Polar Interactions at the Dimer–Dimer Interface of Methionine Adenosyltransferase MAT I Control Tetramerization

Catalytic MATα1 subunits associate into kinetically distinct homo-dimers (MAT III) and homo-tetramers (MAT I) that synthesize S-adenosylmethionine in the adult liver. Pathological reductions in S-adenosylmethionine levels correlate with MAT III accumulation; thus, it is important to know the determinants of dimer–dimer associations. Here, polar interactions (<3.5 Å) at the rat MAT I dimer–dimer interface were disrupted by site-directed mutagenesis. Heterologous expression rendered decreased soluble mutant MATα1 levels that appeared mostly as dimers. Substitutions at the B1–B2 or B3–C1 β-strand loops, or changes in charge on helix α2 located behind, induced either MAT III or MAT I accumulation. Notably, double mutants combining neutral changes on helix α2 with substitutions at either β-strand loop further increased MAT III content. Mutations had negligible impact on secondary or tertiary protein structure, but induced changes of 5–10 °C in thermal stability. All mutants preserved tripolyphosphatase activity, although AdoMet synthesis was only detected in single mutants. Kinetic parameters were altered in all purified proteins, their AdoMet synthesis Vmax and methionine affinities correlating with the association state induced by the corresponding mutations. In conclusion, polar interactions control MATα1 tetramerization and kinetics, diverse effects being induced by changes on opposite β-sheet loops putatively leading to subtle variations in central domain β-sheet orientation.

Mass Spectrometric and Bio-Computational Binding Strength Analysis of Multiply Charged RNAse S Gas-Phase Complexes Obtained by Electrospray Ionization from Varying In-Solution Equilibrium Conditions

We investigated the influence of a solvent’s composition on the stability of desorbed and multiply charged RNAse S ions by analyzing the non-covalent complex’s gas-phase dissociation processes. RNAse S was dissolved in electrospray ionization-compatible buffers with either increasing organic co-solvent content or different pHs. The direct transition of all the ions and the evaporation of the solvent from all the in-solution components of RNAse S under the respective in-solution conditions by electrospray ionization was followed by a collision-induced dissociation of the surviving non-covalent RNAse S complex ions. Both types of changes of solvent conditions yielded in mass spectrometrically observable differences of the in-solution complexation equilibria. Through quantitative analysis of the dissociation products, i.e., from normalized ion abundances of RNAse S, S-protein, and S-peptide, the apparent kinetic and apparent thermodynamic gas-phase complex properties were deduced. From the experimental data, it is concluded that the stability of RNAse S in the gas phase is independent of its in-solution equilibrium but is sensitive to the complexes’ gas-phase charge states. Bio-computational in-silico studies showed that after desolvation and ionization by electrospray, the remaining binding forces kept the S-peptide and S-protein together in the gas phase predominantly by polar interactions, which indirectly stabilized the in-bulk solution predominating non-polar intermolecular interactions. As polar interactions are sensitive to in-solution protonation, bio-computational results provide an explanation of quantitative experimental data with single amino acid residue resolution.

Improving Coarse Grain Models of Protein Folding through Weighting of Polar-polar/hydrophobic-hydrophobic Interactions into Crowded Spaces

In this piece of work were tested 7 Hydrophobic-Polar sequences in two types of 2D-square space lattices, homogeneous and correlated, the latter simulating molecular crowding included as a geometric boundary restriction. The optimization of the 2D structures was carried out using a variant of Dill's model, inspired by the convex function, which takes into account both the hydrophobic (Dill’s model) and polar interactions, aimed to include more structural information to reach better folding solutions. While using correlated networks, the degrees of freedom in the folding of sequences were limited, and as a result in all cases more successful structural trials were found in comparison to the homogeneous lattice. In particular, the S5 sequence turned out to be the most difficult sequence of the seven folded, this perhaps due to the intrinsic i) degrees of freedom and ii) motifs of the expected 2D HP structure. Regarding S2 and S6 sequences, although optimal folding was not achieved for neither of the two approaches, folding with correlated network approach not only produced better results than homogeneous space, but for both sequences the best values found with crowding were very close to the expected optimal fitness. The sequences S1-S4 and S6 were better folded with medium lattice units for the correlated media, instead, S5 and S7 were better folded with a bit larger degree of lattice unit, revealing that depending on the degrees of freedom and particular folding motifs in each sequence would require particular crowding to achieve better folding. Finally, we claim that in all folded sequences in crowded spaces achieve better results than homogeneous ones.

