CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone H-1(alpha) and C-13' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to alpha-helical/beta-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.

Urey-Bradley potential function for the in-plane vibrations of boric acid

The Urey-Bradley force constants for the in-plane vibrations of the boric acid molecule are calculated using the Wilson's F-G matrix method. They are as follows: KO-H=5·23, KB-O=4·94, HBOH=0·36, {Mathematical expression}, F00=0·68 and FBH=0·98 in units of 105 dynes/cm. Using the force constants, the frequencies are recalculated and the calculated values agree with the observed values satisfactorily. The in-plane vibrational frequencies of deuterated boric acid are also calculated and again satisfactory agreement with the observed values is found.

High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination

Three-dimensional (3D) structure determination of proteins is benefitted by long-range distance constraints comprising the methyl groups, which constitute the hydrophobic core of proteins. However, in methyl groups (of Ala, Ile, Leu, Met, Thr and Val) there is a significant overlap of C-13 and H-1 chemical shifts. Such overlap can be resolved using the recently proposed (3,2)D HCCH-COSY, a G-matrix Fourier transform (GFT) NMR based experiment, which facilitates editing of methyl groups into distinct spectral regions by combining their C-13 chemical shifts with that of the neighboring, directly attached, C-13 nucleus. Using this principle, we present three GFT experiments: (a) (4,3)D NOESY-HCCH, (b) (4,3)D H-1-TOCSY-HCCH and (c) (4,3)D C-13-TOCSY-HCCH. These experiments provide unique 4D spectral information rapidly with high sensitivity and resolution for side-chain resonance assignments and NOE analysis of methyl groups. This is exemplified by (4,3)D NOESY-HCCH data acquired for 17.9 kDa non-deuterated cytosolic human J-protein co-chaperone, which provided crucial long-range distance constraints for its 3D structure determination.

NMR methods for fast data acquisition

NMR spectroscopy has witnessed tremendous advancements in recent years with the development of new methodologies for structure determination and availability of high-field strength spectrometers equipped with cryogenic probes. Supported by these advancements, a new dimension in NMR research has emerged which aims to increase the speed with data is collected and analyzed. Several novel methodologies have been proposed in this direction. This review focuses on the principles on which these different approaches are based with an emphasis on G-matrix Fourier transform NMR spectroscopy.

GFT projection NMR for efficient H-1/C-13 sugar spin system identification in nucleic acids

A newly implemented G-matrix Fourier transform (GFT) (4,3)D HC(C)CH experiment is presented in conjunction with (4,3)D HCCH to efficiently identify H-1/C-13 sugar spin systems in C-13 labeled nucleic acids. This experiment enables rapid collection of highly resolved relay 4D HC(C)CH spectral information, that is, shift correlations of C-13-H-1 groups separated by two carbon bonds. For RNA, (4,3)D HC(C)CH takes advantage of the comparably favorable 1'- and 3'-CH signal dispersion for complete spin system identification including 5'-CH. The (4,3)D HC(C)CH/HCCH based strategy is exemplified for the 30-nucleotide 3'-untranslated region of the pre-mRNA of human U1A protein.

A fast NMR method for resonance assignments: application to metabolomics

We present a new method for rapid NMR data acquisition and assignments applicable to unlabeled (C-12) or C-13-labeled biomolecules/organic molecules in general and metabolomics in particular. The method involves the acquisition of three two dimensional (2D) NMR spectra simultaneously using a dual receiver system. The three spectra, namely: (1) G-matrix Fourier transform (GFT) (3,2)D C-13, H-1] HSQC-TOCSY, (2) 2D H-1-H-1 TOCSY and (3) 2D C-13-H-1 HETCOR are acquired in a single experiment and provide mutually complementary information to completely assign individual metabolites in a mixture. The GFT (3,2)D C-13, H-1] HSQC-TOCSY provides 3D correlations in a reduced dimensionality manner facilitating high resolution and unambiguous assignments. The experiments were applied for complete H-1 and C-13 assignments of a mixture of 21 unlabeled metabolites corresponding to a medium used in assisted reproductive technology. Taken together, the experiments provide time gain of order of magnitudes compared to the conventional data acquisition methods and can be combined with other fast NMR techniques such as non-uniform sampling and covariance spectroscopy. This provides new avenues for using multiple receivers and projection NMR techniques for high-throughput approaches in metabolomics.

Simultaneous acquisition of three NMR spectra in a single experiment for rapid resonance assignments in metabolomics

NMR-based approach to metabolomics typically involves the collection of two-dimensional (2D) heteronuclear correlation spectra for identification and assignment of metabolites. In case of spectral overlap, a 3D spectrum becomes necessary, which is hampered by slow data acquisition for achieving sufficient resolution. We describe here a method to simultaneously acquire three spectra (one 3D and two 2D) in a single data set, which is based on a combination of different fast data acquisition techniques such as G-matrix Fourier transform (GFT) NMR spectroscopy, parallel data acquisition and non-uniform sampling. The following spectra are acquired simultaneously: (1) C-13 multiplicity edited GFT (3,2)D HSQC-TOCSY, (2) 2D H-1- H-1] TOCSY and (3) 2D C-13- H-1] HETCOR. The spectra are obtained at high resolution and provide high-dimensional spectral information for resolving ambiguities. While the GFT spectrum has been shown previously to provide good resolution, the editing of spin systems based on their CH multiplicities further resolves the ambiguities for resonance assignments. The experiment is demonstrated on a mixture of 21 metabolites commonly observed in metabolomics. The spectra were acquired at natural abundance of C-13. This is the first application of a combination of three fast NMR methods for small molecules and opens up new avenues for high-throughput approaches for NMR-based metabolomics.

