Monomer Dimer Research Articles

Langmuir-Schaefer films based on cyclotriphosphazene-substituted phthalocyanines: Supramolecular organization, UV/Vis study, and laser-induced nonlinear absorption

Low-defective thin films of 2-hydroxy-9(10),16(17),23(24)-tri-tert-butylphthalocyanine (1), as well as its cyclotriphosphazene-substituted derivatives, monomer (2) and clamshell-like dimer (3), have been obtained and extensively studied. It is shown that these dyes produce stable floating layers with a certain number of three-dimensional aggregates at the air/water interface. The floating layers retain their structure when transferred to a glass substrate by the Langmuir-Schaefer method, demonstrating the H-aggregation of the dyes. In contrast to the initial monohydroxyphthalocyanine 1, thin films of its derivatives, cyclotriphosphazene-substituted monomer 2 and dimer 3, show a slight increase in absorption when the number of deposited layers exceeds 100. It is shown that thin films of the studied dyes 1–3 can be used in the technology of optical limitation of laser radiation, demonstrating a good cutting efficiency of dangerous nanosecond pulses.

High-Throughput Characterization and Optimization of Polyamide Hydrolase Activity Using Open Port Sampling Interface Mass Spectrometry.

Enzymatic biodegradation of polymers, such as polyamides (PA), has the potential to cost-effectively reduce plastic waste, but enhancements in degradation efficiency are needed. Engineering enzymes through directed evolution is one pathway toward identification of critical domains needed for improving activity. However, screening such enzymatic libraries (100s-to-1000s of samples) is time-consuming. Here we demonstrate the use of robotic autosampler (PAL) and immediate drop on demand technology (I.DOT) liquid handling systems coupled with open-port sampling interface-mass spectrometry (OPSI-MS) to screen for PA6 and PA66 hydrolysis by 6-aminohexanoate-oligomer endo-hydrolase (nylon hydrolase, NylC) in a high-throughput (8-20 s/sample) manner. The OPSI-MS technique required minimal sample preparation and was amenable to 96-well plate formats for automated processing. Enzymatic hydrolysis of PA characteristically produced soluble linear oligomer products that could be identified by OPSI-MS. Incubation temperatures and times were optimized for PA6 (65 °C, 24 h) and PA66 (75 °C, 24 h) over 108 experiments. In addition, the I.DOT/OPSI-MS quantified production of PA6 linear dimer (8.3 ± 1.6 μg/mL) and PA66 linear monomer (13.5 ± 1.5 μg/mL) by NylC with a lower limit of detection of 0.029 and 0.032 μg/mL, respectively. For PA6 and PA66, linear oligomer production corresponded to 0.096 ± 0.018% and 0.204 ± 0.028% conversion of dry pellet mass, respectively. The developed methodology is expected to be utilized to assess enzymatic hydrolysis of engineered enzyme libraries, comprising hundreds to thousands of individual samples.

Post-harvest ripening affects drying behavior, antioxidant capacity and flavor release of peach via alteration of cell wall polysaccharides content and nanostructures, water distribution and status

Effect of post-harvest ripening on cell wall polysaccharides nanostructures, water status, physiochemical properties of peaches and drying behavior under hot air-infrared drying was evaluated. Results showed that the content of water soluble pectins (WSP) increased by 94 %, while the contents of chelate-soluble pectins (CSP), Na2CO3-soluble pectins (NSP) and hemicelluloses (HE) decreased during post-harvest ripening by 60 %, 43 %, and 61 %, respectively. The drying time increased from 3.5 to 5.5 h when the post-harvest time increased from 0 to 6 days. Atomic force microscope analysis showed that depolymerization of hemicelluloses and pectin occurred during post-harvest ripening. Time Domain -NMR observations indicated that reorganization of cell wall polysaccharides nanostructure changed water spatial distribution and cell internal structure, facilitated moisture migration, and affected antioxidant capacity of peaches during drying. This leads to the redistribution of flavor substances (heptanal, n-nonanal dimer and n-nonanal monomer). The current work elucidates the effect of post-harvest ripening on the physiochemical properties and drying behavior of peaches.

