PUBLICATIONS

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Independent work at Univ of Guelph :

Vahidi Lab trainees and staff scientists are underlined.

Y. Feng, M. M. Goncalves, Y. Jitkova, A. F. A. Keszei, Y. Yan, C. Sarathy, J. St-Germain, T. M. G. Kenney, M. Tcheng, V. Trudel, R. S. Mancini, R. Upadhyay, R. Hurren, M. Gronda, M. Schultz, K. Soriano, K. Lees, N. C. Pomroy, S. Q. W. Currie, G. G. Privé, M. A. Reed, A. K. Yudin, L. Z. Penn, C. H. Arrowsmith, B. Raught, M. T. Mazhab-Jafari, S. Vahidi*, A. D. Schimmer* “Serine phosphorylation facilitates protein degradation by the human mitochondrial ClpXP protease” Proc. Natl. Acad. Sci. U.S.A. 122 (5) e2422447122 (2025) * corresponding author

 
 

M. K. Black, A. S. Kim, C. Y Chen, M. M. Goncalves, S. Waseem, S. Vahidi*, and R. Huang “Characterization of conformational dynamics and allostery of the catalytic domain of human mitochondrial YME1L protease” bioRxiv (2025) * corresponding author

A. Plourde, J. C. Ogata-Bean, and S. Vahidi* “Probing the structural heterogeneity of Pup ligase PafA using H/D exchange mass spectrometry” bioRxiv (2024) * corresponding author

M. Goncalves^, A. B. Uday^, T. J. B. Forrester^, S. Q. W. Currie1, A. S. Kim, Y. Feng, Y. Jitkova, A. Velyvis, R. W. Harkness*, M. S. Kimber*, A. D. Schimmer*, N. Zeytuni*, S. Vahidi* “Mechanism of allosteric activation in human mitochondrial ClpP protease“ bioRxiv (2024) ^co-first authorship * corresponding author

K. R. Vosper, A. Velyvis*, S. Vahidi*, “HDgraphiX: A web-based tool for visualization of hydrogen deuterium exchange mass spectrometry data” bioRxiv (2024)* corresponding author | Check out HDgraphiX.net

HDgraphiX.net landing page

An example data output from HDgraphiX.net

M. Turner^, A. B. Uday^, A. Velyvis, E. Rennella, N. Zeytuni*, S. Vahidi*, “Structural basis for allosteric regulation of the proteasome core particle” bioRxiv (2024) ^co-first authorship * corresponding author

M. L. Nosella, T. H. Kim, S. K. Huang, R. W. Harkness, M. M. Goncalves, A. Pan, M. Tereshchenko, S. Vahidi, J. L. Rubinstein, H. O. Lee, J. D. Forman-Kay, L. E. Kay, “Poly-ADP-ribosylation enhances nucleosome dynamics and organizes DNA damage repair components within biomolecular condensates”, Molecular Cell, 84 (3), 429-446 (2024).

 
 

B. T. V. Davis, A. Velyvis*, and S. Vahidi*, “Fluorinated ethylamines as electrospray-compatible neutral pH buffers for native mass spectrometry”, Analytical Chemistry, 95 (48) 17525-17532 (2023). ACS Editors’ Choice and Cover Feature, U of G news release * corresponding author

XFEA Brad Analytical Chemistry Cover

J. M. Di Trani, A. A. Gheorghita, M. Turner, P. Brzezinski, P. Ädelroth, S. Vahidi, P. L. Howell, and J. L. Rubinstein, “Structure of the bc1-cbb3 respiratory supercomplex from Pseudomonas aeruginosa” Proc. Natl. Acad. Sci. U.S.A. 120 (40) e2307093120 (2023).

 
Structure of the bc1-cbb3 respiratory supercomplex from Pseudomonas aeruginosa
 

Y. Liang, A. Plourde, S. A. Bueler, J. Liu, P. Brzezinski*, S. Vahidi*, and J. L. Rubinstein*, “Structure of mycobacterial respiratory Complex I” Proc. Natl. Acad. Sci. U.S.A. 120 (13) e2214949120 (2023).* corresponding author

See SickKids Hospital and U of Guelph news release.

