Cédric Grauffel

Academia Sinica · Institute of Biomedical Sciences

Antibodies conjugated with diagnostic/therapeutic radionuclides are attractive options for inoperable cancers lacking accurate imaging methods and effective therapeutics, such as pancreatic cancer. Hence, we have produced an antibody radionuclide conjugate termed TE-1132 comprising a α-CA19-9 scFv-Fc that is site-specifically conjugated at each C-t...

Strontium (Sr), an alkali metal with properties similar to calcium, in the form of soluble salts is used to treat osteoporosis. Despite the information accumulated on the role of Sr2+ as a Ca2+ mimetic in biology and medicine, there is no systematic study of how the outcome of the competition between the two dications depends on the physicochemical...

Because Li+ and Ca2+ differ in both charge and size, the possibility that monovalent Li+ could dislodge the bulkier, divalent Ca2+ in Ca2+ proteins had not been considered. However, our recent density functional theory/continuum dielectric calculations predicted that Li+ could displace the native Ca2+ from the C2 domain of cytosolic PKCα/γ. This wo...

One strategy to counter viruses that persistently cause outbreaks is to design molecules that can specifically inhibit an essential multifunctional viral protease. Herein, we present such a strategy using well-established methods to first identify a region present only in viral (but not human) proteases and find peptides that can bind specifically...

Opening of two-pore domain K⁺ channels (K2Ps) is regulated by various external cues, such as pH, membrane tension, or temperature, which allosterically modulate the selectivity filter (SF) gate. However, how these cues cause conformational changes in the SF of some K2P channels remains unclear. Herein, we investigate the mechanisms by which extrace...

Lithium (Li⁺) is the first-line therapy for bipolar disorder and a candidate drug for various diseases such as amyotrophic lateral sclerosis, multiple sclerosis, and stroke. Despite being the captivating subject of many studies, the mechanism of lithium’s therapeutic action remains unclear. To date, it has been shown that Li⁺ competes with Mg²⁺ and...

Correction for ‘Multi-targeting of functional cysteines in multiple conserved SARS-CoV-2 domains by clinically safe Zn-ejectors’ by Karen Sargsyan et al. , Chem. Sci. , 2020, 11 , 9904–9909, DOI: 10.1039/D0SC02646H.

Monophosphate, an essential component of nucleic acids, as well as cell membranes and signaling molecules, is often bound to metal cations. Despite the biological importance of monophosphate-containing cell-signaling or lipid molecules, their propensity to bind the two most abundant cellular dications, Mg2+ and Ca2+, in a particular mode (inner/out...

Whole-cell biosensors are useful for monitoring heavy metal toxicity in public health and ecosystems, but their development has been hindered by intrinsic trade-offs between sensitivity and specificity. Here, we demonstrated an effective engineering solution by building a sensitive, specific, and high-response biosensor for carcinogenic cadmium ion...

We present a near-term treatment strategy to tackle pandemic outbreaks of coronaviruses with no specific drugs/vaccinesby combining evolutionary and physical principles to identify conserved viral domains containing druggable Zn-sites that can be targeted by clinically safe Zn-ejecting compounds. By applying this strategy to SARS-CoV-2 polyprotein-...

div> We present a near-term treatment strategy to tackle pandemic outbreaks of coronaviruses with no specific drugs/vaccines by combining evolutionary and physical principles to identify conserved viral domains containing druggable Zn-sites that can be targeted by clinically safe Zn-ejecting compounds. By applying this strategy to SARS-CoV-2 polyp...

The Covid-19 outbreak requires prompt response, but developing Covid-19-specific antivirals/vaccine takes time. Near-term alternatives are needed. Based on evolutionary and physical principles of the key factors controlling the reactivity of Zn-bound Cys, we have identified putative labile Zn-sites in Covid-19 that can be targeted by Zn-ejector dru...

Di/triphosphates perform a multitude of essential tasks, being important components of many vital organic cofactors such as adenosine/guanosine di/triphosphate (ADP/GDP, ATP/GTP), flavin adenine dinucleotide, and nicotinamide adenine dinucleotide and its phosphate derivative. They are generally bound to cations inside cells, in particular Mg2+ in t...

Lithium, a first-line therapy for bipolar disorder, is effective in preventing suicide and new depressive/manic episodes. Yet, how this beguilingly simple monocation with only two electrons could yield such profound therapeutic effects remains unclear. An in-depth understanding of lithium's mechanisms of actions would help one to develop better tre...

To facilitate proper mitotic cell partitioning, the Golgi disassembles by suppressing vesicle fusion. However, the underlying mechanism has not been characterized previously. Here, we report a Ran pathway-independent attenuation mechanism that allows Importin-α (a nuclear transport factor) to suppress the vesicle fusion mediated by p115 (a vesicula...

In Zn-proteins, structural Znsites are mostly Cys-rich lined by two or more Cys residues, whereas catalytic Zn-sites usually contain His or Asp/Glu residues and a water molecule. Here, we reveal many examples outside this trend with Zn2+ bound to ligands commonly found in both structural and catalytic Znsites, namely, Zn-CC(C/H)x (x = D, E, or H2...

