Quantitative analysis of conformational exchange contributions to 1H-15N multiple-quantum relaxation using field-dependent measurements. Time scale and structural characterization of exchange in a calmodulin C-terminal domain mutant

Multiple-quantum spin relaxation is a sensitive probe for correlated conformational exchange dynamics on microsecond to millisecond time scales in biomolecules. We measured differential 1H-15N multiple-quantum relaxation rates for the backbone amide groups of the E140Q mutant of the C-terminal domain of calmodulin at three static magnetic field strengths. The differential multiple-quantum relaxation rates range between -88.7 and 92.7 s(-1), and the mean and standard deviation are 7.0 +/- 24 s(-1), at a static magnetic field strength of 14.1 T. Together with values of the 1H and 15N chemical shift anisotropies (CSA) determined separately, the field-dependent data enable separation of the different contributions from dipolar-dipolar, CSA-CSA, and conformational exchange cross-correlated relaxation mechanisms to the differential multiple-quantum relaxation rates. The procedure yields precise quantitative information on the dominant conformational exchange contributions observed in this protein. The field-dependent differences between double- and zero-quantum relaxation rates directly benchmark the rates of conformational exchange, showing that these are fast on the chemical shift time scale for the large majority of residues in the protein. Further analysis of the differential 1H-15N multiple-quantum relaxation rates using previously determined exchange rate constants and populations, obtained from 15N off-resonance rotating-frame relaxation data, enables extraction of the product of the chemical shift differences between the resonance frequencies of the 1H and 15N spins in the exchanging conformations, deltasigma(H)deltasigma(N). Thus, information on the 1H chemical shift differences is obtained, while circumventing complications associated with direct measurements of conformational exchange effects on 1H single-quantum coherences in nondeuterated proteins. The method significantly increases the information content available for structural interpretation of the conformational exchange process, partly because deltasigma(H)deltasigma(N) is a signed quantity, and partly because two chemical shifts are probed simultaneously. The present results support the hypothesis that the exchange in the calcium-loaded state of the E140Q mutant involves conformations similar to those of the wild-type apo (closed) and calcium-loaded (open) states.     

Characterization of specific protein association by 15N CPMG relaxation dispersion NMR: the GB1(A34F) monomer-dimer equilibrium

The Carr-Purcell-Meiboom-Gill (CPMG) transverse relaxation dispersion NMR experiment is a powerful means for detecting and characterizing conformational exchange. This experiment reports the exchange of chemical shifts and therefore can monitor all chemical exchange phenomena, not only intramolecular conformational exchange. Here, we report a CPMG transverse relaxation dispersion study for the monomer-dimer equilibrium of the GB1 point mutant, Ala-34-Phe (GB1(A34F)). This variant exists predominantly as a side-by-side dimer at high concentration (>1 mM). We demonstrate that the dispersion experiment is exceptionally valuable for studying association equilibria since it is extremely sensitive to the minor population in the equilibrium. Twenty-eight individual amide sites in the GB1(A34F) dimer protein were monitored via a 2D (15)N-(1)H HSQC spectroscopy, and all relaxation-derived data are consistent with predominantly an exchange process between dimer and monomer species.     

Two-dimensional Fourier-transform infrared correlation spectroscopy study of the high-pressure tuning of proteins

2D FTIR gives new information about the pressure effect on the structure and dynamics of macromolecular systems. Application of this analysis to proteins can unravel the relation of conformational changes and H/D exchange processes. For lipoxygenase, a pressure of 6.5 kbar induces irreversible conformational changes resulting in an increased exposure of interior parts of the protein to the solvent. At the transition pressure the spectral changes indicate a correlation between conformational changes and H/D exchange. Below and above this pressure, the effects of H/D exchange on the spectral changes are predominant.     

核磁共振研究二茂铁硒铂配合物构象交换热焓

The intramolecular conformational exchange thermodynamics of cis-PtCl[1,1'bis(undecenylseleno)ferrocene](B11SeFcPt) in CDCl3 solution was studied by one dimensional proton NMR． The chemical equilibrium constants were obtained directly from the integration of the 1H NMR spectra and the enthalpy as a function of temperature for the conformational exchange of B11SeFcPt was calculated from the equilibrium constant.     

Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy

We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond time scales can be detected and quantified by solid-state NMR spectroscopy. We show two independent approaches that measure the effect of conformational exchange on transverse relaxation parameters, namely Carr-Purcell-Meiboom-Gill relaxation-dispersion experiments and measurement of differential multiple-quantum coherence decay. Long coherence lifetimes, as required for these experiments, are achieved by the use of highly deuterated samples and fast magic-angle spinning. The usefulness of the approaches is demonstrated by application to microcrystalline ubiquitin. We detect a conformational exchange process in a region of the protein for which dynamics have also been observed in solution. Interestingly, quantitative analysis of the data reveals that the exchange process is more than 1 order of magnitude slower than in solution, and this points to the impact of the crystalline environment on free energy barriers.     

The anisotropic effect of functional groups in 1H NMR spectra is the molecular response property of spatial nucleus independent chemical shifts (NICS)--conformational equilibria of exo/endo tetrahydrodicyclopentadiene derivatives

The inversion of the flexible five-membered ring in tetrahydrodicyclopentadiene (TH-DCPD) derivatives remains fast on the NMR timescale even at 103 K. Since the intramolecular exchange process could not be sufficiently slowed for spectroscopic evaluation, the conformational equilibrium is thus inaccessible by dynamic NMR. Fortunately, the spatial magnetic properties of the aryl and carbonyl groups attached to the DCPD skeleton can be employed in order to evaluate the conformational state of the system. In this context, the anisotropic effects of the functional groups in the (1)H NMR spectra prove to be the molecular response property of spatial nucleus independent chemical shifts (NICS).     

Far‐ and Mid‐Infrared Spectroscopic Analysis of the Substrate‐Induced Structural Dynamics of Respiratory Complex I

The catalytic activity of the respiratory NADH:ubiquinone oxidoreductase (complex I) is based on conformational reorganizations. Herein we probe the effect of substrates on the conformational flexibility of complex I by means of ¹H/²H exchange kinetics at the level of the amide proton in the mid‐infrared spectral range (1700–1500 cm^?1). Slow, medium, and fast exchanging domains are distinguished that reveal different accessibilities to the solvent. Whereas amide hydrogens undergo rapid exchange with the solvent in an open structure, hydrogens experience much slower exchange when they are involved in H‐bonded structures or when they are sterically inaccessible for the solvent. The results indicate a structure that is more open in the presence of both NADH and quinon. Complementary information on the overall internal hydrogen bonding of the protein was probed in the far infrared (300–30 cm^?1), a spectral range that includes a continuum mode of the hydrogen bonding signature.     

Dynamic NMR study of dinitrophenyl derivatives of seven‐membered cyclic ketals of pyridoxine

Two pyridoxine derivatives containing a dinitrophenyl moiety were investigated by ¹H NMR spectroscopy. Conformational dynamics in solution were studied for each compound using dynamic NMR experiments. It was shown that both compounds studied are involved into two conformational exchange processes. The first process is a transformation of the seven‐membered cycle conformation between the enantiomeric P‐twist and M‐twist forms, and the second is a rotation of the dinitrophenyl fragment of the molecules around the C–O bond. Energy barriers of both conformational transitions were determined. Copyright © 2015 John Wiley & Sons, Ltd.     

Localized changes in the structural stability of myoglobin upon adsorption onto silica particles,as studied with hydrogen/deuterium exchange mass spectrometry

A new method is presented for monitoring the conformational stability of various parts of a protein that is physically adsorbed onto nanometer-sized silica particles. The method employs hydrogen/deuterium (H/D) exchange of amide hydrogens, a process that is extremely sensitive to structural features of proteins. The resulting mass increase is analyzed with Fourier transform ion cyclotron resonance (FTICR) mass spectrometry. Higher structural specificity is obtained by enzymatically cleaving the adsorbed proteins prior to mass spectrometric analysis. The mass increases of four peptic fragments of myoglobin are followed as a function of the H/D exchange time. The four peptic fragments cover 90% of the myoglobin structure. Two of the peptic fragments, located in the middle of the myoglobin sequence and close to the heme group, do not show any adsorption-induced changes in their structural stability, whereas the more stable C- and N-terminal fragments are destabilized. Interestingly, for the N-terminal fragment, comprising residues 1-29, two distinct and equally large conformational populations are observed. One of these populations has a stability similar to that in solution (-23 kJ/mol), whereas the other population is highly destabilized upon adsorption (-11 kJ/mol).     

