Conformational Behavior and Flexibility of Terminally Blocked Cysteine and Cystine

Conformational potential energy hypersurfaces, PES, for the terminally blocked L-Cysteine, L,L-Cystine and D,L-Cystine have been analyzed by means of molecular mechanics in combination with the programs ROSE, CICADA, PANIC and COMBINE. Low energy conformations and conformational transitions, conformational channels, have been located. Global and fragmental flexibility and conformational softness have been calculated for each conformer as well as for the entire molecule. The PES analyses were used for simulation of conformational movement based on Boltzmann probability of the points obtained on the PES. Boltzmann travelling revealed interesting correlated conformational movement where three or even more dihedral angles changed simultaneously. It could be shown that conformational behavior and flexibility were strongly influenced by the absolute configurations of the amino acids in the peptides.     

Conformational Flexibility of Two RNA Trimers Explored by Computational Tools and Database Search

Abstract

Two RNA sequences, AAA and AUG, were studied by the conformational search program CICADA and by molecular dynamics (MD) in the framework of the AMBER force field, and also via thorough PDB database search. CICADA was used to provide detailed information about conformers and conformational interconversions on the energy surfaces of the above molecules. Several conformational families were found for both sequences. Analysis of the results shows differences, especially between the energy of the single families, and also in flexibility and concerted conformational movement. Therefore, several MD trajectories (altogether 16 ns) were run to obtain more details about both the stability of conformers belonging to different conformational families and about the dynamics of the two systems. Results show that the trajectories strongly depend on the starting structure. When the MD start from the global minimum found by CICADA, they provide a stable run, while MD starting from another conformational family generates a trajectory where several different conformational families are visited. The results obtained by theoretical methods are compared with the thorough database search data. It is concluded that all except for the highest energy conformational families found in theoretical result also appear in experimental data.

Registry numbers:

adenylyl-(3′ →5′)-adenylyl-(3′ →5′)-adenosine [917-44-2]

adenylyl-(3′ →5′)-uridylyl-(3′ →5′)-guanosine [3494-35-7]     

A quantitative structure-activity relationship study for structurally diverse HIV-1 protease inhibitors: contribution of conformational flexibility to inhibitory activity

In this study, we investigated by linear regression model the SAR data of the 15 HIV-1 protease inhibitors possessing structurally diverse scaffolds. First, a regression model was developed only using the enzyme-inhibitor interaction energy as a term of the model, but did not provide a good correlation with the inhibitory activity (R² = 0.580 and Q² = 0.500). Then, we focused on the conformational flexibility of the inhibitors which may represent the diversity of the inhibitors, and added two conformational parameters into the model, respectively: the number of rotatable bonds of ligands (ΔSrot) and the distortion energy of ligands (ΔElig). The regression model by adding ΔElig successfully improved the quality of the model (R² = 0.771 and Q² = 0.713) while the model with ΔSrot was unsuccessful. The prediction for a training inhibitor by the ΔElig model also showed good agreement with experimental activity. These results suggest that the conformational flexibility of HIV-1 protease inhibitors directly contributes to the enzyme inhibition.     

A molecular mechanics and semiempirical molecular orbital study on the conformation of polynorbornene chains

The conformational analysis of polynorbornene (PNB) chains was investigated with the AM1, MM2, AMBER and OPLS methods taking into consideration the possibility of binding of norbornene monomers to each other at various positions, i.e. exo–exo, exo–endo, endo–endo. The chain that is formed by connecting exo–endo positions of the monomers has lower torsional barrier energy than those formed with bonds at other positions and has more flexibility. It is determined that the thredisyndiotactic chain formed by exo–endo addition adopts a helix structure and has a coil shape. The disyndiotactic chain formed by connecting norbornene monomers in mixed type has a linear structure. It is found that the repeat unit conformations of thredisyndiotactic and disyndiotactic chains of PNB are TGTG^– and (TGTG^–)₂, respectively.     

