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computational structural biology

Su Lui, Xiaohong Joe Zhou, John A Sweeney, Qiyong Gong
Unlike neurologic conditions, such as brain tumors, dementia, and stroke, the neural mechanisms for all psychiatric disorders remain unclear. A large body of research obtained with structural and functional magnetic resonance imaging, positron emission tomography/single photon emission computed tomography, and optical imaging has demonstrated regional and illness-specific brain changes at the onset of psychiatric disorders and in individuals at risk for such disorders. Many studies have shown that psychiatric medications induce specific measurable changes in brain anatomy and function that are related to clinical outcomes...
November 2016: Radiology
Agnieszka Rybarczyk, Paulina Jackowiak, Marek Figlerowicz, Jacek Blazewicz
Since the beginning of the 21st century, an increasing interest in the research of ribonucleic acids has been observed in response to a surprising discovery of the role that RNA molecules play in the biological systems. It was demonstrated that they do not only take part in the protein synthesis (mRNA, rRNA, tRNA) but also are involved in the regulation of gene expression. Several classes of small regulatory RNAs have been discovered (e.g. microRNA, small interfering RNA, piwiRNA). Most of them are excised from specific double-stranded RNA precursors by enzymes that belong to the RNaseIII family (Drosha, Dicer or Dicer-like proteins)...
October 19, 2016: Acta Biochimica Polonica
Caterina Catalanotto, Carlo Cogoni, Giuseppe Zardo
The finding that small non-coding RNAs (ncRNAs) are able to control gene expression in a sequence specific manner has had a massive impact on biology. Recent improvements in high throughput sequencing and computational prediction methods have allowed the discovery and classification of several types of ncRNAs. Based on their precursor structures, biogenesis pathways and modes of action, ncRNAs are classified as small interfering RNAs (siRNAs), microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), endogenous small interfering RNAs (endo-siRNAs or esiRNAs), promoter associate RNAs (pRNAs), small nucleolar RNAs (snoRNAs) and sno-derived RNAs...
October 13, 2016: International Journal of Molecular Sciences
Alberto Avolio
Blood vessels function as conduits for distribution of blood throughout the circulatory system. Large arteries, in addition to the essential conduit function, also serve to dampen the effect of pulsatile ventricular ejection that generates pulsatile pressure with each cardiac cycle; that is, they exhibit a 'cushion' function. The conduit function can be compromised by intimal effects that cause obstruction to flow, generally attributed to plaque formation due to intimal changes affected by atherosclerotic processes...
September 2016: Journal of Hypertension
Liu Chunbao, Li Li, Lei Yulong, Liu Changsuo, Zhang Yubo
Fish-like, dolphin-like, and bionic nonsmooth surfaces were employed in a hydraulic torque converter to achieve drag reduction and performance improvement, which were aimed at reducing profile loss, impacting loss and friction loss, respectively. YJSW335, a twin turbine torque converter, was bionically designed delicately. The biological characteristics consisted of fish-like blades in all four wheels, dolphin-like structure in the first turbine and the stator, and nonsmooth surfaces in the pump. The prediction performance of bionic YJSW335, obtained by computational fluid dynamics simulation, was improved compared with that of the original model, and then it could be proved that drag reduction had been achieved...
2016: Applied Bionics and Biomechanics
Efeturi Abraham Onoabedje, Akachukwu Ibezim, Sunday Nwankwor Okafor, Ufuoma Shalom Onoabedje, Uchechukwu Chris Okoro
Penicillin binding proteins (PBPs) are normal constituents of bacterial which are absent in mammalian cells. The theoretical binding modes of known oxazin-5-ones toward the protein were used as a guide to synthesis new inhibitors. Structural studies of protein-ligand complexes revealed that conformational discrepancies of the derivatives in the protein's binding site gave rise to the variation in their inhibition constant which ranged from 68.58 μM to 2.04 mM. Biological assay results further confirmed the antibiotic potencies of the studied compounds...
2016: PloS One
Carolyn N Haarmeyer, Matthew D Smith, Shishir Chundawat, Deanne Sammond, Timothy A Whitehead
Biological-mediated conversion of pretreated lignocellulosic biomass to biofuels and biochemicals is a promising avenue towards energy sustainability. However, a critical impediment to the commercialization of cellulosic biofuel production is the high cost of cellulase enzymes needed to deconstruct biomass into fermentable sugars. One major factor driving cost is cellulase adsorption and inactivation in the presence of lignin, yet we currently have a poor understanding of the protein structure-function relationships driving this adsorption...
October 17, 2016: Biotechnology and Bioengineering
Sourabh Boruah, Damien L Subit, Glenn R Paskoff, Barry S Shender, Jeff R Crandall, Robert S Salzar
The strength and compliance of the dense cortical layers of the human skull have been examined since the beginning of the 20th century with the wide range in the observed mechanical properties attributed to natural biological variance. Since this variance may be explained by the difference in structural arrangement of bone tissue, micro-computed tomography (µCT) was used in conjunction with mechanical testing to study the relationship between the microstructure of human skull cortical coupons and their mechanical response...
October 1, 2016: Journal of the Mechanical Behavior of Biomedical Materials
Ron Henkel, Robert Hoehndorf, Tim Kacprowski, Christian Knüpfer, Wolfram Liebermeister, Dagmar Waltemath
Systems biology models are rapidly increasing in complexity, size and numbers. When building large models, researchers rely on software tools for the retrieval, comparison, combination and merging of models, as well as for version control. These tools need to be able to quantify the differences and similarities between computational models. However, depending on the specific application, the notion of 'similarity' may greatly vary. A general notion of model similarity, applicable to various types of models, is still missing...
October 14, 2016: Briefings in Bioinformatics
Melissa L Knothe Tate, Peter W Gunning, Vittorio Sansalone
Stem cell "mechanomics" refers to the effect of mechanical cues on stem cell and matrix biology, where cell shape and fate are intrinsic manifestations of form and function. Before specialization, the stem cell itself serves as a sensor and actuator; its structure emerges from its local mechanical milieu as the cell adapts over time. Coupling of novel spatiotemporal imaging and computational methods allows for linking of the energy of adaptation to the structure, biology and mechanical function of the cell...
October 14, 2016: Bioarchitecture
A F G Glawar, R F Martínez, B J Ayers, M A Hollas, N Ngo, S Nakagawa, A Kato, T D Butters, G W J Fleet, S F Jenkinson
This paper explores the computer modelling aided design and synthesis of β-N-acetylhexosaminidase inhibitors along with their applicability to human disease treatment through biological evaluation in both an enzymatic and cellular setting. We investigated the importance of individual stereocenters, variations in structure-activity relationships along with factors influencing cell penetration. To achieve these goals we modified nitrogen heterocycles in terms of ring size, side chains present and ring nitrogen derivatization...
October 13, 2016: Organic & Biomolecular Chemistry
Andrea Sinz
Chemical cross-linking combined with mass spectrometry (MS) and computational modeling has evolved as an alternative method to address fundamental questions in structural biology. The constraints revealed by the cross-links yield valuable distance information and allow one to deduce three-dimensional structural information on very large and transient protein complexes. During the past few years, technical advances in the cross-linking/MS approach have been enormous, mainly owing to the fantastic advances in MS technology, and it is easily overlooked that significant progress has been made in the design of novel cross-linking reagents...
October 12, 2016: Analytical and Bioanalytical Chemistry
Elizabeth Gross, Brent Davis, Kenneth L Ho, Daniel J Bates, Heather A Harrington
Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation and model selection. These are all optimization problems, well known to be challenging due to nonlinearity, non-convexity and multiple local optima. Furthermore, the challenges are compounded when only partial data are available. Here, we consider polynomial models (e.g. mass-action chemical reaction networks at steady state) and describe a framework for their analysis based on optimization using numerical algebraic geometry...