Behavior of Chemokine Receptor 6 (CXCR6) in Complex with CXCL16 Soluble form Chemokine by Molecular Dynamic Simulations: General Protein‒Ligand Interaction Model and 3D-QSAR Studies of Synthetic Antagonists

The CXCR6‒CXCL16 axis is involved in several pathological processes, and its overexpression has been detected in different types of cancer, such as prostate, breast, ovary, and lung cancer, along with schwannomas, in which it promotes invasion and metastasis. Moreover, this axis is involved in atherosclerosis, type 1 diabetes, primary immune thrombocytopenia, vitiligo, and other autoimmune diseases, in which it is responsible for the infiltration of different immune system cells. The 3D structure of CXCR6 and CXCL16 has not been experimentally resolved; therefore, homology modeling and molecular dynamics simulations could be useful for the study of this signaling axis. In this work, a homology model of CXCR6 and a soluble form of CXCL16 (CXCR6‒CXCL16s) are reported to study the interactions between CXCR6 and CXCL16s through coarse-grained molecular dynamics (CG-MD) simulations. CG-MD simulations showed the two activation steps of CXCR6 through a decrease in the distance between the chemokine and the transmembrane region (TM) of CXCR6 and transmembrane rotational changes and polar interactions between transmembrane segments. The polar interactions between TM3, TM5, and TM6 are fundamental to functional conformation and the meta-active state of CXCR6. The interactions between D77-R280 and T243-TM7 could be related to the functional conformation of CXCR6; alternatively, the interaction between Q195-Q244 and N248 could be related to an inactive state due to the loss of this interaction, and an arginine cage broken in the presence of CXCL16s allows the meta-active state of CXCR6. A general protein‒ligand interaction supports the relevance of TM3‒TM5‒TM6 interactions, presenting three relevant pharmacophoric features: HAc (H-bond acceptor), HDn (H-bond donator), and Hph (hydrophobic), distributed around the space between extracellular loops (ECLs) and TMs. The HDn feature is close to TM3 and TM6; likewise, the HAc and Hph features are close to ECL1 and ECL2 and could block the rotation and interactions between TM3‒TM6 and the interactions of CXCL16s with the ECLs. Tridimensional quantitative structure-activity relationships (3D-QSAR) models show that the positive steric (VdW) and electrostatic fields coincide with the steric and positive electrostatic region of the exo-azabicyclo[3.3.1]nonane scaffold in the best pIC50 ligands. This substructure is close to the E274 residue and therefore relevant to the activity of CXCR6. These data could help with the design of new molecules that inhibit chemokine binding or antagonize the receptor based on the activation mechanism of CXCR6 and provoke a decrease in chemotaxis caused by the CXCR6‒CXCL16 axis.

Screening of Hydrogen Bonding Interactions by a Single Layer Graphene

<p>A single layer of graphene when transferred to a solid substrate has the ability to screen or transmit interactions from the underlying substrate, which has direct consequences in applications of this 2D material to flexible electronics and sensors. Previous reports using a multitude of techniques present contradictory views on graphene’s ability to screen or transmit van der Waals (vdW) and polar interactions. In the present study, we use interface-sensitive spectroscopy to demonstrate that a single layer graphene is opaque to hydrogen bonding interactions (a subset of acid-base interactions), answering a question that has remained unresolved for a decade. Similar frequency shifts of sapphire hydroxyl (OH) for graphene-coated sapphire in contact with air and polydimethylsiloxane (PDMS) demonstrate the insensitivity of sapphire OH to PDMS. The screening ability of graphene is also evident in the smaller magnitude of this frequency shift for graphene-coated sapphire in comparison to that for bare sapphire. The screening of acid-base interactions by a single layer graphene results in the significant reduction of adhesion hysteresis for PDMS lens on graphene-coated substrates (sapphire and silicon wafer, SiO2/Si) than bare substrates. Our</p> <p>results have implications in the use of PDMS stamps to transfer graphene to other substrates eliminating the need for a wet-transfer process</p>