Structural Requirements for Cocaine-Sensitive and -Insensitive Uptake of Phenethylamines into the Adrenal Chromaffin Cell

Abstract: The adrenal medullary chromaffin cell is a commonly used model for the adrenergic neuron. Although much work has been done to study the transport system in the adrenal chromaffin vesicles, relatively little is known about cellular transport, especially with regard to structural features of phenethylamines required for intracellular accumulation. We have now investigated the structural requirements of phenethylamine-related compounds for their accumulation into cultured adrenal chromaffin cells. We find that two types of cellular uptake, previously described only for dopamine, norepinephrine, and epinephrine, are also present for [³H]tyramine. Although two types of accumulation occur, tyramine accumulation occurs mainly via a cocaine-insensitive process, whereas dopamine accumulation occurs predominantly via a cocaine-sensitive process. The accumulation of [¹⁴C]-phenethylamine and p-methoxyphenethylamine is not affected by cocaine, suggesting that a ring hydroxyl substituent is necessary for cocaine-sensitive accumulation. The compounds p-hydroxyphenylpropylamine and p-hydroxyphenyl-2-aminoethyl sulfide accumulate in the cell only via a cocaine-insensitive process, indicating that lengthening of the aminoalkyl side chain prevents cocaine-sensitive accumulation. We have performed conformational analyses of this series of compounds to determine whether the conformation of these compounds can be related to the kinetic data. For dopamine, tyramine, phenethylamine, and p-methoxyphenethylamine, two groups of energy-minimized conformers were found. We find that there is an approximately linear relationship between the K_m values for these phenethylamines and the differences in minimized energies between the low- and highest energy conformer groups of each compound. A similar correlation was found for p-hydroxyphenyl-2-aminoethyl sulfide. These results are consistent with the hypothesis that these compounds undergo a conformational change from the low-energy conformer to the highest energy conformer before their cocaine-insensitive accumulation.     

A salt-bridge switch in the molecular recognition between RS receptor and RGD ligand from the ABEEM σπ molecular dynamics simulations

Abstract

How the receptor and ligand recognise each other is a challenging subject in explaining the mechanism of recognition at the molecular level. As a starting point, here, a synthesised RS receptor and its RGD ligand were investigated as a proper model to simulate their recognition process in terms of ABEEMσπ/MM polarisable force field. It is found that a switch of forming up a salt bridge in the ligand triggers the recognition of the receptor and ligand. Through the salt-bridge switch that undergoes several cycles from on-state with parallel hydrogen bonds to off-state with bifurcated hydrogen bonds, the active site of ligand can flex easily to interact with the active site of the receptor. In addition, the water molecules form a decisive bridge connecting the active sites of the bound system. The salt-bridge switch and water-mediated movement are cooperative as the important factors for the receptor-ligand recognition. In addition, the properties, such as binding free energy, conformational flexibility and solvent accessible surface area have been calculated to provide adequate evidence for the whole recognition process. According to the simulation, a detailed mechanism was derived involving diffusion, a switch triggered cooperative water-mediated movement, and conformational folding, for the flexible recognition.     

DFT-GIAO study of aryltetralin lignan lactones: conformational analyses and chemical shifts calculations

The conformational properties of polygamain and morelensin, two aryltetralin lignan lactones, have been investigated in both the gas-phase and chloroform solution using DFT calculations at the B3LYP/6-311G(d,p) level. Results indicate that the conformation of polygamain is very rigid. Thus, the conformational flexibility of its five-membered rings is considerably restricted as reflects the pseudorotational parameters of the corresponding envelope conformations. On the other hand, morelensin shows a notable conformational flexibility, which is mainly due to its two methoxy groups. Accordingly, 16 minimum energy conformations with relative energies smaller than 2.4 kcal/mol were detected. Furthermore, chemical shifts for 13C nuclei have been calculated using the GIAO method, results being compared with experimental data. A good agreement was found for both polygamain and morelensin.     

Conformational stability and dynamics of cytochrome <Emphasis Type="Italic">c</Emphasis> affect its alkaline isomerization

The alkaline isomerization of horse heart ferricytochrome c (cyt c) has been studied by electronic absorption spectroscopy in the presence of the Hofmeister series of anions: chloride, bromide, rhodanide and perchlorate. The anions significantly affect the apparent pK _a value of the transition in a concentration-dependent manner according to their position in the Hofmeister series. The Soret region of the absorption spectra is not affected by the presence of the salts and shows no significant structural perturbation of the heme crevice. In the presence of perchlorate and rhodanide anions, the cyanide exchange rate between the bulk solvent and the binding site is increased. These results imply higher flexibility of the protein structure in the presence of chaotropic salts. The thermal and isothermal denaturations monitored by differential scanning calorimetry and circular dichroism, respectively, showed a decrease in the conformational stability of cyt c in the presence of the chaotropic salts. A positive correlation between the stability, ΔG, of cyt c and the apparent pK _a values that characterize the alkaline transition indicates the presence of a thermodynamic linkage between these conformational transitions. In addition, the rate constant of the cyanide binding and the partial molar entropies of anions negatively correlate with the pK _a values. This indicates the important role of anion-induced solvent reorganization on the structural flexibility of cyt c in the alkaline transitions. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

