Enantio- and Diastereomerically Pure Titanocenes by Dynamic Conformational Locking

The synthesis of enantiomerically pure titanocenes is limited to cases with enantiomerically pure substituents at the cyclopentadienyl ligands and to ansa-titanocenes. For the latter complexes, the use of achiral ligands requires a resolution of enantiomers and frequently also a separation of the diastereoisomers obtained after metalation. Here, we introduce a new synthetic method that relies on the use of enantiomerically pure camphorsulfonate (CSA) ligands as control elements for the absolute and relative configuration of titanocene complexes. Starting from the conformationally flexible (RC5 H4 )2 TiCl2 , the desired conformationally locked and hence enantio- and diastereomerically pure complexes (RC5 H4 )2 Ti(CSA)2 are obtained in just two steps. According to X-ray crystallography the (RC5 H4 )2 Ti fragment is essentially C2 -symmetric and nuclear magnetic resonance displays overall C2 -symmetry. We applied density functional theory methods to unravel the dynamics of the complexes and the mechanisms and selectivities of their formation.

Effects of quercetin on the gel properties of pork myofibrillar proteins and related changes in protein conformation

BACKGROUND

To study the effects of quercetin on the functionality of myofibrillar proteins (MPs), various levels of quercetin (0, 10, 50, 100 and 200 μmol g^-1 protein) were added to MP solution and the structure and gel properties of MPs were determined.

RESULTS

Compared with the control MPs not treated with quercetin, adding 10, 50 and 100 μmol g^-1 quercetin caused a significant (P < 0.05) loss of sulfhydryls; 10 and 50 μmol g^-1 quercetin enhanced the surface hydrophobicity significantly (P < 0.05), and 50, 100 and 200 μmol g^-1 quercetin reduced the fluorescence intensity of tryptophan. Additions of 50, 100 and 200 μmol g^-1 quercetin resulted in a significant (P < 0.05) reduction in MP solubility. Adding 10, 50 and 100 μmol g^-1 quercetin did not significantly (P > 0.05) change the gel strength and water-holding ability of MPs than control, but 200 μmol g^-1 quercetin declined the gel properties significantly (P < 0.05). The microstructure and dynamic rheological properties confirmed the results of the gel properties of MPs affected by various levels of quercetin.

CONCLUSION

The results obtained in the present study show that mildly high levels of quercetin can maintain the gel properties of MPs, which may be a result of the moderate MP cross-linkage and aggregation caused by the covalent and non-covalent interactions of MPs. © 2023 Society of Chemical Industry.

Wiggle and Shake: Managing and Exploiting Conformational Dynamics during Proteasome Biogenesis

The 26S proteasome is the largest and most complicated protease known, and changes to proteasome assembly or function contribute to numerous human diseases. Assembly of the 26S proteasome from its ~66 individual polypeptide subunits is a highly orchestrated process requiring the concerted actions of both intrinsic elements of proteasome subunits, as well as assistance by extrinsic, dedicated proteasome assembly chaperones. With the advent of near-atomic resolution cryo-electron microscopy, it has become evident that the proteasome is a highly dynamic machine, undergoing numerous conformational changes in response to ligand binding and during the proteolytic cycle. In contrast, an appreciation of the role of conformational dynamics during the biogenesis of the proteasome has only recently begun to emerge. Herein, we review our current knowledge of proteasome assembly, with a particular focus on how conformational dynamics guide particular proteasome biogenesis events. Furthermore, we highlight key emerging questions in this rapidly expanding area.

