Global Minimum Energy Conformation Research Articles

The dead-end elimination theorem and its use in protein side-chain positioning

The prediction of a protein's tertiary structure is still a considerable problem because the huge amount of possible conformational space¹ makes it computationally difficult. With regard to side-chain modelling, a solution has been attempted by the grouping of side-chain conformations into representative sets of rotamers²⁻⁵. Nonetheless, an exhaustive combinatorial search is still limited to carefully indentified packing units⁵⁶ containing a limited number of residues. For larger systems other strategies had to be developed, such as the Monte Carlo Procedure⁶⁷ and the genetic algorithm and clustering approach⁸. Here we present a theorem, referred to as the 'dead-end elimination' theorem, which imposes a suitable condition to identify rotamers that cannot be members of the global minimum energy conformation. Application of this theorem effectively controls the computational explosion of the rotamer combinatorial problem, thereby allowing the determination of the global minimum energy conformation of a large collection of side chains.

Conformational study of α and β epimers of 3-phenethyl-3-azabicyclo[3.3.1]nonan-9-ol.

The conformational preferences of α(I) and β(II) epimers of 3-phenethyl-3-azabicyclo[3.3.1]nonan-9-ol, have been studied using the molecular mechanics method (MM2 and MM2′ programs). In both cases, the global minimum-energy conformer computed correspond to a slightly flattened CC conformation with the 3N-phenethyl group in the β-position. This behaviour is in agreement with the conformation adopted in solution in polar solvents. In relation to the energy differences between N-axial and N-equatorial conformations, these epimers exhibit an intermediate situation between the tropine and the α and β epimers of 3-phenethyl-3-azabicyclo[3.2.1]octan-8-ol.

A rational search for the separation of psychoactivity and analgesia in cannabinoids

The compound 9-beta-hydroxy-hexahydrocannabinol [(−)-9 β-OH-HHC] was designed to fit a combined theoretical profile of an analgesic cannabinoid (equatorial alcohol at C-9, phenol at C-1 and a C-3 side chain) with reduced psychoactivity (axial C-9 substituent which protrudes into the α face). (−)-9 β-OH-HHC was synthesized by the addition of methyl Grignard to 9-oxo-11-nor-HHC. Its α epimer was obtained by the regiospecific epoxide ring opening of 9α, 10 α-epoxy-HHC acetate. (−)-9 β-OH-HHC and (−)-9 α-OH-HHC were each evaluated in a battery of tests in mice and were found to be 10–25 times less potent than (−)-trans- Δ 9-tetrahydrocannabinol ( Δ 9-THC) in all tests including the tail flick test for antinociception (analgesia). Molecular mechanics calculations [MMP2(85)] revealed that, in the global minimum energy conformation of (−)-9 β-OH-HHC, the axial methyl at C-9 protrudes into the α face of the molecule, while the axial hydroxyl at C-9 in (−)-9 α-OH-HHC protrudes into this same face. These calculations also identified a higher energy carbocyclic ring ( twist) conformer of each in which there is no protrusion of a C-9 substituent of the carbocyclic ring into the α face. The minimal activity of both compounds is attributed to these higher energy forms. It is concluded that protrusion of a C-9 substituent into the α-face of the molecule is associated with reduced cannabinoid analgesia, as well as with reduced cannabinoid psychopharmacological activity.

