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Saxena R, Singh R. MALDI-TOF MS and CD spectral analysis for identification and structure prediction of a purified, novel, organic solvent stable, fibrinolytic metalloprotease from Bacillus cereus B80. BIOMED RESEARCH INTERNATIONAL 2015; 2015:527015. [PMID: 25802851 PMCID: PMC4352737 DOI: 10.1155/2015/527015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 08/25/2014] [Accepted: 09/30/2014] [Indexed: 12/01/2022]
Abstract
The ability to predict protein function from structure is becoming increasingly important; hence, elucidation and determination of protein structure become the major steps in proteomics. The present study was undertaken for identification of metalloprotease produced by Bacillus cereus B80 and recognition of characteristics that can be industrially exploited. The enzyme was purified in three steps combining precipitation and chromatographic methods resulting in 33.5% recovery with 13.1-fold purification of enzyme which was detected as a single band with a molecular mass of 26 kDa approximately in SDS-PAGE and zymogram. The MALDI-TOF MS showed that the enzyme exhibited 70-93% similarity with zinc metalloproteases from various strains Bacillus sp. specifically from Bacillus cereus group. The sequence alignment revealed the presence of zinc-binding region VVVHEMCHMV in the most conserved C terminus region. Secondary structure of the enzyme was obtained by CD spectra and I-TASSER. The enzyme kinetics revealed a Michaelis constant (Km) of 0.140 μmol/ml and Vmax of 2.11 μmol/min. The application studies showed that the enzyme was able to hydrolyze various proteins with highest affinity towards casein followed by BSA and gelatin. The enzyme exhibited strong fibrinolytic, collagenolytic, and gelatinolytic properties and stability in various organic solvents.
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102
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Scarlett G, Siligardi G, Kneale GG. Circular Dichroism for the Analysis of Protein-DNA Interactions. Methods Mol Biol 2015; 1334:299-312. [PMID: 26404158 DOI: 10.1007/978-1-4939-2877-4_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The aim of this chapter is to provide information on the practical aspects of circular dichroism (CD) and synchrotron radiation circular dichroism (SRCD) in protein-nucleic acids interaction solution studies. The chapter will describe the guidelines appropriate to designing experiments and conducting correct data interpretation, the use of both benchtop and synchrotron CD approaches is discussed and the advantages of SRCD outlined. Further information and a good general review of the field a can be found in Gray (Circular Dichroism of protein-nucleic acid interactions. In: Fasman GD (ed) Circular dichroism and the conformational analysis of biomolecules. Plenum Press, New York. pp 469-500, 1996).
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Yadav VK, Mandal RS, Puniya BL, Singh S, Yadav S. Studies on the interactions of SAP-1 (an N-terminal truncated form of cystatin S) with its binding partners by CD-spectroscopic and molecular docking methods. J Biomol Struct Dyn 2015; 33:147-57. [PMID: 24261636 DOI: 10.1080/07391102.2013.855882] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
SAP-1 is a 113 amino acid long single-chain protein which belongs to the type 2 cystatin gene family. In our previous study, we have purified SAP-1 from human seminal plasma and observed its cross-class inhibitory property. At this time, we report the interaction of SAP-1 with diverse proteases and its binding partners by CD-spectroscopic and molecular docking methods. The circular dichroism (CD) spectroscopic studies demonstrate that the conformation of SAP-1 is changed after its complexation with proteases, and the alterations in protein secondary structure are quantitatively calculated with increase of α-helices and reduction of β-strand content. To get insight into the interactions between SAP-1 and proteases, we make an effort to model the three-dimensional structure of SAP-1 by molecular modeling and verify its stability and viability through molecular dynamics simulations and finally complexed with different proteases using ClusPro 2.0 Server. A high degree of shape complementarity is examined within the complexes, stabilized by a number of hydrogen bonds (HBs) and hydrophobic interactions. Using HB analyses in different protein complexes, we have identified a series of key residues that may be involved in the interactions between SAP-1 and proteases. These findings will assist to understand the mechanism of inhibition of SAP-1 for different proteases and provide intimation for further research.
