AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions.

Interactions mediated by intrinsically disordered protein regions (IDRs) pose formidable challenges in structural characterization. IDRs are highly versatile, capable of adopting diverse structures and engagement modes. Motivated by recent strides in protein structure prediction, we embarked on exploring the extent to which AlphaFold-Multimer can faithfully reproduce the intricacies of interactions involving IDRs. To this end, we gathered multiple datasets covering the versatile spectrum of IDR binding modes and used them to probe AlphaFold-Multimer's prediction of IDR interactions and their dynamics. Our analyses revealed that AlphaFold-Multimer is not only capable of predicting various types of bound IDR structures with high success rate, but that distinguishing true interactions from decoys, and unreliable predictions from accurate ones is achievable by appropriate use of AlphaFold-Multimer's intrinsic scores. We found that the quality of predictions drops for more heterogeneous, fuzzy interaction types, most likely due to lower interface hydrophobicity and higher coil content. Notably though, certain AlphaFold-Multimer scores, such as the Predicted Aligned Error and residue-ipTM, are highly correlated with structural heterogeneity of the bound IDR, enabling clear distinctions between predictions of fuzzy and more homogeneous binding modes. Finally, our benchmarking revealed that predictions of IDR interactions can also be successful when using full-length proteins, but not as accurate as with cognate IDRs. To facilitate identification of the cognate IDR of a given partner, we established "minD," which pinpoints potential interaction sites in a full-length protein. Our study demonstrates that AlphaFold-Multimer can correctly identify interacting IDRs and predict their mode of engagement with a given partner.

The tick Ixodes scapularis has five different GPCRs specifically activated by ACP (adipokinetic hormone/corazonin-related peptide).

Insects have about 50 neuropeptide genes and about 70 genes, coding for neuropeptide G protein-coupled receptors (GPCRs). An important, but small family of evolutionarily related insect neuropeptides consists of adipokinetic hormone (AKH), corazonin, and AKH/corazonin-related peptide (ACP). Normally, insects have one specific GPCR for each of these neuropeptides. The tick Ixodes scapularis is not an insect, but belongs to the subphylum Chelicerata, which comprises ticks, scorpions, mites, spiders, and horseshoe crabs. Many of the neuropeptides and neuropeptide GPCRs occurring in insects, also occur in chelicerates, illustrating that insects and chelicerates are evolutionarily closely related. The tick I. scapularis is an ectoparasite and health risk for humans, because it infects its human host with dangerous pathogens during a blood meal. Understanding the biology of ticks will help researchers to prevent tick-borne diseases. By annotating the I. scapularis genome sequence, we previously found that ticks contain as many as five genes, coding for presumed ACP receptors. In the current paper, we cloned these receptors and expressed each of them in Chinese Hamster Ovary (CHO) cells. Each expressed receptor was activated by nanomolar concentrations of ACP, demonstrating that all five receptors were functional ACP receptors. Phylogenetic tree analyses showed that the cloned tick ACP receptors were mostly related to insect ACP receptors and, next, to insect AKH receptors, suggesting that ACP receptor genes and AKH receptor genes originated by gene duplications from a common ancestor. Similar duplications have probably occurred for the ligand genes, during a process of ligand/receptor co-evolution. Interestingly, chelicerates, in contrast to all other arthropods, do not have AKH or AKH receptor genes. Therefore, the ancestor of chelicerates might have lost AKH and AKH receptor genes and functionally replaced them by ACP and ACP receptor genes. For the small family of AKH, ACP, and corazonin receptors and their ligands, gene losses and gene gains occur frequently between the various ecdysozoan clades. Tardigrades, for example, which are well known for their survival in extreme environments, have as many as ten corazonin receptor genes and six corazonin peptide genes, while insects only have one of each, or none.

Electrocatalysis of the Oxygen Reduction Reaction by Copper Complexes with Tetradentate Tripodal Ligands.

