Interaction Between Two Residues in the Inter-Domain Interface of Escherichia coli Peptidase N Modulates Catalytic Activity

The role of interaction between Asn259 (catalytic domain) with Gln821 (C-terminal domain) in PeptidaseN was investigated. The k(cat) of PeptidaseN containing Asn259Asp or Gln821Glu is enhanced whereas it is suppressed in Asn259AspGln821Glu. Structural analysis shows this interaction to change the relative disposition of active site residues, which modulates catalytic activity.

Intra and Inter-Molecular Communications Through Protein Structure Network

Communication within and across proteins is crucial for the biological functioning of proteins. Experiments such as mutational studies on proteins provide important information on the amino acids, which are crucial for their function. However, the protein structures are complex and it is unlikely that the entire responsibility of the function rests on only a few amino acids. A large fraction of the protein is expected to participate in its function at some level or other. Thus, it is relevant to consider the protein structures as a completely connected network and then deduce the properties, which are related to the global network features. In this direction, our laboratory has been engaged in representing the protein structure as a network of non-covalent connections and we have investigated a variety of problems in structural biology, such as the identification of functional and folding clusters, determinants of quaternary association and characterization of the network properties of protein structures. We have also addressed a few important issues related to protein dynamics, such as the process of oligomerization in multimers, mechanism on protein folding, and ligand induced communications (allosteric effect). In this review we highlight some of the investigations which we have carried out in the recent past. A review on protein structure graphs was presented earlier, in which the focus was on the graphs and graph spectral properties and their implementation in the study of protein structure graphs/networks (PSN). In this article, we briefly summarize the relevant parts of the methodology and the focus is on the advancement brought out in the understanding of protein structure-function relationships through structure networks. The investigations of structural/biological problems are divided into two parts, in which the first part deals with the analysis of PSNs based on static structures obtained from x-ray crystallography. The second part highlights the changes in the network, associated with biological functions, which are deduced from the network analysis on the structures obtained from molecular dynamics simulations.

Improved Algorithms for Reservoir Capacity Calculation Incorporating Storage-Dependent Losses and Reliability Norm

Two algorithms that improve upon the sequent-peak procedure for reservoir capacity calculation are presented. The first incorporates storage-dependent losses (like evaporation losses) exactly as the standard linear programming formulation does. The second extends the first so as to enable designing with less than maximum reliability even when allowable shortfall in any failure year is also specified. Together, the algorithms provide a more accurate, flexible and yet fast method of calculating the storage capacity requirement in preliminary screening and optimization models.

Effect of inter-edge Coulomb interactions on transport through a point contact in nu=5/2 quantum Hall state

We study transport across a point contact separating two line junctions in a nu = 5/2 quantum Hall system. We analyze the effect of inter-edge Coulomb interactions between the chiral bosonic edge modes of the half-filled Landau level (assuming a Pfaffian wave function for the half-filled state) and of the two fully filled Landau levels. In the presence of inter-edge Coulomb interactions between all the six edges participating in the line junction, we show that the stable fixed point corresponds to a point contact that is neither fully opaque nor fully transparent. Remarkably, this fixed point represents a situation where the half-filled level is fully transmitting, while the two filled levels are completely backscattered; hence the fixed point Hall conductance is given by G(H) = 1/2e(2)/h. We predict the non-universal temperature power laws by which the system approaches the stable fixed point from the two unstable fixed points corresponding to the fully connected case (G(H) = 5/2e(2)/h) and the fully disconnected case (G(H) = 0).

