Physiological Salt Concentrations Research Articles

Anion–Induced Amyloid Fibrillation of Human Insulin In vitro

AbstractIn the present study, we have focused on the effect of three biologically important salt anions on insulin aggregation. The result of the present study reveals that salts differing in their anions (NaI, NaOAc, and NaNO3) induce the self–assembly formation of insulin even at low physiological (in the micromolar range) salt concentration with efficacy that follows the order I−>CH3COO−>NO3−. Here, the anion–driven aggregation of insulin does not follow either the Hofmeister series or electroselectivity series at very low salt concentrations; instead, the binding of anions at low pH to the positively charged residues of insulin is determined by a mechanism where the salt anions promote the fibrillation of insulin and modify the morphology of the monomeric precursor molecule. Both the nucleation and fibril elongation are controlled by the electrostatic forces and hydrophobic interactions. Aggregation mechanism and aggregate morphology were investigated employing a combination of Thioflavin T (ThT) and ANS fluorescence, circular dichroism (CD), dynamic light scattering (DLS), and transmission electron microscopy (TEM). Overall, the present data will enhance the idea to rationalize the anion effects on the aggregation of amyloid‐prone protein and to understand the influence of charged biomolecules in cellular compartments.

Sequence Dependence in Nucleosome Dynamics.

The basic packaging unit of eukaryotic chromatin is the nucleosome that contains 145-147 base pair duplex DNA wrapped around an octameric histone protein. While the DNA sequence plays a crucial role in controlling the positioning of the nucleosome, the molecular details behind the interplay between DNA sequence and nucleosome dynamics remain relatively unexplored. This study analyzes this interplay in detail by performing all-atom molecular dynamics simulations of nucleosomes, comparing the human α-satellite palindromic (ASP) and the strong positioning "Widom-601" DNA sequence at time scales of 12 μs. The simulations are performed at salt concentrations 10-20 times higher than physiological salt concentrations to screen the electrostatic interactions and promote unwrapping. These microsecond-long simulations give insight into the molecular-level sequence-dependent events that dictate the pathway of DNA unwrapping. We find that the "ASP" sequence forms a loop around SHL ± 5 for three sets of simulations. Coincident with loop formation is a cooperative increase in contacts with the neighboring N-terminal H2B tail and C-terminal H2A tail and the release of neighboring counterions. We find that the Widom-601 sequence exhibits a strong breathing motion of the nucleic acid ends. Coincident with the breathing motion is the collapse of the full N-terminal H3 tail and formation of an α-helix that interacts with the H3 histone core. We postulate that the dynamics of these histone tails and their modification with post-translational modifications (PTMs) may play a key role in governing this dynamics.

Coordination of cohesin and DNA replication observed with purified proteins.

Two newly duplicated copies of genomic DNA are held together by the ring-shaped cohesin complex to ensure faithful inheritance of the genome during cell division1-3. Cohesin mediates sister chromatid cohesion by topologically entrapping two sister DNAs during DNA replication4,5, but how cohesion is established at the replication fork is poorly understood. Here, we studied the interplay between cohesin and replication by reconstituting a functional replisome using purified proteins. Once DNA is encircled before replication, the cohesin ring accommodates replication in its entirety, from initiation to termination, leading to topological capture of newly synthesized DNA. This suggests that topological cohesin loading is a critical molecular prerequisite to cope with replication. Paradoxically, topological loading per se is highly rate limiting and hardly occurs under the replication-competent physiological salt concentration. This inconsistency is resolved by the replisome-associated cohesion establishment factors Chl1 helicase and Ctf4 (refs. 6,7), which promote cohesin loading specifically during continuing replication. Accordingly, we found that bubble DNA, which mimics the state of DNA unwinding, induces topological cohesin loading and this is further promoted by Chl1. Thus, we propose that cohesin converts the initial electrostatic DNA-binding mode to a topological embrace when it encounters unwound DNA structures driven by enzymatic activities including replication. Together, our results show how cohesin initially responds to replication, and provide a molecular model for the establishment of sister chromatid cohesion.

Fully activated structure of the sterol-bound Smoothened GPCR-Gi protein complex.