The importance of protein–protein interactions for optimising oxygen activity in photosystem II: reconstitution with a recombinant thioredoxin—manganese stabilising protein

In this paper we describe how photosystem II (PSII) from higher plants, which have been depleted, of the extrinsic proteins can be reconstituted with a chimeric fusion protein comprising thioredoxin from Escherichia coli and the manganese stabilising protein from Thermosynechococcus elongatus. Surprisingly, even though E. coli thioredoxin is completely unrelated to PSII, the fusion protein restores higher rates of activity upon rebinding to PSII than either the native spinach MSP, or T. elongatus MSP. PSII reconstituted with the fusion protein also has a lower requirement for calcium than PSII with the small extrinsic proteins removed, or PSII reconstituted with spinach or T. elongatus MSP. The MSP portion of the fusion protein is less thermally stable compared to isolated MSP from T. elongatus, which could be the key to its superior activation capability through greater flexibility. This work reveals the importance of protein–protein interactions in the water splitting activity of PSII and suggests that conformational configurations, which increase flexibility in MSP, are essential to its function, even when these are induced by an unrelated protein.     

HIV-1 GP120 V3 conformational and informational entropies

In an attempt to analyze structure, function and evolution of HIV-1 GP120 V3, interactions among the Hartree–Fock energy, the conformational entropy and the Shannon entropy were determined for the 1NJ0 set of antibody-bound V3 loop conformers. The Hartree–Fock energy of each conformer was determined at the MINI level with GAMESS. The conformational entropy was determined per conformer and per residue from the mass-weighted covariance matrices. The Shannon entropy per residue was determined from sequence-substitution frequencies. Correlations were determined by linear regression analysis. There was a negative correlation between the Hartree–Fock energy and the conformational entropy (R=−0.4840, p=0.0078, df =28) that enhanced the negative Helmholtz-free-energy change for the binding of the GP120 ligand to target CD4. The Shannon entropy of V3 was a function of the conformational entropy variance (R=0.7225, p=0.00157, df=15) and of the V3 Hartree–Fock energy. Biological implications of this work are that (1) conformational entropy interacts with V3 Hartree–Fock energy to enhance GP120 binding to CD4 cell receptors and that (2) the Hartree–Fock energy of V3 interacts with the evolutionary system to participate in the regulation of V3 diversity.     

Conformational flexibility and binding energy profile of c-Abl tyrosine kinase complexed with Imatinib: an insight from MD study

Structural biology of kinase and in particular of tyrosine kinase has given detailed insights into the intrinsic flexibility of the catalytic domain and has provided a rational basis for obtaining selective inhibitors. In this paper, we have studied the conformational flexibility of c-Abl tyrosine kinase complexed with Imatinib (STI), in the presence of TIP3P water in physiological conditions at neutral pH. The conformational studies suggest that the flexibility of activation loop is responsible to facilitate the nucleotide binding and release. Owing to the conformational adaptability, adenosine triphosphate (ATP) binds at a particular site in the loop region of the tyrosine kinase. The molecular mechanics Poisson–Boltzmann surface area methods are analysed, as is a free-energy pathways method, which shows the stable binding with free energy ? 6.04 kcal/mol for STI. The binding energy calculated by the Sietraj method is approximately the same as the experimental binding energy of STI with c-Abl kinase. It is suggested that the conserved glutamic acid and lysine residues are necessary for the stability and optimum activity of inhibitor. This study may be helpful in rational drug designing of new kinase inhibitors.     

