Siddhartha Sarma

Sodium Channel Modulating Activity in a δ-Conotoxin from an Indian Marine Snail

A 26 residue peptide (Am 2766) with the sequence CKQAGESCDIFSQNCCVG‐TCAFICIE‐NH2 has been isolated and purified from the venom of the molluscivorous snail, Conus amadis, collected off the southeastern coast of India. Chemical modification and mass spectrometric studies establish that Am 2766 has three disulfide bridges. C‐terminal amidation has been demonstrated by mass measurements on the C‐terminal fragments obtained by proteolysis. Sequence alignments establish that Am 2766 belongs to the δ‐conotoxin family. Am 2766 inhibits the decay of the sodium current in brain rNav1.2a voltage‐gated Na+ channel, stably expressed in Chinese hamster ovary cells. Unlike δ‐conotoxins have previously been isolated from molluscivorous snails, Am 2766 inhibits inactivation of mammalian sodium channels.

Solution structure of BTK-2, a novel hK(v)1.1 inhibiting scorpion toxin, from the eastern Indian scorpion Mesobuthus tamulus.

The three dimensional structure of a 32 residue three disulfide scorpion toxin, BTK-2, from the Indian red scorpion Mesobuthus tamulus has been determined using isotope edited solution NMR methods. Samples for structural and electrophysiological studies were prepared using recombinant DNA methods. Electrophysiological studies show that the peptide is active against hK(v)1.1 channels. The structure of BTK-2 was determined using 373 distance restraints from NOE data, 66 dihedral angle restraints from NOE, chemical shift and scalar coupling data, 6 constraints based on disulfide linkages and 8 constraints based on hydrogen bonds. The root mean square deviation (r.m.s.d) about the averaged co-ordinates of the backbone (N, C(α), C) and all heavy atoms are 0.81 ± 0.23Å and 1.51 ± 0.29Å respectively. The backbone dihedral angles (ϕ and ψ) for all residues occupy the favorable and allowed regions of the Ramachandran map. The three dimensional structure of BTK-2 is composed of three well defined secondary structural regions that constitute the α-β-β structural motif. Comparisons between the structure of BTK-2 and other closely related scorpion toxins pointed towards distinct differences in surface properties that provide insights into the structure-function relationships among this important class of voltage-gated potassium channel inhibiting peptides.

Cloning, overexpression, folding and purification of a biosynthetically derived three disulfide scorpion toxin (BTK-2) from Mesobuthus tamulus

BTK-2, a 32 residue scorpion toxin initially identified in the venom of red Indian scorpion Mesobuthus tamulus was cloned, overexpressed and purified using Cytochrome b(5) fusion protein system developed in our laboratory. The synthetic gene coding for the peptide was designed taking into account optimal codon usage by Escherichia coli. High expression levels of the fusion protein enabled facile purification of this peptide. The presence of disulfide bonded isomers, occurring as distinctly populated states even in the fusion protein, were separated by gel filtration chromatography. The target peptide was liberated from the host protein by Tev protease cleavage and subsequent purification was achieved using RP-HPLC methods. Reverse phase HPLC clearly showed the presence of at least two isomeric forms of the peptide that were significantly populated. The oxidative folding of BTK-2 was achieved under ambient conditions during the course of purification. Structural characterization of the two forms, by solution homonuclear and heteronuclear NMR methods, has shown that these two forms exhibit significantly different structural properties, and represent the natively folded and a misfolded form of the peptide. The formation of properly folded BTK-2 as a major fraction without the use of in vitro oxidative refolding methods clearly indicate the versatility of the Cytochrome b(5) fusion protein system for the efficient production of peptides for high resolution NMR studies.

Secure Transmission in Amplify-and-Forward Diamond Networks with a Single Eavesdropper

Unicast communication over a network of M parallel relays in the presence of an eavesdropper is considered. The relay nodes, operating under individual power constraints, amplify and forward the signals received at their inputs. In this scenario, the problem of the maximum secrecy rate achievable with AF relaying is addressed. Previous work on this problem provides iterative algorithms based on semidefinite relaxation. However, those algorithms result in suboptimal performance without any performance and convergence guarantees. We address this problem for two specific network models: (a) degraded eavesdropper channel with complex channel gain and (b) scaled eavesdropper channel with real-valued channel gains. For the first problem, we propose a novel transformation that leads to the global optimum. Our analysis leads to a polynomial-time algorithm to compute the optimal secure AF rate for the other scenario.

Robust Energy Harvesting Based on a Stackelberg Game

We study a Stackelberg game between a base station and a multiantenna power beacon for wireless energy harvesting in a multiple sensor node scenario. Assuming imperfect CSI between the sensor nodes and the power beacon, we propose a utility function that is based on throughput nonoutage probability at the base station. We provide an analytical solution for the equilibrium in case of a single sensor node. For the general case consisting of multiple sensor nodes, we provide upper and lower bounds on the power and price (players strategies). We compare the bounds with solutions resulting from an exhaustive search and a relaxed semidefinite program, and find the upper bound to be tight.

