Dimer Equilibrium Research Articles

Screening for bilayer-active and likely cytotoxic molecules reveals bilayer-mediated regulation of cell function.

A perennial problem encountered when using small molecules (drugs) to manipulate cell or protein function is to assess whether observed changes in function result from specific interactions with a desired target or from less specific off-target mechanisms. This is important in laboratory research as well as in drug development, where the goal is to identify molecules that are unlikely to be successful therapeutics early in the process, thereby avoiding costly mistakes. We pursued this challenge from the perspective that many bioactive molecules (drugs) are amphiphiles that alter lipid bilayer elastic properties, which may cause indiscriminate changes in membrane protein (and cell) function and, in turn, cytotoxicity. Such drug-induced changes in bilayer properties can be quantified as changes in the monomer↔dimer equilibrium for bilayer-spanning gramicidin channels. Using this approach, we tested whether molecules in the Pathogen Box (a library of 400 drugs and drug-like molecules with confirmed activity against tropical diseases released by Medicines for Malaria Venture to encourage the development of therapies for neglected tropical diseases) are bilayer modifiers. 32% of the molecules in the Pathogen Box were bilayer modifiers, defined as molecules that at 10 µM shifted the monomer↔dimer equilibrium toward the conducting dimers by at least 50%. Correlation analysis of the molecules' reported HepG2 cell cytotoxicity to bilayer-modifying potency, quantified as the shift in the gramicidin monomer↔dimer equilibrium, revealed that molecules producing <25% change in the equilibrium had significantly lower probability of being cytotoxic than molecules producing >50% change. Neither cytotoxicity nor bilayer-modifying potency (quantified as the shift in the gramicidin monomer↔dimer equilibrium) was well predicted by conventional physico-chemical descriptors (hydrophobicity, polar surface area, etc.). We conclude that drug-induced changes in lipid bilayer properties are robust predictors of the likelihood of membrane-mediated off-target effects, including cytotoxicity.

Intermolecular-Type Conical Intersections in Benzene Dimer.

The equilibrium and conical intersection geometries of the benzene dimer were computed in the framework of the conventional, linear-response time-dependent and spin-flipped time-dependent density functional theories (known as DFT, TDDFT and SF-TDDFT) as well as using the multiconfigurational complete active space self-consistent field (CASSCF) method considering the minimally augmented def2-TZVPP and the 6-31G(d,p) basis sets. It was found that the stacking distance between the benzene monomers decreases by about 0.5 Å in the first electronic excited state, due to the stronger intermolecular interaction energy, bringing the two monomers closer together. Intermolecular-type conical intersection (CI) geometries can be formed between the two benzene molecules, when (i) both monomer rings show planar deformation and (ii) weaker (approximately 1.6-1.8 Å long) C-C bonds are formed between the two monomers, with parallel and antiparallel orientation with respect to the monomer. These intermolecular-type CIs look energetically more favorable than dimeric CIs containing only one deformed monomer. The validity of the dimer-type CI geometries obtained by SF-TDDFT was confirmed by the CASSCF method. The nudged elastic band method used for finding the optimal relaxation path has confirmed both the accessibility of these intermolecular-type CIs and the possibility of the radiationless deactivation of the electronic excited states through these CI geometries. Although not as energetically favorable as the previous two CI geometries, there are other CI geometries characterized by the relative rotation of monomers at different angles around a vertical C-C axis.

The dependency of slow CLC-ec1 dimerization kinetics on lipid solvent volume.

