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Random Coil (random + coil)
Terms modified by Random Coil Selected AbstractsElectrospun Silk Fibroin Mats for Tissue EngineeringENGINEERING IN LIFE SCIENCES (ELECTRONIC), Issue 3 2008A. Alessandrino Abstract Processing Silk Fibroin (SF) with electrospinning (ES) offers a very attractive opportunity for producing a variety of 2D and 3D matrices with great potential for tissue regeneration and repair due to the superior biocompatibility and mechanical properties of SF. Different combinations of ES parameters were explored to investigate the best experimental set-up related to the dimension and uniformity of the fibers in the electrospun silk fibroin (ES-SF) mats. Using SEM it was found that the ES-SF mats contain uniform fibers with a diameter in the nanometric range obtained by electrospinning a 7.5,% w/v SF solution in formic acid, with an electric field of 2.4,kV/cm and a spinneret-collector distance of 10,cm. FT-IR and DSC analyses were performed to investigate the structure of the ES-SF mats before and after immersion in methanol for different times (5, 10, and 15,min). The methanol treatment was able to promote the crystallization of SF by conformational transition of random coil and other poorly ordered conformations (turns and bends) to the ,-sheet structure. The degree of crystallinity was enhanced as shown by the trend of both the FT-IR crystallinity index and the melting/decomposition peak temperature (from DSC). To study the cytocompatibility of ES-SF mats, tests with L929 murine fibroblasts were carried out. Samples were seeded with the cells and incubated for 1, 3, and 7,days at 37,°C. At each time point, SEM investigations and Alamar blue tests were performed. The SEM images showed cell adhesion and proliferation just after 1,day and cell confluence at 7,days. Alamar blue test demonstrated that there were very low differences between cell viability on ES-SF mats and the tissue culture plastic control. [source] The Alzheimer ,-peptide shows temperature-dependent transitions between left-handed 31 -helix, ,-strand and random coil secondary structuresFEBS JOURNAL, Issue 15 2005Jens Danielsson The temperature-induced structural transitions of the full length Alzheimer amyloid ,-peptide [A,(1,40) peptide] and fragments of it were studied using CD and 1H NMR spectroscopy. The full length peptide undergoes an overall transition from a state with a prominent population of left-handed 31 (polyproline II; PII)-helix at 0 °C to a random coil state at 60 °C, with an average ,H of 6.8 ± 1.4 kJ·mol,1 per residue, obtained by fitting a Zimm,Bragg model to the CD data. The transition is noncooperative for the shortest N-terminal fragment A,(1,9) and weakly cooperative for A,(1,40) and the longer fragments. By analysing the temperature-dependent 3JHNH, couplings and hydrodynamic radii obtained by NMR for A,(1,9) and A,(12,28), we found that the structure transition includes more than two states. The N-terminal hydrophilic A,(1,9) populates PII-like conformations at 0 °C, then when the temperature increases, conformations with dihedral angles moving towards ,-strand at 20 °C, and approaches random coil at 60 °C. The residues in the central hydrophobic (18,28) segment show varying behaviour, but there is a significant contribution of ,-strand-like conformations at all temperatures below 20 °C. The C-terminal (29,40) segment was not studied by NMR, but from CD difference spectra we concluded that it is mainly in a random coil conformation at all studied temperatures. These results on structural preferences and transitions of the segments in the monomeric form of A, may be related to the processes leading to the aggregation and formation of fibrils in the Alzheimer plaques. [source] Protein-Enabled Synthesis of Monodisperse Titania Nanoparticles On and Within Polyelectrolyte MatricesADVANCED FUNCTIONAL MATERIALS, Issue 14 2009Eugenia Kharlampieva Abstract Here, the results of a study of the mechanism of bio-enabled surface-mediated titania nanoparticle synthesis with assistance of polyelectrolyte surfaces are reported. By applying atomic force microscopy, surface force spectroscopy, circular dichroism, and in situ attenuated total reflection Fourier-transform infrared spectroscopy, structural changes of rSilC-silaffin upon its adsorption to polyelectrolyte surfaces prior to and during titania nanoparticle growth are revealed. It is demonstrated that the adhesion of rSilC-silaffin