PMID- 38431839
OWN - NLM
STAT- MEDLINE
DCOM- 20240320
LR  - 20240320
IS  - 2666-1667 (Electronic)
IS  - 2666-1667 (Linking)
VI  - 5
IP  - 1
DP  - 2024 Mar 15
TI  - Protocol for structural modeling of antibody to human leukocyte antigen 
      interaction using discovery and targeted cross-linking mass spectrometry.
PG  - 102927
LID - S2666-1667(24)00092-3 [pii]
LID - 10.1016/j.xpro.2024.102927 [doi]
LID - 102927
AB  - Cross-linking mass spectrometry (XL-MS) provides low-resolution structural 
      information to model protein structures. Here, we present a protocol to identify 
      cross-links of purified antibody binding to purified human leukocyte antigen 
      (HLA). We describe steps for using a discovery-based XL-MS approach followed by a 
      targeted XL-MS approach. We then detail procedures for using the identified 
      cross-links with other structural data for molecular docking of the antibody to 
      HLA. This protocol has applications for modeling the interacting structure of 
      purified antibody to antigen. For complete details on the use and execution of 
      this protocol, please refer to Ser et al.(1).
CI  - Copyright (c) 2024 The Author(s). Published by Elsevier Inc. All rights reserved.
FAU - Ser, Zheng
AU  - Ser Z
AD  - Functional Proteomics Laboratory, SingMass National Laboratory, Institute of 
      Molecular and Cell Biology, Agency for Science, Technology and Research (A *STAR), 
      Singapore 138673, Singapore. Electronic address: ser_zheng@imcb.a-star.edu.sg.
FAU - Gascoigne, Nicholas R J
AU  - Gascoigne NRJ
AD  - Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, 
      National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; 
      Immunology Translational Research Programme, Yong Loo Lin School of Medicine, 
      National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore.
FAU - MacAry, Paul A
AU  - MacAry PA
AD  - Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, 
      National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore; 
      Immunology Translational Research Programme, Yong Loo Lin School of Medicine, 
      National University of Singapore, 5 Science Drive 2, Singapore 117545, Singapore.
FAU - Sobota, Radoslaw M
AU  - Sobota RM
AD  - Functional Proteomics Laboratory, SingMass National Laboratory, Institute of 
      Molecular and Cell Biology, Agency for Science, Technology and Research (A *STAR), 
      Singapore 138673, Singapore. Electronic address: rmsobota@imcb.a-star.edu.sg.
LA  - eng
PT  - Journal Article
DEP - 20240302
PL  - United States
TA  - STAR Protoc
JT  - STAR protocols
JID - 101769501
RN  - 0 (Proteins)
RN  - 0 (Antibodies)
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Humans
MH  - Molecular Docking Simulation
MH  - *Proteins/metabolism
MH  - Mass Spectrometry/methods
MH  - *Antibodies
MH  - HLA Antigens
PMC - PMC10914520
OTO - NOTNLM
OT  - Antibody
OT  - Mass Spectrometry
OT  - Proteomics
OT  - Structural Biology
COIS- Declaration of interests The authors declare no competing interests.
EDAT- 2024/03/03 19:47
MHDA- 2024/03/20 06:45
PMCR- 2024/03/02
CRDT- 2024/03/03 12:36
PHST- 2023/10/24 00:00 [received]
PHST- 2023/12/20 00:00 [revised]
PHST- 2024/02/15 00:00 [accepted]
PHST- 2024/03/20 06:45 [medline]
PHST- 2024/03/03 19:47 [pubmed]
PHST- 2024/03/03 12:36 [entrez]
PHST- 2024/03/02 00:00 [pmc-release]
AID - S2666-1667(24)00092-3 [pii]
AID - 102927 [pii]
AID - 10.1016/j.xpro.2024.102927 [doi]
PST - ppublish
SO  - STAR Protoc. 2024 Mar 15;5(1):102927. doi: 10.1016/j.xpro.2024.102927. Epub 2024 
      Mar 2.