Structural basis for preferential binding of non-ortho-substituted polychlorinated biphenyls by the monoclonal antibody S2B1

被引:17
作者
Pellequer, JL
Chen, SWW
Keum, YS
Karu, AE
Li, QX
Roberts, VA
机构
[1] CEA Valrho, Ctr Marcoule, DSV, DIEPSBTN, F-30207 Bagnols Sur Ceze, France
[2] Scripps Res Inst, Dept Mol Biol, La Jolla, CA 92037 USA
[3] Univ Hawaii, Dept Mol Biosci & Bioengn, Honolulu, HI 96822 USA
关键词
recombinant Fab antibody; PCB; polychlorinated biphenyl; congener-specific; ELISA; docking; cross-reactivity; computational ligand docking; potential of mean force (PMF); X-PLOR; Gaussian94; ActiveSite;
D O I
10.1002/jmr.740
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Polychlorinated biphenyls (PCBs) are a family of 209 isomers (congeners) with a wide range of toxic effects. In structural terms, they are of two types: those with and those without chlorines at the ortho positions (2, 2', 6 and W). Only 20 congeners have no ortho chlorines. Three of these are bound by the aryl hydrocarbon receptor and are one to four orders of magnitude more toxic than all others. A monoclonal antibody, S2B1, and its recombinant Fab have high selectivity and nanomolar binding affinities for two of the most toxic nonortho-chlorinated PCBs, 3,4,3',4-tetrachlorobiphenyl and 3,4,3',4,5-pentachlorobiphenyl. To investigate the basis for these properties, we built a three-dimensional structure model of the S2B1 variable fragment (Fv) based on the high-resolution crystallographic structures of antibodies 48G7 and N1G9. Two plausible conformations for the complementarity-determining region (CDR) H3 loop led to two putative PCB-binding pockets with very different shapes (models A and B). Docking studies using molecular mechanics and potentials of mean force (PMF) indicated that model B was most consistent with the selectivity observed for S2B1 in competition ELISAs. The binding site in model B had a deep, narrow pocket between V-L and V-H, with a slight constriction at the top that opened into a wider pocket between CDRs H1 and H3 on the antibody surface. This binding site resembles those of esterolytic antibodies that bind haptens with phenyl rings. One phenyl ring of the PCB fits into the deep pocket, and the other ring is bound in the shallower one. The bound PCB is surrounded by the side chains of TyrL91, TyrL96 and TrpH98, and it has a pi-cation interaction with ArgL46. The tight fit of the binding pocket around the ortho positions of the bound PCBs indicates that steric hindrance of ortho chlorines in the binding site, rather than induced conformational change of the PCBs, is responsible for the selectivity of S2B1. Copyright (c) 2005 John Wiley & Sons, Ltd.
引用
收藏
页码:282 / 294
页数:13
相关论文
共 96 条
[71]   Evaluation of a knowledge-based potential of mean force for scoring docked protein-ligand complexes [J].
Nobeli, I ;
Mitchell, JBO ;
Alex, A ;
Thornton, JM .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2001, 22 (07) :673-688
[72]   The immunological evolution of catalysis [J].
Patten, PA ;
Gray, NS ;
Yang, PL ;
Marks, CB ;
Wedemayer, GJ ;
Boniface, JJ ;
Stevens, RC ;
Schultz, PG .
SCIENCE, 1996, 271 (5252) :1086-1091
[73]   Stabilization of bound polycyclic aromatic hydrocarbons by a π-cation interaction [J].
Pellequer, JL ;
Zhao, BT ;
Kao, HI ;
Bell, CW ;
Li, K ;
Li, QX ;
Karu, AE ;
Roberts, VA .
JOURNAL OF MOLECULAR BIOLOGY, 2000, 302 (03) :691-699
[74]  
Pellequer JL, 1999, J MOL RECOGNIT, V12, P267, DOI 10.1002/(SICI)1099-1352(199907/08)12:4<267::AID-JMR465>3.3.CO
[75]  
2-0
[76]  
Portmann S, 2000, CHIMIA, V54, P766
[77]   CATALYTIC ANTIBODY MODEL AND MUTAGENESIS IMPLICATE ARGININE IN TRANSITION-STATE STABILIZATION [J].
ROBERTS, VA ;
STEWART, J ;
BENKOVIC, SJ ;
GETZOFF, ED .
JOURNAL OF MOLECULAR BIOLOGY, 1994, 235 (03) :1098-1116
[78]  
Roussel A., 1989, Silicon Graphics Geometry Partners Directory, P77
[79]   POLYCHLORINATED-BIPHENYLS (PCBS) AND POLYBROMINATED BIPHENYLS (PBBS) - BIOCHEMISTRY, TOXICOLOGY, AND MECHANISM OF ACTION [J].
SAFE, S .
CRC CRITICAL REVIEWS IN TOXICOLOGY, 1984, 13 (04) :319-395
[80]   POLYCHLORINATED-BIPHENYLS (PCBS) - ENVIRONMENTAL-IMPACT, BIOCHEMICAL AND TOXIC RESPONSES, AND IMPLICATIONS FOR RISK ASSESSMENT [J].
SAFE, SH .
CRITICAL REVIEWS IN TOXICOLOGY, 1994, 24 (02) :87-149