Conformational Interconversion Research Articles

Theoretical and NMR investigations on the conformations of ( − )-meptazinol hydrochloride in solution

( − )-Meptazinol is an analgesic with an additional acetylcholinesterase (AChE) inhibitory activity. In order to investigate the formation mechanism of its biological conformation observed in AChE-bis( − )-meptazinol complex, two different and naturally stable conformers of ( − )-meptazinol hydrochloride in solution were determined and identified by nuclear magnetic resonance (NMR) and molecular dynamic simulations. Moreover, ab initio calculations and NMR evidence showed the difficulties in conformer interconversion. In combination with the results of conformational comparison, it was proposed that the pharmacophoric conformer of ( − )-meptazinol might come from the conformer with less favourable energy rather than the conformer with the lowest energy.

Activation and Proton Transport Mechanism in Influenza A M2 Channel

Molecular dynamics trajectories 2 μs in length have been generated for the pH-activated, tetrameric M2 proton channel of the influenza A virus in all protonation states of the pH sensor located at the His37 tetrad. All simulated structures are in very good agreement with high-resolution structures. Changes in the channel caused by progressive protonation of His37 provide insight into the mechanism of proton transport. The channel is closed at both His37 and Trp41 sites in the singly and doubly protonated states, but it opens at Trp41 upon further protonation. Anions access the charged His37 and by doing so stabilize the protonated states of the channel. The narrow opening at the His37 site, further blocked by anions, is inconsistent with the water-wire mechanism of proton transport. Instead, conformational interconversions of His37 correlated with hydrogen bonding to water molecules indicate that these residues shuttle protons in high-protonation states. Hydrogen bonds between charged and uncharged histidines are rare. The valve at Val27 remains on average quite narrow in all protonation states but fluctuates sufficiently to support water and proton transport. A proton transport mechanism in which the channel, depending on pH, opens at either the histidine or valine gate is only partially supported by the simulations.

Specific Chemical Reactivities of Spatially Separated 3-Aminophenol Conformers with Cold Ca + Ions

Many molecules exhibit multiple rotational isomers (conformers) that interconvert thermally and are difficult to isolate. Consequently, a precise characterization of their role in chemical reactions has proven challenging. We have probed the reactivity of specific conformers by using an experimental technique based on their spatial separation in a molecular beam by electrostatic deflection. The separated conformers react with a target of Coulomb-crystallized ions in a trap. In the reaction of Ca(+) with 3-aminophenol, we find a twofold larger rate constant for the cis compared with the trans conformer (differentiated by the O-H bond orientation). This result is explained by conformer-specific differences in the long-range ion-molecule interaction potentials. Our approach demonstrates the possibility of controlling reactivity through selection of conformational states.

Computer modeling of the dynamic properties of the cAMP-dependent protein kinase catalytic subunit

The structural dynamics of the cAMP-dependent protein kinase catalytic subunit were modeled using molecular dynamics computational methods. It was shown that the structure of this protein as well as its complexes with ATP and peptide ligand PKI(5-24) consisted of a large number of rapidly inter-converting conformations which could be grouped into subsets proceeding from their similarity. This cluster analysis revealed that conformations which correspond to the “opened” and “closed” structures of the protein were already present in the free enzyme, and most surprisingly co-existed in enzyme–ATP and enzyme–PKI(5-24) complexes as well as in the ternary complex, which included both of these ligands. The results also demonstrated that the most mobile structure segments of the protein were located in the regions of substrate binding sites and that their dynamics were most significantly affected by the binding of the ATP and peptide ligand.

