Results 1 to 10 of about 452,634 (352)

Investigate the Binding of Catechins to Trypsin Using Docking and Molecular Dynamics Simulation

PLOS ONE, 2015
To explore the inhibitory mechanism of catechins for digestive enzymes, we investigated the binding mode of catechins to a typical digestive enzyme-trypsin and analyzed the structure-activity relationship of catechins, using an integration of molecular docking, molecular dynamics simulation and binding free energy calculation.
Yunqi Li, Kecheng Yang, Fengchao Cui
openaire   +6 more sources

Data of the molecular dynamics simulations of mutations in the human connexin46 docking interface

Data in Brief, 2016
The structure of hCx26 derived from the X-ray analysis was used to generate a homology model for hCx46. Interacting connexin molecules were used as starting model for the molecular dynamics (MD) simulation using NAMD and allowed us to predict the dynamic behavior of hCx46wt and the cataract related mutant hCx46N188T as well as two artificial mutants ...
Patrik Schadzek, Frank Schaarschmidt, Michael Koval, Anaclet Ngezahayo, Julia Lindner, Alexander Heisterkamp, Barbara Schlingmann, Matthias Preller   +7 more
openaire   +4 more sources

The integrin-binding defective FGF2 mutants potently suppress FGF2 signalling and angiogenesis. [PDF]

, 2017
We recently found that integrin αvβ3 binds to fibroblast growth factor (FGF)-αvβ31 (FGF1), and that the integrin-binding defective FGF1 mutant (Arg-50 to glutamic acid, R50E) is defective in signalling and antagonistic to FGF1 signalling. R50E suppressed
Hamada, Yoshinosuke, Hatori, Nobuaki, Kawaguchi, Naomasa, Lam, Kit S, Matsuura, Nariaki, Mori, Seiji, Shih, Tsung-Chieh, Takada, Yoko K, Takada, Yoshikazu, Wu, Chun-Yi, Yamamoto, Hirofumi   +10 more
core   +2 more sources

Docking and Molecular Dynamic Simulation of Temozolomide with Carbonic Anhydrase XIII

Asian Journal of Organic & Medicinal Chemistry, 2020
The effect of inhibition of temozolomide, an alkylating agent widely used in cancer treatments, with carbonic anhydrase XIII protein was investigated using docking studies. The stability of temozolomide in the protein environment was assessed and analyzed by molecular dynamics simulation.
K. Selvaraju, P. V. Nidhin, R. Meenashi, P. Jayalakshmi, A. David Stephen   +4 more
openaire   +2 more sources

Neck linker docking is critical for Kinesin-1 force generation in cells but at a cost to motor speed and processivity. [PDF]

, 2019
Kinesin force generation involves ATP-induced docking of the neck linker (NL) along the motor core. However, the roles of the proposed steps of NL docking, cover-neck bundle (CNB) and asparagine latch (N-latch) formation, during force generation are ...
Budaitis, Breane G, Grant, Barry J, Jariwala, Shashank, Lang, Matthew J, Reinemann, Dana N, Scarabelli, Guido, Schimert, Kristin I, Sept, David, Verhey, Kristen J   +8 more
core   +1 more source

Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners [PDF]

, 2018
Lysyl oxidase (LOX) catalyzes the oxidative deamination of lysine and hydroxylysine residues in collagens and elastin, which is the first step of the cross-linking of these extracellular matrix proteins.
Duclos, Bertrand, Liwo, Adam, Miele, Adriana E., Ricard-Blum, Sylvie, Samsonov, Sergey A., Uciechowska-Kaczmarzyk, Urszula, Vallet, Sylvain D.   +6 more
core   +3 more sources

Evaluation of active designs of cephalosporin C acylase by molecular dynamics simulation and molecular docking [PDF]

Journal of Molecular Modeling, 2014
Optimization to identify the global minimum energy conformation sequence in in silico enzyme design is computationally non-deterministic polynomial-time (NP)-hard, with the search time growing exponentially as the number of design sites increases. This drawback forces the modeling of protein-ligand systems to adopt discrete amino acid rotamers and ...
Li, Q, Huang, X, Zhu, Y
openaire   +3 more sources

Secretory vesicles are preferentially targeted to areas of low molecular SNARE density [PDF]

, 2012
Intercellular communication is commonly mediated by the regulated fusion, or exocytosis, of vesicles with the cell surface. SNARE (soluble N-ethymaleimide sensitive factor attachment protein receptor) proteins are the catalytic core of the secretory ...
Dun, Alison, Duncan, Rory R, Dunn, Andrew, Lord, Gabriel J, Lu, Weiping, Martin, Kirsty J, Qiu, Zhen, Rickman, Colin, Yang, Lei   +8 more
core   +4 more sources

Molecular mechanism of MBX2319 inhibition of Escherichia coli AcrB multidrug efflux pump and comparison with other inhibitors [PDF]

, 2014
Efflux pumps of the resistance nodulation division (RND) superfamily, such as AcrB, make a major contribution to multidrug resistance in Gram-negative bacteria. The development of inhibitors of the RND pumps would improve the efficacy of current and next-
Nguyen, ST, Nikaido, H, Opperman, TJ, Ruggerone, P, Vargiu, AV   +4 more
core   +2 more sources

Innovative in silico approaches to address avian flu using grid technology [PDF]

, 2008
The recent years have seen the emergence of diseases which have spread very quickly all around the world either through human travels like SARS or animal migration like avian flu.
Breton, V. Vincent, Da Costa, A. L., De Vlieger, P., Hai, T. N., Kim, D., Kim, Y. -M., Maigne, L., Nguyen, H. Q., Sarramia, D., Solomonides, T., Wu, Y. -T.   +10 more
core   +2 more sources