Although protein association equilibrium has been vastly studied in water, questions remain about how membrane proteins assemble and operate within the oily solvent environment of the membrane. However, recent developments in the field provide the potential for understanding the molecular basis of these reactions. In particular, our lab has developed approaches for quantifying the equilibrium affinities of membrane protein oligomers in membranes, a physical model for protein association and folding. Using single-molecule photobleaching microscopy, the lab has demonstrated CLC-ec1 participates in a fully reversible, equilibrium dimerization reaction in membranes. Our studies reveal the kinetics of dimerization are slower than most biological reactions taking days to equilibrate at 37 ºC in 2:1 POPE/POPG lipid bilayers. Here, we investigate the molecular basis for the slow kinetics by measuring subunit exchange kinetics in membranes. We hypothesize the dimerization reaction involves a high-energy transition state that requires the formation of a vacuum cavity in between the two subunits inaccessible to the surrounding solvent. We expect measuring the reaction in mixed lipid bilayers that include smaller lipoidal molecules will lead to a reduced cavity volume along the reaction pathway, decreasing the transition state energy barrier, which will be observed by speeding up of the reaction kinetics. To test this, CLC-ec1-Cy3 and CLC-ec1-Cy5 subunit exchange equilibration rates are measured by bulk Förster Resonance Energy Transfer at 37 ºC in 2:1 POPE/POPG while titrating benzene, n-Octyl-β-D-Glucoside, and 2:1 PE/PG lysolipids. In parallel, coarse-grained molecular dynamics simulations are carried out on the same mixed lipid systems to calculate the solvent-inaccessible cavity volumes between subunits as they are separated from 8 to 24 Å. The results from this investigation will provide a quantitative analysis offering insight into why membrane protein complexes are often kinetically trapped in lipid bilayers.

The role of protein-protein interactions in Fluc dimerization stability and function.

Functional ion channel assembly often requires subunit oligomerization. Yet the molecular factors that define the stability of ion channel complexes in membranes remain to be delineated. Here we investigate this question by studying the dynamic dimerization reaction of the model system Fluc to map out the molecular and physical forces driving this reaction in membranes. Fluc is dual-topology homodimer, where dimerization confers the highly specific fluoride permeation pathway. Our previous analysis demonstrated that a sodium titratable mutant of Fluc participates in a two-step equilibrium dimerization reaction in membranes. First, membrane-dependent dimerization drives subunits to assemble and form a non-contact lipid-solvated stable dimer intermediate by burying a membrane defect imposed in the monomer. However, the fluoride conducting state requires the protein subunits to come closer and expel the lipids to form the fluoride permeation pathway. High resolution crystal structures of Fluc show numerous protein-protein interactions across the dimerization interface, suggesting these interactions might be involved in stabilizing the close-contact dimer state. Alternatively, these contacts may not play a major role in the overall dimer stability but may be important for conferring function. Here, we will investigate how disruption of these protein-protein interactions affects dimerization stability, channel activity or both. Site-directed mutagenesis was employed following four strategies of disruption: (1) reduction of van der Waals interactions by leucine-to-alanine substitutions; (2) removal of potential hydrogen bonds by threonine-to-valine substitutions; (3) decrease backbone flexibility by glycine-to-alanine mutations of the GxxxG dimerization motif; (4) and introduction of bulky tryptophan residues at the interface. Using single-molecule photobleaching analysis to investigate dimer stability in membranes combined with single channel bilayer recordings, these results will provide a quantitative characterization of the contribution of protein-protein interactions to Fluc dimer stability and activity.

Characterization of heterogeneous dimer and oligomer formation of amyloid-beta using single-molecule FRET.

Protein aggregation is implicated as the cause of pathology in various diseases. Polymorphism in the structure of fibrils formed by aggregation suggests the existence of many different assembly pathways and therefore a heterogeneous ensemble of soluble oligomers. Characterization of this heterogeneity is the key to understanding the aggregation mechanism and toxicity of specific oligomers, but in practice it is extremely difficult to probe individual aggregation pathways in a mixture. Using fluorescence lifetime imaging and deep learning, we have recently visualized the formation of highly diverse fibrils of amyloid-beta (Abeta) in real time (PNAS_2022_e2116736119). Here, we further characterize the heterogeneity in the early stages of aggregation, dimerization and oligomerization of 42-residue Abeta (Abeta42), using single-molecule FRET. We found the dimerization of Abeta is extremely rare. The dimer dissociation constant is unexpectedly high, >5 mM. In addition, the dimerization is highly heterogeneous in terms of the FRET efficiency and kinetics. At least 6 clusters of dimers were needed to fit the entire equilibrium dimerization trajectories. This structural and kinetic diversity suggests that the heterogeneous fibril formation starts from the beginning of the assembly, the dimerization step. Then, we sought the formation of larger stable oligomers of Abeta42 that appear during aggregation. Combination of peptide incubation in a plate reader, single-molecule free-diffusion FRET experiment, and a newly-developed maximum likelihood method based on the rigorous photon statistics and diffusion theory allows for the accurate characterization of stable oligomers appearing at various stages of aggregation. We found that the size of these oligomers ranges from 30- to 100-mer and their overall population is unexpectedly low, less than 1 nM, before and during aggregation of 1-µM Abeta42 peptide. The amounts of small oligomers such as dimers and tetramers are negligible.