An Optimal g-Guidance Scheme for Satellite Launch Vehicles

A closed-loop steering logic based on an optimal (2-guidance is developed here. The guidance system drives the satellite launch vehicle along a two- or three- dimensional trajectory for placing the payload into a specified circular orbit. The modified g-guidance algorithm makes use of the optimal required velocity vector, which minimizes the total impulse needed for an equivalent two-impluse transfer from the present state to the final orbit. The required velocity vector is defined as velocity of the vehicle on the hypothetical transfer orbit immediately after the application of the first impulse. For this optimal transfer orbit, a simple and elegant expression for the Q-matrix is derived. A working principle for the guidance algorithm in terms of the major and minor cycles, and also for the generation of the steering command, is outlined.

Coherent potential approximation, averaged T-matrix approximation and Lloyd's model

It is shown how the single-site coherent potential approximation and the averaged T-matrix approximation become exact in the calculation of the averaged single-particle Green function of the electron in the Anderson model when the site energy is distributed randomly with lorentzian distribution. Using these approximations, Lloyd's exact result is reproduced.

Modified density matrix renormalization group algorithm for the zigzag spin-1/2 chain with frustrated antiferromagnetic exchange: Comparison with field theory at large J(2)/J(1)

A modified density matrix renormalization group (DMRG) algorithm is applied to the zigzag spin-1/2 chain with frustrated antiferromagnetic exchange J(1) and J(2) between first and second neighbors. The modified algorithm yields accurate results up to J(2)/J(1) approximate to 4 for the magnetic gap Delta to the lowest triplet state, the amplitude B of the bond order wave phase, the wavelength lambda of the spiral phase, and the spin correlation length xi. The J(2)/J(1) dependences of Delta, B, lambda, and xi provide multiple comparisons to field theories of the zigzag chain. The twist angle of the spiral phase and the spin structure factor yield additional comparisons between DMRG and field theory. Attention is given to the numerical accuracy required to obtain exponentially small gaps or exponentially long correlations near a quantum phase transition.

An alternate form of the ramberg-osgood formula for matrix displacement analysis

A new stress-strain law, which is a three parameter representation of stress in terms of strain has been proposed for the matrix displacement analysis of structures made of non-hookean materials. This formula has been utilized to study three typical problems. These studies brought out the effectiveness and suitability of this law for matrix displacement analysis.

Antimicrobial activity of highly stable silver nano particles embedded in agar-agar matrix as a thin film

Highly stable silver nanoparticles (Ag NPs) in agar-agar (Ag/agar) as inorganic-organic hybrid were obtained as free-standing film by in situ reduction of silver nitrate by ethanol. The antimicrobial activity of Ag/agar film on Escherichia coli (E. coil), Staphylococcus aureus (S. aureus), and Candida albicans (C albicans) was evaluated in a nutrient broth and also in saline solution. In particular, films were repeatedly tested for antimicrobial activity after recycling. UV-vis absorption and TEM studies were carried out on films at different stages and morphological studies on microbes were carried out by SEM. Results showed spherical Ag NPs of size 15-25 nm, having sharp surface plasmon resonance (SPR) band. The antimicrobial activity of Ag/agar film was found to be in the order, C. albicans > E. coil > S. aureus, and antimicrobial activity against C. albicans was almost maintained even after the third cycle. Whereas, in case of E. coil and S. aureus there was a sharp decline in antimicrobial activity after the second cycle. Agglomeration of Ag NPs in Ag/agar film on exposure to microbes was observed by TEM studies. Cytotoxic experiments carried out on HeLa cells showed a threshold Ag NPs concentration of 60 mu g/mL, much higher than the minimum inhibition concentration of Ag NPs (25.8 mu g/mL) for E. coli. The mechanical strength of the film determined by nanoindentation technique showed almost retention of the strength even after repeated cycle. (C) 2010 Elsevier Ltd. All rights reserved.

Magnetic, electric, and dielectric properties of FeCo alloy nanoparticles dispersed in amorphous matrix

Nanocrystalline Fe53Co47 alloy was synthesized by a single-step transmetallation chemical method at room temperature. The Fe53Co47 alloy nanoparticles of 77 and 47 wt% were dispersed in silica matrix by the sol-gel process using tetraethyl orthosilcate. Structural studies reveal that the as-prepared alloy powders are in bcc phase and silica is in an amorphous state. The phase-transition temperature and Mossbauer spectra analysis of the Fe-Co alloy establishes the homogeneous alloy formation. A saturation magnetization of 218 emu/g was obtained for pure FeCo alloy at room temperature. Scanning electron microscopic analysis demonstrates the hollow-sphere morphology for FeCo alloy particles. Magnetic nanocomposite consisting of 47 wt% FeCo-silica shows enhanced thermal stability over the native FeCo alloy. Electrical and dielectric properties of 47 wt% FeCo-silica nanocomposites were investigated as a function of frequency and temperature. It was found that the dielectric constants and dielectric loss were stable throughout the measured temperature (310-373 K). Our results indicate that FeCo-silica nanocomposite is a promising candidate for high-frequency applications. (C) 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim