Re-assessing the importance of linear type traits in predicting genetic merit for survival in an aging Holstein-Friesian dairy cow population

The cumulative improvement achieved in the genetic merit for reproductive performance in dairy populations will likely improve dairy cow longevity; therefore, it is time to reassess whether linear type traits are still suitable predictors of survival in an aging dairy cow population. The objective of the present study was therefore to estimate the genetic correlations between linear type traits and survival from one parity to the next and, in doing so, evaluate if those genetic correlations change with advancing parity. After edits, 152,894 lactation survival records (first to ninth parity) were available from 52,447 Holstein-Friesian cows, along with linear type trait records from 52,121 Holstein-Friesian cows. A series of bivariate random regression models were used to estimate the genetic covariances between survival in different parities and each linear type trait. Heritability estimates for survival per parity ranged from 0.02 (SE = 0.004; first parity) to 0.05 (SE = 0.01; ninth parity). Pairwise genetic correlations between survival among different parities varied from 0.42 (first and ninth parity) to 1.00 (eighth to ninth parity), with the strength of these genetic correlations being inversely related to the interval between the compared parities. The genetic correlations between survival and the individual linear type traits varied across parities for 9 of the 20 linear type traits examined, but the correlations with only 3 of these linear type traits strengthened as the cows aged; these 3 traits were rear udder height, teat length, and udder depth. Given that linear type traits are frequently scored in first parity and are genetically correlated with survival in older parities, they may be suitable early predictors of survival, especially for later parity cows. Additionally, the direction of the genetic correlations between survival and rear udder height, teat length, and udder depth did not change between parities; hence, selection for survival in older parities using these linear type traits should not hinder genetic improvement for survival in younger parities.

Solo vs. Chorus: Monomers and Oligomers of Arrestin Proteins

Three out of four subtypes of arrestin proteins expressed in mammals self-associate, each forming oligomers of a distinct kind. Monomers and oligomers have different subcellular localization and distinct biological functions. Here we summarize existing evidence regarding arrestin oligomerization and discuss specific functions of monomeric and oligomeric forms, although too few of the latter are known. The data on arrestins highlight biological importance of oligomerization of signaling proteins. Distinct modes of oligomerization might be an important contributing factor to the functional differences among highly homologous members of the arrestin protein family.

Integration of Adenylate Kinase 1 with Its Peptide Conformational Imprint

In the present study, molecularly imprinted polymers (MIPs) were used as a tool to grasp a targeted α-helix or β-sheet of protein. During the fabrication of the hinge-mediated MIPs, elegant cavities took shape in a special solvent on quartz crystal microbalance (QCM) chips. The cavities, which were complementary to the protein secondary structure, acted as a peptide conformational imprint (PCI) for adenylate kinase 1 (AK1). We established a promising strategy to examine the binding affinities of human AK1 in conformational dynamics using the peptide-imprinting method. Moreover, when bound to AK1, PCIs are able to gain stability and tend to maintain higher catalytic activities than free AK1. Such designed fixations not only act on hinges as accelerators; some are also inhibitors. One example of PCI inhibition of AK1 catalytic activity takes place when PCI integrates with an AK1_9-23 β-sheet. In addition, conformation ties, a general MIP method derived from random-coil AK1_133-144 in buffer/acetonitrile, are also inhibitors. The inhibition may be due to the need for this peptide to execute conformational transition during catalysis.

Theoretical Studies on the Structure and Intramolecular Interactions of Fagopyrins-Natural Photosensitizers of Fagopyrum

Simple Summary

The study determines the spatial structure and intramolecular interactions of fagopyrins—natural photosensitizers of Fagopyrum species. In silico calculations show many fagopyrin conformers characterized by the formation of strong intramolecular interactions.

Abstract

Compounds characterized by a double-anthrone moiety are found in many plant species. One of them are fagopyrins—naturally occurring photosensitizers of Fagopyrum. The photosensitizing properties of fagopyrins are related to the selective absorption of light, which is a direct result of their spatial and electronic structure and many intramolecular interactions. The nature of the interactions varies in different parts of the molecule. The aim of this study is to determine the structure and intramolecular interactions of fagopyrin molecules. For this purpose, in silico calculations were used to perform geometry optimization in the gas phase. QTAIM and NCI analysis suggest the formation of the possible conformers in the fagopyrin molecules. The presence of a strong OHO hydrogen bond was shown in the anthrone moiety of fagopyrin. The minimum energy difference for selected conformers of fagopyrins was 1.1 kcal∙mol⁻¹, which suggested that the fagopyrin structure may exist in a different conformation in plant material. Similar interactions were observed in previously studied structures of hypericin and sennidin; however, only fagopyrin showed the possibility of brake the strong OHO hydrogen bond in favor of forming a new OHN hydrogen bond.

The HIV Env Glycoprotein Conformational States on Cells and Viruses

The HIV Env glycoprotein is the surface glycoprotein responsible for viral entry into CD4+ immune cells. During infection, Env also serves as a primary target for antibody responses, which are robust but unable to control virus replication. Immune evasion by HIV-1 Env appears to employ complex mechanisms to regulate what antigenic states are presented to the immune system. Immunodominant features appear to be distinct from epitopes that interfere with Env functions in mediating infection. Further, cell-cell transmission studies indicate that vulnerable conformational states are additionally hidden from recognition on infected cells, even though the presence of Env at the cell surface is required for viral infection through the virological synapse. Cell-cell infection studies support that Env on infected cells is presented in distinct conformations from that on virus particles. Here we review data regarding the regulation of conformational states of Env and assess how regulated sorting of Env within the infected cell may underlie mechanisms to distinguish Env on the surface of virus particles versus Env on the surface of infected cells. These mechanisms may allow infected cells to avoid opsonization, providing cell-to-cell infection by HIV with a selective advantage during evolution within an infected individual. Understanding how distinct Env conformations are presented on cells versus viruses may be essential to designing effective vaccine approaches and therapeutic strategies to clear infected cell reservoirs.

Molecular Structure of Single-Stranded DNA on the ZnS Surface of Quantum Dots

DNA-based nanoparticle assemblies have emerged as leading candidates in the development of bioimaging materials, photonic devices, and computing materials. Here, we combine atomistic simulations and experiments to characterize the wrapping mechanism of chimeric single-stranded DNA (ssDNA) on CdSe-ZnS (core-shell) quantum dots (QDs) at different ratios of the phosphorothioate (PS) modification of the bases. We use an implicit solvent, all-atom ssDNA model to match the experimentally calculated ssDNA conformation at low salt concentrations. Through simulation, we find that 3-mercaptopropionic acid (MPA) induces electrostatic repulsion and O-(2-mercaptoethyl)-Ó-methyl-hexa (ethylene glycol) (mPEG) induces steric exclusion, and both reduce the binding affinity of ssDNA. In both simulation and experiment, we find that ssDNA is closer to the QD surface when the QD size is larger. The effect of the PS-base ratio on the conformation of ssDNA is also elaborated in this work. We found through MD simulations, and confirmed by transmission electron microscopy, that the maximum valence numbers are 1, 2, and 3 on QDs of 6, 9, and 14 nm in diameter, respectively. We conclude that the maximum ssDNA valence number is linearly related to the QD size, n ∝ R, and justify this finding through an electrostatic repulsion mechanism.

Structure Identification of Two Polysaccharides from Morchella sextelata with Antioxidant Activity

Mushrooms of the Morchella genus exhibit a variety of biological activities. Two polysaccharides (MSP1-1, 389.0 kDa; MSP1-2, 23.4 kDa) were isolated from Morchella sextelata by subcritical water extraction and column chromatography fractionation. Methylation and nuclear magnetic resonance analysis determined MSP1-1 as a glucan with a backbone of (1→4)-α-D-glucan branched at O-6, and MSP1-2 as a galactomannan with coextracted α-glucan. Light scattering analysis and transmission electron microscopy revealed that MSP1-1 possessed a random coil chain and that MSP1-2 had a network chain. This is the first time that a network structure has been observed in a polysaccharide from M. sextelata. Despite the differences in their chemical structures and conformations, both MSP1-1 and MSP1-2 possessed good thermal stability and showed antioxidant activity. This study provides fundamental data on the structure-activity relationships of M. sextelata polysaccharides.

3D Printing of Monolithic Proteinaceous Cantilevers Using Regenerated Silk Fibroin

Silk fibroin, regenerated from Bombyx mori, has shown considerable promise as a printable, aqueous-based ink using a bioinspired salt-bath system in our previous work. Here, we further developed and characterized silk fibroin inks that exhibit concentration-dependent fluorescence spectra at the molecular level. These insights supported extrusion-based 3D printing using concentrated silk fibroin solutions as printing inks. 3D monolithic proteinaceous structures with high aspect ratios were successfully printed using these approaches, including cantilevers only supported at one end. This work provides further insight and broadens the utility of 3D printing with silk fibroin inks for the microfabrication of proteinaceous structures.