Conformational analysis of sialyloligosaccharides

The conformational properties of several sialyloligosaccharides present as terminal sequences in N- and O-linked carbohydrate groups of glycoproteins, have been analyzed based on the n.m.r. data of selected sialosides. The compounds examined include representatives of the α- d-NeuAc-(2→6)-β- d-Gal-(1→4)-β- d-GlcNAc, α- d-NeuAc-(2→3)-β- d-Gal-(1→4)-β- d-GlcNAc, α- d-NeuAc-(2→3)-β- d-Gal-(1→3)-β- d-GlcNAc, and α- d-NeuAc-(2→3)-β- d-Gal-(1→3)-β- d-GalNac series. Two deuterated sialosides were prepared by enzymic sialylation of 6-deuterated galactose derivatives of methyl β- d-galactopyranoside and lactoside. These were useful for the unambiguous establishment of the “ gt” orientation of the flexible C-6 methylene unit of the galactose through 1H- 1H coupling constants. Of all the (2→6) sialosides examined, only the deuterated di- and tri-saccharide afforded useful nuclear Overhauser enhancement data that could be used to evaluate the global minimum-energy conformations. Hard-sphere exoanomeric effect calculations estimated the glycosidic torsion angles for the global minimum-energy conformer of α- d-NeuAc-(2→6)-β- d-Gal linkages to be −163/−132/61° (θ, ψ, and gw, respectively). However, the potential energy well surrounding this global minimum was very shallow and indicated a broad population distribution of conformers. These are illustrated by the isoenergy contour maps. The observation of n.O.e. between the H-3 ax and H-6 R of the galactose in two deuterate (2→6) sialosides, indeed supported the presence of one of the global minimum-energy conformers. The conformational analysis carried out for the di- and trisaccharide [α- d-NeuAc-(2→6)-β- d-Gal-OMe and α- d-NeuAc-(2→6)-β- d-Gal-(1→4)-β- d-Glc-Ome respectively] was then extended to sialoside linkages of other tri- and penta-saccharides by comparison of their 1H- and 13C-n.m.r. chemical shifts. HSEA calculations for the (2→3) sialosides indicated the potential energy well containing the global minimum energy-conformer (θ, ψ = −160 ± 4, −11 ± 2°) was deeper than the one estimated for the (2→6) sialosides. The n.O.e. data are consistent with the distribution of the majority of conformers around the lowest-energy one in solution. CPK models highlighting the topographical differences between the lowest-energy conformations of α-(2→6) and α-(2→3) sialosides are presented.

Global Minimum Energy Conformations of Thyrotropin Releasing Hormone Analogs by Simulated Annealing.II

Lowest conformational energy structures of seventeen thyrotropin releasing hormone analogs have been studied by simulated annealing. A surprising conformational similarity was observed for the peptide backbone. The possible role of each substituent in its biological activity is inferred. A composite hydrogen-bonding environment is proposed for the TRH with respect to receptor binding.

Correlation of the structure of the transmembrane domain of the neu oncogene-encoded p185 protein with its function.

The human homologue of the neu oncogene is frequently found in human tumors. Certain amino acid substitutions at position 664 in the transmembrane domain of the neu oncogene-encoded p185 protein product are known to cause malignant transformation of cells. Using conformational energy analysis based on ECEPP (empirical conformational energies for polypeptides program), we have previously determined the preferred three-dimensional structures for the transmembrane domain of the p185 protein with a transforming (glutamic acid) and a nontransforming (valine) substitution at the critical position 664 and found that the global minimum-energy conformation of this region in the nontransforming protein contains a sharp bend, whereas the global minimum-energy conformation for this region from the transforming protein is entirely alpha-helical. We now demonstrate that this result holds for other known nontransforming (glycine, histidine, tyrosine, and lysine) and transforming (glutamine) substitutions at position 664. Furthermore, a simple statistical thermodynamic analysis of the results indicates that approximately 85% of each of the nontransforming sequences exist with the bend at positions 664 and 665, while approximately 90% of each of the transforming sequences exist as an alpha-helix. About 9% of the nontransforming sequences exist as the alpha-helix. These results suggest that if the intracellular concentration of the normal protein is increased at least 10-fold, thereby increasing the alpha-helical form by this factor, cell transformation should result. This conclusion is directly supported by genetic experiments in which this level of overexpression of the normal protein was achieved with attendant cell transformation.

Molecular mechanics calculations of several lanthanide complexes: An application of the random incremental pulse search

AbstractA new method for the evaluation of metal complexes with molecular mechanics calculations is described. The method has been employed to determine the global minimum energy conformations of three seven‐coordinate lanthanide complexes. The method searches the potential energy surface of the metal complexes for the global minimum structure using the recently reported Random Incremental Pulse Search (RIPS). The molecular mechanics calculations were performed using the MM2 metal‐extended force field (MM2MX). This force field excludes 1‐3 bending terms about the metal center and, instead, explicitly includes 1‐3 nonbonded van der Waals interactions. This affords a model based mainly on steric interactions about the ligating atoms, and removes the necessity of specifying ligand‐metal‐ligand bond angles for seven‐coordinate and higher metal complexes in which no preferred bond angle can be proficiently determined. The calculated minimum‐energy structures were well known seven‐coordinate conformations in all cases, and a comparison with X‐ray crystallographic is presented.