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Kott L, Petrovic J, Phelps D, Roginski R, Schubert J. Determination of a low-level percent enantiomer of a compound with no ultraviolet chromophore using vibrational circular dichroism (VCD): enantiomeric purity by VCD of a compound with three chiral centers. APPLIED SPECTROSCOPY 2014; 68:1108-1115. [PMID: 25199054 DOI: 10.1366/13-07112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The chiral configuration of three of the four chiral centers in the investigational drug MLN4924 is locked by an intermediate (1S,2S,4R)-4-amino-2-(hydroxymethyl)cyclopentanol (designated as INT1a). The intermediate INT1a is a key component to the molecule, but its multiple chiral centers and lack of chromophore make it challenging to analyze for chiral purity of the desired enantiomer when it is contaminated with a small amount of its undesired enantiomer. Vibrational circular dichroism (VCD) is a technique that uses the infrared (IR) regions of the electromagnetic spectrum and as INT1a contains IR active groups, we considered using VCD to determine the chiral purity of INT1a. Since the VCD spectra of enantiomers are of equal intensity and opposite in sign, it was possible to construct calibration curves to detect the presence of low levels of this compound in the presence of its enantiomer. By normalizing the observed intensities of the VCD signals with the observed IR spectra, a partial least squares model was constructed having a root mean squared error of cross validation of 0.46% absolute over a range of 97 to 99.9% pure enantiomer (or 97-99.8% enantiomeric excess). This work demonstrates that VCD can be used for the low-level detection of a compound in the presence of its enantiomer and thus eliminates the need for an ultraviolet chromophore and chromatographic separation of the two enantiomers.
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105
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Reed CJ, Bushnell S, Evilia C. Circular dichroism and fluorescence spectroscopy of cysteinyl-tRNA synthetase from Halobacterium salinarum ssp. NRC-1 demonstrates that group I cations are particularly effective in providing structure and stability to this halophilic protein. PLoS One 2014; 9:e89452. [PMID: 24594651 PMCID: PMC3940603 DOI: 10.1371/journal.pone.0089452] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/21/2014] [Indexed: 12/24/2022] Open
Abstract
Proteins from extremophiles have the ability to fold and remain stable in their extreme environment. Here, we investigate the presence of this effect in the cysteinyl-tRNA synthetase from Halobacterium salinarum ssp. NRC-1 (NRC-1), which was used as a model halophilic protein. The effects of salt on the structure and stability of NRC-1 and of E. coli CysRS were investigated through far-UV circular dichroism (CD) spectroscopy, fluorescence spectroscopy, and thermal denaturation melts. The CD of NRC-1 CysRS was examined in different group I and group II chloride salts to examine the effects of the metal ions. Potassium was observed to have the strongest effect on NRC-1 CysRS structure, with the other group I salts having reduced strength. The group II salts had little effect on the protein. This suggests that the halophilic adaptations in this protein are mediated by potassium. CD and fluorescence spectra showed structural changes taking place in NRC-1 CysRS over the concentration range of 0-3 M KCl, while the structure of E. coli CysRS was relatively unaffected. Salt was also shown to increase the thermal stability of NRC-1 CysRS since the melt temperature of the CysRS from NRC-1 was increased in the presence of high salt, whereas the E. coli enzyme showed a decrease. By characterizing these interactions, this study not only explains the stability of halophilic proteins in extremes of salt, but also helps us to understand why and how group I salts stabilize proteins in general.
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106
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Bokkhim H, Tran T, Bansal N, Grøndahl L, Bhandari B. Evaluation of different methods for determination of the iron saturation level in bovine lactoferrin. Food Chem 2013; 152:121-7. [PMID: 24444915 DOI: 10.1016/j.foodchem.2013.11.132] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 11/04/2013] [Accepted: 11/23/2013] [Indexed: 11/18/2022]
Abstract
Lactoferrin (Lf) samples with ca. 25%, 50%, 75%, 85% and 100% iron saturation were prepared for the purpose of evaluating Chromametry, Differential Scanning Calorimetry (DSC) and Circular Dichroism (CD) spectropolarimetry for their suitability in determining the iron saturation level. Numerical values for colour from Chromametry, enthalpy change of denaturation (ΔHcal) from DSC and molar ellipticities from CD were statistically analysed to evaluate their correlation with the level of iron saturation in Lf. Linear regression analysis of colour coordinates Chroma (C(∗)) and hue (h°) angle on percentage iron saturation level of Lf showed that the values can be used to estimate the iron saturation level. The ΔHcal for the iron saturated peak and the CD ellipticities in the 310-340 nm region provided reliable data for the estimation of iron saturation level of Lf up to 75%. Mono- and di-saturated Lf displayed the same thermal stability and very similar tertiary structures.
