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1.
Despite recent breakthroughs in the structural characterization of G‐protein‐coupled receptors (GPCRs), there is only sparse data on how GPCRs recognize larger peptide ligands. NMR spectroscopy, molecular modeling, and double‐cycle mutagenesis studies were integrated to obtain a structural model of the peptide hormone neuropeptide Y (NPY) bound to its human G‐protein‐coupled Y2 receptor (Y2R). Solid‐state NMR measurements of specific isotope‐labeled NPY in complex with in vitro folded Y2R reconstituted into phospholipid bicelles provided the bioactive structure of the peptide. Guided by solution NMR experiments, it could be shown that the ligand is tethered to the second extracellular loop by hydrophobic contacts. The C‐terminal α‐helix of NPY, which is formed in a membrane environment in the absence of the receptor, is unwound starting at T32 to provide optimal contacts in a deep binding pocket within the transmembrane bundle of the Y2R.  相似文献   

2.
Aha1 is the only co-chaperone known to strongly stimulate the ATPase activity of Hsp90. Meanwhile, besides the well-studied co-chaperone function, human Aha1 has also been demonstrated to exhibit chaperoning activity against stress-denatured proteins. To provide structural insights for a better understanding of Aha1’s co-chaperone and chaperone-like activities, nuclear magnetic resonance (NMR) techniques were used to reveal the unique structure and internal dynamics features of full-length human Aha1. We then found that, in solution, both the two domains of Aha1 presented distinctive thermal stabilities and dynamics behaviors defined by their primary sequences and three-dimensional structures. The low thermal stability (melting temperature of Aha128–162: 54.45 °C) and the internal dynamics featured with slow motions on the µs-ms time scale were detected for Aha1’s N-terminal domain (Aha1N). The aforementioned experimental results suggest that Aha1N is in an energy-unfavorable state, which would therefore thermostatically favor the interaction of Aha1N with its partner proteins such as Hsp90’s middle domain. Differently from Aha1N, Aha1C (Aha1’s C-terminal domain) exhibited enhanced thermal stability (melting temperature of Aha1204–335: 72.41 °C) and the internal dynamics featured with intermediate motions on the ps-ns time scale. Aha1C’s thermal and structural stabilities make it competent for the stabilization of the exposed hydrophobic groove of dimerized Hsp90’s N-terminal domain. Of note, according to the NMR data and the thermal shift results, although the very N-terminal region (M1-W27) and the C-terminal relaxin-like factor (RLF) motif showed no tight contacts with the remaining parts of human Aha1, they were identified to play important roles in the recognition of intrinsically disordered pathological α-synuclein.  相似文献   

3.
Functional motions of 15N‐labeled proteins can be monitored by solution NMR spin relaxation experiments over a broad range of timescales. These experiments however typically take of the order of several days to a week per protein. Recently, NMR chemical exchange saturation transfer (CEST) experiments have emerged to probe slow millisecond motions complementing R1ρ and CPMG‐type experiments. CEST also simultaneously reports on site‐specific R1 and R2 parameters. It is shown here how CEST‐derived R1 and R2 relaxation parameters can be measured within a few hours at an accuracy comparable to traditional relaxation experiments. Using a “lean” version of the model‐free approach S2 order parameters can be determined that match those from the standard model‐free approach applied to 15N R1, R2, and {1H}‐15N NOE data. The new methodology, which is demonstrated for ubiquitin and arginine kinase (42 kDa), should serve as an effective screening tool of protein dynamics from picosecond‐to‐millisecond timescales.  相似文献   

4.
Neuropeptide Y (NPY) acts via multiple receptor subtypes termed Y1, Y2 and Y5. While Y1 receptor-mediated effects, e.g., in the vasculature, are often sensitive to inhibitors of L-type Ca2+ channels such as nifedipine, little is known about the role of such channels in Y5-mediated effects such as diuresis and natriuresis. Therefore, we explored whether nifedipine affects NPY-induced diuresis and natriuresis. After pre-treatment with nifedipine or vehicle, anesthetized rats received infusions or bolus injections of NPY. Infusion NPY (1 µg/kg/min) increased diuresis and natriuresis, and this was attenuated by intraperitoneal injection of nifedipine (3 µg/kg). Concomitant decreases in heart rate and reductions of renal blood flow were not attenuated by nifedipine. Bolus injections of NPY (0.3, 1, 3, 10 and 30 μg/kg) dose-dependently increased mean arterial pressure and renovascular vascular resistance; only the higher dose of nifedipine (100 μg/kg/min i.v.) moderately inhibited these effects. We conclude that Y5-mediated diuresis and natriuresis are more sensitive to inhibition by nifedipine than Y1-mediated renovascular effects. Whether this reflects a general sensitivity of Y5 receptor-mediated responses or is specific for diuresis and natriuresis remains to be investigated.  相似文献   