October 2016: Journal of the Royal Society, Interface
James Rafferty, Lance Farr, Tim James, David Chase, John Heinrich, Michael Brady
We present a novel, high-resolution magnetic resonance technique, fine structure analysis (FSA) for the quantification and analysis of amorphous and quasi-amorphous biological structures. The one-dimensional technique is introduced mathematically and then applied to one simulated phantom, two physical phantoms and a set of ex vivo biological samples, scanned with interpoint spacings of 0.0038-0.195 mm and cross-sectional sizes of 3 × 3 or 5 × 5 mm. The simulated phantom and one of the physical phantoms consists of randomly arranged beads of known size in two and three dimensions, respectively...
October 2016: Journal of the Royal Society, Interface
Qin Wang, Simone Sciabola, Gabriela Barreiro, Xinjun Hou, Guoyun Bai, Michael J Shapiro, Frank E Koehn, Anabella Villalobos, Matthew P Jacobson
Macrocycles pose challenges for computer-aided drug design due to their conformational complexity. One fundamental challenge is identifying all low-energy conformations of the macrocyclic ring, which is important for modeling target binding, passive membrane permeation, and other conformation-dependent properties. Macrocyclic polyketides are medically and biologically important natural products characterized by structural and functional diversity. Advances in synthetic biology and semi-synthetic methods may enable creation of an even more diverse set of non-natural product polyketides for drug discovery and other applications...
October 12, 2016: Journal of Chemical Information and Modeling
H Chai, J Zhang, G Yang, Z Ma
DNA-binding proteins play a pivotal role in various biological activities. Identification of DNA-binding residues (DBRs) is of great importance for understanding the mechanism of gene regulations and chromatin remodeling. Most traditional computational methods usually construct their predictors on static non-redundant datasets. They excluded many homologous DNA-binding proteins so as to guarantee the generalization capability of their models. However, those ignored samples may potentially provide useful clues when studying protein-DNA interactions, which have not obtained enough attention...
October 12, 2016: Molecular BioSystems
Thomas Gueudré, Carlo Baldassi, Marco Zamparo, Martin Weigt, Andrea Pagnani
Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are urgently needed. Such methods should connect multiple scales from evolutionary conserved interactions between families of homologous proteins, over the identification of specifically interacting proteins in the case of multiple paralogs inside a species, down to the prediction of residues being in physical contact across interaction interfaces...
October 11, 2016: Proceedings of the National Academy of Sciences of the United States of America
Bo Lin, Shihua Xiang, Mengsen Li
Nicotinic acetylcholine receptors (nAChRs) are targets for developing new drugs to treat severe pain, nicotine addiction, Alzheimer disease, epilepsy, etc. α-Conotoxins are biologically and chemically diverse. With 12-19 residues and two disulfides, they can be specifically selected for different nAChRs. Acetylcholine-binding proteins from Aplysia californica (Ac-AChBP) are homologous to the ligand-binding domains of nAChRs and pharmacologically similar. X-ray structures of the α-conotoxin in complex with Ac-AChBP in addition to computer modeling have helped to determine the binding site of the important residues of α-conotoxin and its affinity for nAChR subtypes...
October 11, 2016: Marine Drugs
Hessam Malmir, Muhammad Sahimi, M Reza Rahimi Tabar
Understanding the properties of random packings of solid objects is of critical importance to a wide variety of fundamental scientific and practical problems. The great majority of the previous works focused, however, on packings of spherical and sphere-like particles. We report the first detailed simulation and characterization of packings of non-overlapping cubic particles. Such packings arise in a variety of problems, ranging from biological materials, to colloids and fabrication of porous scaffolds using salt powders...
October 11, 2016: Scientific Reports
Shunian Xiang, Ke Liu, Zhangming Yan, Yaou Zhang, Zhirong Sun
N6-Methyladenosine (m6A) is the most common mRNA modification; it occurs in a wide range of taxon and is associated with many key biological processes. High-throughput experiments have identified m6A-peaks and sites across the transcriptome, but studies of m6A sites at the transcriptome-wide scale are limited to a few species and tissue types. Therefore, the computational prediction of mRNA m6A sites has become an important strategy. In this study, we integrated multiple features of mRNA (flanking sequences, local secondary structure information, and relative position information) and trained a SVM classifier to predict m6A sites in mammalian mRNA sequences...
2016: PloS One
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