Protein docking using case‐based reasoning

Inhibition or genetic deletion of poly(ADP-ribose) (PAR) polymerase-1 (PARP-1) is protective against toxic insults in many organ systems. The molecular mechanisms underlying PARP-1–dependent cell death involve release of mitochondrial apoptosis-inducing factor (AIF) and its translocation to the nucleus, which results in chromatinolysis. We identified macrophage migration inhibitory factor (MIF) as a PARP-1–dependent AIF-associated nuclease (PAAN). AIF was required for recruitment of MIF to the nucleus, where MIF cleaves genomic DNA into large fragments. Depletion of MIF, disruption of the AIF-MIF interaction, or mutation of glutamic acid at position 22 in the catalytic nuclease domain blocked MIF nuclease activity and inhibited chromatinolysis, cell death induced by glutamate excitotoxicity, and focal stroke. Inhibition of MIF's nuclease activity is a potential therapeutic target for diseases caused by excessive PARP-1 activation.

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“…protein-DNA docking program (46, 47). The HEX program uses a surface complementarity algorithm to identify contact between protein and DNA.…”

Section: Methodsmentioning

confidence: 99%

A nuclease that mediates cell death induced by DNA damage and poly(ADP-ribose) polymerase-1

Wang

Umanah

et al. 2016

Science

302

265

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“…The structures of different modulators were retrieved from NCBI PubChem search engine and were docked to the protein's predicted active binding site using Schrodinger GLIDE version 9.7 and HEX: version 8.0.0 [20,21].…”

Section: In Silico Interaction Studies Of Rubiscomentioning

confidence: 99%

In silico Identification of Ergosterol as a Novel Fungal Metabolite Enhancing RuBisCO Activity in Lycopersicum esculentum

Mitra

Narad

Sengupta

et al. 2015

Interdiscip Sci Comput Life Sci

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RuBisCO (EC 4.1.1.39), a key enzyme found in stroma of chloroplast, is important for fixing atmospheric CO2 in plants. Alterations in the activity of RuBisCO could influence photosynthetic yield. Therefore, to understand the activity of the protein, knowledge about its structure is pertinent. Though the structure of Nicotiana RuBisCO has been modeled, the structure of tomato RuBisCO is still unknown. RuBisCO extracted from chloroplasts of tomato leaves was subjected to MALDI-TOF-TOF followed by Mascot Search. The protein sequence based on gene identification numbers was subjected to in silico model construction, characterization and docking studies. The primary structure analysis revealed that protein was stable, neutral, hydrophilic and has an acidic pI. The result though indicates a 90 % homology with other members of Solanaceae but differs from the structure of Arabidopsis RuBisCO. Different ligands were docked to assess the activity of RuBisCO against these metabolite components. Out of the number of modulators tested, ergosterol had the maximum affinity (E = -248.08) with RuBisCO. Ergosterol is a major cell wall component of fungi and has not been reported to be naturally found in plants. It is a known immune elicitor in plants. The current study throws light on its role in affecting RuBisCO activity in plants, thereby bringing changes in the photosynthetic rate.

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“…2). In the default HADDOCK protocol, the rigid-body energy minimization stage produces and scores 1000 models (effectively sampling The research group responsible for GRAMM-X has recently developed an alternative technique to predict the structure of protein-protein complexes based on structural similarity with (distant) homologues [104]. This method is reviewed in greater detail in the 'Beyond Docking' section of this article.…”

Section: State-of-the-art Of Integrative Modeling Softwarementioning

confidence: 99%

“…Among these, a few particular methods deserve praise: the integrative modeling platform [100] and the modeling of complexes based on experimentally determined homologues [101][102][103][104].…”

Section: Predicting From Predictions: Bioinformatics Interface Predicmentioning

confidence: 99%

“…Kundrotas et al claimed that 'there are enough templates to model nearly all protein complexes' [103] and developed a method to rigidly superimpose the interacting proteins on homologous complexes. Finally, KBDOCK [104] was also recently developed and uses domain-domain homology to model protein complexes.…”

Section: Predicting From Predictions: Bioinformatics Interface Predicmentioning

confidence: 99%

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Integrative computational modeling of protein interactions

Rodrigues

Bonvin

2014

The FEBS Journal

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Protein interactions define the homeostatic state of the cell. Our ability to understand these interactions and their role in both health and disease is tied to our knowledge of the 3D atomic structure of the interacting partners and their complexes. Despite advances in experimental method of structure determination, the majority of known protein interactions are still missing an atomic structure. High‐resolution methods such as X‐ray crystallography and NMR spectroscopy struggle with the high‐throughput demand, while low‐resolution techniques such as cryo‐electron microscopy or small‐angle X‐ray scattering provide data that are too coarse. Computational structure prediction of protein complexes, or docking, was first developed to complement experimental research and has since blossomed into an independent and lively field of research. Its most successful products are hybrid approaches that combine powerful algorithms with experimental data from various sources to generate high‐resolution models of protein complexes. This minireview introduces the concept of docking and docking with the help of experimental data, compares and contrasts the available integrative docking methods, and provides a guide for the experimental researcher for what types of data and which particular software can be used to model a protein complex.

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Protein docking using case‐based reasoning

Cited by 105 publications

References 44 publications

A nuclease that mediates cell death induced by DNA damage and poly(ADP-ribose) polymerase-1

A nuclease that mediates cell death induced by DNA damage and poly(ADP-ribose) polymerase-1

In silico Identification of Ergosterol as a Novel Fungal Metabolite Enhancing RuBisCO Activity in Lycopersicum esculentum

Integrative computational modeling of protein interactions

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