5.
Several routes were used to achieve silicon nanocomposites. The first and second one are the melt intercalation of polydimethylsiloxane (PDMS), which is a mechanical blending of the polymer in the molten state with the untreated inorganic filler or intercalated nanoparticles. The last one is an in situ polymerization, which previously requires the intercalation of hexamethylcyclotrisiloxane (D3) followed by a subsequent polymerization step. We used synthetic mineral oxide HTiNbO5 as nanofiller. These systems were investigated by differential scanning calorimetry (DSC) and solid state NMR in order to better understand the relation between the nanocomposites dynamics, and crystallisation. The efficiency of grafting reactions was studied by 29Si CP/MAS NMR. The nature of the interfacial interactions seems to play the major role. Indeed, the nanocomposites 1 and 2 for which only physical interactions are expected do not exhibit any Tg deviation whereas the nanocomposite 3, for which chemical grafting is achieved, increases strongly the Tg. Crystallization is more sensitive to density and strength of interfacial interactions which are maximum for the pristine filler.  相似文献   

6.
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of Mpro, a cysteine protease, have been determined, facilitating structure-based drug design. Mpro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41–Cys145, Mpro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nucleophile Cys145 have been debated in previous studies of SARS-CoV Mpro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 Mpro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of Mpro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α-ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored Nδ (HD) and Nϵ (HE) protonation of His41 and His164, respectively, the α-ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 Mpro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.

The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.  相似文献   

7.
The thermodynamic, kinetic, and structural properties of Ln3+ complexes with the bifunctional DO3A-ACE4− ligand and its amide derivative DO3A-BACE4− (modelling the case where DO3A-ACE4− ligand binds to vector molecules) have been studied in order to confirm the usefulness of the corresponding Gd3+ complexes as relaxation labels of targeted MRI contrast agents. The stability constants of the Mg2+ and Ca2+ complexes of DO3A-ACE4− and DO3A-BACE4− complexes are lower than for DOTA4− and DO3A3−, while the Zn2+ and Cu2+ complexes have similar and higher stability than for DOTA4− and DO3A3− complexes. The stability constants of the Ln(DO3A-BACE) complexes increase from Ce3+ to Gd3+ but remain practically constant for the late Ln3+ ions (represented by Yb3+). The stability constants of the Ln(DO3A-ACE)4− and Ln(DO3A-BACE)4− complexes are several orders of magnitude lower than those of the corresponding DOTA4− and DO3A3− complexes. The formation rate of Eu(DO3A-ACE) is one order of magnitude slower than for Eu(DOTA), due to the presence of the protonated amine group, which destabilizes the protonated intermediate complex. This protonated group causes the Ln(DO3A-ACE) complexes to dissociate several orders of magnitude faster than Ln(DOTA) and its absence in the Ln(DO3A-BACE) complexes results in inertness similar to Ln(DOTA) (as judged by the rate constants of acid assisted dissociation). The 1H NMR spectra of the diamagnetic Y(DO3A-ACE) and Y(DO3A-BACE) reflect the slow dynamics at low temperatures of the intramolecular isomerization process between the SA pair of enantiomers, R-Λ(λλλλ) and S-Δ(δδδδ). The conformation of the Cα-substituted pendant arm is different in the two complexes, where the bulky substituent is further away from the macrocyclic ring in Y(DO3A-BACE) than the amino group in Y(DO3A-ACE) to minimize steric hindrance. The temperature dependence of the spectra reflects slower ring motions than pendant arms rearrangements in both complexes. Although losing some thermodynamic stability relative to Gd(DOTA), Gd(DO3A-BACE) is still quite inert, indicating the usefulness of the bifunctional DO3A-ACE4− in the design of GBCAs and Ln3+-based tags for protein structural NMR analysis.  相似文献   

