For simulations of membranes and membrane proteins, the generation of the lipid bilayer is a critical step in the setup of the system. Membranes comprising multiple components pose a particular challenge, because the relative abundances need to be controlled and the equilibration of the system may take several microseconds. Here we present a comprehensive method for building membrane containing systems, characterized by simplicity and versatility. The program uses preset, coarse-grain lipid templates to build the membrane, and also allows on-the-fly generation of simple lipid types by specifying the headgroup, linker, and lipid tails on the command line. The resulting models can be equilibrated, after which a relaxed atomistic model can be obtained by reverse transformation. For multicomponent membranes, this provides an efficient means for generating equilibrated atomistic models. The method is called insane, an acronym for INSert membrANE. The program has been made available, together with the complemen...

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

Objective(s): Gallic acid is a natural phenolic compound found in several fruits and medicinal plants. It is reported to have several health-promoting effects. This review aims to summarize the pharmacological and biological activities of gallic acid in vitro and animal models to depict the pharmacological status of this compound for future studies.Materials and Methods: All relevant papers in the English language were collected up to June 2018. The keywords of gallic acid, antioxidant, anticancer, antimicrobial, gastrointestinal-, cardiovascular-, metabolic-, neuropsychological-, and miscellaneous- diseases were searched in Google Scholar, PubMed, and Scopus.Results: Several beneficial effects are reported for gallic acid, including antioxidant, anti-inflammatory, and antineoplastic properties. This compound has been reported to have therapeutic activities in gastrointestinal, neuropsychological, metabolic, and cardiovascular disorders. Conclusion: Current evidence confirms the pharmacological and therapeutic interventions of gallic acid in multiple health complications; however, available data are limited to just cellular and animal studies. Future investigations are essential to further define the safety and therapeutic efficacy of gallic acid in humans.

https://ijbms.mums.ac.ir/article_12251_1e2b9a1363690fd784d6b16a6d3a5d5a.pdf

Pharmacological effects of gallic acid in health and diseases: A mechanistic review.

The conformation space of a 20 residue antiparallel β-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Snapshots saved along the trajectory are grouped according to secondary structure into nodes of the network and the transitions between them are links. The conformation space network describes the significant free energy minima and their dynamic connectivity without requiring arbitrarily chosen reaction coordinates. As previously found for the Internet and the World-Wide Web as well as for social and biological networks, the conformation space network is scale-free and contains highly connected hubs like the native state which is the most populated free energy basin. Furthermore, the native basin exhibits a hierarchical organization, which is not found for a random heteropolymer lacking a predominant free-energy minimum. The network topology is used to identify conformations in the folding transition state (TS) ensemble, and provides a basis for understanding the heterogeneity of the TS and denatured state ensemble as well as the existence of multiple pathways.

The protein folding network

Enzyme-based biosensing devices have been extensively developed over the last few decades, and have proven to be innovative techniques in the qualitative and quantitative analysis of a variety of target substrates over a wide range of applications. Distinct advantages that enzyme-based biosensors provide, such as high sensitivity and specificity, portability, cost-effectiveness, and the possibilities for miniaturization and point-of-care diagnostic testing make them more and more attractive for research focused on clinical analysis, food safety control, or disease monitoring purposes. Therefore, this review article investigates the operating principle of enzymatic biosensors utilizing electrochemical, optical, thermistor, and piezoelectric measurement techniques and their applications in the literature, as well as approaches in improving the use of enzymes for biosensors.

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Immobilized enzymes in biosensor applications

Accurate prediction of relative solvent accessibilities (RSAs) of amino acid residues in proteins may be used to facilitate protein structure prediction and functional annotation. Toward that goal we developed a novel method for improved prediction of RSAs. Contrary to other machine learning-based methods from the literature, we do not impose a classification problem with arbitrary boundaries between the classes. Instead, we seek a continuous approximation of the real-value RSA using nonlinear regression, with several feed forward and recurrent neural networks, which are then combined into a consensus predictor. A set of 860 protein structures derived from the PFAM database was used for training, whereas validation of the results was carefully performed on several nonredundant control sets comprising a total of 603 structures derived from new Protein Data Bank structures and had no homology to proteins included in the training. Two classes of alternative predictors were developed for comparison with the regression-based approach: one based on the standard classification approach and the other based on a semicontinuous approximation with the so-called thermometer encoding. Furthermore, a weighted approximation, with errors being scaled by the observed levels of variability in RSA for equivalent residues in families of homologous structures, was applied in order to improve the results. The effects of including evolutionary profiles and the growth of sequence databases were assessed. In accord with the observed levels of variability in RSA for different ranges of RSA values, the regression accuracy is higher for buried than for exposed residues, with overall 15.3-15.8% mean absolute errors and correlation coefficients between the predicted and experimental values of 0.64-0.67 on different control sets. The new method outperforms classification-based algorithms when the real value predictions are projected onto two-class classification problems with several commonly used thresholds to separate exposed and buried residues. For example, classification accuracy of about 77% is consistently achieved on all control sets with a threshold of 25% RSA. A web server that enables RSA prediction using the new method and provides customizable graphical representation of the results is available at http://sable.cchmc.org.

