keyword
MENU ▼
Read by QxMD icon Read
search

computational structural biology

keyword
https://www.readbyqxmd.com/read/28736737/diffraction-tomography-with-fourier-ptychography
#1
Roarke Horstmeyer, Jaebum Chung, Xiaoze Ou, Guoan Zheng, Changhuei Yang
This paper presents a technique to image the complex index of refraction of a sample across three dimensions. The only required hardware is a standard microscope and an array of LEDs. The method, termed Fourier ptychographic tomography (FPT), first captures a sequence of intensity-only images of a sample under angularly varying illumination. Then, using principles from ptychography and diffraction tomography, it computationally solves for the sample structure in three dimensions. The experimental microscope demonstrates a lateral spatial resolution of 0...
August 2016: Optica
https://www.readbyqxmd.com/read/28735540/the-n%C3%A2-%C3%AF-interaction
#2
Robert W Newberry, Ronald T Raines
The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group...
July 23, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28733924/cellular-mechanosensitivity-to-substrate-stiffness-decreases-with-increasing-dissimilarity-to-cell-stiffness
#3
Tamer Abdalrahman, Laura Dubuis, Jason Green, Neil Davies, Thomas Franz
Computational modelling has received increasing attention to investigate multi-scale coupled problems in micro-heterogeneous biological structures such as cells. In the current study, we investigated for a single cell the effects of (1) different cell-substrate attachment (2) and different substrate modulus [Formula: see text] on intracellular deformations. A fibroblast was geometrically reconstructed from confocal micrographs. Finite element models of the cell on a planar substrate were developed. Intracellular deformations due to substrate stretch of [Formula: see text], were assessed for: (1) cell-substrate attachment implemented as full basal contact (FC) and 124 focal adhesions (FA), respectively, and [Formula: see text]140 KPa and (2) [Formula: see text], 140, 1000, and 10,000 KPa, respectively, and FA attachment...
July 21, 2017: Biomechanics and Modeling in Mechanobiology
https://www.readbyqxmd.com/read/28732461/a-deep-convolutional-neural-network-approach-to-single-particle-recognition-in-cryo-electron-microscopy
#4
Yanan Zhu, Qi Ouyang, Youdong Mao
BACKGROUND: Single-particle cryo-electron microscopy (cryo-EM) has become a mainstream tool for the structural determination of biological macromolecular complexes. However, high-resolution cryo-EM reconstruction often requires hundreds of thousands of single-particle images. Particle extraction from experimental micrographs thus can be laborious and presents a major practical bottleneck in cryo-EM structural determination. Existing computational methods for particle picking often use low-resolution templates for particle matching, making them susceptible to reference-dependent bias...
July 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28730495/modeling-of-receptor-tyrosine-kinase-signaling-computational-and-experimental-protocols
#5
Dirk Fey, Edita Aksamitiene, Anatoly Kiyatkin, Boris N Kholodenko
The advent of systems biology has convincingly demonstrated that the integration of experiments and dynamic modelling is a powerful approach to understand the cellular network biology. Here we present experimental and computational protocols that are necessary for applying this integrative approach to the quantitative studies of receptor tyrosine kinase (RTK) signaling networks. Signaling by RTKs controls multiple cellular processes, including the regulation of cell survival, motility, proliferation, differentiation, glucose metabolism, and apoptosis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28730431/protocols-for-molecular-dynamics-simulations-of-rna-nanostructures
#6
Taejin Kim, Wojciech K Kasprzak, Bruce A Shapiro
Molecular dynamics (MD) simulations have been used as one of the main research tools to study a wide range of biological systems and bridge the gap between X-ray crystallography or NMR structures and biological mechanism. In the field of RNA nanostructures, MD simulations have been used to fix steric clashes in computationally designed RNA nanostructures, characterize the dynamics, and investigate the interaction between RNA and other biomolecules such as delivery agents and membranes.In this chapter we present examples of computational protocols for molecular dynamics simulations in explicit and implicit solvent using the Amber Molecular Dynamics Package...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729343/flowtrace-simple-visualization-of-coherent-structures-in-biological-fluid-flows
#7
William Gilpin, Vivek N Prakash, Manu Prakash
We present a simple, intuitive algorithm for visualizing time-varying flow fields that can reveal complex flow structures with minimal user intervention. We apply this technique to a variety of biological systems, including the swimming currents of invertebrates and the collective motion of swarms of insects. We compare our results to more experimentally-difficult and mathematically-sophisticated techniques for identifying patterns in fluid flows, and suggest that our tool represents an essential "middle ground" allowing experimentalists to easily determine whether a system exhibits interesting flow patterns and coherent structures without resorting to more intensive techniques...
