Solvation Free Energies and Transfer Free Energies for Amino Acids from Hydrophobic Solution to Water Solution from a Very Simple Residue Model

Plausible Emergence of Autocatalytic Cycles under Prebiotic Conditions

The emergence of life in a prebiotic world is an enormous scientific question of paramount philosophical importance. Even when life (in any sense we can define it) can be observed and replicated in the laboratory, it is only an indication of one possible pathway for life emergence, and is by no means be a demonstration of how life really emerged. The best we can hope for is to indicate plausible chemical–physical conditions and mechanisms that might lead to self-organizing and autopoietic systems. Here we present a stochastic simulation, based on chemical reactions already observed in prebiotic environments, that might help in the design of new experiments. We will show how the definition of simple rules for the synthesis of random peptides may lead to the appearance of networks of autocatalytic cycles and the emergence of memory.

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Maintaining a proper balance between specific intermolecular interactions and non-specific solvent interactions is of critical importance in molecular simulations, especially when predicting binding affinities or reaction rates in the condensed phase. The most rigorous metric for characterizing solvent affinity are solvation free energies, which correspond to a transfer from the gas phase into solution. Due to the drastic change of the electrostatic environment during this process, it is also a stringent test of polarization response in the model. Here, we employ both the CHARMM fixed charge and polarizable force fields to predict hydration free energies of twelve simple solutes. The resulting classical ensembles are then reweighted to obtain QM/MM hydration free energies using a variety of QM methods, including MP2, Hartree⁻Fock, density functional methods (BLYP, B3LYP, M06-2X) and semi-empirical methods (OM2 and AM1 ). Our simulations test the compatibility of quantum-mechanical methods with molecular-mechanical water models and solute Lennard⁻Jones parameters. In all cases, the resulting QM/MM hydration free energies were inferior to purely classical results, with the QM/MM Drude force field predictions being only marginally better than the QM/MM fixed charge results. In addition, the QM/MM results for different quantum methods are highly divergent, with almost inverted trends for polarizable and fixed charge water models. While this does not necessarily imply deficiencies in the QM models themselves, it underscores the need to develop consistent and balanced QM/MM interactions. Both the QM and the MM component of a QM/MM simulation have to match, in order to avoid artifacts due to biased solute⁻solvent interactions. Finally, we discuss strategies to improve the convergence and efficiency of multi-scale free energy simulations by automatically adapting the molecular-mechanics force field to the target quantum method.

Capping effects on polymorphic Aβ16-21 amyloids depend on their size: A molecular dynamics simulation study

Understanding Aβ amyloid oligomers associated with neuro-degenerative diseases is needed due to their toxic characteristics and mediation of amyloid fibril growth. Depending on various physiological circumstances such as ionic strength, metal ion, and point-residue mutation, oligomeric amyloids exhibit polymorphic behavior and structural stabilities, i.e. showing different conformation and stabilities. Specifically, experimental and computational researchers have found that the capping modulates the physical and chemical properties of amyloids by preserving electrostatic energy interactions, which is one of the dominant factors for amyloid stability. Still, there is no detailed knowledge for the polymorphic amyloids with reflecting the terminal capping effects. In the present study, we investigated the role of terminal capping (i.e. N-terminal acetylation and C-terminal amidation) on polymorphic Aβ_16-21 amyloid oligomer and protofibrils via molecular dynamics (MD) simulations. We found that the capping effects have differently altered the conformation of polymorphic antiparallel-homo and -hetero Aβ_16-21 amyloid oligomer, but not Aβ_16-21 amyloid protofibrils. However, regardless of polymorphic composition of the amyloids, the capping induces the thermodynamic instabilities of Aβ_16-21 amyloid oligomers, but does not show any distinct affect on Aβ_16-21 amyloid protofibrils. Specifically, among the molecular mechanic factors, electrostatic energy dominantly contributes the thermodynamic stability of the Aβ_16-21 amyloids. We hope that our computation study about the role of the capping effects on the polymorphic amyloids will facilitate additional efforts to enhance degradation of amyloids and to design a selective drug in the future.

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility

Oligoglycine is a backbone mimic for all proteins and is prevalent in the sequences of intrinsically disordered proteins. We have computed the absolute chemical potential of glycine oligomers at infinite dilution by simulation with the CHARMM36 and Amber ff12SB force fields. We performed a thermodynamic decomposition of the solvation free energy (ΔG(sol)) of Gly2-5 into enthalpic (ΔH(sol)) and entropic (ΔS(sol)) components as well as their van der Waals and electrostatic contributions. Gly2-5 was either constrained to a rigid/extended conformation or allowed to be completely flexible during simulations to assess the effects of flexibility on these thermodynamic quantities. For both rigid and flexible oligoglycine models, the decrease in ΔG(sol) with chain length is enthalpically driven with only weak entropic compensation. However, the apparent rates of decrease of ΔG(sol), ΔH(sol), ΔS(sol), and their elec and vdw components differ for the rigid and flexible models. Thus, we find solvation entropy does not drive aggregation for this system and may not explain the collapse of long oligoglycines. Additionally, both force fields yield very similar thermodynamic scaling relationships with respect to chain length despite both force fields generating different conformational ensembles of various oligoglycine chains.

Interaction of glycine, lysine, proline and histidine with dipalmitoylphosphatidylcholine lipid bilayers: a theoretical and experimental study

The interaction of unblocked glycine, lysine, proline and histidine with a DPPC bilayer was assessed using extensive atomistic molecular dynamics simulations.

