共查询到20条相似文献,搜索用时 46 毫秒
1.
tRNA molecules contain 93 chemically unique nucleotide base modifications that expand the chemical and biophysical diversity of RNA and contribute to the overall fitness of the cell. Nucleotide modifications of tRNA confer fidelity and efficiency to translation and are important in tRNA-dependent RNA-mediated regulatory processes. The three-dimensional structure of the anticodon is crucial to tRNA-mRNA specificity, and the diverse modifications of nucleotide bases in the anticodon region modulate this specificity. We have determined the solution structures and thermodynamic properties of Bacillus subtilis tRNATyr anticodon arms containing the natural base modifications N6-dimethylallyl adenine (i6A37) and pseudouridine (ψ39). UV melting and differential scanning calorimetry indicate that the modifications stabilize the stem and may enhance base stacking in the loop. The i6A37 modification disrupts the hydrogen bond network of the unmodified anticodon loop including a C32-A38+ base pair and an A37-U33 base-base interaction. Although the i6A37 modification increases the dynamic nature of the loop nucleotides, metal ion coordination reestablishes conformational homogeneity. Interestingly, the i6A37 modification and Mg2+ are sufficient to promote the U-turn fold of the anticodon loop of Escherichia coli tRNAPhe, but these elements do not result in this signature feature of the anticodon loop in tRNATyr. 相似文献
2.
Observation of allosteric transition in hemoglobin 总被引:6,自引:0,他引:6
Two conclusions have been drawn from NMR studies of mixed state hemoglobins. First the α and β subunits in hemoglobin are not equivalent in their conformational properties. Second the mixed state hemoglobin (αIIICN βII)2 can take two different quaternary structures without changing the degree of ligation. One of the two structures is similar to that of deoxyhemoglobin and the other to that of oxyhemoglobin. 相似文献
3.
Andrea Pavlou Hideaki Yoshimura Shigetoshi Aono Eftychia Pinakoulaki 《Biophysical journal》2018,114(3):584-591
The heme-based aerotactic transducer (HemAT) is an oxygen-sensor protein consisting of a sensor and a signaling domain in the N- and C-terminal regions, respectively. Time-resolved step-scan FTIR spectroscopy was employed to characterize protein intermediate states obtained by photolysis of the carbon monoxide complexes of sensor-domain, full-length HemAT, and the Y70F (B-helix), L92A (E-helix), T95A (E-helix), and Y133F (G-helix) HemAT mutants. We assign the spectral components to discrete substructures, which originate from a helical structure that is solvated (1638 cm?1) and a native helix that is protected from solvation by interhelix tertiary interactions (1654 cm?1). The full-length protein is characterized by an additional amide I absorbance at 1661 cm?1, which is attributed to disordered structure suggesting that further protein conformational changes occur in the presence of the signaling domain in the full-length protein. The kinetics monitored within the amide I absorbance of the polypeptide backbone in the sensor domain exhibit two distinct relaxation phases (t1 = 24 and t2 = 694 μs), whereas that of the full-length protein exhibits monophasic behavior for all substructures in a time range of t = 1253–2090 μs. These observations can be instrumental in monitoring helix motion and the role of specific mutants in controlling the dynamics in the communication pathway from the sensor to the signaling domain. The kinetics observed for the amide I relaxation for the full-length protein indicate that the discrete substructures within full-length HemAT, unlike those of the sensor domain, relax independently. 相似文献
4.
Michael G. Duncan Michael D. Williams Bruce E. Bowler 《Protein science : a publication of the Protein Society》2009,18(6):1155-1164
Evolutionary conservation of substructure architecture between yeast iso-1-cytochrome c and the well-characterized horse cytochrome c is studied with limited proteolysis, the alkaline conformational transition and global unfolding with guanidine-HCl. Mass spectral analysis of limited proteolysis cleavage products for iso-1-cytochrome c show that its least stable substructure is the same as horse cytochrome c. The limited proteolysis data yield a free energy of 3.8 ± 0.4 kcal mol−1 to unfold the least stable substructure compared with 5.05 ± 0.30 kcal mol−1 for global unfolding of iso-1-cytochrome c. Thus, substructure stabilities of iso-1-cytochrome c span only ∼1.2 kcal mol−1 compared with ∼8 kcal mol−1 for horse cytochrome c. Consistent with the less cooperative folding thus expected for the horse protein, the guanidine-HCl m-values are ∼3 kcal mol−1M−1 versus ∼4.5 kcal mol−1M−1 for horse versus yeast cytochrome c. The tight free energy spacing of the yeast cytochrome c substructures suggests that its folding has more branch points than for horse cytochrome c. Studies on a variant of iso-1-cytochrome c with an H26N mutation indicate that the least and most stable substructures unfold sequentially and the two least stable substructures unfold independently as for horse cytochrome c. Thus, important aspects of the substructure architecture of horse cytochrome c, albeit compressed energetically, are preserved evolutionally in yeast iso-1-cytochrome c. 相似文献
5.
