Search

Amphiphilic nanoparticles are highly biocompatible frameworks widely used for shuttling hydrophobic molecules across hydrophilic cellular environments. Their use can also span applications focused on achieving a selective binding against a target receptor. However, the molecular factors leading to an optimal binding often remain a critical step to assess. Here we have evaluated through advanced sampling free-energy simulations, combined with electronic circular dichroism spectra predictions, the binding of an amphiphilic polyethylene glycol (PEG)-based nanoparticle incorporating folate monomers with human folate receptor alpha. It turns out from the free-energy predictions that the optimal binding is achieved when the receptor target and the ligand-mimicking nanoparticle have a comparable size and the shortest spacer length of the folate monomer. Furthermore, we calculated the ECD spectrum of the folate monomer binding the target receptor, as well as that of the binding pocket of the receptor. Noteworthy, only when the optimal binding is achieved, the two ECD spectra closely match each other. Shape factors control the binding efficacy of nanoparticles with target receptors.

In recent years, pi-conjugated polymers are attracting considerable interest in view of their light-dependent torsional reorganization around the pi-conjugated backbone, which determines peculiar light-emitting properties. Motivated by the interest in designing conjugated polymers with tunable photoswitchable pathways, we devised a computational framework to enhance the sampling of the torsional conformational space and at the same time estimate ground to excited-state free-energy differences. This scheme is based on a combination of Hamiltonian Replica Exchange (REM), Parallel Bias metadynamics, and free-energy perturbation theory. In our scheme, each REM replica samples an intermediate unphysical state between the ground and the first two excited states, which are characterized by TD-DFT simulations at the B3LYP/6-31G* level of theory. We applied the method to a 5-mer of 9,9-dioctylfluorene and found that upon irradiation this system can undergo a dihedral inversion from 155 to -155 degrees crossing a barrier that decreases from 0.1 eV in the ground state (S0) to 0.05 eV and 0.04 eV in the first (S1) and second (S2) excited states. Furthermore, S1 and even more S2 were predicted to stabilize coplanar dihedrals, with a local free-energy minimum located at +-44 degrees. The presence of a free-energy barrier of 0.08 eV for the S1 and 0.12 eV for the S2 state can trap this conformation in a basin far from the global free-energy minimum located at 155 degrees. The simulation results were compared with the experimental emission spectrum, showing a quantitative agreement with the predictions provided by our framework., Comment: 14 pages, 6 figures. The present article has been accepted in The Journal of Chemical Physics

The sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT) in cyanobacteria allows the incorporation of ammonium into carbon skeletons. In the cyanobacterium Synechocystis sp. PCC 6803, the activity of GS is modulated by the interaction with proteins, which include a 65-residue-long intrinsically disordered protein (IDP), the inactivating factor IF7. This interaction is regulated by the presence of charged residues in both IF7 and GS. To understand how charged amino acids can affect the binding of an IDP with its target and to provide clues on electrostatic interactions in disordered states of proteins, we measured the pKa values of all IF7 acidic groups (Glu32, Glu36, Glu38, Asp40, Asp58, and Ser65, the backbone C-terminus) at 100 mM NaCl concentration, by using NMR spectroscopy. We also obtained solution structures of IF7 through molecular dynamics simulation, validated them on the basis of previous experiments, and used them to obtain theoretical estimates of the pKa values. Titration values for the two Asp and three Glu residues of IF7 were similar to those reported for random-coil models, suggesting the lack of electrostatic interactions around these residues. Furthermore, our results suggest the presence of helical structure at the N-terminus of the protein and of conformational changes at acidic pH values. The overall experimental and in silico findings suggest that local interactions and conformational equilibria do not play a role in determining the electrostatic features of the acidic residues of IF7.

The comprehensive characterization of Intramolecular Charge Transfer (ICT) stemming in push-pull molecules with a delocalized π-system of electrons is noteworthy for a bespoke design of organic materials, spanning widespread applications from photovoltaics to nanomedicine imaging devices. Photo-induced ICT is characterized by structural reorganizations, which allows the molecule to adapt to the new electronic density distribution. Herein, we discuss recent photophysical advances combined with recent progresses in the computational chemistry of photoactive molecular ensembles. We focus the discussion on femtosecond Transient Absorption Spectroscopy (TAS) enabling us to follow the transition from a Locally Excited (LE) state to the ICT and to understand how the environment polarity influences radiative and non-radiative decay mechanisms. In many cases, the charge transfer transition is accompanied by structural rearrangements, such as the twisting or molecule planarization. The possibility of an accurate prediction of the charge-transfer occurring in complex molecules and molecular materials represents an enormous advantage in guiding new molecular and materials design. We briefly report on recent advances in ultrafast multidimensional spectroscopy, in particular, Two-Dimensional Electronic Spectroscopy (2DES), in unraveling the ICT nature of push-pull molecular systems. A theoretical description at the atomistic level of photo-induced molecular transitions can predict with reasonable accuracy the properties of photoactive molecules. In this framework, the review includes a discussion on the advances from simulation and modeling, which have provided, over the years, significant information on photoexcitation, emission, charge-transport, and decay pathways. Density Functional Theory (DFT) coupled with the Time-Dependent (TD) framework can describe electronic properties and dynamics for a limited system size. More recently, Machine Learning (ML) or deep learning approaches, as well as free-energy simulations containing excited state potentials, can speed up the calculations with transferable accuracy to more complex molecules with extended system size. A perspective on combining ultrafast spectroscopy with molecular simulations is foreseen for optimizing the design of photoactive compounds with tunable properties.

International audience; The π-rich rings of conjugated polymers and molecular rotors shape their typical properties, allowing a variety of chemical and photoresponsive phenomena. Herein, we present a computational method in the framework of classical simulations to estimate the free-energy gap between ground and excited states of oligofluorenes, which is a class of molecular rotors widely used in optoelectronic devices, because of the inner torsional rotation triggered by light irradiation. We devised multiple sets of free-energy simulations in combination with free-energy perturbation theory to predict the free-energy gap between the ground state and the first excited state. The computed excitation energies show good agreement with experiments. The approach presented herein allows one to achieve comprehensive sampling of the conformational landscape and accurate estimates of the excited state free-energy landscapes at the same time.

The phosphotransferase system (PTS) controls the preferential use of sugars in bacteria and it is also involved in other processes, such as chemotaxis. It is formed by a protein cascade in which the first two proteins are general (namely, EI and HPr) and the others are sugar-specific permeases. The Rsd protein binds specifically to the RNA polymerase (RNAP) σ factor. We first characterized the conformational stability of Escherichia coli Rsd. And second, we delineated the binding regions of Streptomyces coelicolor, HPr, and E. coli Rsd, by using fragments derived from each protein. To that end, we used several biophysical probes, namely, fluorescence, CD, NMR, ITC and BLI. Rsd had a free energy of unfolding of 15 kcal mol at 25 °C, and a thermal denaturation midpoint of 103 °C at pH 6.5. The affinity between Rsd and HPr was 2 μM. Interestingly enough, the isolated helical-peptides, comprising the third (RsdH3) and fourth (RsdH4) Rsd helices, also interacted with HPr in a specific manner, and with affinities similar to that of the whole Rsd. Moreover, the isolated peptide of HPr, HPr, comprising the active site, His15, also was bound to intact Rsd with similar affinity. Therefore, binding between Rsd and HPr was modulated by the two helices H3 and H4 of Rsd, and the regions around the active site of HPr. This implies that specific fragments of Rsd and HPr can be used to interfere with other protein-protein interactions (PPIs) of each other protein.

The temperature dependence of the UV absorption spectra of biphenyl in solution is herein reported. The UV spectral shapes vary with an increase in temperature, where a decrease in intensity (hypochromism) and blue shifts are observed. The predicted UV spectra in the Time Dependent-Density Functional Theory (TD-DFT) framework within the B97D3 functional indicate a lowering of the biphenyl conjugation band and a blue shift of the spectra upon increasing the biphenyl twist dihedral angle.

The sequential action of glutamine synthetase (GS) and glutamate synthase (GOGAT) in cyanobacteria allows the incorporation of ammonium into carbon skeletons. In the cyanobacterium Synechocystis sp. PCC 6803, the activity of GS is modulated by the interaction with proteins, which include a 65‐residue‐long intrinsically disordered protein (IDP), the inactivating factor IF7. This interaction is regulated by the presence of charged residues in both IF7 and GS. To understand how charged amino acids can affect the binding of an IDP with its target and to provide clues on electrostatic interactions in disordered states of proteins, we measured the pK a values of all IF7 acidic groups (Glu32, Glu36, Glu38, Asp40, Asp58, and Ser65, the backbone C‐terminus) at 100 mM NaCl concentration, by using NMR spectroscopy. We also obtained solution structures of IF7 through molecular dynamics simulation, validated them on the basis of previous experiments, and used them to obtain theoretical estimates of the pK a values. Titration values for the two Asp and three Glu residues of IF7 were similar to those reported for random‐coil models, suggesting the lack of electrostatic interactions around these residues. Furthermore, our results suggest the presence of helical structure at the N‐terminus of the protein and of conformational changes at acidic pH values. The overall experimental and in silico findings suggest that local interactions and conformational equilibria do not play a role in determining the electrostatic features of the acidic residues of IF7.