Specific interactions of sodium salts with alanine dipeptide and tetrapeptide in water: insights from molecular dynamics

A Heteronuclear NMR Study of Aqueous Lithium Salt Solutions of l-Alanine: Revealing Solute Hydrophobic Association through the NMR B' Coefficient

In the present study, a set of heteronuclear NMR approaches has been adopted to investigate the solution behavior of a small hydrophobic solute l-alanine in the presence of lithium (Li) salts. The presence of salts plays a major role in determining the structure and solvation of biomolecules. It therefore evokes interest to understand the effect of Li salts on amino acids (alanine), the building block of biomolecules. The ionic solute dynamics in the present case has been probed using 1H, 7Li, and 13C nuclei available in the aqueous Li salt solution of l-alanine. Nuclear longitudinal spin relaxation of alanine protons was examined at a variable concentration range of three lithium salts, i.e., LiCl, Li2SO4 and LiClO4, to introduce the NMR B' coefficient for each salt defining ionic solute/solvent interaction in the solution. Analysis of the active relaxation mechanism of 7Li spin-lattice relaxation further revealed the presence of alanine in the solvation shell of Li ion depending on the anionic counterpart.

Surface Energies and Structure of Salt-Brine Interfaces

Permeability of salt formations is controlled by the equilibrium between the salt-brine and salt-salt interfaces described by the dihedral angle, which can change with the composition of the intergranular brine. Here, classical molecular dynamics (MD) simulations were used to investigate the structure and properties of the salt-brine interface to provide insight into the stability of salt systems. Mixed NaCl-KCl brines were investigated to explore differences in ion size on the surface energy and interface structure. Nonlinearity was noted in the salt-brine surface energy with increasing KCl concentration, and the addition of 10% KCl increased surface energies by 2-3 times (5.0 M systems). Size differences in Na⁺ and K⁺ ions altered the packing of dissolved ions and water molecules at the interface, impacting the surface energy. Additionally, ions at the interface had lower numbers of coordinating water molecules than those in the bulk and increased hydration for ions in systems with 100% NaCl or 100% KCl brines. Ultimately, small changes in brine composition away from pure NaCl altered the structure of the salt-brine interface, impacting the dihedral angle and the predicted equilibrium permeability of salt formations.

Bifurcate localization modes of excess electron in aqueous Ca(2+)amide solution revealed by ab initio molecular dynamics simulation: towards hydrated electron versus hydrated amide anion

In this work, we conduct ab initio molecular dynamics simulations on the localization dynamics of an excess electron (EE) in acetamide/Ca(2+) aqueous solutions with three different interaction modes of Ca(2+) with acetamide: tight contact, solvent-shared state, and separated interaction. The simulated results reveal that an EE could exhibit two different localization behaviors in these acetamide/Ca(2+) aqueous solutions depending on different amideCa(2+) interactions featuring different contact distances. For the tight contact and solvent-shared state of amideCa(2+) solutions, vertically injected diffuse EEs follow different mechanisms with different dynamics, forming a cavity-shaped hydrated electron or a hydrated amide anion, respectively. Meanwhile, for the separated state, only one localization pattern of a vertically injected diffuse EE towards the formation of hydrated amide anion is observed. The hindrance of hydrated Ca(2+) and the attraction of the hydrated amide group originating from its polarity and low energy π* orbital are the main driving forces. Additionally, different EE localization modes have different effects on the interaction between the amide group and Ca(2+) in turn. This work provides an important basis for further understanding the mechanisms and dynamics of localizations/transfers of radiation-produced EEs and associated EE-induced lesions and damage to biological species in real biological environments or other aqueous solutions.

Understanding the conformational behaviour of Ac-Ala-NHMe in different media. A joint NMR and DFT study

The conformational behaviour of Ac-Ala-NHMe was studied in the gas-phase and in solution by theoretical calculations (B3LYP-D3/aug-cc-pVDZ level) and experimental (1)H NMR. The conformational preferences of this compound were shown to result from a complex interplay between the strengths of possible intramolecular hydrogen bonds, steric interactions, hyperconjugation, entropy effects and the overall dipole moments. The Ac-Ala-N(Me)2 derivative was studied in addition, to design a system akin to Ac-Ala-NHMe, but with disrupted intramolecular hydrogen bonds involving the -NHMe group, mimicking the effect of polar protic solvents.

Self-assembly of dipeptide sodium salts derived from alanine: a molecular dynamics study

The dipeptides self-assemble into a helical structure after a 200 ns MD simulation.

Local order in the unfolded state: conformational biases and nearest neighbor interactions

The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed.

Electric field effects on alanine tripeptide in sodium halide solutions

The electric field effects on conformational properties of trialanine in different halide solutions were explored with long-scale molecular dynamics simulations. NaF, NaCl, NaBr and NaI solutions of low (0.2 M) and high (2 M) concentrations were exposed to a constant electric field of 1000 V/m. Generally, the electric field does not disturb trialanine's structure. Large structural changes appear only in the case of the supersaturated 2.0 M NaF solution containing NaF crystals. Although the electric field affects in a complex way, all the ions-water-peptide interactions, it predominantly affects the electroselectivity effect, which describes specific interactions such as the ion-pair formation.