Global minimum energy conformations of thyrotropin releasing hormone analogs by simulated annealing

The global minimum energy of the conformations of several tripeptides, analogs of the thyrotropin releasing hormone (TRH), are located employing simulated annealing. These structures are compared with others previously reported and found to be the lowest in conformational energy. The energy function does not take into account the solvent effect. However, the technique seems to be appropriate to conduct further research in computer-assisted design of TRH analogs.

Disaccharide conformational flexibility. II. Molecular dynamics simulations of sucrose

Molecular dynamics simulations have been used to study the motions in vacuum of the disaccharide sucrose. Ensembles of trajectories were calculated for each of the five local minimum energy conformations identified in the adiabatic conformational energy mapping of this molecule. The model sucrose molecules were found to exhibit a variety of motions, although the global minimum energy conformation was found to be dynamically stable, and no transitions away from this structure were observed to occur spontaneously. In all but one of these vacuum trajectories, the intramolecular hydrogen bond between residues was maintained, in accord with recent nmr studies of this molecule in aqueous solution. Considerable flexibility of the furanoid ring was found in the trajectories. No "flips" to the opposite puckering for this ring were found in the simulations starting from the global minimum, although such a transition was observed for a trajectory initiated with one of the higher local minimum energy conformations. Overall, the observed structural fluctuations were consistent with the experimental picture of sucrose as a relatively rigid molecule.

Comparative conformational study of α and β epimers of 3-phenethyl-3-azabicyclo [3.2.1] octan-8-ol with atropine and azaprophen.

Conformational analysis of α(I) and β(II) epimers of 3-phenethyl-3-azabicyclo [3.2.1] octan-8-ol has been performed using the Molecular Mechanics Method (MM2). In both cases, the global minimum-energy conformer was the slight distorted chair form with the N-phenethyl group in equatorial position. The preferred conformation is in agreement with the form adopted in solid state and in solution in polar solvents. Higher energy differences between N-axial and N-equatorial conformations have been found with respect to tropine and 6-methyl-6-azabicyclo [3.2.1] octan-3-α-ol, the am i noalcohols components of atropine and azaprophen.

Conformational changes induced by the transforming amino acid substitution in the transmembrane domain of the neu oncogene-encoded p185 protein.

The neu oncogene is frequently found in certain types of human carcinomas and has been shown to be activated in animal models by nitrosourea-induced mutation. The activating mutation in the neu oncogene results in the substitution of a glutamic acid for a valine at position 664 in the transmembrane domain of the encoded protein product of 185 kda (designated p185), which, on the basis of homology studies, is presumed to be a receptor for an as yet unidentified growth factor. It has been proposed that activating amino acid substitutions in this region of p185 lead to a conformational change in the protein which causes signal transduction via an increase in tyrosine kinase activity in the absence of any external signal. Using conformational energy analysis, we have determined the preferred three-dimensional structures for the transmembrane decapeptide (residues 658-667) of the p185 protein with valine and glutamic acid at the critical position 664. The results indicate that the global minimum energy conformation of the decapeptide from the normal protein with Val at position 664 is an alpha-helix with a sharp bend (CD conformation at residues 664 and 665) in this region, whereas the global minimum conformation for the decapeptide from the mutant transforming protein with Glu at position 664 assumes an all alpha-helical configuration. Furthermore, the second highest energy conformation for the decapeptide from the normal protein is identical to the global minimum energy conformation for the decapeptide from the transforming protein, providing a possible explanation why overexpression of the normal protein also has a transforming effect.(ABSTRACT TRUNCATED AT 250 WORDS)

Conformational energy analysis of the leucine repeat regions of C/EBP, GCN4, and the proteins of themyc, jun, andfos oncogenes

