Macromolecular crowding effects on protein–protein binding affinity and specificity

2010 ◽  
Vol 133 (20) ◽  
pp. 205101 ◽  
Author(s):  
Young C. Kim ◽  
Robert B. Best ◽  
Jeetain Mittal
Keyword(s):  
Protein Binding ◽  
Binding Affinity ◽  
Macromolecular Crowding ◽  
Crowding Effects

scholarly journals Macromolecular Crowding Effects on Reactions of TePixD (Tll0078)†

2010 ◽  
Vol 87 (3) ◽  
pp. 584-589 ◽  
Author(s):  
Tsuguyoshi Toyooka ◽  
Keisuke Tanaka ◽  
Koji Okajima ◽  
Masahiko Ikeuchi ◽  
Satoru Tokutomi ◽  
...  
Keyword(s):  
Macromolecular Crowding ◽  
Crowding Effects

scholarly journals Learning protein binding affinity using privileged information

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Wajid Arshad Abbasi ◽  
Amina Asif ◽  
Asa Ben-Hur ◽  
Fayyaz ul Amir Afsar Minhas
Keyword(s):  
Protein Binding ◽  
Binding Affinity ◽  
Privileged Information

Evaluation for Protein Binding Affinity of Maghemite and Magnetite Nanoparticles

2007 ◽  
Vol 7 (11) ◽  
pp. 3706-3708 ◽  
Author(s):  
Se Chan Kang ◽  
Yong Jun Jo ◽  
Jong Phil Bak ◽  
Ki-Chul Kim ◽  
Young-Sung Kim
Keyword(s):  
Protein Binding ◽  
Binding Affinity ◽  
Magnetite Nanoparticles ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Human Lung Cancer ◽  
Maghemite Nanoparticles ◽  
Binding Ability ◽  
Sds Page ◽  
Lung Cancer A549 Cell

We investigated the protein binding affinity of magnetite (Fe3O4) and maghemite (γ-Fe2O3) nanoparticles with against non-characterized protein from human lung cancer A549 cell line on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The binding ability of maghemite was 400 ng/mg. According to the SDS-PAGE results, the protein binding affinity of maghemite nanoparticles is stronger than magnetite nanoparticles. These data suggest that a protein can be detected with maghemite nanoparticles.

Using an oxidized porous silicon interferometer for determination of relative protein binding affinity through non-covalent capture probe immobilization

2007 ◽  
Vol 204 (5) ◽  
pp. 1444-1448 ◽  
Author(s):  
Michael P. Schwartz ◽  
Christine Yu ◽  
Sara D. Alvarez ◽  
Benjamin Migliori ◽  
Denis Godin ◽  
...  
Keyword(s):  
Porous Silicon ◽  
Protein Binding ◽  
Binding Affinity ◽  
Capture Probe ◽  
Oxidized Porous Silicon

scholarly journals RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features

2020 ◽  
Author(s):  
Stefan Holderbach ◽  
Lukas Adam ◽  
Bhyravabhotla Jayaram ◽  
Rebecca Wade ◽  
Goutam Mukherjee
Keyword(s):  
Machine Learning ◽  
Ligand Binding ◽  
Protein Binding ◽  
Binding Affinity ◽  
Binding Free Energy ◽  
Rapid Screening ◽  
Scoring Functions ◽  
Energy Prediction ◽  
Molecular Features ◽  
Physicochemical Descriptors

The virtual screening of large numbers of compounds against target protein binding sites has become an integral component of drug discovery workflows. This screening is often done by computationally docking ligands into a protein binding site of interest, but this has the drawback that a large number of poses must be evaluated to obtain accurate estimates of protein-ligand binding affinity. We here introduce a fast prefiltering method for ligand prioritization that is based on a set of machine learning models and uses simple pose-invariant physicochemical descriptors of the ligands and the protein binding pocket. Our method, Rapid Screening with Physicochemical Descriptors + machine learning (RASPD+), is trained on PDBbind data and achieves a regression performance better than for the original RASPD method and comparable to traditional scoring functions on a range of different test sets without the need for generating ligand poses. Additionally, we use RASPD+ to identify molecular features important for binding affinity and assess the ability of RASPD+ to enrich active molecules from decoys.

scholarly journals Residue-Level Interrogation of Macromolecular Crowding Effects on Protein Stability

2008 ◽  
Vol 130 (21) ◽  
pp. 6826-6830 ◽  
Author(s):  
Lisa M. Charlton ◽  
Christopher O. Barnes ◽  
Conggang Li ◽  
Jillian Orans ◽  
Gregory B. Young ◽  
...  
Keyword(s):  
Protein Stability ◽  
Macromolecular Crowding ◽  
Residue Level ◽  
Crowding Effects

Macromolecular crowding: effects on actin polymerisation

1997 ◽  
Vol 66 (1) ◽  
pp. 57-66 ◽  
Author(s):  
Robyn A. Lindner ◽  
Gregory B. Ralston
Keyword(s):  
Macromolecular Crowding ◽  
Crowding Effects
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