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Engen JR, Wales TE, Chen S, Marzluff EM, Hassell KM, Weis DD, Smithgall TE. Partial cooperative unfolding in proteins as observed by hydrogen exchange mass spectrometry. INT REV PHYS CHEM 2013; 32:96-127. [PMID: 23682200 DOI: 10.1080/0144235x.2012.751175] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Many proteins do not exist in a single rigid conformation. Protein motions, or dynamics, exist and in many cases are important for protein function. The analysis of protein dynamics relies on biophysical techniques that can distinguish simultaneously existing populations of molecules and their rates of interconversion. Hydrogen exchange (HX) detected by mass spectrometry (MS) is contributing to our understanding of protein motions by revealing unfolding and dynamics on a wide timescale, ranging from seconds to hours to days. In this review we discuss HX MS-based analyses of protein dynamics, using our studies of multi-domain kinases as examples. Using HX MS, we have successfully probed protein dynamics and unfolding in the isolated SH3, SH2 and kinase domains of the c-Src and Abl kinase families, as well as the role of inter- and intra-molecular interactions in the global control of kinase function. Coupled with high-resolution structural information, HX MS has proved to be a powerful and versatile tool for the analysis of the conformational dynamics in these kinase systems, and has provided fresh insight regarding the regulatory control of these important signaling proteins. HX MS studies of dynamics are applicable not only to the proteins we illustrate here, but to a very wide range of proteins and protein systems, and should play a role in both classification of and greater understanding of the prevalence of protein motion.
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Affiliation(s)
- John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115 USA
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Species restriction of Herpesvirus saimiri and Herpesvirus ateles: Human lymphocyte transformation correlates with distinct signaling properties of viral oncoproteins. Virus Res 2012; 165:179-89. [DOI: 10.1016/j.virusres.2012.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/06/2012] [Accepted: 02/16/2012] [Indexed: 01/05/2023]
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Sophocleous AM, Topp EM. Localized hydration in lyophilized myoglobin by hydrogen-deuterium exchange mass spectrometry. 2. Exchange kinetics. Mol Pharm 2012; 9:727-33. [PMID: 22352990 DOI: 10.1021/mp2004093] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Solid-state hydrogen-deuterium exchange with mass spectrometric analysis (ssHDX) is a promising method for characterizing proteins in amorphous solids. Though analysis of HDX kinetics is informative and well-established in solution, application of these methods to solid samples is complicated by possible heterogeneities in the solid. The studies reported here provide a detailed analysis of the kinetics of hydration and ssHDX for equine myoglobin (Mb) in solid matrices containing sucrose or mannitol. Water sorption was rapid relative to ssHDX, indicating that ssHDX kinetics was not limited by bulk water transport. Deuterium uptake in solids was well-characterized by a biexponential model; values for regression parameters provided insight into differences between the two solid matrices. Analysis of the widths of peptide mass envelopes revealed that, in solution, an apparent EX2 mechanism prevails, consistent with native conformation of the protein. In contrast, in mannitol-containing samples, a smaller non-native subpopulation exchanges by an EX1-like mechanism. Together, the results indicate that the analysis of ssHDX kinetic data and of the widths of peptide mass envelopes is useful in screening solid formulations of protein drugs for the presence of non-native species that cannot be detected by amide I FTIR.
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Affiliation(s)
- Andreas M Sophocleous
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, Indiana 47901, USA
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Keppel TR, Howard BA, Weis DD. Mapping Unstructured Regions and Synergistic Folding in Intrinsically Disordered Proteins with Amide H/D Exchange Mass Spectrometry. Biochemistry 2011; 50:8722-32. [DOI: 10.1021/bi200875p] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Theodore R. Keppel
- Department
of Chemistry and ‡Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, 1251 Wescoe Hall
Drive, Lawrence, Kansas 66045, United States
| | - Brent A. Howard
- Department
of Chemistry and ‡Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, 1251 Wescoe Hall
Drive, Lawrence, Kansas 66045, United States
| | - David D. Weis
- Department
of Chemistry and ‡Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, 1251 Wescoe Hall
Drive, Lawrence, Kansas 66045, United States
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Chen S, Brier S, Smithgall TE, Engen JR. The Abl SH2-kinase linker naturally adopts a conformation competent for SH3 domain binding. Protein Sci 2007; 16:572-81. [PMID: 17327393 PMCID: PMC2203333 DOI: 10.1110/ps.062631007] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The core of the Abelson tyrosine kinase (c-Abl) is structurally similar to Src-family kinases where SH3 and SH2 domains pack against the backside of the kinase domain in the down-regulated conformation. Both kinase families depend upon intramolecular association of SH3 with the linker joining the SH2 and kinase domains for suppression of kinase activity. Hydrogen deuterium exchange (HX) and mass spectrometry (MS) were used to probe intramolecular interaction of the c-Abl SH3 domain with the linker in recombinant constructs lacking the kinase domain. Under physiological conditions, the c-Abl SH3 domain undergoes partial unfolding, which is stabilized by ligand binding, providing a unique assay for SH3:linker interaction in solution. Using this approach, we observed dynamic association of the SH3 domain with the linker in the absence of the kinase domain. Truncation of the linker before W254 completely prevented cis-interaction with SH3, while constructs containing amino acids past this point showed SH3:linker interactions. The observation that the Abl linker sequence exhibits SH3-binding activity in the absence of the kinase domain is unique to Abl and was not observed with Src-family kinases. These results suggest that SH3:linker interactions may have a more prominent role in Abl regulation than in Src kinases, where the down-regulated conformation is further stabilized by a second intramolecular interaction between the C-terminal tail and the SH2 domain.
