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https://www.readbyqxmd.com/read/28330175/exploration-of-the-binding-modes-of-l-asparaginase-complexed-with-its-amino-acid-substrates-by-molecular-docking-dynamics-and-simulation
#1
Erva Rajeswara Reddy, Rajulapati Satish Babu, Potla Durthi Chandrasai, Pola Madhuri
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-glutamine (L-Gln) deamination plays crucial role in ALL treatment. Role of Erwinaze(®) (L-asparaginase from Erwinia chrysanthemi) in regulation of L-Asn and L-Gln has been confirmed by the experimental studies. Therapeutic research against ALL remained elusive with the lack of structural information on Erwinaze(®) enzyme. In this present study, homology model of the Erwinaze(®) was developed using MODELLER and the same was validated by various quality indexing tools...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330072/molecular-dynamic-simulations-of-escherichia-coli-l-asparaginase-to-illuminate-its-role-in-deamination-of-asparagine-and-glutamine-residues
#2
Rajeswara Reddy Erva, Satish Babu Rajulapati, Chandrasai Potla Durthi, Mayuri Bhatia, Madhuri Pola
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-Glutamine (L-Gln) deamination play a crucial role in ALL treatment. Role of Elspar(®) (L-asparaginase from Escherichia coli) in regulation of L-Asn and L-Gln has been confirmed by the other researchers through experimental studies. Therapeutic research against ALL remained elusive with the lack of information on molecular interactions of Elspar(®) with amino acid substrates. In the present study, using different docking tools binding cavities, key residues in binding and ligand binding mechanisms were identified...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329914/ginsenoside-rg3-restores-hepatitis-c-virus-induced-aberrant-mitochondrial-dynamics-and-inhibits-virus-propagation
#3
Seong-Jun Kim, Jae Young Jang, Eun-Jung Kim, Eun Kyung Cho, Dae Gyun Ahn, Chonsaeng Kim, Han Seul Park, Soung Won Jeong, Sae Hwan Lee, Sang Gyune Kim, Young Seok Kim, Hong Soo Kim, Boo Sung Kim, Ji-Hyung Lee, Aleem Siddiqui
Hepatitis C virus (HCV) alters mitochondrial dynamics associated with persistent viral infection and suppression of innate immunity. Mitochondrial dysfunction is also a pathologic feature of direct-acting antiviral (DAA) treatment. Despite the high efficacy of DAAs, their treatment of patients with chronic hepatitis C in interferon-sparing regimens occasionally produces undesirable side effects such as fatigue, migraine and other conditions, which may be linked to mitochondrial dysfunction. Here we show that clinically prescribed DAAs, including Sofosbuvir, affect mitochondrial dynamics...
March 22, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28329727/theoretical-study-on-the-alkylation-of-o-xylene-with-styrene-in-alcl3-ionic-liquid-catalytic-system
#4
Bobo Cao, Jiuyao Du, Ziping Cao, Haitao Sun, Xuejun Sun, Hui Fu
To explore sustainable catalysts with innovative mechanisms, the alkylation mechanism of o-xylene with styrene was studied using DFT method in AlCl3-ionic liquid catalytic system. The reaction pathway was consisted of CC coupling and a hydrogen shift, in which two transition states were found and further discussed. The reactive energy catalyzed by superelectrophilic AlCl2(+) (12.6kcal/mol) was distinctly lower than AlCl3 (43.0kcal/mol), which was determined as the rate-determining step. Mulliken charge along IRC gave a comprehensive understanding of charge distribution and electron transfer in dynamic progress...
March 6, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28329460/model-based-comparison-of-the-normal-and-fontan-circulatory-systems-part-iii
#5
Raymond L Watrous, Alvin J Chin
BACKGROUND: For patients with the Fontan circulatory arrangement, angiotensin-converting enzyme inhibition, guanylate cyclase activation, phosphodiesterase 5 inhibition, and endothelin receptor antagonism have so far resulted in little or no improvement in [Formula: see text] or peak cardiac index (CI), suggesting that our understanding of the factors that most impact the exercise hemodynamics is incomplete. METHODS: To facilitate comparisons with clinical reports of the exercise performance of preadolescent Fontan patients, we rescaled our previously reported computational models of a two-year-old normal child and similarly aged Fontan patient, extended our Fontan model to capture the nonlinear relationship between flow and resistance quantified from previous computational fluid dynamic analyses of the total cavopulmonary connection (TCPC), and added respiration as well as skeletal muscle contraction...
March 2017: World Journal for Pediatric & Congenital Heart Surgery
https://www.readbyqxmd.com/read/28328933/water-borne-pharmaceuticals-reduce-phenotypic-diversity-and-response-capacity-of-natural-phytoplankton-communities
#6
Francesco Pomati, Jukka Jokela, Sara Castiglioni, Mridul K Thomas, Luca Nizzetto
Chemical micropollutants occur worldwide in the environment at low concentrations and in complex mixtures, and how they affect the ecology of natural systems is still uncertain. Dynamics of natural communities are driven by the interaction between individual organisms and their growth environment, which is mediated by the organisms' expressed phenotypic traits. We tested whether exposure to a mixture of 12 pharmaceuticals and personal care products (PPCP) influences phenotypic trait diversity in lake phytoplankton communities and their ability to regulate biomass production to fit environmental changes (response capacity)...
