[HTML][HTML] Profiling of protein interaction networks of protein complexes using affinity purification and quantitative mass spectrometry

RM Kaake, X Wang, L Huang - Molecular & cellular proteomics, 2010 - Elsevier
Protein-protein interactions are important for nearly all biological processes, and it is known
that aberrant protein-protein interactions can lead to human disease and cancer. Recent …

Computational and informatics strategies for identification of specific protein interaction partners in affinity purification mass spectrometry experiments

AI Nesvizhskii - Proteomics, 2012 - Wiley Online Library
Analysis of protein interaction networks and protein complexes using affinity purification and
mass spectrometry (AP/MS) is among most commonly used and successful applications of …

Refinements to label free proteome quantitation: how to deal with peptides shared by multiple proteins

Y Zhang, Z Wen, MP Washburn, L Florens - Analytical chemistry, 2010 - ACS Publications
Quantitative shotgun proteomics is dependent on the detection, identification, and
quantitative analysis of peptides. An issue arises with peptides that are shared between …

Combinatorial depletion analysis to assemble the network architecture of the SAGA and ADA chromatin remodeling complexes

KK Lee, ME Sardiu, SK Swanson… - Molecular systems …, 2011 - embopress.org
Despite the availability of several large‐scale proteomics studies aiming to identify protein
interactions on a global scale, little is known about how proteins interact and are organized …

Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex

AB Patel, J Qing, KH Tam, S Zaman, M Luiso… - Nature …, 2023 - nature.com
The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex
conserved in a broad range of eukaryotes that performs localized deacetylation at or near …

[HTML][HTML] Highly reproducible label free quantitative proteomic analysis of RNA polymerase complexes

AL Mosley, ME Sardiu, SG Pattenden… - Molecular & Cellular …, 2011 - Elsevier
The use of quantitative proteomics methods to study protein complexes has the potential to
provide in-depth information on the abundance of different protein components as well as …

Rpd3L HDAC links H3K4me3 to transcriptional repression memory

BB Lee, A Choi, JH Kim, Y Jun, H Woo… - Nucleic acids …, 2018 - academic.oup.com
Transcriptional memory is critical for the faster reactivation of necessary genes upon
environmental changes and requires that the genes were previously in an active state …

The Fng3 ING protein regulates H3 acetylation and H4 deacetylation by interacting with two distinct histone‐modifying complexes

H Xu, M Ye, A **a, H Jiang, P Huang, H Liu… - New …, 2022 - Wiley Online Library
The steady‐state level of histone acetylation is maintained by histone acetyltransferase
(HAT) and histone deacetylase (HDAC) complexes. INhibitor of Growth (ING) proteins are …

[HTML][HTML] Proteomic approaches to the study of papillomavirus–host interactions

EA White, PM Howley - Virology, 2013 - Elsevier
The identification of interactions between viral and host cellular proteins has provided major
insights into papillomavirus research, and these interactions are especially relevant to the …

[HTML][HTML] Exploring the yeast acetylome using functional genomics

SK Duffy, H Friesen, A Baryshnikova, JP Lambert… - Cell, 2012 - cell.com
Lysine acetylation is a dynamic posttranslational modification with a well-defined role in
regulating histones. The impact of acetylation on other cellular functions remains relatively …