From noncovalent to covalent bonds: a paradigm shift in target protein identification

2013 ◽  
Vol 9 (4) ◽  
pp. 544 ◽  
Author(s):  
Jongmin Park ◽  
Minseob Koh ◽  
Seung Bum Park
Keyword(s):  
Paradigm Shift ◽  
Protein Identification ◽  
Target Protein ◽  
Covalent Bonds

Target Protein Identification on Photocatalyst‐Functionalized Magnetic Affinity Beads

2020 ◽  
Vol 101 (1) ◽  
Author(s):  
Michihiko Tsushima ◽  
Shinichi Sato ◽  
Keita Nakane ◽  
Hiroyuki Nakamura
Keyword(s):  
Protein Identification ◽  
Target Protein ◽  
Affinity Beads

Celastrol binds to its target protein via specific noncovalent interactions and reversible covalent bonds

2018 ◽  
Vol 54 (91) ◽  
pp. 12871-12874 ◽  
Author(s):  
Duo Zhang ◽  
Ziwen Chen ◽  
Chaochao Hu ◽  
Siwei Yan ◽  
Zhuoer Li ◽  
...  
Keyword(s):  
Noncovalent Interactions ◽  
Binding Specificity ◽  
Target Protein ◽  
Covalent Bonds ◽  
Reversible Covalent

Celastrol binding to its target protein Nur77 requires specific noncovalent interactions that position celastrol close to a specific cysteine and furthermore confer its binding specificity.

scholarly journals Carbohydrate-Encapsulated Gold Nanoparticles for Rapid Target-Protein Identification and Binding-Epitope Mapping

ChemBioChem ◽  
2005 ◽  
Vol 6 (7) ◽  
pp. 1169-1173 ◽  
Author(s):  
Yu-Ju Chen ◽  
Shu-Hua Chen ◽  
Yuh-Yih Chien ◽  
Yu-Wan Chang ◽  
Hsin-Kai Liao ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Epitope Mapping ◽  
Protein Identification ◽  
Target Protein ◽  
Binding Epitope

scholarly journals PatchSearch: a web server for off-target protein identification

2019 ◽  
Vol 47 (W1) ◽  
pp. W365-W372 ◽  
Author(s):  
Julien Rey ◽  
Inès Rasolohery ◽  
Pierre Tufféry ◽  
Frédéric Guyon ◽  
Gautier Moroy
Keyword(s):  
Protein Identification ◽  
Protein Structures ◽  
Scoring Function ◽  
Web Server ◽  
Binding Mode ◽  
Target Protein ◽  
Local Alignment ◽  
Protein Surfaces ◽  
Target Proteins ◽  
Potential Interactions

Abstract The large number of proteins found in the human body implies that a drug may interact with many proteins, called off-target proteins, besides its intended target. The PatchSearch web server provides an automated workflow that allows users to identify structurally conserved binding sites at the protein surfaces in a set of user-supplied protein structures. Thus, this web server may help to detect potential off-target protein. It takes as input a protein complexed with a ligand and identifies within user-defined or predefined collections of protein structures, those having a binding site compatible with this ligand in terms of geometry and physicochemical properties. It is based on a non-sequential local alignment of the patch over the entire protein surface. Then the PatchSearch web server proposes a ligand binding mode for the potential off-target, as well as an estimated affinity calculated by the Vinardo scoring function. This novel tool is able to efficiently detects potential interactions of ligands with distant off-target proteins. Furthermore, by facilitating the discovery of unexpected off-targets, PatchSearch could contribute to the repurposing of existing drugs. The server is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/PatchSearch.

An Automated Model for Target Protein prediction in PPI

2020 ◽  
Vol 15 ◽  
Author(s):  
G. Naveen Sundar ◽  
D. Narmadha
Keyword(s):  
Protein Identification ◽  
Research Work ◽  
Target Protein ◽  
Centrality Measures ◽  
Essential Proteins ◽  
Machine Learning Model ◽  
Computer Based ◽  
Living Organisms ◽  
Protein Essentiality ◽  
Sensitivity Specificity

Background: Essential proteins play a crucial role in most of the living organisms. The computer-based task of predicting essential proteins is important for target protein identification, disease treatment and suitable drug development. Objective: Traditionally many experimental and centrality measures have been proposed by researchers to predict protein essentiality. Methods: The prediction accuracy, sensitivity, specificity identified by the traditional methods is very low. Results and Discussion: In this research work, a novel computational based approach such NC-KNN model has been proposed to identify the most essential proteins. The proposed work uses a combination of network topology measure and machine learning model to predict the essential proteins. Conclusion: The proposed work shows a remarkable improvement than seven traditional centrality based measures such as DC, BC, CC, EC, NC, ECC and SC in terms of the metrics such as accuracy(A1), precision(P1), recall(R1), sensitivity(SE) and specificity(SP).

