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Different Secondary Structures (different + secondary_structure)
Selected AbstractsConfined dynamics of a ribosome-bound nascent globin: Cone angle analysis of fluorescence depolarization decays in the presence of two local motionsPROTEIN SCIENCE, Issue 10 2009Jamie P. Ellis Abstract We still know very little about how proteins achieve their native three-dimensional structure in vitro and in the cell. Folding studies as proteins emerge from the mega Dalton-sized ribosome pose special challenges due to the large size and complicated nature of the ribosome-nascent chain complex. This work introduces a combination of three-component analysis of fluorescence depolarization decays (including the presence of two local motions) and in-cone analysis of diffusive local dynamics to investigate the spatial constraints experienced by a protein emerging from the ribosomal tunnel. We focus on E. coli ribosomes and an all-,-helical nascent globin in the presence and absence of the cotranslationally active chaperones DnaK and trigger factor. The data provide insights on the dynamic nature and structural plasticity of ribosome-nascent chain complexes. We find that the sub-ns motions of the N-terminal fluorophore, reporting on the globin dynamics in the vicinity of the N terminus, are highly constrained both inside and outside the ribosomal tunnel, resulting in high-order parameters (>0.85) and small cone semiangles (<30°). The shorter globin chains buried inside the tunnel are less spatially constrained than those of a reference sequence from a natively unfolded protein, suggesting either that the two nascent chain sequences have a different secondary structure and therefore sample different regions of the tunnel or that the tunnel undergoes local structural adjustments to accommodate the globin sequence. Longer globins emerging out of the ribosomal tunnel are also found to have highly spatially constrained slow (ns) motions. There are no observable spectroscopic changes in the absence of bound chaperones. [source] Poly(L-lysine) as a model drug macromolecule with which to investigate secondary structure and membrane transport, part I: physicochemical and stability studiesJOURNAL OF PHARMACY AND PHARMACOLOGY: AN INTERNATI ONAL JOURNAL OF PHARMACEUTICAL SCIENCE, Issue 3 2002Montakarn Chittchang Low oral bioavailability of therapeutic peptides and proteins generally results from their poor permeability through biological membranes and enzymatic degradation in the gastrointestinal tract. Since different secondary structures exhibit different physicochemical properties such as hydrophobicity, size and shape, changing the secondary structure of a therapeutic polypeptide may be another approach to increasing its membrane permeation. Poly(L-lysine) was used as a model polypeptide. The objectives of this study were to induce secondary structural changes in poly(L-lysine) and to determine the time course over which a given conformer was retained. In addition, the hydrophobicity of each secondary structure of poly(L-lysine) was assessed. The circular dichroism (CD) studies demonstrated that the conditions employed could successfully induce the desired secondary structural changes in poly(L-lysine). The ,-helix conformer appeared to be more stable at 25° C whereas the ,-sheet conformer could be preserved at 37° C. On the other hand, the random coil conformer was retained at both temperatures. Significant losses of the ,-helix and the ,-sheet conformers were observed when the pH was reduced. The change in ionic strength did not affect any of the conformers. The octanol/buffer partitioning studies indicated that the ,-helix and the ,-sheet conformers exhibited significantly different (P< 0.05) hydrophobicities. In conclusion, variation of pH and temperature conditions can be used to induce secondary structural changes in poly(L-lysine). These changes are reversible when the stimuli are removed. The ,-helix and the ,-sheet conformers of poly(L-lysine) are more lipophilic than the native random coil conformer. Thus, poly(L-lysine) may represent an ideal model polypeptide with which to further investigate the effects of secondary structure on membrane diffusion or permeation. [source] Terahertz time-domain spectroscopy of poly- L -lysineBIOPOLYMERS, Issue 8 2010Ohki Kambara Abstract Poly- L -lysine is known to have three different secondary structures depending on solvent conditions because of its flexible nature. In previous work (Kambara et al., Phys Chem Chem Phys 2008, 10, 5042-5044), we observed two different types of structural changes in poly- L -lysine. In the present study, we investigated the low-frequency spectrum of poly- L -lysine with a ,-sheet structure in the solid state by terahertz time-domain spectroscopy. On the basis of this spectroscopic analysis, we found that the low-frequency dynamics differed from those of other polypeptides. Furthermore, we performed powder X-ray diffraction measurement on poly- L -lysine, which was found to be highly amorphous compared with other polypeptides. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 735,739, 2010. This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Fourier transform infrared spectroscopy suggests unfolding of loop structures precedes complete unfolding of pig citrate synthaseBIOPOLYMERS, Issue 4 2003Feride Severcan Abstract Pig citrate synthase (PCS) can be used as a model enzyme to gain some insight into the structural basis of protein thermostability. The thermal unfolding characteristics of the specific secondary structure elements within PCS were monitored in detail by following changes in its amide I band components. The result of our study indicates that PCS undergoes irreversible thermal denaturation. Detailed analysis reveals that the different secondary structures display a multistep transition with a major and a minor transition at different temperatures and a very small initial transition at the same temperature (30°C). A plot of temperature-induced changes in 1H,2H exchange, the decrease in the absorbance of the ,-helical structures, and the increase in the absorbance of aggregated structures all have in common a multistep transition, the minor one centered at 45°C and the major one around 59°C. In contrast, a band that is tentatively assigned to loop structures displays these same minor and major transitions but at lower temperatures (39 and 52°C, respectively). The transition, which occurs at 39,45°C, is not associated with the appearance of aggregated structures. This transition may reflect a change in the tertiary structure of the protein. However, the final transition, which occurs at a higher temperature (52,59°C), reflects unfolding and aggregation of the polypeptide chains. The Fourier transform infrared (FTIR) analysis suggests that PCS has a thermolabile region that unfolds first, some 7°C below the main unfolding of the protein. We propose that this reflects the unfolding of the highly flexible loop segments, which in turn triggers the unfolding of the predominantly helical core structure of PCS. © 2003 Wiley Periodicals, Inc. Biopolymers 69: 440,447, 2003 [source] New Fourier transform infrared based computational method for peptide secondary structure determination.BIOPOLYMERS, Issue 2 2001Abstract Fourier transform infrared (FTIR) experiments in dimethylsulfoxide, a solvent incapable of H donation, demonstrate that H , D isotopic replacement on the amide side of peptide bonds involves modifications of both the position and intensity of the amide I band. The effect of the isotopic substitution is particularly significant in the 1710,1670 and 1670,1650 cm,1 regions, which are generally associated with ,-turns and ,-helices. This behavior, attributed to the existence of intramolecular H-bonds in the polypeptide chain, is directly correlated to the presence of different secondary structures. Utilizing the effects induced by isotopic substitution, a method for the quantitative determination of the percentage of intramolecular H-bonds and the correlated secondary structures is proposed. The method consists of three principal steps: resolution of the fine structure of the amide I band with the determination of the number and position of the different components; reconstruction of the experimentally measured amide I band as a combination of Gaussian and Lorentzian functions, centered on the wave numbers set by band-narrowing methods, through a curve-fitting program; and quantitative determination of the population of the H-bonded carbonyls and the correlated secondary structures by comparison of the integrated intensities pertaining to the components with homologous wave numbers before and after isotopic exchange. The method is tested on a synthetic fragment of proocytocin that was previously analyzed by NMR techniques using the same solvent systems. © 2001 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 62: 95,108, 2001 [source] | ||||||||||