It has been recently proposed that certain DNA binding proteins (including C/EBP, GCN4 and the myc, jun, and fos oncogene proteins) share a common structural motif based on helix-promoting regions containing heptad repeat sequences of leucines. It has been suggested that this structure is critical to the biological activity of these proteins, since it facilitates the formation of functional dimers held together by interdigitating leucine side-chains along the hydrophobic interfaces between long alpha-helical regions of the polypeptide chains in a configuration termed the "leucine zipper." In this paper, conformational energy analysis is used to deterrmine the preferred three-dimensional structures of the leucine repeat regions of these proteins. The results indicate that, in all cases, the global minimum energy conformation for these regions is an amphipathic alpha-helix with the leucine side-chains arrayed on one side in such a way to favor "leucine zipper" dimerization. Furthermore, amino acid substitutions in these regions (such as Pro for Leu), that are known to inhibit dimer formation and prevent DNA binding, are found to produce significant conformational changes that disrupt the amphipathic helical structure. Thus, these results provide support for the proposed "leucine zipper" configuration as a critical structural feature of this class of DNA binding proteins.

Analysis of the in vitro antiviral activity of certain ribonucleosides against parainfluenza virus using a novel computer aided receptor modeling procedure

The in vitro antiviral activity of 28 nucleosides against the parainfluenza virus type 3 has been analyzed by using a novel computer aided receptor modeling procedure. The method involves an extensive modification of our earlier work (Ghose, A. K.; Crippen, G. M. J. Med. Chem. 1985, 28, 333). It presents a more straightforward algorithm for the steps that suffered from subjectivity in the earlier method. The method first determines the possible low-energy conformations of the nucleosides, and assigns a priority value for each conformation of each molecule. It then performs the following steps repeatedly, until it finds an acceptable solution. Starting from the conformation of highest priority, the various energetically allowed conformations of the other molecules are superimposed on it. On the basis of the physicochemical property matching (or overlapping), the best superposition is determined. The superimposed molecules are dissected into a minimum number of parts and the local physicochemical properties at different regions are correlated with their binding data (antiviral activity). A modified version of distance geometry has been used for geometric comparison of the structure of the molecules. On the basis of the virus rating (VR) of 28 ribonucleosides, this procedure hypothesized the minimum-energy conformation of 6-(methylthio)-9-beta-D-ribofuranosylpurine as a reference conformation and used three physicochemical properties, namely hydrophobicity, molar refractivity, and formal charge density for property matching. The binding-site cavity was divided into seven regions or pockets to differentiate the nature of interaction quantitatively. The model suggests that the 2- and 3-positions of the purine ring and the corresponding atoms of the other rings get some steric repulsion, and nucleosides having a single five-membered heterocyclic ring will better fit this virus. The methylthio group gets a strong attraction from dispersive interaction. Both hydrophilic and dispersive groups are attractive here. Although our calculation supports the previously suggested active conformation of ribavirin, it shows that it is not the global minimum-energy conformation. The difference lies in the orientation of the amide group. The calculated viral rating from this model showed a correlation coefficient of 0.971 with the observed values, and the explained variance and the standard deviation of the fit were 0.880 and 0.125, respectively.

Conformational Analysis of Flexible Molecules: Location of the Global Minimum Energy Conformation by the Simulated Annealing Method

A new computational method for the location of the lowest energy conformation of flexible molecules is reported. The technique, called simulated annealing, is discussed and several applications are described.