Hexahexyloxycalix[6]arene, a Conformationally Adaptive Host for the Complexation of Linear and Branched Alkylammonium Guests

Hexahexyloxycalix[6]arene 2b leads to the endo-cavity complexation of linear and branched alkylammonium guests showing a conformational adaptive behavior in CDCl₃ solution. Linear n-pentylammonium guest 6a⁺ induces the cone conformation of 2b at the expense of the 1,2,3-alternate, which is the most abundant conformer of 2b in the absence of a guest. In a different way, branched alkylammonium guests, such as tert-butylammonium 6b⁺ and isopropylammonium 6c⁺, select the 1,2,3-alternate as the favored 2b conformation (6b⁺/6c⁺&sub;2b^1,2,3-alt), but other complexes in which 2b adopts different conformations, namely, 6b⁺/6c⁺&sub;2b^cone, 6b⁺/6c⁺&sub;2b^paco, and 6b⁺/6c⁺&sub;2b^1,2-alt, have also been revealed. Binding constant values determined via NMR experiments indicated that the 1,2,3-alternate was the best-fitting 2b conformation for the complexation of branched alkylammonium guests, followed by cone > paco > 1,2-alt. Our NCI and NBO calculations suggest that the H-bonding interactions (⁺N-H···O) between the ammonium group of the guest and the oxygen atoms of calixarene 2b are the main determinants of the stability order of the four complexes. These interactions are weakened by increasing the guest steric encumbrance, thus leading to a lower binding affinity. Two stabilizing H-bonds are possible with the 1,2,3-alt- and cone-2b conformations, whereas only one H-bond is possible with the other paco- and 1,2-alt-2b stereoisomers.

GPCR Binding and JNK3 Activation by Arrestin-3 Have Different Structural Requirements

Arrestins bind active phosphorylated G protein-coupled receptors (GPCRs). Among the four mammalian subtypes, only arrestin-3 facilitates the activation of JNK3 in cells. In available structures, Lys-295 in the lariat loop of arrestin-3 and its homologue Lys-294 in arrestin-2 directly interact with the activator-attached phosphates. We compared the roles of arrestin-3 conformational equilibrium and Lys-295 in GPCR binding and JNK3 activation. Several mutants with enhanced ability to bind GPCRs showed much lower activity towards JNK3, whereas a mutant that does not bind GPCRs was more active. The subcellular distribution of mutants did not correlate with GPCR recruitment or JNK3 activation. Charge neutralization and reversal mutations of Lys-295 differentially affected receptor binding on different backgrounds but had virtually no effect on JNK3 activation. Thus, GPCR binding and arrestin-3-assisted JNK3 activation have distinct structural requirements, suggesting that facilitation of JNK3 activation is the function of arrestin-3 that is not bound to a GPCR.

Photoallosteric Polymersomes toward On-Demand Drug Delivery and Multimodal Cancer Immunotherapy

Allosteric transitions can modulate the self-assembly and biological function of proteins. It remains, however, tremendously challenging to design synthetic allosteric polymeric assemblies with spatiotemporally switchable hierarchical structures and functionalities. Here, a photoallosteric polymersome is constructed that undergoes a rapid conformational transition from β-sheet to α-helix upon exposure to near-infrared light irradiation. In addition to improving nanoparticle cell penetration and lysosome escape, photoinduced allosteric behavior reconstructs the vesicular membrane structure, which stimulates the release of hydrophilic cytolytic peptide melittin and hydrophobic kinase inhibitor sorafenib. Combining on-demand delivery of multiple therapeutics with phototherapy results in apoptosis and immunogenic death of tumor cells, remold the immune microenvironment and achieve an excellent synergistic anticancer efficacy in vivo without tumor recurrence and metastasis. Such a light-modulated allosteric transition in non-photosensitive polymers provides new insight into the development of smart nanomaterials for biosensing and drug delivery applications.

Application of the method for visualization of noncovalent interactions in conformational polymorphs of four organic acids

A method for the visualization of noncovalent interactions using examples of the conformational polymorphs of four organic compounds: 2-(phenylamino)nicotinic, 2-(3-chloro-2-methylphenylamino)nicotinic, N-(3-chloro-2-methylphenyl)anthranilic and 2-(methylphenylamino)nicotinic acids is examined. The changes in noncovalent contacts are plotted against the angle between the planes of aromatic rings allowing a visual representation of conformational adjustment of molecules as well as packing features of crystal structures. According to the k-Φ criterion, the studied structures represent conformational polymorphs. Different types of hydrogen bonding are discussed within the framework of the method of visualization and molecular Voronoi-Dirichlet polyhedra. Good correlations are found between calculated and experimental data for several cases, such as the agreement between π stacking and polymorphic transition temperatures as well as between the area of a contact and the energy of conjugation. Also, an attempt has been made to assess the relative contributions of conformational and packing polymorphism in the formation of polymorphs.

