[NMR paper] The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids.
The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids.
Related ArticlesThe application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids.
Biopolymers. 2013 Aug;99(8):548-61
Authors: Clark TD, Bartolotti L, Hicks RP
Abstract
Anionic and zwitterionic micelles are often used as simple models for the lipids found in bacterial and mammalian cell membranes to investigate antimicrobial peptide-lipid interactions. In our laboratory we have employed a variety of 1D, 2D, and diffusion ordered (DOSY) NMR experiments to investigate the interactions of antimicrobial peptides containing unnatural amino acids with SDS and DPC micelles. Complete assignment of the proton spectra of these peptides is prohibited by the incorporation of a high percentage of unnatural amino acids which don't contain amide protons into the backbone. However preliminary assignment of the TOCSY spectra of compound 23 in the presence of both micelles indicated multiple conformers are present as a result of binding to these micelles. Chemical Shift Indexing agreed with previously collected CD spectra that indicated on binding to SDS micelles compound 23 adopts a mixture of ?-helical structures and on binding to DPC micelles this peptide adopts a mixture of helical and ?-turn/sheet like structures. DOSY NMR experiments also indicated that the total positive charge and the relative placement of that charge at the N-terminus or C-terminus are important in determining the mole fraction of the peptide that will bind to the different micelles. DOSY and (1) H-NMR experiments indicated that the length of Spacer #1 plays a major role in defining the binding conformation of these analogs with SDS micelles. Results obtained from molecular simulations studies of the binding of compounds 23 and 36 with SDS micelles were consistent with the observed NMR results.
[NMR paper] Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.
Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.
Related Articles Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field.
J Chem Theory Comput. 2015 Mar 10;11(3):1315-1329
Authors: Li S, Andrews CT, Frembgen-Kesner T, Miller MS, Siemonsma SL, Collingsworth TD, Rockafellow IT, Ngo NA,...
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[NMR paper] Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies.
Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies.
Related Articles Searching For Protein Binding Sites From Molecular Dynamics Simulations and Paramagnetic Fragment-based NMR Studies.
Biochim Biophys Acta. 2013 Dec 26;
Authors: Bernini A, De Angelis LH, Morandi E, Spiga O, Santucci A, Assfalg M, Molinari H, Pillozzi S, Arcangeli A, Niccolai N
Abstract
Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces....
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations.
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations.
Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations.
Biochim Biophys Acta. 2011 Aug;1808(8):2019-30
Authors: Romo TD, Bradney LA, Greathouse DV, Grossfield A
Abstract
One approach to the growing health problem of antibiotic resistant bacteria is the development of antimicrobial peptides (AMPs) as alternative treatments. The...
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08-19-2011 02:56 PM
Site-specific labeling of proteins with NMR-active unnatural amino acids
Site-specific labeling of proteins with NMR-active unnatural amino acids
Abstract A large number of amino acids other than the canonical amino acids can now be easily incorporated in vivo into proteins at genetically encoded positions. The technology requires an orthogonal tRNA/aminoacyl-tRNA synthetase pair specific for the unnatural amino acid that is added to the media while a TAG amber or frame shift codon specifies the incorporation site in the protein to be studied. These unnatural amino acids can be isotopically labeled and provide unique opportunities for site-specific labeling...
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01-09-2011 12:46 PM
[NMR paper] The solution conformations of amino acids from molecular dynamics simulations of Gly-
The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters.
Related Articles The solution conformations of amino acids from molecular dynamics simulations of Gly-X-Gly peptides: comparison with NMR parameters.
Biochem Cell Biol. 1998;76(2-3):164-70
Authors: van der Spoel D
The conformations that amino acids can adopt in the random coil state are of fundamental interest in the context of protein folding research and studies of protein-peptide interactions. To date, no...
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11-17-2010 11:06 PM
Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Stru
Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy-Entropy Compensation in SH2-Ligand Binding.
Related Articles Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy-Entropy Compensation in SH2-Ligand Binding.
J Am Chem Soc. 2010 Aug 18;132(32):11058-70
Authors: Ward JM, Gorenstein NM, Tian J, Martin SF, Post CB
NMR spectroscopy and molecular dynamics (MD) simulations were used to probe the structure and dynamics...
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Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Stru
Constraining Binding Hot Spots: NMR and Molecular Dynamics Simulations Provide a Structural Explanation for Enthalpy−Entropy Compensation in SH2−Ligand Binding
Joshua M. Ward<sup>†</sup>, Nina M. Gorenstein<sup>†</sup>, Jianhua Tian<sup>‡</sup>, Stephen F. Martin<sup>‡</sup> and Carol Beth Post*<sup>†</sup>
Department of Medicinal Chemistry, Markey Center for Structural Biology, and Purdue Cancer Center, Purdue University, West Lafayette, Indiana 47907, and Department of Chemistry and Biochemistry and The Institute of Cellular and Molecular Biology, The University of Texas,...
The application of DOSY NMR and molecular dynamics simulations to explore the mechanism(s) of micelle binding of antimicrobial peptides containing unnatural amino acids.
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