 
Structure of mycobacterial respiratory Complex I
 

Graduate and postdoctoral work:

Z. A. Ripstein*, S. Vahidi*, J. L. Rubinstein, and L. E. Kay, “A pH-Dependent Conformational Switch Controls N. meningitidis ClpP Protease Function” J. Am. Chem. Soc. 142, 20519–20523 (2020). * Co-first authorship and corresponding author

 
A pH-Dependent Conformational Switch Controls N. meningitidis ClpP Protease Function
 

S. Vahidi*, Z. A. Ripstein*, J. B. Juravsky, E. Rennella, A. L Goldberg, A. K. Mittermaier, J. L. Rubinstein, and L. E. Kay, “An allosteric switch regulates Mycobacterium tuberculosis ClpP1P2 protease function as established by cryo-EM and methyl-TROSY NMR” Proc. Natl. Acad. Sci. U.S.A. 117, 5895-5906 (2020).  * Co-first authorship.

 
Structures of active and inactive MtClpP1P2, with the corresponding sizes of the complexes. A typical NMR spectrum is shown as well.
 

Read commentary by Dr. Andrew Byrd, Structural Biophysics Laboratory, National Cancer Institute, Frederick, MD, USA, in PNAS “Could confounding the allosteric communication of biotic machinery be an alternative path to antibiotics?” DOI: 10.1073/pnas.2002666117

Z. A. Ripstein*, S. Vahidi*, W. A. Houry, J. L. Rubinstein, and L. E. Kay, “A processive rotary mechanism couples substrate unfolding and proteolysis in the ClpXP degradation machinery” eLife 9:e52158, DOI: 10.7554/eLife.52158 (2020). * Co-first authorship and corresponding author

 
Cryo-EM structure of the NmClpXP complex.
 

Read Insight Article by Profs. Francis TF Tsai and Christopher Hill, Baylor College of Medicine & University of Utah School of Medicine, US in eLife “Protein Unfolding: Same structure, different mechanisms?” DOI: 10.7554/eLife.56501

M. F. Mabanglo*, E. Leung*, S. Vahidi*, T. V. Seraphim*, B. T. Eger, S. Bryson, V. Bhandari, J. L. Zhou, Y. Mao, K. Rizzolo, M. M Barghash, J. D Goodreid, S. Phanse, M. Babu, L. RS. Barbosa, C. H. Ramos, R. A. Batey, L. E. Kay, E. F. Pai, W. A. Houry, “ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores” Commun. Biol. 2, 410 (2019). * Co-first authorship.

Crystal structures of ClpP in free and bound forms highlight the state of the gating residues.

S. Vahidi*, Z. A. Ripstein*, M. Bonomi, T. Yuwen, M. F. Mabanglo, J. B. Juravsky, K. Rizzolo, A. Velyvis, W. A. Houry, M. Vendruscolo, J. L. Rubinstein, and L. E. Kay, “Reversible inhibition of the ClpP protease via an N-terminal conformational switch” Proc. Natl. Acad. Sci. U.S.A. 115, E6447-E6456 (2018).  * Co-first authorship.

 
The introduction of a V7A mutation in SaClpP leads to the formation of a non-canonical conformation, presented along with the corresponding methyl-TROSY NMR spectrum.
 

A. Murcia-Rios*, S. Vahidi*, S. D. Dunn, and L. Konermann, “Evidence for a Partially Stalled Gamma Rotor in F1-ATPase from H/D Exchange Experiments and Molecular Dynamics Simulations” J. Am. Chem. Soc. 140, 14860-14869(2018). * Co-first authorship.

 
Schematic representation of the FoF1 ATP synthase system in the cell membrane is presented.
 

C. S. Fast, S. Vahidi, and L. Konermann, “Changes in Enzyme Structural Dynamics Studied by Hydrogen Exchange-Mass Spectrometry: Ligand Binding Effects or Catalytically Relevant Motions?” Anal. Chem. 89, 13326-13333 (2017).

 
HDX cannot distinguish between catalytically active and dead enzymes.
 

S. C. Mandacaru, L. H.F. do Vale, S. Vahidi, Y. Xiao, O. S Skinner, C. A. O. Ricart, N. L. Kelleher, M. V. de Sousa, and L. Konermann, “Characterizing the Structure and Oligomerization of Major Royal Jelly Protein 1 (MRJP1) by Mass Spectrometry and Complementary Biophysical Tools” Biochemistry 56, 1645-1655 (2017).

 
Schematic representation of the MRJP protein system with key residues highlighted.
 

S. Vahidi, Y. Bi, S. D. Dunn, and L. Konermann, “Load-dependent destabilization of the γ-rotor shaft in FOF1 ATP synthase revealed by H/D-exchange mass spectrometry”Proc. Natl. Acad. Sci. U.S.A. 113, 2412-2417 (2016).

