PDBsum entry 1odp

Go to PDB code: 
protein links
Lipid transport PDB id
Protein chain
20 a.a.
PDB id:
Name: Lipid transport
Title: Peptide of human apoa-i residues 166-185. Nmr, 5 structures at ph 6.6, 37 degrees celsius and peptide:sds mole ratio of 1:40
Structure: Apoa-i peptide. Chain: a. Fragment: residues 166 - 185. Synonym: apoa-i (166 - 185), apolipoprotein a-i (166 - 185). Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606
NMR struc: 5 models
Authors: G.Wang,W.D.Treleaven,R.J.Cushley
Key ref: G.Wang et al. (1996). Conformation of human serum apolipoprotein A-I(166-185) in the presence of sodium dodecyl sulfate or dodecylphosphocholine by 1H-NMR and CD. Evidence for specific peptide-SDS interactions. Biochim Biophys Acta, 1301, 174-184. PubMed id: 8664326 DOI: 10.1016/0005-2760(96)00037-9
02-Mar-96     Release date:   10-Jun-96    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P02647  (APOA1_HUMAN) -  Apolipoprotein A-I
267 a.a.
20 a.a.
Key:    PfamA domain  Secondary structure


DOI no: 10.1016/0005-2760(96)00037-9 Biochim Biophys Acta 1301:174-184 (1996)
PubMed id: 8664326  
Conformation of human serum apolipoprotein A-I(166-185) in the presence of sodium dodecyl sulfate or dodecylphosphocholine by 1H-NMR and CD. Evidence for specific peptide-SDS interactions.
G.Wang, W.D.Treleaven, R.J.Cushley.
The segment, YSDELRQRLAARLEALKENG, corresponding to residues 166 to 185 of human serum apolipoprotein A-I, was studied by circular dichroism and NMR spectroscopy in sodium dodecyl sulfate and dodecylphosphocholine micelles. 2-Dimensional NOESY, TOCSY and DQF-COSY spectra of apoA-I(166-185) in perdeuterated sodium dodecyl sulfate (SDS-d25) and dodecylphosphocholine (DPC-d38) micelles were collected at a peptide/SDS (DPC) ratio of 1:40. Similar CD spectra and NOE connectivity patterns were observed for apoA-I(166-185) in SDS and DPC, indicating a similar helical conformation in both. Conformations of apoA-I(166-185) in DPC-d38 micelles, and in SDS-d25 micelles at two pH values, 6.6 and 3.7, were determined using distance geometry calculations. Backbone superposition (N,C alpha,C = O) for an ensemble of twenty-nine structures in DPC at pH 6.0 gave a RMSD of 0.45 +/- 0.09 A for the region D168 to K182, while for all atoms it was 1.60 +/- 0.17 A. In SDS, the ensemble of nineteen structures each at pH 6.6 and 3.7 gave RMSDs of 0.28 +/- 0.07 A and 0.35 +/- 0.10 A, respectively, for the region D168 to K182. RMSD for superposition of all atoms was 1.36 +/- 0.10 A and 1.38 +/- 0.21 A at the respective pH values. In all cases a highly defined class A amphipathic helical structure was found for the region R171 to K182. Since the same structure occurs in micelles with either negatively charged or zwitterionic head groups it strongly suggests a dominant role for hydrophobic interactions in stabilizing the complex. The Y166 aromatic ring is bent back upon the helix axis at the lower pH. NMR determination of pKa values for D168, E169, E179 and E183 in the presence of SDS or DPC indicated a micro-pH at the micellar surface approximately one pH unit higher than the normal residue pKa. SDS interactions with the peptide were examined by collecting 1H NOESY spectra in the presence of protiated SDS. Residues R171, R173, R177, as well as the aromatic ring of Y166, were shown by intermolecular NOE measurements to interact with SDS, hence a key interaction in stabilizing the complex appears to be between interfacial basic side-chains and SDS alkyl chains.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18818205 G.Wang (2008).
Structures of Human Host Defense Cathelicidin LL-37 and Its Smallest Antimicrobial Peptide KR-12 in Lipid Micelles.
  J Biol Chem, 283, 32637-32643.
PDB code: 2k6o
17144649 R.Renthal (2006).
An unfolding story of helical transmembrane proteins.
  Biochemistry, 45, 14559-14566.  
15678187 G.Di Natale, G.Impellizzeri, and G.Pappalardo (2005).
Conformational properties of peptide fragments homologous to the 106-114 and 106-126 residues of the human prion protein: a CD and NMR spectroscopic study.
  Org Biomol Chem, 3, 490-497.  
15572363 G.Wang, Y.Li, and X.Li (2005).
Correlation of three-dimensional structures with the antibacterial activity of a group of peptides designed based on a nontoxic bacterial membrane anchor.
  J Biol Chem, 280, 5803-5811.
