scholarly journals Effects of Ethanol on Conformational Changes of Akt Studied by Chemical Cross-Linking, Mass Spectrometry, and 18O Labeling

2011 ◽  
Vol 7 (2) ◽  
pp. 387-394 ◽  
Author(s):  
Bill X. Huang ◽  
Hee-Yong Kim
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Cross Linking ◽  
18O Labeling ◽  
Chemical Cross Linking

scholarly journals Probing conformational changes of human serum albumin due to unsaturated fatty acid binding by chemical cross-linking and mass spectrometry

2005 ◽  
Vol 387 (3) ◽  
pp. 695-702 ◽  
Author(s):  
Bill X. HUANG ◽  
Chhabil DASS ◽  
Hee-Yong KIM
Keyword(s):  
Mass Spectrometry ◽  
Fatty Acids ◽  
Fatty Acid ◽  
Human Serum Albumin ◽  
Serum Albumin ◽  
Human Serum ◽  
Conformational Changes ◽  
Cross Linking ◽  
X Ray ◽  
Chemical Cross Linking

Mass spectrometry with chemical cross-linking was used to probe the conformational changes of HSA (human serum albumin) in solution on interaction with monounsaturated OA (oleic acid) or polyunsaturated AA (arachidonic acid) or DHA (docosahexaenoic acid). Fatty acid-free or -bound HSA was modified with lysine-specific cross-linkers and digested with trypsin. Cross-linked peptides were analysed by nano-electrospray ionization MS to localize the sites of cross-linking. Our data indicated that a local conformational change involving movement of the side chains of Lys-402 of subdomain IIIA or Lys-541 of subdomain IIIB occurred upon binding of all three fatty acids. Our data also indicated that the side chains of Lys-205 (IIA) and Lys-466 (IIIA) moved closer towards each other upon binding AA or DHA, but not OA, suggesting that the conformations of HSA when bound to mono- and poly-unsaturated fatty acids are distinctively different. While these observations agreed with previous X-ray crystallographic studies, the distances between ε-amino groups of most cross-linked lysine pairs were shorter than the crystal structure predicted, possibly reflecting a discrepancy between the solution and crystal structures. This method can serve as a useful complement to X-ray crystallography, particularly in probing the structure of a protein in solution.

Monitoring Conformational Changes in Protein Complexes Using Chemical Cross-Linking and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry: The Effect of Calcium Binding on the Calmodulin—Melittin Complex

2007 ◽  
Vol 13 (4) ◽  
pp. 281-290 ◽  
Author(s):  
Petr Novak ◽  
Vladimir Havlicek ◽  
Peter J. Derrick ◽  
Kyle A. Beran ◽  
Sajid Bashir ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Fourier Transform ◽  
Conformational Changes ◽  
Calcium Binding ◽  
Cyclotron Resonance ◽  
Structural Changes ◽  
Cross Linking ◽  
Ion Cyclotron Resonance ◽  
Ion Cyclotron ◽  
Chemical Cross Linking

Calmodulin is an EF hand calcium binding protein. Its binding affinities to various protein/peptide targets often depend on the conformational changes induced by the binding of calcium. One such target is melittin, which binds tightly to calmodulin in the presence of calcium, and inhibits its function. Chemical cross-linking combined with Fourier transform ion cyclotron resonance mass spectrometry has been employed to investigate the coordination of calmodulin and melittin in the complex at different concentrations of calcium. This methodology can be used to monitor structural changes in proteins induced by ligand binding and to study the effects these changes have on non-covalent interactions between proteins. Cross-linking results indicate that the binding place of the first melittin in the calcium-free calmodulin form is the same as in the calcium-loaded calmodulin/melittin complex.

scholarly journals Comparative cross-linking and mass spectrometry of an intact F-type ATPase suggest a role for phosphorylation

2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Carla Schmidt ◽  
Min Zhou ◽  
Hazel Marriott ◽  
Nina Morgner ◽  
Argyris Politis ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Mass Spectra ◽  
Nucleotide Binding ◽  
Cross Linking ◽  
Spinach Chloroplasts ◽  
Cross Links ◽  
Chemical Cross Linking

Abstract F-type ATPases are highly conserved enzymes used primarily for the synthesis of ATP. Here we apply mass spectrometry to the F1FO-ATPase, isolated from spinach chloroplasts, and uncover multiple modifications in soluble and membrane subunits. Mass spectra of the intact ATPase define a stable lipid ‘plug’ in the FO complex and reveal the stoichiometry of nucleotide binding in the F1 head. Comparing complexes formed in solution from an untreated ATPase with one incubated with a phosphatase reveals that the dephosphorylated enzyme has reduced nucleotide occupancy and decreased stability. By contrasting chemical cross-linking of untreated and dephosphorylated forms we show that cross-links are retained between the head and base, but are significantly reduced in the head, stators and stalk. Conformational changes at the catalytic interface, evidenced by changes in cross-linking, provide a rationale for reduced nucleotide occupancy and highlight a role for phosphorylation in regulating nucleotide binding and stability of the chloroplast ATPase.

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

Three Dimensional Structures of Proteins and Protein Complexes from Chemical Cross-Linking and Mass Spectrometry: A Biochemical and Computational Overview

2006 ◽  
Vol 3 (1) ◽  
pp. 1-21 ◽  
Author(s):  
Bulbul Chakravarti ◽  
Steven Lewis ◽  
Deb Chakravarti ◽  
Alpan Raval
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Cross Linking ◽  
Chemical Cross Linking

Characterization of In Vivo Protein Complexes via Chemical Cross-Linking and Mass Spectrometry

2021 ◽  
Author(s):  
Yuefan Wang ◽  
Yingwei Hu ◽  
Naseruddin Höti ◽  
Lan Huang ◽  
Hui Zhang
Keyword(s):  
Mass Spectrometry ◽  
Protein Complexes ◽  
Cross Linking ◽  
Chemical Cross Linking
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