Secondary Structures of MERS-CoV, SARS-CoV, and SARS-CoV-2 Spike Proteins Revealed by Infrared Vibrational Spectroscopy

All coronaviruses are characterized by spike glycoproteins whose S1 subunits contain the receptor binding domain (RBD). The RBD anchors the virus to the host cellular membrane to regulate the virus transmissibility and infectious process. Although the protein/receptor interaction mainly depends on the spike's conformation, particularly on its S1 unit, their secondary structures are poorly known. In this paper, the S1 conformation was investigated for MERS-CoV, SARS-CoV, and SARS-CoV-2 at serological pH by measuring their Amide I infrared absorption bands. The SARS-CoV-2 S1 secondary structure revealed a strong difference compared to those of MERS-CoV and SARS-CoV, with a significant presence of extended β-sheets. Furthermore, the conformation of the SARS-CoV-2 S1 showed a significant change by moving from serological pH to mild acidic and alkaline pH conditions. Both results suggest the capability of infrared spectroscopy to follow the secondary structure adaptation of the SARS-CoV-2 S1 to different environments.

New Optically Active tert-Butylarylthiophosphinic Acids and Their Selenium Analogues as the Potential Synthons of Supramolecular Organometallic Complexes: Syntheses and Crystallographic Structure Determination

The aim of the research described in this publication is two-fold. The first is a detailed description of the synthesis of a series of compounds containing a stereogenic heteroatom, namely the optically active P-stereogenic derivatives of tert-butylarylphoshinic acids bearing sulfur or selenium. The second is a detailed discussion dedicated to the determination of their structures by an X-ray analysis. Such a determination is needed when considering optically active hetero-oxophosphoric acids as new chiral solvating agents, precursors of new chiral ionic liquids, or ligands in complexes serving as novel organometallic catalysts.

Pyridin-4-ylmethanaminium perchlorate mono-hydrate

Pyridin-4-ylmethanaminium perchlorate monohydrate (synonym: 4-picolyl-ammonium perchlorate monohydrate), C₆H₉N₂ ⁺·ClO₄ ^-·H₂O, crystallizes in the monoclinic system (space group P2₁/n) with the asymmetric unit comprising two formula units (Z' = 2). All mol-ecular entities are located on general positions. The two crystallographically distinct 4-picolyl-ammonium cations exhibit different conformations. The two unique perchlorate anions are non-disordered, showing an r.m.s. deviation of 0.011 Å from mol-ecular T _d symmetry. The supra-molecular structure in the solid state features an intricate tri-periodic network of N-H⋯O, O-H⋯N and O-H⋯O hydrogen bonds.

Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins

Protein regions which are intrinsically disordered, exist as an ensemble of rapidly interconverting structures. Cooling proteins to cryogenic temperatures for dynamic nuclear polarization (DNP) magic angle spinning (MAS) NMR studies suspends most of the motions, resulting in peaks that are broad but not featureless. To demonstrate that detailed conformational restraints can be retrieved from the peak shapes of frozen proteins alone, we developed and used a simulation framework to assign peak features to conformers in the ensemble. We validated our simulations by comparing them to spectra of α-synuclein acquired under different experimental conditions. Our assignments of peaks to discrete dihedral angle populations suggest that structural constraints are attainable under cryogenic conditions. The ability to infer ensemble populations from peak shapes has important implications for DNP MAS NMR studies of proteins with regions of disorder in living cells because chemical shifts are the most accessible measured parameter.