The cytoplasmic N-terminal tail of Zika virus NS4A protein forms oligomers in the absence of detergent or lipids

The non-structural (NS) NS4A protein in flaviviruses has three predicted transmembrane domains, is critical for virulence and participates in membrane morphogenesis. In Dengue virus (DENV), both hydrophylic N-terminal tail and its first transmembrane domain participate in the formation of oligomers which are important for pathogenicity. However, the relative importance of the N-terminal domain in oligomerization has been under debate. In particular, since in the absence of detergent or lipids, this domain (residues 1–48) in both DENV and Zika virus (ZIKV) NS4A, was found to be disordered. Recently, however, we reported preliminary data that showed that peptide ZIKV NS4A 4–58 adopts a defined secondary structure in aqueous solution and forms oligomers, signaling its importance for full length NS4A oligomerization. Herein we have performed detailed analytical ultracentrifugation experiments to further characterize the oligomerization of this peptide and also a shorter variant (residues 4–44). In both cases, sedimentation velocity produced a single species with concentration-dependent sedimentation coefficient, consistent with a fast equilibrium between at least two species. Combining sedimentation velocity and equilibrium experiments, data is best fitted to a monomer–dimer–trimer equilibrium. Possible models of NS4A oligomers obtained with AlphaFold-2 predict the stabilizing role for residues in this N-terminal domain, such as Arg20, Asn27, Ala44 and Glu50, all at highly conserved positions in flavivirus NS4A proteins. Our results are thus consistent with N-terminal domain interactions acting as one of the driving forces for NS4A homo-oligomerization.

Monomeric crystal structure of the vaccine carrier protein CRM197 and implications for vaccine development.

CRM197 is a genetically detoxified mutant of diphtheria toxin (DT) that is widely used as a carrier protein in conjugate vaccines. Protective immune responses to several bacterial diseases are obtained by coupling CRM197 to glycans from these pathogens. Wild-type DT has been described in two oligomeric forms: a monomer and a domain-swapped dimer. Their proportions depend on the chemical conditions and especially the pH, with a large kinetic barrier to interconversion. A similar situation occurs in CRM197, where the monomer is preferred for vaccine synthesis. Despite 30 years of research and the increasing application of CRM197 in conjugate vaccines, until now all of its available crystal structures have been dimeric. Here, CRM197 was expressed as a soluble, intracellular protein in an Escherichia coli strain engineered to have an oxidative cytoplasm. The purified product, called EcoCRM, remained monomeric throughout crystallization. The structure of monomeric EcoCRM is reported at 2.0 Å resolution with the domain-swapping hinge loop (residues 379-387) in an extended, exposed conformation, similar to monomeric wild-type DT. The structure enables comparisons across expression systems and across oligomeric states, with implications for monomer-dimer interconversion and for the optimization of conjugation.

Exploration of Solid-State vs Solution-State Structure in Contact Ion Pair Systems: Synthesis, Characterization, and Solution-State Dynamics of Zinc Diphenyl Phosphate, [Zn{O2P(OPh)2}2], Donor-Base-Supported Complexes.

