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.

Assignment of Fundamental Vibrations of Hydrazo Derivatives. Carbohydrazide and Diprotonated Carbohydrazide

The Infrared spectra of carbohydrazide, diprotonated carbohydrazide and their deuterated compounds have been measured in the solid state. From the results on thio- and selenocarbohydrazides and other related molecules and normal coordinate analyses using a Urey-Bradley force field assignments of the fundamental vibrational frequencies and a description of the normal modes of carbohydrazide, diprotonated carbohydrazide and their deuterated species are given.

Matrix method for eigenstructure assignment - The multi-input case with application

The eigenvalue and eigenstructure assignment procedure has found application in a wide variety of control problems. In this paper a method for assigning eigenstructure to a linear time invariant multi-input system is proposed. The algorithm determines a matrix that has eigenvalues and eigenvectors at the desired locations. It is obtained from the knowledge of the open-loop system and the desired eigenstructure. Solution of the matrix equation, involving unknown controller gams, open-loop system matrices, and desired eigenvalues and eigenvectors, results hi the state feedback controller. The proposed algorithm requires the closed-loop eigenvalues to be different from those of the open-loop case. This apparent constraint can easily be overcome by a negligible shift in the values. Application of the procedure is illustrated through the offset control of a satellite supported, from an orbiting platform, by a flexible tether.

Matrix method for eigenvalue assignment: The single input case

The eigenvalue assignment/pole placement procedure has found application in a wide variety of control problems. The associated literature is rather extensive with a number of techniques discussed to that end. In this paper a method for assigning eigenvalues to a Linear Time Invariant (LTI) single input system is proposed. The algorithm determines a matrix, which has eigenvalues at the desired locations. It is obtained from the knowledge of the open-loop system and the desired eigenvalues. Solution of the matrix equation, involving unknown controller gains, open-loop system matrices and desired eigenvalues, results in the state feedback controller. The proposed algorithm requires the closed-loop eigenvalues to be different from those of the open-loop case. This apparent constraint is easily overcome by a negligible shift in the values. Two examples are considered to verify the proposed algorithm. The first one pertains to the in-plane libration of a Tethered Satellite System (TSS) while the second is concerned with control of the short period dynamics of a flexible airplane. Finally, the method is extended to determine the Controllability Grammian, corresponding to the specified closed-loop eigenvalues, without computing the controller gains.

Matrix method for eigenstructure assignment - The multi-input case with application

The eigenvalue and eigenstructure assignment procedure has found application in a wide variety of control problems. In this paper a method for assigning eigenstructure to a Linear time invariant multi-input system is proposed. The algorithm determines a matrix that has eigenvalues and eigenvectors at the desired locations. It is obtained from the knowledge of the open-loop system and the desired eigenstructure. solution of the matrix equation, involving unknown controller gains, open-loop system matrices, and desired eigenvalues and eigenvectors, results in the state feedback controller. The proposed algorithm requires the closed-loop eigenvalues to be different from those of the open-loop case. This apparent constraint can easily be overcome by a negligible shift in the values. Application of the procedure is illustrated through the offset control of a satellite supported, from an orbiting platform, by a flexible tether,

Matrix method for eigenvalue assignment: The single input case

The eigenvalue assignment/pole placement procedure has found application in a wide variety of control problems. The associated literature is rather extensive with a number of techniques discussed to that end. In this paper a method for assigning eigenvalues to a Linear Time Invariant (LTI) single input system is proposed. The algorithm determines a matrix, which has eigenvalues at the desired locations. It is obtained from the knowledge of the open-loop system and the desired eigenvalues. Solution of the matrix equation, involving unknown controller gains, open-loop system matrices and desired eigenvalues, results in the state feedback controller. The proposed algorithm requires the closed-loop eigenvalues to be different from those of the open-loop case. This apparent constraint is easily overcome by a negligible shift in the values. Two examples are considered to verify the proposed algorithm. The first one pertains to the in-plane libration of a Tethered Satellite System (TSS) while the second is concerned with control of the short period dynamics of a flexible airplane. Finally, the method is extended to determine the Controllability Grammian, corresponding to the specified closed-loop eigenvalues, without computing the controller gains.

Spin-Selective Correlation Experiment for Measurement of Long-Range J Couplings and for Assignment of (R/S) Enantiomers from the Residual Dipolar Couplings and DFT

We report the C-HETSERF experiment for determination of long- and short-range homo- and heteronuclear scalar couplings ((n)J(HH) and (n)J(XH), n >= 1) of organic molecules with a low sensitivity dilute heteronucleus in natural abundance. The method finds significant advantage in measurement of relative signs of long-range heteronuclear total couplings in chiral organic liquid crystal. The advantage of the method is demonstrated for the measurement of residual dipolar couplings (RDCs) in enantiomers oriented in the chiral liquid crystal with a focus to unambiguously assign R/S designation in a 2D spectrum. The alignment tensor calculated from the experimental RDCs and with the computed structures of enantiomers obtained by DFT calculations provides the size of the back-calculated RDCs. Smaller root-mean-square deviations (rmsd) between experimental and calculated RDCs indicate better agreement with the input structure and its correct designation of the stereogenic center.