Seismic reliability assessment of external stability of reinforced soil walls using pseudo-dynamic method

The paper presents a method for the evaluation of external stability of reinforced soil walls subjected to earthquakes in the framework of the pseudo-dynamic method. The seismic reliability of the wall is evaluated by considering the different possible failure modes such as sliding along the base, overturning about the toe point of the wall, bearing capacity and the eccentricity of the resultant force. The analysis is performed considering properties of the reinforced backfill, foundation soil below the base of the wall, length of the geosynthetic reinforcement and characteristics of earthquake ground motions such as shear wave and primary wave velocity as random variables. The optimum length of reinforcement needed to maintain stability against four modes of failure by targeting various component reliability indices is obtained. Differences between pseudo-static and pseudo-dynamic methods are clearly highlighted in the paper. A complete analysis of pseudo-static and pseudo-dynamic methodologies shows that the pseudodynamic method results in realistic design values for the length of geosynthetic reinforcement under earthquake conditions.

Crystallographic and modelling studies on Mycobacterium tuberculosis RuvA: Additional role of RuvB-binding domain and inter species variability

RuvA, along with RuvB, is involved in branch migration of heteroduplex DNA in homologous recombination. The structures of three new crystal forms of RuvA from Mycobacterium tuberculosis (MtRuvA) have been determined. The RuvB-binding domain is cleaved off in one of them. Detailed models of the complexes of octameric RuvA from different species with the Holliday junction have also been constructed. A thorough examination of the structures presented here and those reported earlier brings to light the hitherto unappreciated role of the RuvB-binding domain in determining inter-domain orientation and oligomerization. These structures also permit an exploration of the interspecies variability of structural features such as oligomerization and the conformation of the loop that carries the acidic pin, in terms of amino acid substitutions. These models emphasize the additional role of the RuvB-binding domain in Holliday junction binding. This role along with its role in oligomerization could have important biological implications.

Design of laterally loaded piles in clays based on cone penetration test data: a reliability-based approach

The behaviour of laterally loaded piles is considerably influenced by the uncertainties in soil properties. Hence probabilistic models for assessment of allowable lateral load are necessary. Cone penetration test (CPT) data are often used to determine soil strength parameters, whereby the allowable lateral load of the pile is computed. In the present study, the maximum lateral displacement and moment of the pile are obtained based on the coefficient of subgrade reaction approach, considering the nonlinear soil behaviour in undrained clay. The coefficient of subgrade reaction is related to the undrained shear strength of soil, which can be obtained from CPT data. The soil medium is modelled as a one-dimensional random field along the depth, and it is described by the standard deviation and scale of fluctuation of the undrained shear strength of soil. Inherent soil variability, measurement uncertainty and transformation uncertainty are taken into consideration. The statistics of maximum lateral deflection and moment are obtained using the first-order, second-moment technique. Hasofer-Lind reliability indices for component and system failure criteria, based on the allowable lateral displacement and moment capacity of the pile section, are evaluated. The geotechnical database from the Konaseema site in India is used as a case example. It is shown that the reliability-based design approach for pile foundations, considering the spatial variability of soil, permits a rational choice of allowable lateral loads.

Reliability Optimization using SLUMT

This paper is concerned with the reliability optimization of a spatially redundant system, subject to various constraints, by using nonlinear programming. The constrained optimization problem is converted into a sequence of unconstrained optimization problems by using a penalty function. The new problem is then solved by the conjugate gradient method. The advantages of this method are highlighted.

Performance reliability of high-maintenance systems

The time–history of the performance of a system is treated as a stochastic corrective process, in which deterioration due to aging is counteracted at brief maintenance checks. Using a diffusion approximation for the deterioration, simple models are proposed for describing maintenance either by component replacement or by performance restoration. Equilibrium solutions of the models show that the performance has a probability distribution with exponential tails: the uncritical use of Gaussians can grossly underestimate the probability of poor performance. The proposed models are supported by recent observational evidence on aircraft track-keeping errors, which are shown to follow the modified exponential distribution derived here. The analysis also brings out the relation between the deterioration characteristics of the system and the intensity of the maintenance effort required to achieve a given performance reliability.