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107
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Lehmuskero A, Ogier R, Gschneidtner T, Johansson P, Käll M. Ultrafast spinning of gold nanoparticles in water using circularly polarized light. NANO LETTERS 2013; 13:3129-34. [PMID: 23777484 DOI: 10.1021/nl4010817] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Controlling the position and movement of small objects with light is an appealing way to manipulate delicate samples, such as living cells or nanoparticles. It is well-known that optical gradient and radiation pressure forces caused by a focused laser beam enables trapping and manipulation of objects with strength that is dependent on the particle's optical properties. Furthermore, by utilizing transfer of photon spin angular momentum, it is also possible to set objects into rotational motion simply by targeting them with a beam of circularly polarized light. Here we show that this effect can set ∼200 nm radii gold particles trapped in water in 2D by a laser tweezers into rotation at frequencies that reach several kilohertz, much higher than any previously reported light driven rotation of a microscopic object. We derive a theory for the fluctuations in light scattering from a rotating particle, and we argue that the high rotation frequencies observed experimentally is the combined result of favorable optical particle properties and a low local viscosity due to substantial heating of the particles surface layer. The high rotation speed suggests possible applications in nanofluidics, optical sensing, and microtooling of soft matter.
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108
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Zhang QB, Na XZ, Yin ZN. [Characterization of thermal denaturation process of proteinase K by spectrometry]. GUANG PU XUE YU GUANG PU FEN XI = GUANG PU 2013; 33:1749-1753. [PMID: 24059167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The effect of different temperatures on the activity and conformational changes of proteinase K was studied. Methods Proteinase K was treated with different temperatures, then denatured natural substrate casein was used to assay enzyme activity, steady-state and time-resolved fluorescence spectroscopy was used to study tertiary structure, and circular dichroism was used to study secondary structure. Results show with the temperature rising from 25 to 65 degrees C, the enzyme activity and half-life of proteinase K dropped, maximum emission wavelength red shifted from 335 to 354 nm with fluorescence intensity decreasing. Synchronous fluorescence intensity of tryptophan residues decreased and that of tyrosine residues increased. Fluorescence lifetime of tryptophan residues reduced from 4. 427 1 to 4. 032 4 ns and the fraction of alpha-helix dropped. It was concluded that it is simple and accurate to use steady-state/time-resolved fluorescence spectroscopy and circular dichroism to investigate thermal stability of proteinase K. Thermal denaturation of proteinase K followed a three-state process. Fluorescence intensity of proteinase K was affected by fluorescence resonance energy transfer from tyrosine to tryptophan residues. The alpha-helix was the main structure to maintain conformational stability of enzyme active site of proteinase K.
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109
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Pivonka DE, Wesolowski SS. Vibrational circular dichroism (VCD) chiral assignment of atropisomers: application to γ-aminobutyric acid (GABA) modulators designed as potential anxiolytic drugs. APPLIED SPECTROSCOPY 2013; 67:365-371. [PMID: 23601535 DOI: 10.1366/12-06934] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Atropisomers exist when axial chirality is present as a result of conformationally restricted rotation around a single bond. The interconversion rate of the individual atropisomers is critical to the assessment of chiral stability of a drug throughout scale-up, development, production, and storage as well as in vivo pharmacokinetics. We describe the application of vibrational circular dichroism spectroscopy coupled with quantum mechanics simulations to assign the absolute axial chirality and measure the racemization half-life of a series of potential anxiolytic drugs that act as γ-aminobutyric acid modulators.
