Journal ArticleDOI
Identification of cross-linked peptides from complex samples
Bing Yang,Yan-Jie Wu,Ming Zhu,Sheng-Bo Fan,Jinzhong Lin,Kun Zhang,Shuang Li,Hao Chi,Yu-Xin Li,Hai-Feng Chen,Shukun Luo,Yue-He Ding,Le-Heng Wang,Zhiqi Hao,Li-Yun Xiu,She Chen,Keqiong Ye,Si-Min He,Meng-Qiu Dong +18 more
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TLDR
pLink as mentioned in this paper is a software for data analysis of cross-linked proteins coupled with mass-spectrometry analysis, which is compatible with multiple homo- or hetero-bifunctional cross-linkers.Abstract:
pLink, software for data analysis of cross-linked proteins coupled with mass spectrometry, estimates false discovery rate and enables analysis of protein complexes without extensive purification. We have developed pLink, software for data analysis of cross-linked proteins coupled with mass-spectrometry analysis. pLink reliably estimates false discovery rate in cross-link identification and is compatible with multiple homo- or hetero-bifunctional cross-linkers. We validated the program with proteins of known structures, and we further tested it on protein complexes, crude immunoprecipitates and whole-cell lysates. We show that it is a robust tool for protein-structure and protein-protein–interaction studies.read more
Citations
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Protein Analysis by Shotgun/Bottom-up Proteomics
TL;DR: The progress of proteomics has been driven by the development of new technologies for peptide/protein separation, mass spectrometry analysis, isotope labeling for quantification, and bioinformatics data analysis.
Journal ArticleDOI
Visualization of arrestin recruitment by a G-protein-coupled receptor
Arun K. Shukla,Gerwin Westfield,Kunhong Xiao,Rosana I. Reis,Li-Yin Huang,Prachi Tripathi-Shukla,Jiang Qian,Sheng Li,Adi Blanc,Austin N. Oleskie,Anne M. Dosey,Min Su,Cui Rong Liang,Ling Ling Gu,Jin Ming Shan,Xin Chen,Rachel Hanna,Minjung Choi,Xiao Jie Yao,Bjoern U. Klink,Alem W. Kahsai,Sachdev S. Sidhu,Shohei Koide,Pawel A. Penczek,Anthony A. Kossiakoff,Virgil L. Woods,Brian K. Kobilka,Georgios Skiniotis,Robert J. Lefkowitz +28 more
TL;DR: A strategy for forming and purifying a functional human β2AR–β-arrestin-1 complex is devised that provides a framework for better understanding the basis of GPCR regulation by arrestins.
Journal ArticleDOI
Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes
Nazar Mashtalir,Nazar Mashtalir,Andrew R. D’Avino,Andrew R. D’Avino,Brittany C. Michel,Brittany C. Michel,Jie Luo,Joshua Pan,Joshua Pan,Jordan E. Otto,Jordan E. Otto,Hayley J. Zullow,Hayley J. Zullow,Zachary M. McKenzie,Rachel L. Kubiak,Roodolph St. Pierre,Roodolph St. Pierre,Alfredo M. Valencia,Alfredo M. Valencia,Steven J. Poynter,Steven J. Poynter,Seth H. Cassel,Seth H. Cassel,Jeffrey A. Ranish,Cigall Kadoch,Cigall Kadoch +25 more
TL;DR: This work elucidates the architecture and assembly pathway across three classes of mSWI/SNF complexes-canonical BRG1/BRM-associated factor (BAF), polybromo-associated BAF (PBAF, and newly defined ncBAF complexes) and defines the requirement of each subunit for complex formation and stability.
Journal ArticleDOI
Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry
TL;DR: An integrated workflow that robustly identifies cross-links from endogenous protein complexes in human cellular lysates is described, based on the application of mass spectrometry (MS)-cleavable cross-linkers, sequential collision-induced dissociation (CID)–tandem MS (MS/MS) and electron-transfer Dissociation (ETD)-MS/ MS acquisitions, and a dedicated search engine, XlinkX.
Journal ArticleDOI
Integrative structure and functional anatomy of a nuclear pore complex
Seung Joong Kim,Javier Fernandez-Martinez,Ilona Nudelman,Yi Shi,Wenzhu Zhang,Barak Raveh,Thurston Herricks,Brian D. Slaughter,Joanna A. Hogan,Paula Upla,Ilan E. Chemmama,Riccardo Pellarin,Ignacia Echeverria,Manjunatha Shivaraju,Azraa S. Chaudhury,Junjie Wang,Rosemary Williams,Jay R. Unruh,Charles H. Greenberg,Erica Y. Jacobs,Zhiheng Yu,M. Jason de la Cruz,Roxana Mironska,David L. Stokes,John D. Aitchison,John D. Aitchison,Martin F. Jarrold,Jennifer L. Gerton,Steven J. Ludtke,Christopher W. Akey,Brian T. Chait,Andrej Sali,Michael P. Rout +32 more
TL;DR: The structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae is determined at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents.
References
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Journal ArticleDOI
Identification of cross-linked peptides from large sequence databases
Oliver Rinner,Jan Seebacher,Thomas Walzthoeni,Thomas Walzthoeni,Lukas N. Mueller,Martin Beck,Alexander Schmidt,Alexander Schmidt,Markus Mueller,Ruedi Aebersold,Ruedi Aebersold,Ruedi Aebersold +11 more
TL;DR: It is shown that xQuest can identify cross-linked peptides from a total Escherichia coli lysate with an unrestricted database search and reduces the search space by an upstream candidate-peptide search before the recombination step.