O–H anharmonic vibrational motions in Cl−⋯(CH3OH)1−2 ionic clusters. Combined IRPD experiments and AIMD simulations

The structures of Cl−–(Methanol)1,2 clusters have been unraveled combining Infrared Predissociation (IR-PD) experiments and DFT-based molecular dynamics simulations (DFT-MD) at 100K. The dynamical IR spectra extracted from DFT-MD provide the initial 600cm−1 large anharmonic red-shift of the O–H stretch from uncomplexed methanol (3682cm−1) to Cl−–(Methanol)1 complex (3085cm−1) as observed in the IR-PD experiment, as well as the subtle supplementary blue- and red-shifts of the O–H stretch in Cl−–(Methanol)2 depending on the structure. The anharmonic vibrational calculations remarkably provide the 100cm−1 O–H blue-shift when the two methanol molecules are simultaneously organized in the anion first hydration shell (conformer 2A), while they provide the 240cm−1 O–H red-shift when the second methanol is in the second hydration shell of Cl− (conformer 2B). RRKM calculations have also shown that 2A/2B conformers interconvert on a nanosecond time-scale at the estimated 100K temperature of the clusters formed by evaporative cooling of argon prior to the IR-PD process.

The structure of poly(γ-glutamic acid)/nanoclay hybrids compatibilized by alkylammonium surfactants

Stoichiometric ionic complexes of bacterial poly(γ-glutamic acid) with the cationic N-octadecyl and N-docosyl-N,N,N-trimethylammonium surfactants were mixed with alkylammonium modified bentonite (Cloisite 30B) to generate hybrid compounds covering a wide range of clay/polymer compositions. The structure of these compounds was examined by XRD and cryoTEM, which indicated extensive penetration of the biopolymer into the nanoclay galleries with widening or even destruction of the layered arrangement of the complex and the clay. Simultaneous SAXS/WAXS analysis in real time showed that hybrids with moderate inorganic contents displayed melting/crystallization upon heating/cooling within the 40–70°C interval with concomitant expansion/contraction of the intersheet spacing. 13C CP-MAS NMR revealed that an anti-to-gauche conformational interconversion of the alkyl chains was involved in the melting/crystallization process. The results provided by energy-based dynamical simulations proved the feasibility of the polyacid and the nanoclay to be homogenized in the hybrid due to the compatibilizing effect of the surfactant.

Ultrafast real-time visualization of active site flexibility of flavoenzyme thymidylate synthase ThyX.

In many bacteria the flavoenzyme thymidylate synthase ThyX produces the DNA nucleotide deoxythymidine monophosphate from dUMP, using methylenetetrahydrofolate as carbon donor and NADPH as hydride donor. Because all three substrates bind in close proximity to the catalytic flavin adenine dinucleotide group, substantial flexibility of the ThyX active site has been hypothesized. Using femtosecond time-resolved fluorescence spectroscopy, we have studied the conformational heterogeneity and the conformational interconversion dynamics in real time in ThyX from the hyperthermophilic bacterium Thermotoga maritima. The dynamics of electron transfer to excited flavin adenine dinucleotide from a neighboring tyrosine residue are used as a sensitive probe of the functional dynamics of the active site. The fluorescence decay spanned a full three orders of magnitude, demonstrating a very wide range of conformations. In particular, at physiological temperatures, multiple angstrom cofactor-residue displacements occur on the picoseconds timescale. These experimental findings are supported by molecular dynamics simulations. Binding of the dUMP substrate abolishes this flexibility and stabilizes the active site in a configuration where dUMP closely interacts with the flavin cofactor and very efficiently quenches fluorescence itself. Our results indicate a dynamic selected-fit mechanism where binding of the first substrate dUMP at high temperature stabilizes the enzyme in a configuration favorable for interaction with the second substrate NADPH, and more generally have important implications for the role of active site flexibility in enzymes interacting with multiple poly-atom substrates and products. Moreover, our data provide the basis for exploring the effect of inhibitor molecules on the active site dynamics of ThyX and other multisubstrate flavoenzymes.