Elvy Like Ginting Chihiro Maeganeku Hiroyuki Motoshima Keiichi Watanabe 《The protein journal》2014,33(1):11-17
Mn2+ ions influence the activity, temperature dependence, and thermostability of the psychrophilic Shewanella-PPase (Sh-PPase), and are required to function in cold environments. The functional characteristics of Sh-PPase on activation with Mn2+ ions are possibly related to conformational changes in the molecule. In this study, conformational changes of Sh-PPase on activation with Mn2+ ions were analyzed in solution by fluorescence spectroscopy analysis of intrinsic tryptophan residues, 1-anilino-8-naphthalene sulfonate fluorescence, and circular dichroism spectroscopy. For Sh-PPase, Mn2+ ions did not affect the flexibility of the tryptophan residues and secondary structure of the enzyme. However, the microenvironment of the tryptophan residues and surface area of Sh-PPase were more hydrophilic on activation with Mn2+ ions. These results indicate that activation with Mn2+ ions causes conformational changes around the aromatic amino acid residues and affects the hydrophobicity of the enzyme surface, which results in conformational changes. Substrate-induced conformational changes reflect that metal-free Sh-PPase in solution indicated an open structure and will be a close structure when binding substrate. In combination of our spectroscopic analyses on Sh-PPase, it can be concluded that activation with Mn2+ ions changes some conformation of Sh-PPase molecule in solution. 相似文献
6.
Thomas Biedenbnder Vanessa de
Jesus Martina Schmidt-Dengler Mark Helm Bjrn Corzilius Boris Fürtig 《Nucleic acids research》2022,50(4):2334
A plethora of modified nucleotides extends the chemical and conformational space for natural occurring RNAs. tRNAs constitute the class of RNAs with the highest modification rate. The extensive modification modulates their overall stability, the fidelity and efficiency of translation. However, the impact of nucleotide modifications on the local structural dynamics is not well characterized. Here we show that the incorporation of the modified nucleotides in tRNAfMet from Escherichia coli leads to an increase in the local conformational dynamics, ultimately resulting in the stabilization of the overall tertiary structure. Through analysis of the local dynamics by NMR spectroscopic methods we find that, although the overall thermal stability of the tRNA is higher for the modified molecule, the conformational fluctuations on the local level are increased in comparison to an unmodified tRNA. In consequence, the melting of individual base pairs in the unmodified tRNA is determined by high entropic penalties compared to the modified. Further, we find that the modifications lead to a stabilization of long-range interactions harmonizing the stability of the tRNA’s secondary and tertiary structure. Our results demonstrate that the increase in chemical space through introduction of modifications enables the population of otherwise inaccessible conformational substates. 相似文献
7.
Preconditioning is defined as a range of stimuli that allow cells to withstand subsequent anaerobic and other deleterious conditions. While cell protection under preconditioning is well established, this paper investigates the influence of neuroprotective preconditioning drugs, 4-aminopyridine and bicuculline (4-AP/bic), on synaptic communication across a broad network of in vitro rat cortical neurons. Using a permutation test, we evaluated cross-correlations of extracellular spiking activity across all pairs of recording electrodes on a 64-channel multielectrode array. The resulting functional connectivity maps were analyzed in terms of their graph-theoretic properties. A small-world effect was found, characterized by a functional network with high clustering coefficient and short average path length. Twenty-four hours after exposure to 4-AP/bic, small-world properties were comparable to control cultures that were not treated with the drug. Four hours following drug washout, however, the density of functional connections increased, while path length decreased and clustering coefficient increased. These alterations in functional connectivity were maintained at four days post-washout, suggesting that 4-AP/bic preconditioning leads to long-term effects on functional networks of cortical neurons. Because of their influence on communication efficiency in neuronal networks, alterations in small-world properties hold implications for information processing in brain systems. The observed relationship between density, path length, and clustering coefficient is captured by a phenomenological model where connections are added randomly within a spatially-embedded network. Taken together, results provide information regarding functional consequences of drug therapies that are overlooked in traditional viability studies and present the first investigation of functional networks under neuroprotective preconditioning. 相似文献
8.
