Premium
Structural alignment of ferredoxin and flavodoxin based on electrostatic potentials: Implications for their interactions with photosystem I and ferredoxin‐NADP reductase
Author(s) -
Ullmann G. Matthias,
Hauswald Markus,
Jensen Axel,
Knapp ErnstWalter
Publication year - 2000
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/(sici)1097-0134(20000215)38:3<301::aid-prot6>3.0.co;2-y
Subject(s) - flavodoxin , ferredoxin , photosystem i , ferredoxin—nadp(+) reductase , ferredoxin thioredoxin reductase , chemistry , electron transfer , crystallography , photosystem ii , biochemistry , photosynthesis , photochemistry , enzyme , thioredoxin , thioredoxin reductase
The two proteins ferredoxin and flavodoxin can replace each other in the photosynthetic electron transfer chain of cyanobacteria and algae. However, structure, size, and composition of ferredoxin and flavodoxin are completely different. Ferredoxin is a small iron‐sulfur protein (∼100 amino acids), whereas flavodoxin is a flavin‐containing protein (∼170 amino acids). The crystal structure of both proteins from the cyanobacteria Anabeana PCC 7120 is known. We used these two protein structures to investigate the structural basis of their functional equivalence. We apply the Hodgkin index to quantify the similarity of their electrostatic potentials. The technique has been applied successfully in indirect drug design for the alignment of small molecule and bioisosterism elucidation. It requires no predefined atom‐atom correspondences. As is known from experiments, electrostatic interactions are most important for the association of ferredoxin and flavodoxin with their reaction partners photosystem I and ferredoxin‐NADP reductase. Therefore, use of electrostatic potentials for the structural alignment is well justified. Our extensive search of the alignment space reveals two alignments with a high degree of similarity in the electrostatic potential. In both alignments, ferredoxinoverlaps completely with flavodoxin. The active sites of ferredoxin and flavodoxin rather than their centers of mass coincide in both alignments. This is in agreement with electron microscopy investigations on photosystem I cross‐linked to ferredoxin or flavodoxin. We identify residues that may have the same function in both proteins and relate our results to previous experimental data. Proteins 2000;38:301–309. © 2000 Wiley‐Liss, Inc.