Integrated Calendar

In the past decade, liquid phase separation has been proposed as a mechanism for intracellular
organization. It has been shown that many proteins phase-separate and form liquid-like drops. These liquid-like compartments provide a distinct biochemical environment inside of the cell and sometimes form as a response to changes in the intracellular environment. In particular, a decrease in the pH of the cytosol of yeast cells leads to widespread macromolecular assembly. Inspired by this experimental observation, we construct a minimal model to study this
pH-responsive mechanism. The model consists of a macromolecular mixture in which macromolecules can exist in different charge states and have a tendency to phase-separate. In order to assess the effect of pH on phase separation, we introduce protonation and deprotonation reactions, which are controlled by the pH of the mixture. Using this model, we construct phase diagrams at the isoelectric point of the system and then study what happens when the pH is moved away from the isoelectric point. We find that under most conditions, the broadest region of phase separation is located at the isoelectric point. Interestingly, our minimal model also predicts reentrant behavior as a function of pH. We conclude by discussing the predictions of our model in light of experimental observations on protein phase separation, showing that they are in agreement.

The occurrence and sequela of disorders that lead to hypoxic spells such as asthma, chronic obstructive pulmonary disease, and obstructive sleep apnea (OSA) exhibit daily variance. This prompted us to examine the interaction between the hypoxic response and the circadian clock in vivo. We found that the global transcriptional response to acute hypoxia is tissue-specific and time-of-day dependent. In particular, clock components differentially responded at the transcriptional and post-transcriptional level, and these responses depended on an intact circadian clock. Importantly, exposure to hypoxia phase-shifted clocks in a tissue-dependent manner, leading to inter-tissue circadian clock misalignment. This differential response relied on intrinsic properties of each tissue and could be recapitulated ex vivo. Notably, circadian misalignment was also elicited by intermittent hypoxia, a widely used model for OSA. Given that phase coherence between circadian clocks is considered favorable, we propose that hypoxia leads to circadian misalignment, contributing to the pathophysiology of OSA and potentially other diseases that involve hypoxia.

Our research uses chemistry principles to address questions of importance in life sciences and molecular medicine. This lecture will cover recent examples of emerging areas in our group in:
(i) methods developed for site-selective chemical modification of proteins at cysteine, disulfide and lysine and their use to build stable and functional protein conjugates for in vivo applications [1–4]
(ii) bioorthogonal cleavage reactions for targeted drug activation in cells [5,6]
(iii) by identifying on- and off-targets for anti-cancer entities using our own machine intelligence platform, unveiling the underlying molecular mechanisms of target recognition and linking drug target binding to modulation of disease, we explore the use of natural products as selective cancer modulators [7]

Recent Publications:
1. Bernardim B; Cal PMSD; Matos MJ; Oliveira BL; Martínez-Sáez N; Albuquerque IS; Corzana F; Burtoloso ACB; Jiménez-Osés G; Bernardes GJL* Stoichiometric and Irreversible Cysteine-selective Protein Modification using Carbonylacrylic Reagents. Nat. Commun. 2016, 7, 13128.
2. Martínez-Saez N; Sun S; Oldrini D; Sormanni P; Boutureira O; Carboni F; Compañón I; Deery MJ; Vendruscolo M; Corzana F; Adamo R; Bernardes GJL* Oxetane Grafts Installed Site-Selectively on Native Disulfides to Enhance Protein Stability and Activity In Vivo. Angew. Chem. Int. Ed. 2017, 47, 14963–14967.
3. Freedy AM; Matos MJ; Omar Boutureira O; Corzana F; Guerreiro A; Somovilla VJ; Rodrigues T; Nicholls K; Xie B; Jiménez-Osés G; Brindle KM; Neves AA; Bernardes GJL* Chemoselective Installation of Amine Bonds on Proteins Through Aza-Michael Ligation. J. Am. Chem. Soc. 2017, 139, 18365–18375.
4. Matos MJ; Oliveira BL; Martínez-Sáez N; Guerreiro A; Cal PMSD; Bertoldo J; Maneiro M; Perkins E; Howard J; Deery MJ; Chalker JM; Corzana F; Jiménez-Osés G; Bernardes GJL* Chemo and regioselective lysine modification on native proteins. J. Am. Chem. Soc. 2018, 140, 4004–4017.
5. Stenton BJ; Oliveira BL; Matos MJ; Sinatra L; Bernardes GJL* A Thioether-directed Palladium-cleavable Linker for Targeted Bioorthogonal Drug Decaging. Chem. Sci. 2018, 9, 4185–4189.
6. Sun S; Oliveira BL; Jiménez-Osés G; Bernardes GJL* Radical-mediated thiol-ene strategy for photoactivation of thiol-containing drugs in cancer cells. Angew. Chem. Int. Ed. 2018, DOI: 10.1002/anie.201811338.
7. Rodrigues T; Werner M; Roth J; da Cruz EHG; Marques MC; Akkapeddi P; Lobo SA; Koeberle A; Corzana F; da Silva Júnior EN; Werz O; Bernardes GJL* Machine intelligence decrypts β-lapachone as an allosteric 5-lipoxygenase inhibitor. Chem. Sci. 2018, 9, 6885–7018.