Solution NMR studies of acetohydroxy acid synthase I: Identification of the sites of inter-subunit interactions using multidimensional NMR methods

The novel multidomain organization in the multimeric Escherichia coli AHAS I (ilvBN) enzyme has been dissected to generate polypeptide fragments. These fragments when cloned, expressed and purified reassemble in the presence of cofactors to yield a catalytically competent enzyme. Structural characterization of AHAS has been impeded due to the fact that the holoenzyme is prone to dissociation leading to heterogeneity in samples. Our approach has enabled the structural characterization using high-resolution nuclear magnetic resonance methods. Near complete sequence specific NMR assignments for backbone H-N, N-15, C-13 alpha and C-13(beta) atoms of the FAD binding domain of ilvB have been obtained on samples isotopically enriched in H-2, C-13 and N-15. The secondary structure determined on the basis of observed C-13(alpha) secondary chemical shifts and sequential NOEs indicates that the secondary structure of the FAD binding domain of E. coli AHAS large Subunit (ilvB) is similar to the structure of this domain in the catalytic subunit of yeast AHAS. Protein-protein interactions involving the regulatory subunit (ilvN) and the domains of the catalytic subunit (ilvB) were studied using circular dichroic and isotope edited solution nuclear magnetic resonance spectroscopic methods. Observed changes in circular dichroic spectra indicate that the regulatory subunit (ilvN) interacts with ilvB alpha and ilvB beta domains of the catalytic subunit and not with the ilvB gamma domain. NMR chemical shift mapping methods show that ilvN binds close to the FAD binding site in ilvB beta and proximal to the intrasubunit ilvB alpha/ilvB beta domain interface. The implication of this interaction on the role of the regulatory subunit oil the activity of the holoenzyme is discussed. NMR studies of the regulatory domains show that these domains are structured in solution. Preliminary evidence for the interaction of ilvN with the metabolic end product of the pathway, viz., valine is also presented.

Ligand dependent intra and inter subunit communication in human tryptophanyl tRNA synthetase as deduced from the dynamics of structure networks

Homodimeric protein tryptophanyl tRNA synthetase (TrpRS) has a Rossmann fold domain and belongs to the 1c subclass of aminoacyl tRNA synthetases. This enzyme performs the function of acylating the cognate tRNA. This process involves a number of molecules (2 protein subunits, 2 tRNAs and 2 activated Trps) and thus it is difficult to follow the complex steps in this process. Structures of human TrpRS complexed with certain ligands are available. Based on structural and biochemical data, mechanism of activation of Trp has been speculated. However, no structure has yet been solved in the presence of both the tRNA(Trp) and the activated Trp (TrpAMP). In this study, we have modeled the structure of human TrpRS bound to the activated ligand and the cognate tRNA. In addition, we have performed molecular dynamics (MD) simulations on these models as well as other complexes to capture the dynamical process of ligand induced conformational changes. We have analyzed both the local and global changes in the protein conformation from the protein structure network (PSN) of MD snapshots, by a method which was recently developed in our laboratory in the context of the functionally monomeric protein, methionyl tRNA synthetase. From these investigations, we obtain important information such as the ligand induced correlation between different residues of this protein, asymmetric binding of the ligands to the two subunits of the protein as seen in the crystal structure analysis, and the path of communication between the anticodon region and the aminoacylation site. Here we are able to elucidate the role of dimer interface at a level of detail, which has not been captured so far.

Optimum Design of Bridge Abutments under Seismic Conditions: Reliability-Based Approach

The paper focuses on the reliability-based design optimization of gravity wall bridge abutments when subjected to active condition during earthquakes. An analytical study considering the effect of uncertainties in the seismic analysis of bridge abutments is presented. Planar failure surface has been considered in conjunction with the pseudostatic limit equilibrium method for the calculation of the seismic active earth pressure. Analysis is conducted to evaluate the external stability of bridge abutments when subjected to earthquake loads. Reliability analysis is used to estimate the probability of failure in three modes of failure viz. sliding failure of the wall on its base, overturning failure about its toe (or eccentricity failure of the resultant force) and bearing failure of foundation soil below the base of wall. The properties of backfill and foundation soil below the base of abutment are treated as random variables. In addition, the uncertainties associated with characteristics of earthquake ground motions such as horizontal seismic acceleration and shear wave velocity propagating through backfill soil are considered. The optimum proportions of the abutment needed to maintain the stability are obtained against three modes of failure by targeting various component and system reliability indices. Studies have also been made to study the influence of various parameters on the seismic stability.

Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions

The availability of a significant number of the Structures of helical membrane proteins has prompted us to investigate the mode of helix-helix packing. In the present study, we have considered a dataset of alpha-helical membrane proteins representing Structures solved from all the known superfamilies. We have described the geometry of all the helical residues in terms of local coordinate axis at the backbone level. Significant inter-helical interactions have been considered as contacts by weighing the number of atom-atom contacts, including all the side-chain atoms. Such a definition of local axis and the contact criterion has allowed us to investigate the inter-helical interaction in a systematic and quantitative manner. We show that a single parameter (designated as alpha), which is derived from the parameters representing the Mutual orientation of local axes, is able to accurately Capture the details of helix-helix interaction. The analysis has been carried Out by dividing the dataset into parallel, anti-parallel, and perpendicular orientation of helices. The study indicates that a specific range of alpha value is preferred for interactions among the anti-parallel helices. Such a preference is also seen among interacting residues of parallel helices, however to a lesser extent. No such preference is seen in the case of perpendicular helices, the contacts that arise mainly due to the interaction Of Surface helices with the end of the trans-membrane helices. The Study Supports the prevailing view that the anti-parallel helices are well packed. However, the interactions between helices of parallel orientation are non-trivial. The packing in alpha-helical membrane proteins, which is systematically and rigorously investigated in this study, may prove to be useful in modeling of helical membrane proteins.

Investigation of inter-ion interactions in N,N,N',N'-tetramethylethylenediammonium dithiocyanate via experimental and theoretical charge density studies

The crystal structure of the N,N,N',N'-tetramethylethylenediammonium dithiocyanate salt has been examined by experimental charge density studies from high-resolution X-ray diffraction data. The corresponding results are compared with multipole refinements, using theoretical structure factors obtained from a periodic density functional theory calculation at the B3LYP level with a 6-31G** basis set. The salt crystallizes in space group P (1) over bar and contains only a single ion pair with an inversion center in the cation. The salt has thus one unique classical N+-H center dot center dot center dot(NCS)(-) hydrogen bond but also has six other weaker interactions: four C-H center dot center dot center dot S, one C-H center dot center dot center dot N, and one C-H center dot center dot center dot C-pi. The nature of all these interactions has been examined topologically using Bader's quantum theory of "atoms in molecules" and all eight of the Koch-Popelier criteria. The experimental and theoretical approaches agree well and both show that the inter-ion interactions, even in this simplest of systems, play an integrated and complex role in the packing of the ions in the crystal. Electrostatic potential maps are derived from experimental charge densities. This is the first time such a system has been examined in detail by these methods.

Optimum design of cantilever sheet pile walls in sandy soils using inverse reliability approach

In this paper an approach for obtaining depth and section modulus of the cantilever sheet pile wall using inverse reliability method is described. The proposed procedure employs inverse first order reliability method to obtain the design penetration depth and section modulus of the steel sheet pile wall in order that the reliability of the wall against failure modes must meet a desired level of safety. Sensitivity analysis is conducted to assess the effect of uncertainties in design parameters on the reliability of cantilever sheet pile walls. The analysis is performed by treating back fill soil properties, depth of the water table from the top of the sheet pile wall, yield strength of steel and section modulus of steel pile as random variables. Two limit states, viz., rotational and flexural failure of sheet pile wall are considered. The results using this approach are used to develop a set of reliability based design charts for different coefficients of variation of friction angle of the backfill (5%, 10% and 15%). System reliability considerations in terms of series and parallel systems are also studied.