Amplifiable protein identification via residue-resolved barcoding and composition code counting  

作　　者：Weiming Guo Yuan Liu Yu Han Huan Tang Xinyuan Fan Chu Wang Peng R.Chen 

机构地区：[1]Synthetic and Functional Biomolecules Center,Beijing National Laboratory for Molecular Sciences,Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education,College of Chemistry and Molecular Engineering,Peking University,Beijing 100871,China [2]Peking-Tsinghua Center for Life Sciences,Academy for Advanced Interdisciplinary Studies,Peking University,Beijing 100871,China

出　　处：《National Science Review》2024年第7期199-211,共13页国家科学评论（英文版）

基　　金：supported by the National Key R&D Program of China(2022YFA1304700);Beijing Natural Science Foundation(Z200010);the National Natural Science Foundation of China(21937001,21925701,22137001,22321005,91753000 and 92153301);sponsored by the XPLORER PRIZE.

摘　　要：Ultrasensitive protein identification is of paramount importance in basic research and clinical diagnostics but remains extremely challenging.A key bottleneck in preventing single-molecule protein sequencing is that,unlike the revolutionary nucleic acid sequencing methods that rely on the polymerase chain reaction(PCR)to amplify DNA and RNA molecules,protein molecules cannot be directly amplified.Decoding the proteins via amplification of certain fingerprints rather than the intact protein sequence thus represents an appealing alternative choice to address this formidable challenge.Herein,we report a proof-of-concept method that relies on residue-resolved DNA barcoding and composition code counting for amplifiable protein fingerprinting(AmproCode).In AmproCode,selective types of residues on peptides or proteins are chemically labeled with a DNA barcode,which can be amplified and quantified via quantitative PCR.The operation generates a relative ratio as the residue-resolved‘composition code’for each target protein that can be utilized as the fingerprint to determine its identity from the proteome database.We developed a database searching algorithm and applied it to assess the coverage of the whole proteome and secretome via computational simulations,proving the theoretical feasibility of AmproCode.We then designed the residue-specific DNA barcoding and amplification workflow,and identified different synthetic model peptides found in the secretome at as low as the fmol/L level for demonstration.These results build the foundation for an unprecedented amplifiable protein fingerprinting method.We believe that,in the future,AmproCode could ultimately realize single-molecule amplifiable identification of trace complex samples without further purification,and it may open a new avenue in the development of next-generation protein sequencing techniques.

关 键 词：protein identification amplifiable fingerprinting residue-specific chemistry DNA barcoding composition code counting 

分 类 号：TP183[自动化与计算机技术—控制理论与控制工程]