July 20, 2017: Journal of Experimental Biology
https://www.readbyqxmd.com/read/28727915/improving-accuracy-diversity-and-speed-with-prime-macrocycle-conformational-sampling
#8
Dan Sindhikara, Steven A Spronk, Tyler Day, Ken Borrelli, Daniel L Cheney, Shana L Posy
A novel method for exploring macrocycle conformational space, Prime Macrocycle Conformational Sampling (Prime-MCS), is introduced and evaluated in the context of other available algorithms (Molecular Dynamics, LowModeMD in MOE, and MacroModel Baseline Search). The algorithms were benchmarked on a dataset of 208 macrocycles which was curated for diversity from the Cambridge Structural Database, the Protein Databank, and the Biologically Interesting Molecule Reference Dictionary. The algorithms were evaluated in terms of accuracy (ability to reproduce the crystal structure), diversity (coverage of conformational space), and computational speed...
July 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28726760/synthesis-antitumor-evaluation-and-molecular-docking-of-new-morpholine-based-heterocycles
#9
Zeinab A Muhammad, Mastoura M Edrees, Rasha A M Faty, Sobhi M Gomha, Seham S Alterary, Yahia N Mabkhot
A series of new morpholinylchalcones was prepared and then used as building blocks for constructing a series of 7-morpholino-2-thioxo-2,3-dihydropyrido[2,3-d]pyrimidin-4(1H)-ones via their reaction with 6-aminothiouracil. The latter thiones reacted with the appropriate hydrazonoyl chloride to give the corresponding pyrido[2,3-d][1,2,4]triazolo[4,3-a]pyrimidin-5(1H)-ones. The assigned structures for all the newly synthesized compounds were confirmed on the basis of elemental analyses and spectral data and the mechanisms of their formation were also discussed...
July 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28721665/micro-computed-tomography-characterization-of-tissue-engineering-scaffolds-effects-of-pixel-size-and-rotation-step
#10
Ibrahim Fatih Cengiz, Joaquim Miguel Oliveira, Rui L Reis
Quantitative assessment of micro-structure of materials is of key importance in many fields including tissue engineering, biology, and dentistry. Micro-computed tomography (µ-CT) is an intensively used non-destructive technique. However, the acquisition parameters such as pixel size and rotation step may have significant effects on the obtained results. In this study, a set of tissue engineering scaffolds including examples of natural and synthetic polymers, and ceramics were analyzed. We comprehensively compared the quantitative results of µ-CT characterization using 15 acquisition scenarios that differ in the combination of the pixel size and rotation step...
August 2017: Journal of Materials Science. Materials in Medicine
https://www.readbyqxmd.com/read/28721504/microbial-community-structure-and-function-decoupling-across-a-phosphorus-gradient-in-streams
#11
Erick S LeBrun, Ryan S King, Jeffrey A Back, Sanghoon Kang
Phosphorus (P) is a key biological element with important and unique biogeochemical cycling in natural ecosystems. Anthropogenic phosphorus inputs have been shown to greatly affect natural ecosystems, and this has been shown to be especially true of freshwater systems. While the importance of microbial communities in the P cycle is widely accepted, the role, composition, and relationship to P of these communities in freshwater systems still hold many secrets. Here, we investigated combined bacterial and archaeal communities utilizing 16S ribosomal RNA (rRNA) gene sequencing and computationally predicted functional metagenomes (PFMs) in 25 streams representing a strong P gradient...
July 18, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28718782/prediction-of-protein-hotspots-from-whole-protein-sequences-by-a-random-projection-ensemble-system
#12
Jinjian Jiang, Nian Wang, Peng Chen, Chunhou Zheng, Bing Wang
Hotspot residues are important in the determination of protein-protein interactions, and they always perform specific functions in biological processes. The determination of hotspot residues is by the commonly-used method of alanine scanning mutagenesis experiments, which is always costly and time consuming. To address this issue, computational methods have been developed. Most of them are structure based, i.e., using the information of solved protein structures. However, the number of solved protein structures is extremely less than that of sequences...
July 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28718281/long-distance-modulation-of-disorder-to-order-in-protein-allostery
#13
Jingheng Wang, Gregory S Custer, Dorothy Beckett, Silvina Matysiak
Elucidation of the molecular details of allosteric communication between distant sites in a protein is key to understanding and manipulating many biological regulatory processes. Although protein disorder is acknowledged to play an important thermodynamic role in allostery, the molecular mechanisms by which this disorder is harnessed for long distance communication are known for a limited number of systems. Transcription repression by the E. coli biotin repressor, BirA, is allosterically activated by binding of the small molecule effector biotinoyl-5'-AMP...
