Electrostatic potentials computed from three-dimensional structures of biomolecules by solving the Poisson-Boltzmann equation are widely used in molecular biophysics, structural biology, and medicinal chemistry. Despite the approximate nature of the Poisson-Boltzmann theory, validation of the computed electrostatic potentials around biological macromolecules is rare and methodologically limited. Here, we present a unique and powerful NMR method that allows for straightforward and extensive...
[NMR paper] Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions.
Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions.
Related Articles Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions.
J Biomol Struct Dyn. 2014 Aug 8;:1-10
Authors: Zhang J, Wang F, Zhang Y
Abstract
Prion diseases are invariably fatal and highly infectious neurodegenerative diseases that affect a wide variety of mammalian species such as sheep and...
nmrlearner
Journal club
0
08-12-2014 06:25 PM
[KPWU blog] [PyMOL] side-by-side comparison of 3 electrostatic surface potentials
side-by-side comparison of 3 electrostatic surface potentials
Here is an example using “grid mode” provided in PyMOL to show the charged states of a protein (PDB entry: 1Z66) at pH 4 (left), 7 (center) and 11 (right). *PyMOL script is attached after the figure. First, *the potential maps at three pH states have to be generated. I used APBS web http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=798&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
nmrlearner
News from NMR blogs
0
09-18-2012 02:58 PM
[NMR paper] Validating the use of database potentials in protein structure determination by NMR.
Validating the use of database potentials in protein structure determination by NMR.
Related Articles Validating the use of database potentials in protein structure determination by NMR.
FEBS Lett. 2005 Oct 24;579(25):5542-8
Authors: Mertens HD, Gooley PR
The refinement of protein structures determined by nuclear magnetic resonance spectroscopy against database potentials of mean force allows for the exclusion of unfavourable conformations of the protein backbone during a structure calculation, resulting in protein structures with a marked...
nmrlearner
Journal club
0
12-01-2010 06:56 PM
[NMR paper] Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NM
Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NMR spectroscopy: nociceptin-lipid association.
Related Articles Molecular insight into the electrostatic membrane surface potential by 14n/31p MAS NMR spectroscopy: nociceptin-lipid association.
J Am Chem Soc. 2005 May 11;127(18):6610-6
Authors: Lindström F, Williamson PT, Gröbner G
Exploiting naturally abundant (14)N and (31)P nuclei by high-resolution MAS NMR (magic angle spinning nuclear magnetic resonance) provides a molecular view of the electrostatic...
nmrlearner
Journal club
0
11-25-2010 08:21 PM
[NMR paper] Study of electrostatic potential surface distribution of wild-type plastocyanin Synec
Study of electrostatic potential surface distribution of wild-type plastocyanin Synechocystis solution structure determined by homonuclear NMR.
Related Articles Study of electrostatic potential surface distribution of wild-type plastocyanin Synechocystis solution structure determined by homonuclear NMR.
Biopolymers. 2003 Oct;70(2):212-20
Authors: Monleón D, Celda B
Plastocyanin is a small (approximately 10 kDa), type I blue copper protein that works as an electron donor to photosystem I from cytochrome f in both chloroplast systems and in some...
nmrlearner
Journal club
0
11-24-2010 09:16 PM
[NMR paper] De novo protein structure determination using sparse NMR data.
De novo protein structure determination using sparse NMR data.
Related Articles De novo protein structure determination using sparse NMR data.
J Biomol NMR. 2000 Dec;18(4):311-8
Authors: Bowers PM, Strauss CE, Baker D
We describe a method for generating moderate to high-resolution protein structures using limited NMR data combined with the ab initio protein structure prediction method Rosetta. Peptide fragments are selected from proteins of known structure based on sequence similarity and consistency with chemical shift and NOE data. Models...
nmrlearner
Journal club
0
11-19-2010 08:29 PM
[NMR paper] De novo determination of protein structure by NMR using orientational and long-range
De novo determination of protein structure by NMR using orientational and long-range order restraints.
Related Articles De novo determination of protein structure by NMR using orientational and long-range order restraints.
J Mol Biol. 2000 May 19;298(5):927-36
Authors: Hus JC, Marion D, Blackledge M
Orientational and novel long-range order restraints available from paramagnetic systems have been used to determine the backbone solution structure of the cytochrome c' protein to atomic resolution in the complete absence of restraints derived from...
nmrlearner
Journal club
0
11-18-2010 09:15 PM
[NMR paper] Determination of de novo synthesized amino acids in cellular proteins revisited by 13
Determination of de novo synthesized amino acids in cellular proteins revisited by 13C NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles Determination of de novo synthesized amino acids in cellular proteins revisited by 13C NMR spectroscopy.
NMR Biomed. 1997 Apr;10(2):50-8
Authors: Flögel U, Willker W, Leibfritz D
13C nuclear magnetic resonance spectroscopy was used to determine the absolute amounts to de novo...
De novo determination of near-surface electrostatic potentials by NMR
Linear Mode