Due to the direct correlation among the physical properties and crystal structure of materials, study of the latter is crucial for fundamental understanding of the properties. In the era of nano-science, objects of interest are getting smaller and traditional single-crystal and powder X-ray diffraction methods cannot be applied for characterization of their atomic structures due to the unavailability of single crystals and/or small quantity and size of these crystals in the multiphase specimens. Thus, electron crystallography (EC) (which is defined as a combination of electron diffraction and imaging methods) is sometimes the only viable tool for the analysis of their structure.
In the previous century, electron diffraction (ED) was considered to be unsuitable for structure determination due to the problems of data quality arising from dynamical effects. At the last decades, researchers have shown that influence of dynamical effects can be substantially reduced if beam precession (PED) is used and/or data collection is performed in the off-axis conditions - enabling solution of atomic structures with various complexity (from inorganics to proteins).
Our group focuses on development and application of EC methods for structure solution of nano-sized precipitates and characterization of structural defects in steels and light alloys. This study is technologically essential since precipitates and defects dictate physical properties of these structural materials. It must be noted that, atomic structures of intermetallics were not solved previously using solely ED methods. Reason for that is in the nature of intermetallic compound's structures. Contrarily to other complex materials, the atomic distances and angles of intermetallics are not fixed and coordination polyhedra are usually unknown. Thus, structure solution of these compounds is harder to validate.
In the present seminar, contribution of our group in the development of routine structure solution path for aluminides (as an example of intermetallics) will be presented. In addition, characterization of structural defects, influencing the performance of the studied materials, will be shown.

The oxygen isotopic signature of marine deep-sea cherts was previously used to reconstruct past ocean temperature and bottom water δ18O through the Cenozoic and Mesozoic periods. Oxygen isotopes of deep-sea cherts, which were never exposed to meteoric water, exhibit a wide range of values indicating that the evolution and maturation of biogenic amorphous opal (opal-A) to opal-CT and microquartz chert is accompanied by isotopic changes. We measured δ18O of diatom opal-A, opal-CT, and microquartz chert from deep sea cores retrieved from the Japan Sea. The δ18O of opal-CT and microquartz chert phases correspond to the depth in the sediments where these transitions occur, ~400 m and 40 °C for opal-A to opal-CT and ~500 m and 60 °C for opal-CT to microquartz chert. The δ18O values of opal-CT and microquartz chert appear to reflect equilibrium formation temperatures of silica, corresponding to the geothermal gradient and the local porewater δ18O. The δ18O of opal-CT and microquartz chert are controlled by the geothermal gradient and compositions of pore waters during polymorphic transformations deep within the sediment, indicating that the δ18O of these phases cannot be used to determine temperature or composition of seawater during diatom growth.
Opal-A is the most susceptible phase for isotope alteration. We separated opal-A (i.e., diatoms, radiolaria, and siliceous sponge spicules) of Cenozoic age and measured its isotope composition. The results do not indicate any significant change in δ18O. This will be discussed within the general framework of global climatic change.