Smoothened (SMO) is an oncoprotein and signal transducer in the Hedgehog signaling pathway that regulates cellular differentiation and embryogenesis. As a member of the Frizzled (Class F) family of G protein-coupled receptors (GPCRs), SMO biochemically and functionally interacts with Gi family proteins. However, key molecular features of fully activated, G protein-coupled SMO remain elusive. We present the atomistic structure of activated human SMO complexed with the heterotrimeric Gi protein and two sterol ligands, equilibrated at 310 K in a full lipid bilayer at physiological salt concentration and pH. In contrast to previous experimental structures, our equilibrated SMO complex exhibits complete breaking of the pi-cation interaction between R4516.32 and W5357.55, a hallmark of Class F receptor activation. The Gi protein couples to SMO at seven strong anchor points similar to those in Class A GPCRs: intracellular loop 1, intracellular loop 2, transmembrane helix 6, and helix 8. On the path to full activation, we find that the extracellular cysteine-rich domain (CRD) undergoes a dramatic tilt, following a trajectory suggested by positions of the CRD in active and inactive experimental SMO structures. Strikingly, a sterol ligand bound to a shallow transmembrane domain (TMD) site in the initial structure migrates to a deep TMD pocket found exclusively in activator-bound SMO complexes. Thus, our results indicate that SMO interacts with Gi prior to full activation to break the molecular lock, form anchors with Gi subunits, tilt the CRD, and facilitate migration of a sterol ligand in the TMD to an activated position.

Concentration and time-dependent amyloidogenic characteristics of intrinsically disordered N-terminal region of Saccharomyces cerevisiae Stm1

Saccharomyces cerevisiae Stm1 protein is a ribosomal association factor, which plays an important role in preserving ribosomes in a nutrition-deprived environment. It is also shown to take part in apoptosis-like cell death. Stm1 N-terminal region (Stm1_N1-113) is shown to recognize purine motif DNA triplex and G-quadruplex. Circular dichroism (CD) spectra of Stm1_N1-113 (enriched in positively-charged Lysine and Arginine; negatively-charged Aspartate; polar-uncharged Threonine, Asparagine, Proline and Serine; hydrophobic Alanine, Valine, and Glycine) collected after 0 and 24 h indicate that the protein assumes beta-sheet conformation at the higher concentrations in contrast to intrinsically disordered conformation seen for its monomeric form found in the crystal structure. Thioflavin-T kinetics experiments indicate that the lag phase is influenced by the salt concentration. Atomic force microscopy (AFM) images collected for a variety of Stm1_N1-113 concentrations (in the range of 1–400 μM) in the presence of 150 mM NaCl at 0, 24, and 48 h indicate a threshold concentration requirement to observe the time-dependent amyloid formation. This is prominent seen at the physiological salt concentration of 150 mM NaCl with the fibrillation observed for 400 μM concentration at 48 h, whereas oligomerization or proto-fibrillation is seen for the other concentrations. Such concentration-dependent fibrillation of Stm1_N1-113 explains that amyloid fibrils formed during the overexpression of Stm1_N1-113 may act as a molecular device to trigger apoptosis-like cell death.

In-depth biological characterization of two black soldier fly anti-Pseudomonas peptides reveals LPS-binding and immunomodulating effects.

As effector molecules of the innate immune system, antimicrobial peptides (AMPs) have gathered substantial interest as a potential future generation of antibiotics. Here, we demonstrate the anti-Pseudomonas activity and lipopolysaccharide (LPS)-binding ability of HC1 and HC10, two cecropin peptides from the black soldier fly (Hermetia Illucens). Both peptides are active against a wide range of Pseudomonas aeruginosa strains, including drug-resistant clinical isolates. Moreover, HC1 and HC10 can bind to lipid A, the toxic center of LPS and reduce the LPS-induced nitric oxide and cytokine production in murine macrophage cells. This suggests that the peptide-LPS binding can also lower the strong inflammatory response associated with P. aeruginosa infections. As the activity of AMPs is often influenced by the presence of salts, we studied the LPS-binding activity of HC1 and HC10 in physiological salt concentrations, revealing a strong decrease in activity. Our research confirmed the early potential of HC1 and HC10 as starting points for anti-Pseudomonas drugs, as well as the need for structural or formulation optimization before further preclinical development can be considered. IMPORTANCE The high mortality and morbidity associated with Pseudomonas aeruginosa infections remain an ongoing challenge in clinical practice that requires urgent action. P. aeruginosa mostly infects immunocompromised individuals, and its prevalence is especially high in urgent care hospital settings. Lipopolysaccharides (LPSs) are outer membrane structures that are responsible for inducing the innate immune cascade upon infection. P. aeruginosa LPS can cause local excessive inflammation, or spread systemically throughout the body, leading to multi-organ failure and septic shock. As antimicrobial resistance rates in P. aeruginosa infections are rising, the research and development of new antimicrobial agents remain indispensable. Especially, antimicrobials that can both kill the bacteria themselves and neutralize their toxins are of great interest in P. aeruginosa research to develop as the next generation of drugs.

