Cause and Effect of Melittin-Induced Pore Formation: A Computational Approach

Melittin embedded in a palmitoyl oleyl phosphatidylcholine bilayer at a high peptide/lipid ratio (1:30) was simulated in the presence of explicit water and ions. The simulation results indicate the incipience of an ion-permeable water pore through collective membrane perturbation by bound peptides. The positively charged residues of melittin not only act as “anchors” but also disrupt the membrane, leading to cell lysis. A detailed analysis of the lipid tail order parameter profile depicts localized membrane perturbation. The lipids in the vicinity of the aqueous cavity adopt a tilted conformation, which allows local bilayer thinning. The prepore thus formed can be considered as the melittin-induced structural defects in the bilayer membrane. Because of the strong cationic nature, the melittin-induced prepore exhibits selectivity toward anions over cations. As Cl− ions entered into the prepore, they are electrostatically entrapped by positively charged residues located at its wall. The confined motion of the Cl− ions in the membrane interior is obvious from calculated diffusion coefficients. Moreover, reorientation of the local lipids occurs in such a way that few lipid heads along with peptide helices can line the surface of the penetrating aqueous phase. The flipping of lipids argued in favor of melittin-induced toroidal pore over a barrel-stave mechanism. Thus, our result provides atomistic level details of the mechanism of membrane disruption by antimicrobial peptide melittin

Location and orientation of Aβ-monomer at membrane-interfaces.

<p>(a,c,e) Atom density profiles (last 100 ns average) of peptide, lipids and water were plotted along Z-axis. For POPC (green) and GM1 (blue) the shaded area under the curve represented their head-group regions. (b,d,f) The average (last 100 ns) distance of the center of mass of peptide residues from bilayer interfaces. The horizontal lines represent the average planes of GM1 penta-saccharide head (solid line), Chol -OH oxygen (dashed line) and phosphorus atom of POPC (dotted line at Z = 0 position).</p

Computational studies suggest compounds restoring function of p53 cancer mutants can bind SARS-CoV-2 spike protein

It is reasonable to think that cancer patients undergoing chemotherapy or immunotherapy may have a more aggressive course if they are positive for the novel coronavirus disease. Their compulsive condition requires investigation into effective drugs. We applied computational techniques to a series of compounds known for restoring the function of p53 cancer mutant p53R175H and p53G245S. Two potent inhibitors, 1-(3-chlorophenyl)-3-(1, 3 -thiazol-2-yl) urea (CTU, PubChem NSC321792) with the highest binding affinity −6.92 kcal/mol followed by a thiosemicarbazone compound N’-(1-(Pyridin-2-yl)ethylidene) azetidine − 1 -carbothiohydrazide (NPC, PubChem NSC319726) with −6.75 kcal/mol were subjected to Molecular Dynamics simulation with receptor binding domain (RBD) and compared with control ligand dexamethasone. In particular, CTU adheres to pocket 1 with an average free energy of binding −21.65 ± 2.89 kcal/mol at the RBD - angiotensin-converting enzyme 2 binding region with the highest frequency of amino acid residues after reaching a local equilibrium in 100 ns MD simulation trajectory. A significant enthalpy contribution from the independent simulations unfolds the possibility of dual binding sites for NPC as shifted pocket 1 (−15.59 ± 5.98 kcal/mol) and pocket 2 (−18.90 ± 5.02 kcal/mol). The obtained results for these two compounds are in good agreement with dexamethasone (−18.45 ± 2.42 kcal/mol). Taken together our findings could facilitate the discovery of small molecules that restore the function of p53 cancer mutants newly against COVID-19 in cancer patients. Communicated by Ramaswamy H. Sarma</p

Atomistic Mechanism of Protein Denaturation by Urea

Effects of urea on protein stability have been studied from all-atom molecular dynamics simulations of ubiquitin, G311 protein, and immunoglobulin binding domain (B1) of streptococcal protein G (GB1) in water and 8 M aqueous urea solution. The mechanism of the change in the solvent environment and the early events in protein unfolding by urea have been identified with emphasis on the change in the interactions of hydrophilic and hydrophobic parts of the protein by calculating the potential of mean force (PMF). Urea replaces the protein−protein and protein−water contacts by forming stronger contacts with the protein, which is indicated by the longer survival times of the protein−urea hydrogen bonds

