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1.
The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled‐coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand‐binding characteristics of the cavities, we originally designed two other coiled‐coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size‐complementary organic compounds. The dissociation constants, Kd, of AM2W were 220 nM for adamantane, 81 μM for 1‐adamantanol, and 294 μM for 1‐adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.  相似文献   

2.
A new NMR experiment is presented for the measurement of micros-ms time scale dynamics of Asn and Gln side chains in proteins. Exchange contributions to the (15)N line widths of side chain residues are determined via a relaxation dispersion experiment in which the effective nitrogen transverse relaxation rate is measured as a function of the number of refocusing pulses in constant-time, variable spacing CPMG intervals. The evolution of magnetization from scalar couplings and dipole-dipole cross-correlations, which has limited studies of exchange in multi-spin systems in the past, does not affect the extraction of accurate exchange parameters from relaxation profiles of NH(2) groups obtained in the present experiment. The utility of the method is demonstrated with an application to a Leu --> Ala cavity mutant of T4 lysozyme, L99A. It is shown that many of the side chain amide groups of Asn and Gln residues in the C-terminal domain of the protein are affected by a chemical exchange process which may be important in facilitating the rapid binding of hydrophobic ligands to the cavity.  相似文献   

3.
We report here an advanced approach for the characterization of the folding pattern of a de novo designed antiparallel coiled coil peptide by high-resolution methods. Incorporation of two fluorescence labels at the C- and N-terminus of the peptide chain as well as modification of two hydrophobic core positions by Phe/[15N,13C]Leu enable the study of the folding characteristics and of distinct amino acid side chain interactions by fluorescence resonance energy transfer (FRET) and NMR spectroscopy. Results of both experiments reveal the antiparallel alignment of the helices and thus prove the design concept. This finding is also supported by molecular dynamics simulations. Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR-MS) in combination with NMR experiments was used for verification of the oligomerization equilibria of the coiled coil peptide.  相似文献   

4.
Systematic model investigations of the molecular interactions of fluorinated amino acids within native protein environments substantially improve our understanding of the unique properties of these building blocks. A rationally designed heterodimeric coiled coil peptide (VPE/VPK) and nine variants containing amino acids with variable fluorine content in either position a16 or d19 within the hydrophobic core were synthesized and used to evaluate the impact of fluorinated amino acid substitutions within different hydrophobic protein microenvironments. The structural and thermodynamic stability of the dimers were examined by applying both experimental (CD spectroscopy, FRET, and analytical ultracentrifugation) and theoretical (MD simulations and MM‐PBSA free energy calculations) methods. The coiled coil environment imposes position‐dependent conformations onto the fluorinated side chains and thus affects their packing and relative orientation towards their native interaction partners. We find evidence that such packing effects exert a significant influence on the contribution of fluorine‐induced polarity to coiled coil folding.  相似文献   

5.
6.
The reaction of a mixture of 1 equiv of PhPH(2) and 2 equiv of PhNHSiMe(2)CH(2)Cl with 4 equiv of Bu(n)Li followed by the addition of THF generates the lithiated ligand precursor [NPN]Li(2).(THF)(2) (where [NPN] = PhP(CH(2)SiMe(2)NPh)(2)). The reaction of [NPN]Li(2).(THF)(2) with TaMe(3)Cl(2) produces [NPN]TaMe(3), which reacts under H(2) to yield the diamagnetic dinuclear Ta(IV) tetrahydride ([NPN]Ta)(2)(mu-H)(4). This hydride reacts with N(2) with the loss of H(2) to produce ([NPN]Ta(mu-H))(2)(mu-eta(1):eta(2)-N(2)), which was characterized both in solution and in the solid state, and contains strongly activated N(2) bound in the unprecedented side-on end-on dinuclear bonding mode. A density functional theory calculation on the model complex [(H(3)P)(H(2)N)(2)Ta(mu-H)](2)(mu-eta(1):eta(2)-N(2)) provides insight into the molecular orbital interactions involved in the side-on end-on bonding mode of dinitrogen. The reaction of ([NPN]Ta(mu-H))(2)(mu-eta(1):eta(2)-N(2)) with propene generates the end-on bound dinitrogen complex ([NPN]Ta(CH(2)CH(2)CH(3)))(2)(mu-eta(1):eta(1)-N(2)), and the reaction of [NPN]Li(2).(THF)(2) with NbCl(3)(DME) generates the end-on bound dinitrogen complex ([NPN]NbCl)(2)(mu-eta(1):eta(1)-N(2)). These two end-on bound dinitrogen complexes provide evidence that the bridging hydride ligands are responsible for the unusual bonding mode of dinitrogen in ([NPN]Ta(mu-H))(2)(mu-eta(1):eta(2)-N(2)). The dinitrogen moiety in the side-on end-on mode is amenable to functionalization; the reaction of ([NPN]Ta(mu-H))(2)(mu-eta(1):eta(2)-N(2)) with PhCH(2)Br results in C-N bond formation to yield [NPN]Ta(mu-eta(1):eta(2)-N(2)CH(2)Ph)(mu-H)(2)TaBr[NPN]. Nitrogen-15 NMR spectral data are provided for all the tantalum-dinitrogen complexes and derivatives described.  相似文献   

