Publications

For the most recent and complete list of publications, please see my Google Scholar profile or ResearchGate.

* Indicates first or corresponding authorship.

[44] Zhenzhou Q. et al., Sljoka A.*, Kitao A., Prosser S. 19F NMR Studies of the Conformational Ensemble and Allosteric Network of the Fluorotryptophan-enriched Adenosine A2A Receptor. PNAS, 2026. DOI: https://doi.org/10.1073/pnas.2525502123

[43] Colyer A., Wolf E., Lento C., Ustav Jr. M., Sljoka A.*, Wilson D.J. Allostery Links hACE2 Binding, Pan-variant Neutralization and Helical Extension in the SARS-CoV-2 Spike Protein. JOURNAL OF MOLECULAR BIOLOGY, 437(17):169232, 2025.

[42] Wang L., Tučs A., Ding S., Tsuda K.*, Sljoka A.* HDXRank: A Deep Learning Framework for Ranking Protein Complex Predictions with Hydrogen-Deuterium Exchange Data. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2025. DOI: 10.1021/acs.jctc.5c00175. Note: Front cover of JCTC.

[41] Picard L.-P. et al., Tučs A., Tsuda K., Kitao A., Sljoka A.*, Prosser S.P. Balancing Promiscuity and Selectivity: Determining Factors Governing G Protein Selectivity and Efficacy for the Adenosine A2A Receptor. NATURE CHEMICAL BIOLOGY, 2024.

[40] Suleiman M., Frere G.A., Törner R., Tabunar L., Bhole G.V., Taverner K., Tsuchimura N., Pichugin D., Lichtenecker R.J., Vozny O., Gunning P., Arthanari H., Sljoka A., Prosser R.S. Characterization of Conformational States of the Homodimeric Enzyme Fluoroacetate Dehalogenase by 19F-13C Two-Dimensional NMR. RSC CHEMICAL BIOLOGY, 5, 1214-1218, 2024. DOI: 10.1039/D4CB00176A.

[39] Kozome D., Sljoka A., Laurino P. Beyond the Active Site: The Addition of a Remote Loop Reveals a New Complex Biological Function for Chitinase Enzymes. NATURE COMMUNICATIONS, 15(1), 3227, 2024.

[38] Huang K., Rahmatullah R., Pandey A., Sunahara R., Ernst O., Sljoka A.*, Prosser R.S. Mapping the Stimulatory G Protein Conformational Landscape. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 30, 502-511, 2023.

[37] Baksh K.A., Augustine J., Sljoka A.*, Prosser R.S., Zamble D.B. Mechanistic Insights into the Nickel-Dependent Allosteric Response of the Helicobacter pylori NikR Transcription Factor. JOURNAL OF BIOLOGICAL CHEMISTRY, 102785, 2023.

[36] Besaw J.E., Reichenwallner J., De Guzman P. et al., Sljoka A.*, Miller R.J.D., Ernst O.P. Low pH Structure of Heliorhodopsin Reveals Chloride Binding Site and Intramolecular Signaling Pathway. SCIENTIFIC REPORTS, 12, 13955, 2022.

[35] Tučs A., Tsuda K., Sljoka A.* Probing Dynamics of Antibodies with Geometric Dynamics Simulations and Search Algorithms. METHODS IN MOLECULAR BIOLOGY, Computer-Aided Computational Design, 125-139, 2022.

[34] Kumawat N. et al., Sljoka A.*, Chakraborty A. Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex. MOLECULES, 27, 799, 2022.

[33] Huang S.K. et al., Sljoka A., Prosser R.S. Allosteric Modulation of the Adenosine A2A Receptor by Cholesterol. ELIFE, 11:e73901, 2022.

[32] Dasa J.K., Sund G.Q., Sljoka A., Chakraborty A. Mutation-Induced Long-Range Allosteric Interactions in the Spike Protein Determine Infectivity of SARS-CoV-2 Emerging Variants. ACS OMEGA, 6, 46, 31305-31320, 2021.

[31] Fowler N., Sljoka A.*, Williamson M.P. The Accuracy of NMR Structures in Protein Data Bank. STRUCTURE, 29(12), 1430-1439.e2, 2021.

[30] Huang S.K., Pandey A., Tran D.T., Villanueva N.L., Kitao A., Sunahara R.K., Sljoka A.*, Prosser R.S. Delineating the Conformational Landscape of the Adenosine A2A Receptor During G Protein Coupling. CELL, 184(7), 1884-1894.e14, 2021.

[29] Fowler N., Sljoka A.*, Williamson M.P. A Method for Validating the Accuracy of NMR Protein Structures. NATURE COMMUNICATIONS, 11, 6321, 2020.

[28] Bera S., Rashid M., Medvinsky A.B., Sun G.Q., Li B.L., Acquisti C., Sljoka A., Chakraborty A. Allosteric Regulation of Glutamate Dehydrogenase Deamination Activity. SCIENTIFIC REPORTS, 10, 16523, 2020.

[27] Rashid M., Bera S., Sljoka A., Chakraborty A. Feedforward Control of Plant Nitrate Transporter NRT1.1 Biphasic Adaptive Activity. BIOPHYSICAL JOURNAL, 2020.

[26] Mehrabi P., Di Pietrantonio C., Kim T.H., Sljoka A., Taverner K., Ing C., Pomès R., Pai E.F., Prosser R.S. Substrate-Based Allosteric Regulation of a Homodimeric Enzyme. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 141(29), 11540-11556, 2019.

[25] Ye L., Neale C., Sljoka A., Pichugin D., Tsuchimura N., Ernst O.P., Sunahara R., Prosser S. Bidirectional Regulation of the A2A Adenosine G Protein-Coupled Receptor by Physiological Cations. NATURE COMMUNICATIONS, 9:1372, 2018.