The mechanism responsible for extraordinary Cs ion selectivity in crystalline silicotitanate

Combining information from time-resolved X-ray and neutron scattering with theoretical calculations has revealed the elegant mechanism whereby hydrogen crystalline silicotitanate (H-CST; H2Ti2SiO7 x 1.5 H2O) achieves its remarkable ion-exchange selectivity for cesium. Rather than a simple ion-for-ion displacement reaction into favorable sites, which has been suggested by static structural studies of ion-exchanged variants of CST, Cs(+) exchange proceeds via a two-step process mediated by conformational changes in the framework. Similar to the case of ion channels in proteins, occupancy of the most favorable site does not occur until the first lever, cooperative repulsive interactions between water and the initial Cs-exchange site, repels a hydrogen lever on the silicotitanate framework. Here we show that these interactions induce a subtle conformational rearrangement in CST that unlocks the preferred Cs site and increases the overall capacity and selectivity for ion exchange.     

Gas phase RNA and DNA ions 2. Conformational dependence of the gas-phase H/D exchange of nucleotide-5′-monophosphates

The conformational dependence of the gas-phase hydrogen/deuterium (H/D) exchange of nucleotide-5-monophosphate anions with the H/D exchange reagent D2S is reported here. The electrospray-generated [M-H]- anions of adenosine-5'-monophosphate, adenosine-5'-carboxylic acid, ribitol-5-phosphate, and 2-deoxy-ribitol-5-phosphate were reacted with D2S in the gas phase. Their reactivity (adenosine-5'-monophosphate exchanged 2 of 5 labile hydrogens, adenosine-5'-carboxylic acid exchanged 1 of 4, ribitol-5-phosphate exchanged 2 of 3, and 2-deoxy-ribitol-5-phosphate exchanged 1 of 2) suggests that the hydroxyl group in the 2 position of the ribose sugar and the amino hydrogen on the nucleobase do not exchange readily with D2S. Semiempirical molecular orbital calculations suggest that the labile hydrogens in these positions are thermodynamically facile to exchange but as a conformation inaccessible to the presumed phosphate anion, consistent with a mechanism in which the phosphate anion complexes with the exchange reagent and assists H/D exchange at a neighboring site.     

Slow anion exchange,conformational equilibria,and fluorescent sensing in venus flytrap aminopyridinium-based anion hosts

The synthesis, anion binding, and conformational properties of a series of 3-aminopyridinium-based, tripodal, tricationic hosts for anions are described. Slow anion and conformational exchange on the (1)H NMR time scale at low temperature, coupled with NMR titration, results in a high level of understanding of the anion-binding properties of the compounds, particularly with respect to significant conformational change resulting from induced fit complexation. Peak selectivity for halides, particularly Cl(-), is observed. The approach has been extended to dipodal and tripodal podands based on 3-aminopyridinium "arms" containing photoactive anthracenyl moieties. The 1,3,5-tripodal host shows a remarkable selectivity for acetate over other anions, in contrast to the analogous unsubstituted tris(3-aminopyridinium) analogue, despite the fact that low-temperature (1)H NMR experiments reveal a total of four acetate-binding conformations. Photodimerization of anthracene units results in the formation of potential fluorescent anion sensors.     

Conformational changes in beta-endorphin as studied by electrospray ionization mass spectrometry.

Because of a wide range of physiological functions, the structure of beta-endorphin (BE) is of great interest. In this study, conformational changes in BE induced by methanol are explored with electrospray ionization-mass spectrometry (ESI-MS). Differences in the charge-state distribution (CSD) and the extent of hydrogen/deuterium (H/D) exchange were used to monitor the conformational changes. The latter experiments were conducted via time-resolved ESI-MS in a continuous-flow apparatus. Both these techniques demonstrate that BE exists in a random coil open structure in aqueous media, but it acquires a more compact conformation with increased concentration of methanol. The H/D exchange experiments reveal that BE forms 61% alpha-helix in mixed solvents.     