Dietary Trace Elements and the Pathogenesis of Neurodegenerative Diseases

Trace elements such as iron (Fe), zinc (Zn), copper (Cu), and manganese (Mn) are absorbed from food via the gastrointestinal tract, transported into the brain, and play central roles in normal brain functions. An excess of these trace elements often produces reactive oxygen species and damages the brain. Moreover, increasing evidence suggests that the dyshomeostasis of these metals is involved in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease, prion diseases, and Lewy body diseases. The disease-related amyloidogenic proteins can regulate metal homeostasis at the synapses, and thus loss of the protective functions of these amyloidogenic proteins causes neurodegeneration. Meanwhile, metal-induced conformational changes of the amyloidogenic proteins contribute to enhancing their neurotoxicity. Moreover, excess Zn and Cu play central roles in the pathogenesis of vascular-type senile dementia. Here, we present an overview of the intake, absorption, and transport of four essential elements (Fe, Zn, Cu, Mn) and one non-essential element (aluminum: Al) in food and their connections with the pathogenesis of neurodegenerative diseases based on metal-protein, and metal-metal cross-talk.

Decoding the Roles of Amyloid-β (1-42)'s Key Oligomerization Domains toward Designing Epitope-Specific Aggregation Inhibitors

Fibrillar amyloid aggregates are the pathological hallmarks of multiple neurodegenerative diseases. The amyloid-β (1-42) protein, in particular, is a major component of senile plaques in the brains of patients with Alzheimer's disease and a primary target for disease treatment. Determining the essential domains of amyloid-β (1-42) that facilitate its oligomerization is critical for the development of aggregation inhibitors as potential therapeutic agents. In this study, we identified three key hydrophobic sites (¹⁷LVF¹⁹, ³²IGL³⁴, and ⁴¹IA⁴²) on amyloid-β (1-42) and investigated their involvement in the self-assembly process of the protein. Based on these findings, we designed candidate inhibitor peptides of amyloid-β (1-42) aggregation. Using the designed peptides, we characterized the roles of the three hydrophobic regions during amyloid-β (1-42) fibrillar aggregation and monitored the consequent effects on its aggregation property and structural conversion. Furthermore, we used an amyloid-β (1-42) double point mutant (I41N/A42N) to examine the interactions between the two C-terminal end residues with the two hydrophobic regions and their roles in amyloid self-assembly. Our results indicate that interchain interactions in the central hydrophobic region (¹⁷LVF¹⁹) of amyloid-β (1-42) are important for fibrillar aggregation, and its interaction with other domains is associated with the accessibility of the central hydrophobic region for initiating the oligomerization process. Our study provides mechanistic insights into the self-assembly of amyloid-β (1-42) and highlights key structural domains that facilitate this process. Our results can be further applied toward improving the rational design of candidate amyloid-β (1-42) aggregation inhibitors.

Conformation-dependent ligand hot spots in the spliceosomal RNA helicase BRR2

The conversion of hits to leads in drug discovery involves the elaboration of chemical core structures to increase their potency. In fragment-based drug discovery, low-molecular-weight compounds are tested for protein binding and are subsequently modified, with the tacit assumption that the binding mode of the original hit will be conserved among the derivatives. However, deviations from binding mode conservation are rather frequently observed, but potential causes of these alterations remain incompletely understood. Here, two crystal forms of the spliceosomal RNA helicase BRR2 were employed as a test case to explore the consequences of conformational changes in the target protein on the binding behaviour of fragment derivatives. The initial fragment, sulfaguanidine, bound at the interface between the two helicase cassettes of BRR2 in one crystal form. Second-generation compounds devised by structure-guided docking were probed for their binding to BRR2 in a second crystal form, in which the original fragment-binding site was altered due to a conformational change. While some of the second-generation compounds retained binding to parts of the original site, others changed to different binding pockets of the protein. A structural bioinformatics analysis revealed that the fragment-binding sites correspond to predicted binding hot spots, which strongly depend on the protein conformation. This case study offers an example of extensive binding-mode changes during hit derivatization, which are likely to occur as a consequence of multiple binding hot spots, some of which are sensitive to the flexibility of the protein.

