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Protein structure characterization with mass spectrometry

Richard Kriwacki, Nichole Reisdorph, Gary Siuzdak
2004 Spectroscopy (Ottawa)  
Mass spectrometry is now commonly being used to determine both the primary and higher order structures of proteins.  ...  The basis for these investigations lies in the ability of mass analysis techniques to detect changes in protein conformation under differing conditions.  ...  Chemical cross-linking and chemical modification Other methods of probing higher-order structure include investigating the chemical reactivity of individual amino acids in a protein and chemical cross-linking  ... 
doi:10.1155/2004/407960 fatcat:cipizmlayrg3pfoa54bkq3dwki

Mass spectrometry for semi-experimental protein structure determination and modeling [article]

Gerhard Mayer
2020 arXiv   pre-print
We review the methodology and describe software programs supporting such integrated protein structure prediction approaches, making use of distance constraints got from mass spectrometry cross-linking  ...  Then we describe how mass spectrometry is useful for semi-experimental integrative protein structure determination.  ...  The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks.  ... 
arXiv:2003.00328v1 fatcat:er2hzplirjgenpwla6wresatce

Subject index

2004 Journal of the American Society for Mass Spectrometry  
characterization of thiols, 288 Tryptophan, protonated, gas phase reactions of, 65 Tyrosine, chemical cross-linking with lysine, 1604 Ultraviolet-MALDI matrices, liquid based, detection limits of proteins  ...  energy in, 48 Quadrupole tandem mass spectrometry (MS/MS), triple, in molecular characterization of thiols, 288 Quadrupole time-of-flight mass spectrometer, CID in, generating protein sequence tags by,  ... 
doi:10.1016/s1044-0305(04)00746-9 fatcat:7gg3qm3w5bblrphu6mnr3ygcbe

Editorial overview: Carbohydrates: Ménage à trois with glycosaminoglycans — a serious rendezvous, not a gag!

Ralf P Richter, Hugues Lortat-Jacob
2018 Current Opinion in Structural Biology  
They provide evidence that immobilized GAGs can form mechanically soft and swollen brushes that can be cross-linked by binding proteins.  ...  of the buiding blocks, sulfation pattern), the conformation and the dynamics of these molecules.  ... 
doi:10.1016/ pmid:30080481 fatcat:bj4gx6ebhzakxi2gfonfxfnrmm

Mass spectrometry of glycans

Liang Han, Catherine E. Costello
2013 Biochemistry (Moscow)  
They are involved in diverse roles such as molecular recognition, cell-cell and cell-matrix interactions, energy generation, and modification of protein conformations.  ...  Monosaccharides constitute oligosaccharides (2-10 units) Abstract-Powerful new strategies based on mass spectrometry are revolutionizing the structural analysis and profiling of glycans and glycoconjugates  ...  When linked to a specific site on a protein backbone, glycans can modify the structural properties of the protein, affecting its solubility and conformation.  ... 
doi:10.1134/s0006297913070031 pmid:24010834 pmcid:PMC4104780 fatcat:iddoudix3bgzzcmjhoe6ziu76e

Characterization of simple isomeric oligosaccharides and the rapid separation of glycan mixtures by ion mobility mass spectrometry

Jonathan P. Williams, Megan Grabenauer, Richard J. Holland, Catherine J. Carpenter, Mark R. Wormald, Kevin Giles, David J. Harvey, Robert H. Bateman, James H. Scrivens, Michael T. Bowers
2010 International Journal of Mass Spectrometry  
The ion mobility mass spectrometry techniques were used to separate the isomeric oligosaccharides and the glycan mixtures.  ...  of isomeric oligosaccharides and hydrazine-released N-linked glycans from various sources.  ...  Acknowledgments The support of the Department of Food and Rural Affairs, UK, is gratefully acknowledged (JHS and MTB) as is the National Science Foundation, USA (MTB) and the Oxford Glycobiology Institute  ... 
doi:10.1016/j.ijms.2009.08.006 fatcat:hdwtsgoyjndndhpnn77ogqceyu

Use of Proteinase K Nonspecific Digestion for Selective and Comprehensive Identification of Interpeptide Cross-links: Application to Prion Proteins

Evgeniy V. Petrotchenko, Jason J. Serpa, Darryl B. Hardie, Mark Berjanskii, Bow P. Suriyamongkol, David S. Wishart, Christoph H. Borchers
2012 Molecular & Cellular Proteomics  
Cross-linked proteins are usually digested with trypsin to generate cross-linked peptides, which are then analyzed by mass spectrometry.  ...  Chemical cross-linking combined with mass spectrometry is a rapidly developing technique for structural proteomics.  ...  For mass spectrometric determination of the crosslinking sites, the cross-linked protein is typically digested with proteolytic enzymes, and the peptides are examined by mass spectrometry.  ... 
doi:10.1074/mcp.m111.013524 pmid:22438564 pmcid:PMC3394941 fatcat:dz5qajqlozft5eq7qz3uxvasnq

Chemical cross-linking in the structural analysis of protein assemblies

Feixia Chu, Daniel T. Thornton, Hieu T. Nguyen
2018 Methods  
The chemical cross-linking approach has recently been revived by mass spectrometric analysis of the cross-linking reaction products.  ...  Selection of proper chemical cross-linking reagents, strategies for crosslinked peptide identification, and successful application of CXMS in structural characterization of proteins and protein complexes  ...  Acknowledgments This work was supported by grants from the UNH Collaborative Research Excellence (CoRE), National Science Foundation (CLF 1307367) and the National Institute of Health (R01 HD093783).  ... 
doi:10.1016/j.ymeth.2018.05.023 pmid:29857191 pmcid:PMC6051896 fatcat:sz7v2pmhxvglhexio6lswexzku