Single-Molecule Identification of the Conformations of Human C-Reactive Protein and Its Aptamer Complex with Solid-State Nanopores

Human C-reactive protein (CRP) is an established inflammatory biomarker and was proved to be potentially relevant to disease pathology and cancer progression. A large body of methodologies have been reported for CRP analysis, including electrochemical/optical biosensors, aptamer, or antibody-based detection. Although the detection limit is rather low until pg/uL, most of which are time-consuming and relatively expensive, and few of them provided CRP single-molecule information. This work demonstrated the nanopore-based approach for the characterization of CRP conformation under versatile conditions. With an optimized pore of 14 nm in diameter, we achieved the detection limit as low as 0.3 ng/μL, voltage polarity significantly influences the electro-osmotic force and CRP translocation behavior, and the pentameric conformation of CRP may dissociate into pro-inflammatory CRP isoforms and monomeric CRP at bias potential above 300 mV. CRP tends to translocate through nanopores faster along with the increase in pH values, due to more surface charge on both CRP and pore inner wall and stronger electro-osmotic force. The CRP could specifically bind with its aptamer of different concentrations to form complexes, and the complexes exhibited distinguishable nanopore translocation behavior compared with CRP alone. The variation of the molar ratio of aptamer significantly influences the orientation of CRP translocation. The plasma test under physiological conditions displayed the ability of the nanopore system on the CRP identification with a concentration of 3 ng/μL.

Boosting of cross-reactive antibodies to endemic coronaviruses by SARS-CoV-2 infection but not vaccination with stabilized spike

Preexisting antibodies to endemic coronaviruses (CoV) that cross-react with SARS-CoV-2 have the potential to influence the antibody response to COVID-19 vaccination and infection for better or worse. In this observational study of mucosal and systemic humoral immunity in acutely infected, convalescent, and vaccinated subjects, we tested for cross-reactivity against endemic CoV spike (S) protein at subdomain resolution. Elevated responses, particularly to the β-CoV OC43, were observed in all natural infection cohorts tested and were correlated with the response to SARS-CoV-2. The kinetics of this response and isotypes involved suggest that infection boosts preexisting antibody lineages raised against prior endemic CoV exposure that cross-react. While further research is needed to discern whether this recalled response is desirable or detrimental, the boosted antibodies principally targeted the better-conserved S2 subdomain of the viral spike and were not associated with neutralization activity. In contrast, vaccination with a stabilized spike mRNA vaccine did not robustly boost cross-reactive antibodies, suggesting differing antigenicity and immunogenicity. In sum, this study provides evidence that antibodies targeting endemic CoV are robustly boosted in response to SARS-CoV-2 infection but not to vaccination with stabilized S, and that depending on conformation or other factors, the S2 subdomain of the spike protein triggers a rapidly recalled, IgG-dominated response that lacks neutralization activity.

Metallo-Supramolecular Complexation Behavior of Terpyridine- and Ferrocene-Based Polymers in Solution-A Molecular Hydrodynamics Perspective

The contribution deals with the synthesis of the poly(methacrylate)-based copolymers, which contain ferrocene and/or terpyridine moieties in the side chains, and the subsequent analysis of their self-assembly behavior upon supramolecular/coordination interactions with Eu3+ and Pd2+ ions in dilute solutions. Both metal ions provoke intra and inter molecular complexation that results in the formation of large supra-macromolecular assembles of different conformation/shapes. By applying complementary analytical approaches (i.e., sedimentation-diffusion analysis in the analytical ultracentrifuge, dynamic light scattering, viscosity and density measurements, morphology studies by electron microscopy), a map of possible conformational states/shapes was drawn and the corresponding fundamental hydrodynamic and macromolecular characteristics of metallo-supramolecular assemblies at various ligand-to-ion molar concentration ratios (M/L) in extremely dilute polymer solutions (c[η]≈0.006) were determined. It was shown that intramolecular complexation is already detected at (L≈0.1), while at M/L>0.5 solution/suspension precipitates. Extreme aggregation/agglomeration behavior of such dilute polymer solutions at relatively “high” metal ion content is explained from the perspective of polymer-solvent and charge interactions that will accompany the intramolecular complexation due to the coordination interactions.

