Few weeks ago, I posted a blog that provides a newer collected/organized dataset for the torsional angles of proteins. I played around and try to use GnuPlot 4.4 to make my own Ramachandran plots. Here are three examples of the residual Ramachandran space regarding to the helical, extend or coil regions. I used STRIDE to [...]
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Sequence correction of random coil chemical shifts: correlation between neighbor correction factors and changes in the Ramachandran distribution
Abstract Random coil chemical shifts are necessary for secondary chemical shift analysis, which is the main NMR method for identification of secondary structure in proteins. One of the largest challenges in the determination of random coil chemical shifts is accounting for the effect of neighboring residues. The contributions from the neighboring residues are typically removed by using neighbor correction factors determined based on each...
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[NMR paper] Solid-state NMR data support a helix-loop-helix structural model for the N-terminal h
Solid-state NMR data support a helix-loop-helix structural model for the N-terminal half of HIV-1 Rev in fibrillar form.
Related Articles Solid-state NMR data support a helix-loop-helix structural model for the N-terminal half of HIV-1 Rev in fibrillar form.
J Mol Biol. 2001 Nov 2;313(4):845-59
Authors: Blanco FJ, Hess S, Pannell LK, Rizzo NW, Tycko R
Rev is a 116 residue basic protein encoded by the genome of human immunodeficiency virus type 1 (HIV-1) that binds to multiple sites in the Rev response element (RRE) of viral mRNA transcripts in...
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11-19-2010 08:44 PM
[NMR paper] Prion protein fragments spanning helix 1 and both strands of beta sheet (residues 125
Prion protein fragments spanning helix 1 and both strands of beta sheet (residues 125-170) show evidence for predominantly helical propensity by CD and NMR.
Related Articles Prion protein fragments spanning helix 1 and both strands of beta sheet (residues 125-170) show evidence for predominantly helical propensity by CD and NMR.
Fold Des. 1998;3(5):313-20
Authors: Sharman GJ, Kenward N, Williams HE, Landon M, Mayer RJ, Searle MS
BACKGROUND: Transmissible spongiform encephalopathies are a group of neurodegenerative disorders of man and animals...
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11-17-2010 11:06 PM
Complete (1)H, (13)C and (15)N NMR assignments for donor-strand complemented AafA, th
Complete (1)H, (13)C and (15)N NMR assignments for donor-strand complemented AafA, the major pilin of aggregative adherence fimbriae (AAF/II) from enteroaggregative E. coli.
Related Articles Complete (1)H, (13)C and (15)N NMR assignments for donor-strand complemented AafA, the major pilin of aggregative adherence fimbriae (AAF/II) from enteroaggregative E. coli.
Biomol NMR Assign. 2010 Aug 17;
Authors: Yang Y, Berry AA, Lee WC, Garnett JA, Marchant J, Levine JA, Simpson PJ, Fogel SA, Varney KM, Matthews SJ, Nataro JP, Inman KG
Aggregative...
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[NMR paper] The helix-hinge-helix structural motif in human apolipoprotein A-I determined by NMR
The helix-hinge-helix structural motif in human apolipoprotein A-I determined by NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles The helix-hinge-helix structural motif in human apolipoprotein A-I determined by NMR spectroscopy.
Biochemistry. 1997 Nov 4;36(44):13657-66
Authors: Wang G, Sparrow JT, Cushley RJ
The conformation of a synthetic peptide of 46 residues from apoA-I was investigated by fluorescence, CD, and 2D NMR spectroscopies in lipid-mimetic environments....
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08-22-2010 05:08 PM
[NMR paper] High helicity of peptide fragments corresponding to beta-strand regions of beta-lacto
High helicity of peptide fragments corresponding to beta-strand regions of beta-lactoglobulin observed by 2D-NMR spectroscopy.
Related Articles High helicity of peptide fragments corresponding to beta-strand regions of beta-lactoglobulin observed by 2D-NMR spectroscopy.
Fold Des. 1996;1(4):255-63
Authors: Kuroda Y, Hamada D, Tanaka T, Goto Y
BACKGROUND: Whereas protein fragments, when they are structured, adopt conformations similar to that found in the native state, the high helical propensity of beta-lactoglobulin, a predominantly beta-sheet...
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[NMR paper] PhoE signal peptide inserts into micelles as a dynamic helix-break-helix structure, w
PhoE signal peptide inserts into micelles as a dynamic helix-break-helix structure, which is modulated by the environment. A two-dimensional 1H NMR study.
Related Articles PhoE signal peptide inserts into micelles as a dynamic helix-break-helix structure, which is modulated by the environment. A two-dimensional 1H NMR study.
Biochemistry. 1995 Sep 12;34(36):11617-24
Authors: Chupin V, Killian JA, Breg J, de Jongh HH, Boelens R, Kaptein R, de Kruijff B
Proteins that are destined for export out of the cytoplasm of Escherichia coli cells are...
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[NMR paper] Determination of helix-helix interactions in membranes by rotational resonance NMR.
Determination of helix-helix interactions in membranes by rotational resonance NMR.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Determination of helix-helix interactions in membranes by rotational resonance NMR.
Proc Natl Acad Sci U S A. 1995 Jan 17;92(2):488-91
Authors: Smith SO, Bormann BJ
Dimerization of human glycophorin A in erythrocyte membranes is mediated by specific interactions within the helical transmembrane domain of the protein. Rotational...
Examples of Ramachandran plots of residues in helix, strand or coil regions
Linear Mode