A family of zinc phosphate complexes supported by nitrogen donor-base ligands have been synthesized, and their molecular structures were identified in both the solid (X-ray crystallography) and solution state (DOSY NMR spectroscopy). [Zn{O2P(OPh)2}2]∞ (1), formed from the reaction of Zn[N(SiMe3)2]2 with HO(O)P(OPh)2 coordinates to donor-base ligands, i.e., pyridine (Py), 4-methylpyridine (4-MePy), 2,2-bipyridine (bipy), tetramethylethylenediamine (TMEDA), pentamethyldiethylenetriamine (PMDETA), and 1,3,5-trimethyl-1,3,5-triazacyclohexane (Me3-TAC), to produce polymeric 1D structures, [(Py)2Zn{O2P(OPh)2}2]∞ (2) and [(4-MePy)2Zn{O2P(OPh)2}2]∞ (3), the bimetalic systems, [(Bipy)Zn{O2P(OPh)2}2]2 (4), [(TMEDA)Zn{O2P(OPh)2}2]2 (5), and [(Me3-TAC)Zn{O2P(OPh)2}2]2 (7), as well as a mono-nuclear zinc bis-diphenylphosphate complex, [(PMDETA)Zn{O2P(OPh)2}2] (6). 1H NMR DOSY has been used to calculate averaged molecular weights of the species. Studies are consistent with the disassembly of polymeric 3 into the bimetallic species [(Me-Py)2·Zn2{O2P(OPh)2}4], where the Me-Py ligand is in rapid exchange with free Me-Py in solution. Further 1H DOSY NMR studies of 4 and 5 reveal that dissolution of the complex results in a monomer dimer equilibrium, i.e., [(Bipy)Zn{O2P(OPh)2}2]2 ⇆ 2[(Bipy)Zn{O2P(OPh)2}2] and [(TMEDA)Zn{O2P(OPh)2}2]2 ⇆ 2[(TMEDA)Zn{O2P(OPh)2}2], respectively, in which the equilibria lie toward formation of the monomer. As part of our studies, variable temperature 1H DOSY experiments (223 to 313 K) were performed upon 5 in d8-tol, which allowed us to approximate the enthalpy [ΔH = -43.2 kJ mol-1 (±3.79)], entropy [ΔS = 109 J mol-1 K-1 (±13.9)], and approximate Gibbs free energy [ΔG = 75.6 kJ mol-1 (±5.62) at 293 K)] of monomer-dimer equilibria. While complex 6 is shown to maintain its monomeric solid-state structure, 1H DOSY experiments of 7 at 298 K reveal two separate normalized diffusion coefficients consistent with the presence of the bimetallic species [(TAC)2-xZn2{O2P(OPh)2}4], (x = 1 or 0) and free TAC ligand.

An Investigation of the Temperature Dependence of a Monomer–Dimer Equilibrium Using UV–Vis and 1H NMR Spectroscopies

A laboratory experiment in which 1H NMR and UV–vis spectroscopies are applied to probe the temperature dependence of a monomer–dimer equilibrium involving a cyclopentadienone derivative is described and discussed. Details of the data analysis for extraction of equilibrium constants from the raw experimental data from both techniques are provided, leading to the determination of thermodynamic parameters (ΔrH° and ΔrS°) via van’t Hoff analysis. Fully analyzed datasets are provided in the Supporting Information to aid adaptation of the experiment or its use as a data analysis activity.

Lactose and Galactose Promote the Crystallization of Human Galectin-10.

Galectin-10 (Gal-10) forms Charcot-Leyden crystals (CLCs), which play a key role in the symptoms of asthma and allergies and some other diseases. Gal-10 has a carbohydrate-binding site; however, neither the Gal-10 dimer nor the CLCs can bind sugars. To investigate the monomer-dimer equilibrium of Gal-10, high-performance size-exclusion chromatography (SEC) was employed to separate serial dilutions of Gal-10 with and without carbohydrates. We found that both the dimerization and crystallization of Gal-10 were promoted by lactose/galactose binding. A peak position shift for the monomer was observed after treatment with either lactose or galactose, implying that the polarity of the monomer was reduced by lactose/galactose binding. Further experiments indicated that alkaline conditions of pH 8.8 mimicked the lactose/galactose-binding environment, and the time interval between monomers and dimers in the chromatogram decreased from 0.8 min to 0.4 min. Subsequently, the electrostatic potential of the Gal-10 monomers was computed. After lactose/galactose binding, the top side of the monomer shifted from negatively charged to electrically neutral, allowing it to interact with the carbohydrate-binding site of the opposing subunit during dimerization. Since lactose/galactose promotes the crystallization of Gal-10, our findings implied that dairy-free diets (free of lactose/galactose) might be beneficial to patients with CLC-related diseases.