July 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28716931/combining-experimental-and-simulation-data-of-molecular-processes-via-augmented-markov-models
#14
Simon Olsson, Hao Wu, Fabian Paul, Cecilia Clementi, Frank Noé
Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few [Formula: see text], which may lead to significant discrepancies when comparing to experimentally measured rates or state populations...
July 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28716449/venom-derived-peptides-inhibiting-kir-channels-past-present-and-future
#15
REVIEW
Craig A Doupnik
Inwardly rectifying K+ (Kir) channels play a significant role in vertebrate and invertebrate biology by regulating the movement of K+ ions involved in membrane transport and excitability. Yet unlike other ion channels including their ancestral K + -selective homologs, there are very few venom toxins known to target and inhibit Kir channels with the potency and selectivity found for the Ca2+-activated and voltage-gated K+ channel families. It is unclear whether this is simply due to a lack of discovery, or instead a consequence of the evolutionary processes that drive the development of venom components towards their targets based on a collective efficacy to 1) elicit pain for defensive purposes, 2) promote paralysis for prey capture, or 3) facilitate delivery of venom components into the circulation...
July 14, 2017: Neuropharmacology
https://www.readbyqxmd.com/read/28715615/rational-design-chemical-development-and-stability-assessment-of-a-new-macrocyclic-four-hydroxamates-bearing-bifunctional-chelating-agent-for-89zr
#16
Uwe Seibold, Björn Wängler, Carmen Wängler
89Zr is a positron-emitting radionuclide being of high interest for medical imaging applications with Positron Emission Tomography. For the introduction of this radiometal into biologically active targeting vectors, the chelating agent desferrioxamine B (DFO) is commonly applied which is however known to form 89Zr-complexes of limited in vivo stability. We herein describe the rational design and chemical development a new, macrocyclic, four hydroxamates-bearing chelating agent (CTH36) for the stable complexation of Zr4+...
July 17, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28713017/intracellular-co-delivery-of-sr-ion-and-phenamil-drug-through-mesoporous-bioglass-nanocarriers-synergizes-bmp-signaling-and-tissue-mineralization
#17
Jung-Hwan Lee, Nandin Mandakhbayar, Ahmed El-Fiqi, Haw-Won Kim
Inducing differentiation and maturation of resident multipotent stem cells (MSCs) is an important strategy to regenerate hard tissues in mal-calcification conditions. Here we explore a co-delivery approach of therapeutic molecules comprised of ion and drug through a mesoporous bioglass nanoparticle (MBN) for this purpose. Recently, MBN has offered unique potential as a nanocarrier for hard tissues, in terms of high mesoporosity, bone bioactivity (and possibly degradability), tunable delivery of biomolecules, and ionic modification...
July 13, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28710037/rna-editing-independently-occurs-at-three-mir-376a-1-sites-and-may-compromise-the-stability-of-the-microrna-hairpin
#18
Alicia Gallego, Diego A Hartasánchez, Marina Brasó-Vives, Eva Garcia-Ramallo, Maria Lopez-Valenzuela, Neus Baena, Miriam Guitart, Hugo Fernández-Bellon, Ivanela Kondova, Ronald Bontrop, Yukio Kawahara, Yolanda Espinosa-Parrilla
RNA editing is being recognized as an important post-transcriptional mechanism that may have crucial roles in introducing genetic variation and phenotypic diversity. Despite microRNA editing recurrence, defining its biological relevance is still under extended debate. To better understand microRNA editing function and regulation we performed an exhaustive characterization of the A-to-I site-specific patterns in mir-376a-1, a mammalian microRNA which RNA editing is involved in the regulation of development and in disease...
July 11, 2017: Gene
https://www.readbyqxmd.com/read/28709206/spectral-partitioning-in-equitable-graphs
#19
Paolo Barucca
Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of equitable graphs, i.e., random graphs with a block-regular structure, is studied, for which analytical results can be obtained. In particular, the spectral density of this ensemble is computed exactly for a modular and bipartite structure. Kesten-McKay's law for random regular graphs is found analytically to apply also for modular and bipartite structures when blocks are homogeneous...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28709120/advances-in-design-of-protein-folds-and-assemblies
#20
REVIEW
Ajasja Ljubetič, Helena Gradišar, Roman Jerala
Conceptual and computational advances triggered an explosion of designed protein structures in the recent years. Various protein fold geometries have been robustly designed with atomic accuracy, including protein folds unseen in nature. The same principles and tools have been extended to design multi-chain assemblies. By exploiting symmetry, mega-Dalton structures have been created with exciting potential applications for synthetic biology. In this review we focus on design of single chain and multi polypeptide chain assemblies of defined size and composition...
July 11, 2017: Current Opinion in Chemical Biology
keyword
keyword
41524
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"