Lanthanides as NMR Probes of Fast Molecular Dynamics at High Magnetic Fields and Temperature Sensors: Conformational Interconversion of Erbium Ethylenediaminetetraacetate Complexes

(1)H NMR measurements are reported for D2O solutions of paramagnetic complex [Er(H2O)(EDTA(4-))](-) (I) for temperature interval 273-319 K. Diamagnetic complex [Lu(H2O)(EDTA(4-))](-) (II) was used as an NMR reference compound. The spectra obtained have been analyzed using a band-shape analysis technique in the framework of dynamic NMR (DNMR) taking into account the temperature dependence of lanthanide-induced shifts. Intramolecular dynamics in I was assigned to the interconversion of Δ-λE-δδδδ and Δ-δE-δδδδ conformers with estimated activation free energy ΔG(‡)(298 K) = 50 ± 4 kJ/mol. The methodology of paramagnetic 4f-element probe applications on the example of Er(3+) for the study of free-energy changes in chemical exchange processes, as well as the advantages of this method in comparison with DNMR studies of diamagnetic substances, is discussed. In accordance with the literature reviewed, the fulfilled experimental study is the first example of intramolecular dynamics determination for erbium complexes. An additional advantage of the investigation is in the approach proposed which extends the range of measurement of the NMR rate constants for paramagnetic 4f-element complexes compared to diamagnetic ones. Coordination compounds investigated represent a new type of thermometric NMR sensors and lanthanide paramagnetic probes for in situ temperature control in solutions.

Nonamethylcyclopentyl Cation Rearrangement Mysteries Solved

The C1 nonamethylcyclopentyl cation minimum undergoes complete methyl scrambling in SbF5 with a 7 kcal/mol barrier. This corresponds to the rate-limiting conformational interconversion of enantiomeric hyperconjomers via a C(s) transition structure (above right). A remarkable, more rapid, second process only exchanges methyls within sets of four and five (blue and red, see above), as has been observed experimentally at low temperatures. The computed ∼2 kcal/mol barrier involves a C(s) [1s,2s] sigmatropic methyl shift transition structure (above left).

A Designed Three-Stranded β-Sheet in an α/β Hybrid Peptide

The incorporation of β-amino acid residues into the antiparallel β-strand segments of a multi-stranded β-sheet peptide is demonstrated for a 19-residue peptide, Boc-LV(β)FV(D)PGL(β)FVVL(D)PGLVL(β)FVV-OMe (BBH19). Two centrally positioned (D)Pro-Gly segments facilitate formation of a stable three-stranded β-sheet, in which β-phenylalanine ((β)Phe) residues occur at facing positions 3, 8 and 17. Structure determination in methanol solution is accomplished by using NMR-derived restraints obtained from NOEs, temperature dependence of amide NH chemical shifts, rates of H/D exchange of amide protons and vicinal coupling constants. The data are consistent with a conformationally well-defined three-stranded β-sheet structure in solution. Cross-strand interactions between (β)Phe3/(β)Phe17 and (β)Phe3/Val15 residues define orientations of these side-chains. The observation of close contact distances between the side-chains on the N- and C-terminal strands of the three-stranded β-sheet provides strong support for the designed structure. Evidence is presented for multiple side-chain conformations from an analysis of NOE data. An unusual observation of the disappearance of the Gly NH resonances upon prolonged storage in methanol is rationalised on the basis of a slow aggregation step, resulting in stacking of three-stranded β-sheet structures, which in turn influences the conformational interconversion between type I' and type II' β-turns at the two (D)Pro-Gly segments. Experimental evidence for these processes is presented. The decapeptide fragment Boc-LV(β)FV(D)PGL(β)FVV-OMe (BBH10), which has been previously characterized as a type I' β-turn nucleated hairpin, is shown to favour a type II' β-turn conformation in solution, supporting the occurrence of conformational interconversion at the turn segments in these hairpin and sheet structures.