Evaluation of Bile Salts on the Survival and Modulation of Virulence of Aliarcobacter butzleri.

Aliarcobacter butzleri is a Gram-negative bacterium associated with infections of the gastrointestinal tract and widely distributed in various environments. For successful infection, A. butzleri should be able to tolerate various stresses during gastrointestinal passage, such as bile. Bile represents an antimicrobial host barrier that acts against external noxious agents and consists of a variety of bile salts. The intestinal bile salts act as detergents involved in the antimicrobial host defense; although, on the bacterial side, they could also serve as a signal to activate virulence mechanisms. The aim of this work was to understand the effects of bile salts on the survival and virulence of A. butzleri. In our study, A. butzleri was able to survive in the presence of human physiological concentrations of bile salts. Regarding the virulence features, an increase in cellular hydrophobicity, a decrease in motility and expression of flaA gene, as well as an increase in biofilm formation with a concomitant change in the type of biofilm structure were observed in the presence of sub-inhibitory concentration of bile salts. Concerning adhesion and invasion ability, no significant difference was observed. Overall, the results demonstrated that A. butzleri is able to survive in physiological concentrations of bile salts and that exposure to bile salts could change its virulence mechanisms.

Exploring the impact of nucleic acids on protein stability in bacterial cell lysate

- Addition of salt enhanced thermal stability of model substrate proteins by reducing electrostatic repulsion between protein molecules.- However, the opposite effect was observed with bacterial cell lysate, indicating that certain molecules within the lysate could enhance protein stability via electrostatic interactions.- Such molecules present in cell lysate were found to be nucleic acids known to have a potent anti-aggregation activity toward proteins involving electrostatic interactions.- Nucleic acids showed chaperone activity in physiological salt concentration within cells and in buffer or medium commonly used in experiments.- The chaperone activity of nucleic acids should be taken into account when performing various in vitro assays using cell lysate or samples containing nucleic acids.

Acidity/hydrogen peroxide-responsive PEGylated chitosan-modified polydopamine nanoparticles to realize effective photothermal conversion and intracellular drug delivery

To realize effective photothermal conversion and intracellular drug delivery for application of cancer treatment, an acidity/hydrogen peroxide-responsive nanoparticle system comprising melanin-like polydopamine (PDA) as the hydrophobic core covered by PEGylated chitosan (PEG-CS) conjugates is created herein. The PEG-CS/PDA nanoparticles characterized with a well-dispersed spherical shape exhibited prominent colloidal stability in the milieu of physiological salt concentration. Through π- π stacking and hydrophobic interactions between doxorubicin (DOX) and PDA, DOX molecules were efficiently incorporated into the PEG-CS/PDA nanoparticles. With solution pH being adjusted from 7.4 to 5.0, the ionic complexation of protonated chitosan with negatively-charged PDA enabled the embedding of outer PEG segments of DOX@PEG-CS/PDA nanoparticles into the neutral and gel-like surfaces, thus eliciting interparticle aggregation. The same pH stimulation also accelerated DOX release due to the declined interactions of DOX and PDA combined with enhanced repulsion force between positively-charged chitosan and DOX. Notably, the PEG-CS/PDA nanoparticles not only showed robust photothermal effect and stability, but also were significantly degraded by hydrogen peroxide. After being endocytosed by TRAMP-C1 cells, the DOX@PEG-CS/PDA nanoparticles gradually released drug within acidic organelles, thus promoting drug accumulation in nuclei to kill cancer cells. This work indicates the feasibility for applying such DOX@PEG-CS/PDA nanoparticles in cancer treatment.

