Prediction of Protein Tertiary Structure using Genetic Algorithm

Proteins are essential for the biological processes in the human body. They can only perform their functions when they fold into their tertiary structure .Protein structure can be determined experimentally and computationally. Experimental methods are time consuming and high-priced and it is not always feasible to identify the protein structure experimentally. In order to predict the protein structure using computational methods, the problem is formulated as an optimization problem and the goal is to find the lowest free energy conformation. In this paper, Genetic Algorithm (GA) based optimization is used. This algorithm is adapted to search the protein conformational search space to find the lowest free energy conformation. Interestingly, the algorithm was able to find the lowest free energy conformation for a test protein (i.e. Met enkephalin) using ECEPP force fields

Genetic algorithm in ab initio protein structure prediction using low resolution model : a review

Proteins are sequences of amino acids bound into a linear chain that adopt a specific folded three-dimensional (3D) shape. This specific folded shape enables proteins to perform specific tasks. The protein structure prediction (PSP) by ab initio or de novo approach is promising amongst various available computational methods and can help to unravel the important relationship between sequence and its corresponding structure. This article presents the ab initio protein structure prediction as a conformational search problem in low resolution model using genetic algorithm. As a review, the essence of twin removal, intelligence in coding, the development and application of domain specific heuristics garnered from the properties of the resulting model and the protein core formation concept discussed are all highly relevant in attempting to secure the best solution

Global gene expression profiling of healthy human brain and its application in studying neurological disorders

The human brain is the most complex structure known to mankind and one of the greatest challenges in modern biology is to understand how it is built and organized. The power of the brain arises from its variety of cells and structures, and ultimately where and when different genes are switched on and off throughout the brain tissue. In other words, brain function depends on the precise regulation of gene expression in its sub-anatomical structures. But, our understanding of the complexity and dynamics of the transcriptome of the human brain is still incomplete. To fill in the need, we designed a gene expression model that accurately defines the consistent blueprint of the brain transcriptome; thereby, identifying the core brain specific transcriptional processes conserved across individuals. Functionally characterizing this model would provide profound insights into the transcriptional landscape, biological pathways and the expression distribution of neurotransmitter systems. Here, in this dissertation we developed an expression model by capturing the similarly expressed gene patterns across congruently annotated brain structures in six individual brains by using data from the Allen Brain Atlas (ABA). We found that 84% of genes are expressed in at least one of the 190 brain structures. By employing hierarchical clustering we were able to show that distinct structures of a bigger brain region can cluster together while still retaining their expression identity. Further, weighted correlation network analysis identified 19 robust modules of coexpressing genes in the brain that demonstrated a wide range of functional associations. Since signatures of local phenomena can be masked by larger signatures, we performed local analysis on each distinct brain structure. Pathway and gene ontology enrichment analysis on these structures showed, striking enrichment for brain region specific processes. Besides, we also mapped the structural distribution of the gene expression profiles of genes associated with major neurotransmission systems in the human. We also postulated the utility of healthy brain tissue gene expression to predict potential genes involved in a neurological disorder, in the absence of data from diseased tissues. To this end, we developed a supervised classification model, which achieved an accuracy of 84% and an AUC (Area Under the Curve) of 0.81 from ROC plots, for predicting autism-implicated genes using the healthy expression model as the baseline. This study represents the first use of healthy brain gene expression to predict the scope of genes in autism implication and this generic methodology can be applied to predict genes involved in other neurological disorders

Assembling the Tat protein translocase

The twin-arginine protein translocation system (Tat) transports folded proteins across the bacterial cytoplasmic membrane and the thylakoid membranes of plant chloroplasts. The Tat transporter is assembled from multiple copies of the membrane proteins TatA, TatB, and TatC. We combine sequence co-evolution analysis, molecular simulations, and experimentation to define the interactions between the Tat proteins of Escherichia coli at molecular-level resolution. In the TatBC receptor complex the transmembrane helix of each TatB molecule is sandwiched between two TatC molecules, with one of the inter-subunit interfaces incorporating a functionally important cluster of interacting polar residues. Unexpectedly, we find that TatA also associates with TatC at the polar cluster site. Our data provide a structural model for assembly of the active Tat translocase in which substrate binding triggers replacement of TatB by TatA at the polar cluster site. Our work demonstrates the power of co-evolution analysis to predict protein interfaces in multi-subunit complexes

Aerospace medicine and biology: A continuing bibliography with indexes (supplement 333)

This bibliography lists 122 reports, articles and other documents introduced into the NASA Scientific and Technical Information System during January, 1990. Subject coverage includes: aerospace medicine and psychology, life support systems and controlled environments, safety equipment, exobiology and extraterrestrial life, and flight crew behavior and performance