Intermolecular interactions in clusters of ethylammonium nitrate and 1-amino-1,2,3-triazole.

The intermolecular interaction energies, including hydrogen bonds (H-bonds), of clusters of the ionic liquid ethylammonium nitrate (EAN) and 1-amino-1,2,3-triazole (1-AT) based deep eutectic propellants (DeEP) are examined. 1-AT is introduced as a neutral hydrogen bond donor (HBD) to EAN in order to form a eutectic mixture. The effective fragment potential (EFP) is used to examine the bonding interactions in the DeEP clusters. The resolution of the Identity (RI) approximated second order Møller-Plesset perturbation theory (RI-MP2) and coupled cluster theory (RI-CCSD(T)) are used to validate the EFP results. The EFP method predicts that there are significant polarization and charge transfer effects in the EAN:1-AT complexes, along with Coulombic, dispersion and exchange repulsion interactions. The EFP interaction energies are in good agreement with the RI-MP2 and RI-CCSD(T) results. The quasi-atomic orbital (QUAO) bonding and kinetic bond order (KBO) analyses are additionally used to develop a conceptual and semi-quantitative understanding of the H-bonding interactions as a function of the size of the system. The QUAO and KBO analyses suggest that the H-bonds in the examined clusters follow the characteristic hydrogen bonding three-center four electron interactions. The strongest H-bonding interactions between the (EAN)1:(1-AT)n and (EAN)2:(1-AT)n (n = 1-5) complexes are observed internally within EAN; that is, between the ethylammonium cation [EA]+ and the nitrate anion ([NO3]-). The weakest H-bonding interactions occur between [NO3]- and 1-AT. Consequently, the average strengths of the H-bonds within a given (EAN)x:(1-AT)n complex decrease as more 1-AT molecules are introduced into the EAN monomer and EAN dimer. The QUAO bonding analysis suggests that 1-AT in (EAN)x:(1-AT)n can act as both a HBD and a hydrogen bond acceptor simultaneously. It is observed that two 1-AT molecules can form H-bonds to each other. Although the KBOs that correspond to H-bonding interactions in [EA]+:1-AT, [NO3]-:1-AT and between two 1-AT molecules are weaker than the H-bonds in EAN, those weak H-bond networks with 1-AT could be important to form a stable DeEP.

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.

SARS-CoV-2 accessory protein 7b forms homotetramers in detergent

A global pandemic is underway caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The SARS-CoV-2 genome, like its predecessor SARS-CoV, contains open reading frames that encode accessory proteins involved in virus-host interactions active during infection and which likely contribute to pathogenesis. One of these accessory proteins is 7b, with only 44 (SARS-CoV) and 43 (SARS-CoV-2) residues. It has one predicted transmembrane domain fully conserved, which suggests a functional role, whereas most variability is contained in the predicted cytoplasmic C-terminus. In SARS-CoV, 7b protein is expressed in infected cells, and the transmembrane domain was necessary and sufficient for Golgi localization. Also, anti-p7b antibodies have been found in the sera of SARS-CoV convalescent patients. In the present study, we have investigated the hypothesis that SARS-2 7b protein forms oligomers with ion channel activity. We show that in both SARS viruses 7b is almost completely α-helical and has a single transmembrane domain. In SDS, 7b forms various oligomers, from monomers to tetramers, but only monomers when exposed to reductants. Combination of SDS gel electrophoresis and analytical ultracentrifugation (AUC) in both equilibrium and velocity modes suggests a dimer-tetramer equilibrium, but a monomer–dimer–tetramer equilibrium in the presence of reductant. This data suggests that although disulfide-linked dimers may be present, they are not essential to form tetramers. Inclusion of pentamers or higher oligomers in the SARS-2 7b model were detrimental to fit quality. Preliminary models of this association was generated with AlphaFold2, and two alternative models were exposed to a molecular dynamics simulation in presence of a model lipid membrane. However, neither of the two models provided any evident pathway for ions. To confirm this, SARS-2 p7b was studied using Planar Bilayer Electrophysiology. Addition of p7b to model membranes produced occasional membrane permeabilization, but this was not consistent with bona fide ion channels made of a tetrameric assembly of α-helices.

