Structural alignment of ferredoxin and flavodoxin based on electrostatic potentials: Implications for their interactions with photosystem I and ferredoxin-NADP reductase

The two proteins ferredoxin and flavodoxin can replace each other in the ph otosynthetic electron transfer chain of cyanobacteria and algae, However, s tructure, size, and composition of ferredoxin and flavodoxin are completely different. Ferredoxin is a small iron sulfur protein (similar to 100 amino acids), whereas flavodoxin is a flavin-containing protein (similar to 170 amino acids). The crystal structure of both proteins from the cyanobacteria Anabeana PCC 7120 is known. We used these two protein structures to invest igate the structural basis of their functional equivalence, We apply the Ho dgkin index to quantify the similarity of their electrostatic potentials. T he technique has been applied successfully in indirect drug design for the alignment of small molecule and bioisosterism elucidation. It requires no p redefined atom-atom correspondences, As is known from experiments, electros tatic 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 al ignment is well justified, Our extensive search of the alignment space reve als two alignments with a high degree of similarity in the electrostatic po tential. In both alignments, ferredoxin overlaps completely with flavodoxin , The active sites of ferredoxin and flavodoxin rather than their centers o f mass coincide in both alignments. This is in agreement with electron micr oscopy investigations on photosystem I cross-linked to ferredoxin or flavod oxin, We identify residues that may have the same function in both proteins and relate our results to previous experimental data. (C) 2000 Wiley-Liss, Inc.