Conformation of HIV-1 Envelope Governs Rhesus CD4 Usage and Simian-Human Immunodeficiency Virus Replication

Infection of rhesus macaques with simian-human immunodeficiency viruses (SHIVs) is the preferred model system for vaccine development because SHIVs encode human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins (Envs)-a key target of HIV-1 neutralizing antibodies. Since the goal of vaccines is to prevent new infections, SHIVs encoding circulating HIV-1 Env are desired as challenge viruses. Development of such biologically relevant SHIVs has been challenging, as they fail to infect rhesus macaques, mainly because most circulating HIV-1 Envs do not use rhesus CD4 (rhCD4) receptor for viral entry. Most primary HIV-1 Envs exist in a closed conformation and occasionally transit to a downstream, open conformation through an obligate intermediate conformation. Here, we provide genetic evidence that open Env conformations can overcome the rhCD4 entry barrier and increase replication of SHIVs in rhesus lymphocytes. Consistent with prior studies, we found that circulating HIV-1 Envs do not use rhCD4 efficiently for viral entry. However, by using HIV-1 Envs with single amino acid substitutions that alter their conformational state, we found that transitions to intermediate and open Env conformations allow usage of physiological levels of rhCD4 for viral entry. We engineered these single amino acid substitutions in the transmitted/founder HIV-1_BG505 Envs encoded by SHIV-BG505 and found that open Env conformation enhances SHIV replication in rhesus lymphocytes. Lastly, CD4-mediated SHIV pulldown, sensitivity to soluble CD4, and fusogenicity assays indicated that open Env conformation promotes efficient rhCD4 binding and viral-host membrane fusion. These findings identify the conformational state of HIV-1 Env as a major determinant for rhCD4 usage, viral fusion, and SHIV replication. IMPORTANCE Rhesus macaques are a critical animal model for preclinical testing of HIV-1 vaccine and prevention approaches. However, HIV-1 does not replicate in rhesus macaques, and thus, chimeric simian-human immunodeficiency viruses (SHIVs), which encode HIV-1 envelope glycoproteins (Envs), are used as surrogate challenge viruses to infect rhesus macaques for modeling HIV-1 infection. Development of SHIVs encoding Envs from clinically relevant, circulating HIV-1 variants has been extremely challenging, as such SHIVs replicate poorly, if at all, in rhesus lymphocytes. This is most probably because many circulating HIV-1 Envs do not use rhesus CD4 efficiently for viral entry. In this study, we identified conformational state of HIV-1 envelope as a key determinant for rhesus CD4 usage, viral-host membrane fusion, and SHIV replication in rhesus lymphocytes.

Conformation-driven strategy for resilient and functional protein materials

The exceptional elastic resilience of some protein materials underlies essential biomechanical functions with broad interest in biomedical fields. However, molecular design of elastic resilience is restricted to amino acid sequences of a handful of naturally occurring resilient proteins such as resilin and elastin. Here, we exploit non-resilin/elastin sequences that adopt kinetically stabilized, random coil-dominated conformations to achieve near-perfect resilience comparable with that of resilin and elastin. We also show a direct correlation between resilience and Raman-characterized protein conformations. Furthermore, we demonstrate that metastable conformation of proteins enables the construction of mechanically graded protein materials that exhibit spatially controlled conformations and resilience. These results offer insights into molecular mechanisms of protein elastomers and outline a general conformation-driven strategy for developing resilient and functional protein materials.

Effect of Conformation of Sugar Beet Pectin on the Interfacial and Emulsifying Properties

The influence of the conformation of sugar beet pectin (SBP) on the interfacial and emulsifying properties was investigated. The colloidal properties of SBP, such as zeta potential and hydrodynamic diameter, were characterized at different pH levels. Furthermore, pendant drop tensiometry and quartz crystal microgravimetry were used to study adsorption behavior (adsorbed mass and adsorption rate) and stabilizing mechanism (layer thickness and interfacial tension). A more compact conformation resulted in a faster reduction of interfacial tension, higher adsorbed mass, and a thicker adsorption layer. In addition, emulsions were prepared at varying conditions (pH 3-5) and formulations (1-30 wt% MCT oil, 0.1-2 wt% SBP), and their droplet size distributions were measured. The smallest oil droplets could be stabilized at pH 3. However, significantly more pectin was required at pH 3 compared to pH 4 or 5 to sufficiently stabilize the oil droplets. Both phenomena were attributed to the more compact conformation of SBP at pH < pKa: On the one hand, pectins adsorbed faster and in greater quantity, forming a thicker interfacial layer. On the other hand, they covered less interfacial area per SBP molecule. Therefore, the SBP concentration must be chosen appropriately depending on the conformation.