Applications of spectroscopic techniques to the study of monomer–dimer equilibria for methylene blue in aqueous solutions containing ionic liquid: Probing the structural interactions involving water and ionic liquids

An understanding of the nature of interaction and bonding in dye aggregation process is important for such diverse problems and applications such as stacking interactions in biomolecules, staining properties, photodynamic therapy for cancer, energy transfer in lasing technology and energy transfer and electron transfer processes. In present communication we report visible absorption spectrums and their analysis for the dye methylene blue (MB) in concentration range of 1∙10–6 – 1∙10–4 M in aqueous solutions containing ionic liquids namely, 1–ethyl–3–methyl–imidazolium bromide, 1–butyl–3–methyl–imidazolium bromide and 1–hexyl–3–methyl–imidazolium bromide at 298 ± 1. In this concentration range of MB only Monomer ⇌ Dimer equilibria for the dye exist and hence the spectral characteristics in the visible range of 550–700 nm have been examined. The spectrums obtained are compared with those obtained in aqueous solutions of NaCl. Using suitable developed method of estimating molar absorption extinction coefficient values, the equilibrium constant values are obtained at various ionic strengths of imidazolium ions. It has been found that monomer and dimer absorption maximum occur at 665 and ≈605/610 nm, respectively, do not get much altered on addition of imidazolium ions. The extent of interaction between the MB and imidazolium cations varies with the concentration of imidazolium cations as well as the nature of imidazolium cations, that is, the chain length of the substituents. The dimer dissociation constant values extrapolated to zero ionic strength of ionic liquids exhibit systematic alteration with respect to alteration of chain length in imidazolium cations. The different interactional phenomena such as the formation of ion–pairs, ion–pair complexes, dimer dissociation, solubilization of monomers and binding of MB with imidazolium cations have been examined. The transfer standard free energy changes have been calculated for the transfer of dimers from aqueous solutions to aqueous solutions containing ionic liquids. The changes in dimer geometry from sandwich type and end–on–end types also have been studied. It is observed that the contribution to the interaction energy is mainly from van der Waals type and dispersion forces, in addition to short range forces involving multipoles. The binding of monomers with imidazolium cations is also examined in terms of formation of micellar type aggregates in solution phase. It is proposed that the water structural interaction and hydrophobic interactions are the major factors in the formation and dissociation of aggregates.

Molecular Insights into the Misfolding and Dimerization Dynamics of the Full-Length α-Synuclein from Atomistic Discrete Molecular Dynamics Simulations.