Abiogenic lead (Pb2+), present in the environment in elevated levels due to human activities, has detrimental effects on human health. Metal-binding sites in proteins have been identified as primary targets for lead substitution resulting in malfunction of the host protein. Although Pb2+ is known to be a potent competitor of Ca2+ in protein binding...

Lysine acetylation is a widespread post-translational modification regulating various biological processes. To characterize cellular functions of the human lysine acetyltransferases KAT2A (GCN5) and KAT2B (PCAF), we determined their acetylome by shotgun proteomics. One of the newly identified KAT2A/2B substrate is polo-like kinase 4 (PLK4), a key r...

Supplementary Figures 1-8

PKAT2A/KAT2B-dependent acetylome data

Cation-π interactions between tyrosine amino acids and compounds containing a N,N,N-trimethylethanolammonium (N(CH3)3) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet the lack of explicit polarization or charge transfer effects in mo...

Proteinase 3 (PR3), the autoantigen in granulomatosis with polyangiitis, is expressed at the plasma membrane of resting neutrophils and this membrane expression increases during both activation and apoptosis. Using surface plasmon resonance and protein-lipid overlay assays, this study demonstrates that PR3 is a phosphatidylserine-binding protein an...

Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) is a secreted virulence factor that binds specifically to phosphatidylcholine (PC) bilayers containing negatively charged phospholipids. BtPI-PLC carries a negative net charge and its interfacial binding site has no obvious cluster of basic residues. Continuum electrost...

How do phospholipase Cs associated with bacterial virulence bind to membranes and search for substrates? The virulence factor Bacillus thuringiensis phosphatidylinositol‐specific phospholipase C ( Bt PI‐PLC) cleaves GPI‐anchored proteins off the outer leaflet of eukaryotic cells, helping the bacteria evade host defenses. Single molecule fluorescenc...

Transient binding of amphitropic proteins to membranes can be mediated by phospholipid cation / tyrosine π interactions. Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (BtPI-PLC) is a secreted virulence factor that targets GPI-anchored proteins in the outer surface of eukaryotic plasma membranes, a bilayer rich in choline-cont...

Neutrophil serine proteases Proteinase 3 (PR3) and human neutrophil elastase (HNE) are considered as targets for chronic inflammatory diseases. Despite sharing high sequence similarity, the two enzymes have different substrate specificities and functions. While a plethora of HNE inhibitors exist, PR3 specific inhibitors are still in their infancy....

Background: Post-translational modifications of histones, and in particular of their disordered N-terminal tails, play a major role in epigenetic regulation. The identification of proteins and proteic domains that specifically bind modified histones is therefore of paramount importance to understand the molecular mechanisms of epigenetics. Method...

Neutrophil serine proteases Proteinase 3 (PR3) and human neutrophil elastase (HNE) are homologous antibiotic serine proteases of the polymorphonuclear neutrophils. Despite sharing a 56% sequence identity they have been shown to have different functions and localizations in the neutrophils. In particular, and in contrast to HNE, PR3 has been detecte...

Enterotoxigenic Escherichia coli (ETEC) expressing the heat-stable toxin (ST; variants STh and STp) is among the five most important enteric pathogens in young children living in low-and middle income countries. ST mediates diarrheal disease through activation of the guanylate cyclase C (GC-C) receptor and is an attractive vaccine target with the p...

The X-linked lethal Ogden syndrome was the first reported human genetic disorder associated with a mutation in an N-terminal acetyltransferase (NAT) gene. The affected males harbour a Ser37Pro mutation in the gene encoding hNaa10, the catalytic subunit of NatA, the major human NAT involved in the co-translational acetylation of proteins. Structural...

Neutrophil serine proteases are specific regulators of the immune response, and Proteinase3 is a major target antigen in antineutrophil cytoplasmic antibody-associated vasculitis. FRET peptides containing 2-aminobenzoic acid (Abz) and N-(2,4-dinitrophenyl)-ethylenediamine (EDDnp) as fluorophore and quencher groups, respectively, have been widely us...

Amphitropic proteins, such as the virulence factor phosphatidylinositol-specific phospholipase C (PI-PLC) from Bacillus thuringiensis, often depend on lipid-specific recognition of target membranes. However, the recognition mechanisms for zwitterionic lipids such as phosphatidylcholine, which is enriched in the outer leaflet of eukaryotic cells, ar...

Phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes transiently interact with target membranes. Previous fluorescence correlation spectroscopy (FCS) experiments showed that Bacillus thuringiensis PI-PLC specifically binds to phosphatidylcholine (PC)--rich membranes and preferentially interacts with unilamellar vesicles that show larger c...

The N-terminal domain of huntingtin (Htt17), located immediately upstream of the decisive polyglutamine tract, strongly influences important properties of this large protein and thereby the development of Huntington's disease. Htt17 markedly increases polyglutamine aggregation rates and huntingtin's interactions with biological membranes. Here, an...