[24] Jeliazkov J.R., Sljoka A.*, Kuroda D., Tsuchimura N., Katoh N., Tsumoto K., Gray J.J. Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification. FRONTIERS IN IMMUNOLOGY, 9, 413, 2018.

[23] Deng B., Zhu S., Macklin A.M., Xu J., Lento C., Sljoka A., Wilson D. Suppressing Allostery in Epitope Mapping Experiments Using Millisecond Hydrogen-Deuterium Exchange Mass Spectrometry. MABS, 10(1), 2017.

[22] Kim T., Mehrabi P., Sljoka A., Ing C., Bezginov A., Pomès R., Prosser S., Pai E. The Role of Dimer Asymmetry and Protomer Dynamics in Enzyme Catalysis. SCIENCE, 355, 262, 2017.

[21] Higashikawa Y., Katoh N., Kobayashi Y., Sljoka A. Characterizing Redundant Rigidity and Redundant Global Rigidity of Body-Hinge Graphs. INFORMATION PROCESSING LETTERS, 116(2), 175-178, 2016.

[20] Zhu S., Shala A., Bezginov A., Sljoka A., Audette G., Wilson D. Hyperphosphorylation of Intrinsically Disordered Tau Protein Induces an Amyloidogenic Shift in Its Conformational Ensemble. PLOS ONE, 10(3), 2015.

[19] Nixon A., Schulze B., Sljoka A.*, Whiteley W. Symmetry Adapted Assur Decompositions. SYMMETRY, 6(3), 516-550, 2014.

[18] Porta J.M., Ros L., Schulze B., Sljoka A.*, Whiteley W. On the Symmetric Molecular Conjectures. BOOK CHAPTER / CONFERENCE VOLUME, Computational Kinematics, Vol. 15 of Mechanisms and Machine Science, pp. 175-184, Springer, 2014.

[17] Schulze B., Sljoka A., Whiteley W. How Does Symmetry Impact the Flexibility of Proteins? PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A, 372, 20120041, 2014.

[16] Sljoka A.*, Wilson D. Probing Protein Ensemble Rigidity and Predictions of Hydrogen-Deuterium Exchange. PHYSICAL BIOLOGY, 10, 056013, 2013.

[15] Shai O., Sljoka A.*, Whiteley W. Directed Graphs, Decompositions and Spatial Decompositions. DISCRETE APPLIED MATHEMATICS, 161, 3028-3047, 2013.

[14] Sljoka A.* Structural and Functional Analysis of Proteins Using Rigidity Theory, Sublinear Computation Paradigm. Book: SPRINGER NATURE, 2022.

[13] Katoh N., Shibuya T., Sljoka A. et al. Sublinear Computation Paradigm: Algorithmic Revolution in the Big Data Era. Book: SPRINGER NATURE, 2022.

[12] Sljoka A.* Probing Allosteric Communication with Long-Range Rigidity Transmission Across Protein Networks. Book Chapter: METHODS IN MOLECULAR BIOLOGY, vol. 2253, Humana, New York, NY, 2021.

[11] Tsuchimura S., Sljoka A. Distributed Computation for Protein Structure Analysis. INCOS-2018, Lecture Notes in Data Engineering and Communication Technologies Series, Springer, 2018.

[10] Sljoka A.*, Saitoh T. Validation of NMR Protein Structures Using Rigidity Theory and Chemical Shifts. JOURNAL OF INFORMATION PROCESSING INFORMATION, Research Report Bioinformatics, 2018.

[9] Cheng S.W., Yuya H., Katoh N., Sljoka A. Characterizing Minimal Rigidity of Square-Grid Frameworks with Holes. 10th Japanese-Hungarian Symposium on Discrete Mathematics and Its Applications, 2017.

[8] Hahn E., Sljoka A., Muller A. Applications of Constraint Graphs and Assur Groups in Mechanism Analysis and Synthesis. ASME IDETC2017, Cleveland, Ohio, USA, 2017.

[7] Higashikawa Y., Katoh N., Kobayashi Y., Sljoka A. Characterizing Redundant Rigidity and Redundant Global Rigidity of Body-Hinge Graphs. INFORMATION PROCESSING LETTERS, 116(2), 175-178, 2016.

[6] Sljoka A.*, Shai O., Whiteley W. Checking Mobility and Decomposition of Linkages via Pebble Game Algorithm. ASME IDETC/CIE 2011, Washington, DC, USA, 2011.

[5] Sljoka A.*, Bezginov A. Predicting Hinge Motions and Allostery Using Rigidity Theory. International Conference on Applied Mathematics, Modeling and Computational Science, Volume 1368, pp. 167-170, Waterloo, Canada, 2011.

[4] Schulze B., Sljoka A., Whiteley W. Protein Flexibility of Dimers: Do Symmetric Motions Play Role in Allosteric Interactions? International Conference on Applied Mathematics, Modeling and Computational Science, Volume 1368, pp. 135-138, Waterloo, Canada, 2011.

[3] Sljoka A. Counting for Rigidity, Flexibility and Extensions via the Pebble Game Algorithm – Hinge Predictions and Other Biological Applications. Third Canadian Student Conference on Biomedical Computing, 2008. Note: Second prize.

[2] Sljoka A. Algorithms in Rigidity Theory with Applications to Protein Flexibility and Mechanical Linkages. PhD Dissertation, York University, Toronto, 2012. Supervisor: Walter Whiteley.

[1] Sljoka A. Counting for Rigidity, Flexibility and Extensions via the Pebble Game Algorithm. Master’s Thesis, York University, Toronto, 2006. Note: Best Thesis Prize.