A Holistic Approach to Determining Stereochemistry of Potential Pharmaceuticals by Circular Dichroism with β-Lactams as Test Cases

This paper's main objective is to show that many different factors must be considered when solving stereochemical problems to avoid misleading conclusions and obtain conclusive results from the analysis of spectroscopic properties. Particularly in determining the absolute configuration, the use of chiroptical methods is crucial, especially when other techniques, including X-ray crystallography, fail, are not applicable, or give inconclusive results. Based on various β-lactam derivatives as models, we show how to reliably determine their absolute configuration (AC) and preferred conformation from circular dichroism (CD) spectra. Comprehensive CD analysis, employing both approaches, i.e., traditional with their sector and helicity rules, and state-of-the-art supported by quantum chemistry (QC) calculations along with solvation models for both electronic (ECD) and vibrational (VCD) circular dichroism ranges, allows confident defining stereochemistry of the β-lactams studied. Based on an in-depth analysis of the results, we have shown that choosing a proper chiroptical method/s strictly depends on the specific case and certain structural features.

Binding mechanism of lipase with Lentinus edodes mycelia polysaccharide by multi-spectroscopic methods

It is an effective strategy to avoid obesity by inhibiting the activity of lipase. In this study, the binding mechanism of lipase and Lentinus edodes mycelia polysaccharide (LMP) were explored with multi-spectral methods, for example, three-dimensional (3D) fluorescence, Fourier-transformed infrared (FT-IR), and Raman spectra. At 290 K, the binding constant was 2.44 × 10⁵  L/mol, there was only one binding site between LMP and lipase. Static quenching was the quenching mechanism. The major forces were hydrogen bonding and van der Waals force. The binding of LMP to lipase impacted the microenvironment around tyrosine and tryptophan residues. The polarity around these residues was decreased and hydrophobicity was enhanced. This study not only revealed the binding mechanism of LMP on lipase but also provided scientific evidence for expanding the application of LMP in functional food industries.

Impact of Hydroxypropyl Methylcellulose Acetate Succinate Critical Aggregation Concentration on Celecoxib Supersaturation

Polymers play an important role in amorphous solid dispersions (ASDs), enhancing stability in the solid state and maintaining supersaturation in aqueous solutions of intrinsically low-water-soluble drug candidates. Hydroxypropyl methylcellulose acetate succinate (HPMCAS) is widely used in ASDs due to its hydrophobic/hydrophilic balance and ionizability of the substituent functionalities. While colloid formation of HPMCAS in solution due to this hydrophobic/hydrophilic balance has been studied, the impact of the polymer conformation (random coil vs aggregated) on drug supersaturation of ASDs is not well understood. To our knowledge, this is the first report where the critical aggregation concentration for three grades of HPMCAS (HF/MF/LF) has been determined via fluorescence spectroscopy using the environment-sensitive probe pyrene. The specific impact of polymer conformation (random coil vs aggregate) on the model drug celecoxib (CLX) has been elucidated with fluorescence quenching and nuclear magnetic resonance (NMR) spectroscopy. A negative deviation of the Stern-Volmer plot indicated that aggregated HPMCAS effectively blocked the quencher's access to CLX. This is further supported by NMR observations, where NMR spectra indicate a larger change of chemical shift of the -NH group of CLX when HPMCAS is above its aggregated concentration, suggesting strong H-bonding interactions between aggregated HPMCAS and CLX. Finally, the supersaturation-precipitation study shows that all three grades of HPMCAS in the aggregated state significantly enhanced CLX supersaturation compared to the nonaggregated state, indicating that polymer aggregation plays a critical role in maintaining drug supersaturation.

Effect of Disease Causing Missense Mutations on Intrinsically Disordered Regions in Proteins

BACKGROUND

It is well known that disease-causing missense mutations (DCMMs) reduce the structural stability/integrity of the proteins with well-defined 3D structures, thereby impacting their molecular functions. However, it is not known in what way DCMMs affect the intrinsically disordered proteins (IDPs) that do not adopt well defined stable 3D structures.

