniz Özalp-Yaman
Keyword(s):  
Docking Studies ◽  
Platinum Agent ◽  
Dna Docking

scholarly journals A knowledge-based orientation potential for transcription factor-DNA docking

2012 ◽  
Vol 29 (3) ◽  
pp. 322-330 ◽  
Author(s):  
Takako Takeda ◽  
Rosario I. Corona ◽  
Jun-tao Guo
Keyword(s):  
Transcription Factor ◽  
Knowledge Based ◽  
Dna Docking

scholarly journals Modulation of current through a nanopore induced by a charged globule: Implications for DNA-docking

2014 ◽  
Vol 108 (4) ◽  
pp. 46002 ◽  
Author(s):  
Mauro Chinappi ◽  
Carlo Massimo Casciola ◽  
Fabio Cecconi ◽  
Umberto Marini Bettolo Marconi ◽  
Simone Melchionna
Keyword(s):  
Dna Docking

A GPU-Based Approach to Accelerate Computational Protein-DNA Docking

2012 ◽  
Vol 14 (3) ◽  
pp. 20-29 ◽  
Author(s):  
Jiadong Wu ◽  
Chunlei Chen ◽  
Bo Hong
Keyword(s):  
Dna Docking

scholarly journals Optimized structure of monoubiquitinated FANCD2 (human) at Lys 561: a theoretical approach

2021 ◽  
Author(s):  
Sudipa Mondal ◽  
Subba Reddy ◽  
Sudit S. Mukhopadhyay
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Theoretical Approach ◽  
Md Simulation ◽  
Docking Studies ◽  
Fanconi Anaemia ◽  
Cross Linking ◽  
Structural Differences ◽  
The Stability ◽  
Dna Docking

AbstractFanconi anaemia pathway repairs inter-strand cross linking damage (ICL) of the DNA. Monoubiquitination of FANCD2 and FANCI is very crucial for ICL repairing. In this work we have tried to understand the monoubiquitinated FANCD2 structure, which facilitates the FANCD2 for binding the damage part of the chromatin. Crystal structure of the monoubiquitinated FANCD2 alone is not available, therefore we have developed the optimized structure of the human monoubiquitinated (Lys 561) FANCD2. As there is no suitable software or web server we have developed a method for building up monoubiquitinated product and validated on simplest monoubiquitinated protein, diubiquitin. We have predicted the structure of human monoubiquitinated FANCD2 by using our method and studied the interaction with DNA by docking studies. Molecular Dynamics (MD) simulation was used to understand the stability of the structure. Large structural differences have been observed between FANCD2 and monoubiquitinated FANCD2. DNA docking studies suggest that the binding site varies for the FANCD2 and monoubiquitinated FANCD2.

scholarly journals Hypothalamus-Pituitary-Adrenal Axis, Hair Cortisol, Chronic Stress, Metabolic Syndrome, and Mindfulness

2016 ◽  
Vol 1 (2) ◽  
Keyword(s):  
Metabolic Syndrome ◽  
The Body ◽  
Receptor Complex ◽  
Hair Cortisol ◽  
Adrenal Axis ◽  
The Past ◽  
Exponential Expansion ◽  
Hypothalamus Pituitary Adrenal Axis ◽  
Dna Docking ◽  
Pituitary Adrenal Axis

Over the past 60 years, there has been an exponential expansion in the field of neuroendocrinology. The HPA (HypothalamusPituitary-Adrenal) Axis is affected by both internal physiological stressors (cytokines, hypoxia, macromolecules, etc), and by external stressors (source of anxiety, fear, etc), which threaten the organism’s homeostasis. Cortisol binds to cortisol receptors throughout the body. The hormone receptor complex is to be found in the nucleus of the cells, where it binds to DNA (docking). The consequences of this bond vary considerably. In some cells cortisol can induce some genes and repress others. When the HPA Axis is overactive, the amount of cortisol in the nucleus of the cells may increase tenfold.

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