Investigation of Hydrophobic Interactions in Colloidal and Biological Systems by Molecular Dynamics Simulations and NMR Spectroscopy

Langmuir ◽  
1997 ◽  
Vol 13 (7) ◽  
pp. 2007-2018 ◽  
Author(s):  
M. H. Alaimo ◽  
T. F. Kumosinski
Keyword(s):  
Molecular Dynamics ◽  
Nmr Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Hydrophobic Interactions ◽  
Biological Systems ◽  
Dynamics Simulations

Molecular Basis of Iterative C–H Oxidation by TamI, a Multifunctional P450 Monooxygenase from the Tirandamycin Biosynthetic Pathway

2020 ◽  
Author(s):  
Sean A. Newmister ◽  
Kinshuk Raj Srivastava ◽  
Rosa V. Espinoza ◽  
Kersti Caddell Haatveit ◽  
Yogan Khatri ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Basis ◽  
Hydrophobic Interactions ◽  
Cytochromes P450 ◽  
Targeted Mutagenesis ◽  
P450 Monooxygenase ◽  
Bond Functionalization ◽  
Dynamics Simulations

Biocatalysis offers an expanding and powerful strategy to construct and diversify complex molecules by C-H bond functionalization. Due to their high selectivity, enzymes have become an essential tool for C-H bond functionalization and offer complementary reactivity to small-molecule catalysts. Hemoproteins, particularly cytochromes P450, have proven effective for selective oxidation of unactivated C-H bonds. Previously, we reported the in vitro characterization of an oxidative tailoring cascade in which TamI, a multifunctional P450 functions co-dependently with the TamL flavoprotein to catalyze regio- and stereoselective hydroxylations and epoxidation to yield tirandamycin A and tirandamycin B. TamI follows a defined order including 1) C10 hydroxylation, 2) C11/C12 epoxidation, and 3) C18 hydroxylation. Here we present a structural, biochemical, and computational investigation of TamI to understand the molecular basis of its substrate binding, diverse reactivity, and specific reaction sequence. The crystal structure of TamI in complex with tirandamycin C together with molecular dynamics simulations and targeted mutagenesis suggest that hydrophobic interactions with the polyene chain of its natural substrate are critical for molecular recognition. QM/MM calculations and molecular dynamics simulations of TamI with variant substrates provided detailed information on the molecular basis of sequential reactivity, and pattern of regio- and stereo-selectivity in catalyzing the three-step oxidative cascade.<br>

Molecular Conformations in the Pentasaccharide LNF-1 Derived from NMR Spectroscopy and Molecular Dynamics Simulations

2011 ◽  
Vol 115 (21) ◽  
pp. 7109-7121 ◽  
Author(s):  
Elin Säwén ◽  
Baltzar Stevensson ◽  
Jennie Östervall ◽  
Arnold Maliniak ◽  
Göran Widmalm
Keyword(s):  
Molecular Dynamics ◽  
Nmr Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Molecular Conformations ◽  
Dynamics Simulations

Drug-dendrimer supramolecular complexation studied from molecular dynamics simulations and NMR spectroscopy

2014 ◽  
Vol 25 (5) ◽  
pp. 1443-1455 ◽  
Author(s):  
Pabla A. Barra ◽  
Luis F. Barraza ◽  
Verónica A. Jiménez ◽  
José A. Gavin ◽  
Joel B. Alderete
Keyword(s):  
Molecular Dynamics ◽  
Nmr Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Supramolecular Complexation
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