Structures of permuted halves of a modern ribose-binding protein.

Periplasmic binding proteins (PBPs) are a class of proteins that participate in the cellular transport of various ligands. They have been used as model systems to study mechanisms in protein evolution, such as duplication, recombination and domain swapping. It has been suggested that PBPs evolved from precursors half their size. Here, the crystal structures of two permuted halves of a modern ribose-binding protein (RBP) from Thermotoga maritima are reported. The overexpressed proteins are well folded and show a monomer-dimer equilibrium in solution. Their crystal structures show partially noncanonical PBP-like fold type I conformations with structural deviations from modern RBPs. One of the half variants forms a dimer via segment swapping, suggesting a high degree of malleability. The structural findings on these permuted halves support the evolutionary hypothesis that PBPs arose via a duplication event of a flavodoxin-like protein and further support a domain-swapping step that might have occurred during the evolution of the PBP-like fold, a process that is necessary to generate the characteristic motion of PBPs essential to perform their functions.

Destabilizers of the thymidylate synthase homodimer accelerate its proteasomal degradation and inhibit cancer growth.

Drugs that target human thymidylate synthase (hTS), a dimeric enzyme, are widely used in anticancer therapy. However, treatment with classical substrate-site-directed TS inhibitors induces over-expression of this protein and development of drug resistance. We thus pursued an alternative strategy that led us to the discovery of TS-dimer destabilizers. These compounds bind at the monomer-monomer interface and shift the dimerization equilibrium of both the recombinant and the intracellular protein toward the inactive monomers. A structural, spectroscopic, and kinetic investigation has provided evidence and quantitative information on the effects of the interaction of these small molecules with hTS. Focusing on the best among them, E7, we have shown that it inhibits hTS in cancer cells and accelerates its proteasomal degradation, thus causing a decrease in the enzyme intracellular level. E7 also showed a superior anticancer profile to fluorouracil in a mouse model of human pancreatic and ovarian cancer. Thus, over sixty years after the discovery of the first TS prodrug inhibitor, fluorouracil, E7 breaks the link between TS inhibition and enhanced expression in response, providing a strategy to fight drug-resistant cancers.

Unmasking the Conformational Stability and Inhibitor Binding to SARS-CoV-2 Main Protease Active Site Mutants and Miniprecursor

We recently demonstrated that inhibitor binding reorganizes the oxyanion loop of a monomeric catalytic domain of SARS CoV-2 main protease (MPro) from an unwound (E) to a wound (active, E*) conformation, independent of dimerization. Here we assess the effect of the flanking N-terminal residues, to imitate the MPro precursor prior to its autoprocessing, on conformational equilibria rendering stability and inhibitor binding. Thermal denaturation (Tm) of C145A mutant, unlike H41A, increases by 6.8 °C, relative to wild-type mature dimer. An inactivating H41A mutation to maintain a miniprecursor containing TSAVL[Q or E] of the flanking nsp4 sequence in an intact form [(-6)MProH41A and (-6*)MProH41A, respectively], and its corresponding mature MProH41A were systematically examined. While the H41A mutation exerts negligible effect on Tm and dimer dissociation constant (Kdimer) of MProH41A, relative to the wild type MPro, both miniprecursors show a 4–5 °C decrease in Tm and > 85-fold increase in Kdimer as compared to MProH41A. The Kd for the binding of the covalent inhibitor GC373 to (-6*)MProH41A increases ∼12-fold, relative to MProH41A, concomitant with its dimerization. While the inhibitor-free dimer exhibits a state in transit from E to E* with a conformational asymmetry of the protomers’ oxyanion loops and helical domains, inhibitor binding restores the asymmetry to mature-like oxyanion loop conformations (E*) but not of the helical domains. Disorder of the terminal residues 1–2 and 302–306 observed in both structures suggest that N-terminal autoprocessing is tightly coupled to the E-E* equilibrium and stable dimer formation.

