title: Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly.
abstract: BACKGROUND
  Binding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearrangement in Apaf-1, which leads to oligomerization of Apaf-1/cytochrome c complexes into an apoptosome. Despite the availability of crystal structures of cytochrome c and Apaf-1 and cryo-electron microscopy models of the entire apoptosome, the binding mode of cytochrome c to Apaf-1, as well as the nature of the amino acid residues of Apaf-1 involved remain obscure.
  
  
  RESULTS
  We investigated the interaction between cytochrome c and Apaf-1 by combining several modeling approaches. We have applied protein-protein docking and energy minimization, evaluated the resulting models of the Apaf-1/cytochrome c complex, and carried out a further analysis by means of molecular dynamics simulations. We ended up with a single model structure where all the lysine residues of cytochrome c that are known as functionally-relevant were involved in forming salt bridges with acidic residues of Apaf-1. This model has revealed three distinctive bifurcated salt bridges, each involving a single lysine residue of cytochrome c and two neighboring acidic resides of Apaf-1. Salt bridge-forming amino acids of Apaf-1 showed a clear evolutionary pattern within Metazoa, with pairs of acidic residues of Apaf-1, involved in bifurcated salt bridges, reaching their highest numbers in the sequences of vertebrates, in which the cytochrome c-mediated mechanism of apoptosome formation seems to be typical.
  
  
  CONCLUSIONS
  The reported model of an Apaf-1/cytochrome c complex provides insights in the nature of protein-protein interactions which are hard to observe in crystallographic or electron microscopy studies. Bifurcated salt bridges can be expected to be stronger than simple salt bridges, and their formation might promote the conformational change of Apaf-1, leading to the formation of an apoptosome. Combination of structural and sequence analyses provides hints on the evolution of the cytochrome c-mediated apoptosis.
authors.affiliation: School of Physics, Osnabrück University, 49069, Osnabrück, Germany. dshalaeva@uni-osnabrueck.de.|School of Bioengineering and Bioinformatics, 117999, Moscow, Russia. dshalaeva@uni-osnabrueck.de.
authors.forename: Daria N
authors.initials: DN
authors.lastname: Shalaeva
authors.affiliation: A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia. udavdasha@belozersky.msu.ru.
authors.forename: Daria V
authors.initials: DV
authors.lastname: Dibrova
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 20894, Bethesda, MD, USA. galperin@ncbi.nlm.nih.gov.
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Galperin
authors.affiliation: School of Physics, Osnabrück University, 49069, Osnabrück, Germany. amulkid@uos.de.|School of Bioengineering and Bioinformatics, 117999, Moscow, Russia. amulkid@uos.de.|A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 117999, Moscow, Russia. amulkid@uos.de.
authors.forename: Armen Y
authors.initials: AY
authors.lastname: Mulkidjanian
mesh_terms: D000818:Animals; D017209:Apoptosis; D053478:Apoptosomes; D053477:Apoptotic Protease-Activating Factor 1 / Q000737:chemistry*; D045304:Cytochromes c / Q000737:chemistry*; D006736:Horses; D006801:Humans; D006860:Hydrogen Bonding; D008239:Lysine / Q000737:chemistry; D008854:Microscopy, Electron; D056004:Molecular Dynamics Simulation; D010802:Phylogeny; D011485:Protein Binding; D025941:Protein Interaction Mapping; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012492:Salts / Q000737:chemistry; D055672:Static Electricity
chemical_list: C506592:APAF1 protein, human; D053478:Apoptosomes; D053477:Apoptotic Protease-Activating Factor 1; D012492:Salts; D045304:Cytochromes c; D008239:Lysine