Model for the conformational analysis of hydrated peptides. Effect of hydration on the conformational stability of the terminally blocked residues of the 20 naturally occurring amino acids

The effects of hydration are included in empirical conformational energy computations on oligopeptides by means of a modified hydration-shell model. Free energy terms are introduced to account for “specific hydration” due to water–solute hydrogen bonding and for “nonspecific hydration” describing the interaction of the solute with water molecules in a first-neighbor shell. The dielectric constant has been doubled (over the value used for calculations in the absence of water) to take into account the presence of solvent. Computations were carried out for the N-acetyl-N′-methylamides of the 20 naturally occurring amino acids. Conformational energy maps are compared with similar maps calculated in the absence of hydration. Minimum-energy conformations are located and compared with the corresponding minima for unhydrated peptides in terms of ordering with respect to potential energy, the dihedral angles at the minima, and the presence of intramolecular hydrogen bonds. The Boltzmann factors for various conformational regions are altered significantly on hydration in some cases. These changes can be explained in terms of differences in the hydration free energy terms for various conformations.     

A molecular dynamics study of the C-terminal fragment of the L7/L12 ribosomal protein

The crystallographic dimer of the C-terminal fragment (CTF) of the L7/L12 ribosomal protein has been subjected to molecular dynamics (MD) simulations. A 90 picosecond (ps) trajectory for the protein dimer, 19 water molecules and two counter ions has been calculated at constant temperature. Effects of intermolecular interactions on the structure and dynamics have been studied. The exact crystallographic symmetry is lost and the atomic fluctuations differ from one monomer to the other. The average MD structure is more stable than the X-ray one, as judged by accessible surface area and energy calculations. Crystal (non-dimeric) interactions have been simulated in another 40 ps trajectory by using harmonic restraints to represent intermolecular hydrogen bonds. The conformational changes with respect ot the X-ray structure are then virtually suppressed.The unrestrained dimer trajectory has been scanned for cooperative motions involving secondary structure elements. The intrinsic collective motions of the monomer are transmitted via intermolecular contacts to the dimer structure.The existence of a stable dimeric form of CTF, resembling the crystallographic one, has been documented. At the cost of fairly small energy expenditure the dimer has considerable conformational flexibility. This flexibility may endow the dimer with some functional potential as an energy transducer.     

Differences in Conformational Behavior of ATA and TAT Sequences in Single Strand DNA Trimer

Abstract

The conformational behavior of single strand (ss) TAT and ATA trimers of DNA have been studied by computational chemistry tools including CICADA software interfaced with AMBER molecular mechanics and dynamics. The Single-Coordinate-Driving (SCD) method has been used in conjunction with molecular dynamics simulated annealing. It has been revealed that the conformational flexibility of each sequence differs substantially from the other one. Four common conformational families have been found for both trimers. These are: helical, reverse-stacked (base 3), half-stacked (base 3), reverse-stacked (base 1). However, the energies of conformers representing the families are different for both the studied systems. An additional conformational family, bulged, has been found for ss(ATA), while ss(TAT) has been found also in half-stacked (base 1) conformation. In general, ss(TAT) exhibits a higher number of low energy conformations while ss(ATA) shows one interesting low energy conformational interconversion between reverse-stacked (A3) family and half-stacked (A3) family. The high conformational variability of the trimers has been confirmed by flexibility analysis and by molecular dynamics simulations, which have also shown the conformational stability of single conformational families. It has been concluded that the methodology used is able to provide a very detailed picture of the conformational space of these molecules.     

Ab initio conformational maps for disaccharides in gas phase and aqueous solution

Ab initio conformational maps for beta-lactose in both the gas phase and in aqueous solution have been constructed at the HF/6-31G(d,p) level of calculation. The results of the gas-phase ab initio calculations allow us to conclude that a rigid conformational map is able to predict the regions of the minima in the potential energy surface of beta-lactose, in full agreement with those found in the relaxed conformational map. The solvation effects do not give rise to any new local minimum in the potential energy surface of beta-lactose, but just change the relative Boltzmann populations of the conformers found in the gas-phase calculations. The values obtained for heteronuclear spin coupling constant (3J(H,C)), using the seven most stable conformers in solution are in good agreement with the available experimental values. This is a good indication that ab initio rigid conformational maps can be reliably used to sort the most stable conformers of beta-lactose.     