N-O Ligand Supported Stannylenes: Preparation, Crystal, and Molecular Structures

A new series of tin(II) complexes (1, 2, 4, and 5) were successfully synthesized by employing hydroxy functionalized pyridine ligands, specifically 2-hydroxypyridine (hpH), 8-hydroxyquinoline (hqH), and 10-hydroxybenzo[h]quinoline (hbqH) as stabilizing ligands. Complexes [Sn(μ-κ2ON-OC5H4N)(N{SiMe3}2)]2 (1) and [Sn4(μ-κ2ON-OC5H4N)6(κ1O-OC5H4N)2] (2) are the first structurally characterized examples of tin(II) oxypyridinato complexes exhibiting {Sn2(OCN)2} heterocyclic cores. As part of our study, 1H DOSY NMR experiments were undertaken using an external calibration curve (ECC) approach, with temperature-independent normalized diffusion coefficients, to determine the nature of oligomerisation of 2 in solution. An experimentally determined diffusion coefficient (298 K) of 6.87 × 10−10 m2 s−1 corresponds to a hydrodynamic radius of Ca. 4.95 Å. This is consistent with the observation of an averaged hydrodynamic radii and equilibria between dimeric [Sn{hp}2]2 and tetrameric [Sn{hp}2]4 species at 298 K. Testing this hypothesis, 1H DOSY NMR experiments were undertaken at regular intervals between 298 K–348 K and show a clear change in the calculated hydrodynamic radii form 4.95 Å (298 K) to 4.35 Å (348 K) consistent with a tetramer ⇄ dimer equilibria which lies towards the dimeric species at higher temperatures. Using these data, thermodynamic parameters for the equilibrium (ΔH° = 70.4 (±9.22) kJ mol−1, ΔS° = 259 (±29.5) J K−1 mol−1 and ΔG°298 = −6.97 (±12.7) kJ mol−1) were calculated. In the course of our studies, the Sn(II) oxo cluster, [Sn6(m3-O)6(OR)4:{Sn(II)(OR)2}2] (3) (R = C5H4N) was serendipitously isolated, and its molecular structure was determined by single-crystal X-ray diffraction analysis. However, attempts to characterise the complex by multinuclear NMR spectroscopy were thwarted by solubility issues, and attempts to synthesise 3 on a larger scale were unsuccessful. In contrast to the oligomeric structures observed for 1 and 2, single-crystal X-ray diffraction studies unambiguously establish the monomeric 4-coordinate solid-state structures of [Sn(κ2ON-OC9H6N)2)] (4) and [Sn(κ2ON-OC13H8N)2)] (5).

Membrane-mediated dimerization potentiates PIP5K lipid kinase activity.

The phosphatidylinositol 4-phosphate 5-kinase (PIP5K) family of lipid-modifying enzymes generate the majority of phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] lipids found at the plasma membrane in eukaryotic cells. PI(4,5)P2 lipids serve a critical role in regulating receptor activation, ion channel gating, endocytosis, and actin nucleation. Here, we describe how PIP5K activity is regulated by cooperative binding to PI(4,5)P2 lipids and membrane-mediated dimerization of the kinase domain. In contrast to constitutively dimeric phosphatidylinositol 5-phosphate 4-kinase (PIP4K, type II PIPK), solution PIP5K exists in a weak monomer-dimer equilibrium. PIP5K monomers can associate with PI(4,5)P2-containing membranes and dimerize in a protein density-dependent manner. Although dispensable for cooperative PI(4,5)P2 binding, dimerization enhances the catalytic efficiency of PIP5K through a mechanism consistent with allosteric regulation. Additionally, dimerization amplifies stochastic variation in the kinase reaction velocity and strengthens effects such as the recently described stochastic geometry sensing. Overall, the mechanism of PIP5K membrane binding creates a broad dynamic range of lipid kinase activities that are coupled to the density of PI(4,5)P2 and membrane-bound kinase.

Ca 2+ Regulates Dimerization of the BAR Domain Protein PICK1 and Consequent Membrane Curvature.