Internally versus Externally Solvated Derivatives of Doubly Bridged 1,4-Dilithio-2-butene: Structures and Dynamic Behavior. A “T” Shaped Dimeric Cluster in the Solid State

X-ray crystallographic NMR and calculational modeling studies using B3LYP/6-311G* of selected dilithium derivatives of the 1,3-butadiene dianion including cis-dilithio-1,4-bis(TMS)-2-butene·(TMEDA)(2)2, internally solvated cis-dilithio-1,4-bis[bis(2-methoxyethyl)aminomethyldimethylsilyl]-2-butene 5, and using only modeling, 1,4-dilithio-2-butene·(TMEDA)(2)9 reveal remarkably similar structural and NMR parameters. In the solid, 5 consists of unusual "T" shaped dynamic clusters. In all three bridging lithiums are sited between 1.8 and 1.9 Å normal to the centroids of opposite faces of the near coplanar of the 2-butene component. Typical bond lengths of the latter are 1.458 ± 0.004, 1.385 ± 0.006, and 1.459 ± 0.003 Å, for C1-C2, C2-C3, and C3-C4, respectively. The (13)C chemical shifts lie within the ranges δ 21 ± 0.5, 99 ± 0.7, 99 ± 0.7 and 21 ± 0.5 for C1, C2 and C3 together, and C4, respectively. Dynamic (13)C NMR provides activation parameters for nitrogen inversion in 2 and 5, overall molecular inversion of 5, and conformational interconversion of 2.

Conformational Analysis of δ-Lactones by DFT Calculations: The Parent Compound and its Monomethyl and Selected Dimethyl Derivatives

The static and dynamic stereochemistry of unsubstituted δ-valerolactone, all monomethylated δ-lactones, and all nongeminally dimethylated δ-lactones was explored with the B3LYP functional and def2-TZVPP basis set. A search strategy was employed which allowed the entire conformational space of any (poly-)substituted δ-lactone to be scanned. It allowed the lowest threshold conformational interconversion pathways to be mapped. The latter can be visualized in appealingly intuitive yet unprecedented diagrams. They trace the energy versus a circular abscissa which describes the passage of the molecule through one complete conformation interchange. The respective plot is C(2)-symmetrical for the parent compound, which is achiral, and C(1)-symmetrical for all methylated δ-lactones, which are chiral.

Importance of cholesterol in dopamine transporter function

The conformation and function of the dopamine transporter (DAT) can be affected by manipulating membrane cholesterol, yet there is no agreement as to the impact of cholesterol on the activity of lipid-raft localized DATs compared with non-raft DATs. Given the paucity of information regarding the impact of cholesterol on substrate efflux by the DAT, this study explores its influence on the kinetics of DAT-mediated DA efflux induced by dextroamphetamine, as measured by rotating disk electrode voltammetry (RDEV). Treatment with methyl-β-cyclodextrin (mβCD), which effectively depletes total membrane cholesterol--uniformly affecting cholesterol-DAT interactions in both raft and non-raft membrane domains--reduced both DA uptake and efflux rate. In contrast, disruption of raft-localized DAT by cholesterol chelation with nystatin had no effect, arguing against a vital role for raft-localized DAT in substrate uptake or efflux. Supranormal repletion of cholesterol-depleted cells with the analog desmosterol, a non-raft promoting sterol, was as effective as cholesterol itself in restoring transport rates. Further studies with Zn(2+) and the conformationally biased W84L DAT mutant supported the idea that cholesterol is important for maintaining the outward-facing DAT with normal rates of conformational interconversions. Collectively, these results point to a role for direct cholesterol-DAT interactions in regulating DAT function.

Dynamic behaviour of ubiquitin receptor S5a in free and complex with K48-linked diubiquitin

S5a is a critical component of proteasome and carries ubiquitin recognition function. Previous nuclear magnetic resonance (NMR) experiments have shown that K48-linked diubiquitin binds to S5a through a major and a minor conformational species. Molecular dynamics simulations have been performed on S5a and S5a:K48-linked diubiquitin complex extracted from both species to investigate the essential dynamic behaviour of the receptor S5a in free and complex with the diubiquitin. It shows that structures of S5a as well as S5a:diubiquitin complex are very mobile during the simulations, which enables the receptor to undergo a conformational interconversion from the minor to major species or vice versa, though finally the receptor alone tends to adopt a tight packed structure. The binding of diubiquitin to S5a reduces the structural mobility of the receptor, however, it is still able to cover the different conformations within each species of the complex. Despite the high mobility of the structures, the binding of ubiquitin interacting with motif 2 (UIM2) is always stronger than the UIM1 to the ubiquitin subunit. Accordingly, the current dynamic study provides a vivid view how the receptor in free and complex with diubiquitin sampled the multiple conformations as well as their exchanges revealed in two NMR structures.