The tetradentate tripodal ligand scaffold is capable of supporting the expected geometries of the copper ion during the oxygen reduction reaction (ORR) catalysis. As such, we probed the reactivity of copper complexes with these types of ligands by electronically and structurally tweaking the tris(pyridin 2-ylmethyl)amine (tmpa) scaffold by progressively replacing the terminal pyridines with carboxylate donors. This work shows that systems with one carboxylato donor (bpg = bis(pyridin-2-ylmethyl)glycine), (bpp = (3-(bis(pyridin-2-ylmethyl)amino)propanoic acid)) are active in electrocatalyzing the homogeneous ORR under circumneutral aqueous conditions. Turnover frequencies in the range from 105 to 106 s-1, on par with that for Cu-tmpa under identical conditions, were obtained. It is noteworthy that the CuII/CuI redox potentials for the Cu-bpg, Cu-bpp, and Cu-tmpa systems in phosphate-buffered water (pH 7, under Ar) are similar at -0.409, -0.375, and -0.401 V vs Ag/AgCl, respectively. This is rationalized by the influence of the Lewis acidity of the copper ions on the water coligand. Corroborating this are pKa values for [Cu(tmpa)(H2O)]2+, Cu(bpg)(H2O)]+, and [Cu(bpp)(H2O)]+ of 6.6, 8.8, and 10.2, respectively. Thus, the overall charge of the solution species for all three complexes will be +1 at pH 7 and this will be an important determinant for the redox potentials and, in turn, the catalytic overpotentials, which are also similar. A cis carboxylato donor offers H-bonding possibilities for exogenous resting state water and intermediate hydroperoxo coligands. This is reflected by the higher pKa values for Cu-bpp and Cu-bpg compared with that for Cu-tmpa, with the Cu-bpp system furnishing the least strained H-bonding.

Sulfonamido-Pincer Complexes of Cu(II) and the Electrocatalysis of O2 Reduction.

Heteroleptic copper complexes of an asymmetrical pincer ligand containing a central anionic sulfonamide donor (pyridine-2-yl-sulfonyl)(quinolin-8-yl)-amide (psq), which contains a central anionic sulfonamido donor have been prepared. Meridional κ3-N,N″,N‴ binding with the co-ligands acetate, chloride, or acetonitrile (MeCN), trans to the central sulfonamido N-donor, is revealed by the X-ray crystal structures of [Cu(OAc)(psq)(H2O)], [CuCl(psq)]2, and [Cu(psq)(MeCN)](PF6). Either overall distorted square pyramidal or octahedral geometries of the copper atom are satisfied by coordinated water in the case of the acetate complex or interactions with periphery sulfonamido oxygen atoms on adjacent molecules in the dimeric chloride and 1D polymeric acetonitrile complexes. The cyclic voltammogram (CV) of [Cu(OAc)(psq)(H2O)] shows a quasi-reversible CuII/CuI reduction at -0.930 V (vs Fc+/Fc0, MeCN), and an irreversible CuII/CuI reduction for [Cu(psq)(MeCN)](PF6) is seen at -0.838 V. This signal is split into two quasi-reversible redox processes on the addition of 2,2,2-trifluoroethanol (TFE). This suggests that TFE pushes a solution equilibrium toward a dimeric acetate complex analogous to [CuCl(psq)]2, which shows two quasi-reversible waves at -0.666 V and -0.904 V vs Fc+/Fc0 consistent with its dimeric solid-state structure. A comparison of the CVs of [Cu(OAc)(psq)(H2O)] under either a N2 or an O2 atmosphere revealed that this complex catalyzes turnover electro-reduction of O2 to H2O2 and H2O. The rate of reaction increases on addition of a weak organic acid, and a coulombic efficiency of 48% for H2O2 was determined by iodometric titration. We propose that a CuI complex formed on electroreduction binds O2 to yield an intermediate superoxide complex. On electron and proton transfer to this species, a bifurcated route back to the O2-activating CuI complex is feasible with either release of H2O2 or O-O cleavage resulting in the liberation of H2O. The CuI complex is regenerated by subsequent reduction and protonation to close the cycle.

Structure Activity Relationships for Reversible O2 Chemisorption by the Solid Phases of Co(salen) and Co(3F-salen).

The potential of solid-state materials comprising Co(salen) units for concentrating dioxygen from air was recognized over 80 years ago. While the chemisorptive mechanism at the molecular level is largely understood, the bulk crystalline phase plays important, yet unidentified roles. We have reverse crystal-engineered these materials and can for the first time describe the nanostructuring requisite for achieving reversible O2 chemisorption by Co(3R-salen) R = H or F, the simplest and most effective of the many known derivatives of Co(salen). Of the six phases of Co(salen) identified, α-ζ: α = ESACIO, ß = VEXLIU, γ, δ, ε, and ζ (this work), only γ, δ, ε, and ζ are capable of reversible O2 binding. Class I materials (phases γ, δ, and ε) are obtained by desorption (40-80 °C, atmospheric pressure) of the co-crystallized solvent from Co(salen)·(solv), solv = CHCl3, CH2Cl2, or 1.5 C6H6. The oxy forms comprise between 1:5 and 1:3 O2:[Co] stoichiometries. Class II materials achieve an apparent maximum of 1:2 O2:Co(salen) stoichiometries. The precursors for the Class II materials comprise [Co(3R-salen)(L)·(H2O)x], R = H, L = pyridine, and x = 0; R = F, L = H2O, and x = 0; R = F, L = pyridine, and x = 0; R = F, L = piperidine, and x = 1. Activation of these depends on the desorption of the apical ligand (L) that templates channels through the crystalline compounds with the Co(3R-salen) molecules interlocked in a Flemish bond brick pattern. The 3F-salen system produces F-lined channels proposed to facilitate O2 transport through the materials through repulsive interactions with the guest O2. We postulate that a moisture dependence of the activity of the Co(3F-salen) series is due to a highly specific binding pocket for locking in water via bifurcated hydrogen bonding to the two coordinated phenolato O atoms and the two ortho F atoms.

