Conformation of the sebacyl beta1Lys82-beta2Lys82 crosslink in T-state human hemoglobin.
The crystal structure of human T state hemoglobin crosslinked with bis(3,5-dibromo-salicyl) sebacate has been determined at 1.9 A resolution. The final crystallographic R factor is 0.168 with root-mean-square deviations (RMSD) from ideal bond distance of 0.018 A. The 10-carbon sebacyl residue found in the beta cleft covalently links the two betaLys82 residues. The sebacyl residue assumes a zigzag conformation with cis amide bonds formed by the NZ atoms of betaLys82's and the sebacyl carbonyl oxygens. The atoms of the crosslink have an occupancy factor of 1.0 with an average temperature factor for all atoms of 34 A2. An RMSD of 0.27 for all CA's of the tetramer is observed when the crosslinked deoxyhemoglobin is compared with deoxyhemoglobin refined by using a similar protocol, 2HHD [Fronticelli et al. J. Biol. Chem. 269: 23965-23969, 1994]. Thus, no significant perturbations in the tertiary or quaternary structure are introduced by the presence of the sebacyl residue. However, the sebacyl residue does displace seven water molecules in the beta cleft and the conformations of the beta1Lys82 and beta2Lys82 are altered because of the crosslinking. The carbonyl oxygen that is part of the amide bond formed with the NZ of beta2Lys82 forms a hydrogen bond with side chain of beta2Asn139 that is in turn hydrogen-bonded to the side chain of beta2Arg104. A comparison of the observed conformation with that modeled [Bucci et al. Biochemistry 35:3418-3425, 1996] shows significant differences. The differences in the structures can be rationalized in terms of compensating changes in the estimated free-energy balance, based on differences in exposed surface areas and the observed shift in the side-chain hydrogen-bonding pattern involving beta2Arg104, beta2Asn139, and the associated sebacyl carbonyl group.
Ji
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Center for Advanced Research in Biotechnology of the University of Maryland Biotechnology Institute, Rockville, Maryland 20850, USA.
Braxenthaler
M
M
Moult
J
J
Fronticelli
C
C
Bucci
E
E
Gilliland
G L
GL
D003432:Cross-Linking Reagents / Q000378:metabolism; D018360:Crystallography, X-Ray; D003652:Decanoic Acids / Q000378:metabolism; D006454:Hemoglobins / Q000737:chemistry*; D006801:Humans; D006860:Hydrogen Bonding; D008239:Lysine / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012459:Salicylates / Q000378:metabolism
D003432:Cross-Linking Reagents; D003652:Decanoic Acids; D006454:Hemoglobins; D012459:Salicylates; C089663:bis(3,5-dibromosalicyl)sebacate; C100003:deoxyhemoglobin; D008239:Lysine