Schematic representation of the FoF1 ATP synthase system, along with example peptide mass spectra of key regions.

S. Vahidi, and L. Konermann, “Probing the Time Scale of FPOP (Fast Photochemical Oxidation of Proteins): Radical Reactions Extend Over Tens of Milliseconds” J. Am. Soc. Mass Spectrom. 27, 1156-1164 (2016).

 
Measurement of radical lifetimes using an optical device highlights the difference between measured and expected FPOP kinetics.
 

Y. Sun, S. Vahidi, M. A. Sowole, and L. Konermann, “Protein Structural Studies by Traveling Wave Ion Mobility Spectrometry: A Critical Look at Electrospray Sources and Calibration Issues” J. Am. Soc. Mass Spectrom. 27, 31-40 (2016).

 
Collision cross section of a typical protein ion in the gas phase is displayed.
 

X. Yue *, S. Vahidi *, and L. Konermann, “Insights into the Mechanism of Protein Electrospray Ionization from Salt Adduction Measurements” J. Am. Soc. Mass Spectrom. 25, 1322-1331 (2014) * Co-first authorship.

 
Schematic showing the mechanism of salt reduction during the ESI process.
 

 L. Konermann, S. Vahidi, and M. A. Sowole, “Mass Spectrometry Methods for Studying Structure and Dynamics of Biological Macromolecules” Anal. Chem. 86, 213-232 (2014).

Title page of a scientific paper linked above.

S. Vahidi, B. B. Stocks, and L. Konermann, “Partially Disordered Proteins Studied by Ion Mobility-Mass Spectrometry: Implications for the Preservation of Solution Phase Structure in the Gas Phase” Anal. Chem. 85, 10471-10478 (2013).

Collision cross sections of representative protein conformations.

S. Vahidi, B. B. Stocks, Y. Liaghati-Mobarhan, and L. Konermann, “Submillisecond Protein Folding Events Monitored by Rapid Mixing and Mass Spectrometry-Based Oxidative Labeling” Anal. Chem. 85, 8618-8625 (2013).Cover Feature.

 
A UV laser is illuminating proteins as they fold on various timescales.
 
Cover image shows a protein in solution attacked by radicals.

J. B. Hedges, S. Vahidi, X. Yue, and L. Konermann, “Effects of Ammonium Bicarbonate on the Electrospray Mass Spectra of Proteins: Evidence for Bubble-Induced Unfolding” Anal. Chem. 85, 6469-6476 (2013).

Formation of droplets, as seen in beer, leads to the production of high charge states in ESI-MS spectra.

L. Konermann, E. Ahadi, A. D. Rodriguez, and S. Vahidi, "Unraveling The Mechanism of Electrospray Ionization" Anal. Chem. 85, 2-9 (2013). Cover Feature. 4th Most Read Article in Anal. Chem. from 2013.

 
Schematic showing the IEM, CRM, and CEM mechanism of the ESI process.
 
Cover image shows a protein emerging from an ESI droplet, with a few mass spectra in the background.

S. Vahidi, B. B. Stocks, Y. Liaghati-Mobarhan, and L. Konermann, "Mapping pH-Induced Protein Structural Changes Under Equilibrium Conditions by Pulsed Oxidative Labeling and Mass Spectrometry" Anal. Chem. 84, 9124-9130 (2012).

Differences in the levels of protein oxidation for myoglobin at pH 2 and 7.

H. Ebrahimzadeh, N. Tavassoli, O. Sadeghi, M. M. Amini, S. Vahidi, S. M. Aghigh, and E. Moazzen, “Extraction of Nickel from Soil, Water, Fish, and Plants on Novel Pyridine-Functionalized MCM-41 and MCM-48 Nanoporous Silicas and Its Subsequent Determination by FAAS” Food Anal. Method. 5, 1070-1078 (2012).

S. S. H. Davarani, N. Sheijooni-Fumani, A. Morteza Najarian, M. A. Tabatabaei, and S. Vahidi, “Preconcentration of Lead in Sugar Samples by Solid Phase Extraction and Its Determination by Flame Atomic Absorption Spectrometry” Am. J. Anal. Chem. 2, 626-631 (2011).

S. S. H. Davarani, N. Sheijooni-Fumani, S. Vahidi, M. A. Tabatabaei, and H. Arvin-Nezhad, “Electro-organic Synthesis of New pyrimidine and Uracil Derivatives” J. Heterocycle Chem. 47, 40-45 (2010).