Amphiphilic tribasic galactosamines potentiate rifampicin in Gram-negative bacteria at low Mg++/Ca++concentrations

Many antibiotics specific to Gram-positive bacteria like rifampicin (RIF) are inactive in Gram-negative bacteria because of outer membrane (OM) impermeability. Enhancing the OM permeability of these antibiotics with the help of OM perturbants is a promising strategy to develop new agents against Gram-negative bacteria. Here we report the synthesis and biological properties of amphiphilic tribasic galactosamines as potential RIF potentiators. Our results demonstrate that tribasic galactose-based amphiphiles potentiate RIF in multidrug-resistant Acinetobacter baumannii and Escherichia coli but not Pseudomonas aeruginosa in low salt-containing media. Under these conditions, lead compounds 20, 22 and 35 lowered the minimum inhibitory concentration of RIF by 64- to 256-fold against Gram-negative bacteria. However, the RIF-potentiating effect was reduced when bivalent Mg++ or Ca++ ions were added in the media at physiological concentrations. Overall, our results indicate that amphiphilic tribasic galactosamine-based compounds show reduced RIF-potentiating effects when compared to amphiphilic tobramycin antibiotics at physiological salt concentrations.

Aβ40 Aggregation under Changeable Conditions.

Homeostasis is crucial for cell function, and disturbances in homeostasis can lead to health disorders. Under normal conditions, intracellular pH is maintained between 7.35 and 7.45. Altered endosomal and lysosomal pH together with a general drop in brain pH are associated with the aggregation of amyloid-β-peptide (Aβ) and the development of Alzheimer's disease. Under acidic conditions, close to the Aβ isoelectric point, the absence of charges favors the formation of intermolecular contacts and promotes aggregation. Here, we analyzed how pH levels affect the aggregation of Aβ40 considering the variations in brain pH and the coexistence of different aggregated conformations. Our results suggest that different macromolecular conformations can interact with each other and influence the aggregation process. In addition, we showed that neutral pH and physiological salt concentrations favor a slow aggregation, resulting in ordered, stable fibrils, with low cytotoxic effects. Overall, we highlight the complexity of the aggregation processes occurring in different physiological and pathological environments.

OmpC-Dependent Bile Tolerance Contributes to E. coli Colonization of the Mammalian Intestine.

Escherichia coli persistently colonizes the mammalian intestine by mechanisms that are not fully understood. Previously, we found when streptomycin-treated mice were fed E. coli MG1655, the intestine selected for envZ missense mutants that outcompeted the wild type. The better-colonizing envZ mutants had a higher level of OmpC and reduced OmpF. This suggested the EnvZ/OmpR two-component system and outer membrane proteins play a role in colonization. In this study, we show that wild-type E. coli MG1655 outcompetes an envZ-ompR knockout mutant. Moreover, ompA and ompC knockout mutants are outcompeted by the wild type, while an ompF knockout mutant colonizes better than the wild type. Outer membrane protein gels show the ompF mutant overproduces OmpC. An ompC mutant is more sensitive to bile salts than the wild type and ompF mutant. The ompC mutant initiates colonization slowly because it is sensitive to physiological concentrations of bile salts in the intestine. Overexpression of ompC under the control of a constitutive promoter confers a colonization advantage only when ompF is deleted. These results indicate that fine-tuning of OmpC and OmpF levels is needed to maximize competitive fitness in the intestine. RNA sequencing reveals the EnvZ/OmpR two-component system is active in the intestine: ompC is upregulated and ompF is downregulated. While other factors could also contribute to the advantage provided by OmpC, we provide evidence that OmpC is important for E. coli to colonize the intestine because its smaller pore size excludes bile salts or other unknown toxic substances, while OmpF is deleterious because its larger pore size allows bile salts or other unknown toxic substances to enter the periplasm. IMPORTANCE Every mammalian intestine is colonized with Escherichia coli. Although E. coli is one of the most studied model organisms, how it colonizes the intestine is not fully understood. Here, we investigated the role of the EnvZ/OmpR two-component system and outer membrane proteins in colonization of the mouse intestine by E. coli. We report that an ompC mutant is a poor colonizer, while an ompF mutant, which overproduces OmpC, outcompetes the wild type. OmpF has a larger pore size that allows toxic bile salts or other toxic compounds into the cell and is deleterious for colonization of the intestine. OmpC has a smaller pore size and excludes bile salts. Our findings provide insights into why E. coli fine-tunes the levels of OmpC and OmpF during colonization via the EnvZ/OmpR two-component system.