Secure Communication in Amplify-and-Forward Networks with Multiple Eavesdroppers: Decoding with SNR Thresholds

The problem of secure unicast communication over a two hop Amplify-and-Forward wireless relay network with multiple eavesdroppers is considered. Assuming that a receiver (destination or eavesdropper) can decode a message only if the received SNR is above a predefined threshold, we consider this problem in two scenarios. In the first scenario, we maximize the SNR at the legitimate destination, subject to the condition that the received SNR at each eavesdropper is below the target threshold. Due to the non-convex nature of the objective function and eavesdroppers’ constraints, we transform variables and obtain a quadratically constrained quadratic program (QCQP) with convex constraints, which can be solved efficiently. When the constraints are not convex, we consider a semidefinite relaxation (SDR) to obtain computationally efficient approximate solution. In the second scenario, we minimize the total power consumed by all relay nodes, subject to the condition that the received SNR at the legitimate destination is above the threshold and at every eavesdropper, it is below the corresponding threshold. We propose a semidefinite relaxation of the problem in this scenario and also provide an analytical lower bound.

Optimal power allocation for protective jamming in wireless networks

We address the problem of passive eavesdroppers in multi-hop wireless networks using the technique of friendly jamming. The network is assumed to employ Decode and Forward (DF) relaying. Assuming the availability of perfect channel state information (CSI) of legitimate nodes and eavesdroppers, we consider a scheduling and power allocation (PA) problem for a multiple-source multiple-sink scenario so that eavesdroppers are jammed, and source-destination throughput targets are met while minimizing the overall transmitted power. We propose activation sets (AS-es) for scheduling, and formulate an optimization problem for PA. Several methods for finding AS-es are discussed and compared. We present an approximate linear program for the original nonlinear, non-convex PA optimization problem, and argue that under certain conditions, both the formulations produce identical results. In the absence of eavesdroppers CSI, we utilize the notion of Vulnerability Region (VR), and formulate an optimization problem with the objective of minimizing the VR. Our results show that the proposed solution can achieve power-efficient operation while defeating eavesdroppers and achieving desired source-destination throughputs simultaneously.

Robust Power Allocation and Outage Analysis for Secrecy in Independent Parallel Gaussian Channels

This letter studies parallel independent Gaussian channels with uncertain eavesdropper channel state information (CSI). First, we evaluate the probability of zero secrecy rate in this system for 1) given instantaneous channel conditions and 2) a Rayleigh fading scenario. Second, when nonzero secrecy is achievable in the low SNR regime, we aim to solve a robust power allocation problem, which minimizes the outage probability at a target secrecy rate. We bound the outage probability and obtain a linear fractional program that takes into account the uncertainty in eavesdropper CSI while allocating power on the parallel channels. Problem structure is exploited to solve this optimization problem efficiently. We find the proposed scheme effective for uncertain eavesdropper CSI in comparison with conventional power allocation schemes.

Nuclear Magnetic Resonance Structure of a Major Lens Protein, Human gamma C-Crystallin: Role of the Dipole Moment in Protein Solubility.

A hallmark of the crystallin proteins is their exceptionally high solubility, which is vital for maintaining the high refractive index of the eye lens. Human γC-crystallin is a major γ-crystallin whose mutant forms are associated with congenital cataracts but whose three-dimensional structure is not known. An earlier study of a homology model concluded that human γC-crystallin has low intrinsic solubility, mainly because of the atypical magnitude and fluctuations of its dipole moment. On the contrary, the high-resolution tertiary structure of human γC-crystallin determined here shows unequivocally that it is a highly soluble, monomeric molecule in solution. Notable differences between the orientations and interactions of several side chains are observed upon comparison to those in the model. No evidence of the pivotal role ascribed to the effect of dipole moment on protein solubility was found. The nuclear magnetic resonance structure should facilitate a comprehensive understanding of the deleterious effects of cataract-associated mutations in human γC-crystallin.

A Disulfide Stabilized beta-Sandwich Defines the Structure of a New Cysteine Framework M-Superfamily Conotoxin

The structure of a new cysteine framework (-C-CC-C-C-C-) M-superfamily conotoxin, Mo3964, shows it to have a β-sandwich structure that is stabilized by inter-sheet cross disulfide bonds. Mo3964 decreases outward K(+) currents in rat dorsal root ganglion neurons and increases the reversal potential of the NaV1.2 channels. The structure of Mo3964 (PDB ID: 2MW7 ) is constructed from the disulfide connectivity pattern, i.e., 1-3, 2-5, and 4-6, that is hitherto undescribed for the M-superfamily conotoxins. The tertiary structural fold has not been described for any of the known conus peptides. NOE (549), dihedral angle (84), and hydrogen bond (28) restraints, obtained by measurement of (h3)JNC scalar couplings, were used as input for structure calculation. The ensemble of structures showed a backbone root mean square deviation of 0.68 ± 0.18 Å, with 87% and 13% of the backbone dihedral (ϕ, ψ) angles lying in the most favored and additional allowed regions of the Ramachandran map. The conotoxin Mo3964 represents a new bioactive peptide fold that is stabilized by disulfide bonds and adds to the existing repertoire of scaffolds that can be used to design stable bioactive peptide molecules.