Slow exchange in the chromophore of a green fluorescent protein variant

Green fluorescent protein and its mutants have become valuable tools in molecular biology. They also provide systems rich in photophysical and photochemical phenomena of which an understanding is important for the development of new and optimized variants of GFP. Surprisingly, not a single NMR study has been reported on GFPs until now, possibly because of their high tendency to aggregate. Here, we report the (19)F nuclear magnetic resonance (NMR) studies on mutants of the green fluorescent protein (GFP) and cyan fluorescent protein (CFP) labeled with fluorinated tryptophans that enabled the detection of slow molecular motions in these proteins. The concerted use of dynamic NMR and (19)F relaxation measurements, supported by temperature, concentration- and folding-dependent experiments provides direct evidence for the existence of a slow exchange process between two different conformational states of CFP. (19)F NMR relaxation and line shape analysis indicate that the time scale of exchange between these states is in the range of 1.2-1.4 ms. Thermodynamic analysis revealed a difference in enthalpy (Delta)H(0) = (18.2 +/- 3.8) kJ/mol and entropy T(Delta)S(0) = (19.6 +/- 1.2) kJ/mol at T = 303 K for the two states involved in the exchange process, indicating an entropy-enthalpy compensation. The free energy of activation was estimated to be approximately 60 kJ/mol. Exchange between two conformations, either of the chromophore itself or more likely of the closely related histidine 148, is suggested to be the structural process underlying the conformational mobility of GFPs. The possibility to generate a series of single-atom exchanges ("atomic mutations") like H --> F in this study offers a useful approach for characterizing and quantifying dynamic processes in proteins by NMR.     

Dynamics of proton exchange in a model phosphonic acid‐functionalized polymer

The dynamics and mechanism of proton exchange in phosphonic acid‐functionalized polymers were studied using poly(vinyl‐phosphonic acid) (PVPA) as a model system along with quantum chemical calculations and Born–Oppenheimer molecular dynamics (BOMD) simulations at the B3LYP/TZVP level as model calculations. This theoretical study began with searching for the smallest, most active polymer segments and their intermediate conformations which could be involved in the local proton‐exchange process. The B3LYP/TZVP results confirmed that a low local dielectric environment and excess proton conditions are required to generate the intermediate conformations, and the shapes of the potential energy curves of the proton exchange between the two phosphonic acid functional groups are sensitive to the local conformational changes. In contrast, a high local dielectric environment increases the energy barriers, thereby preventing the proton from returning to the original functional group. Based on the static results, a mechanism for the proton exchange between the two functional groups involving fluctuations in the local dielectric environment and a local conformational change was proposed. The BOMD results confirmed the proposed mechanism by showing that the activation energies for the proton exchange in the hydrogen bond between two immobilized phosphonic acid moieties, obtained from the exponential relaxation behaviors of the envelopes of the velocity autocorrelation functions and the ¹H Nuclear Magnetic Resonance (NMR) line‐shape analyses, are too low to be the rate‐determining process. Instead, coupled librational motion in the backbone which leads to the interconversion between the two intermediate conformations possesses higher activation energy, and therefore represents one of the most important rate‐determining processes. These findings suggested that the rate of the proton exchange in the model phosphonic acid‐functionalized polymer is determined by the polymer mobility which, in this case, is the large‐amplitude librational motion of the vinyl backbone. © 2015 Wiley Periodicals, Inc.     

Chemical shift assignment and conformational analysis of monoalkylated acylguanidines

Monoalkylated acylguanidines are important functional groups in many biologically active compounds and additionally applied in coordination chemistry. Yet a straightforward assignment of the individual NH chemical shifts and the acylguanidine conformations is still missing. Therefore, in this study, NMR spectroscopic approaches for the chemical and especially the conformational assignment of protonated monoalkylated acylguanidines are presented. While NOESY and ³J_{H, H} scalar couplings cannot be applied successfully for the assignment of acylguanidines, ⁴J_{H, H} scalar couplings in ¹H,¹H COSY spectra allow for an unambiguous chemical shift and conformational assignment. It is shown that these ⁴J_{H, H} long‐range couplings between individual acylguanidinium NH resonances are observed solely across all‐trans (w) pathways. Already one cis orientation in the magnetisation transfer pathway leads to signal intensities below the actual detection limit and significantly lower than cross‐peaks from ²J_{NH, NH} couplings or chemical exchange. However, it should be noted that also in the case of conformational exchange being fast on the NMR time scale, averaged cross‐peaks from all‐trans ⁴J_{H, H} scalar couplings are detected, which may lead at first glance to an incomplete or even wrong conformational analysis. Copyright © 2010 John Wiley & Sons, Ltd.     