onto polyelectrolyte surfaces results in its reorganization from a random-coil conformation in solution into a mixed secondary structure with both random coil and , -sheet structures presented. Moreover, the protein forms a continuous molecularly thin layer with well-defined monodisperse nanodomains of lateral dimensions below 20,nm. It is also shown that rSilC embedded inside the polylelectrolyte matrix preserves its titania formation activity. It is suggested that the surface-mediated, bio-enabled synthesis of nanostructured materials might be useful to develop general procedures for controlled growth of inorganic nanomaterials on reactive organic surfaces, which opens new perspectives in the design of tailored, in situ grown, hybrid inorganic,organic nanomaterials. [source] A minor ,-structured conformation is the active state of a fusion peptide of vesicular stomatitis virus glycoprotein,JOURNAL OF PEPTIDE SCIENCE, Issue 4 2008Carolina G. Sarzedas Abstract Entry of enveloped animal viruses into their host cells always depends on a step of membrane fusion triggered by conformational changes in viral envelope glycoproteins. Vesicular stomatitis virus (VSV) infection is mediated by virus spike glycoprotein G, which induces membrane fusion at the acidic environment of the endosomal compartment. In a previous work, we identified a specific sequence in the VSV G protein, comprising the residues 145,164, directly involved in membrane interaction and fusion. In the present work we studied the interaction of pep[145,164] with membranes using NMR to solve the structure of the peptide in two membrane-mimetic systems: SDS micelles and liposomes composed of phosphatidylcholine and phosphatidylserine (PC:PS vesicles). The presence of medium-range NOEs showed that the peptide has a tendency to form N - and C -terminal helical segments in the presence of SDS micelles. Analysis of the chemical shift index indicated helix,coil equilibrium for the C -terminal helix under all conditions studied. At pH 7.0, the N -terminal helix also displayed a helix,coil equilibrium when pep[145-164] was free in solution or in the presence of PC:PS. Remarkably, at the fusogenic pH, the region of the N -terminal helix in the presence of SDS or PC:PS presented a third conformational species that was in equilibrium with the helix and random coil. The N -terminal helix content decreases pH and the minor ,-structured conformation becomes more prevalent at the fusogenic pH. These data point to a ,-conformation as the fusogenic active structure-which is in agreement with the X-ray structure, which shows a ,-hairpin for the region corresponding to pep[145-164]. Copyright © 2007 European Peptide Society and John Wiley & Sons, Ltd. [source] Conformation of N-terminal HIV-1 tat (fragment 1,9) peptide by NMR and MD simulationsJOURNAL OF PEPTIDE SCIENCE, Issue 11 2001Meena Kanyalkar Abstract The N -terminal portion of HIV-1 Tat covering residues 1,9 is a competitive inhibitor of dipeptidyl peptidase IV (DP IV). We have used 1H NMR techniques, coupled with molecular dynamics methods, to determine the conformation of this peptide in the three diverse media: DMSO-d6, water (pH 2.7) and 40% HFA solution. The results indicate that in both DMSO-d6 and HFA the peptide has a tendency to acquire a type I ,-turn around the segment Asp5 -Pro6 -Asn7 -Ile8. The N -terminal end is seen to be as a random coil. In water, the structure is best described as a left-handed polyproline type II (PPII) helix for the mid segment region Asp2 to Pro6. The structures obtained in this study have been compared with an earlier report on Tat (1,9). Copyright © 2000 European Peptide Society and John Wiley & Sons, Ltd. [source] Functionally relevant motions of haloalkane dehalogenases occur in the specificity-modulating cap domainsPROTEIN SCIENCE, Issue 5 2002Michal Otyepka Abstract One-nanosecond molecular dynamics trajectories of three haloalkane dehalogenases (DhlA, LinB, and DhaA) are compared. The main domain was rigid in all three dehalogenases, whereas the substrate specificity-modulating cap domains showed considerably higher mobility. The functionally relevant motions were spread over the entire cap domain in DhlA, whereas they were more localized in LinB and DhaA. The highest amplitude of essential motions of DhlA was noted in the ,4,-helix-loop-,4-helix region, formerly proposed to participate in the large conformation change needed for product release. The highest amplitude of essential