7.
The active sites of metalloenzymes are often deeply buried inside a hydrophobic protein sheath, which protects them from undesirable hydrolysis and polymerization reactions, allowing them to achieve their normal functions. In order to mimic the hydrophobic environment of the active sites in bacterial monooxygenases, diiron(II) compounds of the general formula [Fe2([G-3]COO)4(4-RPy)2] were prepared, where [G-3]COO- is a third-generation dendrimer-appended terphenyl carboxylate ligand and 4-RPy is a pyridine derivative. The dendrimer environment provides excellent protection for the diiron center, reducing its reactivity toward dioxygen by about 300-fold compared with analogous complexes of terphenyl carboxylate ([G-1]COO-) ligands. An FeIIFeIII intermediate was characterized by electronic, electron paramagnetic resonance, M?ssbauer, and X-ray absorption spectroscopic analyses following the oxygenation of [Fe2([G-3]COO)4(4-PPy)2], where 4-PPy is 4-pyrrolidinopyridine. The results are consistent with the formation of a superoxo species. This diiron compound, in the presence of dioxygen, can oxidize external substrates.  相似文献   

8.
The kinetics and mechanism of the self-assemblies of alpha- and beta-cyclodextrin (CD) [2]rotaxanes, [(NC)5Fe-[pyRpy.CD]Fe(CN)5]6-, containing pentacyanoferrate(II)-stoppered 4,4'-bis(pyridyl) threads pyRpy (R = -CH = CH-, -N=N-, -CH=N-N=CH-, and -C(CH3)=N-N=C(CH3)-) have been investigated in aqueous solution by using visible and 1H NMR spectroscopy. The rotaxanes may be formed rapidly by the addition of the [Fe(CN)5OH2]3- ion to the CD-included pyRpy thread or slowly by the addition of an excess of CD to the dimeric [(NC)5Fe(pyRpy)Fe(CN)5]6- complex. In the latter method, the mechanism involves a rate-determining dissociation of a [Fe(CN)5]3- center to form the monomeric complex, which subsequently includes the coordinated pyRpy in the CD cavity to yield the semirotaxane, which is rapidly recomplexed by the [Fe(CN)5OH2]3- ion, generating the [2]rotaxane. Rate and activation parameters and CD inclusion stability constants have been determined for the ligand substitution reactions involving the formations and dissociations of the semirotaxanes and rotaxanes. The extents of the decreases in the formation (kf) and dissociation (kd) rate constants upon CD inclusions of the free and coordinated ligands, respectively, are related to the natures of the CD hosts and the R linkage on the pyRpy guests. The semirotaxanes and rotaxanes exhibit significant bathochromic shifts in their visible MLCT transitions compared with the corresponding monomeric and dimeric iron complexes. A correlation between the extent of the decrease in kd and the change in the MLCT energy upon alpha-CD inclusions of [Fe(CN)5L]3-, where L is an aromatic N-heterocyclic 4-Rpy or pyRpy ligand, has been observed.  相似文献   

9.
A relaxation dispersion-based NMR experiment is presented for the measurement and quantitation of micros-ms dynamic processes at methyl side-chain positions in proteins. The experiment measures the exchange contribution to the 13C line widths of methyl groups using a constant-time CPMG scheme. The effects of cross-correlated spin relaxation between dipole-dipole and dipole-CSA interactions as well as the effects of scalar coupling responsible for mixing of magnetization modes during the course of the experiment have been investigated in detail both theoretically and through simulations. It is shown that the complex relaxation properties of the methyl spin system do not complicate extraction of accurate exchange parameters as long as care is taken to ensure that appropriate magnetization modes are interchanged in the middle of the constant-time CPMG period. An application involving the measurement of relaxation dispersion profiles of methionine residues in a Leu99Ala substitution of T4 lysozyme is presented. All of the methionine residues are sensitive to an exchange event with a rate on the order of 1200 s(-1) at 20 degrees C that may be linked to a process in which hydrophobic ligands are able to rapidly bind to the cavity that is present in this mutant.  相似文献   

10.
A number of mono(imidazole)-ligated complexes of perchloro(meso-tetramesitylporphyrinato)iron(III), [Fe(TMP)L]ClO(4), have been prepared, and their spin states have been examined by (1)H NMR, (13)C NMR, and EPR spectroscopy as well as solution magnetic moments. All the complexes examined have shown a quantum mechanical spin admixed state of high and intermediate-spin (S = 5/2 and 3/2) states though the contribution of the S = 3/2 state varies depending on the nature of axial ligands. While the complex with extremely bulky 2-tert-butylimidazole (2-(t)()BuIm) has exhibited an essentially pure S = 5/2 state, the complex with electron-deficient 4,5-dichloroimidazole (4,5-Cl(2)Im) adopts an S = 3/2 state with 30% of the S = 5/2 spin admixture. On the basis of the (1)H and (13)C NMR results, we have concluded that the S = 3/2 contribution at ambient temperature increases according to the following order: 2-(t)BuIm < 2-(1-EtPr)Im < 2-MeIm 相似文献   

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