8.
Nonspherical cages in inclusion compounds can result in non‐uniform motion of guest species in these cages and anisotropic lineshapes in NMR spectra of the guest. Herein, we develop a methodology to calculate lineshape anisotropy of guest species in cages based on molecular dynamics simulations of the inclusion compound. The methodology is valid for guest atoms with spin 1/2 nuclei and does not depend on the temperature and type of inclusion compound or guest species studied. As an example, the nonspherical shape of the structure I (sI) clathrate hydrate large cages leads to preferential alignment of linear CO2 molecules in directions parallel to the two hexagonal faces of the cages. The angular distribution of the CO2 guests in terms of a polar angle θ and azimuth angle ? and small amplitude vibrational motions in the large cage are characterized by molecular dynamics simulations at different temperatures in the stability range of the CO2 sI clathrate. The experimental 13C NMR lineshapes of CO2 guests in the large cages show a reversal of the skew between the low temperature (77 K) and the high temperature (238 K) limits of the stability of the clathrate. We determine the angular distributions of the guests in the cages by classical MD simulations of the sI clathrate and calculate the 13C NMR lineshapes over a range of temperatures. Good agreement between experimental lineshapes and calculated lineshapes is obtained. No assumptions regarding the nature of the guest motions in the cages are required.  相似文献   

9.
The CB1 cannabinoid receptor (CB1R) contains one of the longest N termini among class A G protein-coupled receptors. Mutagenesis studies suggest that the allosteric binding site of cannabidiol (CBD) involves residues from the N terminal domain. In order to study the allosteric binding of CBD to CB1R we modeled the whole N-terminus of this receptor using the replica exchange molecular dynamics with solute tempering (REST2) approach. Then, the obtained structures of CB1R with the N terminus were used for ligand docking. A natural cannabinoid receptor agonist, Δ9-THC, was docked to the orthosteric site and a negative allosteric modulator, CBD, to the allosteric site positioned between extracellular ends of helices TM1 and TM2. The molecular dynamics simulations were then performed for CB1R with ligands: (i) CBD together with THC, and (ii) THC-only. Analyses of the differences in the residue-residue interaction patterns between those two cases allowed us to elucidate the allosteric network responsible for the modulation of the CB1R by CBD. In addition, we identified the changes in the orthosteric binding mode of Δ9-THC, as well as the changes in its binding energy, caused by the CBD allosteric binding. We have also found that the presence of a complete N-terminal domain is essential for a stable binding of CBD in the allosteric site of CB1R as well as for the allosteric-orthosteric coupling mechanism.  相似文献   

10.
Magic‐angle spinning solid‐state NMR spectroscopy has been applied to study the dynamics of CBM3b–Cbh9A from Clostridium thermocellum (ctCBM3b), a cellulose binding module protein. This 146‐residue protein has a nine‐stranded β‐sandwich fold, in which 35 % of the residues are in the β‐sheet and the remainder are composed of loops and turns. Dynamically averaged 1H‐13C dipolar coupling order parameters were extracted in a site‐specific manner by using a pseudo‐three‐dimensional constant‐time recoupled separated‐local‐field experiment (dipolar‐chemical shift correlation experiment; DIPSHIFT). The backbone‐Cα and Cβ order parameters indicate that the majority of the protein, including turns, is rigid despite having a high content of loops; this suggests that restricted motions of the turns stabilize the loops and create a rigid structure. Water molecules, located in the crystalline interface between protein units, induce an increased dynamics of the interface residues thereby lubricating crystal water‐mediated contacts, whereas other crystal contacts remain rigid.  相似文献   

11.
We demonstrate phage-display screening on self-assembled ligands that enables the identification of oligopeptides that selectively bind dynamic supramolecular targets over their unassembled counterparts. The concept is demonstrated through panning of a phage-display oligopeptide library against supramolecular tyrosine-phosphate ligands using 9-fluorenylmethoxycarbonyl-phenylalanine-tyrosine-phosphate (Fmoc-FpY) micellar aggregates as targets. The 14 selected peptides showed no sequence consensus but were enriched in cationic and proline residues. The lead peptide, KVYFSIPWRVPM-NH2 (P7) was found to bind to the Fmoc-FpY ligand exclusively in its self-assembled state with KD = 74 ± 3 μM. Circular dichroism, NMR and molecular dynamics simulations revealed that the peptide interacts with Fmoc-FpY through the KVYF terminus and this binding event disrupts the assembled structure. In absence of the target micellar aggregate, P7 was further found to dynamically alternate between multiple conformations, with a preferred hairpin-like conformation that was shown to contribute to supramolecular ligand binding. Three identified phages presented appreciable binding, and two showed to catalyze the hydrolysis of a model para-nitro phenol phosphate substrate, with P7 demonstrating conformation-dependent activity with a modest kcat/KM = 4 ± 0.3 × 10−4 M−1 s−1.

