Rigorous 3D inversion of marine CSEM data based on the integral equation method

Journal ArticleMarine controlled-source electromagnetic (MCSEM) surveys have become an important part of offshore petroleum exploration. However, due to enormous computational difficulties with full 3D inversion, practical interpretation of MCSEM data is still a very challenging problem. We present a new approach to 3D inversion of MCSEM data based on rigorous integral-equation (IE) forward modeling and a new IE representation of the sensitivity (Fréchet derivative matrix) of observed data to variations in sea-bottom conductivity. We develop a new form of the quasi-analytical approximation for models with variable background conductivity (QAVB) and apply this form for more efficient Fréchet derivative calculations. This approach requires just one forward modeling on every iteration of the regularized gradient-type inversion algorithm, which speeds up the computations significantly. We also use a regularized focusing inversion method, which provides a sharp boundary image of the petroleum reservoir. The methodology is tested on a 3D inversion of the synthetic EM data representing a typical MCSEM survey conducted for offshore petroleum exploration

3D inversion of towed streamer EM data: a model study of the Harding field with comparison to CSEM

provide an early study of the challenges involved in validating offshore electromagnetic (EM) data acquired using a towed streamer receiver (currently under development) and compare the results with existing seabed-based marine controlled source electromagnetic (CSEM) technology. T he premise of the various marine controlled source electromagnetic (CSEM) methods is sensitivity to the lateral extents and thicknesses of resistive bodies embedded in conductive hosts. Over the past decade, CSEM surveys have been characterized by arrays of fixed ocean bottom receivers and towed transmitters, and applied to de-risking exploration and appraisal projects with direct hydrocarbon indication. The most successful applications of CSEM to date have been in complement to those seismic interpretations where lithological or fluid variations cannot be adequately discriminated by seismic methods alone (e.g., Hesthammer et al., 2010). However, relatively high acquisition costs have represented a significant obstacle to widespread adoption of conventional CSEM technology, particularly in frontier basins. To this end, a towed streamer system capable of simultaneous seismic and electromagnetic (EM) data acquisition has recently been developed and tested in the North Sea In exploration, hydrocarbon reserves and resources are estimated with varying confidence from volumetrics that are predicted from different 3D earth models and scenarios. Quantitative interpretation of EM data is inherently reliant upon 3D earth models derived from inversion since EM data cannot simply be separated or transformed with linear operators as per seismic methods. However, methods for inverting CSEM data are complicated by the very small, nonunique and non-linear responses of hydrocarbon-bearing reservoir units when compared to the measured total fields. Moreover, 3D inversion of towed streamer EM data poses a significant challenge because of the increased scale of the surveys, the requirement for high resolution models, and the significantly increased number of transmitter-receiver pairs. Inverting towed streamer EM data Large-scale conventional CSEM surveys may have in the order of hundreds of fixed receivers, and in the order of thousands of transmitter positions. Reciprocity is routinely exploited in 3D conventional CSEM modelling and inversion to minimize the number of source terms that need to be solved (e.g.

Inferring stabilizing mutations from protein phylogenies : application to influenza hemagglutinin

One selection pressure shaping sequence evolution is the requirement that a protein fold with sufficient stability to perform its biological functions. We present a conceptual framework that explains how this requirement causes the probability that a particular amino acid mutation is fixed during evolution to depend on its effect on protein stability. We mathematically formalize this framework to develop a Bayesian approach for inferring the stability effects of individual mutations from homologous protein sequences of known phylogeny. This approach is able to predict published experimentally measured mutational stability effects (ΔΔG values) with an accuracy that exceeds both a state-of-the-art physicochemical modeling program and the sequence-based consensus approach. As a further test, we use our phylogenetic inference approach to predict stabilizing mutations to influenza hemagglutinin. We introduce these mutations into a temperature-sensitive influenza virus with a defect in its hemagglutinin gene and experimentally demonstrate that some of the mutations allow the virus to grow at higher temperatures. Our work therefore describes a powerful new approach for predicting stabilizing mutations that can be successfully applied even to large, complex proteins such as hemagglutinin. This approach also makes a mathematical link between phylogenetics and experimentally measurable protein properties, potentially paving the way for more accurate analyses of molecular evolution

Stabilization by Fusion to the C-terminus of Hyperthermophile Sulfolobus tokodaii RNase HI: A Possibility of Protein Stabilization Tag

RNase HI from the hyperthermophile Sulfolobus tokodaii (Sto-RNase HI) is stabilized by its C-terminal residues. In this work, the stabilization effect of the Sto-RNase HI C-terminal residues was investigated in detail by thermodynamic measurements of the stability of variants lacking the disulfide bond (C58/145A), or the six C-terminal residues (ΔC6) and by structural analysis of ΔC6. The results showed that the C-terminal does not affect overall structure and stabilization is caused by local interactions of the C-terminal, suggesting that the C-terminal residues could be used as a “stabilization tag.” The Sto-RNase HI C-terminal residues (-IGCIILT) were introduced as a tag on three proteins. Each chimeric protein was more stable than its wild-type protein. These results suggested the possibility of a simple stabilization technique using a stabilization tag such as Sto-RNase HI C-terminal residues

A Rigidifying Salt-Bridge Favors the Activity of Thermophilic Enzyme at High Temperatures at the Expense of Low-Temperature Activity

Although enzymes from thermophiles thriving in hot habitats are more stable than their mesophilic homologs, they are often less active at low temperatures. One theory suggests that extra stabilizing interactions found in thermophilic enzymes may increase their rigidity and decrease enzymatic activity at lower temperatures. We used acylphosphatase as a model to study how flexibility affects enzymatic activity. This enzyme has a unique structural feature in that an invariant arginine residue, which takes part in catalysis, is restrained by a salt-bridge in the thermophilic homologs but not in its mesophilic homologs. Here, we demonstrate the trade-offs between flexibility and enzymatic activity by disrupting the salt-bridge in a thermophilic acylphosphatase and introducing it in the mesophilic human homolog. Our results suggest that the salt-bridge is a structural adaptation for thermophilic acylphosphatases as it entropically favors enzymatic activity at high temperatures by restricting the flexibility of the active-site residue. However, at low temperatures the salt-bridge reduces the enzymatic activity because of a steeper temperature-dependency of activity

Role of Active Site Rigidity in Activity: MD Simulation and Fluorescence Study on a Lipase Mutant

Relationship between stability and activity of enzymes is maintained by underlying conformational flexibility. In thermophilic enzymes, a decrease in flexibility causes low enzyme activity while in less stable proteins such as mesophiles and psychrophiles, an increase in flexibility is associated with enhanced enzyme activity. Recently, we identified a mutant of a lipase whose stability and activity were enhanced simultaneously. In this work, we probed the conformational dynamics of the mutant and the wild type lipase, particularly flexibility of their active site using molecular dynamic simulations and time-resolved fluorescence techniques. In contrast to the earlier observations, our data show that active site of the mutant is more rigid than wild type enzyme. Further investigation suggests that this lipase needs minimal reorganization/flexibility of active site residues during its catalytic cycle. Molecular dynamic simulations suggest that catalytically competent active site geometry of the mutant is relatively more preserved than wild type lipase, which might have led to its higher enzyme activity. Our study implies that widely accepted positive correlation between conformation flexibility and enzyme activity need not be stringent and draws attention to the possibility that high enzyme activity can still be accomplished in a rigid active site and stable protein structures. This finding has a significant implication towards better understanding of involvement of dynamic motions in enzyme catalysis and enzyme engineering through mutations in active site

Stabilizing Salt-Bridge Enhances Protein Thermostability by Reducing the Heat Capacity Change of Unfolding

Most thermophilic proteins tend to have more salt bridges, and achieve higher thermostability by up-shifting and broadening their protein stability curves. While the stabilizing effect of salt-bridge has been extensively studied, experimental data on how salt-bridge influences protein stability curves are scarce. Here, we used double mutant cycles to determine the temperature-dependency of the pair-wise interaction energy and the contribution of salt-bridges to ΔCp in a thermophilic ribosomal protein L30e. Our results showed that the pair-wise interaction energies for the salt-bridges E6/R92 and E62/K46 were stabilizing and insensitive to temperature changes from 298 to 348 K. On the other hand, the pair-wise interaction energies between the control long-range ion-pair of E90/R92 were negligible. The ΔCp of all single and double mutants were determined by Gibbs-Helmholtz and Kirchhoff analyses. We showed that the two stabilizing salt-bridges contributed to a reduction of ΔCp by 0.8–1.0 kJ mol−1 K−1. Taken together, our results suggest that the extra salt-bridges found in thermophilic proteins enhance the thermostability of proteins by reducing ΔCp, leading to the up-shifting and broadening of the protein stability curves

Joining S100 proteins and migration:for better or for worse, in sickness and in health

The vast diversity of S100 proteins has demonstrated a multitude of biological correlations with cell growth, cell differentiation and cell survival in numerous physiological and pathological conditions in all cells of the body. This review summarises some of the reported regulatory functions of S100 proteins (namely S100A1, S100A2, S100A4, S100A6, S100A7, S100A8/S100A9, S100A10, S100A11, S100A12, S100B and S100P) on cellular migration and invasion, established in both culture and animal model systems and the possible mechanisms that have been proposed to be responsible. These mechanisms involve intracellular events and components of the cytoskeletal organisation (actin/myosin filaments, intermediate filaments and microtubules) as well as extracellular signalling at different cell surface receptors (RAGE and integrins). Finally, we shall attempt to demonstrate how aberrant expression of the S100 proteins may lead to pathological events and human disorders and furthermore provide a rationale to possibly explain why the expression of some of the S100 proteins (mainly S100A4 and S100P) has led to conflicting results on motility, depending on the cells used. © 2013 Springer Basel