PD Research Report for the 2016 year
Adnan Sljoka: Katoh Crest Big Data Project（Katoh Group, Graduate School of Science and Technology）
Research Theme: Applications of rigidity and algorithm protein function
April 1st, 2016 ~ June 30th, 2016

Dee understanding of protein function requires knowledge about its motions and dynamics,
which is critical in medicine and drug design. Advancements in the rigidity theory have led tofast computational predictions of flexibility/rigidity and protein motions. I have made anumber of key contributions to this field by developing various algorithms and methods forstudying a functionally critical protein motions. The methods provide novel andcomputationally efficient insights related to protein functions and their motions. This includes,
but is not limited to, protein allosteric interactions, predictions of hydrogen-deuterium
exchange, the role of intrinsically flexible proteins and others. We have obtained a number of
new results over the past year in allostery, redundant rigidity, and are continuing to work on
applications of rigidity to mechanical engineering.
Allosteric regulation of the protein function occurs when a binding event at one site of theprotein leads to changes in the conformation, dynamics, and shape of a distant functional site.
Allostery is a long-standing unsolved biological problems with direct implications inmedicine and drug design. In spite of its importance, the molecular mechanisms that give riseto allostery remain poorly understood. We have previously developed a novel
computationally fast rigidity-based allostery detection algorithm. Our method not only
provides an entirely new mechanistic view of allostery but it can quantify the strength ofallosteric signalling and detect the regions in the protein that are crucial for the allostericcommunication. This should eventually allow us to tackle the more difficult signalling eventsin the cell. Recently a key component of our research has been to link our predictions toexperimental data and at the same time seek novel insights on allosteric communication invarious proteins, such as enzymes, GPCRs and other allosteric proteins
We have recently been collaborating with a couple of biochemistry groups in University ofToronto, who have gathered various invaluable experimental data on enzyme dehalogenase
fluoroacetate. We have performed computational allostery predictions on several structures ofthis enzyme and the findings indicate that rigidity changes in the substrate binding pocket
propagate across to the regions in the other monomer, which is in line with experimental data.
This demonstrates the presence of rigidity-based allostery and its role in the function of thisenzyme. Moreover, we have recently performed the identification of allosteric pathway
between the two monomers and our predicting are in high coloration with experimentalevidence. Our findings may have wide encompassing consequences on understanding the roleof allostery in enzyme activation. We are continuing to explore the role of rigidity-based
allostery and collaborate with biochemists and understand how our predictions provide better
understanding of allostery.
We have also focused our attention on the G-protein coupled receptors (GPCRs). GPCRs are
the cell surface proteins which detect and govern enormous number of signaling processes
associated with vision, inflammation, neurotransmitters and hormones such as adrenaline,
dopamine and caffeine. Pharmacologically these drugs are the most common drug targets,with some estimates suggesting that more than 50% of the current drugs on the market aredesigned to target GPCRs. How these receptors transmit the allosteric signal across themembrane is still not well understood. To shed some light on the allosteric mechanism inGPCRs, we have recently presented our work on rigidity-based alloseric signalling at twoleading international conferences on GPCRs in Hawaii and Keystone. Our findings on a typeof GPCR called adenosine A2A receptor, which is a drug target for treatments ofinflammation, cancer, diabetes, infectious diseases and neuronal defect disorders, suggest thattransmissions of rigidity upon binding of adenosine A2A agonists (natural activating ligandsthat bind to GPCRs) are important for structural and conformational changes at the distant site
on GPCR responsible for binding a partner G protein. Moreover, the antagonist ligands(inactivating ligands) were found to contribute little or no rigidity-based allosterictransmission. We are also currently examining the role of rigidity-based allostery in A2A
receptor and how to identify the allosteric hotspot regions, where binding a ligand at a hotspot
region causes rigidity and conformational changes at the important functional G-protein
binding regions. The results we presented at GPCR conferences have resulted in a few key
collaborations, in particular with the Prof. Scott Prosser in University of Toronto andmembers of the Biozentrum group of Prof. Stephan Grzesiek at the University of Basel. This
group collects experimental evidence using NMR and mutation studies and should provide
rich data for corroborating the rigidity allosteric predictions. Moreover, we hope to be able tomap the allosteric pathway in the protein network responsible for transmitting the allostericsignals.
As we are proposing a general mechanism for allosteric communication in proteins and sincemost proteins are believed to function through allostery, the number of possible applications
and research directions is quite rich. As such, one directions we started to explore is ofengineering allosteric control of proteins (detection and design of new allosteric sites that alter
active site conformations and rigidity) by predicting regions in the protein that are inrigidity-based allosteric communication with the active sites. In collaboration with Andrew
Wooley at University of Toronto who uses light-switchable proteins to control proteinfunction, our initial results show that our predictions on the key translation initiation factor
protein 4E (a common cancer target protein) are in direct agreement with previously predicted
allosteric drug binding regions. Such collaboration is currently ongoing.

Papers 2016:[12] Zhu S., Shala A., Bezginov A., Sljoka A., Audette G. and Wilson D.,
Hyperphosphorylation of Intrinsically Disordered Tau Protein Induces an Amyloidogenic
Shift in Its Conformational Ensemble, PLoS ONE, 10(3), 2015.
Yuki Kobayashi, Yuya Higashikawa, Naoki Katoh, Adnan Sljoka:
Characterizing redundant rigidity and redundant global rigidity of body-hinge graphs. Inf.
Process. Lett. 116(2): 175-178 (2016) DOI: 10.1016/j.ipl.2015.08.011
Taehun Kim, Pedram Mehrabi, Adnan Sljoka, Cris Ing, Alexandr Bezginov, Regis Pomes,Emil Pai, Scott Prosser, Dimer Asymmetry and Subunit Dynamics, Key Factors in Enzyme
Catalysis, 2016, submitted.
Adnan Sljoka, Nobuyuki TSUCHIMURA, additional authors to be determined,
Rigidity-based allostery as a tool for detection of allosteric control of Translation Initiation
Factor 4E, in planning.
Libin Ye, Chris Neil, Adnan Sljoka, Nobuyuki Tsuchimura, Scott Prosser, additional authors
to be determined, Bidirectional Regulation of the A2A Adenosine G Protein Coupled
Receptor by Physiological Cations, 2016, draft in preparation.
Conference presentations:
Adnan Sljoka, Probing GPCR allosteric communication via transmissions of rigidity, GPCR
Workshop, Hawaii, 2015
Adnan Sljoka, Transmission of rigidity at a distance in GPCR alllostery, G Protein-Coupled
Receptors: Structure, Signaling and Drug Discovery, Keystone, 2016
Adnan Sljoka, Probing protein flexibility and function via rigidity theory, ANMA,
Kathmandu, Nepal