Conformational Control of the Electronic Properties of an α-β Terthiophene: Lessons from a Precursor Towards Dendritic Hyperbranched Oligo- and Poly-Thiophenes

Herein we investigate the conformational and electronic properties of the 2,2';3',2"-terthiophene (B3T) unit as the building block of thiophene dendrimeric materials. By means of DFT ground electronic state dihedral energy profiles, we get insight in the flexibility of B3 T as the prominent feature promoting the 3D arrangement. The presence of diverse conformers is explored by Raman and (1)H NMR spectroscopies. A theoretical estimation of the Raman and (1)H NMR spectra over the most energetically accessible conformers is found to be crucial for the appropriate assignment of the major conformer population derived from the experimental spectra. We show that energy barriers for the interconversion of conformers also play a role. Finally, the impact on the optical spectra (absorption and emission) of the α-α and α-β connections is studied and addressed by scanning the properties of the relevant low-lying excited states. These studies highlight the relevance of the architecture of the basic molecular unit to understand charge and exciton behavior in organic semiconductors, particularly for those useful in photovoltaics.

Entropic and Surprisingly Small Intramolecular Polarization Effects in the Mechanism of Cyclophilin A

The precise catalytic mechanism of peptidyl-prolyl cis-trans isomerases (PPIases) has been elusive, despite many experimental and computational studies. The more than 5 orders of magnitude speedup achieved in catalysis by cyclophilin A (CypA) has been attributed to several factors, including substrate desolvation, enzyme dynamics, and preferential binding of the transition state. Here, we explore the conformational space of a substrate analogue of CypA using accelerated molecular dynamics, free in solution and in the active site of CypA, in order to probe its conformational interconversion during catalysis. We show that the undemanding exchange of the free substrate between β- and α-helical regions is lost in the active site of the enzyme, where it is mainly in the β-region. Our results suggest that the loss in conformational entropy at the transition state relative to the cis and trans states in the free substrate is decreased in the complex. This relative change in conformational entropy contributes favorable to the free energy of stabilizing the transition state by CypA. We also show that the ensuing intramolecular polarization, as a result of the loss in pseudo double bond character of the peptide bond at the transition state, contributes only about -1.0 kcal/mol to stabilizing the transition state. This relatively small contribution demonstrates that routinely used fixed charge classical force fields can reasonably describe these types of biological systems. Our results provide further insights into the mechanism of CypA, a member of a poorly understood family of enzymes that are central to many biological processes.

Flexible-meccano: a tool for the generation of explicit ensemble descriptions of intrinsically disordered proteins and their associated experimental observables

Intrinsically disordered proteins (IDPs) represent a significant fraction of the human proteome. The classical structure function paradigm that has successfully underpinned our understanding of molecular biology breaks down when considering proteins that have no stable tertiary structure in their functional form. One convenient approach is to describe the protein in terms of an equilibrium of rapidly inter-converting conformers. Currently, tools to generate such ensemble descriptions are extremely rare, and poorly adapted to the prediction of experimental data. We present flexible-meccano-a highly efficient algorithm that generates ensembles of molecules, on the basis of amino acid-specific conformational potentials and volume exclusion. Conformational sampling depends uniquely on the primary sequence, with the possibility of introducing additional local or long-range conformational propensities at an amino acid-specific resolution. The algorithm can also be used to calculate expected values of experimental parameters measured at atomic or molecular resolution, such as nuclear magnetic resonance (NMR) and small angle scattering, respectively. We envisage that flexible-meccano will be useful for researchers who wish to compare experimental data with those expected from a fully disordered protein, researchers who see experimental evidence of deviation from 'random coil' behaviour in their protein, or researchers who are interested in working with a broad ensemble of conformers representing the flexibility of the IDP of interest. A fully documented multi-platform executable is provided, with examples, at http://www.ibs.fr/science-213/scientific-output/software/flexible-meccano/ martin.blackledge@ibs.fr.