Bin-Amphiphysin-Rvs (BAR) domain proteins are critical regulators of membrane geometry. They induce and stabilize membrane curvature for processes, such as clathrin-coated pit formation and endosomal membrane tubulation. BAR domains form their characteristic crescent-shaped structure in the dimeric form, indicating that the formation of the dimer is critical to their function of inducing membrane curvature and suggesting that a dynamic monomer–dimer equilibrium regulated by cellular signaling would be a powerful mechanism for controlling BAR domain protein function. However, to the best of our knowledge, cellular mechanisms for regulating BAR domain dimerization remain unexplored. PICK1 is a Ca2+-binding BAR domain protein involved in the endocytosis and endosomal recycling of neuronal AMPA receptors and other transmembrane proteins. In this study, we demonstrated that PICK1 dimerization is regulated by a direct effect of Ca2+ ions via acidic regions in the BAR domain and at the N-terminus. While the cellular membrane tubulating activity of PICK1 is absent under basal conditions, Ca2+ influx causes the generation of membrane tubules that originate from the cell surface. Furthermore, in neurons, PICK1 dimerization increases transiently following NMDA receptor stimulation. We believe that this novel mechanism for regulating BAR domain dimerization and function represents a significant conceptual advance in our knowledge about the regulation of cellular membrane curvature.

Fluorescence Lifetime Phasor Analysis of the Decamer-Dimer Equilibrium of Human Peroxiredoxin 1.

Protein self-assembly is a common feature in biology and is often required for a myriad of fundamental processes, such as enzyme activity, signal transduction, and transport of solutes across membranes, among others. There are several techniques to find and assess homo-oligomer formation in proteins. Naturally, all these methods have their limitations, meaning that at least two or more different approaches are needed to characterize a case study. Herein, we present a new method to study protein associations using intrinsic fluorescence lifetime with phasors. In this case, the method is applied to determine the equilibrium dissociation constant (KD) of human peroxiredoxin 1 (hPrx1), an efficient cysteine-dependent peroxidase, that has a quaternary structure comprised of five head-to-tail homodimers non-covalently arranged in a decamer. The hPrx1 oligomeric state not only affects its activity but also its association with other proteins. The excited state lifetime of hPrx1 has distinct values at high and low concentrations, suggesting the presence of two different species. Phasor analysis of hPrx1 emission lifetime allowed for the identification and quantification of hPrx1 decamers, dimers, and their mixture at diverse protein concentrations. Using phasor algebra, we calculated the fraction of hPrx1 decamers at different concentrations and obtained KD (1.1 × 10−24 M4) and C0.5 (1.36 μM) values for the decamer–dimer equilibrium. The results were validated and compared with size exclusion chromatography. In addition, spectral phasors provided similar results despite the small differences in emission spectra as a function of hPrx1 concentration. The phasor approach was shown to be a highly sensitive and quantitative method to assess protein oligomerization and an attractive addition to the biophysicist’s toolkit.

The thermodynamics of the van der Waals dimer and trimer formation in gaseous carbon dioxide and methane and their heterodimers with dinitrogen

The equilibrium thermochemical properties of the dimers and trimers of the greenhouse gases carbon dioxide and methane, as well as their heterodimers with dinitrogen, have been calculated from the CO2 and CH4 equations of state (EOSs) and statistical mechanics. The standard dimer and trimer equilibrium constants, along with the respective ΔHoandΔSo values are reported for CO2 and CH4 between 220 and 260, and 95 and 135 K, respectively, and for the heterodimers between 100 and 250 K. Statistical mechanical calculations based on experimental and computational data of the dimers provide qualitative agreement with the EOS results. The equilibrium thermochemical properties of the CH4 dimer and the CO2–N2 and CH4–N2 heterodimers are calculated using a Morse potential to represent pairwise interactions in an “atom–diatom” model that accounts for both bound and metastable rovibrational states.

Equilibrium Thermodynamics of the Dimers and Trimers of H2 and D2 and Their Heterodimer (H2)(D2).

The equilibrium thermochemical properties of the dimers and trimers of H2 and D2 are obtained from the equations of state (EOSs) of normal H2 and D2. The standard dimer and trimer equilibrium constants K D o and K T o and ΔH D,T o and ΔS D,T o are reported for these weakly bound van der Waals molecules between 25 and 45 K. Statistical thermodynamics (ST) calculations of H2 and D2 dimerization using Morse pair potentials to account for intermolecular interactions, obtained from recent experimental work, are in qualitative agreement with the EOS results. The entropies of the H2 and D2 dimers and trimers are calculated from the EOS ΔS o values and ST calculations of the monomer entropies.

The use of DOSY experiments to determine the solution structures of coinage metal pyrazolates: The case of {[3,5-(CF3 )2 Pz]Ag}3.

A series of DOSY experiments have been carried out to determine the solution stoichiometry of silver(I) 3,5-bis (trifluoromethyl)pyrazolate species. This compound exists as a trimer in the solid state (n = 3) but in solutions of chlorinated solvents, the DOSY data suggest the presence of a mixture of solvent stabilized monomer (n = 1) and dimer (n = 2) in equilibrium. Different approximations have been used including the Stokes-Einstein and the Stokes-Einstein-Gierer-Wirtz equations. Some methodological problems are discussed.

Organic Host Encapsulation Effects on Nitrosobenzene Monomer-Dimer Distribution and C-NO Bond Rotation in an Aqueous Solution.

The intermolecular (monomer-dimer equilibrium) and intramolecular (C-NO and C-NMe2 rotations) dynamics of 4-nitrosocumene (1a) and 4-(N,N-dimethylamino)nitrosobenzene (1b), respectively, were found to be controlled by the medium (water) and the host environment (organic capsules and cavitands). The ability of water to shift the equilibrium toward the dimer appears to result from dipolar stabilization of the polar dimer structure and has a resemblance to water's known ability to favor organic cycloaddition reactions. In an aqueous medium, a range of organic hosts selectively include only the nitrosocumene monomer 1a. Encapsulation in the octa acid duplex (OA2) selects two 1a monomers rather than a dimer structure. Octa acid encapsulation also results in more restricted intramolecular C-N rotations of the guest 1b.

Photophysics of a cyanine dye in the protein-surfactant aggregates

In this work we have studied the photophysical properties of a cyanine dye merocyanine 540 (MC540) in the presence as well as in the absence of bovine serum albumin (BSA) along with anionic surfactants sodium dodecyl sulfate(SDS) and sodium tetradecyl sulfate (STDS) and cationic surfactants cetrimonium bromide (CTAB) and dodecyltrimethylammonium bromide (DTAB) with the help of various spectroscopic methods. MC540 in protein-surfactant aggregates as well as surfactant aggregates interacts differently with anionic and cationic surfactants. MC540 exits in both monomer and dimer form in the buffer medium however, in protein-surfactant aggregates and surfactant aggregates monomer–dimer equilibrium is perturbed, where only the monomer form exists. By employing various spectroscopic methods it is evident that in the presence of cationic and anionic surfactants, MC540 strongly interacts with cationic micelles compared to anionic micelles. MC540 being a negatively charged molecule in the buffer medium, electrostatic repulsion is predominant with anionic surfactants whereas, electrostatic attraction is predominant with cationic surfactants in protein-surfactant aggregates as well as in micelles.

Probing the equilibrium between mono- and di-nuclear nickel(II)-diamidate {[NiII(DQPD)]x, x = 1,2} complexes in chloroform solutions by combining acoustic and vibrational spectroscopies and molecular orbital calculations

