Binding of Antimicrobial Peptide Indolicidin to DMPC Bilayer Using Replica-Exchange Molecular Dynamics.

Cationic antimicrobial peptides (AMPs) are toxic to microbes, such as bacteria and fungi, and have been increasingly studied as an alternative to traditional antibiotics, in part because AMPs are bactericidal with a minimum risk of developing bacterial resistance. Indolicidin (IL) is an AMP derived from bovine neutrophils that is unique due to its high prevalence of tryptophan and proline amino acids and its disordered structure. In addition to its antimicrobial activity, IL has exhibited toxicity toward mammalian cells, resulting in hemolysis.

The decameric repeat (DR) of PSGL-1 functions as a basic antiviral unit in restricting HIV-1 infectivity.

PSGL-1 (P-selectin glycoprotein ligand-1) is a dimeric, mucin-like surface glycoprotein that interacts with selectins on the endothelium, facilitating leukocyte tethering and rolling during transmigration. Previous studies have demonstrated that PSGL-1 acts as an HIV restriction factor, blocking HIV infectivity by hindering particle attachment to target cells. A large part of PSGL-1's extracellular region consists of a mucin-like domain, characterized by decameric repeats (DR), which comprise 14 to 16 DR tandems.

Applying Absolute Free Energy Perturbation Molecular Dynamics to Diffusively Binding Ligands.

We have developed and tested an absolute free energy perturbation (FEP) protocol, which combines all-atom molecular dynamics, replica exchange with solute tempering (REST) enhanced sampling, and a spherical harmonic restraint applied to a ligand. Our objective was to compute the binding free energy together with the underlying binding mechanism for a ligand, which binds diffusively to a protein. Such ligands represent nearly impossible targets for traditional FEP simulations.

CD34 serves as an intrinsic innate immune guardrail protecting stem cells from replicating retroviruses.

Stem cells are highly resistant to viral infection compared to their differentiated progeny, and this resistance is associated with stem cell-specific restriction factors and intrinsic interferon stimulated genes (ISGs). In HIV infection, proviral DNA has been detected in certain bone marrow hematopoietic stem cells, yet widespread stem cell infection is restricted. Intriguingly, exposing bone marrow stem cells to HIV led to viral replication selectively only in the CD34 population, but not in the CD34 cells.

Structural Analysis of Amylin and Amyloid β Peptide Signaling in Alzheimer's Disease.

Amylin and amyloid β belong to the same protein family and activate the same receptors. Amyloid β levels are elevated in Alzheimer's disease. Recent studies have demonstrated that amylin-based peptides can reduce the symptoms of Alzheimer's disease in animal models.

PSGL-1 excludes HIV Env from virion surface through spatial hindrance involving structural folding of the decameric repeats (DR).

P-selectin glycoprotein ligand-1 (PSGL-1), a mucin-like surface glycoprotein, is primarily expressed on lymphoid and myeloid cells. PSGL-1 has recently been identified as an HIV restriction factor, blocking HIV infectivity mainly through virion incorporation that sterically hinders virion attachment to target cells. PSGL-1 also inhibits HIV Env incorporation into virions.

Proteomics in Acute Heart Transplant Rejection, on Behalf of the GRAfT Investigators.

Background: Proteomic phenotyping can provide insights into rejection pathophysiology, novel biomarkers, and therapeutic targets.

Methods: Within the prospective, multicenter Genomic Research Alliance for Transplantation study, 181 proteins were evaluated from blood drawn at the time of endomyocardial biopsy; protein fold change, logistic regression, and pathway analyses were conducted, with protein discovery adjusted for a 5% false discovery rate.

Results: Among 104 adult heart transplant patients (31% female sex, 53% Black race, median age 52 y), 74 had no rejection, 18 developed acute cellular rejection (ACR), and 12 developed antibody-mediated rejection (AMR).

Binding of Inhibitors to Nuclear Localization Signal Peptide from Venezuelan Equine Encephalitis Virus Capsid Protein Explored with All-Atom Replica Exchange Molecular Dynamics.

Several small molecule inhibitors have been designed to block binding of the Venezuelan equine encephalitis virus (VEEV) nuclear localization signal (NLS) sequence to the importin-α nuclear transport protein. To probe the inhibition mechanism on a molecular level, we used all-atom explicit water replica exchange molecular dynamics to study the binding of two inhibitors, I1 and I2, to the coreNLS peptide, representing the core fragment of the VEEV NLS sequence. Our objective was to evaluate the possibility of masking wherein binding of these inhibitors to the coreNLS occurs prior to its binding to importin-α.

Competitive Binding of Viral Nuclear Localization Signal Peptide and Inhibitor Ligands to Importin-α Nuclear Transport Protein.

