Conformational free energy of alkylsilanes by nonequilibrium-pulling Monte Carlo simulation

The stationary phase in supercritical fluid chromatography includes alkylsilanes, bearing typically 18-carbon alkane chains, bonded to silica. The silanes are in contact with supercritical carbon dioxide. Interaction of the stationary phase with analytes from the mobile phase depends on conformation of the silanes, whether they form a collapsed layer between the silica and the carbon dioxide or are extended into the carbon dioxide. Although equilibrium conformation of alkylsilanes can be determined by equilibrium Monte Carlo (MC) simulation, that is hampered by slow relaxation of the chains. An alternative is to pull alkylsilanes from collapsed to extended conformations, then calculate free energy change from the Jarzynski equality. This work compares conformational results from equilibrium MC simulation to free energies from nonequilibrium pulling simulations. Because both equilibrium and nonequilibrium simulations are faster for shorter silanes, this work also compares results from 8-carbon and 18-carbon silanes. Free energies from nonequilibrium pulling predict that alkylsilanes tend to bend over and form a layer between silica and carbon dioxide. Results from equilibrium simulations are qualitatively consistent with results from nonequilibrium pulling. Longer-chain silanes have greater tendency to extend slightly into the carbon dioxide.     

Conformational analysis of endothelin-1: Effects of solvation free energy

In order to investigate conformational preferences of the 21-residue peptide hormone endothelin-1 (ET-1), an extensive conformational search was carried out in vacuo using a combination of high temperature molecular dynamics / annealing and a Monte Carlo / minimization search in torsion angle space. Fully minimized conformations from the search were grouped into families using a clustering technique based on rms fitting over the Cartesian coordinates of the atoms of the peptide backbone of the ring region. A wide range of local energy minima were identified even though two disulfide bridges (Cys¹-Cys¹⁵ and Cys³-Cys¹¹) constrain the structure of the peptide. Low energy conformers of ET-1 as a nonionized species in vacuo arestabilized by intramolecular interaction of the ring region (residues 1-15) with the tail (residues 16–21). Strained conformations for individual residues are observed. Conformational similarity to protein loops is established by matching to protein crystal structures In order to assess the influence of aqueous environment on conformational preference, the electrostatic contribution to the solvation energy was calculated for ET-1 as a fully ionized species (Asp⁸, Lys⁹, Glu¹⁰, Asp¹⁸, N- and C-terminus) using a continuum electrostatics model (DelPhi) for each of the conformed generated in vacuo, and the total solvation free energy was estimated by adding a hydrophobic contribution proportional to solvent accessible surface area. Solvation dramatically alters the relative energetics of ET-1 conformers from that calculated in vacuo. Conformers of ET-1 favored by the electrostatic salvation energy in water include conformers with helical secondary structure in the region of residues 9–15. Perhaps of most importance, it was demonstrated that the contribution tosolvation by an individual charge depends not only on its solvent accessibility but on the proximity of other charges, i.e., it is a cooperative effect. This was shown by the calculation of electrostatic solvation energy as afunction of conformation with individual charges systematically turned “on” and “off”. The cooperative effect of multiple charges on solvation demonstrated in this manner calls into question models that relate solvation energysimply to solvent accessibility by atom or residue alone. © 1995 John Wiley & Sons, Inc.     

Conformational changes in sperm-whale metmyoglobin due to combination with antibodies to apomyoglobin

1. No ferrihaem was detected in the precipitate formed by metmyoglobin with an antiserum to apomyoglobin and the extinction at 410mmu of metmyoglobin, due to ferrihaem, was decreased by the univalent fragments of apomyoglobin antibodies. It was concluded that the combination of apomyoglobin antibodies with metmyoglobin caused the release of ferrihaem. As the removal of ferrihaem from metmyoglobin is accompanied by a conformational change, it was concluded that the conformation of metmyoglobin was altered by the apomyoglobin antibodies. 2. Antisera to metmyoglobin were divided into two groups; antisera of the first group revealed differences between the immunological reactivities of metmyoglobin and apomyoglobin, whereas no differences were detected with antisera of the second group. 3. Metmyoglobin was only partially re-formed by adding haematin to the precipitate produced by apomyoglobin with an antiserum of the first group, whereas complete re-formation of metmyoglobin was achieved in the presence of antisera of the second group. No metmyoglobin was formed on the addition of haematin to the precipitates produced by either metmyoglobin or apomyoglobin with the anti-apomyoglobin serum. 4. Immune precipitates formed by antisera to metmyoglobin dissociated at pH1.8, whereas those formed by the anti-apomyoglobin serum did not dissociate. 5. These results suggest that apomyoglobin possessed different conformations when combined with metmyoglobin antibodies and apomyoglobin antibodies.     