Differential regulation of phosphorylation, structure and stability of circadian clock protein FRQ isoforms

Neurospora crassa is an important model for circadian clock research. The Neurospora core circadian component FRQ protein has two isoforms, large FRQ (l-FRQ) and small FRQ (s-FRQ), of which l-FRQ bears an additional N-terminal 99-amino acid fragment. However, how the FRQ isoforms operate differentially in regulating the circadian clock remains elusive. Here, we show l-FRQ and s-FRQ play different roles in regulating the circadian negative feedback loop. Compared to s-FRQ, l-FRQ is less stable at three temperatures, and undergoes hypophosphorylation and faster degradation. The phosphorylation of the C-terminal l-FRQ 794-aa fragment was markedly higher than that of s-FRQ, suggesting the l-FRQ N-terminal 99-aa region may regulate phosphorylation of the entire FRQ protein. Quantitative label-free LC/MS analysis identified several peptides that were differentially phosphorylated between l-FRQ and s-FRQ, which were distributed in FRQ in an interlaced fashion. Furthermore, we identified two novel phosphorylation sites, S765 and T781; mutations S765A and T781A showed no significant effects on conidiation rhythmicity, although T781 conferred FRQ stability. These findings demonstrate that FRQ isoforms play differential roles in the circadian negative feedback loop and undergo different regulation of phosphorylation, structure, and stability. The l-FRQ N-terminal 99-aa region plays an important role in regulating the phosphorylation, stability, conformation, and function of the FRQ protein. As the FRQ circadian clock counterparts in other species also have isoforms or paralogues, these findings will also further our understanding of the underlying regulatory mechanisms of the circadian clock in other organisms based on the high conservation of circadian clocks in eukaryotes.

Conformational and Supramolecular Aspects in Chirality of Flexible Camphor-Containing Schiff Base as an Inducer of Helical Liquid Crystals

The experimental and theoretical study of influence of the conformational state and association on the chirality of the stereochemically nonrigid biologically active bis-camphorolidenpropylenediamine (CPDA) and its ability to induce the helical mesophase of alkoxycyanobiphenyls liquid-crystalline binary mixture was carried out. On the basis of quantum-chemical simulation of the CPDA structure, four relatively stable conformers were detected. A comparison of the calculated and experimental electronic circular dichroism (ECD) and ¹H, ¹³C, ¹⁵N NMR spectra, as well as specific optical rotation and dipole moments, allowed to establish the most probable trans-gauche conformational state (tg) of dicamphorodiimine and CPDA dimer with a predominantly mutually parallel arrangement of molecular dipoles. The induction of helical phases in LC mixtures based on cyanobiphenyls and bis-camphorolidenpropylenediamine was studied by polarization microscopy. The clearance temperatures and the helix pitch of the mesophases were measured. The helical twisting power (HTP) was calculated. The decrease in HTP with increasing dopant concentration was shown to be connected with the CPDA association process in the LC phase. The effect of camphor-containing chiral dopants of various structures on nematic LCs was compared. The values of the permittivity and birefringence components of the CPDA solutions in CB-2 were measured experimentally. A strong effect of this dopant on the anisotropic physical properties of the induced chiral nematic was established. A significant decrease in the dielectric anisotropy was associated with the 3D compensation of the LC dipoles during the formation of the helix.

Improved NMR-data-compliant protein structure modeling captures context-dependent variations and expands the scope of functional inference