motions of LinB and DhaA was observed in the random coil before helix 4, linking two domains of these proteins. This flexibility is the consequence of the modular composition of haloalkane dehalogenases. Two members of the catalytic triad, that is, the nucleophile and the base, showed a very high level of rigidity in all three dehalogenases. This rigidity is essential for their function. One of the halide-stabilizing residues, important for the catalysis, shows significantly higher flexibility in DhlA compared with LinB and DhaA. Enhanced flexibility may be required for destabilization of the electrostatic interactions during the release of the halide ion from the deeply buried active site of DhlA. The exchange of water molecules between the enzyme active site and bulk solvent was very different among the three dehalogenases. The differences could be related to the flexibility of the cap domains and to the number of entrance tunnels. [source] Probability-based protein secondary structure identification using combined NMR chemical-shift dataPROTEIN SCIENCE, Issue 4 2002Yunjun Wang Abstract For a long time, NMR chemical shifts have been used to identify protein secondary structures. Currently, this is accomplished through comparing the observed 1H,, 13C,, 13C,, or 13C, chemical shifts with the random coil values. Here, we present a new protocol, which is based on the joint probability of each of the three secondary structural types (,-strand, ,-helix, and random coil) derived from chemical-shift data, to identify the secondary structure. In combination with empirical smooth filters/functions, this protocol shows significant improvements in the accuracy and the confidence of identification. Updated chemical-shift statistics are reported, on the basis of which the reliability of using chemical shift to identify protein secondary structure is evaluated for each nucleus. The reliability varies greatly among the 20 amino acids, but, on average, is in the order of: 13C,>13C,>1H,>13C,>15N>1HN to distinguish an ,-helix from a random coil; and 1H,>13C, >1HN ,13C,,13C,,15N for a ,-strand from a random coil. Amide 15N and 1HN chemical shifts, which are generally excluded from the application, in fact, were found to be helpful in distinguishing a ,-strand from a random coil. In addition, the chemical-shift statistical data are compared with those reported previously, and the results are discussed. A JAVA User Interface program has been developed to make the entire procedure fully automated and is available via http://ccsr3150-p3.stanford.edu. [source] ,-Sheet aggregation of kisspeptin-10 is stimulated by heparin but inhibited by amphiphilesBIOPOLYMERS, Issue 8 2010Søren B. Nielsen Abstract The murine 10-residue neurohormone kisspeptin (YNWNSFGLRY) is an important regulator of reproductive behavior and gonadotrophin secretion. It is known to form a random coil in solution, but undergoes a structural change in the presence of membranes although the nature of this change is not fully determined. The peptide's conformational versatility raises the question whether it is also able to form ordered aggregates under physiological conditions, which might be relevant as a storage mechanism. Here we show that heparin induces kisspeptin to form ,-sheet rich amyloid aggregates both at neutral (pH 7.0) and slightly acidic (pH 5.2) conditions. Addition of heparin leads to aggregation after a certain lag phase, irrespective of the time of addition of heparin, indicating that heparin is needed to facilitate the formation of fibrillation nuclei. Aggregation is completely inhibited by submicellar concentrations of zwitterionic and anionic surfactants. Unlike previous reports, our NMR data do not indicate persistent structure in the presence of zwitterionic surfactant micelles. Thus kisspeptin can aggregate under physiologically relevant conditions provided heparin is present, but the process is highly sensitive to the presence of amphiphiles, highlighting the very dynamic nature of the peptide conformation and suggesting that kisspeptin aggregation is a biologically regulatable process. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 678,689, 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] Determination of the secondary structure of proteins in different environments by FTIR-ATR spectroscopy and PLS regressionBIOPOLYMERS, Issue 11 2008Yeqiu Wang Abstract The secondary structures of proteins (,-helical, ,-sheet, ,-turn, and random coil) in the solid state and when bound to polymer beads, containing immobilized phenyl and butyl ligands such as those as commonly employed in hydrophobic interaction chromatography, have been investigated using FTIR-ATR spectroscopy and partial least squares (PLS) methods. Proteins with known structural features were used as models, including 12 proteins in the solid state and 7 proteins adsorbed onto the hydrophobic surfaces. A strong PLS correlation was achieved between predictions derived from the experimental data for 4 proteins adsorbed onto the phenyl-modified beads and reference data obtained from the X-ray crystallographic structures with r2 values of 0.9974, 0.9864, 0.9924, and 0.9743 for ,-helical, ,-sheet, ,-turn, and random coiled structures, respectively. On the other hand, proteins adsorbed onto the butyl sorbent underwent greater secondary structural changes compared to the phenyl sorbent as evidenced from the poorer PLS r2 values (r2 are 0.9658, 0.9106, 0.9571, and 0.9340). The results thus indicate that the secondary structures for these proteins were more affected by the butyl sorbent, whereas the secondary structure remains relatively unchanged for the proteins adsorbed onto the phenyl sorbent. This study has important ramifications for understanding the nature of protein secondary structural changes following adsorption onto hydrophobic sorbent surfaces. This knowledge could also enable the development of useful protocols for enhancing the chromatographic purification of proteins in their native bioactive states. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 895,905, 2008. 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] Titration of poly(dA-dT) · poly(dA-dT) in solution at variable NaCl concentrationBIOPOLYMERS, Issue 2 2004Marta Airoldi Abstract CD and uv absorption data showed that high molecular weight poly(dA-dT) · poly(dA-dT), at 298 K, undergoes an acid-induced transition from B-double helix to random coil in NaCl solutions of different concentrations, ranging from 0.005 to 0.600M. Similarly, titration of the polynucleotide with a strong base causes duplex-to-single strands transition. The base- and acid-induced transitions were both reversible by back-titration (with an acid or, respectively, with a base): the apparent pKa were the same in both directions. However, the number of protons per titratable site (adenine N1) required to reach half-denaturation was in great excess over the stoichiometric value; to a much larger extent, the same effect was observed also for the deprotonation of the N3H sites of thymine. Moreover, in the basic denaturation experiments, at low salt concentrations ([NaCl],0.300M) less acid than calculated was needed to back-titrate the base excess to half-denaturation. Both effects could be qualitatively justified on the basis of the counterion condensation theory of polyelectrolytes and considering the energy barrier created by the negatively charged phosphodiester groups to the penetration of the OH, ions inside the double helix and the screening effect of the Na+ ions on such charges, in the deprotonation experiments. © 2004 Wiley Periodicals, Inc. Biopolymers, 2004 [source] Design of a pH-sensitive pore-forming peptide with improved performanceCHEMICAL BIOLOGY & DRUG DESIGN, Issue 1 2004D.H. Haas Abstract:, GALA is a 30 residue synthetic peptide designed to interact with membranes in a pH-sensitive manner, with potential applications for intracellular drug and gene delivery. Upon reduction of the pH from neutral to acidic, GALA switches from random coil to , -helix, inserts into lipid bilayers, and forms oligomeric pores of defined size. Its simple sequence and well-characterized behavior make the peptide an excellent starting point to explore the effects of sequence on structure, pH sensitivity, and membrane affinity. We describe synthesis and characterization of two derivatives of GALA, termed GALAdel3E and YALA. GALAdel3E has a deletion of three centrally located glutamate residues from GALA, while YALA replaces one glutamate residue with the unusual amino acid 3,5-diiodotyrosine. Both derived peptides retain pH sensitivity, showing no ability to cause leakage of an encapsulated dye from unilamellar vesicles at pH 7.4 but substantial activity at pH 5. Unlike GALA, neither peptide undergoes a conformational change upon reduction of the pH, remaining , -helical throughout. Interestingly, the pH at which the peptides activate is shifted, with GALA becoming active at pH ,5.7, GALAdel3E at pH ,6.2, and YALA at pH ,6.7. Furthermore, the peptides GALAdel3E and YALA show improved activity compared with GALA for cholesterol-containing membranes, with YALA retaining the greatest activity. Improved activity in the presence of cholesterol and onset of activity in the critical range between pH 6 and 7 may make these peptides useful in applications requiring intracellular delivery of macromolecules, such as gene delivery or anti-cancer treatments. [source] Reversible Double-Helix,Random-Coil Transition Process of Bis{hexa(ethynylhelicene)}sCHEMISTRY - AN ASIAN JOURNAL, Issue 2 2008Hiroki Sugiura Dr. Abstract Two compounds with two hexa(ethynylhelicene) parts connected by a flexible haxadecamethylene and a rigid butadiyne linker were synthesized. The 1H,NMR spectroscopic and CD analyses and vapor-pressure osmometry (VPO) of these two compounds revealed intramolecular double-helix formation. Upon heating a 5-,M solution in toluene, the double-helix structure unfolded to form a random coil, and on cooling it folded again into a double helix. The thermodynamic stabilities of both structures were dependent on temperature, and the structural change in both compounds is due to the large enthalpies and entropies under equilibrium. The rate constants of their unfolding were obtained by assuming a pseudo-first-order reaction; the compound with a rigid linker unfolded slower than that with a flexible linker. The former has a larger activation energy, and its double-helix and random-coil conformers were separated by chromatography. The rate of folding was also faster for the flexible-linker compound with larger activation energy. The rate constants for the folding of both compounds slightly decreased with increasing temperature, which was ascribed to the presence of exothermic pre-equilibrium and rate-determining steps. The folding was markedly accelerated with increasing random-coil concentration, which suggests the involvement of self-catalysis. A mechanism of folding was proposed. The involvement of different mechanisms of folding and unfolding was suggested by the kinetic studies, and it was confirmed by the presence of hysteresis in the melting profiles. The difference in linker structure also affected the thermal-switching profiles of the double-helix,random-coil structural changes. [source] Electrostatic screening and backbone preferences of amino acid residues in urea-denatured ubiquitinPROTEIN SCIENCE, Issue 2 2007Franc Avbelj Abstract Local structures in denatured proteins may be important in guiding a polypeptide chain during the folding and misfolding processes. Existence of local structures in chemically denatured proteins is a highly controversial issue. NMR parameters [coupling constants 3J(H,,HN) and chemical shifts] of chemically denatured proteins in general deviate little from their values in small peptides. These peptides were presumed to be completely unstructured; therefore, it was considered that chemically denatured proteins are random coils. But recent experimental studies show that small peptides adopt relatively stable structures in aqueous solutions. Small deviations of the NMR parameters from their values in small peptides may thus actually indicate the existence of local structures in chemically denatured proteins. Using NMR data and theoretical predictions we show here that fluctuating ,-strands exist in urea-denatured ubiquitin (8 M urea at pH 2). Residues in such ,-strands populate more frequently the left side of the broad , region of ,,, space. Urea-denatured ubiquitin contains no detectable ,-sheet secondary structures; nevertheless, the fluctuating ,-strands in urea-denatured ubiquitin coincide to the ,-strands in the native state. Formation of ,-strands is in accord with the electrostatic screening model of unfolded proteins. The free energy of a residue in an unfolded protein is in this model determined by the local backbone electrostatics and its screening by backbone solvation. These energy terms introduce strong electrostatic coupling between neighboring residues, which causes cooperative formation of ,-strands in denatured proteins. We propose that fluctuating ,-strands in denatured proteins may serve as initiation sites to form fibrils. [source] Molecular chemical structure of barley proteins revealed by ultra-spatially resolved synchrotron light sourced FTIR microspectroscopy: Comparison of barley varietiesBIOPOLYMERS, Issue 4 2007Peiqiang Yu Abstract Barley protein