2017: PloS One
https://www.readbyqxmd.com/read/28328746/cross-talk-between-insulin-signaling-and-gpcrs
#7
Qin Fu, Qian Shi, Toni M West, Yang K Xiang
Diabetes is a major risk factor for the development of heart failure. One of the hallmarks of diabetes is insulin resistance associated with hyperinsulinemia. The literature shows that insulin and adrenergic signaling is intimately linked to each other; however, whether and how insulin may modulate cardiac adrenergic signaling and cardiac function remains unknown. Notably, recent studies have revealed that insulin receptor and β2 adrenergic receptor (β2AR) forms a membrane complex in animal hearts, bringing together the direct contact between two receptor signaling systems, and forming an integrated and dynamic network...
March 17, 2017: Journal of Cardiovascular Pharmacology
https://www.readbyqxmd.com/read/28328671/hemorrhagic-blood-failure-oxygen-debt-coagulopathy-and-endothelial-damage
#8
Nathan J White, Kevin R Ward, Shibani Pati, Geir Strandenes, Andrew P Cap
Our understanding of the events taking place within the blood following severe injury with hemorrhagic shock is quickly evolving. Traditional concepts have given way to a detailed and nuanced understanding of coagulopathy, bleeding, and shock at the cellular and biochemical levels. In doing so, the tremendous complexity of events taking place within the blood have been illuminated and present an additional challenge. In this review, we seek to understand shock, endotheliopathy, and coagulopathy not as isolated events, but rather as the result of changes taking place within a single dynamic organ system...
March 20, 2017: Journal of Trauma and Acute Care Surgery
https://www.readbyqxmd.com/read/28328515/solving-multiextremal-problems-by-using-recurrent-neural-networks
#9
Alaeddin Malek, Najmeh Hosseinipour-Mahani
In this paper, a neural network model for solving a class of multiextremal smooth nonconvex constrained optimization problems is proposed. Neural network is designed in such a way that its equilibrium points coincide with the local and global optimal solutions of the corresponding optimization problem. Based on the suitable underestimators for the Lagrangian of the problem, one give geometric criteria for an equilibrium point to be a global minimizer of multiextremal constrained optimization problem with or without bounds on the variables...
March 16, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28328514/dynamic-uncertain-causality-graph-for-knowledge-representation-and-reasoning-utilization-of-statistical-data-and-domain-knowledge-in-complex-cases
#10
Qin Zhang, Quanying Yao
The dynamic uncertain causality graph (DUCG) is a newly presented framework for uncertain causality representation and probabilistic reasoning. It has been successfully applied to online fault diagnoses of large, complex industrial systems, and decease diagnoses. This paper extends the DUCG to model more complex cases than what could be previously modeled, e.g., the case in which statistical data are in different groups with or without overlap, and some domain knowledge and actions (new variables with uncertain causalities) are introduced...
March 17, 2017: IEEE Transactions on Neural Networks and Learning Systems
https://www.readbyqxmd.com/read/28327752/umbrella-sampling-molecular-dynamics-simulations-reveal-concerted-ion-movement-through-g-quadruplex-dna-channels
#11
Parisa Akhshi, Gang Wu
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28327745/dynamics-of-miura-patterned-foldable-sheets-in-shear-flow
#12
Sarit Dutta, Michael D Graham
We study the dynamics of piecewise rigid sheets containing predefined crease lines in shear flow. The crease lines act like hinge joints along which the sheet may fold rigidly, i.e. without bending any other crease line. We choose the crease lines such that they tessellate the sheet into a two-dimensional array of parallelograms. Specifically, we focus on a particular arrangement of crease lines known as a Miura-pattern in the origami community. When all the hinges are fully open the sheet is planar, whereas when all are closed the sheet folds over itself to form a compact flat structure...