Pseudo-Complementary G:C Base Pair for Mixed Sequence dsDNA Invasion and Its Applications in Diagnostics (SARS-CoV-2 Detection).

Pseudo-complementary oligonucleotides contain artificial nucleobases designed to reduce duplex formation in the pseudo-complementary pair without compromising duplex formation to targeted (complementary) oligomers. The development of a pseudo-complementary A:T base pair, Us:D, was important in achieving dsDNA invasion. Herein, we report pseudo-complementary analogues of the G:C base pair leveraged on steric and electrostatic repulsion between the cationic phenoxazine analogue of cytosine (G-clamp, C+) and N-7 methyl guanine (G+), which is also cationic. We show that while complementary peptide nucleic acids (PNA) form a much more stable homoduplex than the PNA:DNA heteroduplex, oligomers based on pseudo-C:G complementary PNA favor PNA:DNA hybridization. We show that this enables dsDNA invasion at physiological salt concentration and that stable invasion complexes are obtained with low equivalents of PNAs (2-4 equiv). We harnessed the high yield of dsDNA invasion for the detection of RT-RPA amplicon using a lateral flow assay (LFA) and showed that two strains of SARS-CoV-2 can be discriminated owing to single nucleotide resolution.

Lipid droplets as flexible substrates for protein phase separation.

Biomolecular condensates have been shown to nucleate the formation of amyloid fibrils for many proteins implicated in neurodegenerative disorders, such as alpha synuclein in Parkinson's disease and fused in sarcoma (FUS) in amyotrophic lateral sclerosis. Within these fibrils, a distinct lipid signal is often observable, and indeed, a membrane environment is favorable for the formation of amyloid fibrils for a variety of biophysical reasons, including an increase in local protein concentration and conformational shift upon membrane binding. How might intracellular lipid substrates contribute to nucleation of phase separation? Here we observe for the first time that intrinsically disordered proteins can undergo phase separation on the surface of lipid droplets. We find that the low complexity domain of FUS (FUSLC) separates into protein-rich and protein-depleted phases at physiological salt (150mM) and protein concentrations (<5μM) when recruited to the surfaces of lipid droplets through a histidine-Ni-NTA headgroup interaction. The number of LDs showing FUSLC phase separation is strongly affected by variations in the protein and salt concentration, and it follows the trend seen previously with FUSLC droplets in solution. Further, these phase-separated patches demonstrate molecular mobility when assessed using fluorescence recovery after photobleaching (FRAP), which is indicative of a liquid-like state. This phenomenon extends to other well-known phase separating domains, such as LAF1-RGG. Overall, these results demonstrate the potential of monolayer substrates to nucleate protein phase separation and could have important implications for the assembly of intrinsically disordered lipid droplet-binding proteins.

DNA bending facilitates the formation of Z-DNA investigated by single-molecule FRET.

Z-DNA, a noncanonical helical structure of double-stranded DNA (dsDNA), plays essential roles in diverse biological processes such as transcription regulation. Mechanical stresses on dsDNA, such as torsion and tension, could form Z-DNA more easily. However, the effect of DNA bending, one of the most common deformations of DNA, on Z-DNA formation is utterly elusive. Herein, we show that DNA bending facilitates the formation of Z-DNA, that is, Z-DNA is formed at lower Mg2+ concentration as the bending force becomes stronger. We regulated the bending force on dsDNA via D-shaped DNA nanostructures and observed the B-Z transition by single-molecule FRET. In the presence of the bending force, the B-Z transition of methylated DNA occurred at a 28-fold lower Mg2+ condition (2.8 mM) which is in the range of physiological salt concentrations. Monte Carlo simulation suggested that the base extrusion at the B-Z junction according to the B-Z transition may stabilize the Z-DNA form via releasing the bending stress on dsDNA. Our results certainly show that DNA bending force induces the formation of Z-DNA and provide a new insight into the effect of DNA bending.