《Journal of steroid biochemistry》1976,7(6-7):497-500
The13C-,1H- and19F magnetic resonance spectra of cortisol and of some of its 9α-fluorinated derivatives are analyzed and compared with the results obtained by X-ray diffraction.No major conformational differences are detected after 9α-fluorination of cortisol and of prednisolone. However, modifications of the electronic structures occur in the moiety of the molecule centred on the 9α-F.These modifications may be taken as responsible for the increase in the mineralocorticoid activity of those molecules. On the contrary the decrease in biological activity of the 9α-fluorinated derivatives methylated or hydroxylated at C16 is very likely dependent upon conformational and electronic changes in the D-ring and in the side chain. 相似文献
9.
The formation of fibrillar amyloid is most often associated with protein conformational disorders such as prion diseases, Alzheimer disease and Huntington disease. Interestingly, however, an increasing number of studies suggest that amyloid structures can sometimes play a functional role in normal biology. Several proteins form self-propagating amyloids called prions in the budding yeast Saccharomyces cerevisiae. These unique elements operate by creating a reversible, epigenetic change in phenotype. While the function of the non-prion conformation of the Rnq1 protein is unclear, the prion form, [RNQ+], acts to facilitate the de novo formation of other prions to influence cellular phenotypes. The [RNQ+] prion itself does not adversely affect the growth of yeast, but the overexpression of Rnq1p can form toxic aggregated structures that are not necessarily prions. The [RNQ+] prion is also involved in dictating the aggregation and toxicity of polyglutamine proteins ectopically expressed in yeast. Thus, the [RNQ+] prion provides a tractable model that has the potential to reveal significant insight into the factors that dictate how amyloid structures are initiated and propagated in both physiological and pathological contexts.Key words: [RNQ+], [PSI+], prion, polyglutamine, functional amyloid, toxic amyloid, chaperones, epigenetic 相似文献
10.
11.
R. Bryn Fenwick David Oyen Henry van den Bedem H. Jane Dyson Peter E. Wright 《Biophysical journal》2021,120(2):296-305
NMR relaxation dispersion measurements report on conformational changes occurring on the μs-ms timescale. Chemical shift information derived from relaxation dispersion can be used to generate structural models of weakly populated alternative conformational states. Current methods to obtain such models rely on determining the signs of chemical shift changes between the conformational states, which are difficult to obtain in many situations. Here, we use a “sample and select” method to generate relevant structural models of alternative conformations of the C-terminal-associated region of Escherichia coli dihydrofolate reductase (DHFR), using only unsigned chemical shift changes for backbone amides and carbonyls (1H, 15N, and 13C′). We find that CS-Rosetta sampling with unsigned chemical shift changes generates a diversity of structures that are sufficient to characterize a minor conformational state of the C-terminal region of DHFR. The excited state differs from the ground state by a change in secondary structure, consistent with previous predictions from chemical shift hypersurfaces and validated by the x-ray structure of a partially humanized mutant of E. coli DHFR (N23PP/G51PEKN). The results demonstrate that the combination of fragment modeling with sparse chemical shift data can determine the structure of an alternative conformation of DHFR sampled on the μs-ms timescale. Such methods will be useful for characterizing alternative states, which can potentially be used for in silico drug screening, as well as contributing to understanding the role of minor states in biology and molecular evolution. 相似文献
12.
The incorporation of [35S]methionine into polypeptides during progesterone-induced meiotic maturation of Xenopus laevis oocytes was studied by two-dimensional polyacrylamide gel electrophoresis. Five modifications were consistently observed: two polypeptides of an approximate molecular weight of 150K daltons and pI 5 were new proteins, two represent increased incorporation and one was decreased incorporation. Cholera toxin inhibited the appearance of the modifications induced by progesterone. Actinomycin and enucleation did not significantly alter the modifications. These data indicate that a good correlation exists between the modifications in protein synthesis induced by progesterone and the resumption of meiotic cell division. 相似文献
13.