Conformational equilibria and free energy profiles for the allosteric transition of the ribose-binding protein

The ribose-binding protein (RBP) is a sugar-binding bacterial periplasmic protein whose function is associated with a large allosteric conformational change from an open to a closed conformation upon binding to ribose. The crystal structures of RBP in open and closed conformations have been solved. It has been hypothesized that the open and closed conformations exist in a dynamic equilibrium in solution, and that sugar binding shifts the population from open conformations to closed conformations. Here, we study by computer simulations the thermodynamic changes that accompany this conformational change, and model the structural changes that accompany the allosteric transition, using umbrella sampling molecular dynamics and the weighted histogram analysis method. The open state is comprised of a diverse ensemble of conformations; the open ribose-free X-ray crystal conformations being representative of this ensemble. The unligated open form of RBP is stabilized by conformational entropy. The simulations predict detectable populations of closed ribose-free conformations in solution. Additional interdomain hydrogen bonds stabilize this state. The predicted shift in equilibrium from the open to the closed state on binding to ribose is in agreement with experiments. This is driven by the energetic stabilization of the closed conformation due to ribose-protein interactions. We also observe a significant population of a hitherto unobserved ribose-bound partially open state. We believe that this state is the one that has been suggested to play a role in the transfer of ribose to the membrane-bound permease complex.     

Conformational energy analysis of melanostatin

Conformational energy calculations were carried out on the hypothalamic hormone melanostatin, a tripeptide with the primary structure H-L-Pro-L-Leu-Gly-NH2. The calculated lowest energy conformation was a type II beta bend, very similar to that reported in an X-ray crystal study. This conformation, however, was only one of 109 low-energy structures (less than or equal to 3 kcal/mol above the global minimum), indicating that the molecule in solution exists as an ensemble of conformations and is very flexible, in agreement with relaxation data from n.m.r. measurements. A statistical analysis yielded an average end-to-end distance of 6.8 A and a bend probability of 0.62, suggesting that, in nonpolar solvents, bend structures predominate within the statistical ensemble. The statistical analysis, however, also yielded a probability of only 0.11 for the occurrence of a 4 leads to 1 hydrogen bond. Hence, the calculations show that, although bend conformations predominate, bends would be difficult to observe in solution if the experiments were designed only to detect 4 leads to 1 hydrogen bonds.     

Conformational effects on the activation free energy of diffusion through membranes as influenced by electric fields

In biological membranes there are large differences in the permeabilities of K⁺ and Na⁺, the permeability of K⁺ being the higher in the polarized membrane. In excitable membranes both the absolute and relative permeabilities are strongly affected by the electric field. It is shown that these changes can be explained by simple electrostatically induced conformational changes at the mouths of pores, due to the deflection of ionized long-chain molecules. A conformational change requiring a low free energy for its production, may result in a large change in the free energy of activation, as a result of the relative magnitudes of elastic and inertial forces. The energy required to partially dehydrate the two ion species plays an essential role in the process.     

Conformational energy analysis of retro-all-Dmethionine enkephalin

Empirical conformational energy calculations have been carried out on the molecule retro-all-D -methionine enkephalin. Low-energy conformers were found by energy minimization and conformational search procedures. The lowest energy conformers wee found toi have some stereochemical relationship to the calculated normal met-enkephalin conformers, but they were not retro-all-D -equivalent to the Met-enkephalin structures. The retro-all-D -equivalent conformations were ～10 kcal/mol higher energy than the low-energy conformers found here. A structural comparison between the retro-all-D -conformers and the met-enkephalin conformers shows hat one cannot rely solely on topochemical analysis to predict biological activity for linear retro-all-D -peptides.     