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110
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Karabencheva-Christova TG, Carlsson U, Balali-Mood K, Black GW, Christov CZ. Conformational effects on the circular dichroism of Human Carbonic Anhydrase II: a multilevel computational study. PLoS One 2013; 8:e56874. [PMID: 23526922 PMCID: PMC3582176 DOI: 10.1371/journal.pone.0056874] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 01/15/2013] [Indexed: 11/25/2022] Open
Abstract
Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions.
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111
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Nicolas Filippin A, Borras A, Rico VJ, Frutos F, González-Elipe AR. Laser induced enhancement of dichroism in supported silver nanoparticles deposited by evaporation at glancing angles. NANOTECHNOLOGY 2013; 24:045301. [PMID: 23291348 DOI: 10.1088/0957-4484/24/4/045301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Silver nanoparticles (NPs) depicting well defined surface plasmon resonance (SPR) absorption were deposited on flat substrates by physical vapor deposition in a glancing angle configuration. The particles were characterized by scanning electron microscopy and atomic force microscopy and their optical properties examined by UV-vis absorption spectroscopy using linearly polarized light. It was found that, depending on the amount of deposited silver and the evaporation angle, part of the 'as-prepared' samples present NPs characterized by an anisotropic shape and a polarization dependent SPR absorption and different colors when using polarized white light at 0° and 90°. Low-power irradiation of these materials with an infrared Nd-YAG nanosecond laser in ambient conditions produced an enhancement in such dichroism. At higher powers, the dichroism was lost and the SPR bands shifted to lower wavelengths as a result of the reshaping of the silver NPs in the form of spheres. The possible factors contributing to the observed changes in dichroism are discussed.
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112
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Hidalgo F, Noguez C. Optical activity of achiral ligand SCH3 adsorbed on achiral Ag55 clusters: relationship between adsorption site and circular dichroism. ACS NANO 2013; 7:513-521. [PMID: 23256525 DOI: 10.1021/nn3046083] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The electronic circular dichroism (CD) spectra of a methyl-thiol adsorbed at different sites on an icosahedral silver nanoparticle is studied by using time-perturbed density functional theory. Despite that separately molecule and nanoparticle are achiral and consequently optically inactive, the Ag(55)-SCH(3) compound emerges with a new symmetry, which may be chiral or not depending on the adsorption site and orientation of the molecule. It is found that chirality is favored when the thiol is adsorbed between two atoms of different coordination number. Chiral compounds have characteristic CD spectra in the UV-visible region, where Ag(55) shows optical absorption but SCH(3) does not; revealing that highly degenerated molecular-like electronic states of Ag(55) are modified by the presence of the molecule inducing optical activity. It is concluded that CD line-shapes and magnitude strongly depend on the site where the adsorption takes place, while its intensity is modulated by the molecule orientation.
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113
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Sato H, Yamagishi A. VCD studies on chiral characters of metal complex oligomers. Int J Mol Sci 2013; 14:964-78. [PMID: 23296273 PMCID: PMC3565301 DOI: 10.3390/ijms14010964] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Revised: 12/27/2012] [Accepted: 12/31/2012] [Indexed: 12/31/2022] Open
Abstract
The present article reviews the results on the application of vibrational circular dichroism (VCD) spectroscopy to the study of stereochemical properties of chiral metal complexes in solution. The chiral characters reflecting on the vibrational properties of metal complexes are revealed by measurements of a series of β-diketonato complexes with the help of theoretical calculation. Attention is paid to the effects of electronic properties of a central metal ion on vibrational energy levels or low-lying electronic states. The investigation is further extended to the oligomers of β-diketonato complex units. The induction of chiral structures is confirmed by the VCD spectra when chiral inert moieties are connected with labile metal ions. These results have demonstrated how VCD spectroscopy is efficient in revealing the static and dynamic properties of mononuclear and multinuclear chiral metal complexes, which are difficult to clarify by means of other spectroscopes.