Nuclear magnetic resonance (NMR) spectroscopy can reveal conformational states of a protein in physiological conditions. However, sparsely available NMR data for a protein with large degrees of freedom can introduce structural artifacts in the built models. Currently used state-of-the-art methods deriving protein structure and conformation from NMR deploy molecular dynamics (MD) coupled with simulated annealing for building models. We provide an alternate graph-based modeling approach, where we first build substructures from NMR-derived distance-geometry constraints combined in one shot to form the core structure. The remaining molecule with inadequate data is modeled using a hybrid approach respecting the observed distance-geometry constraints. One-shot structure building is rarely undertaken for large and sparse data systems, but our data-driven bottom-up approach makes this uniquely feasible by suitable partitioning of the problem. A detailed comparison of select models with state-of-art methods reveals differences in the secondary structure regions wherein the correctness of our models is confirmed by NMR data. Benchmarking of 106 protein-folds covering 38-282 length structures shows minimal experimental-constraint violations while conforming to other structure quality parameters such as the proper folding, steric clash, and torsion angle violation based on Ramachandran plot criteria. Comparative MD studies using select protein models from a state-of-art method and ours under identical experimental parameters reveal distinct conformational dynamics that could be attributed to protein structure-function. Our work is thus useful in building enhanced NMR-evidence-based models that encapsulate the contextual secondary and tertiary structure variations present during the experimentation and expand the scope of functional inference.

Structural and Functional Implication of Natural Variants of Gαs

Heterotrimeric guanine nucleotide-binding proteins (G proteins) are among the most important cellular signaling components, especially G protein-coupled receptors (GPCRs). G proteins comprise three subunits, Gα, Gβ, and Gγ. Gα is the key subunit, and its structural state regulates the active status of G proteins. Interaction of guanosine diphosphate (GDP) or guanosine triphosphate (GTP) with Gα switches G protein into basal or active states, respectively. Genetic alteration in Gα could be responsible for the development of various diseases due to its critical role in cell signaling. Specifically, loss-of-function mutations of Gαs are associated with parathyroid hormone-resistant syndrome such as inactivating parathyroid hormone/parathyroid hormone-related peptide (PTH/PTHrP) signaling disorders (iPPSDs), whereas gain-of-function mutations of Gαs are associated with McCune-Albright syndrome and tumor development. In the present study, we analyzed the structural and functional implications of natural variants of the Gαs subtype observed in iPPSDs. Although a few tested natural variants did not alter the structure and function of Gαs, others induced drastic conformational changes in Gαs, resulting in improper folding and aggregation of the proteins. Other natural variants induced only mild conformational changes but altered the GDP/GTP exchange kinetics. Therefore, the results shed light on the relationship between natural variants of Gα and iPPSDs.

The effect of a methyl group on structure and function: Serine vs. threonine glycosylation and phosphorylation

A variety of glycan structures cover the surface of all cells and are involved in myriad biological processes, including but not limited to, cell adhesion and communication, protein quality control, signal transduction and metabolism, while also being intimately involved in innate and adaptive immune functions. Immune surveillance and responses to foreign carbohydrate antigens, such as capsular polysaccharides on bacteria and surface protein glycosylation of viruses, are the basis of microbial clearance, and most antimicrobial vaccines target these structures. In addition, aberrant glycans on tumors called Tumor-Associated Carbohydrate Antigens (TACAs) elicit immune responses to cancer, and TACAs have been used in the design of many antitumor vaccine constructs. A majority of mammalian TACAs are derived from what are referred to as mucin-type O-linked glycans on cell-surface proteins and are linked to the protein backbone through the hydroxyl group of either serine or threonine residues. A small group of structural studies that have compared mono- and oligosaccharides attached to each of these residues have shown that there are distinct differences in conformational preferences assumed by glycans attached to either "unmethylated" serine or ß-methylated threonine. This suggests that the linkage point of antigenic glycans will affect their presentation to the immune system as well as to various carbohydrate binding molecules (e.g., lectins). This short review, followed by our hypothesis, will examine this possibility and extend the concept to the presentation of glycans on surfaces and in assay systems where recognition of glycans by proteins and other binding partners can be defined by different attachment points that allow for a range of conformational presentations.