C.d. measurements on amylose iodine solutions carried out at different degrees of iodine saturation show that the decrease of the Cotton effect, observed earlier below DP 5011,12, is mainly due to the decreasing complex formation constants. The continuous decrease of the Cotton effect above DP 50 is even more pronounced at higher iodine concentration. Slow addition of iodine leads to especially high Cotton effects with a marked maximum at DP 47–50 and only a small increase of the Cotton effect upon standing of the solutions. Rapid addition of iodine leads to considerably lower Cotton effects but a prolonged time-dependent increase. Further ordering, however, does not reach the same high degree as when ioidine is added slowly. The results are discussed in the light of a single and multichain initiation process. Studies with aggregating solutions on the one hand and with very dilute solutions on the other hand, strongly indicate that the c.d. intensity is related to a conformational state of helix ordering and not to an ordering by chain folding or regular intermolecular association. Thus, the slow, time-dependent increase of the Cotton effect reflects substantial conformational changes of amylose on binding iodine. The results indicate that in the range of DP 47–50 a particularly well ordered helix is formed. For production of the typical blue colour in aqueous soluton and stabilization of aligned polyiodide subunits there is no need to stipulate a special colloid or crystalline state of the complex. 相似文献
14.
An increasing attention has been dedicated to the characterization of complex networks within the protein world. Before now most investigations about protein structures were only considered where the interactive cutoff distance Rc=5 or 7 Å. It is noteworthy that the length of peptide bond is about 1.5 Å, the length of hydrogen bond is about 3 Å, the range of London-van der Waals force is about 5 Å and the range of hydrophobic effect can reach to 12 Å in protein molecule. Present work reports a study on the topological properties of the amino acid network constructed by different interactions above. The results indicate that the small-world property of amino acid network constructed by the peptide and hydrogen bond, London-van der Waals force and the hydrophobic effect is strong, very strong and relatively weak, respectively. Besides, there exists a precise exponential relation C∝k−0.5 at Rc=12 Å. It means that the amino acid network constructed by the hydrophobic effect tend to be hierarchical. Functional modules could be the cause for hierarchical modularity architecture in protein structures. This study on amino acid interactive network for different interactions facilitates the identification of binding sites which is strongly linked with protein function, and furthermore provides reasonable understanding of the underlying laws of evolution in genomics and proteomics. 相似文献
15.
The biophysical properties of oligodeoxyribonucleotides (ODNs) selectively modified with conformationally ‘locked’ bicyclo[3.1.0]hexane pseudosugars (Maier,M.A., Choi,Y., Gaus,H., Barchi,J.J. Jr, Marquez,V.E., Manoharan,M. (2004) Synthesis and characterization of oligonucleotides containing conformationally constrained bicyclo[3.1.0]hexane pseudosugar analogs Nucleic Acids Res., 32, 3642–3650) have been studied by various techniques. Six separate synthetic ODNs based on the Dickerson Drew dodecamer sequence (CGCGAAT*T*CGCG) were examined where each one (or both) of the thymidines (T*) were substituted with a bicyclic pseudosugar locked in either a North (2′-exo) or South (3′-exo) ring pucker. Circular dichroism spectroscopy, differential scanning calorimetry and 1H NMR spectroscopy were used to examine the duplex stability and conformational properties of the ODNs. Replacement of one or both thymidines with North-locked sugars (RNA-like) into the dodecamer did not greatly affect duplex formation or melt temperatures but distinct differences in thermodynamic parameters were observed. In contrast, incorporation of South-locked sugar derivatives that were predicted to stabilize this standard B-DNA, had the unexpected effect of causing a conformational equilibrium between different duplex forms at specific strand and salt concentrations. Our data and those of others suggest that although DNA can tolerate modifications with RNA-like (North) nucleotides, a more complicated spectrum of changes emerges with modifications restricted to South (DNA-like) puckers. 相似文献
16.
17.
18.
Makoto Murakami 《The protein journal》1995,14(3):111-114
Calcium ion is thought to be one of the initial signals in the process of synaptic modification. Various reports have described that the critical amino acids responsible for determining calcium permeability of ion channels are glutamic acid, glutamine, arginine, and asparagine. By using a computational method (MacPROT) distinguishing transmembrane, globular, and surface sequences of proteins, the present work predicts that the critical amino acids exist within surface regions of the proteins. Furthermore, occurrence ofβ-turn probabilities can be predicted around these critical residues by the protein conformational prediction method of Chou and Fasman. The results suggest that the critical amino acids exist at hydrophilic spaces or canals of membranous channel proteins and that the redirection potential of the protein chain induced by the turn structures provides the conformational change requisite for the ion selectivity and gating (opening/closing) of the channels. 相似文献
19.
20.
Three new orthopalladated chromophores based on push-pull π conjugated ligands have been prepared and characterized. The second order molecular NLO activity has been determined by EFISH measurements giving μgβ values up to 610×10−48 esu at an incident laser wavelength of 1.907 μm. The X-ray structures of two different polymorphs of one chromophore are also reported and polymorphism is discussed in terms of conformational changes. 相似文献