Experimental Probing and Molecular Dynamics Simulation of the Molecular Recognition of DNA Duplexes by the Flavonoid Luteolin

2017 ◽  
Vol 57 (9) ◽  
pp. 2237-2249 ◽  
Author(s):  
Varughese Mary ◽  
P. Haris ◽  
Mathew K. Varghese ◽  
P. Aparna ◽  
C. Sudarsanakumar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Recognition ◽  
Dynamics Simulation ◽  
Dna Duplexes

Conformational and energetic properties of pyrrolidinyl PNA-DNA duplexes: A molecular dynamics simulation

2017 ◽  
Vol 1122 ◽  
pp. 27-33 ◽  
Author(s):  
Nattawee Poomsuk ◽  
Tawun Remsungnen ◽  
Tirayut Vilaivan ◽  
Andrew J. Hunt ◽  
Khatcharin Siriwong
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Dna Duplexes ◽  
Energetic Properties

Molecular recognition of bio-active flavonoids quercetin and rutin by bovine hemoglobin: an overview of the binding mechanism, thermodynamics and structural aspects through multi-spectroscopic and molecular dynamics simulation studies

2018 ◽  
Vol 20 (33) ◽  
pp. 21668-21684 ◽  
Author(s):  
Sourav Das ◽  
Nikita Bora ◽  
Mostofa Ataur Rohman ◽  
Raju Sharma ◽  
Anupam Nath Jha ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Recognition ◽  
Computational Analysis ◽  
Dynamics Simulation ◽  
Bovine Hemoglobin ◽  
Simulation Studies ◽  
Binding Mechanism ◽  
Structural Aspects

A spectroscopic and computational analysis of the interactions of two bio-active flavonoids with bovine hemoglobin (BHb) has been carried out.

Understanding selective molecular recognition in integrated carbon nanotube–polymer sensors by simulating physical analyte binding on carbon nanotube–polymer scaffolds

Soft Matter ◽  
2014 ◽  
Vol 10 (32) ◽  
pp. 5991-6004 ◽  
Author(s):  
Shangchao Lin ◽  
Jingqing Zhang ◽  
Michael S. Strano ◽  
Daniel Blankschtein
Keyword(s):  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulation ◽  
Molecular Recognition ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Binding Affinities ◽  
Polymer Scaffolds ◽  
Polymer Sensors ◽  
Coarse Grained Molecular Dynamics

Coarse-grained molecular dynamics simulation (left) is used to predict various analyte binding affinities onto SWCNT-polymer scaffolds (new sensor motifs), which are correlated with their photoluminescence signals (right) to understand sensing selectivity.

Hole-transfer Mechanism in Hydrated DNA Duplexes: Direct Ab Initio Molecular Dynamics Simulation

2019 ◽  
Vol 16 (24) ◽  
pp. 53-64
Author(s):  
Hajime Wakabayashi ◽  
Yasuyuki Ishikawa ◽  
Takayuki Tsukamoto ◽  
Noriyuki Kurita
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Transfer Mechanism ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Dna Duplexes ◽  
Hole Transfer

Molecular Recognition Mechanisms of Calmodulin Examined by Perturbation-Response Scanning

2011 ◽  
Vol 1301 ◽  
Author(s):  
A. Ozlem Aykut ◽  
Ali Rana Atilgan ◽  
Canan Atilgan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Recognition ◽  
Conformational Change ◽  
Linear Response ◽  
Direct Contact ◽  
Dynamics Simulation ◽  
Binding Region ◽  
Selective Binding ◽  
C Terminus

ABSTRACTWe analyze the apo and holo calmodulin (CaM) structures by sequentially inserting a perturbation on every residue of the protein, and monitoring the linear response. Residue crosscorrelation matrices obtained from 20 ns long molecular dynamics simulation of the apo-form are used as the kernel in the linear response. We determine two residues whose perturbation equivalently yields the experimentally determined displacement profiles of CaM, relevant to the binding of the trifluoperazine (TFP) ligand. They reside on structurally equivalent positions on the N- and C-terminus lobes of CaM, and are not in direct contact with the binding region. The direction of the perturbation that must be inserted on these residues is an important factor in recovering the conformational change, implying that highly selective binding must occur near these sites to invoke the necessary conformational change.

scholarly journals 139 Analysis of structure and thermodynamics of modified DNA duplexes using molecular dynamics simulation

2015 ◽  
Vol 33 (sup1) ◽  
pp. 90-91 ◽  
Author(s):  
Alexander A. Lomzov ◽  
Vitaly V. Gorelov ◽  
Victor M. Golyshev ◽  
Tatiana V. Abramova ◽  
Dmitrii V. Pyshnyi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Dynamics Simulation ◽  
Dna Duplexes ◽  
Modified Dna
Sign in / Sign up

Export Citation Format

Share Document