Diazobicycloalkanes with bridgehead nitrogen atoms in nodal positions. 22. Conformational analysis of benzodiazabicycloalkenes. Iterative evaluation of spectral and thermodynamic parameters

¹H and ¹³C NMR were used to investigate the conformational equilibrium of benzo[f]-1,5-diazabicyclo[3,2.2]nonene and benzo[g]-1,6-diazabicyclo[4.2.2]decene in solution at temperatures from 20 to–110C. Benzo[f]-1,5-diazabicyclo[3.2.2]nonene in this temperature interval undergoes rapid conformational exchange, while the conformation ratio changes from 7327 to 5545. The thermodynamic characteristics of this equilibrium were obtained and some NMR parameters of the individual conformers were estimated. For benzo[g]-1,6-diazabicyclo-[4.2.2]decene it was possible to attain conditions of slow exchange between two conformations whose proportion in the temperature interval studied were almost identical. The kinetics of conformational exchange were investigated and the energy of activation of the process was found to equal 42.3 kJ/mole.For Communication 21 see [1].Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1402–1407, October, 1991.     

Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics

Histone tails are highly flexible N- or C-terminal protrusions of histone proteins which facilitate the compaction of DNA into dense superstructures known as chromatin. On a molecular scale histone tails are polyelectrolytes with high degree of conformational disorder which allows them to function as biomolecular "switches", regulating various genetic processes. Unfortunately, their intrinsically disordered nature creates obstacles for comprehensive experimental investigation of both the structural and dynamical aspects of histone tails, because of which their conformational behaviors are still not well understood. In this work we have carried out ～3 microsecond long all atom replica exchange molecular dynamics (REMD) simulations for each of four histone tails, H4, H3, H2B, and H2A, and probed their intrinsic conformational preferences. Our subsequent free energy landscape analysis demonstrated that most tails are not fully disordered, but show distinct conformational organization, containing specific flickering secondary structural elements. In particular, H4 forms β-hairpins, H3 and H2B adopt α-helical elements, while H2A is fully disordered. We rationalized observed patterns of conformational dynamics of various histone tails using ideas from physics of polyelectrolytes and disordered systems. We also discovered an intriguing re-entrant contraction-expansion of the tails upon heating, which is caused by subtle interplay between ionic screening and chain entropy.     

Deciphering the Conformational Choreography of Zinc Coordination Complexes with Standard and Novel Proton NMR Techniques Combined with DFT Methods

The presence of water has been shown to deeply impact the stability and geometry of Zn complexes in solution. Evidence for tetra‐ and penta‐coordinated species in a pyridylmethylamine–Zn^II model complex is presented. Novel ¹H NMR tools such as T₁‐filtered selective exchange spectroscopy and pure shifted gradient‐encoded selective refocusing as well as classical 2D (¹H–¹H) exchange spectroscopy, diffusion‐ordered spectroscopy and T₁(¹H) measurements, in combination with density functional theory methods allow the full conformational dynamics of a pyridylmethylamine–Zn^II complex to be revealed. Four conformers and two families of complexes depending on the hydration states are elucidated.     

Improving hydrogen/deuterium exchange mass spectrometry by reduction of the back-exchange effect

The measurement of deuterium incorporation kinetics using hydrogen/deuterium (H/D) exchange experiments is a valuable tool for the investigation of the conformational dynamics of biomolecules in solution. Experiments consist of two parts when using H/D exchange mass spectrometry to analyse the deuterium incorporation. After deuterium incorporation at high D(2)O concentration, it is necessary to decrease the D(2)O concentration before the mass analysis to avoid deuterium incorporation under artificial conditions of mass spectrometric preparation and measurement. A low D(2)O concentration, however, leads to back-exchange of incorporated deuterons during mass analysis. This back-exchange is one of the major problems in H/D exchange mass spectrometry and must be reduced as much as possible. In the past, techniques using electrospray ionization (ESI) had the lowest back-exchange values possible in H/D exchange mass spectrometry. Methods for the measurement of H/D exchange by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) that have been developed since 1998 have some significant advantages, but they could not achieve the back-exchange minima of ESI methods. Here, we present a protocol for H/D exchange MALDI-MS which allows for greater minimization of back-exchange compared with H/D exchange ESI-MS under similar conditions.