METHODS

In order to investigate how DCMMs may impact intrinsically disordered regions (IDRs) in proteins, we undertook Molecular Dynamics (MD) based studies on three different examples of functionally important IDRs with known DCMMs. Our studies revealed that the functional impact of DCMMs is in reducing the conformational heterogeneity of IDRs, which is intrinsic and quintessential for their multi-faceted cellular roles.

RESULTS

These results are reinforced by energy landscapes of the wildtype and mutant IDRs where the former is characterized by many local minima separated by low barriers, whereas the latter are characterized by one global minimum and several local minima separated by high energy barriers. Our MD based studies also indicate that DCMMs stabilize very few structural possibilities of IDRs either by the newly formed interactions induced by the substituted side chains or by means of restricted or increased flexibilities of the backbone conformations at the mutation sites.

CONCLUSION

Furthermore, the structural possibilities stabilized by DCMMs do not support the native functional roles of the IDRs, thereby leading to disease conditions.

Asymmetric Structures and Conformational Plasticity of the Uncleaved Full-Length Human Immunodeficiency Virus Envelope Glycoprotein Trimer

The functional human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer [(gp120/gp41)3] is produced by cleavage of a conformationally flexible gp160 precursor. gp160 cleavage or the binding of BMS-806, an entry inhibitor, stabilizes the pretriggered, "closed" (state 1) conformation recognized by rarely elicited broadly neutralizing antibodies. Poorly neutralizing antibodies (pNAbs) elicited at high titers during natural infection recognize more "open" Env conformations (states 2 and 3) induced by binding the receptor, CD4. We found that BMS-806 treatment and cross-linking decreased the exposure of pNAb epitopes on cell surface gp160; however, after detergent solubilization, cross-linked and BMS-806-treated gp160 sampled non-state-1 conformations that could be recognized by pNAbs. Cryo-electron microscopy of the purified BMS-806-bound gp160 revealed two hitherto unknown asymmetric trimer conformations, providing insights into the allosteric coupling between trimer opening and structural variation in the gp41 HR1N region. The individual protomer structures in the asymmetric gp160 trimers resemble those of other genetically modified or antibody-bound cleaved HIV-1 Env trimers, which have been suggested to assume state-2-like conformations. Asymmetry of the uncleaved Env potentially exposes surfaces of the trimer to pNAbs. To evaluate the effect of stabilizing a state-1-like conformation of the membrane Env precursor, we treated cells expressing wild-type HIV-1 Env with BMS-806. BMS-806 treatment decreased both gp160 cleavage and the addition of complex glycans, implying that gp160 conformational flexibility contributes to the efficiency of these processes. Selective pressure to maintain flexibility in the precursor of functional Env allows the uncleaved Env to sample asymmetric conformations that potentially skew host antibody responses toward pNAbs. IMPORTANCE The envelope glycoprotein (Env) trimers on the surface of human immunodeficiency virus (HIV-1) mediate the entry of the virus into host cells and serve as targets for neutralizing antibodies. The functional Env trimer is produced by cleavage of the gp160 precursor in the infected cell. We found that the HIV-1 Env precursor is highly plastic, allowing it to assume different asymmetric shapes. This conformational plasticity is potentially important for Env cleavage and proper modification by sugars. Having a flexible, asymmetric Env precursor that can misdirect host antibody responses without compromising virus infectivity would be an advantage for a persistent virus like HIV-1.

Temperature Dependence of Conformational Relaxation of Poly(ethylene oxide) Melts

The time-temperature superposition (TTS) principle, employed extensively for the analysis of polymer dynamics, is based on the assumption that the different normal modes of polymer chains would experience identical temperature dependence. We aim to test the critical assumption for TTS principle by investigating poly(ethylene oxide) (PEO) melts, which have been considered excellent solid polyelectrolytes. In this work, we perform all-atom molecular dynamics simulations up to 300 ns at a range of temperatures for PEO melts. We find from our simulations that the conformations of strands of PEO chains in melts show ideal chain statistics when the strand consists of at least 10 monomers. At the temperature range of T= 400 to 300 K, the mean-square displacements (⟨Δr2(t)⟩) of the centers of mass of chains enter the Fickian regime, i.e., ⟨Δr2(t)⟩∼t1. On the other hand, ⟨Δr2(t)⟩ of the monomers of the chains scales as ⟨Δr2(t)⟩∼t1/2 at intermediate time scales as expected for the Rouse model. We investigate various relaxation modes of the polymer chains and their relaxation times (τn), by calculating for each strand of n monomers. Interestingly, different normal modes of the PEO chains experience identical temperature dependence, thus indicating that the TTS principle would hold for the given temperature range.

