Free Energy Of Amino Acids Research Articles

Binding mechanism and binding free energy of amino acids and citrate to hydroxyapatite surfaces as a function of crystallographic facet, pH, and electrolytes

Hydroxyapatite (HAP) is the major mineral phase in bone and teeth. The interaction of individual amino acids and citrate ions with different crystallographic HAP surfaces has remained uncertain for decades, creating a knowledge gap to rationally design interactions with peptides, proteins, and drugs. In this contribution, we quantify the binding mechanisms and binding free energies of the 20 end-capped natural amino acids and citrate ions on the basal (001) and prismatic (010)/(020) planes of hydroxyapatite at pH values of 7 and 5 for the first time at the molecular scale. We utilized over 1500 steered molecular dynamics simulations with highly accurate potentials that reproduce surface and hydration energies of (hkl) hydroxyapatite surfaces at different pH values. Charged residues demonstrate a much higher affinity to HAP than charge-neutral species due to the formation of superficial ion pairs and ease of penetration into layers of water molecules on the mineral surface. Binding free energies range from 0 to −60 kJ/mol and were determined with ∼ 10% uncertainty. The highest affinity was found for citrate, followed by Asp(-) and Glu(-), and followed after a gap by Arg(+), Lys(+), as well as by His(+) at pH 5. The (hkl)-specific area density of calcium ions, the protonation state of phosphate ions, and subsurface directional order of the ions in HAP lead to surface-specific binding patterns. Amino acids without ionic side groups exhibit weak binding, between −3 and 0 kJ/mol, due to difficulties to penetrate the first layer of water molecules on the apatite surfaces. We explain recognition processes that remained elusive in experiments, in prior simulations, discuss agreement with available data, and reconcile conflicting interpretations. The findings can serve as useful input for the design of peptides, proteins, and drug molecules for the modification of bone and teeth-related materials, as well as control of apatite mineralization.

The Roots of Genetic Coding in Aminoacyl-tRNA Synthetase Duality.

Codon-dependent translation underlies genetics and phylogenetic inferences, but its origins pose two challenges. Prevailing narratives cannot account for the fact that aminoacyl-tRNA synthetases (aaRSs), which translate the genetic code, must collectively enforce the rules used to assemble themselves. Nor can they explain how specific assignments arose from rudimentary differentiation between ancestral aaRSs and corresponding transfer RNAs (tRNAs). Experimental deconstruction of the two aaRS superfamilies created new experimental tools with which to analyze the emergence of the code. Amino acid and tRNA substrate recognition are linked to phase transfer free energies of amino acids and arise largely from aaRS class-specific differences in secondary structure. Sensitivity to protein folding rules endowed ancestral aaRS-tRNA pairs with the feedback necessary to rapidly compare alternative genetic codes and coding sequences. These and other experimental data suggest that the aaRS bidirectional genetic ancestry stabilized the differentiation and interdependence required to initiate and elaborate the genetic coding table.

Efficient computation of transfer free energies of amino acids in beta-barrel membrane proteins

Transmembrane beta-barrel proteins (TMBs) serve a multitude of essential cellular functions in Gram-negative bacteria, mitochondria and chloroplasts. Transfer free energies (TFEs) of residues in the transmembrane (TM) region provides fundamental quantifications of thermodynamic stabilities of TMBs, which are important for the folding and the membrane insertion processes, and may help in understanding the structure-function relationship. However, experimental measurement of TFEs of TMBs is challenging. Although a recent computational method can be used to calculate TFEs, the results of which are in excellent agreement with experimentally measured values, this method does not scale up, and is limited to small TMBs. We have developed an approximation method that calculates TFEs of TM residues in TMBs accurately, with which depth-dependent transfer free energy profiles can be derived. Our results are in excellent agreement with experimental measurements. This method is efficient and applicable to all bacterial TMBs regardless of the size of the protein. An online webserver is available at http://tanto.bioe.uic.edu/tmb-tfe . : jliang@uic.edu. Supplementary data are available at Bioinformatics online.

Outer Membrane Protein Folding and Topology from a Computational Transfer Free Energy Scale.