Characterization of protein glycosylation using chip-based infusion nanoelectrospray linear ion trap tandem mass spectrometry

Sheng Zhang, Dirk Chelius
2004 Journal of Biomolecular Techniques  
Mass spectrometry (MS) has the potential to revolutionize structural glycobiology and help in the understanding of how post-translation events such as glycosylation affect protein activities.  ...  of the linear ion trap and the extended analysis time provided by the ionization technique.  ...  We also thank Professor Jack Henion and Dr. Colleen Van Pelt for reviewing this manuscript and for providing helpful comments.  ... 
pmid:15190085 pmcid:PMC2291675 fatcat:sufg33gqwbemnnwzyqfpoys5ze

Page 549 of Journal of Mass Spectrometry Vol. 37, Issue 5 [page]

2002 Journal of Mass Spectrometry  
Proteins, Tissue Proteomics Unit, Bethesda, Md 20892, USA Dis Marker 2001 17 (4) 301 Intramolecular cross-linking experiments on cytochrome c and ribonuclease A using an isotope multiplet method Pearson  ...  : Characterization by proteolytic degradation of monoclonal antibody-bound antigen and mass spectrometry Michel S, Forest E, Petillot Y, Deleage G, Heuze-Vourch N, Courty Y, Lascoux D, Jolivet M, Jolivet  ... 

Amino Acid Proximities in Two Sup35 Prion Strains Revealed by Chemical Cross-linking

Shenq-Huey Wong, Chih-Yen King
2015 Journal of Biological Chemistry  
Intra-and intermolecular cross-linking were distinguished by tandem mass spectrometry analysis on fibers seeded from solutions containing equal amounts of 14 N-and 15 N-labeled protein.  ...  A, chain folding topology of the VL fiber constrained by cross-linking between residue 3 and 28 and residues 32 and 55.  ...  The cross-linking induced by UV irradiation was subsequently analyzed by tandem mass spectrometry.  ... 
doi:10.1074/jbc.m115.676379 pmid:26265470 pmcid:PMC4599010 fatcat:xib7f6meyfe33jqz4hmei3dbpq

In vivo Cross-Linking MS of the Complement System MAC Assembled on Live Gram-Positive Bacteria

Hamed Khakzad, Lotta Happonen, Guy Tran Van Nhieu, Johan Malmström, Lars Malmström
2021 Frontiers in Genetics  
Protein cross-linking combined with mass spectrometry (MS) and computational modeling is gaining increased recognition as a viable tool in protein interaction studies.  ...  Proteinprotein interactions are central in many biological processes, but they are challenging to characterize, especially in complex samples.  ...  Here, we applied a simplified version (see the Materials and Methods section for details) of the recently developed targeted cross-linking mass spectrometry (TX-MS) approach to study the formation of  ... 
doi:10.3389/fgene.2020.612475 pmid:33488677 pmcid:PMC7820895 fatcat:bfsuuo6f2fcdnm722lvxvqp6oa


Magdaléna Prokšová, Jiří Stulík, Klára Kubelková
2020 Military Medical Science Letters  
To increase their sensitivity and accuracy, these methods are commonly used in combinations, such as affinity purification and liquid chromatographymass spectrometry analysis, cross-linking together with  ...  liquid chromatography-mass spectrometry analysis, or stable isotope labeling with amino acids in cell culture with affinity purification.  ...  Protein complexes are purified (by immunopurification) and followed by enzymatic digestion and mass spectrometry analysis after cross-linking reaction.  ... 
doi:10.31482/mmsl.2020.010 fatcat:jlemtmdbvfa2pnc4uobdgqorxm

Eisosomes and Plasma Membrane Domain Formation

Agustina Olivera-Couto, Michelle Digman, Valentina Salzman, Milagros Mailhos, Enrico Gratton, Pablo S. Aguilar
2014 Biophysical Journal  
We then compare that information with that garnered from intrinsic tyrosine absorbance to understand the changes in structural conformations as a function of the mutation and lipid binding.  ...  Amots are adaptor proteins which coordinate signaling for cellular differentiation and proliferation. Their ACCH domain binds lipids with specificity leading to membrane deformation.  ...  Here, we describe an integrative approach to determine the topologies of heteromeric assemblies using structural information derived from native mass spectrometry (MS), proteomics and chemical cross-linking  ... 
doi:10.1016/j.bpj.2013.11.2636 fatcat:vaypbd6efvdxtmmpigcq6xlzeu

Lipidated apolipoprotein E4 structure and its receptor binding mechanism determined by a combined cross-linking coupled to mass spectrometry and molecular dynamics approach

Nicolas Henry, Eva-Maria Krammer, Florian Stengel, Quentin Adams, François Van Liefferinge, Ellen Hubin, Rui Chaves, Rouslan Efremov, Ruedi Aebersold, Guy Vandenbussche, Martine Prévost, Vincent Raussens (+2 others)
2018 PLoS Computational Biology  
Chemical cross-linking combined with mass spectrometry provided distance restraints, characterizing the three-dimensional organization of apoE4 molecules at the surface of lipidic nanoparticles.  ...  Overall, our results show how apoE4 adapts its conformation for the recognition of the low density lipoprotein receptor and we propose a novel mechanism of activation for apoE4 that is based on accessibility  ...  The advancement of chemical cross-linking and mass spectrometry for structural proteomics: from single proteins to protein interaction networks.  ... 
doi:10.1371/journal.pcbi.1006165 pmid:29933361 pmcid:PMC6033463 fatcat:up63t2cfbvatbkokwkf76vk5ky
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