1H-NMR Karplus Analysis of Molecular Conformations of Glycerol under Different Solvent Conditions: A Consistent Rotational Isomerism in the Backbone Governed by Glycerol/Water Interactions

Glycerol is a symmetrical, small biomolecule with high flexibility in molecular conformations. Using a ¹H-NMR spectroscopic Karplus analysis in our way, we analyzed a rotational isomerism in the glycero backbone which generates three kinds of staggered conformers, namely gt (gauche-trans), gg (gauche-gauche), and tg (trans-gauche), at each of sn-1,2 and sn-2,3 positions. The Karplus analysis has disclosed that the three rotamers are consistently equilibrated in water keeping the relation of 'gt:gg:tg = 50:30:20 (%)' at a wide range of concentrations (5 mM~540 mM). The observed relation means that glycerol in water favors those symmetric conformers placing 1,2,3-triol groups in a gauche/gauche geometry. We have found also that the rotational isomerism is remarkably changed when the solvent is replaced with DMSO-d₆ or dimethylformamide (DMF-d₇). In these solvents, glycerol gives a relation of 'gt:gg:tg = 40:30:30 (%)', which means that a remarkable shift occurs in the equilibrium between gt and tg conformers. By this shift, glycerol turns to also take non-symmetric conformers orienting one of the two vicinal diols in an antiperiplanar geometry.

Anchoring of Amyloid-β onto Polyunsaturated Phospholipid Membranes

The interaction between the toxic amyloid-β and phospholipid membranes in the early stage of Alzheimer's disease is complicated and depends on many factors. It was found that polyunsaturated fatty acids affect the incidence of Alzheimer's disease. The number of double bonds in the phospholipid layer may play an important role in the molecular dynamic behavior of amyloid-β on cell membranes. In the present paper, the interactions between Aβ(25-35) and each of four phospholipids, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-stearoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (SAPC), 1-stearoyl-2-docosahexaenooyl-sn-glycero-3-phosphocholine (SDPC), and 1,2-diarachidonoyl-sn-glycero-3-phosphocholine (DAPC), are investigated by using all-atom molecular dynamics simulation. It is interesting that, as the number of double bonds in the membrane increases, the peptide fragment prefers to stay in the surface region of the membrane rather than penetrates deeply into the membrane. With the increasing number of double bonds, the interaction between Aβ(25-35) and the membrane surface becomes stronger, especially for the interaction between the residue 28 (LYS28) in Aβ(25-35) and the phospholipids, anchoring Aβ(25-35) onto the membrane. The double bonds in phospholipid determine not only the adsorption of the peptide fragment Aβ(25-35) but also its conformation, which will influence further aggregation of Aβ in later stages.Communicated by Ramaswamy H. Sarma.

Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats

Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up- and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.

Characterization of a Novel CD4 Mimetic Compound YIR-821 against HIV-1 Clinical Isolates

Small CD4-mimetic compound (CD4mc), which inhibits the interaction between gp120 with CD4, acts as an entry inhibitor and induces structural changes in the HIV-1 envelope glycoprotein trimer (Env) through its insertion within the Phe43 cavity of gp120. We recently developed YIR-821, a novel CD4mc, that has potent antiviral activity and lower toxicity than the prototype NBD-556. To assess the possibility of clinical application of YIR-821, we tested its antiviral activity using a panel of HIV-1 pseudoviruses from different subtypes. YIR-821 displayed entry inhibitor activity against 53.5% (21/40) of the pseudoviruses tested and enhanced neutralization mediated by coreceptor binding site (CoRBS) antibodies in 50% (16/32) of these. Furthermore, when we assessed the antiviral effects using a panel of pseudoviruses and autologous plasma IgG, enhancement of antibody-mediated neutralization activity was observed for 48% (15/31) of subtype B strains and 51% (28/55) of non-B strains. The direct antiviral activity of YIR-821 as an entry inhibitor was observed in 53% of both subtype B (27/51) and non-B subtype (40/75) pseudoviruses. Enhancement of antibody-dependent cellular cytotoxicity was also observed with YIR-821 for all six selected clinical isolates, as well as for the transmitted/founder (T/F) CH58 virus-infected cells. The sequence diversity in the CD4 binding site as well as other regions, such as the gp120 inner domain layers or gp41, may be involved in the multiple mechanisms related to the sensitive/resistant phenotype of the virus to YIR-821. Our findings may facilitate the clinical application of YIR-821. IMPORTANCE Small CD4-mimetic compound (CD4mc) interacts with the Phe43 cavity and triggers conformational changes, enhancing antibody-mediated neutralization and antibody-dependent cellular cytotoxicity (ADCC). Here, we evaluated the effect of YIR-821, a novel CD4mc, against clinical isolates, including both subtype B and non-B subtype viruses. Our results confirm the desirable properties of YIR-821, which include entry inhibition, enhancement of IgG-neutralization, binding, and ADCC, in addition to low toxicity and long half-life in a rhesus macaque model, that might facilitate the clinical application of this novel CD4mc. Our observation of primary viruses that are resistant to YIR-821 suggests that further development of CD4mcs with different structural properties is required.

