Diproline Templates as Folding Nuclei in Designed Peptides. Conformational Analysis of Synthetic Peptide Helices Containing Amino Terminal Pro-Pro Segments

The effect of N-terminal diproline segments in nucleating helical folding in designed peptides has been studied in two model sequences Piv-Pro-Pro-Aib-Leu-Aib-Phe-OMe (1) and Boc-Aib-Pro-Pro-Aib-Val-Ala-Phe-OMe (2). The structure of 1 in crystals, determined by X-ray diffraction, reveals a helical (RR) conformation for the segment residues 2 to 5, stabilized by one 4 -> 1 hydrogen bond and two 5 -> 1 interactions. The N-terminus residue, Pro(1) adopts a polyproline II (P-II) conformation. NMR studies in three different solvent systems support a conformation similar to that observed in crystals. In the apolar solvent CDCl3, NOE data favor the population of both completely helical and partially unfolded structures. In the former, the Pro-Pro segment adopts an alpha(R)-alpha(R) conformation, whereas in the latter, a P-II-alpha(R) structure is established. The conformational equilibrium shifts in favor of the P-II-alpha(R) structure in solvents like methanol and DMSO. A significant population of the Pro(1)- Pro(2) cis conformer is also observed. The NMR results are consistent with the population of at least three conformational states about Pro- Pro segment: trans alpha(R)-alpha(R), trans P-II-alpha(R) and cis P-II-alpha(R). Of these, the two trans conformers are in rapid dynamic exchange on the NMR time scale, whereas the interconversion between cis and trans form is slow. Similar results are obtained with peptide 2. Analysis of 462 diproline segments in protein crystal structures reveals 25 examples of the alpha(R)-alpha(R) conformation followed by a helix. Modeling and energy minimization studies suggest that both P-II-alpha(R) and alpha(R)-alpha(R) conformations have very similar energies in the model hexapeptide 1

Modes of binding of guanosine monophosphates to ribonuclease T1 - A computer modelling study

Computer-modelling studies on the modes of binding of the three guanosine monophosphate inhibitors 2'-GMP, 3'-GMP, and 5'-GMP to ribonuclease (RNase) T1 have been carried out by energy minimization in Cartesian-coordinate space. The inhibitory power was found to decrease in the order 2'-GMP > 3'-GMP > 5'-GMP in agreement with the experimental observations. The ribose moiety was found to form hydrogen bonds with the protein in all the enzyme-inhibitor complexes, indicating that it contributes to the binding energy and does not merely act as a spacer between the base and the phosphate moieties as suggested earlier. 2'-GMP and 5'-GMP bind to RNase T1 in either of the two ribose puckered forms (with C3'-endo more favoured over the C2'-endo) and 3'-GMP binds to RNase T1 predominantly in C3'-endo form. The catalytically important residue His-92 was found to form hydrogen bond with the phosphate moiety in all the enzyme-inhibitor complexes, indicating that this residue may serve as a general acid group during catalysis. Such an interaction was not found in either X-ray or two-dimensional NMR studies.

Structure of valinomycin by molecular dynamics studies

Valinomycin is an important ionophore which exhibits a high conformational flexibility. The study of various conformations adopted by this molecule together with the study of flexibility in a given conformation can throw light on the ion transport by the ionophore across the membrane. Molecular dynamics (MD) studies are ideal to characterize the flexibility in different parts of the molecule and can also give an idea of various conformations adopted by the molecule at a given temperature. Hence MD studies at 100K have been carried out on the minimized crystal structure of the molecule to scan the possible conformations in the neighbourhood of the well known 'bracelet' like structure of uncomplexed Valinomycin, Properties, like the flexibility, average values, r.m.s. fluctuations of the various intramolecular hydrogen bonds are discussed. Energy minimization has been carried out on selected MD simulated points to analyze the characteristics of the unique conformation adopted by this molecule at this temperature.