PDB codes: 1vm2 1vm3 1vm4 1vm5
14739294 H.S.Won, S.J.Jung, H.E.Kim, M.D.Seo, and B.J.Lee (2004).
Systematic peptide engineering and structural characterization to search for the shortest antimicrobial peptide analogue of gaegurin 5.
  J Biol Chem, 279, 14784-14791.  
12717030 G.Wang, P.A.Keifer, and A.Peterkofsky (2003).
Solution structure of the N-terminal amphitropic domain of Escherichia coli glucose-specific enzyme IIA in membrane-mimetic micelles.
  Protein Sci, 12, 1087-1096.
PDB codes: 1o0z 1o53
12324439 D.E.Otzen (2002).
Protein unfolding in detergents: effect of micelle structure, ionic strength, pH, and temperature.
  Biophys J, 83, 2219-2230.  
12199716 H.S.Won, S.H.Park, H.E.Kim, B.Hyun, M.Kim, B.J.Lee, and B.J.Lee (2002).
Effects of a tryptophanyl substitution on the structure and antimicrobial activity of C-terminally truncated gaegurin 4.
  Eur J Biochem, 269, 4367-4374.  
11988467 R.J.Cushley, and M.Okon (2002).
NMR studies of lipoprotein structure.
  Annu Rev Biophys Biomol Struct, 31, 177-206.  
11278170 C.G.Brouillette, G.M.Anantharamaiah, J.A.Engler, and D.W.Borhani (2001).
Structural models of human apolipoprotein A-I: a critical analysis and review.
  Biochim Biophys Acta, 1531, 4.  
11072226 X.Gao, and T.C.Wong (2001).
NMR studies of adrenocorticotropin hormone peptides in sodium dodecylsulfate and dodecylphosphocholine micelles: proline isomerism and interactions of the peptides with micelles.
  Biopolymers, 58, 20-32.  
  10975576 G.W.Buchko, A.Rozek, P.Kanda, M.A.Kennedy, and R.J.Cushley (2000).
Structural studies of a baboon (Papio sp.) plasma protein inhibitor of cholesteryl ester transferase.
  Protein Sci, 9, 1548-1558.
PDB code: 1eze
10913242 R.Montserret, M.J.McLeish, A.Böckmann, C.Geourjon, and F.Penin (2000).
Involvement of electrostatic interactions in the mechanism of peptide folding induced by sodium dodecyl sulfate binding.
  Biochemistry, 39, 8362-8373.
PDB codes: 1djf 1dn3 1dng
  10493581 D.Clayton, I.M.Brereton, P.A.Kroon, and R.Smith (1999).
NMR studies of the low-density lipoprotein receptor-binding peptide of apolipoprotein E bound to dodecylphosphocholine micelles.
  Protein Sci, 8, 1797-1805.  
  10548051 O.Gursky (1999).
Probing the conformation of a human apolipoprotein C-1 by amino acid substitutions and trimethylamine-N-oxide.
  Protein Sci, 8, 2055-2064.  
  9521109 J.Wang, V.Narayanaswami, B.D.Sykes, and R.O.Ryan (1998).
Interhelical contacts are required for the helix bundle fold of apolipophorin III and its ability to interact with lipoproteins.
  Protein Sci, 7, 336-341.  
9693002 M.Coles, W.Bicknell, A.A.Watson, D.P.Fairlie, and D.J.Craik (1998).
Solution structure of amyloid beta-peptide(1-40) in a water-micelle environment. Is the membrane-spanning domain where we think it is?
  Biochemistry, 37, 11064-11077.
PDB code: 1ba4
9565601 M.G.Sorci-Thomas, L.Curtiss, J.S.Parks, M.J.Thomas, M.W.Kearns, and M.Landrum (1998).
The hydrophobic face orientation of apolipoprotein A-I amphipathic helix domain 143-164 regulates lecithin:cholesterol acyltransferase activation.
  J Biol Chem, 273, 11776-11782.  
  9300485 A.Rozek, G.W.Buchko, P.Kanda, and R.J.Cushley (1997).
Conformational studies of the N-terminal lipid-associating domain of human apolipoprotein C-I by CD and 1H NMR spectroscopy.
  Protein Sci, 6, 1858-1868.
PDB code: 1opp
9354635 G.Wang, J.T.Sparrow, and R.J.Cushley (1997).
The helix-hinge-helix structural motif in human apolipoprotein A-I determined by NMR spectroscopy.
  Biochemistry, 36, 13657-13666.
PDB codes: 1gw3 1gw4
9218415 J.Wang, S.M.Gagné, B.D.Sykes, and R.O.Ryan (1997).
Insight into lipid surface recognition and reversible conformational adaptations of an exchangeable apolipoprotein by multidimensional heteronuclear NMR techniques.
  J Biol Chem, 272, 17912-17920.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.