1mic: Difference between revisions
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'''GRAMICIDIN A: LEFT-HANDED PARALLEL DOUBLE HELICAL FORM IN METHANOL IN THE PRESENCE OF CACL2, NMR, 20 STRUCTURES''' | {{Structure | ||
|PDB= 1mic |SIZE=350|CAPTION= <scene name='initialview01'>1mic</scene> | |||
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|LIGAND= <scene name='pdbligand=FOR:FORMYL GROUP'>FOR</scene> | |||
|ACTIVITY= | |||
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}} | |||
'''GRAMICIDIN A: LEFT-HANDED PARALLEL DOUBLE HELICAL FORM IN METHANOL IN THE PRESENCE OF CACL2, NMR, 20 STRUCTURES''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1MIC is a [ | 1MIC is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1MIC OCA]. | ||
==Reference== | ==Reference== | ||
Solution structure of a parallel left-handed double-helical gramicidin-A determined by 2D 1H NMR., Chen Y, Tucker A, Wallace BA, J Mol Biol. 1996 Dec 13;264(4):757-69. PMID:[http:// | Solution structure of a parallel left-handed double-helical gramicidin-A determined by 2D 1H NMR., Chen Y, Tucker A, Wallace BA, J Mol Biol. 1996 Dec 13;264(4):757-69. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8980684 8980684] | ||
[[Category: Brevibacillus brevis]] | [[Category: Brevibacillus brevis]] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
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[[Category: peptide antibiotic]] | [[Category: peptide antibiotic]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:43:46 2008'' | ||
Revision as of 13:43, 20 March 2008
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GRAMICIDIN A: LEFT-HANDED PARALLEL DOUBLE HELICAL FORM IN METHANOL IN THE PRESENCE OF CACL2, NMR, 20 STRUCTURES
OverviewOverview
The structure of a parallel left-handed double-helical form of gramicidin was detected by circular dichroism spectroscopy and determined using 500 and 600 MHz NMR in CaCl2/methanol solution. Measurements of TOCSY, DQF-COSY and NOESY spectra were converted into 604 distance and 48 torsional angle constraints for structure calculations. Stereospecific assignments and chi 1 angles were calculated using 3J alpha beta, d alpha beta (i,i), dN beta(i,i) and dN gamma(i,i). chi 2 angles were determined using d alpha beta(i,i), dN beta(i,i), d beta delta(i,i), dN gamma(i,i) and d alpha gamma(i,i). The calculations of initial structures were performed using the distance geometry/simulated annealing method in XPLOR. The initial structures were further refined and energy minimized using simulated annealing/molecular dynamics methods. Back-calculations for every generated structure were also performed to check their consistency with the experimental data. 187 final structures with no violations above the threshold conditions (0.05 A, 5 degrees, 5 degrees, 0.5 A and 5 degrees for bonds, angles, improper, NOE and cdihe, respectively) were produced from the 200 initial structures. Twenty structures with the lowest NOE energies were used for further analysis. The average r.m.s. deviations for the 20 structures are 0.64 A for backbone and 1.1 A for all non-hydrogen atoms. Gramicidin in this form, with approximately 5.7 residues per turn, is a parallel double helical dimer. The length along the helix axis is about 30 A and the inner pore diameter varies from 1 to 2 A. It is different from all other gramicidin structures determined to date. The presence of Ca2+ stabilises a conformation that prevents the binding of monovalent cations. It is likely that this structure is related to a non-channel, antibiotic role of gramicidin.
About this StructureAbout this Structure
1MIC is a Protein complex structure of sequences from Brevibacillus brevis. Full crystallographic information is available from OCA.
ReferenceReference
Solution structure of a parallel left-handed double-helical gramicidin-A determined by 2D 1H NMR., Chen Y, Tucker A, Wallace BA, J Mol Biol. 1996 Dec 13;264(4):757-69. PMID:8980684
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