Advances in identification and validation of protein targets of natural products without chemical modification

2016 ◽  
Vol 33 (5) ◽  
pp. 719-730 ◽  
Author(s):  
J. Chang ◽  
Y. Kim ◽  
H. J. Kwon
Keyword(s):  
Natural Products ◽  
Chemical Modification ◽  
Case Studies ◽  
Protein Identification ◽  
Target Protein ◽  
Label Free ◽  
Protein Targets ◽  
Identification Methods ◽  
Drug Candidates ◽  
New Drug

This review focuses on and reports case studies of the latest advances in target protein identification methods for label-free natural products. The integration of newly developed technologies will provide new insights and highlight the value of natural products for use as biological probes and new drug candidates.

Temperature Dependence of the Critical Electron Dose for Fatty Acid Monolayers

1982 ◽  
Vol 40 ◽  
pp. 78-79
Author(s):  
Kenneth H. Downing ◽  
Robert M. Glaeser
Keyword(s):  
Electron Beam ◽  
Fatty Acid ◽  
Inelastic Scattering ◽  
Temperature Dependence ◽  
Structural Damage ◽  
Direct Result ◽  
Second Step ◽  
Strong Temperature Dependence ◽  
Electron Dose ◽  
Covalent Bonds

The structural damage of molecules irradiated by electrons is generally considered to occur in two steps. The direct result of inelastic scattering events is the disruption of covalent bonds. Following changes in bond structure, movement of the constituent atoms produces permanent distortions of the molecules. Since at least the second step should show a strong temperature dependence, it was to be expected that cooling a specimen should extend its lifetime in the electron beam. This result has been found in a large number of experiments, but the degree to which cooling the specimen enhances its resistance to radiation damage has been found to vary widely with specimen types.

Structural Transformation of a Germanium Σ=13 (510) [001] Tilt Grain Boundary under the Electron Beam

1990 ◽  
Vol 48 (1) ◽  
pp. 52-53 ◽  
Author(s):  
Jean-Luc Rouvière ◽  
Alain Bourret
Keyword(s):  
Electron Microscopy ◽  
High Resolution ◽  
Grain Boundary ◽  
Structural Transformation ◽  
Mirror Symmetry ◽  
High Resolution Electron Microscopy ◽  
Structural Transformations ◽  
Covalent Bonds ◽  
Resolution Electron ◽  
Tilt Grain Boundary

The possible structural transformations during the sample preparations and the sample observations are important issues in electron microscopy. Several publications of High Resolution Electron Microscopy (HREM) have reported that structural transformations and evaporation of the thin parts of a specimen could happen in the microscope. Diffusion and preferential etchings could also occur during the sample preparation.Here we report a structural transformation of a germanium Σ=13 (510) [001] tilt grain boundary that occurred in a medium-voltage electron microscopy (JEOL 400KV).Among the different (001) tilt grain boundaries whose atomic structures were entirely determined by High Resolution Electron Microscopy (Σ = 5(310), Σ = 13 (320), Σ = 13 (510), Σ = 65 (1130), Σ = 25 (710) and Σ = 41 (910), the Σ = 13 (510) interface is the most interesting. It exhibits two kinds of structures. One of them, the M-structure, has tetracoordinated covalent bonds and is periodic (fig. 1). The other, the U-structure, is also tetracoordinated but is not strictly periodic (fig. 2). It is composed of a periodically repeated constant part that separates variable cores where some atoms can have several stable positions. The M-structure has a mirror glide symmetry. At Scherzer defocus, its HREM images have characteristic groups of three big white dots that are distributed on alternatively facing right and left arcs (fig. 1). The (001) projection of the U-structure has an apparent mirror symmetry, the portions of good coincidence zones (“perfect crystal structure”) regularly separate the variable cores regions (fig. 2).

Sign in / Sign up

Export Citation Format

Share Document