Solvent effects on kinetic mechanisms of self-assembly by peptide amphiphiles via molecular dynamics simulations

Peptide amphiphiles are known to form a variety of distinctive self-assembled nanostructures (including cylindrical nanofibers in hydrogels) dependent upon the solvent conditions. Using a novel coarse-grained model, large-scale molecular dynamics simulations are performed on a system of 800 peptide amphiphiles (sequence, palmitoyl-Val3Ala3Glu3) to elucidate kinetic mechanisms of molecular assembly as a function of the solvent conditions. The assembly process is found to occur via a multistep process with transient intermediates that ultimately leads to the stabilized nanostructures including open networks of β-sheets, cylindrical nanofibers, and elongated micelles. Different kinetic mechanisms are compared in terms of peptide secondary structures, solvent-accessible surface area, radius of gyration, relative shape anisotropy, intra/intermolecular interactions, and aggregate size dynamics to provide insightful information for the design of functional biomaterials.

Role of hydrophobicity on self-assembly by peptide amphiphiles via molecular dynamics simulations

Using a novel coarse-grained model, large-scale molecular dynamics simulations were performed to examine self-assembly of 800 peptide amphiphiles (sequence palmitoyl-V3A3E3). Under suitable physiological conditions, these molecules readily assemble into nanofibers leading to hydrogel construction as observed in experiments. Our simulations capture this spontaneous self-assembly process, including formation of secondary structure, to identify morphological transitions of distinctive nanostructures. As the hydrophobic interaction is increased, progression from open networks of secondary structures toward closed cylindrical nanostructures containing either β-sheets or random coils are observed. Moreover, temperature effects are also determined to play an important role in regulating formation of secondary structures within those nanostructures. These understandings of the molecular interactions involved and the role of environmental factors on hydrogel formation provide useful insight for development of innovative smart biomaterials for biomedical applications.

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 - 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 - 30 μs simulations, to its native states (C(α) RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins.

Biomolecular electrostatics and solvation: a computational perspective

An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view toward describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g. solvent structure, polarization, ion binding, and non-polar behavior) in order to provide a background to understand the different types of solvation models.

Backbone additivity in the transfer model of protein solvation

The transfer model implying additivity of the peptide backbone free energy of transfer is computationally tested. Molecular dynamics simulations are used to determine the extent of change in transfer free energy (DeltaG(tr)) with increase in chain length of oligoglycine with capped end groups. Solvation free energies of oligoglycine models of varying lengths in pure water and in the osmolyte solutions, 2M urea and 2M trimethylamine N-oxide (TMAO), were calculated from simulations of all atom models, and DeltaG(tr) values for peptide backbone transfer from water to the osmolyte solutions were determined. The results show that the transfer free energies change linearly with increasing chain length, demonstrating the principle of additivity, and provide values in reasonable agreement with experiment. The peptide backbone transfer free energy contributions arise from van der Waals interactions in the case of transfer to urea, but from electrostatics on transfer to TMAO solution. The simulations used here allow for the calculation of the solvation and transfer free energy of longer oligoglycine models to be evaluated than is currently possible through experiment. The peptide backbone unit computed transfer free energy of -54 cal/mol/M compares quite favorably with -43 cal/mol/M determined experimentally.

Hydration free energies of amino acids: why side chain analog data are not enough

Using molecular dynamics based free energy simulations, we computed relative solvation free energies for pairs of N-acetyl-methylamide amino acids (Ala-Ser, Val-Thr, Phe-Tyr, Val-Ala, Thr-Ser, Phe-Ala, and Tyr-Ser) and compared the results with the relative solvation free energies of the corresponding pairs of side chain analogs. We observed differences in (relative) solvent affinity DeltaDeltaDeltaA between amino acids and side chain analogs of up to 66% or, in absolute numbers, 4.9 kcal/mol (Ala-Ser). To rationalize these findings, we estimated separately contributions from what we refer to as solvent exclusion and self-solvation. While the former accounts for the reduction in solute-solvent interactions as one part of the solute occludes other parts of the solute, the latter turned out to be the determining contribution for small polar amino acids and could be shown to arise from interactions between the polar backbone and the polar functional group of the respective side chain in the gas phase. Consequently, the solvent affinity of small polar amino acids depends strongly on the backbone conformation. Our results indicate that the still widely used group additivity-solvent exclusion assumption to estimate solvation free energies for large(r) molecules (such as peptides and proteins) from model compound data (such as side chain analogs) is insufficient. To illustrate practical consequences, we compare the explicit solvent results with those of implicit solvent models. While approaches based on the generalized Born model give results in (mostly) good agreement with explicit solvent, approaches relying (primarily) on the group additivity-solvent exclusion assumption fail to reproduce DeltaDeltaDeltaA. Finally, we briefly discuss the implications of our results for hydrophobicity scales.

Molecular-dynamics evaluation of fluid-phase equilibrium properties by a novel free-energy perturbation approach: Application to gas solubility and vapor pressure of liquid hexane

A novel free-energy perturbation method is developed for the computation of the free energy of transferring a molecule between fluid phases. The methodology consists in drawing a free-energy profile of the target molecule moving across a binary-phase structure built in the computer. The novelty of the method lies in the difference of the definition of the free-energy profile from the common definition. As an important element of the method, the process of making a correction to the transfer free energy with respect to the cutoff of intermolecular forces is elucidated. In order to examine the performance of the method in the application to fluid-phase equilibrium properties, molecular-dynamics computations are carried out for the evaluation of gas solubility and vapor pressure of liquid n-hexane at 298.15 K. The gas species treated are methane, ethane, propane, and n-butane, with the gas solubility expressed as Henry's constant. It is shown that the method works fine and calculated results are generally in good agreement with experiments. It is found that the cutoff correction is strikingly large, constituting a dominant part of the calculated transfer free energy at the cutoff of 8 A.