Determination of atomic desolvation energies from the structures of crystallized proteins

Zhang, Chao; Vasmatzis, George; Cornette, James L.; DeLisi, Charles

doi:10.1006/jmbi.1996.0859

Cited by 509 publications

(503 citation statements)

References 58 publications

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“…Protein-protein docking of PTEN with the N-terminal C2, WW1, and WW2 domains of NEDD4-1 and p34 was sequentially performed using ZDOCK 29 and RDOCK [29][30][31] (Accelrys Software) (Discovery studio, version 2.1., 2007). In the docking studies, the structure of PTEN was taken from PDB 1D5R (http://www.rcsb.org), in which the structure was resolved in a complex that was bound to L-tartrate.…”

Section: Methodsmentioning

confidence: 99%

p34 is a novel regulator of the oncogenic behavior of NEDD4-1 and PTEN

Hong

et al. 2013

Cell Death Differ

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PTEN is one of the most frequently mutated or deleted tumor suppressors in human cancers. NEDD4-1 was recently identified as the E3 ubiquitin ligase for PTEN; however, a number of important questions remain regarding the role of ubiquitination in regulating PTEN function and the mechanisms by which PTEN ubiquitination is regulated. In the present study, we demonstrated that p34, which was identified as a binding partner of NEDD4-1, controls PTEN ubiquitination by regulating NEDD4-1 protein stability. p34 interacts with the WW1 domain of NEDD4-1, an interaction that enhances NEDD4-1 stability. Expression of p34 promotes PTEN poly-ubiquitination, leading to PTEN protein degradation, whereas p34 knockdown results in PTEN mono-ubiquitination. Notably, an inverse correlation between PTEN and p34/NEDD4-1 levels was confirmed in tumor samples from colon cancer patients. Thus, p34 acts as a key regulator of the oncogenic behavior of NEDD4-1 and PTEN.

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Section: Methodsmentioning

confidence: 99%

p34 is a novel regulator of the oncogenic behavior of NEDD4-1 and PTEN

Hong

et al. 2013

Cell Death Differ

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“…After validating the methods, each studied molecules optimized using all three methods were docked in the protein following mentioned parameters. Scoring function that considers both geometric fit and atomic desolvation energy [38] was used to evaluate each candidate transformation. Based on the atomic contact energy or desolvation energy, docking score, and approximate interface area of the complex, best docking solution was selected for further refinement and rescoring analysis by FireDock (Fast Interaction REfinement in molecular DOCKing) algorithm.…”

Section: Docking Approachmentioning

confidence: 99%

A comprehensive computational analysis of cathinone and its metabolites using quantum mechanical approaches and docking studies

et al. 2016

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Conformers of the psychoactive compound of the Khat plant cathinone along with its amino alcohol metabolites norephedrine and norpseudoephedrine have been calculated using DFT (M062X/B3LYP) and MP2 levels of theory for gas and solution phases. Gas-phase studies revealed that cathinone has two, norephedrine has four and norpseudoephedrine has three low-energy conformations with all conformers connected by rotational transition states. To understand the solvent effect to the energetic profiles of the studied species, the conductor-like screening model is employed within aqueous medium. It explains lowering of energy of all studied conformers in solution. The molecular electrostatic potential surface data for each molecule revealed likely reaction sites for the studied molecules. The computed IR spectra for cathinone and its metabolites have been compared with experimental data and rotational transition states connecting all conformers have been reported. The natural bond orbital analyses for only ligands and separately for their complexes with amino acid residues in protein pockets from the docking results are also performed to corroborate the results obtained from the MP2 and DFT calculations. The comprehensive computational study explore important amino acid residues and stabilizing energy of the studied molecules with the interacting proteins along with the reason behind the difference in potency for cathinone's metabolites.

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“…If we consider the interaction between the ith atom of a ligand and the jth atom of a receptor, then e ij is the atomic contact potential between them and g(r) is a smooth function based on their distance (Zhang et al 1997). For simplicity, we consider the smooth function to be linear.…”

Section: Desolvation Energymentioning

confidence: 99%

Using desolvation energies of structural domains to predict stability of protein complexes

Maleki

Hall

Rueda

2013

Netw Model Anal Health Inform Bioinforma

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Employing domain knowledge for prediction of particular types of protein-protein interactions (PPIs) is a problem that has become increasingly important in the past few years, due to the fundamental role of domains in protein function. We propose a model to predict obligate and non-obligate protein interaction types using desolvation energies of structural domains that are present in the interfaces of protein complexes, which are extracted from the CATH database. The prediction is performed using several state-of-the-art classification techniques, including linear dimensionality reduction, a support vector machine based on sequential minimal optimization, naive Bayes, and k-nearest neighbour. Our results on two well-known datasets demonstrate that (a) domain-based features of higher levels of CATH, especially level 2, are more powerful and discriminative than features of other levels, and (b) properties taken from different levels of the CATH hierarchy yield higher accuracies than properties taken from each level of the hierarchy separately. Furthermore, analysis of structural properties suggests that domaindomain interactions that have at least a mainly-beta secondary structure in one sub-unit are more informative for predicting obligate and non-obligate PPIs.

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Determination of atomic desolvation energies from the structures of crystallized proteins

Cited by 509 publications

References 58 publications

p34 is a novel regulator of the oncogenic behavior of NEDD4-1 and PTEN

p34 is a novel regulator of the oncogenic behavior of NEDD4-1 and PTEN

A comprehensive computational analysis of cathinone and its metabolites using quantum mechanical approaches and docking studies

Using desolvation energies of structural domains to predict stability of protein complexes

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