Hems distortions in sperm-whale carbonmonoxy myoglobin: Correlations between rotational strengths and heme distortions in MD-generated structures

被引:40
作者
Kiefl, C
Sreerama, N
Haddad, R
Sun, LS
Jentzen, W
Lu, Y
Qiu, Y
Shelnutt, JA
Woody, RW
机构
[1] Sandia Natl Labs, Biomol Mat & Interfaces Dept, Albuquerque, NM 87185 USA
[2] Colorado State Univ, Dept Biochem & Mol Biol, Ft Collins, CO 80523 USA
[3] Univ New Mexico, Dept Chem, Albuquerque, NM 87131 USA
关键词
D O I
10.1021/ja011961w
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
We have investigated the effects of hems rotational isomerism in sperm-whale carbonmonoxymyoglobin using computational techniques. Several molecular dynamics simulations have bean performed for the two rotational isomers A and B, which are related by a 180degrees rotation around the alpha-gamma axis of the hems, of sperm-whale carbonmonoxy myoglobin in water. Both neutron diffraction and NMR structures were used as starting structures. In the absence of an experimental structure, the structure of isomer B was generated by rotating the hems in the structure of isomer A. Distortions of the hems from planarity were characterized by normal coordinate structural decomposition and by the angle of twist of the pyrrole rings from the hems plane. The hems distortions of the neutron diffraction structure were conserved in the MD trajectories, but in the NMR-based trajectories, where the hems distortions are less well defined, they differ from the original hems deformations. The protein matrix induced similar distortions on the heroes in orientations A and B. Our results suggest that the binding site prefers a particular macrocycle conformation, and a 180degrees rotation of the hems does not significantly alter the protein's preference for this conformation. The intrinsic rotational strengths of the two Soret transitions, separated according to their polarization in the hems plane, show strong correlations with the ruffling deformation and the average Twist angle of the pyrrole rings. The total rotational strength, which includes contributions from the chromophores in the protein, shows a weaker correlation with hems distortions.
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收藏
页码:3385 / 3394
页数:10
相关论文
共 37 条
[1]   H-1-NMR AND CD STUDIES OF HEME ORIENTATIONAL DISORDER IN SPERM-WHALE MYOGLOBIN AND HUMAN-HEMOGLOBIN [J].
AOJULA, HS ;
WILSON, MT ;
MOORE, GR ;
WILLIAMSON, DJ .
BIOCHEMICAL JOURNAL, 1988, 250 (03) :853-858
[2]   FUNCTIONAL CONSEQUENCES OF HEME ORIENTATIONAL DISORDER IN SPERM-WHALE AND YELLOW-FIN-TUNA MYOGLOBINS [J].
AOJULA, HS ;
WILSON, MT ;
MORRISON, IEG .
BIOCHEMICAL JOURNAL, 1987, 243 (01) :205-210
[3]   CHARACTERIZATION OF HEME DISORDER BY CIRCULAR-DICHROISM [J].
AOJULA, HS ;
WILSON, MT ;
DRAKE, A .
BIOCHEMICAL JOURNAL, 1986, 237 (02) :613-616
[4]   THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS [J].
BERENDSEN, HJC ;
GRIGERA, JR ;
STRAATSMA, TP .
JOURNAL OF PHYSICAL CHEMISTRY, 1987, 91 (24) :6269-6271
[5]  
BERENDSEN HJC, 1985, MOL DYNAMICS PROTEIN, P43
[6]   MOLECULAR-DYNAMICS FREE-ENERGY CALCULATION IN 4 DIMENSIONS [J].
BEUTLER, TC ;
VANGUNSTEREN, WF .
JOURNAL OF CHEMICAL PHYSICS, 1994, 101 (02) :1417-1422
[7]   FREE-ENERGY VIA MOLECULAR SIMULATION - APPLICATIONS TO CHEMICAL AND BIOMOLECULAR SYSTEMS [J].
BEVERIDGE, DL ;
DICAPUA, FM .
ANNUAL REVIEW OF BIOPHYSICS AND BIOPHYSICAL CHEMISTRY, 1989, 18 :431-492
[8]   SIMULATED ANNEALING IN CRYSTALLOGRAPHY [J].
BRUNGER, AT .
ANNUAL REVIEW OF PHYSICAL CHEMISTRY, 1991, 42 :197-223
[9]   KINETIC-STUDY OF CO AND O-2 BINDING TO HORSE HEART MYOGLOBIN RECONSTITUTED WITH SYNTHETIC HEMES LACKING METHYL AND VINYL SIDE-CHAINS [J].
CHANG, CK ;
WARD, B ;
EBINA, S .
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 1984, 231 (02) :366-371
[10]   NEUTRON-DIFFRACTION STUDY OF CARBONMONOXYMYOGLOBIN [J].
CHENG, XD ;
SCHOENBORN, BP .
JOURNAL OF MOLECULAR BIOLOGY, 1991, 220 (02) :381-399