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Affiliation(s)
- Shugui Chen
- Chemistry and Chemical Biology, The Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, Massachusetts 02115, USA
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Mitchell JL, Trible RP, Emert-Sedlak LA, Weis DD, Lerner EC, Applen JJ, Sefton BM, Smithgall TE, Engen JR. Functional characterization and conformational analysis of the Herpesvirus saimiri Tip-C484 protein. J Mol Biol 2006; 366:1282-93. [PMID: 17207813 PMCID: PMC2262936 DOI: 10.1016/j.jmb.2006.12.026] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2006] [Revised: 12/06/2006] [Accepted: 12/07/2006] [Indexed: 11/15/2022]
Abstract
Tyrosine kinase interacting protein (Tip) of Herpesvirus saimiri (HVS) activates the lymphoid-specific member of the Src family kinase Lck. The Tip:Lck interaction is essential for transformation and oncogenesis in HVS-infected cells. As there are no structural data for Tip, hydrogen-exchange mass spectrometry was used to investigate the conformation of a nearly full-length form (residues 1-187) of Tip from HVS strain C484. Disorder predictions suggested that Tip would be mostly unstructured, so great care was taken to ascertain whether recombinant Tip was functional. Circular dichroism and gel-filtration analysis indicated an extended, unstructured protein. In vitro and in vivo binding and kinase assays confirmed that purified, recombinant Tip interacted with Lck, was capable of activating Lck kinase activity strongly and was multiply phosphorylated by Lck. Hydrogen-exchange mass spectrometry of Tip then showed that the majority of backbone amide hydrogen atoms became deuterated after only 10 s of labeling. Such a result suggested that Tip was almost totally unstructured in solution. Digestion of deuterium-labeled Tip revealed some regions with minor protection from exchange. Overall, it was found that, although recombinant Tip is still functional and capable of binding and activating its target Lck, it is largely unstructured.
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Affiliation(s)
| | - Ronald P. Trible
- Molecular Genetics & Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Lori A. Emert-Sedlak
- Molecular Genetics & Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - David D. Weis
- Department of Chemistry, University of New Mexico, Albuquerque, NM 87131
| | - Edwina C. Lerner
- Molecular Genetics & Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - Jeremy J. Applen
- Department of Chemistry, University of New Mexico, Albuquerque, NM 87131
| | | | - Thomas E. Smithgall
- Molecular Genetics & Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261
| | - John R. Engen
- Department of Chemistry, University of New Mexico, Albuquerque, NM 87131
- Chemistry & Chemical Biology and The Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston, MA 02115
- *Address correspondence: John R. Engen, 341 Mugar Life Sciences, The Barnett Institute, Northeastern University, 360 Huntington Ave., Boston, MA 02115-5000,
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Weis DD, Wales TE, Engen JR, Hotchko M, Ten Eyck LF. Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2006; 17:1498-1509. [PMID: 16875839 DOI: 10.1016/j.jasms.2006.05.014] [Citation(s) in RCA: 176] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2006] [Revised: 05/24/2006] [Accepted: 05/24/2006] [Indexed: 05/11/2023]
Abstract
Proteins that undergo cooperative unfolding events display EX1 kinetic signatures in hydrogen exchange mass spectra. The hallmark bimodal isotope pattern observed for EX1 kinetics is distinct from the binomial isotope pattern for uncorrelated exchange (EX2), the normal exchange regime for folded proteins. Detection and characterization of EX1 kinetics is simple when the cooperative unit is large enough that the isotopic envelopes in the bimodal pattern are resolved in the m/z scale but become complicated in cases where the unit is small or there is a mixture of EX1 and EX2 kinetics. Here we describe a data interpretation method involving peak width analysis that makes characterization of EX1 kinetics simple and rapid. The theoretical basis for EX1 and EX2 isotopic signatures and the effects each have on peak width are described. Modeling of EX2 widening and analysis of empirical data for proteins and peptides containing purely EX2 kinetics showed that the amount of widening attributable to stochastic forward- and back exchange in a typical experiment is small and can be quantified. Proteins and peptides with both obvious and less obvious EX1 kinetics were analyzed with the peak width method. Such analyses provide the half-life for the cooperative unfolding event and the relative number of residues involved. Automated analysis of peak width was performed with custom Excel macros and the DEX software package. Peak width analysis is robust, capable of automation, and provides quick interpretation of the key information contained in EX1 kinetic events.
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Affiliation(s)
- David D Weis
- Department of Chemistry, University of New Mexico, Clark Hall 242, MSC03-2060, 87131-0001, Albuquerque, NM, USA
| | - Thomas E Wales
- Department of Chemistry, University of New Mexico, Clark Hall 242, MSC03-2060, 87131-0001, Albuquerque, NM, USA
| | - John R Engen
- Department of Chemistry, University of New Mexico, Clark Hall 242, MSC03-2060, 87131-0001, Albuquerque, NM, USA.
| | - Matthew Hotchko
- Department of Chemistry and Biochemistry and San Diego Supercomputer Center, University of California-San Diego, La Jolla, California, USA
| | - Lynn F Ten Eyck
- Department of Chemistry and Biochemistry and San Diego Supercomputer Center, University of California-San Diego, La Jolla, California, USA
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