An approach to the multiple-minima problem in protein folding by relaxing dimensionality: Tests on enkephalin

An algorithm for locating the region in conformational space containing the global energy minimum of a polypeptide is described. Distances are used as the primary variables in the minimization of an objective function that incorporates both energetic and distancegeometric terms. The latter are obtained from geometry and energy functions, rather than nuclear magnetic resonance experiments, although the algorithm can incorporate distances from nuclear magnetic resonance data if desired. The polypeptide is generated originally in a space of high dimensionality. This has two important consequences. First, all interatomic distances are initially at their energetically most favorable values; i.e. the polypeptide is initially at a global minimum-energy conformation, albeit a high-dimensional one. Second, the relaxation of dimensionality constraints in the early stages of the minimization removes many potential energy barriers that exist in three dimensions, thereby allowing a means of escaping from three-dimensional local minima. These features are used in an algorithm that produces short trajectories of three-dimensional minimum-energy conformations. A conformation in the trajectory is generated by allowing the previous conformation in the trajectory to evolve in a high-dimensional space before returning to three dimensions. The resulting three-dimensional structure is taken to be the next conformation in the trajectory, and the process is iterated. This sequence of conformations results in a limited but efficient sampling of conformational space. Results for test calculations on Met-enkephalin, a pentapeptide with the amino acid sequence H-Tyr-Gly-Gly-Phe-Met-OH, are presented. A tight cluster of conformations (in three-dimensional space) is found with ECEPP energies (Empirical Conformational Energy Program for Peptides) lower than any previously reported. This cluster of conformations defines a region in conformational space in which the global-minimum-energy conformation of enkephalin appears to lie.

Conformation of d(CpG) modified by the carcinogen 4-aminobiphenyl: a combined experimental and theoretical analysis.

The change in DNA conformation produced by the attachment of a reactive substance is likely to be a vital factor in determining the biological consequences of the reaction. We have prepared a deoxydinucleoside monophosphate containing the major adduct derived from the carcinogenic amine 4-aminobiphenyl and analyzed its conformation by theoretical and experimental methods. Reaction of d(CpG) with N-acetoxy-N-(trifluoroacetyl)-4-aminobiphenyl afforded the product modified at C-8 of guanine with 4-aminobiphenyl. After purification by reverse-phase high-performance liquid chromatography, milligram amounts of product were obtained. It was analyzed by circular dichroism, proton magnetic resonance, and minimized potential-energy calculations. A flexible molecule with a mixture of conformers is indicated. Both carcinogen-base-stacked states and base-base-stacked states, with guanine both syn anti, contribute to the population mixture on the dimer level. The global minimum-energy conformation has syn-guanine and carcinogen-base stacking. Forms of this type are calculated to represent roughly 58% of the conformer population. Because of the twisted nature of the biphenyl moiety, carcinogen-base stacking inherently involves less overlap than that in the planar and rigid three-ringed aminofluorene analogue. This difference might relate to the diminished effectiveness of the aminobiphenyl vs. the aminofluorene adduct as a frameshift mutagen in Salmonella typhimurium 1538.

Molecular Conformation, Receptor Binding, and Hormone Action of Natural and Synthetic Estrogens and Antiestrogens

The X-ray crystallographic structural determinations of synthetic estrogens and antiestrogens provide reliable information on the global minimum energy conformation of these molecules or a local minimum energy conformation that is within 1 or 2 kcal/mole of the global minimum. In favorable cases, state-of-the-art molecular mechanics calculations provide quantitative agreement with X-ray results and information on the relative energy of other local minimum energy conformations not observed crystallographically. Because the conformation of diethylstilbestrol (DES) observed in solvated crystals has an overall conformation and dipole moment more similar to estradiol it is the form more likely to bind to the receptor and produce hormone activity. Either phenol ring of DES can successfully mimic the estradiol A-ring in binding to the receptor. Indenestrol A (INDA) and indenestrol B (INDB) have nearly identical fully extended planar conformations. Either the alpha or gamma rings of these compounds may mimic the A ring of estradiol and compete for the estrogen receptor. Although there are eight distinct ways in which molecules of a racemic mixture of INDA or INDB can bind to the receptor, not all of them may be able to elicit a hormonal response. This may account for the reduced biological activity of the compounds despite their successful competition for receptor binding. The minimum energy conformations of Z-pseudodiethylstilbestrol (ZPD) and E-pseudodiethylstilbestrol (EPD) are bent in a fashion similar to that of indanestrol (INDC). These molecules have good binding affinity suggesting that the receptor does not require a flat molecule. Therefore these conformations would appear to be compatible with receptor binding, but only the Z isomer has an energetically allowed extended conformation that accounts for its observed biological activity relative to DES.