A channel-aware, fast sub-channel to user assignment algorithm in OFDMA systems

Channel-aware assignment of sub-channels to users in the downlink of an OFDMA system demands extensive feedback of channel state information (CSI) to the base station. Since the feedback bandwidth is often very scarce, schemes that limit feedback are necessary. We develop a novel, low feedback splitting-based algorithm for assigning each sub-channel to its best user, i.e., the user with the highest gain for that sub-channel among all users. The key idea behind the algorithm is that, at any time, each user contends for the sub-channel on which it has the largest channel gain among the unallocated sub-channels. Unlike other existing schemes, the algorithm explicitly handles multiple access control aspects associated with the feedback of CSI. A tractable asymptotic analysis of a system with a large number of users helps design the algorithm. It yields 50% to 65% throughput gains compared to an asymptotically optimal one-bit feedback scheme, when the number of users is as small as 10 or as large as 1000. The algorithm is fast and distributed, and scales with the number of users.

Ternary ion-pair complexation: a protocol for chiral discrimination and the assignment of absolute configuration of chiral hydroxy acids

The study demonstrates the utility of ternary ion-pair complex formed among BINOL (1,1'-Bi-2-naphthol), a carboxylic acid and an organic base, such as, dimethylpyridine (DMAP), 1,4-diazabicyclo2.2.2]octane (DABCO), as a versatile chiral solvating agent (CSA) for the enantiodiscrimination of carboxylic acids, measurement of enantiomeric excess (ee) and the assignment of absolute configuration of hydroxy acids. The proposed mechanism of ternary complex has wider application for testing the enantiopurity owing to the fact that the binary mixture using BINOL alone does not serve as a solvating agent for their discrimination. In addition, the developed protocol has an excellent utility for the assignment of the absolute configurations of hydroxy acids.

Facile protocols for the configurational assignment of primary amines and hydroxy acids by NMR

Three-component chiral derivatization protocols are proposed for the assignment of the absolute configurations of chiral primary amines and chiral hydroxy acids using H-1-NMR. The protocols involve simple mixing of the ternary components in CDCl3, followed by stirring for 15 min. The spectra can be recorded directly, without invoking any separation method, unlike many other chiral derivatizing agents. The protocols permit the analysis in less than 15 min, making them convenient and effective for the assignment of the absolute configurations of primary amines and hydroxy acids.

SecB binds only to a late native-like intermediate in the folding pathway of barstar and not to the unfolded state

SecB is a cytosolic, tetrameric chaperone of Escherichia coli which maintains precursor proteins in a translocation competent state. We have investigated the effect of SecB on the refolding kinetics of the small protein barstar in I M guanidine hydrochloride at pH 7.0 and 25 degrees C using fluorescence spectroscopy. We show that SecB does not bind either the native or the unfolded states of barstar but binds to a late near-native intermediate along the folding pathway. For barstar, polypeptide collapse and formation of a hydrophobic surface are required for binding to SecB. SecB does not change the apparent rate constant of barstar refolding. The kinetic data for SecB binding to barstar are not consistent with simple kinetic partitioning models.

Electronic Properties of the Vortex State in Cuprate Superconductors

The superconducting state of the cuprates in the presence of a magnetic field has been investigated very actively in the past few years through measurements of electrical and thermal transport, ac conductivity, specific heat, and other quantities. The observed behavior is not well understood; it probes the nature of quasiparticies, vortices, and their interactions in a superconductor with nodes in the pair amplitude. We summarize here experimental results and our attempts to understand the phenomena.

Sizable photocurrent and emission from solid state devices based on CdS nanoparticles

CdS nanoparticles exhibit size dependent optical and electrical properties. We report here the photocurrent and I-V characteristic studies of CdS nanoparticle devices. A sizable short circuit photocurrent was observed in the detection range governed by the size of the clusters. We speculate on the mechanisms leading to the photocurrent and emission in these nanometer scale systems.

Stress-state permeability relationships for clays with coarse fraction

In standard laboratory consolidation tests, only the fraction of soil passing through a particular size of the sieve, called the matrix material, is used. This size is usually restricted to 1/10 of the height of the consolidation ring. Particles larger than this size that are removed before the test may consist of gravel, fragments of rock, or other coarse materials. Hence, it is not possible to estimate the compressibility and permeability of the total material based on the compressibility and permeability behavior obtained from laboratory consolidation tests on the matrix material. In the present investigation an attempt has been made to estimate the compressibility and permeability behavior of the total material based on the compressibility and permeability behavior of the matrix material. The results indicate that the presence of coarse particles will reduce the compressibility of the soil in proportion to the coarse fraction present in the whole soil and will not affect the permeability of the soil for the range investigated. If the coarse fraction exceeds the Limiting percentage, the void ratio-vertical effective stress path will also start to deviate from the predicted path. An expression has been developed to estimate approximately the deviating pressure, and it is found to depend on the soil type as well as the percent clay fraction.

Exact ground state and kink-like excitations of a two-dimensional Heisenberg antiferromagnet

A rare example of a two-dimensional Heisenberg model with an exact dimerized ground state is presented. This model, which can be regarded as a variation on the kagome' lattice, has several features of interest: it has a highly (but not macroscopically) degenerate ground state; it is closely related to spin chains studied by earlier authors; in particular, it exhibits domain-wall-like "kink" excitations normally associated only with one-dimensional systems. In some limits it decouples into noninteracting chains; unusually, this happens in the limit of strong, rather than weak, interchain coupling. [S0163-1829(99)50338-X].