structure affects the barley quality, fermentation, and degradation behavior in both humans and animals among other factors such as protein matrix. Publications show various biological differences among barley varieties such as Valier and Harrington, which have significantly different degradation behaviors. The objectives of this study were to reveal the molecular structure of barley protein, comparing various varieties (Dolly, Valier, Harrington, LP955, AC Metcalfe, and Sisler), and quantify protein structure profiles using Gaussian and Lorentzian methods of multi-component peak modeling by using the ultra-spatially resolved synchrotron light sourced Fourier transform infrared microspectroscopy (SFTIRM). The items of the protein molecular structure revealed included protein structure ,-helices, ,-sheets, and others such as ,-turns and random coils. The experiment was performed at the National Synchrotron Light Source in Brookhaven National Laboratory (BNL, US Department of Energy, NY). The results showed that with the SFTIRM, the molecular structure of barley protein could be revealed. Barley protein structures exhibited significant differences among the varieties in terms of proportion and ratio of model-fitted ,-helices, ,-sheets, and others. By using multi-component peaks modeling at protein amide I region of 1710,1576 cm,1, the results show that barley protein consisted of approximately 18,34% of ,-helices, 14,25% of ,-sheets, and 44,69% others. AC Metcalfe, Sisler, and LP955 consisted of higher (P < 0.05) proportions of ,-helices (30,34%) than Dolly and Valier (,-helices 18,23%). Harrington was in between which was 25%. For protein ,-sheets, AC Metcalfe, and LP955 consisted of higher proportions (22,25%) than Dolly and Valier (13,17%). Different barley varieties contained different ,-helix to ,-sheet ratios, ranging from 1.4 to 2.0, although the difference were insignificant (P > 0.05). The ratio of ,-helices to others (0.3 to 1.0, P < 0.05) and that of ,-sheets to others (0.2 to 0.8, P < 0.05) were different among the barley varieties. It needs to be pointed out that using a multi-peak modeling for protein structure analysis is only for making relative estimates and not exact determinations and only for the comparison purpose between varieties. The principal component analysis showed that protein amide I Fourier self-deconvolution spectra were different among the barley varieties, indicating that protein internal molecular structure differed. The above results demonstrate the potential of the SFTIRM to localize relatively pure protein areas in barley tissues and reveal protein molecular structure. The results indicated relative differences in protein structures among the barley varieties, which may partly explain the biological differences among the barley varieties. Further study is needed to understand the relationship between barley molecular chemical structure and biological features in terms of nutrient availability and digestive behavior. © 2006 Wiley Periodicals, Inc. Biopolymers 85:308,317, 2007. 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] Site-directed PEGylations of Thymosin , 1 Analogs and Evaluation of Their ImmunoactivityCHINESE JOURNAL OF CHEMISTRY, Issue 4 2009Jiankun QIE Abstract PEGylation is an effective way to improve the pharmacokinetic profiles of pharmaceutical proteins or peptides. But the relatively large and long PEG chains would be likely to shelter the active site of a small peptide because of its small size, compared with a protein. Therefore, the positions and numbers of PEGylation are crucial for the bioactivity of a PEGylated peptide. To elucidate the relationship between the PEGylated positions and bioactivity of a peptide drug, site-specific PEGylations were performed on Zadaxin (Thymosin , 1, T,1), which is a pharmaceutical peptide with an , -helix region, a , -turn region, and random coils. Site-specific mono-PEGylations of T,1 in different conformational regions were realized through introducing one cysteine residue into the desired positions of the peptide, followed by a coupling reaction with a thiol-attached maleimide-PEG reagent. Primary data from IFN- , production of splenocytes induced by Con A showed that the influence of PEGylation on Zadaxin was position-dependent, and mostly, positive effects were observed after PEGylation, which indicated that the position of PEGylation is important for maintaining the bioactivity of a peptide. [source] | |||||||||||||||||||||||||