The misfolding and pathological aggregation of α-synuclein forming insoluble amyloid deposits is associated with Parkinson's disease, the second most common neurodegenerative disease in the world population. Characterizing the self-assembly mechanism of α-synuclein is critical for discovering treatments against synucleinopathies. The intrinsically disordered property, high degrees of freedom, and macroscopic timescales of conformational conversion make its characterization extremely challenging in vitro and in silico. Here, we systematically investigated the dynamics of monomer misfolding and dimerization of the full-length α-synuclein using atomistic discrete molecular dynamics simulations. Our results suggested that both α-synuclein monomers and dimers mainly adopted unstructured formations with partial helices around the N-terminus (residues 8-32) and various β-sheets spanning the residues 35-56 (N-terminal tail) and residues 61-95 (NAC region). The C-terminus mostly assumed an unstructured formation wrapping around the lateral surface and the elongation edge of the β-sheet core formed by an N-terminal tail and NAC regions. Dimerization enhanced the β-sheet formation along with a decrease in the unstructured content. The inter-peptide β-sheets were mainly formed by the N-terminal tail and NACore (residues 68-78) regions, suggesting that these two regions played critical roles in the amyloid aggregation of α-synuclein. Interactions of the C-terminus with the N-terminal tail and the NAC region were significantly suppressed in the α-synuclein dimer, indicating that the interaction of the C-terminus with the N-terminal tail and NAC regions could prevent α-synuclein aggregation. These results on the structural ensembles and early aggregation dynamics of α-synuclein will help understand the nucleation and fibrillization of α-synuclein.

Protein adsorption and separation with monomodal and multimodal anion exchange chromatography resins. Part II. Mechanisms of protein aggregation on the chromatographic surface

AbstractBACKGROUNDProteins on chromatographic surfaces can undergo conformational changes, leading to aggregate formation. Such effects have been reported previously for hydrophobic interaction and cation exchange chromatography. In Part I of this work, we examined protein adsorption behavior on monomodal (Nuvia HP‐Q) and multimodal anion exchangers (Nuvia aPrime and Capto Adhere), observing that aggregates are also formed on these multimodal resins. In this work we examine the underlying mechanisms and the conditions that affect aggregate formation.RESULTSIncubating the multimodal anion exchangers with pure bovine serum albumin monomer at low ionic strength results in the formation of dimer and higher‐order oligomers (up to hexamers) to an extent that depends on the incubation time. The percentage of total protein initially bound that is desorbed decreased from >85% with a 5 min incubation to <40% with 24 h incubation at pH 7.0, indicating that additional irreversibly bound species are formed on the resin surface. Load buffers leading to stronger binding (higher pH and/or lower salt) and higher temperatures (32 °C) result in more extensive aggregation. Minimal aggregation occurs, instead, for Nuvia HP‐Q.CONCLUSIONBSA oligomers are formed directly on the surface of the multimodal resins studied and are eluted as discrete species at increasing salt concentrations. Aggregate formation is promoted by the ligand hydrophobicity and affects the separation of monomer–dimer mixtures by frontal chromatography, as the ability of the dimer in the feed to displace the adsorbed protein is impaired by gradual conversion of the monomer to stronger bound species. © 2022 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).

Protein adsorption and separation with monomodal and multimodal anion exchange chromatography resins. Part I. Multicomponent adsorption properties and frontal chromatography

AbstractBACKGROUNDMultimodal ion exchangers, containing ligands combining charged and hydrophobic moieties, exhibit enhanced separation compared to monomodal ion exchangers under low loading conditions. Commercial applications often require high protein loads and such conditions have not been investigated extensively, especially for multimodal anion exchangers. This work compares protein adsorption and separation by frontal chromatography for a commercial monomodal (Nuvia HP‐Q) and two multimodal anion exchangers (Nuvia aPrime and Capto Adhere) using bovine serum albumin (BSA) monomer and dimer as a model.RESULTSGreater dimer–monomer selectivity is observed for Nuvia aPrime and Capto Adhere than for Nuvia HP‐Q at low protein loads. However, binary adsorption isotherms at high protein loads show higher binding capacity and greater selectivity for Nuvia HP‐Q, despite having the same ligand density. Higher salt concentrations reduce the binding strength in all cases, but this reduction is less pronounced for the multimodal resins. As a result, selectivity increases for the latter at higher salt concentrations. Confocal laser scanning microscopy shows that, during co‐adsorption, displacement of the monomer by the dimer occurs for each resin. However, displacement becomes very slow for the multimodal resins during sequential adsorption. The multimodal resins give poorer separation by frontal chromatography, accompanied by low recovery and substantial on‐column formation of protein aggregates.CONCLUSIONThe selectivity of multimodal anion exchangers for separation of the model proteins studied varies with salt concentration and protein load. At high protein loads, multimodal resins can result in on‐column aggregate formation negatively impacting the kinetics of competitive binding and separation. © 2022 The Authors. Journal of Chemical Technology and Biotechnology published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry (SCI).