Knowledge of the transfer free energy of amino acids from aqueous solution to a lipid bilayer is essential for understanding membrane protein folding and for predicting membrane protein structure. Here we report a computational approach that can calculate the folding free energy of the transmembrane region of outer membrane β-barrel proteins (OMPs) by combining an empirical energy function with a reduced discrete state space model. We quantitatively analyzed the transfer free energies of 20 amino acid residues at the center of the lipid bilayer of OmpLA. Our results are in excellent agreement with the experimentally derived hydrophobicity scales. We further exhaustively calculated the transfer free energies of 20 amino acids at all positions in the TM region of OmpLA. We found that the asymmetry of the Gram-negative bacterial outer membrane as well as the TM residues of an OMP determine its functional fold in vivo. Our results suggest that the folding process of an OMP is driven by the lipid-facing residues in its hydrophobic core, and its NC-IN topology is determined by the differential stabilities of OMPs in the asymmetrical outer membrane. The folding free energy is further reduced by lipid A and assisted by general depth-dependent cooperativities that exist between polar and ionizable residues. Moreover, context-dependency of transfer free energies at specific positions in OmpLA predict regions important for protein function as well as structural anomalies. Our computational approach is fast, efficient and applicable to any OMP.

Peptide Recognition Capabilities of Cellulose in Molecular Dynamics Simulations

Knowing the amino acid discriminating capacity of the surface of cellulose can be valuable information toward the rational design and re-engineering of the cellulosome in order to improve its catalytic properties. This aim can be achieved by the determination of the binding free energies of amino acids in molecular dynamics simulations. Conventional simulations do not always allow for sufficient sampling of the configuration space, especially in a system where large energy barriers occur. A better sampling can be obtained by replica exchange molecular dynamics (REMD). Here, we use REMD combined with umbrella sampling to determine the potential of the mean force for amino acids, analogues of their side chains, dipeptides, and tripeptides for the interactions with the (100) face of the crystalline cellulose Iβ. We also use REMD to characterize the adsorption dynamics of a small protein, tryptophan cage. Our results show that all 20 standard amino acids adsorb on the surface of cellulose with binding energie...

Evaluating the transfer free energies of amino acids from water to ammonium-based ionic liquids at 298.15 K

The interactions between ionic liquids (ILs) and amino acids (AAs) can easily be quantified using the apparent transfer free energy (∆G′tr) values that can be used to interpret the stability of the proteins in the same solvent medium. In this study, ∆G′tr values of AAs such as phenylalanine (Phe), histidine (His), threonine (Thr), glutamine (Gln) and serine (Ser) from the water to ILs have been obtained from the solubility measurements, as a function of IL concentration at 298.15K under atmospheric pressure. The investigated ILs contain diethylammonium acetate (DEAA), diethylammonium hydrogen sulfate (DEAS), triethylammonium acetate (TEAA), triethylammonium hydrogen sulfate (TEAS), triethylammonium dihydrogen phosphate (TEAP), and trimethylammonium acetate (TMAA). The results reveal that the IL effect was specific and independent for each AA in the aqueous medium. Apparently, we observed a positive as well as negative ∆G′tr values for Phe, His, Glu, Thr, and Ser AAs in the ammonium-based ILs.

On the transferability of fractional contributions to the hydration free energy of amino acids

This study reports the application of the quantum mechanical self-consistent reaction field MST method to compute the solvation profile in water of the twenty natural amino acids. The aim is to derive intrinsic fractional contributions to the hydration free energy and to examine their transferability to peptides. To this end, IEF-MST calculations have been performed at the B3LYP/6-31G(d) level for the series of acetyl amino acid amides, which were chosen as model compounds. In order to account for the flexibility of both the backbone and the side chain in deriving the hydration fractional contributions, calculations have been performed for representative conformers taken from the Dunbrack’s backbone-dependent conformational library. The results allow us to dissect the hydration free energy into backbone and side chain contributions and examine the conformational dependence of the fragmental contributions to hydration. For the backbone, different hydration contributions are found for α-helical and β-sheet conformations, which mainly reflect differences in the electrostatic contribution to hydration of the carbonyl group. In contrast, the conformational flexibility of the side chain is found to have little impact on the fractional contribution to hydration. These findings should be valuable to refine semiempirical methods for predicting solvation properties of peptides and proteins in large-scale genomic studies.

