= Emerging. More than 5 years before clinical availability. (29.54%)
= Expected to be clinically available in 1 to 4 years. (38.82%)
= Clinically available now. (31.65%)
MSACL 2020 US : Yates

MSACL 2020 US Abstract

Topic: Proteomics

Podium Presentation in Room 5 on Wednesday at 9:40 (Chair: Stephen Pennington)

The 3D Proteome and the Potential for Conformational Biomarkers

John Yates (Presenter)
Scripps Research

Presenter Bio(s): John R. Yates is the Ernest W. Hahn Professor in the Departments of Molecular Medicine and Neurobiology at The Scripps Research Institute. His research interests include development of integrated methods for tandem mass spectrometry analysis of protein mixtures, bioinformatics using mass spectrometry data, and biological studies involving proteomics. He is the lead inventor of the SEQUEST software for correlating tandem mass spectrometry data to sequences in the database and developer of the shotgun proteomics technique for the analysis of protein mixtures. His laboratory has developed the use of proteomic techniques to analyze protein complexes, posttranslational modifications, organelles and quantitative analysis of protein expression for the discovery of new biology. Many proteomic approaches developed by Yates have become a national and international resource to many investigators in the scientific community. He has received the American Society for Mass Spectrometry research award, the Pehr Edman Award in Protein Chemistry, the American Society for Mass Spectrometry Biemann Medal, the HUPO Distinguished Achievement Award in Proteomics, Herbert Sober Award from the ASBMB, and the Christian Anfinsen Award from The Protein Society, the 2015 ACS’s Analytical Chemistry award, 2015 The Ralph N. Adams Award in Bioanalytical Chemistry, the 2018 Thomson Medal from the International Mass Spectrometry Society, and the 2019 John B. Fenn Distinguished Contribution to Mass Spectrometry award from the ASMS. He was ranked by Citation Impact, Science Watch as one of the Top 100 Chemists for the decade, 2000-2010. He was #1 on a List of Most Influential in Analytical Chemistry compiled by The Analytical Scientist 10/30/2013 and is on the List Of Most Highly Influential Biomedical Researchers, 1996-2011, European J. Clinical Investigation 2013, 43, 1339-1365 and the Thomson Reuters 2015 List of Highly Cited Scientists. He has published over 950 scientific articles with >125,000 citations, and an H index of 174 (Google Scholar). Dr. Yates served as an Associate Editor at Analytical Chemistry for 15 years and is currently the Editor in Chief at the Journal of Proteome Research.

Authors: John R. Yates, III, Casimir Bamberger, Hyunsoo Yu, and Sandra Pankow
The Scripps Research Institute, Lajolla, CA 92037


INTRODUCTION: Proteins have exquisite three-dimensional structure. Their structures dictate the functions and interactions within the cell. Most of what we know about the structures of proteins comes from methods like x-ray crystallography, NMR and more recently cyro-EM. These methods are all in vitro methods that often look at proteins as single entities or as a protein complex. What is often missing is the in vivo context to the protein structure, e.g. what is the structure that exists in the cell. Several mass spectrometry-based methods are emerging to examine the 3D proteome or the conformations of proteins in their in vivo context.

OBJECTIVES: The primary objective of this work is to develop methods to measure the "structures" or confirmations of protein in the in vivo environment and to apply them to common diseases.

METHODS: We’ve developed a strategy to measure the surface accessibility of proteins in vivo that provides information about protein conformations and does so in a quantitative manner.

RESULTS: This method has been used to study protein misfolding diseases. This method has been applied to WT and mutant DF508 CFTR to examine structural changes induced by the mutation. A significant change has been observed at a critical interface between the NBD1 and NBD2 domains. This method is also being applied in Alzheimer's disease (AD)and Lewy body disease (LBD) to measure extent of conformational changes to proteins. This method is applied to AD and LBD patient brain tissue lysates and extensive protein comformational changes are observed.

CONCLUSIONS: Substantial changes beyond misfolded aBeta and Tau are observed and based on the molecular changes observed it is difficult to distinguish at the molecular level between advanced AD and LBD suggesting in neurodegenerative misfolding diseases the collapse of proteostasis has a similar endpoint. The studies of CFTR show a critical interface is disrupted between WT and DF508.

Financial Disclosure

SalaryyesThermofisher, CIL
Board MemberyesIntegrated Proteomics
Stockyes Integrated Proteomics
IP RoyaltyyesUniversity of Washington

Planning to mention or discuss specific products or technology of the company(ies) listed above: