Kinetics Of Dimer Formation Research Articles

Soluble State of Villin Headpiece Protein as a Tool in the Assessment of MD Force Fields.

Protein self-assembly plays an important role in cellular processes. Whereas molecular dynamics (MD) represents a powerful tool in studying assembly mechanisms, its predictions depend on the accuracy of underlying force fields, which are known to overly promote protein assembly. We here examine villin headpiece domain, HP36, which remains soluble at concentrations amenable to MD studies. The experimental characterization of soluble HP36 at concentrations of 0.05 to 1 mM reveals concentration-independent 90% monomeric and 10% dimeric populations. Extensive all-atom MD simulations at two protein concentrations, 0.9 and 8.5 mM, probe the HP36 dimer population, stability, and kinetics of dimer formation within two MD force fields, Amber ff14SB and CHARMM36m. MD results demonstrate that whereas CHARMM36m captures experimental HP36 monomer populations at the lower concentration, both force fields overly promote HP36 association at the higher concentration. Moreover, contacts stabilizing HP36 dimers are force-field-dependent. CHARMM36m produces consistently higher HP36 monomer populations, lower association rates, and weaker dependence of these quantities on the protein concentration than Amber ff14SB. Nonetheless, the highest monomer populations and dissociation constants are observed when the TIP3P water model in Amber ff14SB is replaced by TIP4P/2005, showcasing the critical role of the water model in addressing the protein solubility problem in MD.

Dynamic PCBM:Dimer Population in Solar Cells under Light and Temperature Fluctuations

AbstractPhotoinduced dimerization of phenyl‐C61‐butyric acid methyl ester (PCBM) has a significant impact on the stability of polymer:PCBM organic solar cells (OSCs). This reaction is reversible, as dimers can be thermally decomposed at sufficiently elevated temperatures and both photodimerization and decomposition are temperature dependent. In operando conditions of OSCs evidently involve exposure to both light and heat, following periodic diurnal and seasonal profiles. In this work, the kinetics of dimer formation and decomposition are examined and quantified as a function of temperature, light intensity, blend composition, and time. The activation energy for photodimerization is estimated to be 0.021(3) eV, considerably smaller than that for decomposition (0.96 eV). The findings are benchmarked with a variety of conjugated polymer matrices to propose a descriptive dynamic model of PCBM:dimer population in OSCs, and a framework is proposed to rationalize its interplay with morphology evolution and charge quenching. The model and parameters enable the prediction of the dynamic and long‐term PCBM:dimer populations, under variable temperature and light conditions, which impact the morphological stability of OSCs.

Contributions of fluorescence techniques to understanding G protein-coupled receptor dimerisation.

G protein-coupled receptors (GPCRs) are the largest class of eukaryotic cell-surface receptors and, over the last decade, it has become clear that they are capable of dimerisation. Whilst many biochemical and biophysical approaches have been used to study dimerisation, fluorescence techniques, including Förster resonance energy transfer and single molecule fluorescence, have been key players. Here we review recent contributions of fluorescence techniques to investigate GPCR dimers, including dimerisation in cell membranes and native tissues, the effect of ligand binding on dimerisation and the kinetics of dimer formation and dissociation. The challenges of studying multicomponent membrane protein systems have led to the development and refinement of many fluorescence assays, allowing the functional consequences of receptor dimerisation to be investigated and individual protein molecules to be imaged in the membranes of living cells. It is likely that the fluorescence techniques described here will be of use for investigating many other multicomponent membrane protein systems.

Characterization of an unfolding intermediate and kinetic analysis of guanidine hydrochloride-induced denaturation of the colicin E1 channel peptide.

The equilibrium unfolding pathway of the colicin E1 channel peptide was shown in a previous study to involve an unfolding intermediate, stable in approximately 4 M guanidine hydrochloride, which comprised primarily the C-terminal hydrophobic alpha-helical hairpin segment of the peptide [Steer, B. A., & Merrill, A. R. (1995) Biochemistry 34, 7225-7233]. In this study, the structural nature of this unfolding intermediate was investigated further, and it was found that the intermediate primarily consists of a dimer species and is comprised of two partially denatured monomeric peptides, which appear to be associated by hydrophobic interactions. The dimerized structure was detected by size-exclusion high-performance liquid chromatography, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, chemical cross-linking, and intermolecular fluorescence energy transfer. Using stopped-flow fluorescence spectroscopy, the kinetics of the denaturation and dimerization of the colicin E1 channel peptide in 4 M guanidine hydrochloride were examined. Denaturation kinetics were also investigated by wild-type peptide Trp fluorescence and 1-anilinonaphthalene-8-sulfonic acid binding. The kinetics of dimer formation were examined by monitoring the time dependence of intermolecular Trp to 5-[[2-[(iodoacetyl)amino]ethyl]amino]naphthalene-1-sulfonic acid fluorescence resonance energy transfer upon denaturation in 4 M guanidine hydrochloride. In addition, single Trp mutant peptides were employed as site-specific fluorescent probes of unfolding kinetics and reported diverse and characteristic unfolding kinetics. However, it was shown that following a rapid and major unfolding transition the peptide's core residues cluster slowly, by hydrophobic association, forming an intermediate species which is a prerequisite to dimerization. These equilibrium and kinetic unfolding data describe a unique unfolding mechanism where the channel peptide forms a partially unfolded dimerized structure in 4 M guanidine hydrochloride.

Raman studies of argon dimers in a supersonic expansion. II. Kinetics of dimer formation

Results of a systematic study of the formation of dimers in a supersonic free-jet expansion of argon as studied by Raman scattering are presented. By seeding the expansion with ${\mathrm{N}}_{2}$, measurements of temperature and density were obtained in the part of the flow field where dimers were observed. Temperature was also measured in the remaining part of the expansion showing large deviations from the behavior of an isentropic expansion due to condensation. The condensation was observed directly by Rayleigh scattering as well. From the Raman spectra it was shown that the dimers can relax their internal energy rapidly enough to come into thermal equilibrium with the translational degrees of freedom. By relating the intensity of dimer transitions to that of the simultaneously measured ${\mathrm{N}}_{2}$ $J=0\ensuremath{\rightarrow}2$ Raman transition, we were able to measure the concentration of dimers in the expansion. The measurements were compared to the predictions of equilibrium theory for a chemical equilibrium between dimers and monomers. The predictions of two- and three-body collision dimer-formation models were also tested.

Kinetics of dimer formation in rarefied water vapor streams

Kinetics of dimer formation in rarefied water vapor streams