Conformational free energies of myoglobins of small mammals

Myoglobins from three small placental mammals and one small marsupial were isolated from cardiac or skeletal muscle. The conformational free energies of these four myoglobins were estimated from guanidinium chloride unfolding data at pH 8 and 25 degrees. The myoglobins from rat and rabbit are more stable than that of the most stable myoglobin previously studied, that of the sperm whale. In addition, these two myoglobins unfold with greater cooperativity than previously characterized myoglobins. The data obtained herein demonstrate unequivocally for the first time that the stability of homeotherm myoglobins correlates with neither the size of the organism nor its metabolic rate.     

Conformational energy studies of linear dipeptides H-X-L-Pro-OH

Empirical conformational energy calculations with the use of ECEPP energy functions have been carried out for linear dipeptides H-X-L -Pro-OH, with X = Gly, L -Ala, D -Ala, L -Leu, D -Leu, L -Phe, and D -Phe, in different states of protonation of the end groups. The results of these calculations are compared with the previously reported experimental equilibrium populations for the cis and trans isomers of the X-Pro bond in the different species. For all the protonation states of the seven dipeptides, the calculated nonbonded interactions and the conformational entropy term lead to a preference of the trans forms over the cis isomers by at least 1 kcal/mol. The electrostatic interactions stabilize the cis conformations in all species except the cationic forms of the D ,L -peptides, and it could further be shown that only the carbonyl group of X and the two end groups contribute significantly to the total electrostatic energy. One of the principal results of the experimental studies, i.e., the occurrence of 5–15% cis-proline in all the peptides with an uncharged C-terminus, was corroborated by our investigation of the cationic species. A detailed assessment of the electrostatic contribution to the total energy of the different conformations of H-Gly-L -Pro-OH indicates that the standard ECEPP parameters tend to overestimate the electrostatic interactions in aqueous solutions of the X-Pro dipeptides.     

Conformational transitions in RNA single uridine and adenosine bulge structures: a molecular dynamics free energy simulation study

Extra unmatched nucleotides (single base bulges) are common structural motifs in folded RNA molecules and can participate in RNA-ligand binding and RNA tertiary structure formation. Often these processes are associated with conformational transitions in the bulge region such as flipping out of the bulge base from an intrahelical stacked toward a looped out state. Knowledge of the flexibility of bulge structures and energetics of conformational transitions is an important prerequisite to better understand the function of this RNA motif. Molecular dynamics simulations were performed on single uridine and adenosine bulge nucleotides at the center of eight basepair RNA molecules and indicated larger flexibility of the bulge bases compared to basepaired regions. The umbrella sampling method was applied to study the bulge base looping out process and accompanying conformational and free energy changes. Looping out toward the major groove resulted in partial disruption of adjacent basepairs and was found to be less favorable compared to looping out toward the minor groove. For both uridine and adenosine bulges, a positive free energy change for full looping out was obtained which was approximately 1.5 kcal mol-1 higher in the case of the adenosine compared to the uridine bulge system. The simulations also indicated stable partially looped out states with the bulge bases located in the RNA minor groove and forming base triples with 5'-neighboring basepairs. In the case of the uridine bulge this state was more stable than the intrahelical stacked bulge structure. Induced looping out toward the minor groove involved crossing of an energy barrier of approximately 3.5 kcal mol-1 before reaching the base triple state. A continuum solvent analysis of intermediate bulge states indicated that electrostatic interactions stabilize looped out and base triple states, whereas van der Waals interactions and nonpolar contributions favor the stacked bulge conformation.     

Conformational energy calculations on alginic acid. II. Conformational statistics of the copolymers

Conformational energy maps have been calculated for α-D -mannuronic acid (1–4) α-L -guluronic acid and for α-L -guluronic acid (1–4) β-D -mannuronic acid. These have been used, together with maps previously calculated for the homomonomeric dimers, to estimate the characteristic ratios and Kuhn lengths of the alternating copolymer and of a stochastic copolymer similar in composition to that extracted from L. digitata.The results show that the alternating copolymer is less extended than either homopolymer. Kuhn lengths calculated for the stochastic copolymer agree well with experimental results on high ionic strength solutions of alginate isolated from L digitata.     

Conformational energy refinement of horse-heart ferricytochrome c.

The reported X-ray structure of horse-heart ferricytochrome c has been refined by conformational energy calculations, using a three-stage computational procedure. In stage I, the atomic positions are adjusted to conform to idealized bond lengths and bond angles characteristic of small amino acid derivatives, while yet remaining as close as possible to the X-ray coordinates. In stage II, atomic overlaps are eliminated by adjusting the backbone and side-chain dihedral angles to minimize the nonbonded energy, hydrogen-bonded energy, and rotational energy contributions. In the final stage of refinement, the electrostatic energy and a more accurate hydrogen-bonded energy treatment are considered, in addition to the energy contributions of stage II. A "fitting potential" of gradually decreasing strength is imposed in both stages II and III, in order to keep the computed structure as similar to the x-ray structure as is consistent with a low-energy conformation. The final computed structure of cytochrome c exhibits a very low conformational energy (-504 kcal/mol) and also closely resembles the X-ray structure (RMS deviation = 0.77 A for all atoms). However, a special treatment was required in order to alter the location of the phenyl ring of phenylalanine-82. In contrast to the originally published X-ray structure, which shows the phenyl ring pointing away from the heme, the phenyl ring in the computed structure is tucked into the heme crevice, in a position similar to that observed in the reduced form of tuna cytochrome c, in the oxidized form of Rhodospirillum rubrum cytochrome c2, and also in the recently determined structure of oxidized tuna cytochrome c.     

Conformational properties of alpha-synuclein in its free and lipid-associated states

alpha-Synuclein (alphaS) is a presynaptic terminal protein that is believed to play an important role in the pathogenesis of Parkinson's disease (PD). We have used NMR spectroscopy to characterize the conformational properties of alphaS in solution as a free monomer and when bound to lipid vesicles and lipid-mimetic detergent micelles. Free wild-type alphaS is largely unfolded in solution, but exhibits a region with a preference for helical conformations that may be important in the aggregation of alphaS into fibrils. The N-terminal region of alphaS binds to synthetic lipid vesicles and detergent micelles in vitro and adopts a highly helical conformation, consistent with predictions based on sequence analysis. The C-terminal part of the protein does not associate with either vesicles or micelles, remaining free and unfolded. These results suggest that one function of alphaS may be to tether as of yet unidentified partners to lipid surfaces via interactions with its C-terminal tail.     

Conformational energy calculations on glycosylated turns in glycoproteins

Analysis of the amino acid sequence of glycoproteins has suggested the β-turn as a likely site of glycosylation in glycoproteins. According to this model, the peptide chain traverses the interior of a globular protein, reversing its direction at the protein surface, a likely point for the attachment of hydrophilic carbohydrate residues. In order to search for plausible conformations of glycosylated β-turns in asparagine-linked glycoproteins, we have adapted the conformational energy calculation method of Scheraga and coworkers for use in carbohydrates. The parameters for nonbonded and hydrogen-bonded interactions have been published, and electrostatic parameters are derived from a CNDO calculation on a model glycopeptide. Our results indicate that the orientation of the glycosyl amide bond having the amide proton nearly trans to the anomeric proton of the sugar has the lowest energy. Although CD and nmr experiments in our laboratory have consistently found this conformation, our calculations show the conformation having these two protons in a cis relationship to lie very close in energy. Calculations on the glycopeptide linkage model, α-N-acetyl, δ-N(2-acetamido-1,2-dideoxy-β-D -glucopyranosyl)-N′-methyl-L -asparaginyl amide show that several distinct geometries are allowed for glycosylated β-turns. For a type I β-turn, three conformations of the glycosylated side chain are found within 4 kcal of the minimum, while two conformations of the glycosylated side chain are allowed for a type II turn. The hydrogen-bonded C7 conformation is also allowed. Stereoviews of the low-energy conformations reveal no major hydrogen-bonding interaction between the peptide and sugar.