Opposite Regulatory Effects of Immobilized Cations on the Folding Vs. Assembly of Melittin

Ions are crucial in modulating the protein structure. For the free ions in bulk solution, ammonium is kosmotropic (structure forming) and guanidinium is chaotropic (structure breaking) to the protein structure within the Hofmeister series. However, the effect of immobilized ions on a protein surface is less explored. Herein, we explored the influence of two immobilized cations (ammonium in the side chain of lysine and guanidinium in the side chain of arginine) on the folding and assembly of melittin. Melittin adopts an α-helix structure and is driven by hydrophobic interactions to associate into a helical bundle. To test the influence of immobilized cations on the peptide structure, we designed the homozygous mutants exclusively containing ammonium (melittin-K) or guanidinium (melittin-R) and compared the differences of melittin-K vs. melittin-R in their folding, assembly, and molecular functions. The side chains of lysine and arginine differ in their influences on the folding and assembly of melittin. Specifically, the side chain of R increases the α-helical propensity of melittin relative to that of K, following an inverse Hofmeister series. In contrast, the side chain of K favors the assembly of melittin relative to the side chain of R in line with a direct Hofmeister series. The opposite regulatory effects of immobilized cations on the folding and assembly of melittin highlight the complexity of the noncovalent interactions that govern protein intermolecular architecture.

NEAR HYDRATION OF SINGLY CHARGED MONOATOMIC IONS IN EXTREMELY DILUTED SOLUTIONS: THE EFFECT OF TEMPERATURE AND PRESSURE

The diffusion coefficient and the distance of translational displacement of Li+, Na+ K+, Cs+, Cl– and Br– ions in water at 298.15 K – 423.15 K (25 K step) and pressure from 0.0981 to 784.5 MPa (98.1 MPa step) were calculated from the literature data on limiting molar electrical conductivity. The values for these ions increase with pressure growth from 0.0981 to 98.1 MPa at 298.15 K. Further pressure increase (up to 785 MPa) leads to decrease in . Temperature growth under isobaric conditions leads to an increase in . Parameter (– ri) (deviation from the Stokes–Einstein law, ri is ion structural radius) was used as a criterion for the type of ion solvation. It is shown that Li+ and Na+ ions behave as cosmotropes, or positively solvated structure–forming ions having (– ri) > 0. The Cs+, Cl–, Br– ions behave as chaotropes, or negatively solvated structure–breaking ions having (– ri) < 0. For the K+ ion, the (– ri) deviation is alternating. At 0.0981 MPa and 298.15 K, the K+ ion is a chaotrope. But at 320 K (Tlim) parameter (– ri) = 0. It corresponds to the transition from negative to positive solvation. Above Tlim at P = const, the K+ ion is a cosmotrope. At 298.15 K and up to 98.1 MPa, the pressure causes the same change in the (– ri) deviation as the temperature. On the contrary, at 320 K and higher, the pressure affects the near hydration in the direction opposite to the temperature.

Effect of the Temperature and Solvents on the Solvolysis of Barium Bromide in Aqueous-Organic Solutions: Volumetric and Viscometric Study

Volumetric and viscometric properties of solutions containing barium bromide in an aqueous solution of ethylene glycol and 1,4-dioxane have been discussed at different temperatures such as 298.15K 303.15K, 308.15K, and 313.15K. The Masson’s equation was used to determine the apparent molar volume, V_ϕ, standard partial molar volume, V_ϕ^0, molar expansibilities,E_ϕ^0 by taking the density data. The values of viscosity and density were used in the Jones-Dole equation to find the viscosity B coefficients, which were used to estimate the ion-solvent interactions. The values of Hepler’s constant (∂^2 V_ϕ^0/ ∂T2)p and the viscosity B-coefficients have been used to deduce the solvent structure-promoting or structure breaking tendency of the salt in the studied mixtures. In the current study, the positive values of Hepler’s constant and the negative values of dB/dT show that barium bromide in the considered solvents mainly behaves as a structure promoter.

Transformations, Comparisons, and Analysis of Down to Up Protomer States of Variants of the SARS-CoV-2 Prefusion Spike Protein Including the UK Variant B.1.1.7

Monitoring and strategic response to variants in SARS-CoV-2 represents a considerable challenge in the current pandemic, as well as potentially future viral outbreaks of similar magnitude. In particular mutations and deletions involving the virion’s prefusion Spike protein has significant potential impact on vaccines and therapeutics that utilize this key structural viral protein in their mitigation strategies. In this study, we have demonstrated how dominant energetic landscape mappings (“glue points”) coupled with sequence alignment information can potentially identify or flag key residue mutations and deletions associated with variants. Surprisingly, we also found excellent homology of stabilizing residue glue points across the lineage of β coronavirus Spike proteins, and we have termed this as “sequence homologous glue points”. In general, these flagged residue mutations and/or deletions are then computationally studied in detail using all-atom biocomputational molecular dynamics over approximately one microsecond in order to ascertain structural and energetic changes in the Spike protein associated variants. Specifically, we examined both a theoretically-based triple mutant and the so called UK or B.1.1.7 variant. For the theoretical triple mutant, we demonstrated through Alanine mutations, which help “unglue” key residue-residue interactions, that these three key stabilizing residues could cause the transition of Down to Up protomer states, where the Up protomer state allows binding of the prefusion Spike protein to hACE2 host cell receptors, whereas the Down state is believed inaccessible. For the B.1.1.7 variant, we demonstrated the critical importance of D614G and N5017 on the structure and binding of the Spike protein associated variant. In particular, we had previously identified D614 as a key glue point in the inter-protomer stabilization of the Spike protein. Other mutations and deletions associated with this variant did not appear to play a pivotal role in structure or binding changes. The mutant D614G is a structure breaking Glycine mutation demonstrating a relatively large hinge angle and highly stable Up conformation in agreement with previous studies. In addition, we demonstrate that the mutation N501Y may significantly increase the Spike protein binding to hACE2 cell receptors through its interaction with Y41 of hACE2 forming a potentially strong hydrophobic residue binding pair. We note that these two key mutations, D614G and N501Y, are also found in the so-called South African (SA; B.1.351) variant of SARS-CoV-2. Future studies along these lines are therefore aimed at mapping glue points to residue mutations and deletions of associated prefusion Spike protein variants in order to help direct and optimize efforts aimed at the mitigation of this deadly virion.