Phosphatidylinositol specific phospholipase Cs (PI-PLCs) from extra-cellular bacterial pathogens are associated with bacterial virulence. Membrane binding and enzymatic activity of many of these PI-PLCs are specifically enhanced by the presence of phosphatidylcholine (PC), an abundant phospholipid in the outer plasma membrane of eukaryotic cells ta...

The enzymatic activity of secreted phosphatidylinositol-specific phospholipase C (PI-PLC) enzymes is associated with bacterial virulence. Although the PI-PLC active site has no obvious lid, molecular-dynamics simulations suggest that correlated loop motions may limit access to the active site, and two Pro residues, Pro(245) and Pro(254), are associ...

Nt-acetylation is among the most common protein modifications in eukaryotes. Although thought for a long time to protect proteins from degradation, the role of Nt-acetylation is still debated. It is catalyzed by enzymes called N-terminal acetyltransferases (NATs). In eukaryotes, several NATs, composed of at least one catalytic domain, target differ...

Contributions to the free energy of binding in hNaa50p. Amino acid residues of hNaa50p/MLG (black) and hNaa50p/MKG (grey) with the highest contribution to the free energy of binding (MM/PBSA). The contributions are divided between backbone (bb) and side chains (sc) contributions. (TIF)

Distance (Å) between the N-terminal nitrogen of Met1 and the carbon atom of Ac-CoA carbonyl in hNaa10p complexed with EEE (top) and MLG (bottom). In each case we represent the evolution of the distance for the five simulations of the corresponding complex. (TIF)

CHARMM force field parameters for AcCoA. Parameters provided in the CHARMM topology format. (PDF)

Backbone RMSD of hNaa50p during MD simulations. The plots correspond to the simulations of the alanine mutants (F27A, P28A, V29A, Y31A, F35A, Y73A, H112A, Y139A and I142A) in complex with an MLG peptide, of a wild-type/MKG complex, and of the apo form of the F27A mutant. RMSD has been calculated after superposition of the trajectory on the starting...

Free energy decompositions (expressed in kcal/mol) of alanine point-mutants of hNaa50p/MLG. Black bars are used for the wild-type hNaa50p/MLG and white dashed bars for the mutant (F27A, P28A, V29A, Y31A, F35A, Y73A, H112A, Y139A, I142A). (PDF)

Correlation maps of hNaa50p apo (above diagonal) hNaa50p/MLG (below diagonal). Correlations are shown in a yellow to red gradient, and anti-correlations in blue. The position of the helix is highlighted by the dashed lines. (TIF)

Change in backbone atomic fluctuations of hNaa50p/MLG resulting from alanine point-mutations. Plots (left) compare the atomic fluctuations of the mutant (P28A, V29A, Y31A, F35A, Y73A, H112A, Y139A, I142A) and wild-type, while the relative difference is shown on the structure (right). Amino acids of the protein are shown in sticks if the difference...

Detailed atomic fluctuations during the simulations of hNaa50p. Data is provided for the 5 simulations of the enzyme in complex with MLG (red) and EEE (green), and the 2 simulations of the apo hNaa50p (blue). (TIF)

Sequence alignment between hNaa10p and the template from Sulfolobus Solfataricus (PDBid 2X7B ) (TIF)

Phosphatidylinositol specific phospholipase Cs (PI-PLCs) from extra-cellular bacterial pathogens are associated with bacterial virulence. Membrane binding and enzymatic activity of many of these PI-PLCs is specifically enhanced by the presence of phosphatidylcholine (PC), an abundant phospholipid in the outer plasma membrane of eukaryotic cells tar...

Proteinase 3 (PR3) is a serine protease of the neutrophils involved in inflammation processes. Its membrane expression is a risk factor for chronic inflammatory diseases. Experimental data led to divergent hypotheses on the binding mode of PR3 to the plasma membrane of neutrophils. While several studies performed on cell lines have identified a num...

We describe the development of force field parameters for methylated lysines and arginines, and acetylated lysine for the CHARMM all-atom force field. We also describe a CHARMM united-atom force field for modified sidechains suitable for use with fragment-based docking methods. The development of these parameters is based on results of ab initio qu...

Condensation of chromatin, mediated in part by posttranslational modifications of histones, is essential for cell division during mitosis. Histone H3 tails are dimethylated on lysine (Kme2) and become phosphorylated on serine (Sp) residues during mitosis. We have explored the possibility that these double modifications are involved in the establish...

Guanine nucleotide exchange factors (GEFs), which activate small GTP-binding proteins (SMG) by stimulating their GDP/GTP exchange, are emerging as candidate targets for the inhibition of cellular pathways involved in diseases. However, their specific inhibition by competitive inhibitors is challenging, because GEF and SMG families comprise highly s...

Density functional theory B3LYP calculations have been carried out for the Pd(diimine)(C2H2)+H2Pd(diimine)(C2H4) reaction, which is the key reaction in the semihydrogenation of alkynes homogeneously catalyzed by (diimine)palladium(0) complexes. The results show that a H2 heterolytic addition across one Pd–N bond opens a feasible zwitterionic pathwa...