Statistical Mechanical Model for the Transfer Free Energy of Amino Acids in the Context of Membrane Protein OmpLA

Transfer free energy scale of amino acids is fundamental for understanding membrane protein folding and for predicting membrane protein structures. Several experimental studies have been carried out to measure the free energy of partitioning amino acids to artificial lipid bilayer or biological membranes in the context of model peptides. A recent study measured water-to-bilayer transfer free energy in the context of a native β-barrel transmembrane protein OmpLA[1]. Here we report the development of a computational free energy scale based on an empirical potential energy function and statistical mechanical model. Our energy function incorporates the energy contribution of single-body burial, inter-strand interaction and sequential nearest neighbor contact interaction. Using a statistical mechanical model with a reduced state space, we computed the full partition function of OmpLA and the relative insertion free energy of amino acids replacing Ala210. The computed relative free energy scale correlates well with experimental data (r2 =0.79 with water-to-bilayer scale[1] and r2=0.88 with translocon scale[2]). In addition, depth dependency profiles of Arg and Leu are in excellent agreement with those measured by Moon and Flemming [1]. We also obtained depth dependency profiles of all 20 amino acids which provide insight to the folding process of membrane protein. Furthermore, our model showed strong coopperativity of Arg-Arg, consistent with experimental founds[1]. We further predicted that Lys-Lys show significant cooperativity, which is subject to future experimental verification.1. Moon CP, Fleming KG (2011) Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers. Proc Natl Acad Sci USA108:10174-101772. Hessa, T, Kim, H, Bihlmaier, K, Lundin, C, Boekel, J, Andersson, H, Nilsson, I, White, SH, von Heijne, G (2005). Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature, 433, 7024:377-81.

Computational Prediction of Solvation Free Energies of Amino Acids with Genetic Algorithm

We propose an improved solvent contact model to estimate the solvation free energies of amino acids from individual atomic contributions. The modification of the solvation model involves the optimization of three kinds of parameters in the solvation free energy function: atomic fragmental volume, maximum atomic occupancy, and atomic solvation parameters. All of these atomic parameters for 17 atom types are developed by the operation of a standard genetic algorithm in such a way to minimize the difference between experimental and calculated solvation free energies. The present solvation model is able to predict the experimental solvation free energies of amino acids with the squared correlation coefficients of 0.94 and 0.93 for the parameterization with Gaussian and screened Coulomb potential as the envelope functions, respectively. This result indicates that the improved solvent contact model with the newly developed atomic parameters would be a useful tool for the estimation of the molecular solvation free energy of a protein in aqueous solution.

Solvation Free Energy of Amino Acids and Side-Chain Analogues

The solvation free energies of amino acids and their side-chain analogues in water and cyclohexane are calculated by using Monte Carlo simulation. The molecular interactions are described by the OPLS-AA force field for the amino acids and the TIP4P model for water, and the free energies are determined by using the Bennett acceptance method. Results for the side-chain analogues in cyclohexane and in water are used to evaluate the performance of the force field for the van der Waals and the electrostatic interactions, respectively. Comparison of the calculated hydration free energies for the amino acid analogues and the full amino acids allows assessment of the additivity of the side chain contributions on the number of hydrating water molecules. The hydration free energies of neutral amino acids can be reasonably approximated by adding the contributions of their side chains to that of the hydration of glycine. However, significant nonadditivity in the free energy is found for the zwitterionic form of amino acids with polar side chains. In serine and threonine, intramolecular hydrogen bonds are formed between the polar side chains and backbone groups, leading to weaker solvation than for glycine. In contrast, such nonadditivity is not observed in tyrosine, in which the hydroxyl group is farther separated from, and therefore cannot form an intramolecular hydrogen bond with, the backbone. For histidine we find that a water molecule can form a bridge when the intramolecular hydrogen bond between the polar group and the backbone is broken.

Are Solvation Free Energies of Homogeneous Helical Peptides Additive?

We investigated the additivity of the solvation free energy of amino acids in homogeneous helices of different length in water and in chloroform. Solvation free energies were computed by multiconfiguration thermodynamic integration involving extended molecular dynamics simulations and by applying the generalized-born surface area solvation model to static helix geometries. The investigation focused on homogeneous peptides composed of uncharged amino acids, where the backbone atoms are kept fixed in an ideal helical conformation. We found nonlinearity especially for short peptides, which does not allow a simple treatment of the interaction of amino acids with their surroundings. For homogeneous peptides longer than five residues, the results from both methods are in quite good agreement and solvation energies are to a good extent additive.

Development of Fast Disintegrating Compressed Tablets Using Amino Acid as Disintegratation Accelerator: Evaluation of Wetting and Disintegration of Tablet on the Basis of Surface Free Energy

A fast disintegrating compressed tablet was formulated using amino acids, such as L-lysine HCl, L-alanine, glycine and L-tyrosine as disintegration accelerator. The tablets having the hardness of about 4 kgf were prepared and the effect of amino acids on the wetting time and disintegration time in the oral cavity of tablets was examined on the basis of surface free energy of amino acids. The wetting time of the tablets increased in the order of L-lysine HCl, L-alanine, glycine and L-tyrosine, whereas the disintegration time in the oral cavity of the tablets increased in the order of L-alanine, glycine, L-lysine HCl and L-tyrosine. These behaviors were well analyzed by the introduction of surface free energy. When the polar component of amino acid was large value or the dispersion component was small value, faster wetting of tablet was observed. When the dispersion component of amino acid was large value or the dispersion component was small value, faster disintegration of tablet was observed, expect of L-tyrosine tablet. The fast disintegration of tablets was explained by the theory presented by Matsumaru.