Rational design of elastin-like polypeptide fusion proteins to tune self-assembly and properties of protein vesicles.

Protein vesicles made from bioactive proteins have potential value in drug delivery, biocatalysis, and as artificial cells. As the proteins are produced recombinantly, the ability to precisely tune the protein sequence provides control not possible with polymeric vesicles. The tunability and biocompatibility motivated this work to develop protein vesicles using rationally designed protein building blocks to investigate how protein sequence influences vesicle self-assembly and properties. We have reported an elastin-like polypeptide (ELP) fused to an arginine-rich leucine zipper (ZR) and functional, globular proteins fused to a glutamate-rich leucine zipper (ZE) that self-assemble into protein vesicles when warmed from 4 to 25 °C due to the hydrophobic transition of ELP. Previously, we demonstrated the ability to tune vesicle properties by changing protein and salt concentration, ZE : ZR ratio, and warming rate. However, there is a limit to the properties that can be achieved via assembly conditions. In order to access a wider range of vesicle diameter and stability profiles, this work investigated how modifiying the hydrophobicity and length of the ELP sequence influenced self-assembly and the final properties of protein vesicles using mCherry as a model globular protein. The results showed that both transition temperature and diameter of protein vesicles were inversely correlated to the ELP guest residue hydrophobicity and the number of ELP pentapeptide repeats. Additionally, sequence manipulation enabled assembly of vesicles with properties not accessible by changes to assembly conditions. For example, introduction of tyrosine at 5 guest residue positions in ELP enabled formation of nanoscale vesicles stable at physiological salt concentration. This work yields design guidelines for modifying the ELP sequence to manipulate protein vesicle transition temperature, size and stability to achieve desired properties for particular biofunctional applications.

Onion-like doxorubicin-carrying polymeric nanomicelles with tumor acidity-sensitive dePEGylation to expose positively-charged chitosan shell for enhanced cancer chemotherapy

To effectively promote antitumor potency of doxorubicin (DOX), a regularly used chemotherapy drug, the tumor acidity-responsive polymeric nanomicelles from self-assembly of the as-synthesized amphiphilic benzoic imine-containing PEGylated chitosan-g-poly(lactic-co-glycolic acid) (PLGA) conjugates were developed as vehicles of DOX. The attained PEGylated chitosan-g-PLGA nanomicelles with high PEGylation degree (H-PEG-CSPNs) were characterized to exhibit a “onion-like” core-shell-corona structure consisting of a hydrophobic PLGA core covered by benzoic imine-rich chitosan shell and outer hydrophilic PEG corona. The DOX-carrying H-PEG-CSPNs (DOX@H-PEG-CSPNs) displayed robust colloidal stability under large-volume dilution condition and in a serum-containing aqueous solution of physiological salt concentration. Importantly, the DOX@H-PEG-CSPNs in weak acidic milieu undergoing the hydrolysis of benzoic imine bonds and increased protonation of chitosan shell showed dePEGylation and surface charge conversion. Also, the considerable swelling of protonated chitosan shell within DOX@H-PEG-CSPNs accelerated drug release. Notably, the cellular internalization of DOX@H-PEG-CSPNs by TRAMP-C1 prostate cancer cells under mimic acidic tumor microenvironment was efficiently boosted upon acidity-triggered detachment of PEG corona and exposure of positively-charged chitosan shell, thus augmenting DOX-mediated anticancer effect. Compared to free DOX molecules, the DOX@H-PEG-CSPNs appreciably suppressed TRAMP-C1 tumor growth in vivo, thereby showing great promise in improving DOX chemotherapy.