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Pivato M, De Franceschi G, Tosatto L, Frare E, Kumar D, Aioanei D, Brucale M, Tessari I, Bisaglia M, Samori B, de Laureto PP, Bubacco L. Covalent α-synuclein dimers: chemico-physical and aggregation properties. PLoS One 2012; 7:e50027. [PMID: 23272053 PMCID: PMC3521728 DOI: 10.1371/journal.pone.0050027] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Accepted: 10/15/2012] [Indexed: 11/29/2022] Open
Abstract
The aggregation of α-synuclein into amyloid fibrils constitutes a key step in the onset of Parkinson's disease. Amyloid fibrils of α-synuclein are the major component of Lewy bodies, histological hallmarks of the disease. Little is known about the mechanism of aggregation of α-synuclein. During this process, α-synuclein forms transient intermediates that are considered to be toxic species. The dimerization of α-synuclein could represent a rate-limiting step in the aggregation of the protein. Here, we analyzed four covalent dimers of α-synuclein, obtained by covalent link of the N-terms, C-terms, tandem cloning of two sequences and tandem juxtaposition in one protein of the 1–104 and 29–140 sequences. Their biophysical properties in solution were determined by CD, FT-IR and NMR spectroscopies. SDS-induced folding was also studied. The fibrils formation was analyzed by ThT and polarization fluorescence assays. Their morphology was investigated by TEM and AFM-based quantitative morphometric analysis. All dimers were found to be devoid of ordered secondary structure under physiological conditions and undergo α-helical transition upon interaction with SDS. All protein species are able to form amyloid-like fibrils. The reciprocal orientation of the α-synuclein monomers in the dimeric constructs affects the kinetics of the aggregation process and a scale of relative amyloidogenic propensity was determined. Structural investigations by FT IR spectroscopy, and proteolytic mapping of the fibril core did not evidence remarkable difference among the species, whereas morphological analyses showed that fibrils formed by dimers display a lower and diversified level of organization in comparison with α-synuclein fibrils. This study demonstrates that although α-synuclein dimerization does not imply the acquisition of a preferred conformation by the participating monomers, it can strongly affect the aggregation properties of the molecules. The results presented highlight a substantial role of the relative orientation of the individual monomer in the definition of the fibril higher structural levels.
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115
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Xu L, Rainey JK, Meng Q, Liu XQ. Recombinant minimalist spider wrapping silk proteins capable of native-like fiber formation. PLoS One 2012; 7:e50227. [PMID: 23209681 PMCID: PMC3509139 DOI: 10.1371/journal.pone.0050227] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 10/22/2012] [Indexed: 11/19/2022] Open
Abstract
Spider silks are desirable biomaterials characterized by high tensile strength, elasticity, and biocompatibility. Spiders produce different types of silks for different uses, although dragline silks have been the predominant focus of previous studies. Spider wrapping silk, made of the aciniform protein (AcSp1), has high toughness because of its combination of high elasticity and tensile strength. AcSp1 in Argiope trifasciata contains a 200-aa sequence motif that is repeated at least 14 times. Here, we produced in E. coli recombinant proteins consisting of only one to four of the 200-aa AcSp1 repeats, designated W1 to W4. We observed that purified W2, W3 and W4 proteins could be induced to form silk-like fibers by shear forces in a physiological buffer. The fibers formed by W4 were ∼3.4 µm in diameter and up to 10 cm long. They showed an average tensile strength of 115 MPa, elasticity of 37%, and toughness of 34 J cm−3. The smaller W2 protein formed fewer fibers and required a higher protein concentration to form fibers, whereas the smallest W1 protein did not form silk-like fibers, indicating that a minimum of two of the 200-aa repeats was required for fiber formation. Microscopic examinations revealed structural features indicating an assembly of the proteins into spherical structures, fibrils, and silk-like fibers. CD and Raman spectral analysis of protein secondary structures suggested a transition from predominantly α-helical in solution to increasingly β-sheet in fibers.