Reliable oligonucleotide conformational ensemble generation in explicit solvent for force field assessment using reservoir replica exchange molecular dynamics simulations

Molecular dynamics force field development and assessment requires a reliable means for obtaining a well-converged conformational ensemble of a molecule in both a time-efficient and cost-effective manner. This remains a challenge for RNA because its rugged energy landscape results in slow conformational sampling and accurate results typically require explicit solvent which increases computational cost. To address this, we performed both traditional and modified replica exchange molecular dynamics simulations on a test system (alanine dipeptide) and an RNA tetramer known to populate A-form-like conformations in solution (single-stranded rGACC). A key focus is on providing the means to demonstrate that convergence is obtained, for example, by investigating replica RMSD profiles and/or detailed ensemble analysis through clustering. We found that traditional replica exchange simulations still require prohibitive time and resource expenditures, even when using GPU accelerated hardware, and our results are not well converged even at 2 μs of simulation time per replica. In contrast, a modified version of replica exchange, reservoir replica exchange in explicit solvent, showed much better convergence and proved to be both a cost-effective and reliable alternative to the traditional approach. We expect this method will be attractive for future research that requires quantitative conformational analysis from explicitly solvated simulations.

pH-Independence of trialanine and the effects of termini blocking in short peptides: a combined vibrational, NMR, UVCD, and molecular dynamics study

Several lines of evidence now well establish that unfolded peptides in general, and alanine in specific, have an intrinsic preference for the polyproline II (pPII) conformation. Investigation of local order in the unfolded state is, however, complicated by experimental limitations and the inherent dynamics of the system, which has in some cases yielded inconsistent results from different types of experiments. One method of studying these systems is the use of short model peptides, and specifically short alanine peptides, known for predominantly sampling pPII structure in aqueous solution. Recently, He et al. ( J. Am. Chem. Soc. 2012 , 134 , 1571 - 1576 ) proposed that unblocked tripeptides may not be suitable models for studying conformational propensities in unfolded peptides due to the presence of end effect, that is, electrostatic interactions between investigated amino acid residues and terminal charges. To determine whether changing the protonation states of the N- and C-termini influence the conformational manifold of the central amino acid residue in tripeptides, we have examined the pH-dependence of unblocked trialanine and the conformational preferences of alanine in the alanine dipeptide. To this end, we measured and globally analyzed amide I' band profiles and NMR J-coupling constants. We described conformational distributions as the superposition of two-dimensional Gaussian distributions assignable to specific subspaces of the Ramachandran plot. Results show that the conformational ensemble of trialanine as a whole, and the pPII content (χpPII = 0.84) in particular, remains practically unaffected by changing the protonation state. We found that compared to trialanine, the alanine dipeptide has slightly lower pPII content (χpPII = 0.74) and an ensemble more reminiscent of the unblocked Gly-Ala-Gly model peptide. In addition, a two-state thermodynamic analysis of the conformational sensitive Δε(T) and (3)J(H(N)H(α))(T) data obtained from electronic circular dichroism and H NMR spectra indicate that the free energy landscape of trialanine is similar in all protonation states. MD simulations for the investigated peptides corroborate this notion and show further that the hydration shell around unblocked trialanine is unaffected by the protonation/deprotonation of the C-terminal group. In contrast, the alanine dipeptide shows a reduced water density around the central residue as well as a less ordered hydration shell, which decreases the pPII propensity and reduces the lifetime of sampled conformations.

Disorder and order in unfolded and disordered peptides and proteins: a view derived from tripeptide conformational analysis. II. Tripeptides with short side chains populating asx and β-type like turn conformations

In the preceding paper, we found that ensembles of tripeptides with long or bulky chains can include up to 20% of various turns. Here, we determine the structural and thermodynamic characteristics of GxG peptides with short polar and/or ionizable central residues (D, N, C), whose conformational distributions exhibit higher than average percentage (>20%) of turn conformations. To probe the side-chain conformations of these peptides, we determined the (3)J(H(α),H(β)) coupling constants and derived the population of three rotamers with χ1 -angles of -60°, 180° and 60°, which were correlated with residue propensities by DFT-calculations. For protonated GDG, the rotamer distribution provides additional evidence for asx-turns. A comparison of vibrational spectra and NMR coupling constants of protonated GDG, ionized GDG, and the protonated aspartic acid dipeptide revealed that side chain protonation increases the pPII content at the expense of turn populations. The charged terminal groups, however, have negligible influence on the conformational properties of the central residue. Like protonated GDG, cationic GCG samples asx-turns to a significant extent. The temperature dependence of the UVCD spectra and (3)J(H(N)H(α)) constants suggest that the turn populations of GDG and GNG are practically temperature-independent, indicating enthalpic and entropic stabilization. The temperature-independent J-coupling and UVCD spectra of GNG require a three-state model. Our results indicate that short side chains with hydrogen bonding capability in GxG segments of proteins may serve as hinge regions for establishing compact structures of unfolded proteins and peptides.