March 22, 2017: Soft Matter
https://www.readbyqxmd.com/read/28327711/a-global-coupled-cluster-potential-energy-surface-for-hcl-oh-%C3%A2-cl-h2o
#13
Junxiang Zuo, Bin Zhao, Hua Guo, Daiqian Xie
A new and more accurate full-dimensional global potential energy surface (PES) for the ground electronic state of the ClH2O system is developed by fitting 15 777 points obtained using an explicitly correlated unrestricted coupled-cluster method with single, double, and perturbative triple excitations (UCCSD(T)-F12b). The fitting is carried out using the permutation invariant polynomial-neural network (PIP-NN) method and has an error of 6.9 meV. The new PES has a slightly lower barrier for the atmospherically important HCl + OH → Cl + H2O reaction than the previous PES based on multi-reference configuration interaction (MRCI) calculations...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28327590/elaboration-and-controlling-excited-state-double-proton-transfer-mechanism-of-2-5-bis-benzoxazol-2-yl-thiophene-3-4-diol
#14
Jinfeng Zhao, Yujun Zheng
In the present work, we theoretically illuminate the excited state double proton transfer (ESDPT) process about a novel synthesized system 2,5-bis(benzoxazol-2-yl)thiophene-3,4-diol (BBTD). Minor changes of both structure and charge redistribution deriving from photoexcitation result in obviously different excited state dynamical process. Exploration about our constructed S1-state potential energy surface (PES) indicates a stepwise ESDPT mechanism for BBTD. In addition, we present a new mechanism about regulating and controlling stepwise ESDPT process via external electric field...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327505/technical-aspects-and-validation-of-a-new-biofeedback-system-for-measuring-lower-limb-loading-in-the-dynamic-situation
#15
Marco Raaben, Herman R Holtslag, Robin Augustine, Rutger O van Merkerk, Bart F J M Koopman, Taco J Blokhuis
BACKGROUND: A variety of techniques for measuring lower limb loading exists, each with their own limitations. A new ambulatory biofeedback system was developed to overcome these limitations. In this study, we described the technical aspects and validated the accuracy of this system. METHODS: A bench press was used to validate the system in the static situation. Ten healthy volunteers were measured by the new biofeedback system and a dual-belt instrumented treadmill to validate the system in the dynamic situation...
March 22, 2017: Sensors
https://www.readbyqxmd.com/read/28327454/collective-variables-for-the-study-of-long-time-kinetics-from-molecular-trajectories-theory-and-methods
#16
REVIEW
Frank Noé, Cecilia Clementi
Collective variables are an important concept to study high-dimensional dynamical systems, such as molecular dynamics of macromolecules, liquids, or polymers, in particular to define relevant metastable states and state-transition or phase-transition. Over the past decade, a rigorous mathematical theory has been formulated to define optimal collective variables to characterize slow dynamical processes. Here we review recent developments, including a variational principle to find optimal approximations to slow collective variables from simulation data, and algorithms such as the time-lagged independent component analysis...
March 16, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28327183/modeling-multi-mutation-and-drug-resistance-analysis-of-some-case-studies
#17
Mitra Shojania Feizabadi
BACKGROUND: Drug-induced resistance is one the major obstacles that may lead to therapeutic failure during cancer treatment. Different genetic alterations occur when tumor cells divide. Among new generations of tumor cells, some may express intrinsic resistance to a specific chemotherapeutic agent. Also, some tumor cells may carry a gene that can develop resistance induced by the therapeutic drug. The methods by which the therapeutic approaches need to be revised in the occurrence of drug induced resistance is still being explored...
March 21, 2017: Theoretical Biology & Medical Modelling
https://www.readbyqxmd.com/read/28326779/illuminating-photochemistry-of-an-excitation-ratiometric-fluorescent-protein-calcium-biosensor
#18
Longteng Tang, Yanli Wang, Weimin Liu, Yongxin Zhao, Robert E Campbell, Chong Fang
Fluorescent protein (FP) based biosensors have become an important and promising tool to track metal ion movement inside living systems. Their working principles after light irradiation, however, remain elusive. To facilitate the rational design of biosensors, we dissect the fluorescence modulation mechanism of a newly developed excitation ratiometric green FP-based Ca(2+) biosensor, GEX-GECO1, using femtosecond stimulated Raman spectroscopy (FSRS) in the electronic excited state. Upon 400 nm photoexcitation, characteristic vibrational marker bands at ~1180 and 1300 cm(-1) show concomitant decay and rise dynamics, probing the progression of an ultrafast excited state proton transfer (ESPT) reaction...
March 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28326054/dynamical-constants-and-time-universals-a-first-step-toward-a-metrical-definition-of-ordered-and-abnormal-cognition
#19
REVIEW
Mark A Elliott, Naomi du Bois
From the point of view of the cognitive dynamicist the organization of brain circuitry into assemblies defined by their synchrony at particular (and precise) oscillation frequencies is important for the correct correlation of all independent cortical responses to the different aspects of a given complex thought or object. From the point of view of anyone operating complex mechanical systems, i.e., those comprising independent components that are required to interact precisely in time, it follows that the precise timing of such a system is essential - not only essential but measurable, and scalable...
2017: Frontiers in Psychology
https://www.readbyqxmd.com/read/28326032/a-dynamic-circuit-hypothesis-for-the-pathogenesis-of-blepharospasm
#20
David A Peterson, Terrence J Sejnowski
Blepharospasm (sometimes called "benign essential blepharospasm," BEB) is one of the most common focal dystonias. It involves involuntary eyelid spasms, eye closure, and increased blinking. Despite the success of botulinum toxin injections and, in some cases, pharmacologic or surgical interventions, BEB treatments are not completely efficacious and only symptomatic. We could develop principled strategies for preventing and reversing the disease if we knew the pathogenesis of primary BEB. The objective of this study was to develop a conceptual framework and dynamic circuit hypothesis for the pathogenesis of BEB...
2017: Frontiers in Computational Neuroscience
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