Unraveling the Molecular Structure of the Catalytic Domain of Matrix Metalloproteinase-2 in Complex with a Triple-Helical Peptide by Means of Molecular Dynamics Simulations

Biochemistry ◽  
2013 ◽  
Vol 52 (47) ◽  
pp. 8556-8569 ◽  
Author(s):  
Natalia Díaz ◽  
Dimas Suárez ◽  
Haydeé Valdés
Keyword(s):  
Molecular Structure ◽  
Molecular Dynamics ◽  
Matrix Metalloproteinase ◽  
Molecular Dynamics Simulations ◽  
Catalytic Domain ◽  
Matrix Metalloproteinase 2 ◽  
Helical Peptide ◽  
Dynamics Simulations

scholarly journals Studi Dinamika Molekul Stabilisasi Metaloproteinase Matriks 9 oleh Asam Kafeat

2020 ◽  
Vol 6 (2) ◽  
Author(s):  
Enade Perdana Istyastono
Keyword(s):  
Molecular Dynamics ◽  
Matrix Metalloproteinase ◽  
Molecular Dynamics Simulations ◽  
Caffeic Acid ◽  
Matrix Metalloproteinase 9 ◽  
Atomic Mechanism ◽  
Ic50 Value ◽  
Dynamics Simulations ◽  
20 Nm ◽  
Metalloproteinase 9

Caffeic acid, a cathecol-containing phytochemical found in coffee, has been reported as a potent matrix metalloproteinase 9 (MMP9) inhibitor. The IC50 value of caffeic acid as MMP9 inhibitor could reach below 20 nM. The research presented in this article employed molecular dynamics simulations to unravel the atomic mechanism of the MMP9 inhibition by caffeic acid. Molecular dynamics simulations of MMP9 for 10 ns using YASARA-Structure were performed with and without caffeic acid as the studied ligand. The results showed that caffeic acid stabilized the stucture of the MMP9.

scholarly journals Molecular Mechanism of Light-Induced Acceleration of the Adenosine Triphosphate Conversion to the Cyclic Adenosine Monophosphate Catalyzed by the Photoactivated Adenylyl Cyclase bPAC

2020 ◽  
Author(s):  
Alexander Nemukhin ◽  
Maria Khrenova ◽  
Anna M. Kulakova
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Adenylyl Cyclase ◽  
Adenosine Triphosphate ◽  
Catalytic Domain ◽  
Cyclic Adenosine Monophosphate ◽  
Adenosine Monophosphate ◽  
Bluf Domain ◽  
Dynamics Simulations ◽  
Photoactivated Adenylyl Cyclase

<p>We report the first computational characterization of an optogenetic system composed of two photosensing BLUF (<u>b</u>lue <u>l</u>ight sensor <u>u</u>sing <u>f</u>lavin adenine dinucleotide) domains and two catalytic adenylyl cyclase (AC) domains. Conversion of adenosine triphosphate (ATP) to cyclic adenosine monophosphate (cAMP) and pyrophosphate (PPi) catalyzed by ACs coupled with excitation in photosensing domains has emerged in the focus of modern optogenetic applications because of the request in photoregulated enzymes to modulate cellular concentrations of signaling messengers. The photoactivated adenylyl cyclase from the soil bacterium <i>Beggiatoa sp.</i> (bPAC) is an important model showing considerable increase of the ATP to cAMP conversion rate in the catalytic domain after the illumination of the BLUF domain. The 1 μs classical molecular dynamics simulations reveal that the activation of the BLUF domain leading to tautomerization of Gln49 in the chromophore binding pocket results in switching of position of the side chain of Arg278 in the active site of AC. Allosteric signal transmission pathways between Gln49 from BLUF and Arg278 from AC were revealed by the dynamical network analysis. The Gibbs energy profiles of the ATP → cAMP + PPi reaction computed using QM(DFT(ωB97X-D3/6-31G**))/MM(CHARMM) molecular dynamics simulations for both Arg278 conformations in AC clarify the reaction mechanism. In the light-activated system, the corresponding arginine conformation stabilizes the pentacoordinated phosphorus of the α-phosphate group in the transition state, thus lowering the activation energy. Simulations of the bPAC system with the Tyr7Phe replacement in BLUF demonstrate occurrence of both arginine conformations in an equal ratio, explaining the experimentally observed intermediate catalytic activity of the bPAC-Y7F variant as compared with the dark and light states of the wild type bPAC. </p>

Effect of Two Dental Restorative Materials on Adhesion and Molecular Structure of Oral Bacteria

2020 ◽  
Vol 20 (8) ◽  
pp. 4643-4647
Author(s):  
Shuai Xu ◽  
Junfeng Guo ◽  
Junjie Huang ◽  
Gang Zhang ◽  
Yinghui Tan
Keyword(s):  
Molecular Structure ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Substrate Surface ◽  
Oral Bacteria ◽  
Oral Rehabilitation ◽  
Dental Restorative Materials ◽  
Restorative Materials ◽  
Dynamics Simulations ◽  
Dental Restorative

Dental restorative materials are widely used to repair teeth and dentition defects. However, the dental restorative materials tend to react with oral bacteria when they are exposed to oral conditions, which leads to a change in the oral microecology. Herein, we have employed molecular dynamics simulations to investigate the interaction between different dental restorative materials and oral bacteria. It was found that the staphylococcal protein A (SPA) is more likely to attach on the surface of silicon carbide (SiC) substrate than hematite (Fe2O3) substrate surface. Furthermore, the tightly adhesion and accumulation of SPA on SiC surface changes the molecular structure of SPA, which will induce a change in the oral microecology. This study has demonstrated that the adhesion and molecular structure of oral bacteria is strongly dependent on dental restorative materials by molecular dynamics simulations, and Fe2O3 is more suitable to be a dental restorative material. It is therefore believed that molecular dynamics simulations can be used to further screen suitable materials for oral rehabilitation.

Sign in / Sign up

Export Citation Format

Share Document