Theoretical studies of the conformational behavior of chain molecules containing polar groups: simulations of a poly(vinylidene fluoride) model

Atomistic Monte Carlo simulations have been conducted to elucidate the conformational behavior of a single chain molecule containing polar functional groups. Here, we resort to an atomistic poly(vinylidene fluoride) (PVDF) chain model as a representative example. The model is modified in such a way that bond lengths and bond angles are fixed, aiming to manifest the role of dipolar interactions. For a given chain length, chain conformation is sensitive to two environmental parameters, temperature and dielectric constant. The mean chain size increases when temperature and/or dielectric constant are increased. The conformational behavior is further characterized by chain size distribution function, and our findings show that temperature induced conformational transition for a chain molecule can be discrete or continuous, depending on its chain length. Also, the dipolar interactions in PVDF are effectively attractive, and enhance chain contraction. As a result, when the strength of dipolar interactions is increased, the discrete conformational transition shifts toward longer chains; and for a given chain length, such a transition occurs at higher temperatures.Figure Variation of R² with temperature for different dielectric constants =1 and 8, denoted by dotted and solid lines, respectively, and for different chain lengths M=8 and 12, as marked. Lines are meant for eye guidance     

Reducing Molecular Flexibility by Cyclization for Elucidation of Absolute Configuration by CD Calculations: Daurichromenic Acid

Circular dichroism (CD) calculations of flexible natural products have been difficult because of the large number of low‐energy conformers and ambiguous Boltzmann distributions. In this article, through electronic (ECD) and vibrational (VCD) studies on a natural product, (+)‐daurichromenic acid, we demonstrate that derivatization of a flexible molecule can dramatically reduce its flexibility. This work also shows the usefulness of derivatization for diminishing computational expenses required for optimization and CD calculations, and for increasing the reliability of the assignment of absolute configuration. Chirality 28:453–459, 2016. © 2016 Wiley Periodicals, Inc.     

Structural and thermodynamic behavior of cytochrome c assembled with glutathione-covered gold nanoparticles

The conformational changes of horse heart ferricytochrome c (cyt c) after association of gold nanoparticles have been studied by electronic absorption spectroscopy and circular dichroism (CD). Our results show that the structural stability around the heme of complexed cyt c was increased successfully. Glutathione-layered gold nanoparticles caused a significant increase of the apparent pK values of the cyt c alkaline transition. Similarly, the heme crevice became more stable to heat after assembly of cyt c with gold nanoparticles. In contrast, gold nanoparticles weaken the overall thermal stability of the cyt c by decreasing the denaturation temperature estimated from far-UV CD measurements. Similar behavior has previously been reported for cyt c complexed with physiological redox partners as well as hydrophilic polyanions. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

An activating amino acid substitution in the c-abl oncogene protein fails to produce a local conformational change

Thebcr-abl chimeric gene of Philadelphia chromosome positive chronic myelogenous leukemias is only weakly transforming. This transformation activity is greatly enhanced by a Lys-for-Glu substitution at position 832 in the c-abl gene, as occurs in the highly transforming v-abl genes. It has been suggested that this mutation results in a significant structural change in the encoded protein product. Using conformational energy analysis, we have determined the allowed low-energy conformations for residues 828–836 of this protein with Lys and Glu at position 832. In both cases, the overwhelmingly preferred conformation for this region is a bend-helix motif. The helix terminates at residue 836, and there are no discernible differences in conformation between the Lys- and Glu-containing sequences. These results suggest that the activating amino acid substitution at position 832 in the c-abl protein product does not produce its effect via a local conformational change.     

Solvent modulation of the structural heterogeneity in FeIII myoglobin samples: a low temperature EPR investigation

High spin FeIII myoglobin samples in solutions with different solvent composition have been investigated at low temperature by Electron Paramagnetic Resonance spectroscopy. The g = 6 line of the spectrum has been analyzed in terms of a distribution of the two crystal field parameters ₁ and ₂. By means of the Angular Overlap Method, it has been shown that these distributions entail, in turn, a distribution in the iron-heme displacement along the normal to the heme-plane. The spread in this iron-heme distance, which can be connected with the binding action of the proximal histidine, has been proposed as a quantitative measurement of the structural heterogeneity (conformational substate landscape) displayed by the protein molecules. The results point out, moreover, that the solvent composition can affect the structural heterogeneity of the protein system. In particular, addition of glycerol, ethylene glycol and sucrose yields a significant reduction in the spread of the ironheme displacement, while the presence of ammonium sulfate induces a change in the average position of the iron in the heme-plane. The role played by the solvent in the structure and dynamics of the protein, in connection also with the conformational substate distribution, is discussed. Correspondence to: S. Cannistraro