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Macwan AS, Kukshal V, Srivastava N, Javed S, Kumar A, Ramachandran R. Crystal structure of the hexachlorocyclohexane dehydrochlorinase (LinA-type2): mutational analysis, thermostability and enantioselectivity. PLoS One 2012; 7:e50373. [PMID: 23209726 PMCID: PMC3507683 DOI: 10.1371/journal.pone.0050373] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 10/19/2012] [Indexed: 12/02/2022] Open
Abstract
Hexachlorocyclohexane dehydrochlorinase (LinA) mediates dehydrochlorination of γ-HCH to 1, 3, 4, 6-tetrachloro-1,4-cyclohexadiene that constitutes first step of the aerobic degradation pathway. We report the 3.5 Å crystal structure of a thermostable LinA-type2 protein, obtained from a soil metagenome, in the hexagonal space group P6(3)22 with unit cell parameters a = b = 162.5, c = 186.3 Å, respectively. The structure was solved by molecular replacement using the co-ordinates of LinA-type1 that exhibits mesophile-like properties. Structural comparison of LinA-type2 and -type1 proteins suggests that thermostability of LinA-type2 might partly arise due to presence of higher number of ionic interactions, along with 4% increase in the intersubunit buried surface area. Mutational analysis involving the differing residues between the -type1 and -type2 proteins, circular dichroism experiments and functional assays suggest that Q20 and G23 are determinants of stability for LinA-type2. It was earlier reported that LinA-type1 exhibits enantioselectivity for the (-) enantiomer of α-HCH. Contrastingly, we identified that -type2 protein prefers the (+) enantiomer of α-HCH. Structural analysis and molecular docking experiments suggest that changed residues K20Q, L96C and A131G, vicinal to the active site are probably responsible for the altered enantioselectivity of LinA-type2. Overall the study has identified features responsible for the thermostability and enantioselectivity of LinA-type2 that can be exploited for the design of variants for specific biotechnological applications.
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Dietrich K, Lehr D, Helgert C, Tünnermann A, Kley EB. Circular dichroism from chiral nanomaterial fabricated by on-edge lithography. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2012; 24:OP321-OP325. [PMID: 23042699 DOI: 10.1002/adma.201203424] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 09/18/2012] [Indexed: 06/01/2023]
Abstract
A novel-shaped plasmonic chiral nanomaterial exhibiting circular dichroism in the near-infrared spectral range is presented. Applying on-edge lithography, a large area with these nanostructures is efficiently covered. This fabrication method offers tunability of the operation bandwidth by tailoring the chiral shape.
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118
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Barthem VMTS, Rogalev A, Wilhelm F, Sant'anna MM, Mello SLA, Zhang Y, Bayle-Guillemaud P, Givord D. Spin fluctuations of paramagnetic Rh clusters revealed by x-ray magnetic circular dichroism. PHYSICAL REVIEW LETTERS 2012; 109:197204. [PMID: 23215422 DOI: 10.1103/physrevlett.109.197204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Indexed: 06/01/2023]
Abstract
The magnetic moment induced on Rh atoms, forming 1.6 nm average diameter clusters, embedded in an Al(2)O(3) matrix, has been determined using x-ray magnetic circular dichroism measurements. The magnetic moment varies linearly with the applied magnetic field. At 2.3 K and under 17 T, the spin magnetic moment amounts to 0.067(2) μ(B)/Rh atom. The orbital moment does not exceed 2% of the spin moment. The susceptibility is highly temperature dependent. This is in agreement with a prediction due to Moriya and Kawabata, that in itinerant electron systems, close to the onset of magnetism, the renormalization of the magnetic susceptibility by electron correlations, leads to a Curie-like behavior.
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Shih MD, Hsieh TY, Jian WT, Wu MT, Yang SJ, Hoekstra FA, Hsing YIC. Functional studies of soybean (Glycine max L.) seed LEA proteins GmPM6, GmPM11, and GmPM30 by CD and FTIR spectroscopy. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 196:152-9. [PMID: 23017910 DOI: 10.1016/j.plantsci.2012.07.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 07/25/2012] [Accepted: 07/27/2012] [Indexed: 05/06/2023]
Abstract
The protein and mRNA levels of late embryogenesis abundant (LEA) genes may be linked to osmotic stresses. Here, we characterized three soybean hydrophilic LEA proteins--GmPM11 (LEA I), GmPM6 (LEA II), and GmPM30 (LEA III)--by circular dichroism and Fourier transform infrared spectroscopy. Structural analysis revealed that the LEA proteins adopted high amounts of disordered conformations in solution and underwent conformational changes with hydrophobicity and desiccation induction. Macromolecular interaction studies revealed that the GmPM proteins interact with non-reducing sugars and phospholipids. GmPM6 and GmPM30 but not GmPM11 could prevent beta-aggregation of poly-L-lysine after slow drying. We discuss the possible functions of hydrophilic LEA proteins in maturing seeds.