Voluntary Energy Harvesting Relays and Selection in Cooperative Wireless Networks

The use of energy harvesting (EH) nodes as cooperative relays is a promising and emerging solution in wireless systems such as wireless sensor networks. It harnesses the spatial diversity of a multi-relay network and addresses the vexing problem of a relay's batteries getting drained in forwarding information to the destination. We consider a cooperative system in which EH nodes volunteer to serve as amplify-and-forward relays whenever they have sufficient energy for transmission. For a general class of stationary and ergodic EH processes, we introduce the notion of energy constrained and energy unconstrained relays and analytically characterize the symbol error rate of the system. Further insight is gained by an asymptotic analysis that considers the cases where the signal-to-noise-ratio or the number of relays is large. Our analysis quantifies how the energy usage at an EH relay and, consequently, its availability for relaying, depends not only on the relay's energy harvesting process, but also on its transmit power setting and the other relays in the system. The optimal static transmit power setting at the EH relays is also determined. Altogether, our results demonstrate how a system that uses EH relays differs in significant ways from one that uses conventional cooperative relays.

An Algebraic Implicitization and Specialization of Minimum KL-Divergence Models

In this paper we study representation of KL-divergence minimization, in the cases where integer sufficient statistics exists, using tools from polynomial algebra. We show that the estimation of parametric statistical models in this case can be transformed to solving a system of polynomial equations. In particular, we also study the case of Kullback-Csiszar iteration scheme. We present implicit descriptions of these models and show that implicitization preserves specialization of prior distribution. This result leads us to a Grobner bases method to compute an implicit representation of minimum KL-divergence models.

A Numerical-Simulation Of The Gneiss-Charnockite Transformations In Southern India

This paper presents a numerical simulation of the well-documented, fluid-controlled Kabbal and Ponmudi type gneiss-chamockite transformations in southern India using a free energy minimization method. The computations have considered all the major solid phases and important fluid species in the rock - C-O-H and rock - C-O-H-N systems. Appropriate activity-composition relations for the solid solutions and equations of state for the fluids have been included in order to evaluate the mineral-fluid equilibria attending the incipient chamockite development in the gneisses. The C-O-H fluid speciation pattern in both the Kabbal and Ponmudi type systems indicates that CO2 and H2O make up the bulk of the fluid phase with CO, CH4, H-2 and O2 as minor constituents. In the graphite-buffered Ponmudi-system, the abundance of CO, CH4 and H-2 is orders of magnitude higher than that in the graphite-free Kabbal system. Simulation with C-O-H-N fluids of varying composition demonstrates the complementary role of CO2 and N2 as rather inert dilutants of H2O in the fluid phase. The simulation, carried out on available whole-rock data, has demonstrated the dependence of the transformation X(H2O) on P,T, and phase and chemical composition of the precursor gneiss.

Conformational studies on beta-bend containing a cis peptide unit

Conformational studies have been carried out on the X-cis-Pro tripeptide system (a system of three linked peptide units, in the trans-cis-trans configuration) using energy minimization techniques. For X, residues Gly, L-Ala, D-Ala and L-Pro have been used. The energy minima have been classified into different groups based upon the conformational similarity. There are 15, 20, 18 and 6 minima that are possible for the four cases respectively and these fall into 11 different groups. A study of these minima shows that, (i) some minima contain hydrogen bonds - either 4-->1 or 1-->2 type, (ii) the low energy minima qualify themselves as bend conformations, (iii) cis' and trans' conformations are possible for the prolyl residue as also the C(gamma)-endo and C(gamma)-exo puckerings, and (iv) for Pro-cis-Pro, cis' at the first prolyl residue is ruled out, due to the high energy. The available crystal structure data on proteins and peptides, containing cis-Pro segment have been examined with a view to find the minima that occur in solid state. The data from protein show that they fall under two groups. The conformation at X in X-cis-Pro is near extended when it is a non-glycyl residue. In both peptides and proteins there exists a preference for trans' conformation at prolyl residue over cis' when X is a non-glycyl residue. The minima obtained can be useful in modelling studies.