Phage-display screening on self-assembled tyrosine-phosphate ligands enables the identification of oligopeptides selective to dynamic supramolecular targets, with the lead peptide showing a preferred hairpin-like conformation and catalytic activity.  相似文献   

12.
The dissociative photodetachment dynamics of the oxalate anion, C2O4H + hν → CO2 + HOCO + e, were theoretically studied using the on-the-fly path-integral and ring-polymer molecular dynamics methods, which can account for nuclear quantum effects at the density-functional theory level in order to compare with the recent experimental study using photoelectron–photofragment coincidence spectroscopy. To reduce computational time, the force acting on each bead of ring-polymer was approximately calculated from the first and second derivatives of the potential energy at the centroid position of the nuclei beads. We find that the calculated photoelectron spectrum qualitatively reproduces the experimental spectrum and that nuclear quantum effects are playing a role in determining spectral widths. The calculated coincidence spectrum is found to reasonably reproduce the experimental spectrum, indicating that a relatively large energy is partitioned into the relative kinetic energy between the CO2 and HOCO fragments. This is because photodetachment of the parent anion leads to Franck–Condon transition to the repulsive region of the neutral potential energy surface. We also find that the dissociation dynamics are slightly different between the two isomers of the C2O4H anion with closed- and open-form structures.  相似文献   

13.
The breathing effects of functionalized MIL-53-X (X=H, CH3, NH2, OH, and NO2) induced by the inclusions of water, methanol, acetone, and N,N-dimethylformamide solvents were comprehensively investigated by solid-state NMR spectroscopy. 2D homo-nuclear correlation NMR provided direct experimental evidence for the host-guest interaction between the guest solvents and the MOF frameworks. The variations of the 1H and 13C NMR chemical shifts in functionalized MIL-53 from the narrow pore phase transitions to large pore forms due to solvent inclusions were clearly identified. The influence of functionalized linkers and their host-guest interactions with the confined solvents on the rotational dynamics of the linkers was examined by separated-local-field MAS NMR experiments in conjunction with DFT theoretical calculations. It is found that the linker rotational dynamics of functionalized MIL-53 in narrow pore form is closely related to the computational rotational energy barrier. The BDC-NO2 linker of activated MIL-53-NO2 undergoes relatively faster rotation, whereas the BDC-NH2 and BDC-OH linkers of activated MIL-53-NH2 and MIL-53-OH exhibit relatively slower rotation. The host-guest interactions between confined solvents and MIL-53-NO2, MIL-53-CH3 would significantly induce an increase of the order parameters of unsubstituted carbon and reduce the rotational frequency of linkers. This study provides a spectroscopic approach for the investigation of linker rotation in functionalized MOFs at natural abundance with solvents inclusions.  相似文献   

14.
Following an earlier study of the 1H relaxation and NMR line shapes, we have carried out selective one‐dimensional and two‐dimensional 13C solid‐state NMR studies that yield to detailed interpretation of the dynamics in form I, II, and III polymorphs of isotactic poly‐1‐butene. A specific defect diffusion along the side group is proposed to account for the temperature dependence of the 13C spectra in form I. The backbone of the helix in forms II and III is shown to undergo large angle motions above the glass‐transition temperature. High‐resolution solid‐state 13C two‐dimensional exchange NMR under magic‐angle spinning with cross‐polarization techniques demonstrates the existence of slow rotational jumps of the helices in form III with typical jump rates of about 10 s−1. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 2611–2624, 2000  相似文献   

15.
The1H and2H NMR spectra were taken for mixed monocrystals of light (C4H8SO2) and perdeuterated sulfolanes in the plastic phase. CNDO/2 and INDO calculations were carried out for the sulfolane molecule to give the geometrical parameters, which strongly affect the molecular energy. The other parameters, which characterize the molecular configuration and intramolecular motions, as well as the orientational order matrix were determined by analysis of the1H and2H NMR spectra.Leningrad State University. Translated from Zhurnal Strukturnoi Khimii, Vol. 30, No. 6, pp. 47–53, November–December, 1989.  相似文献   

16.
Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R) relaxation dispersion solid-state nuclear magnetic resonance spectroscopy over a wide range of spin-lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two-state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited-state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited-state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.  相似文献   

17.
Eukaryotic chromatin structure and dynamics play key roles in genomic regulation. In the current study, the secondary structure and intramolecular dynamics of human histone H4 (hH4) in the nucleosome core particle (NCP) and in a nucleosome array are determined by solid‐state NMR (SSNMR). Secondary structure elements are successfully localized in the hH4 in the NCP precipitated with Mg2+. In particular, dynamics on nanosecond to microsecond and microsecond to millisecond timescales are elucidated, revealing diverse internal motions in the hH4 protein. Relatively higher flexibility is observed for residues participating in the regulation of chromatin mobility and DNA accessibility. Furthermore, our study reveals that hH4 in the nucleosome array adopts the same structure and show similar internal dynamics as that in the NCP assembly while exhibiting relatively restricted motions in several regions consisting of residues in the N‐terminus, Loop 1, and the α3 helix region.  相似文献   