PL‐101‐WK, a novel tryptophan‐ and lysine‐rich peptide with antimicrobial activity against Staphylococcus aureus

AbstractDesigning short antimicrobial peptides (AMPs), which are active against drug‐resistant bacteria, is a promising way to find new therapeutic agents. In this research, a novel short AMP, PL‐101‐WK, was designed based on PL‐101 (a derivative of plicatamide). Here, the substitution of Phe and His with Trp and Lys was considered. The antimicrobial activity and physicochemical properties of PL‐101‐WK were compared with PL‐101 by in silico analysis. The antimicrobial activity in the presence or absence of NaCl concentration, thermal stability, hemolytic activity, and selectivity of the peptides were determined. By substitution of Lys and Trp residues, positive charge, in vitro stability, and hydrophilicity of PL‐101‐WK were raised compared to the template. PL‐101‐WK had the best minimum inhibitory concentration (MIC) value of 64 μg/ml against Staphylococcus aureus strains, which showed at least 16‐fold reduction when compared to the values of PL‐101. The MICs of PL‐101‐WK were retained toward S. aureus strains at physiological salt concentration. While PL‐101‐WK did not display acceptable thermal stability, it had desirable selectivity against bacteria. The maximum hemolytic activity of PL‐101‐WK was 1.65% at 512 μg/ml. Taken together, increasing positive charge and the presence of Trp residues were enhanced the potential of antibacterial activity of PL‐101.

Salt-Induced Transitions in the Conformational Ensembles of Intrinsically Disordered Proteins.

Salts modulate the behavior of intrinsically disordered proteins (IDPs) and influence the formation of membraneless organelles through liquid-liquid phase separation (LLPS). In low ionic strength solutions, IDP conformations are perturbed by the screening of electrostatic interactions, independent of the salt identity. In this regime, insight into the IDP behavior can be obtained using the theory for salt-induced transitions in charged polymers. However, salt-specific interactions with the charged and uncharged residues, known as the Hofmeister effect, influence IDP behavior in high ionic strength solutions. There is a lack of reliable theoretical models in high salt concentration regimes to predict the salt effect on IDPs. We propose a simulation methodology using a coarse-grained IDP model and experimentally measured water to salt solution transfer free energies of various chemical groups that allowed us to study the salt-specific transitions induced in the IDPs conformational ensemble. We probed the effect of three different monovalent salts on five IDPs belonging to various polymer classes based on charged residue content. We demonstrate that all of the IDPs of different polymer classes behave as self-avoiding walks (SAWs) at physiological salt concentration. In high salt concentrations, the transitions observed in the IDP conformational ensembles are dependent on the salt used and the IDP sequence and composition. Changing the anion with the cation fixed can result in the IDP transition from a SAW-like behavior to a collapsed globule. An important implication of these results is that a suitable salt can be identified to induce condensation of an IDP through LLPS.

Structural and functional insight into mismatch extension by human DNA polymerase α

Human DNA polymerase α (Polα) does not possess proofreading ability and plays an important role in genome replication and mutagenesis. Polα extends the RNA primers generated by primase and provides a springboard for loading other replication factors. Here we provide the structural and functional analysis of the human Polα interaction with a mismatched template:primer. The structure of the human Polα catalytic domain in the complex with an incoming deoxycytidine triphosphate (dCTP) and the template:primer containing a T-C mismatch at the growing primer terminus was solved at a 2.9 Å resolution. It revealed the absence of significant distortions in the active site and in the conformation of the substrates, except the primer 3′-end. The T-C mismatch acquired a planar geometry where both nucleotides moved toward each other by 0.4 Å and 0.7 Å, respectively, and made one hydrogen bond. The binding studies conducted at a physiological salt concentration revealed that Polα has a low affinity to DNA and is not able to discriminate against a mispaired template:primer in the absence of deoxynucleotide triphosphate (dNTP). Strikingly, in the presence of cognate dNTP, Polα showed a more than 10-fold higher selectivity for a correct duplex versus a mismatched one. According to pre-steady-state kinetic studies, human Polα extends the T-C mismatch with a 249-fold lower efficiency due to reduction of the polymerization rate constant by 38-fold and reduced affinity to the incoming nucleotide by 6.6-fold. Thus, a mismatch at the postinsertion site affects all factors important for primer extension: affinity to both substrates and the rate of DNA polymerization.