scholarly journals Molecular Dynamics Simulation of the Influenza A(H3N2) Hemagglutinin Trimer Reveals the Structural Basis for Adaptive Evolution of the Recent Epidemic Clade 3C.2a

2017 ◽  
Vol 8 ◽  
Author(s):  
Masaru Yokoyama ◽  
Seiichiro Fujisaki ◽  
Masayuki Shirakura ◽  
Shinji Watanabe ◽  
Takato Odagiri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Adaptive Evolution ◽  
Influenza A ◽  
Dynamics Simulation ◽  
Structural Basis

Molecular dynamics simulation studies on influenza A virus H5N1 complexed with sialic acid and fluorinated sialic acid

2019 ◽  
Vol 37 (18) ◽  
pp. 4813-4824 ◽  
Author(s):  
R. A. Jeyaram ◽  
T. R. K. Priyadarzini ◽  
C. Anu Radha ◽  
N. R. Siva Shanmugam ◽  
C. Ramakrishnan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Sialic Acid ◽  
Molecular Dynamics Simulation ◽  
Influenza A Virus ◽  
Influenza A ◽  
Dynamics Simulation ◽  
Simulation Studies ◽  
Virus H5n1

scholarly journals Probing the Structural Basis of Citrus Phytochrome B using Computational Modelling and Molecular Dynamics Simulation Approaches

2021 ◽  
pp. 116895
Author(s):  
Muhammad Tahir ul Qamar ◽  
Muhammad Usman Mirza ◽  
Jia-Ming Song ◽  
Muhammad Junaid Rao ◽  
Xitong Zhu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Computational Modelling ◽  
Dynamics Simulation ◽  
Structural Basis ◽  
Phytochrome B

scholarly journals HDX-MS Combining Molecular Dynamics Simulation Reveals Structural Basis of Transcriptional Coactivator PC4 Binding to a Platinum Crosslinked Double-Stranded DNA

2021 ◽  
Author(s):  
Yuanyuan Wang ◽  
Zhifeng Du ◽  
Lifang Chen ◽  
Yao Zhao ◽  
Wei Zheng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Dna Damage ◽  
Molecular Dynamics Simulation ◽  
Cellular Response ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Structural Basis ◽  
Future Research ◽  
Deuterium Uptake ◽  
Hdx Ms

<p>Human nuclear protein positive cofactor PC4 is a DNA-binding protein, and plays an important role in the early response to DNA damage by recognizing single-stranded oligodeoxynucleotide domain and facilitating the subsequent steps of DNA repair. Our group previously discovered that PC4 selectively binds to a double-stranded oligodeoxynucleotide (dsODN) damaged by a trans-platinum anticancer complex, trans-[PtCl2(NH3)(thiazole)] (trans-PtTz). However, the molecular basis of this unique recognition and interaction remained unclear. In this work, amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) was applied to dissect the interaction interface between PC4 and a 15-mer double-stranded oligodeoxynucleotide crosslinked by trans-PtTz (trans-PtTz-dsODN). Global deuterium uptake suggested a 1:1 binding stoichiometry of PC4 to trans-PtTz-dsODN. Local deuterium uptake revealed that the flexible N-terminal loop and the β3 – β5-sheet played key roles in the recognition and interaction between PC4 and trans-PtTz-dsODN. In order to locate the key amino acid residues, molecular dynamics simulation was employed, demonstrating that PC4 binds to the trans-PtTz-dsODN at the minor groove via strong H-bonds with the nucleobases of the complementary strand. The minor groove width was broadened to adapt for the binding of PC4. Arg86 residue in PC4 was shown to dominate the recognition and interaction, which was verified by electrophoretic mobility shift assays. This work profiles the detailed interaction mechanism of PC4 with trans-PtTz damaged dsODN, and the combination use of HDX-MS and molecular dynamics simulation provides a new paradigm for the future research of the cellular response to the platinum induced DNA damage.</p>

scholarly journals HDX-MS Combining Molecular Dynamics Simulation Reveals Structural Basis of Transcriptional Coactivator PC4 Binding to a Platinum Crosslinked Double-Stranded DNA

2021 ◽  
Author(s):  
Yuanyuan Wang ◽  
Zhifeng Du ◽  
Lifang Chen ◽  
Yao Zhao ◽  
Wei Zheng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Dna Damage ◽  
Molecular Dynamics Simulation ◽  
Cellular Response ◽  
Minor Groove ◽  
Dynamics Simulation ◽  
Structural Basis ◽  
Future Research ◽  
Deuterium Uptake ◽  
Hdx Ms

<p>Human nuclear protein positive cofactor PC4 is a DNA-binding protein, and plays an important role in the early response to DNA damage by recognizing single-stranded oligodeoxynucleotide domain and facilitating the subsequent steps of DNA repair. Our group previously discovered that PC4 selectively binds to a double-stranded oligodeoxynucleotide (dsODN) damaged by a trans-platinum anticancer complex, trans-[PtCl2(NH3)(thiazole)] (trans-PtTz). However, the molecular basis of this unique recognition and interaction remained unclear. In this work, amide hydrogen/deuterium exchange mass spectrometry (HDX-MS) was applied to dissect the interaction interface between PC4 and a 15-mer double-stranded oligodeoxynucleotide crosslinked by trans-PtTz (trans-PtTz-dsODN). Global deuterium uptake suggested a 1:1 binding stoichiometry of PC4 to trans-PtTz-dsODN. Local deuterium uptake revealed that the flexible N-terminal loop and the β3 – β5-sheet played key roles in the recognition and interaction between PC4 and trans-PtTz-dsODN. In order to locate the key amino acid residues, molecular dynamics simulation was employed, demonstrating that PC4 binds to the trans-PtTz-dsODN at the minor groove via strong H-bonds with the nucleobases of the complementary strand. The minor groove width was broadened to adapt for the binding of PC4. Arg86 residue in PC4 was shown to dominate the recognition and interaction, which was verified by electrophoretic mobility shift assays. This work profiles the detailed interaction mechanism of PC4 with trans-PtTz damaged dsODN, and the combination use of HDX-MS and molecular dynamics simulation provides a new paradigm for the future research of the cellular response to the platinum induced DNA damage.</p>

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