Self-association of a highly charged, arginine-rich cell-penetrating peptide

Small angle X-ray scattering (SAXS) measurements reveal a striking difference in intermolecular interactions between two short, highly charged peptides, namely deca-arginine (R10) and deca-lysine (K10). Comparison of SAXS curves at high and low salt concentration shows that R10 self-associates, while interactions between K10 chains are purely repulsive. The self-association of R10 occurs to a larger extent at low ionic strength indicating that the attraction between R10 molecules has an important electrostatic component. SAXS data is complemented by potentials of mean force between the peptides calculated by means of umbrella sampling molecular dynamics (MD) simulations. Atomistic MD simulations elucidate the origin of the R10-R10 attraction by providing structural information on the dimeric state: the last two C-terminal residues of R10 constitute an adhesive patch achieved by stacking of the side chains of two arginine residues and by salt bridges formed between the like-charge ion-pair and C-terminal carboxyl groups. A statistical analysis of the protein data bank reveals that this mode of interaction commonly occurs in proteins. Please click Additional Files below to see the full abstract

Model simulations of the adsorption of statherin to solid surfaces : Effects of surface charge and hydrophobicity

The structural properties of the salivary protein statherin upon adsorption have been examined using a coarse-grained model and Monte Carlo simulation. A simple model system with focus on electrostatic interactions and short-ranged attractions among the uncharged amino acids has been used. To mimic hydrophobically modified surfaces, an extra short-ranged interaction was implemented between the amino acids and the surface. It has been shown that the adsorption and the thickness of the adsorbed layer are determined by (i) the affinity for the surface, i.e., denser layer with an extrashort-ranged potential, and (ii) the distribution of the charges along the chain. If all the amino acids have a high affinity for the surface, the protein adsorbs in a train conformation, if the surface is negatively charged the protein adsorbs in a tail-train conformation, whereas if the surface is positively charged the protein adsorbs in a loop conformation. The latter gives rise to a more confined adsorbed layer. ©2008 American Institute of Physic

Structure and Phase Stability of Polyelectrolyte-Macroion Solutions

Polyelectrolytes are polymers bearing ionisable groups, which, in polar solvents, can dissociate into charged polymer chains (polyelectrolytes) and small counterions. In aqueous solutions, polyelectrolytes interact strongly with other macroions and in particular they tend to associate with objects of opposite charge and form complexes. Nearly all industrial and biological process involves solutions of charged macromolecules, i.e., paint, detergents, drug delivery, and cosmetics, but also many diseases are associated with malfunctions at the colloidal level. The complexation between one linear flexible polyelectrolyte and one or several oppositely charged macroions was examined by employing a simple model system with focus on the electrostatic interactions. The composition and the structure of the complex as well as conformational data of the polyelectrolyte were obtained by using Monte Carlo simulations. The binding isotherms obtained are Langmuir-like, and in excess of macroions the polyelectrolyte-macroion complex displays a charge reversal. These properties were investigated at different linear charge densities, different lengths, and flexibilities of the polyelectrolyte, and different macroion charges, all at different numbers of macroions at constant volume. The effect of adding simple 1:1 salt has also been investigated. The complexation, phase separation, and redissolution of concentrated polyelectrolyte-macroion solutions have also been examined. As oppositely charged polyelectrolytes were added, the stable macroion solution with repelling macroions became successively less stable. The strong electrostatic attraction brought macroions and polyelectrolytes closely together and slightly before macromolecular charge equivalence, distinct and repelling complexes were established. At macromolecular charge equivalence, the system became unstable and a large and loose cluster of macroions and polyelectrolytes was formed. Finally, in excess of polyelectrolytes, the large cluster was broken up and the macroions were dispersed again – a redissolution had occurred. The effect of the macroion radius, the chain length, and the chain flexibility on the phase separation has also been investigated. A semiflexible chain displayed a smaller tendency to promote phase instability as compared to flexible and stiff chains, the origin most likely arising from the similar chain persistence length and macroion radius

Phosphorylation of a Disordered Peptide - Structural Effects and Force Field Inconsistencies

Phosphorylation is one of the most abundant types of post-translational modifications of intrinsically disordered proteins (IDPs). This study examines the conformational changes in the 15-residue-long N-terminal fragment of the IDP statherin upon phosphorylation, using computer simulations with two different force fields: AMBER ff99SB-ILDN and CHARMM36m. The results from the simulations are compared with experimental small-angle X-ray scattering (SAXS) and circular dichroism data. In the unphosphorylated state, the two force fields are in excellent agreement regarding global structural properties such as size and shape. However, they exhibit some differences in the extent and type of the secondary structure. In the phosphorylated state, neither of the force fields performs well compared to the experimental data. Both force fields show a compaction of the peptide upon phosphorylation, greater than what is seen in SAXS experiments, although they differ in the local structure. While the CHARMM force field increases the fraction of bends in the peptide as a response to strong interactions between the phosphorylated residues and arginines, the AMBER force field shows an increase of the helical content in the N-terminal part of the peptide, where the phosphorylated residues reside, in better agreement with circular dichroism results

Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining

Coarse-graining is commonly used to decrease the computational cost of simulations. However, coarse-grained models are also considered to have lower transferability, with lower accuracy for systems outside the original scope of parametrization. Here, we benchmark a bead-necklace model and a modified Martini 2 model, both coarse-grained models, for a set of intrinsically disordered proteins, with the different models having different degrees of coarse-graining. The SOP-IDP model has earlier been used for this set of proteins; thus, those results are included in this study to compare how models with different levels of coarse-graining compare. The sometimes naive expectation of the least coarse-grained model performing best does not hold true for the experimental pool of proteins used here. Instead, it showed the least good agreement, indicating that one should not necessarily trust the otherwise intuitive notion of a more advanced model inherently being better in model choice

Molecular Dynamics Simulations of Intrinsically Disordered Proteins: On the Accuracy of the TIP4P‐D Water Model and the Representativeness of Protein Disorder Models

Here, we first present a follow-up to a previous work by our group on the problematic of molecular dynamics simulations of intrinsically disordered proteins (IDPs) [Henriques et al. J. Chem. Theory Comput. 2015, 11, 3420−3431], using the recently developed TIP4P-D water model. When used in conjunction with the standard AMBER ff99SB-ILDN force field and applied to the simulation of Histatin 5, our IDP model, we obtain results which are in excellent agreement with the best performing IDP-suitable force field from the earlier study and with experiment. We then assess the representativeness of the IDP models used in these and similar studies, finding that most are too short in comparison to the average IDP and contain a bias toward hydrophilic amino acid residues. Moreover, several key order- and disorder-promoting residues are also found to be misrepresented. It seems appropriate for future studies to address these issues

The effect of multisite phosphorylation on the conformational properties of intrinsically disordered proteins

Intrinsically disordered proteins are involved in many biological processes such as signaling, regulation, and recognition. A common strategy to regulate their function is through phosphorylation, as it can induce changes in conformation, dynamics, and interactions with binding partners. Although phosphorylated intrinsically disordered proteins have received increased attention in recent years, a full understanding of the conformational and structural implications of phosphorylation has not yet been achieved. Here, we present all-atom molecular dynamics simulations of five disordered peptides originated from tau, statherin, and β-casein, in both phosphorylated and non-phosphorylated state, to compare changes in global dimensions and structural elements, in an attempt to gain more insight into the controlling factors. The changes are in qualitative agreement with experimental data, and we observe that the net charge is not enough to predict the impact of phosphorylation on the global dimensions. Instead, the distribution of phosphorylated and positively charged residues throughout the sequence has great impact due to the formation of salt bridges. In statherin, a preference for arginine–phosphoserine interaction over arginine–tyrosine accounts for a global expansion, despite a local contraction of the phosphorylated region, which implies that also non-charged residues can influence the effect of phosphorylation

A coarse-grained model for flexible (phospho)proteins: Adsorption and bulk properties

Protein adsorption is a complex process that it controlled by several different mechanisms, for example: (i) electrostatic interactions between the protein and the surface, and (ii) between adsorbed proteins; (iii) dispersion interactions; (iv) hydration effects; and (v) structural rearrangements of the protein to balance conformational chain entropy with energetics. The aim of this study was to develop a simple model for the adsorption of intrinsically disordered proteins onto surfaces at a mesoscopic level of detail, while retaining protein integrity. Monte Carlo simulations were used in order to study the thermodynamical and structural properties of the flexible phosphoprotein beta-casein, in bulk and adsorbed to hydrophilic silica surfaces, in order to evaluate the effect of varying pH, monovalent salt concentration, and degree of serine phosphorylation. Experimental evidence from our previous study, published in this Journal, was used to set up and tune the Hamiltonian of the model. Our simulations show that protein-surface electrostatic interactions are, indeed, not the main driving force behind adsorption under the simulated conditions. Despite its importance, when taken alone, this type of interaction is not enough to promote the adsorption of beta-casein at any salt concentration. Adsorption is only possible through the inclusion of a protein-surface short-ranged attractive interaction potential with a minimum interaction strength of 2.25 k(B)T. This represents the lowest interaction strength required to mimic experimental adsorption results. An equally important finding is that considerable protein net charge fluctuations, due to phosphorylated serine saturation, have a negligible contribution to the free energy of adsorption. (C) 2014 Elsevier Ltd. All rights reserved