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.

Dimerization processes for light-regulated transcription factor Photozipper visualized by high-speed atomic force microscopy

Dimerization is critical for transcription factors (TFs) to bind DNA and regulate a wide variety of cellular functions; however, the molecular mechanisms remain to be completely elucidated. Here, we used high-speed atomic force microscopy (HS-AFM) to observe the dimerization process for a photoresponsive TF Photozipper (PZ), which consists of light–oxygen–voltage-sensing (LOV) and basic-region-leucine-zipper (bZIP) domains. HS-AFM visualized not only the oligomeric states of PZ molecules forming monomers and dimers under controlled dark–light conditions but also the domain structures within each molecule. Successive AFM movies captured the dimerization process for an individual PZ molecule and the monomer–dimer reversible transition during dark–light cycling. Detailed AFM images of domain structures in PZ molecules demonstrated that the bZIP domain entangled under dark conditions was loosened owing to light illumination and fluctuated around the LOV domain. These observations revealed the role of the bZIP domain in the dimerization processes of a TF.

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.

Comparison of Experimental Approaches Used to Determine the Structure and Function of the Class D G Protein-Coupled Yeast α-Factor Receptor.

The Saccharomyces cerevisiae α-factor mating pheromone receptor (Ste2p) has been studied as a model for the large medically important family of G protein-coupled receptors. Diverse yeast genetic screens and high-throughput mutagenesis of STE2 identified a large number of loss-of-function, constitutively-active, dominant-negative, and intragenic second-site suppressor mutants as well as mutations that specifically affect pheromone binding. Facile genetic manipulation of Ste2p also aided in targeted biochemical approaches, such as probing the aqueous accessibility of substituted cysteine residues in order to identify the boundaries of the seven transmembrane segments, and the use of cysteine disulfide crosslinking to identify sites of intramolecular contacts in the transmembrane helix bundle of Ste2p and sites of contacts between the monomers in a Ste2p dimer. Recent publication of a series of high-resolution cryo-EM structures of Ste2p in ligand-free, agonist-bound and antagonist-bound states now makes it possible to evaluate the results of these genetic and biochemical strategies, in comparison to three-dimensional structures showing activation-related conformational changes. The results indicate that the genetic and biochemical strategies were generally effective, and provide guidance as to how best to apply these experimental strategies to other proteins. These strategies continue to be useful in defining mechanisms of signal transduction in the context of the available structures and suggest aspects of receptor function beyond what can be discerned from the available structures.

Theoretical discussion on the Hydrogen Bond Interactions between Acrylic Acid dimer and dibutyl ether Monomer

Theoretical investigation has been carried out on various acrylic acid (AcA) dimers and dibutyl ether (DBE) + AcA complex structures. The frequency analysis of the structures reveals the dominating effect of dissociation/formation of AcAO-H⋯O=C(AcA) bonds in producing blue/red shifts of ν(O-H) and ν(C=O) bonds. The classical AcAO-H⋯O(DBE) H - bond has high interaction energy as per the NBO analysis. The ESP surface analysis signals that the mesomerism existed in the acid monomers and dimers gets suppressed in the H – bonded structures that have non – classical intermolecular interactions. The non-classical intramolecular H – bond and van der Waals interactions in the acid monomers, dimers and the heteromolecular complexes has been identified using the RDG isosurface. The ρ(r) at the BCP of classical hydrogen bonds of the dimers is slightly greater than the upper limit of the literature value. The ∇2ρr value suggests that the C=O/O-H bond is with the least/highest covalent character.