scholarly journals Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4–protein interaction

2015 ◽  
Vol 17 (48) ◽  
pp. 32257-32267 ◽  
Author(s):  
Yan Li ◽  
Xiang Li ◽  
Zigang Dong
Keyword(s):  
Molecular Dynamics ◽  
Ligand Binding ◽  
Molecular Dynamics Simulations ◽  
Small Molecule ◽  
Protein Interaction ◽  
Allosteric Site ◽  
Binding Process ◽  
Dynamics Simulations

The binding process of a drug-like small molecule through a conformational gate is illustrated by extensive molecular dynamics simulations.

scholarly journals The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (5) ◽  
pp. 1250
Author(s):  
Hien T. T. Lai ◽  
Alejandro Giorgetti ◽  
Giulia Rossetti ◽  
Toan T. Nguyen ◽  
Paolo Carloni ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ligand Binding ◽  
Molecular Dynamics Simulations ◽  
Binding Site ◽  
Transmembrane Protein ◽  
Free Form ◽  
Experimental Investigations ◽  
Terminal Part ◽  
Dynamics Simulations ◽  
Cholesterol Binding

The translocator protein (TSPO) is a 18kDa transmembrane protein, ubiquitously present in human mitochondria. It is overexpressed in tumor cells and at the sites of neuroinflammation, thus representing an important biomarker, as well as a promising drug target. In mammalian TSPO, there are cholesterol–binding motifs, as well as a binding cavity able to accommodate different chemical compounds. Given the lack of structural information for the human protein, we built a model of human (h) TSPO in the apo state and in complex with PK11195, a molecule routinely used in positron emission tomography (PET) for imaging of neuroinflammatory sites. To better understand the interactions of PK11195 and cholesterol with this pharmacologically relevant protein, we ran molecular dynamics simulations of the apo and holo proteins embedded in a model membrane. We found that: (i) PK11195 stabilizes hTSPO structural fold; (ii) PK11195 might enter in the binding site through transmembrane helices I and II of hTSPO; (iii) PK11195 reduces the frequency of cholesterol binding to the lower, N–terminal part of hTSPO in the inner membrane leaflet, while this impact is less pronounced for the upper, C–terminal part in the outer membrane leaflet, where the ligand binding site is located; (iv) very interestingly, cholesterol most frequently binds simultaneously to the so-called CRAC and CARC regions in TM V in the free form (residues L150–X–Y152–X(3)–R156 and R135–X(2)–Y138–X(2)–L141, respectively). However, when the protein is in complex with PK11195, cholesterol binds equally frequently to the CRAC–resembling motif that we observed in TM I (residues L17–X(2)–F20–X(3)–R24) and to CRAC in TM V. We expect that the CRAC–like motif in TM I will be of interest in future experimental investigations. Thus, our MD simulations provide insight into the structural features of hTSPO and the previously unknown interplay between PK11195 and cholesterol interactions with this pharmacologically relevant protein.

Machine learning and molecular dynamics simulations assisted evolutionary design and discovery pipeline to screen the efficient small molecule acceptors for PTB7-Th based organic solar cells with over 15% efficiency

2022 ◽  
Author(s):  
Jin-Liang Wang ◽  
Asif Mahmood ◽  
Ahmad Irfan
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Solar Cells ◽  
Molecular Dynamics Simulations ◽  
Small Molecule ◽  
Organic Solar Cells ◽  
Evolutionary Design ◽  
New Materials ◽  
Dynamics Simulations ◽  
Discovery Pipeline

Organic solar cells are the most promising candidates for future commercialization. This goal can be quickly achieved by designing new materials and predicting their performance without experimentation to reduce the...

scholarly journals DNA triplex structure, thermodynamics, and destabilisation: insight from molecular simulations

2018 ◽  
Vol 20 (20) ◽  
pp. 14013-14023 ◽  
Author(s):  
Belinda J. Boehm ◽  
Charles Whidborne ◽  
Alexander L. Button ◽  
Tara L. Pukala ◽  
David M. Huang
Keyword(s):  
Molecular Dynamics ◽  
Neurodegenerative Disease ◽  
Molecular Dynamics Simulations ◽  
Small Molecule ◽  
Molecular Simulations ◽  
Friedreich’S Ataxia ◽  
Dna Triplexes ◽  
Dna Triplex ◽  
Triplex Structure ◽  
Dynamics Simulations

Molecular dynamics simulations are used to elucidate the structure and thermodynamics of DNA triplexes associated with the neurodegenerative disease Friedreich's ataxia (FRDA), as well as complexes of these triplexes with the small molecule netropsin, which is known to destabilise triplexes.

A molecular dynamics study of the complete binding process of meropenem to New Delhi metallo-β-lactamase 1

2018 ◽  
Vol 20 (9) ◽  
pp. 6409-6420 ◽  
Author(s):  
Juan Duan ◽  
Chuncai Hu ◽  
Jiafan Guo ◽  
Lianxian Guo ◽  
Jia Sun ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Substrate Binding ◽  
New Delhi ◽  
Binding Process ◽  
Dynamics Simulations

We have investigated the substrate-binding pathways of NDM-1 via unbiased molecular dynamics simulations and metadynamics.

Sign in / Sign up

Export Citation Format

Share Document