Conformational Parameters and Hydrodynamic Behavior of Poly(2-Methyl-2-Oxazoline) in a Broad Molar Mass Range

In this work, we report our results on the hydrodynamic behavior of poly(2-methyl-2-oxazoline) (PMeOx). PMeOx is gaining significant attention for use as hydrophilic polymer in pharmaceutical carriers as an alternative for the commonly used poly(ethylene glycol) (PEG), for which antibodies are found in a significant fraction of the human population. The main focus of the current study is to determine the hydrodynamic characteristics of PMeOx under physiological conditions, which serves as basis for better understanding of the use of PMeOx in pharmaceutical applications. This goal was achieved by studying PMeOx solutions in phosphate-buffered saline (PBS) as a solvent at 37 °C. This study was performed based on two series of PMeOx samples; one series is synthesized by conventional living cationic ring-opening polymerization, which is limited by the maximum chain length that can be achieved, and a second series is obtained by an alternative synthesis strategy based on acetylation of well-defined linear poly(ethylene imine) (PEI) prepared by controlled side-chain hydrolysis of a defined high molar mass of poly(2-ethyl-2-oxazoline). The combination of these two series of PMeOx allowed the determination of the Kuhn-Mark-Houwink-Sakurada equations in a broad molar mass range. For intrinsic viscosity, sedimentation and diffusion coefficients, the following expressions were obtained: η=0.015M0.77, s0=0.019M0.42 and D0=2600M-0.58, respectively. As a result, it can be concluded that the phosphate-buffered saline buffer at 37 °C represents a thermodynamically good solvent for PMeOx, based on the scaling indices of the equations. The conformational parameters for PMeOx chains were also determined, revealing an equilibrium rigidity or Kuhn segment length, (A) of 1.7 nm and a polymer chain diameter (d) of 0.4 nm. The obtained value for the equilibrium rigidity is very similar to the reported values for other hydrophilic polymers, such as PEG, poly(vinylpyrrolidone) and poly(2-ethyl-2-oxazoline), making PMeOx a relevant alternative to PEG.

Intensified Nonequilibrium Effect of Polymer Nanocomposites with Decreasing Nanoparticle Size

What are the most important and decisive parameters that determine the structure and the property of polymer nanocomposites (PNCs)? Previous studies answered that controlling the nanoparticle interface is critical, which can be achieved with a choice of a compatible nanoparticle, a proper surface modification, and a change in the polymer chain length. In addition to these parameters, the processing condition of PNCs has recently emerged as an influential parameter for controlling PNC properties, suggesting the existence of the nonequilibrium effect of PNCs. In this regard, we chose the solvent as a main change in the processing condition and investigated the initial solvent-driven nonequilibrium effect of PNCs with varied nanoparticle (NP) sizes. We found that the type of the initial solvent is indeed crucial in determining the ultimate properties of the PNCs, and this becomes more influential as the size of NPs decreases. The decreasing size of NPs causes a conformational change in the adsorbed polymers from tightly packed layers to loosely dangling chains. This results in much greater differences in NP microstructures and rheological properties of PNCs, indicating a stronger nonequilibrium effect with smaller NPs.