Venezuelan equine encephalitis virus (VEEV) is a highly virulent pathogen whose nuclear localization signal (NLS) sequence from capsid protein binds to the host importin-α transport protein and blocks nuclear import. We studied the molecular mechanisms by which two small ligands, termed I1 and I2, interfere with the binding of VEEV's NLS peptide to importin-α protein. To this end, we performed all-atom replica exchange molecular dynamics simulations probing the competitive binding of the VEEV coreNLS peptide and I1 or I2 ligand to the importin-α major NLS binding site.

Repair of a fistula between the aorta and right ventricular outflow tract secondary to infective endocarditis of a unicuspid aortic valve and previously repaired ventricular septal defect.

Background: Infective endocarditis of the aortic valve can result in a wide range of destructive pathology beyond the valve leaflets and annulus which require careful surgical planning to provide appropriate debridement and reconstruction. Failure to do so can result in a failure of surgical treatment, recurrent infection and cardiac failure with concomitant high morbidity and mortality.

Case Report: We describe the case of a 45-year-old male with previous patch repair of a ventricular septal defect, who was diagnosed with sub-acute bacterial endocarditis of the native aortic valve and developed a new fistula from the aorta to the right ventricular outflow tract which.

Binding and dimerization of PGLa peptides in anionic lipid bilayer studied by replica exchange molecular dynamics.

The 21-residue PGLa peptide is well known for antimicrobial activity attributed to its ability to compromize bacterial membranes. Using all-atom explicit solvent replica exchange molecular dynamics with solute tempering, we studied PGLa binding to a model anionic DMPC/DMPG bilayer at the high peptide:lipid ratio that promotes PGLa dimerization (a two peptides per leaflet system). As a reference we used our previous simulations at the low peptide:lipid ratio (a one peptide per leaflet system).

Replica Exchange with Hybrid Tempering Efficiently Samples PGLa Peptide Binding to Anionic Bilayer.

We evaluated the utility of a variant of the replica exchange method, a replica exchange with hybrid tempering (REHT), for all-atom explicit water biomolecular simulations and compared it with a more traditional replica exchange with the solute tempering (REST) algorithm. As a test system, we selected a 21-mer antimicrobial peptide PGLa binding to an anionic DMPC/DMPG lipid bilayer. Application of REHT revealed the following binding mechanism.

Binding of viral nuclear localization signal peptides to importin-α nuclear transport protein.

Using all-atom replica-exchange molecular dynamics simulations, we mapped the mechanisms of binding of the nuclear localization signal (NLS) sequence from Venezuelan equine encephalitis virus (VEEV) capsid protein to importin-α (impα) transport protein. Our objective was to identify the VEEV NLS sequence fragment that confers native, experimentally resolved binding to impα as well as to study associated binding energetics and conformational ensembles. The two selected VEEV NLS peptide fragments, KKPK and KKPKKE, show strikingly different binding mechanisms.

Can Free Energy Perturbation Simulations Coupled with Replica-Exchange Molecular Dynamics Study Ligands with Distributed Binding Sites?

Free energy perturbation coupled with replica exchange with solute tempering (FEP/REST) offers a rigorous approach to compute relative free energy changes for ligands. To determine the applicability of FEP/REST for the ligands with distributed binding poses, we considered two alchemical transformations involving three putative inhibitors I0, I1, and I2 of the Venezuelan equine encephalitis virus nuclear localization signal sequence binding to the importin-α (impα) transporter protein. I0 → I1 and I0 → I2 transformations, respectively, increase or decrease the polarity of the parent molecule.

Binding of Venezuelan Equine Encephalitis Virus Inhibitors to Importin-α Receptors Explored with All-Atom Replica Exchange Molecular Dynamics.

Although Venezuelan equine encephalitis virus (VEEV) is a life-threatening pathogen with a capacity for epidemic outbreaks, there are no FDA-approved VEEV antivirals for humans. VEEV cytotoxicity is partially attributed to the formation of a tetrameric complex between the VEEV capsid protein, the nuclear import proteins importin-α and importin-β, and the nuclear export protein CRM1, which together block trafficking through the nuclear pore complex. Experimental studies have identified small molecules from the CL6662 scaffold as potential inhibitors of the viral nuclear localization signal (NLS) sequence binding to importin-α.

Lysine Acetylation Changes the Mechanism of Aβ25-35 Peptide Binding and Dimerization in the DMPC Bilayer.

The impact of Lys28 acetylation on Alzheimer's Aβ peptide binding to the lipid bilayer has not been previously studied, either experimentally or computationally. To probe this common post-translational modification, we performed all-atom replica exchange molecular dynamics simulations targeting binding and aggregation of acetylated acAβ25-35 peptide within the DMPC bilayer. Using the unmodified Aβ25-35 studied previously as a reference, our results can be summarized as follows.

Transmembrane Aggregation of Aβ10-40 Peptides in an Anionic Lipid Bilayer.

Using the all-atom model and 10 μs serial replica-exchange molecular dynamics (SREMD), we investigated the binding of Alzheimer's Aβ10-40 peptides to the anionic dimyristoylphosphatidylcholine/dimyristoylphosphatidylglycerol (DMPC/DMPG) lipid bilayer. Our objective was to probe transmembrane Aβ10-40 aggregation and to test the utility of SREMD. Our results are threefold.