Molecular dynamics simulations on parallel and antiparallel C.G*G triplexes

Molecular dynamics (MD) studies have been carried out on the Hoogsteen hydrogen bonded parallel and the reverse Hoogsteen hydrogen banded antiparallel C.G*G triplexes. Earlier, the molecular mechanics studies had shown that the parallel structure was energetically more favourable than the antiparallel structure. To characterize the structural stability of the two triplexes and to investigate whether the antiparallel structure can transit to an energetically more favourable structure, due to the local fluctuations in the structure during the MD simulation, the two structures were subjected to 200ps of constant temperature vacuum MD simulations at 300K. Initially no constraints were applied to the structures and it was observed that for the antiparallel tripler, the structure showed a large root mean square deviation from the starting structure within the first 12ps and the N4-H41-O6 hydrogen bond in the WC duplex got distorted due to a high propeller twist and a moderate increase in the opening angle in the basepairs. Starting from an initial value of 30 degrees, helical twist of the average structure from this simulation had a value of 36 degrees, while the parallel structure stabilized at a twist of 33 degrees. In spite of the hydrogen bond distortions in the antiparallel tripler, it was energetically comparable to the parallel tripler. To examine the structural characteristics of an undistorted structure, another MD simulation was performed on the antiparallel tripler by constraining all the hydrogen bonds. This structure stabilized at an average twist of 33 degrees. In the course of the dynamics though the energy of the molecule - compared to the initial structure - improved, it did not become comparable to the parallel structure. Energy minimization studies performed in the presence of explicit water and counterions also showed the two structures to be equally favourable energetically Together these results indicate that the parallel C.G*G tripler with Hoogsteen hydrogen bonds also represents a stereochemically and energetically favourable structure for this class of triplexes.

Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes

Different modes of binding of pyrimidine monophosphates 2'-UMP, 3'-UMP, 2'-CMP and 3'-CMP to ribonuclease (RNase) A are studied by energy minimization in torsion angle and subsequently in Cartesian coordinate space. The results are analysed in the light of primary binding sites. The hydrogen bonding pattern brings out roles for amino acids such as Asn44 and Ser123 apart from the well known active site residues viz., His12,Lys41,Thr45 and His119. Amino acid segments 43-45 and 119-121 seem to be guiding the ligand binding by forming a pocket. Many of the active site charged residues display considerable movement upon nucleotide binding.

Effect of constraints by threonine on proline containing αa-helix—A molecular dynamics approach

Proline plays an important role in the secondary structure of proteins. In the pursuit of understanding its structural role, Proline containing helices with constraints have been studied by employing molecular dynamics (MD) technique. In the present study, the constraint introduced is a threonine residue, whose sidechain has intramolecular hydrogen bond interaction with the backbone oxygen atom. The three systems that have been chosen for characterization are: (1) Ace-(Ala)12−Thr-Pro-(Ala)10−NHMe, (2) Ace-(Ala)13-Pro-Ala-Thr- (Ala)8-NHMe and (3) Ace-(Ala)13-Pro-(Ala)3-Thr-(Ala)6-NHMe. The equilibrium structures and structural transitions have been identified by monitoring the backbone dihedral angles, bend related parameters and the hydrogen bond interactions. The MD averages and root mean square (r.m.s.) fluctuations are compared and discussed. Energy minimization has been carried out on selected MD simulated points in order to analyze the characteristics of different conformations.

On the Milito-Cruz adaptive control scheme for Markov chains

Milito and Cruz have introduced a novel adaptive control scheme for finite Markov chains when a finite parametrized family of possible transition matrices is available. The scheme involves the minimization of a composite functional of the observed history of the process incorporating both control and estimation aspects. We prove the a.s. optimality of a similar scheme when the state space is countable and the parameter space a compact subset ofR.

Phenomenological Ginzburg-Landau-like theory for superconductivity in the cuprates