Regulation of the mammalian-brain V-ATPase through ultraslow mode-switching.

Vacuolar-type adenosine triphosphatases (V-ATPases)1-3 are electrogenic rotary mechanoenzymes structurally related to F-type ATP synthases4,5. They hydrolyse ATP to establish electrochemical proton gradients for a plethora of cellular processes1,3. In neurons, the loading of all neurotransmitters into synaptic vesicles is energized by about one V-ATPase molecule per synaptic vesicle6,7. To shed light on this bona fide single-molecule biological process, we investigated electrogenic proton-pumping by single mammalian-brain V-ATPases in single synaptic vesicles. Here we show that V-ATPases do not pump continuously in time, as suggested by observing the rotation of bacterial homologues8 and assuming strict ATP-proton coupling. Instead, they stochastically switch between three ultralong-lived modes: proton-pumping, inactive and proton-leaky. Notably, direct observation of pumping revealed that physiologically relevant concentrations of ATP do not regulate the intrinsic pumping rate. ATP regulates V-ATPase activity through the switching probability of the proton-pumping mode. By contrast, electrochemical proton gradients regulate the pumping rate and the switching of the pumping and inactive modes. A direct consequence of mode-switching is all-or-none stochastic fluctuations in the electrochemical gradient of synaptic vesicles that would be expected to introduce stochasticity in proton-driven secondary active loading of neurotransmitters and may thus have important implications for neurotransmission. This work reveals and emphasizes the mechanistic and biological importance of ultraslow mode-switching.

Preparation of organocobalt(iii) complexes via O2 activation.

The coupling of selective C-H activation with O2 activation is an important goal for organic synthesis. New experimental and computational results, along with the results from experimental work accumulated over many decades, now unequivocally link O2 activation with C-H activation by the classic Co(salen) complexes. A common holistic mechanistic framework can rationalise the formation of ostensibly diverse peroxo, superoxo, organo and alkoxide complexes of CoIII(salen). DFT calculations show that cobalt(iii)superoxo, dicobalt(iii)peroxo and cobalt(iii)hydroperoxo complexes are all viable intermediates as participants in hydrogen atom transfer reactions, whereas a Co(iv)oxo intermediate is unlikely. The reaction conditions will determine the pathway followed and all pathways are initiated through the initial formation of a superoxo complex, CoIII(salen)(O2˙)(MeOH) (EPR: g = 2.025, A = 19 G). Organo and alkoxide ligands are derived from solvent media and the trends in reactivity reveal that combination of the pKa and BDE of the C-H of the respective solvent substrates are important. These data explain why landmark, structurally characterized, µ2-η1,η2-peroxide and η1-superoxide Co(salen)-O2 adducts were predominantly isolated from solvents with high C-H pKa values (DMSO, DMF, DMA).

NO sorption, in-crystal nitrite and nitrate production with arylamine oxidation in gas-solid single crystal to single crystal reactions.

A bridging nitrite and a nitrate counter anion per Co2 site are generated in-crystal and an arylamine group on the ligand scaffold is oxidised to a nitro group when nitric oxide (NO) is chemisorbed by molecular crystals of cobalt complexes.

Direct observation of proton pumping by a eukaryotic P-type ATPase.

In eukaryotes, P-type adenosine triphosphatases (ATPases) generate the plasma membrane potential and drive secondary transport systems; however, despite their importance, their regulation remains poorly understood. We monitored at the single-molecule level the activity of the prototypic proton-pumping P-type ATPase Arabidopsis thaliana isoform 2 (AHA2). Our measurements, combined with a physical nonequilibrium model of vesicle acidification, revealed that pumping is stochastically interrupted by long-lived (~100 seconds) inactive or leaky states. Allosteric regulation by pH gradients modulated the switch between these states but not the pumping or leakage rates. The autoinhibitory regulatory domain of AHA2 reduced the intrinsic pumping rates but increased the dwell time in the active pumping state. We anticipate that similar functional dynamics underlie the operation and regulation of many other active transporters.