18.
Para-hydroxy methylcinnamate is part of the cinnamate family of molecules. Experimental and computational studies have suggested conflicting non-radiative decay routes after photoexcitation to its S1(ππ*) state. One non-radiative decay route involves intersystem crossing mediated by an optically dark singlet state, whilst the other involves direct intersystem crossing to a triplet state. Furthermore, irrespective of the decay mechanism, the lifetime of the initially populated S1(ππ*) state is yet to be accurately measured. In this study, we use time-resolved ion-yield and photoelectron spectroscopies to precisely determine the S1(ππ*) lifetime for the s-cis conformer of para-hydroxy methylcinnamate, combined with time-dependent density functional theory to determine the major non-radiative decay route. We find the S1(ππ*) state lifetime of s-cis para-hydroxy methylcinnamate to be ∼2.5 picoseconds, and the major non-radiative decay route to follow the [1ππ*→1nπ*→3ππ*→S0] pathway. These results also concur with previous photodynamical studies on structurally similar molecules, such as para-coumaric acid and methylcinnamate.  相似文献   

19.
The development of safe and long‐lasting all‐solid‐state batteries with high energy density requires a thorough characterization of ion dynamics in solid electrolytes. Commonly, conductivity spectroscopy is used to study ion transport; much less frequently, however, atomic‐scale methods such as nuclear magnetic resonance (NMR) are employed. Here, we studied long‐range as well as short‐range Li ion dynamics in the glass‐ceramic Li7P3S11. Li+ diffusivity was probed by using a combination of different NMR techniques; the results are compared with those obtained from electrical conductivity measurements. Our NMR relaxometry data clearly reveal a very high Li+ diffusivity, which is reflected in a so‐called diffusion‐induced 6Li NMR spin‐lattice relaxation peak showing up at temperatures as low as 313 K. At this temperature, the mean residence time between two successful Li jumps is in the order of 3×108 s?1, which corresponds to a Li+ ion conductivity in the order of 10?4 to 10?3 S cm?1. Such a value is in perfect agreement with expectations for the crystalline but metastable glass ceramic Li7P3S11. In contrast to conductivity measurements, NMR analysis reveals a range of activation energies with values ranging from 0.17 to 0.26 eV, characterizing Li diffusivity in the bulk. In our case, through‐going Li ion transport, when probed by using macroscopic conductivity spectroscopy, however, seems to be influenced by blocking grain boundaries including, for example, amorphous regions surrounding the Li7P3S11 crystallites. As a result of this, long‐range ion transport as seen by impedance spectroscopy is governed by an activation energy of approximately 0.38 eV. The findings emphasize how surface and grain boundary effects can drastically affect long‐range ionic conduction. If we are to succeed in solid‐state battery technology, such effects have to be brought under control by, for example, sophisticated densification or through the preparation of samples that are free of any amorphous regions that block fast ion transport.  相似文献   

20.
Understanding the complex thermodynamic behavior of confined amphiphilic molecules in biological or mesoporous hosts requires detailed knowledge of the stacking structures. Here, we present detailed solid‐state NMR spectroscopic investigations on 1‐butanol molecules confined in the hydrophilic mesoporous SBA‐15 host. A range of NMR spectroscopic measurements comprising of 1H spin–lattice (T1), spin–spin (T2) relaxation, 13C cross‐polarization (CP), and 1H,1H two‐dimensional nuclear Overhauser enhancement spectroscopy (1H,1H 2D NOESY) with the magic angle spinning (MAS) technique as well as static wide‐line 2H NMR spectra have been used to investigate the dynamics and to observe the stacking structure of confined 1‐butanol in SBA‐15. The results suggest that not only the molecular reorientation but also the exchange motions of confined molecules of 1‐butanol are extremely restricted in the confined space of the SBA‐15 pores. The dynamics of the confined molecules of 1‐butanol imply that the 1H,1H 2D NOESY should be an appropriate technique to observe the stacking structure of confined amphiphilc molecules. This study is the first to observe that a significant part of confined 1‐butanol molecules are orientated as tilted bilayered structures on the surface of the host SBA‐15 pores in a time‐average state by solid‐state NMR spectroscopy with the 1H,1H 2D NOESY technique.  相似文献   

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