Applications of Artificial Intelligence in Power Systems

Artificial intelligence tools, which are fast, robust and adaptive can overcome the drawbacks of traditional solutions for several power systems problems. In this work, applications of AI techniques have been studied for solving two important problems in power systems. The first problem is static security evaluation (SSE). The objective of SSE is to identify the contingencies in planning and operations of power systems. Numerical conventional solutions are time-consuming, computationally expensive, and are not suitable for online applications. SSE may be considered as a binary-classification, multi-classification or regression problem. In this work, multi-support vector machine is combined with several evolutionary computation algorithms, including particle swarm optimization (PSO), differential evolution, Ant colony optimization for the continuous domain, and harmony search techniques to solve the SSE. Moreover, support vector regression is combined with modified PSO with a proposed modification on the inertia weight in order to solve the SSE. Also, the correct accuracy of classification, the speed of training, and the final cost of using power equipment heavily depend on the selected input features. In this dissertation, multi-object PSO has been used to solve this problem. Furthermore, a multi-classifier voting scheme is proposed to get the final test output. The classifiers participating in the voting scheme include multi-SVM with different types of kernels and random forests with an adaptive number of trees. In short, the development and performance of different machine learning tools combined with evolutionary computation techniques have been studied to solve the online SSE. The performance of the proposed techniques is tested on several benchmark systems, namely the IEEE 9-bus, 14-bus, 39-bus, 57-bus, 118-bus, and 300-bus power systems. The second problem is the non-convex, nonlinear, and non-differentiable economic dispatch (ED) problem. The purpose of solving the ED is to improve the cost-effectiveness of power generation. To solve ED with multi-fuel options, prohibited operating zones, valve point effect, and transmission line losses, genetic algorithm (GA) variant-based methods, such as breeder GA, fast navigating GA, twin removal GA, kite GA, and United GA are used. The IEEE systems with 6-units, 10-units, and 15-units are used to study the efficiency of the algorithms

Applications of Artificial Intelligence in Power Systems

Artificial intelligence tools, which are fast, robust and adaptive can overcome the drawbacks of traditional solutions for several power systems problems. In this work, applications of AI techniques have been studied for solving two important problems in power systems. The first problem is static security evaluation (SSE). The objective of SSE is to identify the contingencies in planning and operations of power systems. Numerical conventional solutions are time-consuming, computationally expensive, and are not suitable for online applications. SSE may be considered as a binary-classification, multi-classification or regression problem. In this work, multi-support vector machine is combined with several evolutionary computation algorithms, including particle swarm optimization (PSO), differential evolution, Ant colony optimization for the continuous domain, and harmony search techniques to solve the SSE. Moreover, support vector regression is combined with modified PSO with a proposed modification on the inertia weight in order to solve the SSE. Also, the correct accuracy of classification, the speed of training, and the final cost of using power equipment heavily depend on the selected input features. In this dissertation, multi-object PSO has been used to solve this problem. Furthermore, a multi-classifier voting scheme is proposed to get the final test output. The classifiers participating in the voting scheme include multi-SVM with different types of kernels and random forests with an adaptive number of trees. In short, the development and performance of different machine learning tools combined with evolutionary computation techniques have been studied to solve the online SSE. The performance of the proposed techniques is tested on several benchmark systems, namely the IEEE 9-bus, 14-bus, 39-bus, 57-bus, 118-bus, and 300-bus power systems. The second problem is the non-convex, nonlinear, and non-differentiable economic dispatch (ED) problem. The purpose of solving the ED is to improve the cost-effectiveness of power generation. To solve ED with multi-fuel options, prohibited operating zones, valve point effect, and transmission line losses, genetic algorithm (GA) variant-based methods, such as breeder GA, fast navigating GA, twin removal GA, kite GA, and United GA are used. The IEEE systems with 6-units, 10-units, and 15-units are used to study the efficiency of the algorithms

Molecular structure of promoter-bound yeast TFIID.

Transcription preinitiation complex assembly on the promoters of protein encoding genes is nucleated in vivo by TFIID composed of the TATA-box Binding Protein (TBP) and 13 TBP-associate factors (Tafs) providing regulatory and chromatin binding functions. Here we present the cryo-electron microscopy structure of promoter-bound yeast TFIID at a resolution better than 5 Å, except for a flexible domain. We position the crystal structures of several subunits and, in combination with cross-linking studies, describe the quaternary organization of TFIID. The compact tri lobed architecture is stabilized by a topologically closed Taf5-Taf6 tetramer. We confirm the unique subunit stoichiometry prevailing in TFIID and uncover a hexameric arrangement of Tafs containing a histone fold domain in the Twin lobe