Resonance assignments of diastereotopic CH2 protons in the anomeric side chain of selenoglycosides by means of 2J(Se,H) spin‐spin coupling constants

Unambiguous resonance assignments of diastereotopic CH(2) protons in the anomeric side chain of nine alkyl- and aralkylselenoglycosides have been carried out on the basis of experimental CPMG-HSQMBC measurements and theoretical second order polarization propagator approach (SOPPA) calculations of geminal (77) Se-(1) H spin-spin coupling constants involving diastereotopic pro-R and pro-S protons. Theoretical conformational analyses have been performed at the MP2/6-311G** level. The conformational space of each of the selenoglycosides under study could be adequately described as a mixture of six interconverting conformers with the molar fractions depending on the nature of the side chain substituent at the selenium atom. The good agreement observed between measured and the weighted conformational averaged values of the calculated coupling constants provides a basis for reliable diastereotopic assignments in this type of carbohydrate structures.

Comparison between Cycloalkyl- and n-Alkyl-Substituted Imidazolium-Based Ionic Liquids in Physicochemical Properties and Reorientational Dynamics

We synthesized three series of imidazolium-based ionic liquids (ILs) containing cycloalkyl groups such as cyclopentyl, cyclohexyl, or cycloheptyl groups incorporating bis(trifluoromethanesulfonyl)amide anions and characterized them with respect to physicochemical properties and molecular reorientational dynamics. A comparison of the physicochemical properties revealed that cycloalkyl-substituted imidazolium ILs have higher densities, viscosities, and glass transition temperatures than the respective n-alkyl-substituted imidazolium ILs. Among three series, the cyclopentyl-substituted IL exhibits exceptionally lower viscosity. Observation of correlation times by (13)C NMR spectroscopy revealed that a remarkably lower viscosity for the cyclopentyl-substituted IL and a considerably higher viscosity for the cyclohexyl- and cycloheptyl-substituted ones are closely related to the respective reorientational motion of the cations. The cause of these distinctions is suggested to be attributed to the difference of activation energy for the conformational interconversion of their substituents.

Solution NMR of a 463-Residue Phosphohexomutase: Domain 4 Mobility, Substates, and Phosphoryl Transfer Defect

Phosphomannomutase/phosphoglucomutase contributes to the infectivity of Pseudomonas aeruginosa, retains and reorients its intermediate by 180°, and rotates domain 4 to close the deep catalytic cleft. Nuclear magnetic resonance (NMR) spectra of the backbone of wild-type and S108C-inactivated enzymes were assigned to at least 90%. (13)C secondary chemical shifts report excellent agreement of solution and crystallographic structure over the 14 α-helices, C-capping motifs, and 20 of the 22 β-strands. Major and minor NMR peaks implicate substates affecting 28% of assigned residues. These can be attributed to the phosphorylation state and possibly to conformational interconversions. The S108C substitution of the phosphoryl donor and acceptor slowed transformation of the glucose 1-phosphate substrate by impairing k(cat). Addition of the glucose 1,6-bisphosphate intermediate accelerated this reaction by 2-3 orders of magnitude, somewhat bypassing the defect and apparently relieving substrate inhibition. The S108C mutation perturbs the NMR spectra and electron density map around the catalytic cleft while preserving the secondary structure in solution. Diminished peak heights and faster (15)N relaxation suggest line broadening and millisecond fluctuations within four loops that can contact phosphosugars. (15)N NMR relaxation and peak heights suggest that domain 4 reorients slightly faster in solution than domains 1-3, and with a different principal axis of diffusion. This adds to the crystallographic evidence of domain 4 rotations in the enzyme, which were previously suggested to couple to reorientation of the intermediate, substrate binding, and product release.