The coronavirus disease pandemic among adult congenital heart disease patients and the lessons learnt - results of a prospective multicenter european registry.

Background: At the beginning of the COVID-19 pandemic, professionals in charge of particularly vulnerable populations, such as adult congenital heart disease (ACHD) patients, were confronted with difficult decision-making. We aimed to assess changes in risk stratification and outcomes of ACHD patients suffering from COVID-19 between March 2020 and April 2021.

Methods And Results: Risk stratification among ACHD experts (before and after the first outcome data were available) was assessed by means of questionnaires.

The sanctity of life: The role of purity in attitudes towards abortion and euthanasia.

Although abortion and euthanasia are highly contested issues at the heart of the culture war, the moral foundations underlying ideological differences on these issues are mostly unknown. Given that much of the extant debate is framed around the sanctity of life, we argued that the moral foundation of purity/sanctity-a core moral belief that emphasises adherence to the "natural order"-would mediate the negative relationship between conservatism and support for abortion and euthanasia. As hypothesised, results from a nation-wide random sample of adults in New Zealand (N = 3360) revealed that purity/sanctity mediated the relationship between conservatism and opposition to both policies.

Mechanisms of Binding of Antimicrobial Peptide PGLa to DMPC/DMPG Membrane.

PGLa belongs to a class of antimicrobial peptides showing strong affinity to anionic bacterial membranes. Using all-atom explicit solvent replica exchange molecular dynamics with solute tempering, we studied binding of PGLa to a model anionic dimyristoylphosphatidylcholine/dimyristoylphosphatidylglycerol (DMPC/DMPG) bilayer. Due to a strong hydrophobic moment, PGLa upon binding adopts a helical structure and two distinct bound states separated by a significant free energy barrier.

Met35 Oxidation Hinders Aβ25-35 Peptide Aggregation within the Dimyristoylphosphatidylcholine Bilayer.

Using all-atom explicit solvent replica exchange molecular dynamics simulations, we studied the aggregation of oxidized (ox) Aβ25-35 peptides into dimers mediated by the zwitterionic dimyristoylphosphatidylcholine (DMPC) lipid bilayer. By comparing oxAβ25-35 aggregation with that observed for reduced and phosphorylated Aβ25-35 peptides, we elucidated plausible impact of post-translational modifications on cytotoxicity of Aβ peptides involved in Alzheimer's disease. We found that Met35 oxidation reduces helical propensity in oxAβ25-35 peptides bound to the lipid bilayer and enhances backbone fluctuations.

Assessment of the conjunctival microcirculation in adult patients with cyanotic congenital heart disease compared to healthy controls.

Purpose: Congenital heart disease (CHD) is the most common live birth defect and a proportion of these patients have chronic hypoxia. Chronic hypoxia leads to secondary erythrocytosis resulting in microvascular dysfunction and increased thrombosis risk. The conjunctival microcirculation is easily accessible for imaging and quantitative assessment.

Partitioning of Aβ Peptide Fragments into Blood-Brain Barrier Mimetic Bilayer.

We used all-atom replica-exchange umbrella sampling molecular dynamics simulations to investigate the partitioning of the charged tetrapeptide KLVF and its neutral apolar counterpart VVIA into the blood-brain barrier (BBB)-mimetic bilayer. Our findings allowed us to reconstruct the partitioning mechanism for these two Aβ peptide fragments. Despite dissimilar sequences, their permeation shares significant common features.

Three Popular Force Fields Predict Consensus Mechanism of Amyloid β Peptide Binding to the Dimyristoylgylcerophosphocholine Bilayer.

Using all-atom explicit water replica-exchange molecular dynamics simulations, we examined the impact of three popular force fields (FF) on the equilibrium binding of Aβ10-40 peptide to the dimyristoylgylcerophosphocholine (DMPC) bilayer. The comparison included CHARMM22 protein FF with CHARMM36 lipid FF (C22), CHARMM36m protein FF with CHARMM36 lipid FF (C36), and Amber14SB protein FF with Lipid14 lipid FF (A14). Analysis of Aβ10-40 binding to the DMPC bilayer in three FFs revealed a consensus binding mechanism.

Do Cholesterol and Sphingomyelin Change the Mechanism of Aβ Peptide Binding to Zwitterionic Bilayer?

Using replica exchange with solute tempering all-atom molecular dynamics, we studied the equilibrium binding of Aβ peptide to the ternary bilayer composed of an equimolar mixture of dimyristoylphosphatidylcholine (DMPC), -palmitoylsphingomyelin (PSM), and cholesterol. Binding of the same peptide to the pure DMPC bilayer served as a control. Due to significant C-terminal hydrophobic moment, binding to the ternary and DMPC bilayers promotes helical structure in the peptide.