Negatively charged residues and hydrogen bonds tune the ligand histidine pKa values of Rieske iron-sulfur proteins

被引:42
作者
Klingen, AR [1 ]
Ullmann, GM [1 ]
机构
[1] Univ Bayreuth, Dept Struct Biol Bioinformat, D-95447 Bayreuth, Germany
关键词
D O I
10.1021/bi0488606
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
Rieske proteins carry a redox-active iron-sulfur cluster, which is bound by two histidine and two cysteine side chains. The reduction potential of Rieske proteins depends on pH. This pH dependence can be described by two pK(a) values, which have been assigned to the two iron-coordinating histidines. Rieske proteins are commonly grouped into two major classes: Rieske proteins from quinol-oxidizing cytochrome bc complexes, in which the ligand histidines titrate in the physiological pH range, and bacterial ferredoxin Rieske proteins, in which the ligand histidines are protonated at physiological pH. In the study presented here, we have calculated pK(a) values of the cluster ligand histidines using a combined density functional theory/continuum electrostatics approach. Experimental pK(a) values for a bc-type and a ferredoxin Rieske protein could be reproduced. We could identify functionally important differences between the two proteins: hydrogen bonds toward the cluster, which are present in bc-type Rieske proteins, and negatively charged residues, which are present in ferredoxin Rieske proteins. We removed these differences by mutating the proteins in our calculations. The Rieske centers in the mutated proteins have very similar pK(a) values. We thus conclude that the studied structural differences are the main reason for the different pH-titration behavior of the proteins. Interestingly, the shift caused by neutralizing the negative charges in ferredoxin Rieske proteins is larger than the shift caused by removing the hydrogen bonds toward the cluster in bc-type Rieske proteins.
引用
收藏
页码:12383 / 12389
页数:7
相关论文
共 39 条
[1]   PKAS OF IONIZABLE GROUPS IN PROTEINS - ATOMIC DETAIL FROM A CONTINUUM ELECTROSTATIC MODEL [J].
BASHFORD, D ;
KARPLUS, M .
BIOCHEMISTRY, 1990, 29 (44) :10219-10225
[2]   Electrochemical and spectroscopic investigations of the cytochrome bc1 complex from Rhodobacter capsulatus [J].
Baymann, F ;
Robertson, DE ;
Dutton, PL ;
Mäntele, W .
BIOCHEMISTRY, 1999, 38 (40) :13188-13199
[3]   VAN DER WAALS VOLUMES + RADII [J].
BONDI, A .
JOURNAL OF PHYSICAL CHEMISTRY, 1964, 68 (03) :441-+
[4]   The structure of the soluble domain of an archaeal Rieske iron-sulfur protein at 1.1 Å resolution [J].
Bönisch, H ;
Schmidt, CL ;
Schäfer, G ;
Ladenstein, R .
JOURNAL OF MOLECULAR BIOLOGY, 2002, 319 (03) :791-805
[5]   DETERMINING ATOM-CENTERED MONOPOLES FROM MOLECULAR ELECTROSTATIC POTENTIALS - THE NEED FOR HIGH SAMPLING DENSITY IN FORMAMIDE CONFORMATIONAL-ANALYSIS [J].
BRENEMAN, CM ;
WIBERG, KB .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1990, 11 (03) :361-373
[6]   Biological identity and diversity in photosynthesis and respiration: structure of the lumen-side domain of the chloroplast Rieske protein [J].
Carrell, CJ ;
Zhang, HM ;
Cramer, WA ;
Smith, JL .
STRUCTURE, 1997, 5 (12) :1613-1625
[7]   A cluster exposed: Structure of the Rieske ferredoxin from biphenyl dioxygenase and the redox properties of Rieske Fe-S proteins [J].
Colbert, CL ;
Couture, MMJ ;
Eltis, LD ;
Bolin, JT .
STRUCTURE, 2000, 8 (12) :1267-1278
[8]   Pathways for proton release during ubihydroquinone oxidation by the bc1 complex [J].
Crofts, AR ;
Hong, SJ ;
Ugulava, N ;
Barquera, B ;
Gennis, R ;
Guergova-Kuras, M ;
Berry, EA .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1999, 96 (18) :10021-10026
[9]   Alteration of the midpoint potential and catalytic activity of the Rieske iron-sulfur protein by changes of amino acids forming hydrogen bonds to the iron-sulfur cluster [J].
Denke, E ;
Merbitz-Zahradnik, T ;
Hatzfeld, OM ;
Snyder, CH ;
Link, TA ;
Trumpower, BL .
JOURNAL OF BIOLOGICAL CHEMISTRY, 1998, 273 (15) :9085-9093
[10]   Crystal structure of the 100 kDa arsenite oxidase from Alcaligenes faecalis in two crystal forms at 1.64 Å and 2.03 Å [J].
Ellis, PJ ;
Conrads, T ;
Hille, R ;
Kuhn, P .
STRUCTURE, 2001, 9 (02) :125-132