• Formation of a mono-nuclear Ni II complex in the solid state. • Formation of two distinct types of Ni II complexes in chloroform solutions. • We propose a dimerization equilibrium between mono- and di-nuclear complexes in solutions. • The [Ni II 2 (DQPD) 2 ] di-nuclear complex as the most thermodynamically favorable. • At low-C or high-T mono-nuclear complex dominates, while in the high-C or low-T di-nuclear abounds. In this work a systematic study has been undertaken by combining vibrational and ultrasonic spectroscopies with molecular orbital calculations in an effort to gain a comprehensive understanding of the structural and dynamic characteristics of the [Ni II (DQPD)] x complexes in the solid state and in chloroform solutions. Vibrational spectra revealed (i) the formation of a mono-nuclear Ni II complex in the solid state and (ii) the formation of two distinct types of Ni II complexes in chloroform solutions. The concentration-dependent vibrational spectroscopic measurements indicated that at low-concentrations mono-nuclear complex dominates, while in the high-concentration limit di-nuclear abounds in the structure. The temperature dependence of the spectra demonstrated the exact opposite behavior to that of concentration. We propose a dimerization equilibrium between mono- and di-nuclear complexes to account for the observed spectral changes. The energy profile of the dimerization reaction was theoretically determined exhibiting the [Ni II 2 (DQPD) 2 ] di-nuclear complex as the most thermodynamically favorable. Ultrasonic relaxation spectroscopy has been employed to establish the proposed dimerization equilibrium. The absorption results demonstrate the existence of a relaxation process which is attributed to the perturbation by the sound wave of an equilibrium between mono-nuclear and di-nuclear complexes. The enthalpy difference between the two states is also evaluated from the analysis of the acoustic results. The acoustically induced birefringence traces (stationary and transient) were also employed to examine the dynamic response of the Ni II complexes in solutions, which directly reflects the structural modifications. From the transient birefringence signals the corresponding relaxation times have been estimated and correlated with the volume change associated to the structural reforms. Complementary computational methodologies have been implemented on isolated molecules in a state free of interactions and in solution with chloroform as solvent medium. The calculations performed provided information concerning the volume change between the two states.

Interactions between semaphorins and plexin–neuropilin receptor complexes in the membranes of live cells

Signaling of semaphorin ligands via their plexin–neuropilin receptors is involved in tissue patterning in the developing embryo. These proteins play roles in cell migration and adhesion but are also important in disease etiology, including in cancer angiogenesis and metastasis. While some structures of the soluble domains of these receptors have been determined, the conformations of the full-length receptor complexes are just beginning to be elucidated, especially within the context of the plasma membrane. Pulsed-interleaved excitation fluorescence cross-correlation spectroscopy allows direct insight into the formation of protein–protein interactions in the membranes of live cells. Here, we investigated the homodimerization of neuropilin-1 (Nrp1), plexin A2, plexin A4, and plexin D1 using pulsed-interleaved excitation fluorescence cross-correlation spectroscopy. Consistent with previous studies, we found that Nrp1, plexin A2, and plexin A4 are present as dimers in the absence of exogenous ligand. Plexin D1, on the other hand, was monomeric under similar conditions, which had not been previously reported. We also found that plexin A2 and A4 assemble into a heteromeric complex. Stimulation with semaphorin 3A or semaphorin 3C neither disrupts nor enhances the dimerization of the receptors when expressed alone, suggesting that activation involves a conformational change rather than a shift in the monomer–dimer equilibrium. However, upon stimulation with semaphorin 3C, plexin D1 and Nrp1 form a heteromeric complex. This analysis of interactions provides a complementary approach to the existing structural and biochemical data that will aid in the development of new therapeutic strategies to target these receptors in cancer.

Structural polymorphism and substrate promiscuity of a ribosome-associated molecular chaperone.

Trigger factor (TF) is a highly conserved multi-domain molecular chaperone that exerts its chaperone activity at the ribosomal tunnel exit from which newly synthesized nascent chains emerge. TF also displays promiscuous substrate binding for a large number of cytosolic proteins independent of ribosome binding. We asked how TF recognizes a variety of substrates while existing in a monomer-dimer equilibrium. Paramagnetic nuclear magnetic resonance (NMR) and electron spin resonance (ESR) spectroscopy were used to show that dimeric TF displays a high degree of structural polymorphism in solution. A series of peptides has been generated to quantify their TF binding affinities in relation with their sequence compositions. The results confirmed a previous predication that TF preferentially binds to peptide fragments that are rich in aromatic and positively charged amino acids. NMR paramagnetic relaxation enhancement analysis showed that TF utilizes multiple binding sites, located in the chaperone domain and part of the prolyl trans-cis isomerization domain, to interact with these peptides. Dimerization of TF effectively sequesters most of the substrate binding sites, which are expected to become accessible upon binding to the ribosome as a monomer. As TF lacks ATPase activity, which is commonly used to trigger conformational changes within molecular chaperones in action, the ribosome-binding-associated disassembly and conformational rearrangements may be the underlying regulatory mechanism of its chaperone activity.