We propose and develop here a phenomenological Ginzburg-Landau-like theory of cuprate high-temperature superconductivity. The free energy of a cuprate superconductor is expressed as a functional F of the complex spin-singlet pair amplitude psi(ij) equivalent to psi(m) = Delta(m) exp(i phi(m)), where i and j are nearest-neighbor sites of the square planar Cu lattice in which the superconductivity is believed to primarily reside, and m labels the site located at the center of the bond between i and j. The system is modeled as a weakly coupled stack of such planes. We hypothesize a simple form FDelta, phi] = Sigma(m)A Delta(2)(m) + (B/2)Delta(4)(m)] + C Sigma(< mn >) Delta(m) Delta(n) cos(phi(m) - phi(n)) for the functional, where m and n are nearest-neighbor sites on the bond-center lattice. This form is analogous to the original continuum Ginzburg-Landau free-energy functional; the coefficients A, B, and C are determined from comparison with experiments. A combination of analytic approximations, numerical minimization, and Monte Carlo simulations is used to work out a number of consequences of the proposed functional for specific choices of A, B, and C as functions of hole density x and temperature T. There can be a rapid crossover of from small to large values as A changes sign from positive to negative on lowering T; this crossover temperature T-ms(x) is identified with the observed pseudogap temperature T*(x). The thermodynamic superconducting phase-coherence transition occurs at a lower temperature T-c(x), and describes superconductivity with d-wave symmetry for positive C. The calculated T-c(x) curve has the observed parabolic shape. The results for the superfluid density rho(s)(x, T), the local gap magnitude , the specific heat C-v(x, T) (with and without a magnetic field), as well as vortex properties, all obtained using the proposed functional, are compared successfully with experiments. We also obtain the electron spectral density as influenced by the coupling between the electrons and the correlation function of the pair amplitude calculated from the functional, and compare the results successfully with the electronic spectrum measured through angle resolved photoemission spectroscopy (ARPES). For the specific heat, vortex structure, and electron spectral density, only some of the final results are reported here; the details are presented in subsequent papers.

Support vector machine for evaluating seismic-liquefaction potential using shear wave velocity

The use of the shear wave velocity data as a field index for evaluating the liquefaction potential of sands is receiving increased attention because both shear wave velocity and liquefaction resistance are similarly influenced by many of the same factors such as void ratio, state of stress, stress history and geologic age. In this paper, the potential of support vector machine (SVM) based classification approach has been used to assess the liquefaction potential from actual shear wave velocity data. In this approach, an approximate implementation of a structural risk minimization (SRM) induction principle is done, which aims at minimizing a bound on the generalization error of a model rather than minimizing only the mean square error over the data set. Here SVM has been used as a classification tool to predict liquefaction potential of a soil based on shear wave velocity. The dataset consists the information of soil characteristics such as effective vertical stress (sigma'(v0)), soil type, shear wave velocity (V-s) and earthquake parameters such as peak horizontal acceleration (a(max)) and earthquake magnitude (M). Out of the available 186 datasets, 130 are considered for training and remaining 56 are used for testing the model. The study indicated that SVM can successfully model the complex relationship between seismic parameters, soil parameters and the liquefaction potential. In the model based on soil characteristics, the input parameters used are sigma'(v0), soil type. V-s, a(max) and M. In the other model based on shear wave velocity alone uses V-s, a(max) and M as input parameters. In this paper, it has been demonstrated that Vs alone can be used to predict the liquefaction potential of a soil using a support vector machine model. (C) 2010 Elsevier B.V. All rights reserved.

A thermodynamic criterion for selection of gas compositions for diamond deposition

Isoactivity lines for carbon with respect to diamond as the standard state have been calculated in the ternary system C-H-O at 1223 K to identify the diamond deposition domain. The gas composition is calculated by suppressing the formation of all condensed forms of carbon using the SOLGASMIX free-energy minimization program. Thirty six gas species were included in the calculation. From the gas composition, isoactivity lines are computed using recent data on the Gibbs energy of diamond. Except for activities less than 0.1, the isoactivity lines are almost linear on the C-H-O ternary diagram. Gas compositions which generate activity of diamond ranging from 1 to 100 at 1223 K fall inside a narrow wedge originating from the point representing CO. This wedge is very similar to the revised lens-shaped diamond growth domain identified by Bachman et al., using inputs from experiment. The small difference between the calculated and observed domains may be attributed to variation in the supersaturation required for diamond deposition with gas composition. The diamond solubility in the gas phase along the isoactivity line for a(di)=100 and P=6.7 kPa exhibits a minimum at 1280 K, which is close to the optimum temperature found experimentally. At higher supersaturations, non-diamond forms of carbon, including amorphous varieties, are expected. The results suggest that thermodynamic calculations can be useful for locating diamond growth domains in more complex CVD systems containing halogens, for which very little experimental data is available.