Molecular conformation, receptor binding, and hormone action of natural and synthetic estrogens and antiestrogens.

The X-ray crystallographic structural determinations of synthetic estrogens and antiestrogens provide reliable information on the global minimum energy conformation of these molecules or a local minimum energy conformation that is within 1 or 2 kcal/mole of the global minimum. In favorable cases, state-of-the-art molecular mechanics calculations provide quantitative agreement with X-ray results and information on the relative energy of other local minimum energy conformations not observed crystallographically. Because the conformation of diethylstilbestrol (DES) observed in solvated crystals has an overall conformation and dipole moment more similar to estradiol it is the form more likely to bind to the receptor and produce hormone activity. Either phenol ring of DES can successfully mimic the estradiol A-ring in binding to the receptor. Indenestrol A (INDA) and indenestrol B (INDB) have nearly identical fully extended planar conformations. Either the alpha or gamma rings of these compounds may mimic the A ring of estradiol and compete for the estrogen receptor. Although there are eight distinct ways in which molecules of a racemic mixture of INDA or INDB can bind to the receptor, not all of them may be able to elicit a hormonal response. This may account for the reduced biological activity of the compounds despite their successful competition for receptor binding. The minimum energy conformations of Z-pseudodiethylstilbestrol (ZPD) and E-pseudodiethylstilbestrol (EPD) are bent in a fashion similar to that of indanestrol (INDC). These molecules have good binding affinity suggesting that the receptor does not require a flat molecule. Therefore these conformations would appear to be compatible with receptor binding, but only the Z isomer has an energetically allowed extended conformation that accounts for its observed biological activity relative to DES.

Sterically crowded five-membered heterocyclic systems. Part 2. Conformation of 2,2,5,5-tetramethylpyrrolidin-3-ol from nuclear magnetic resonance spectroscopy, crystal structure, and molecular mechanics calculations

The conformation of 2,2,5,5-tetramethylpyrrolidin-3-ol (2) was investigated by 1H n.m.r. spectroscopy, X-ray diffraction, and molecular mechanics calculations. In solution there is an equilibrium between the forms of the pyrrolidine ring with axial and equatorial orientations of the hydroxy group. The temperature dependence of the 3J(HH) coupling constants indicates a somewhat lower energy for the axial conformers. The puckering of the CH2CHOH part of the ring was estimated from the extended R value method, optimized for a five-membered ring, to be 32.9° at 263 K. The crystal structure of (2) was solved by direct methods and refined to R = 0.045. Two independent molecules in the asymmetric unit adopt nearly identical conformations with the pyrrolidine ring in the 2T3 twist form with the hydroxy group and the nitrogen proton in an axial orientation. Molecules are connected by O–H ⋯ N hydrogen bonds (O ⋯ N = 2.82 Å) into chains along the z-axis. There are also weak N–H ⋯ O bonds (N ⋯ O = 3.40 Å) between molecules in neighbouring chains. The conformational space of (2) was explored by molecular mechanics calculations. Several local energy minima were characterized. In all of them the ring is flattened around the fully substituted C-2 or C-5 atoms. The energy difference between these conformations is of the order of 5–7 kJ mol–1. The conformation observed in the crystal corresponds very well to the calculated global energy minimum conformation.

AAF linked to the guanine amino group: a B-Z junction.

Minimized conformational potential energy calculations have been performed for AAF linked to dCpdG at the guanine amino group. This is a model for the minor AAF adduct observed in DNA, whose conformational influence has been difficult to ascertain. A global minimum energy conformation was computed with torsion angles like those of the dCpdG residue of Z-DNA. This conformation was incorporated into a larger polymer model at a B-Z junction, with the carcinogen residing in the groove in the Z direction. Local minimum energy conformations of the B type were also computed. In addition, two minima were found with fluorenecytidine stacking. These results suggest that existing B-Z junctions may be vulnerable to modification by AAF at the guanine amino group, or that such junctions may be induced by the carcinogen if the base sequence is appropriate. Otherwise the carcinogen can be located in the minor groove of the B helix (5, 10, 11) or covalently intercalated (13-15).