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 [...]
[KPWU blog] PyMOL-electrostaic surface view
PyMOL-electrostaic surface view
To make electrostatic surface view of protein using PyMOL, two ways are often suggest. One option is using ABPS to generate the electrostatic map. Here is one nice instruction at PyMOLwiki using ABPS. Another option is using Delphi developed by Barry Honig group to generate the electrostatic map of protein. I am writing a note http://stats.wordpress.com/b.gif?host=kpwu.wordpress.com&blog=76132&post=322&subd=kpwu&ref=&feed=1
Go to KPWU blog to read complete post.
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04-13-2011 01:25 PM
Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR.
Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR.
Threonine side chain conformational population distribution of a type I antifreeze protein on interacting with ice surface studied via (13)C-(15)N dynamic REDOR NMR.
Solid State Nucl Magn Reson. 2011 Mar 23;
Authors: Mao Y, Jeong M, Wang T, Ba Y
Antifreeze proteins (AFPs) provide survival mechanism for species living in subzero environments by lowering the freezing points of their...
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04-08-2011 10:00 AM
[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...
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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...
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11-24-2010 09:16 PM
[NMR paper] NMR detection of side chain-side chain hydrogen bonding interactions in 13C/15N-label
NMR detection of side chain-side chain hydrogen bonding interactions in 13C/15N-labeled proteins.
Related Articles NMR detection of side chain-side chain hydrogen bonding interactions in 13C/15N-labeled proteins.
J Biomol NMR. 2000 Aug;17(4):305-10
Authors: Liu A, Hu W, Majumdar A, Rosen MK, Patel DJ
We describe the direct observation of side chain-side chain hydrogen bonding interactions in proteins with sensitivity-enhanced NMR spectroscopy. Specifically, the remote correlation between the guanidinium nitrogen 15Nepsilon of arginine 71,...
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11-19-2010 08:29 PM
[NMR paper] Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics
Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Investigation of a side-chain-side-chain hydrogen bond by mutagenesis, thermodynamics, and NMR spectroscopy.
Protein Sci. 1995 May;4(5):936-44
Authors: Hammen PK, Scholtz...
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08-22-2010 03:41 AM
[NMR paper] Comparison of backbone and tryptophan side-chain dynamics of reduced and oxidized Esc
Comparison of backbone and tryptophan side-chain dynamics of reduced and oxidized Escherichia coli thioredoxin using 15N NMR relaxation measurements.
Related Articles Comparison of backbone and tryptophan side-chain dynamics of reduced and oxidized Escherichia coli thioredoxin using 15N NMR relaxation measurements.
Biochemistry. 1993 Jan 19;32(2):426-35
Authors: Stone MJ, Chandrasekhar K, Holmgren A, Wright PE, Dyson HJ
The backbone and tryptophan side-chain dynamics of both the reduced and oxidized forms of uniformly 15N-labeled Escherichia...
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08-21-2010 11:53 PM
[NMR paper] Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide
Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide spin label and two-dimensional NMR study.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-standard-jbc_full_free.gif Related Articles Surface exposure of the methionine side chains of calmodulin in solution. A nitroxide spin label and two-dimensional NMR study.
J Biol Chem. 1999 Mar 26;274(13):8411-20
Authors: Yuan T, Ouyang H, Vogel HJ
Binding of calcium to calmodulin (CaM) causes a conformational...
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[PyMOL] side-by-side comparison of 3 electrostatic surface potentials
Linear Mode