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Kuepper K, Raekers M, Taubitz C, Uhlarz M, Piamonteze C, de Groot FMF, Arenholz E, Galakhov VR, Mukovskii YM, Neumann M. The x-ray magnetic circular dichroism spin sum rule for 3d4 systems: Mn3+ ions in colossal magnetoresistance manganites. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2012; 24:435602. [PMID: 23034342 DOI: 10.1088/0953-8984/24/43/435602] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The colossal magnetoresistance manganites La(0.87±0.02)Sr(0.12±0.02)MnO(3+δ), La(0.78±0.02)Sr(0.17±0.02)MnO(3+δ), and La(0.66±0.02)Sr(0.36±0.02)MnO(3+δ) (δ close to 0) were investigated by using soft x-ray magnetic circular dichroism (XMCD) and magnetometry. Very good agreement between the values for the average Mn magnetic moments determined with these two methods was achieved by correcting the XMCD spin sum rule results by means of charge transfer multiplet calculations, which also suggest a charge transfer of ~50% for Mn(4+) and approximately equal to 30% for Mn(3+). The magnetic moment was found to be localized at the Mn ions for x = 0.17 and 0.36 at 80 K and for x = 0.12 in the temperature range from 80 to 300 K. We discuss our findings in the light of previously published data, confirming the validity of our approach.
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Alén BO, Nieto L, Gurriarán-Rodríguez U, Mosteiro CS, Álvarez-Pérez JC, Otero-Alén M, Camiña JP, Gallego R, García-Caballero T, Martín-Pastor M, Casanueva FF, Jiménez-Barbero J, Pazos Y. The NMR structure of human obestatin in membrane-like environments: insights into the structure-bioactivity relationship of obestatin. PLoS One 2012; 7:e45434. [PMID: 23056203 PMCID: PMC3464274 DOI: 10.1371/journal.pone.0045434] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 08/17/2012] [Indexed: 11/23/2022] Open
Abstract
The quest for therapeutic applications of obestatin involves, as a first step, the determination of its 3D solution structure and the relationship between this structure and the biological activity of obestatin. On this basis, we have employed a combination of circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy, and modeling techniques to determine the solution structure of human obestatin (1). Other analogues, including human non-amidated obestatin (2) and the fragment peptides (6–23)-obestatin (3), (11–23)-obestatin (4), and (16–23)-obestatin (5) have also been scrutinized. These studies have been performed in a micellar environment to mimic the cell membrane (sodium dodecyl sulfate, SDS). Furthermore, structural-activity relationship studies have been performed by assessing the in vitro proliferative capabilities of these peptides in the human retinal pigmented epithelial cell line ARPE-19 (ERK1/2 and Akt phosphorylation, Ki67 expression, and cellular proliferation). Our findings emphasize the importance of both the primary structure (composition and size) and particular segments of the obestatin molecule that posses significant α-helical characteristics. Additionally, details of a species-specific role for obestatin have also been hypothesized by comparing human and mouse obestatins (1 and 6, respectively) at both the structural and bioactivity levels.
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Fujiwara T, Taniguchi Y, Katsumoto Y, Tanaka T, Ozeki M, Iwasaki H, Node M, Yamashita M, Hosoi S. Novel approach to determining the absolute configurations at the C3-positions of various types of sterols based on an induced circular dichroism. Steroids 2012; 77:1198-204. [PMID: 22842233 DOI: 10.1016/j.steroids.2012.07.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 06/27/2012] [Accepted: 07/03/2012] [Indexed: 11/24/2022]
Abstract
Circular dichroism (CD) spectra of the 2,2'-binaphthyl ester derived from Δ(5)-sterols showed not bisignate CD but diagnostic CD bands at around 210 and 240 nm. These bands might be attributable to an interaction between an olefinic chromophore and a binaphthyl one. Various types of unsaturated sterols were thus derivatized followed by complete hydrogenation, to give saturated sterols. As a result, CD spectra of the binaphthyl derivatives of the saturated sterols showed bisignate curves centered at 240 nm (3S(β): positive chirality; 3R(α): negative one). This suggested a straightforward and practical method for discriminating the absolute stereogenic center at the C-3 positions of sterols based on an induced CD. This finding should contribute significantly to the analysis of metabolites of various types of sterols.