Pushing the Limits of Characterising a Weak Halogen Bond in Solution

Detection and characterisation of very weak, non-covalent interactions in solution is inherently challenging. Low affinity, short complex lifetime and a constant battle against entropy brings even the most sensitive spectroscopic methods to their knees. Herein we introduce a strategy for the accurate experimental description of weak chemical forces in solution. Its scope is demonstrated by the detailed geometric and thermodynamic characterisation of the weak halogen bond of a non-fluorinated aryl iodide and an ether oxygen (0.6 kJ mol^-1 ). Our approach makes use of the entropic advantage of studying a weak force intramolecularly, embedded into a cooperatively folding system, and of the combined use of NOE- and RDC-based ensemble analyses to accurately describe the orientation of the donor and acceptor sites. Thermodynamic constants (ΔG, ΔH and ΔS), describing the specific interaction, were derived from variable temperature chemical shift analysis. We present a methodology for the experimental investigation of remarkably weak halogen bonds and other related weak forces in solution, paving the way for their improved understanding and strategic use in chemistry and biology.

Hydrophobicity-tuned anion responsiveness underlies endosomolytic cargo delivery mediated by amphipathic vehicle peptides

Peptide conformation can change subject to environment cues. This concept also applies to many cationic amphipathic peptides (CAPs) known to have cell membrane lytic or penetrative activities. Well-conditioned CAPs can match the properties of the target membrane to support their intended biological functions, e.g., intracellular cargo delivery; however, the intricacy in such conditioning surpasses our current understanding. Here we focused on hydrophobicity, a key biophysical property that dictates the membrane activity of CAPs, and applied a structure–function strategy to evolve a template peptide for endosomolytic cargo delivery. The template was subjected to iterative adjustment to balance hydrophobicity between its N-terminal linear and C-terminal helical domains. We demonstrate that the obtained peptide, LP6, could dramatically promote cargo cell entry and facilitate cytosolic delivery of biomacromolecules such as FITC-dextran, saporin, and human IgG. Among the evolved peptide series, LP6 has low cytotoxicity and moderate hydrophobicity, exhibits maximum change in helical conformation in response to negatively charged phospholipids, and also shows an apparent aggregational behavior in response to sialic acid enrichment. These attributes of LP6 collectively indicate that its anion-responsive conformational change is a critical underlining of its endosomolytic cargo delivery capability. Our results also suggest that modulation of hydrophobicity serves as a key to the precise tuning of CAP's membrane activity for future biomedical applications.

Investigation on the interaction between Ag+ and bovine hemoglobin using spectroscopic methods

Silver ions (Ag⁺) can be released by silver nanoparticles (AgNPs) which are widely used in diverse fields. Ag⁺ can exist inside cells to produce cytotoxicity. This report uses spectroscopic methods to reveal the interactions between Ag⁺ and bovine hemoglobin (BHb). The results of the quenching rate constant (K_q) and the fluorescence lifetime detection showed that the quenching mechanism of BHb by Ag⁺ was static. Thermodynamic investigations indicated that Ag⁺ can interact with BHb with one binding site to form complex mainly through van der Waals interactions and hydrogen bonds. The UV-vis absorption and synchronous fluorescence spectra showed that Ag⁺ changed the conformation of BHb, which may affect protein functions. This research is favorable for understanding the molecular toxic mechanism of Ag⁺ in vivo.

Biosensors based on peptide exposure show single molecule conformations in live cells

We describe an approach to study the conformation of individual proteins during single particle tracking (SPT) in living cells. "Binder/tag" is based on incorporation of a 7-mer peptide (the tag) into a protein where its solvent exposure is controlled by protein conformation. Only upon exposure can the peptide specifically interact with a reporter protein (the binder). Thus, simple fluorescence localization reflects protein conformation. Through direct excitation of bright dyes, the trajectory and conformation of individual proteins can be followed. Simple protein engineering provides highly specific biosensors suitable for SPT and FRET. We describe tagSrc, tagFyn, tagSyk, tagFAK, and an orthogonal binder/tag pair. SPT showed slowly diffusing islands of activated Src within Src clusters and dynamics of activation in adhesions. Quantitative analysis and stochastic modeling revealed in vivo Src kinetics. The simplicity of binder/tag can provide access to diverse proteins.