Molecular Dynamics Simulations of hydrophobic peptides that form β-hairpin structures in solution

Peptides designed with residues that have high propensity to occur in β-turns, form β-hairpin structures in apolar solvents as well in polar organic solvents such as dimethyl sulfoxide (DMSO), methanol and varying percentages of DMSO in chloroform (CHCl3). Presumably due to limited solubility, their conformations have not been investigated by experimental methods in water. We have examined the conformations of such designed peptides that fold into well-defined β-hairpin structures facilitated by β-turns, in the crystalline state and in solution, by Molecular Dynamics Simulations (MDS). The peptides fold into β-hairpin structures in water, starting from extended conformation. In DMSO, folding into β-hairpin structures was not observed, starting from extended conformation. However, when the starting structure is in β-hairpin conformation, unfolding is not observed during MDS in DMSO. Water clearly favours folding of short, hydrophobic peptides into β-turn and β-hairpin conformations from extended structures. DMSO does not have a denaturing effect on short, hydrophobic peptides.

Molecular Dynamics Simulations of Human FOXO3 Reveal Intrinsically Disordered Regions Spread Spatially by Intramolecular Electrostatic Repulsion

The human transcription factor FOXO3 (a member of the ‘forkhead’ family of transcription factors) controls a variety of cellular functions that make it a highly relevant target for intervention in anti-cancer and anti-aging therapies. FOXO3 is a mostly intrinsically disordered protein (IDP). Absence of knowledge of its structural properties outside the DNA-binding domain constitutes a considerable obstacle to a better understanding of structure/function relationships. Here, I present extensive molecular dynamics (MD) simulation data based on implicit solvation models of the entire FOXO3/DNA complex, and accelerated MD simulations under explicit solvent conditions of a central region of particular structural interest (FOXO3120–530). A new graphical tool for studying and visualizing the structural diversity of IDPs, the Local Compaction Plot (LCP), is introduced. The simulations confirm the highly disordered nature of FOXO3 and distinguish various degrees of folding propensity. Unexpectedly, two ‘linker’ regions immediately adjacent to the DNA-binding domain are present in a highly extended conformation. This extended conformation is not due to their amino acid composition, but rather is caused by electrostatic repulsion of the domains connected by the linkers. FOXO3 is thus an IDP present in an unusually extended conformation to facilitate interaction with molecular interaction partners.

4-(Diphenylmethoxy)-3-ethoxybenzaldehyde

In the title compound, C22H20O3, the dihedral angle between the aromatic rings linked by the methine group is 81.265 (4)° and the ethoxy side chain adopts an extended conformation [C—O—C—C = 177.24 (10)°]. In the crystal, weak C—H...π and C—H...O interactions link the molecules into sheets.

Theoretical study of the electric and the magnetic dipole in UV-Vis and ECD of fluralaner: the folded conformation and the extended conformation

In our contribution, we have carried out a theoretical study of the transition characteristics of one-photon absorption (OPA) spectra of the folded conformation and the extended conformation of fluralaner. The electronic transitions in OPA are visualized with charge difference density (CDD) and transition density matrix (TDM) to explain the charge transfer via hole-electron distribution. We also analyze the transition dipole electric/ magnetic moment by using the isosurface (real space) and TDM diagram in order to determine the portions of molecules which have the most contribution in ECD spectra.

Stabilization of the Hinge Region of Human E-selectin Enhances Binding Affinity to Ligands Under Force

Introduction E-selectin is a member of the selectin family of cell adhesion molecules expressed on the plasma membrane of inflamed endothelium and facilitates initial leukocyte tethering and subsequent cell rolling during the early stages of the inflammatory response via binding to glycoproteins expressing sialyl LewisX and sialyl LewisA (sLeX/A). Existing crystal structures of the extracellular lectin/EGF-like domain of E-selectin complexed with sLeX have revealed that E-selectin can exist in two conformation states, a low affinity (bent) conformation, and a high affinity (extended) conformation. The differentiating characteristic of the two conformations is the interdomain angle between the lectin and the EGF-like domain. Methods Using molecular dynamics (MD) simulations we observed that in the absence of tensile force E-selectin undergoes spontaneous switching between the two conformational states at equilibrium. A single amino acid substitution at residue 2 (serine to tyrosine) on the lectin domain favors the extended conformation. Results Steered molecular dynamics (SMD) simulations of E-selectin and PSGL-1 in conjunction with experimental cell adhesion assays show a longer binding lifetime of E-selectin (S2Y) to PSGL-1 compared to wildtype protein. Conclusions The findings in this study advance our understanding into how the structural makeup of E-selectin allosterically influences its adhesive dynamics.

Ligand-induced conformational rearrangements regulate the switch between membrane-proximal and distal functions of Rho kinase 2

Rho-associated protein kinase 2 (ROCK2) is a membrane-anchored, long, flexible, multidomain, multifunctional protein. Its functions can be divided into two categories: membrane-proximal and membrane-distal. A recent study concluded that membrane-distal functions require the fully extended conformation, and this conclusion was supported by electron microscopy. The present solution small-angle X-ray scattering (SAXS) study revealed that ROCK2 population is a dynamic mixture of folded and partially extended conformers. Binding of RhoA to the coiled-coil domain shifts the equilibrium towards the partially extended state. Enzyme activity measurements suggest that the binding of natural protein substrates to the kinase domain breaks up the interaction between the N-terminal kinase and C-terminal regulatory domains, but smaller substrate analogues do not. The present study reveals the dynamic behaviour of this long, dimeric molecule in solution, and our structural model provides a mechanistic explanation for a set of membrane-proximal functions while allowing for the existence of an extended conformation in the case of membrane-distal functions.

Entropy Rules: Molecular Dynamics Simulations of Model Oligomers for Thermoresponsive Polymers

We attempted to attain atomic-scale insights into the mechanism of the heat-induced phase transition of two thermoresponsive polymers containing amide groups, poly(N-isopropylacrylamide) (PNIPAM) and poly(2-isopropyl-2-oxazoline) (PIPOZ), and we succeeded in reproducing the existence of lower critical solution temperature (LCST). The simulation data are in accord with experimental findings. We found out that the entropy has an important contribution to the thermodynamics of the phase separation transition. Moreover, after decomposing further the entropy change to contributions from the solutes and from the solvent, it appeared out that the entropy of the solvent has the decisive share for the lowering of the free energy of the system when increasing the temperature above the LCST. Our conclusion is that the thermoresponsive behavior is driven by the entropy of the solvent. The water molecules structured around the functional groups of the polymer that are exposed to contact with the solvent in the extended conformation lower the enthalpy of the system, but at certain temperature the extended conformation of the polymer collapses as a result of dominating entropy gain from “released” water molecules. We stress also on the importance of using more than one reference molecule in the simulation box at the setup of the simulation.

Effect of Thermal Annealing on Conformation of MEH-PPV Chains in Polymer Matrix: Coexistence of H- and J-Aggregates

In diluted solid solution using poly(2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene) (MEH-PPV) and polymethyl methacrylate (PMMA) or polystyrene (PS), both aggregated and extended conformations could be formed according to the weight ratio. Aggregated conformation in as-cast MEH-PPV/PMMA film presented a J-aggregate-like photoluminescence (PL) emission. After annealing at 160 °C, its PL showed characteristics of both J- and H-aggregates at the same time; however, extended conformation showed an oligomer-like emission, which was not sensitive to either measurement temperature or annealing temperature. Thus, the conformation transition between aggregated and extended is unlikely to happen in MEH-PPV/PMMA blends during thermal annealing. On the contrary, in MEH-PPV/PS blends, extended conformation dominated in as-cast film with oligomer-like emissions; after annealing at 160 °C, both J- and H- aggregate-like PL emissions were observed, indicating the conformation transitioned from extended to aggregated. Therefore, our work may suggest a new method to manipulate photophysical properties of conjugated polymers by combining appropriate host matrix and thermal annealing processes.

Dipropylammonium 4-aminobenzenesulfonate

In the title molecular salt, NH2(C3H7)2 +·[NH2C6H4SO3]−, the cation displays an extended conformation. In the crystal, anion-to-anion N—H...O and N—H...(O,O) hydrogen bonds generate (101) layers. Cation-to-anion N—H...O hydrogen bonds connect the layers into a three-dimensional network.