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Roman EA, Faraj SE, Gallo M, Salvay AG, Ferreiro DU, Santos J. Protein stability and dynamics modulation: the case of human frataxin. PLoS One 2012; 7:e45743. [PMID: 23049850 PMCID: PMC3458073 DOI: 10.1371/journal.pone.0045743] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 08/24/2012] [Indexed: 01/06/2023] Open
Abstract
Frataxin (FXN) is an α/β protein that plays an essential role in iron homeostasis. Apparently, the function of human FXN (hFXN) depends on the cooperative formation of crucial interactions between helix α1, helix α2, and the C-terminal region (CTR) of the protein. In this work we quantitatively explore these relationships using a purified recombinant fragment hFXN90-195. This variant shows the hydrodynamic behavior expected for a monomeric globular domain. Circular dichroism, fluorescence, and NMR spectroscopies show that hFXN90-195 presents native-like secondary and tertiary structure. However, chemical and temperature induced denaturation show that CTR truncation significantly destabilizes the overall hFXN fold. Accordingly, limited proteolysis experiments suggest that the native-state dynamics of hFXN90-195 and hFXN90-210 are indeed different, being the former form much more sensitive to the protease at specific sites. The overall folding dynamics of hFXN fold was further explored with structure-based protein folding simulations. These suggest that the native ensemble of hFXN can be decomposed in at least two substates, one with consolidation of the CTR and the other without consolidation of the CTR. Explicit-solvent all atom simulations identify some of the proteolytic target sites as flexible regions of the protein. We propose that the local unfolding of CTR may be a critical step for the global unfolding of hFXN, and that modulation of the CTR interactions may strongly affect hFXN physiological function.
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Chen X, Raggio C, Campagnola PJ. Second-harmonic generation circular dichroism studies of osteogenesis imperfecta. OPTICS LETTERS 2012; 37:3837-9. [PMID: 23041876 PMCID: PMC4337953 DOI: 10.1364/ol.37.003837] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We report the use of second-harmonic generation (SHG) microscopy in conjunction with circular dichroism (CD) to differentiate normal skin from that in the connective tissue disorder osteogenesis imperfecta (OI). Osteogenesis imperfecta results from mutations in the collagen triple helix, where the individual chains are defective, leading to abnormal folding, and ultimately, abnormal fibril/fiber organization. Second-harmonic-generation circular dichroism successfully differentiated normal human and OI skin tissues, whereas other SHG polarization schemes did not provide discrimination, suggesting this approach has high sensitivity for studying the difference in chirality in the mutated collagen. We further suggest that the method has clinical diagnostic value, as it could be performed with minimal invasion.
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Réfrégiers M, Wien F, Ta HP, Premvardhan L, Bac S, Jamme F, Rouam V, Lagarde B, Polack F, Giorgetta JL, Ricaud JP, Bordessoule M, Giuliani A. DISCO synchrotron-radiation circular-dichroism endstation at SOLEIL. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:831-835. [PMID: 22898965 DOI: 10.1107/s0909049512030002] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 07/01/2012] [Indexed: 06/01/2023]
Abstract
The new synchrotron-radiation circular-dichroism (SRCD) endstation on the UV-visible synchrotron beamline DISCO has been commissioned at the SOLEIL synchrotron. The design has been focused on preservation of a high degree of linear polarization at high flux and moderate resolving power covering the vacuum ultraviolet to visible spectral range (125-600 nm). The beam dimensions have been set to 4 mm × 4 mm at 1 nm bandwidth for lower sample degradation. The nitrogen-purged sample chamber fits three types of sample holders accommodating conventional round cell mounting, automated rotation of the samples, as well as a microfluidic set-up. Automated temperature-controlled data collection on microvolumes is now available to the biology and chemistry communities. Macromolecules including membrane proteins, soluble proteins, bio-nanotubes, sugars, DNA and RNAs are now routinely investigated.
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