ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers

Pierce, Brian G.; Wiehe, Kevin; Hwang, Howook; Kim, Bong-Hyun; Vreven, Thom; Weng, Zhiping

doi:10.1093/bioinformatics/btu097

Cited by 1,472 publications

(1,161 citation statements)

References 17 publications

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“…suggestive of the presence of conserved ATP signaling via serpentine receptors in Plasmodium. These results were also confirmed using Z-Dock server online (Chen et al 2003;Pierce et al 2014) (data not shown). The identification of ATP binding site could be exploited for development of novel synthetic compounds.…”

Section: Molecular Dockingsupporting

confidence: 56%

In silico characterization of Plasmodium falciparum purinergic receptor: a novel chemotherapeutic target

Gupta

Singh

2015

Syst Synth Biol

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Serpentine receptors with G-protein coupled receptor like seven transmembrane (7 TM) topology are identified in Plasmodium. A class of 7 TM receptors known as purinergic receptors binds to purines such as ADP, ATP and UTP and mediates important physiological functions including regulation of calcium signaling. Here we performed in silico analysis of Plasmodium falciparum serpentine receptors and found that one of the P. falciparum serpentine receptors, PfSR12 possess nucleotide binding consensus P-loop sequence in addition to seven transmembrane domains. The presence of conserved seven transmembrane domains and a consensus nucleotide binding sequence (P-loop) suggest that PfSR12 is a putative purinergic receptor. On further analysis using docking programmes we found four active binding residues Asn149, Lys150, Asn151 and Gly152 in P-loop of PfSR12, interact with ATP. This work gives insights into the interactions between putative purinergic receptor PfSR12 and its ligand ATP which can be explored in structure based drug designing against malaria.

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Section: Molecular Dockingsupporting

confidence: 56%

In silico characterization of Plasmodium falciparum purinergic receptor: a novel chemotherapeutic target

Gupta

Singh

2015

Syst Synth Biol

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“…Initial docking between the E. coli FrdA subunit of QFR (PDB code 1KF6) (24) and SdhE (PDB code 1X6I) (25) with both the distal N and C termini removed was performed using ZDOCK (26). Initial docking calculations constrained SdhE-R8, SdhE-M17, FrdA-M176, and FrdA-E460 as part of the binding surfaces.…”

Section: Expression and Purification Of The Hexahistidine Frdamentioning

confidence: 99%

Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II

Maklashina

Rajagukguk

Starbird³

et al. 2016

Journal of Biological Chemistry

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Escherichia coli harbors two highly conserved homologs of the essential mitochondrial respiratory complex II (succinate: ubiquinone oxidoreductase). Aerobically the bacterium synthesizes succinate:quinone reductase as part of its respiratory chain, whereas under microaerophilic conditions, the quinol: fumarate reductase can be utilized. All complex II enzymes harbor a covalently bound FAD co-factor that is essential for their ability to oxidize succinate. In eukaryotes and many bacteria, assembly of the covalent flavin linkage is facilitated by a small protein assembly factor, termed SdhE in E. coli. How SdhE assists with formation of the covalent flavin bond and how it binds the flavoprotein subunit of complex II remain unknown. Using photo-cross-linking, we report the interaction site between the flavoprotein of complex II and the SdhE assembly factor. These data indicate that SdhE binds to the flavoprotein between two independently folded domains and that this binding mode likely influences the interdomain orientation. In so doing, SdhE likely orients amino acid residues near the dicarboxylate and FAD binding site, which facilitates formation of the covalent flavin linkage. These studies identify how the conserved SdhE assembly factor and its homologs participate in complex II maturation.

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“…24,[30][31][32][33][34][35] Roughly, there are two types of approaches: docking algorithms 30,31,35 whose goal is to predict the quaternary structure a priori and are template free, i.e., they do not require that any previous example of the quaternary structure be known. Others are template based 24,[32][33][34] and predict the interaction pose by copying from a related quaternary structure template.…”

Section: Introductionmentioning

confidence: 99%

Are protein-protein interfaces special regions on a protein’s surface?

Tonddast-Navaei

Skolnick

2015

The Journal of Chemical Physics

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Protein-protein interactions (PPIs) are involved in many cellular processes. Experimentally obtained protein quaternary structures provide the location of protein-protein interfaces, the surface region of a given protein that interacts with another. These regions are termed half-interfaces (HIs). Canonical HIs cover roughly one third of a protein's surface and were found to have more hydrophobic residues than the non-interface surface region. In addition, the classical view of protein HIs was that there are a few (if not one) HIs per protein that are structurally and chemically unique. However, on average, a given protein interacts with at least a dozen others. This raises the question of whether they use the same or other HIs. By copying HIs from monomers with the same folds in solved quaternary structures, we introduce the concept of geometric HIs (HIs whose geometry has a significant match to other known interfaces) and show that on average they cover three quarters of a protein's surface. We then demonstrate that in some cases, these geometric HI could result in real physical interactions (which may or may not be biologically relevant). The composition of the new HIs is on average more charged compared to most known ones, suggesting that the current protein interface database is biased towards more hydrophobic, possibly more obligate, complexes. Finally, our results provide evidence for interface fuzziness and PPI promiscuity. Thus, the classical view of unique, well defined HIs needs to be revisited as HIs are another example of coarse-graining that is used by nature. C

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ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers

Abstract: The ZDOCK server is freely available to all academic and non-profit users at: http://zdock.umassmed.edu. No registration is required.

Cited by 1,472 publications

References 17 publications

In silico characterization of Plasmodium falciparum purinergic receptor: a novel chemotherapeutic target

In silico characterization of Plasmodium falciparum purinergic receptor: a novel chemotherapeutic target

Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II

Are protein-protein interfaces special regions on a protein’s surface?

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