Binding, Conformational Transition and Dimerization of Amyloid-β Peptide on GM1-Containing Ternary Membrane: Insights from Molecular Dynamics Simulation

<div><p>Interactions of amyloid-β (Aβ) with neuronal membrane are associated with the progression of Alzheimer’s disease (AD). Ganglioside GM1 has been shown to promote the structural conversion of Aβ and increase the rate of peptide aggregation; but the exact nature of interaction driving theses processes remains to be explored. In this work, we have carried out atomistic-scale computer simulations (totaling 2.65 µs) to investigate the behavior of Aβ monomer and dimers in GM1-containing raft-like membrane. The oligosaccharide head-group of GM1 was observed to act as scaffold for Aβ-binding through sugar-specific interactions. Starting from the initial helical peptide conformation, a β-hairpin motif was formed at the C-terminus of the GM1-bound Aβ-monomer; that didn’t appear in absence of GM1 (both in fluid POPC and liquid-ordered cholesterol/POPC bilayers and also in aqueous medium) within the simulation time span. For Aβ-dimers, the β-structure was further enhanced by peptide-peptide interactions, which might influence the propensity of Aβ to aggregate into higher-ordered structures. The salt-bridges and inter-peptide hydrogen bonds were found to account for dimer stability. We observed spontaneous formation of intra-peptide D²³-K²⁸ salt-bridge and a turn at V²⁴GSN²⁷ region - long been accepted as characteristic structural-motifs for amyloid self-assembly. Altogether, our results provide atomistic details of Aβ-GM1 and Aβ-Aβ interactions and demonstrate their importance in the early-stages of GM1-mediated Aβ-oligomerisation on membrane surface.</p></div

Evidence for Effect of GM1 on Opioid Peptide Conformation: NMR Study on Leucine Enkephalin in Ganglioside-Containing Isotropic Phospholipid Bicelles

Enkephalins are endogenous neuropeptides that have opioid-like activities and compete with morphines for the receptor binding. The binding of these neuropeptides to membrane appears crucial since enkephalins interact with the nerve cell membranes to achieve bioactive conformations that fit onto multiple receptor sites (μ, δ, and κ). Using NMR spectroscopy, we have determined the solution structure of the small opiate pentapeptide leucine enkephalin in the presence of isotropic phospholipid bicelles: phosphocholine bicelles (DMPC:CHAPS 1:4) and phosphocholine bicelles doped with ganglioside GM1 (DMPC:CHAPS:GM1 1:4:0.3). Bicelles containing GM1 were found to interact strongly with leucine enkephalin, whereas a somewhat weaker interaction was observed in the case of bicelles without GM1. Structure calculation from torsion angles, chemical shifts, and NOE-based distance constraints explored that the peptide could flexibly switch between several μ- and δ-selective conformations in both the bicelles though μ-selective conformations turned out to be geometrically preferred in each bicellar system. A detailed analysis of the structures presented supports the variance over the singly associated conformation of enkephalin in nerve cell membranes

Factors accounting for dimer stability.

<p>(a) The snapshot showed the presence of intra-molecular Lys²⁸-Asp²³ slat-bridge in monomer-1 of Dimer1. Here the corresponding Lys²⁸ and Asp²³ were colored according to atom type: C in red, O in yellow, N in blue and H in white. (b) The time dependence of minimum distance between amide N of Lys²⁸ and carboxyl O of Asp²³ in monomer-1 of Dimer1, as highlighted in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0071308#pone-0071308-g007" target="_blank">Figure 7a</a>. (c) 3D-plot showing the inter-peptide hydrogen-bonding interactions within Dimer1 (last 200 ns average). The notation used here for leveling H-bond between a pair of residues was XA-YB, where X was the amino acid residue of peptide-1 with its corresponding residue number A and Y was the residue of peptide-2 with its corresponding residue number B.</p

Effect of glycosylation on hydration behavior at the ice-binding surface of the Ocean Pout type III antifreeze protein: a molecular dynamics simulation