/pdf/accurate-prediction-of-solvent-accessibility-using-neural-4ph5oz0axm.pdf

Accurate prediction of solvent accessibility using neural networks-based regression.

Motivation: The interactions among proteins and the resulting networks of such interactions have a central role in cell biology. Aligning these networks gives us important information, such as conserved complexes and evolutionary relationships. Although there have been several publications on the global alignment of protein networks; however, none of proposed methods are able to produce a highly conserved and meaningful alignment. Moreover, time complexity of current algorithms makes them impossible to use for multiple alignment of several large networks together. Results: We present a novel algorithm for the global alignment of protein–protein interaction networks. It uses a greedy method, based on the alignment scoring matrix, which is derived from both biological and topological information of input networks to find the best global network alignment. NETAL outperforms other global alignment methods in terms of several measurements, such as Edge Correctness, Largest Common Connected Subgraphs and the number of common Gene Ontology terms between aligned proteins. As the running time of NETAL is much less than other available methods, NETAL can be easily expanded to multiple alignment algorithm. Furthermore, NETAL overpowers all other existing algorithms in term of performance so that the short running time of NETAL allowed us to implement it as the first server for global alignment of protein–protein interaction networks. Availability: Binaries supported on linux are freely available for download at http://www.bioinf.cs.ipm.ir/software/netal. Contact: sh.arab@modares.ac.ir Supplementary information: Supplementary data are available at Bioinformatics online.

NETAL: a new graph-based method for global alignment of protein–protein interaction networks

A new, simple method based on information theory is introduced to predict the solvent accessibility of amino acid residues in various states defined by their different thresholds. Prediction is achieved by the application of information obtained from a single amino acid position or pair-information for a window of seventeen amino acids around the desired residue. Results obtained by pairwise information values are better than results from single amino acids. This reinforces the effect of the local environment on the accessibility of amino acid residues. The prediction accuracy of this method in a jackknife test system for two and three states is better than 70 and 60 %, respectively. A comparison of the results with those reported by others involving the same data set also testifies to a better prediction accuracy in our case.

https://portlandpress.com/biochemsoctrans/article-pdf/28/5/A148/833904/bst028a148b.pdf

Prediction of Protein Surface Accessibility Using Information Theory

Various disciplines are trying to solve one of the most noteworthy queries and broadly used concepts in biology, essentiality. Centrality is a primary index and a promising method for identifying essential nodes, particularly in biological networks. The newly created CentiServer is a comprehensive online resource that provides over 110 definitions of different centrality indices, their computational methods, and algorithms in the form of an encyclopedia. In addition, CentiServer allows users to calculate 55 centralities with the help of an interactive web-based application tool and provides a numerical result as a comma separated value (csv) file format or a mapped graphical format as a graph modeling language (GML) file. The standalone version of this application has been developed in the form of an R package. The web-based application (CentiServer) and R package (centiserve) are freely available at http://www.centiserver.org/

/pdf/centiserver-a-comprehensive-resource-web-based-application-2dwdn24643.pdf

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis

Motivation: Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the ...

/pdf/membuilder-a-web-based-graphical-interface-to-build-2ujn9uyhe4.pdf

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program

In the modern biomedical and therapeutic drug monitoring technology, development of high performance sensing methods for ergoline derivative drug, bromocriptine (BC), is a critical issue due to its plasma low concentration and important function in Parkinson’s disease. The results of the protein-ligand docking simulation consistent with competitive inhibition experimental study strongly support the binding of BC to the laccase active site. Therefore, a new biosensor for direct label-free detection of BC is presented based on surface plasmon resonance (SPR) using laccase from Bacillus sp. HR03 as a recognition element. The biosensor chip surface was constructed by covalent immobilization of the laccase on a SPR carboxymethyl dextran surface. The calculated kinetic affinity (KD) was 5.4 nM, which indicated the high affinity between BC and the immobilized laccase. The biosensor could determine BC in a linear detection range from 0.001 ng/ml to 1000 ng/ml with a lower detection limit of 0.001 ng/ml. The biosensor provided acceptable specificity with suitable recovery in simulated blood samples. This new biosensor represents a novel, fast, sensitive, economic cost effective and accurate method for the therapeutic monitoring and detection of the BC.

Seyed Shahriar Arab

Papers

NETAL: a new graph-based method for global alignment of protein–protein interaction networks

Prediction of Protein Surface Accessibility Using Information Theory

CentiServer: A Comprehensive Resource, Web-Based Application and R Package for Centrality Analysis

MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program

A novel enzyme based SPR-biosensor to detect bromocriptine as an ergoline derivative drug