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

Solvation free energies of neutral amino acids in water and in chloroform were computed from extensive molecular dynamics simulations using multiconfiguration thermodynamic integration. The values computed for the AMBER force field are in very good agreement with available experimental data (rms differences of 5.1 kJ mol-1 for the solvation free energies and 6.4 kJ mol-1 for the transfer free energies of amino acids between water and chloroform) and with existing calculations. We derived an additive residue-scale solvation model formulated as the sum of a nonpolar term that is proportional to the molecular surface area and an electrostatic term (Kirkwood−Onsager model) for the hydration free energy of a dipole in a solvated cavity. This model can surprisingly well describe the solvation free energies in water and chloroform as well as the transfer free energies of amino acids between the two solvents when suitably adapted cavity radii are used. Root-mean-square differences of the predicted values with res...

Calculated Solvation Free Energies of Amino Acids in a Dipolar Approximation

The solvation free energies of amino acids (hydrophobicities) are rationalized here by using a simple electrostatic ab initio model. The parameters of the model are the surface energy density (γ = 9.55 kJ/mol/nm2, the same for all atoms), the fractional charges, and the radii of the atoms of the amino acids. From the fractional charges, dipoles are constructed, and the polarization energies (self-energies) of the dipoles are calculated. The saturation effect of the solvent is included in the model. The dipole electrostatic contribution is in general not very sensitive to the choice of parameters. In contrast, the self-energies of single net charges are extremely sensitive to the choice of the Born radius. However, for amino acids that may carry a net charge, this energy will be prohibitively large in a low-dielectric medium. Therefore, they will in general change their protonation state to become neutral. The energetic cost of this is calculated from the difference between the amino acid side chain pKa's and the pH of the solvent. This results in a hydrophobicity scale for amino acid side chains based on fundamendal physics that agrees well with experimental hydrophobicity scales. The solvation energy for the amino acid backbone (the peptide bond) can also be calculated in this way. This gives good agreement with available experimental data.

Solvation Free Energies of Amino Acids Calculated by Molecular Dynamics/Free Energy Perturbation Method.

It has been accepted that free energy differences between amino acids calculated using computer simulations are in good agreement with the corresponding experimental values. In recent years, however, Sharp et al. [Biochemistry, 30, 9686 (1991)] pointed out that the experimental solvation free energies had been underestimated and suggested reevaluation of the extent of agreement between the experiment and computer simulations. We calculated the free energy differences of transfer from vapor to water between neutral amino acids using molecular dynamics/free energy perturbation method and compared the calculated values (ΔΔGcalc) with both the uncorrected values (ΔΔGuncorr) obtained by Wolfenden et al. [Science, 206, 575 (1979); Biochemistry, 20, 849 (1981)] and the corrected values (ΔΔGcorr) by Sharp et al. considering the effect of solute-solvent size differences. For the uncorrected values, the correlation coefficient was r=0.938 and the simple regression equation was ΔΔGuncorr=0.823ΔΔGcalc-0.235. For the corrected values, the correlation coefficient and the simple regression equation were r=0.987 and ΔΔGcorr=1.042ΔΔGcalc-0.172, respectively. It was shown that the calculated values are in better agreement with the corrected values than with the uncorrected values.

Hydration Thermodynamics of Biomolecules. II. Atomic Transfer Parameters of Amino Acids

Making a least-squares fit of a formula derived in our previous work to published data on the transfer free energy of amino acids from octanol to water, atomic transfer parameters have been estimated for sixteen nonionic amino acids. Among the carbon atoms, those having a partial charge of 0.18 electron charge or more and β-carbon atoms of side chains, were found to have a significantly lower hydrophobicity than other aliphatic and aromatic carbon atoms. The most plausible model for classifying all constituent atoms into six groups is proposed: sulfur, oxygen, nitrogen, aliphatic carbon, aromatic carbon, and partially charged carbon and/or β-carbon. Considering the conformational distribution of amino acids, and evaluating separately the intramolecular interaction energy and the solvation energy of each amino acid, are shown to be essential for estimating accurate atomic transfer parameters.