<p>Antifreeze proteins (AFPs), found in certain vertebrates, plants, fungi and bacteria have the ability to permit their survival in subzero environments by thermal hysteresis mechanism. However, the exact mechanism of ice growth inhibition is still not clearly understood. Here, four long explicit molecular dynamics (MD) simulations have been carried out at two different temperatures (277 and 298 K) with and without glycan to study the conformational rigidity of the Ocean pout type III antifreeze protein in aqueous medium and the structural arrangements of water molecules hydrating its ice-binding surface. It is found that irrespective of the temperature the ice-binding surface (IBS) of the protein is relatively more rigid than its non ice-binding surface (NonIBS) in its native and glycosylated form. Hydrophilic residues N14, T18 and Q44 are essential to antifreeze activity. Radial distribution, density distribution function and nearest neighbor orientation plots with respect to individual two surfaces confirm that density of water molecule near these binding surface in native and glycosylated form are relatively more than the nonbinding surface. The glycosylated form shows a strong peak than the native one. From rotational auto correlation function of water molecules around ice-binding sites, it is prominent that with increase in temperature, strong interaction between the water oxygen and the hydrogen bond acceptor group on the protein-binding surface decreases. This provides a possible molecular reason behind the ice-binding activity of ocean pout at the prism plane of ice.</p

Cause and Effect of Melittin-Induced Pore Formation: A Computational Approach

Melittin embedded in a palmitoyl oleyl phosphatidylcholine bilayer at a high peptide/lipid ratio (1:30) was simulated in the presence of explicit water and ions. The simulation results indicate the incipience of an ion-permeable water pore through collective membrane perturbation by bound peptides. The positively charged residues of melittin not only act as “anchors” but also disrupt the membrane, leading to cell lysis. A detailed analysis of the lipid tail order parameter profile depicts localized membrane perturbation. The lipids in the vicinity of the aqueous cavity adopt a tilted conformation, which allows local bilayer thinning. The prepore thus formed can be considered as the melittin-induced structural defects in the bilayer membrane. Because of the strong cationic nature, the melittin-induced prepore exhibits selectivity toward anions over cations. As Cl− ions entered into the prepore, they are electrostatically entrapped by positively charged residues located at its wall. The confined motion of the Cl− ions in the membrane interior is obvious from calculated diffusion coefficients. Moreover, reorientation of the local lipids occurs in such a way that few lipid heads along with peptide helices can line the surface of the penetrating aqueous phase. The flipping of lipids argued in favor of melittin-induced toroidal pore over a barrel-stave mechanism. Thus, our result provides atomistic level details of the mechanism of membrane disruption by antimicrobial peptide melittin

Urea-Mediated Protein Denaturation: A Consensus View

We have performed all-atom molecular dynamics simulations of three structurally similar small globular proteins in 8 M urea and compared the results with pure aqueous simulations. Protein denaturation is preceded by an initial loss of water from the first solvation shell and consequent in-flow of urea toward the protein. Urea reaches the first solvation shell of the protein mainly due to electrostatic interaction with a considerable contribution coming from the dispersion interaction. Urea shifts the equilibrium from the native to denatured ensemble by making the protein−protein contact less stable than protein−urea contact, which is just the reverse of the condition in pure water, where protein−protein contact is more stable than protein−water contact. We have also seen that water follows urea and reaches the protein interior at later stages of denaturation, while urea preferentially and efficiently solvates different parts of the protein. Solvation of the protein backbone via hydrogen bonding, favorable electrostatic interaction with hydrophilic residues, and dispersion interaction with hydrophobic residues are the key steps through which urea intrudes the core of the protein and denatures it. Why urea is preferred over water for binding to the protein backbone and how urea orients itself toward the protein backbone have been identified comprehensively. All the key components of intermolecular forces are found to play a significant part in urea-induced protein denaturation and also toward the stability of the denatured state ensemble. Changes in water network/structure and dynamical properties and higher degree of solvation of the hydrophobic residues validate the presence of “indirect mechanism” along with the “direct mechanism” and reinforce the effect of urea on protein