keyword
MENU ▼
Read by QxMD icon Read
search

molecular dynamics

keyword
https://www.readbyqxmd.com/read/28343010/structural-and-dynamics-studies-of-the-tetr-family-protein-cprb-from-streptomyces-coelicolor-in-complex-with-its-biological-operator-sequence
#1
Hussain Bhukya, Asis K Jana, Neelanjana Sengupta, Ruchi Anand
In Streptomycetes, tetracycline repressor family of transcription regulators (TetR-FTRs) controls various biological processes including antibiotic biosynthesis, cellular morphology and innate resistance. Here, we focus on understanding the structural basis of transcription regulation by CprB, a member of TetR-FTRs from S. coelicolor. CprB is implicated as a receptor of γ-butyrolactones, a class of quorum sensing molecules, responsible for initiating secondary metabolic pathways. In order to understand the molecular mechanism of DNA recognition, the X-ray structure of CprB in complex with its biological relevant operator sequence was solved to a resolution of 3...
March 22, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28342937/molecular-epidemiology-of-staphylococcus-aureus-nasal-colonization-among-patients-and-their-parents-guardian-in-an-iranian-referral-hospital
#2
Babak Pourakbari, Mahmoud Khodabandeh, Shima Mahmoudi, Farah Sabouni, Alireza Aziz-Ahari, Abbas Bahador, Sepideh Keshavarz Valian, Reihaneh Hosseinpour Sadeghi, Setareh Mamishi
INTRODUCTION: Carriage of Staphylococcus aureus in the nose appears to play a key role in the epidemiology and pathogenesis of infection. It is important to investigate the genetic relatedness of S. aureus and MRSA clones in different geographic regions. The aim of this study was to assess the nasal carriage rate of S. aureus, including MRSA strains in both hospitalized children and general adult population (parents/guardian). In addition, antibiotic susceptibility pattern and molecular diversity of S...
March 22, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28342806/molecular-regulation-of-mitochondrial-dynamics-in-cardiac-disease
#3
REVIEW
Jinliang Nan, Wei Zhu, M S Rahman, Mingfei Liu, Dan Li, Shengan Su, Na Zhang, Xinyang Hu, Hong Yu, Mahesh P Gupta, Jian''an Wang
Mitochondrial homeostasis is critical for keeping functional heart in response to metabolic or environmental stresses. Mitochondrial fission and fusion (mitochondrial dynamics) play essential roles in maintaining mitochondrial homeostasis, defects in mitochondrial dynamics lead to cardiac diseases such as ischemia-reperfusion injury (IRI), heart failure and diabetic cardiomyopathy. Mitochondrial dynamics is determined by mitochondrial fission and fusion proteins, including OPA1, mitofusins and Drp1. These proteins are tightly regulated by a series of signaling pathways through different aspects such as transcription, post translation modifications (PTMs) and proteasome-dependent protein degradation...
March 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28342805/phosphoethanolamine-addition-to-the-heptose-i-of-the-lipopolysaccharide-modifies-the-inner-core-structure-and-has-an-impact-on-the-binding-of-polymyxin-b-to-the-escherichia-coli-outer-membrane
#4
Javier Salazar, Mackarenna Alarcon, Jaime Huerta, Belén Navarro, Daniel Aguayo
Phosphoethanolamine (pEtN) decoration of E. coli Lipopolysaccharide (LPS) provides resistance to the antimicrobial Polymyxin B (PolB). While EptA and EptB enzymes catalyze the addition of pEtN to the Lipid A and Kdo (pEtN-Kdo-Lipid A), EptC catalyzes the pEtN addition to the Heptose I (pEtN-HeptI). In this study, we investigated the contribution of pEtN-HeptI to PolB resistance using eptA/eptB and eptC deficient E. coli K12 and its wild-type parent strains. These mutations were shown to decrease the antimicrobial activity of PolB on cells grown under pEtN-addition inducing conditions...
March 22, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28342732/hydrogen-bond-strength-in-membrane-proteins-probed-by-time-resolved-1-h-detected-solid-state-nmr-and-md-simulations
#5
João Medeiros-Silva, Shehrazade Jekhmane, Marc Baldus, Markus Weingarth
(1)H-detected solid-state NMR in combination with (1)H/(2)D exchange steps allows for the direct identification of very strong hydrogen bonds in membrane proteins. On the example of the membrane-embedded potassium channel KcsA, we quantify the longevity of such very strong hydrogen bonds by combining time-resolved (1)H-detected solid-state NMR experiments and molecular dynamics simulations. In particular, we show that the carboxyl-side chain of the highly conserved residue Glu51 is involved in ultra-strong hydrogen bonds, which are fully-water-exposed and yet stable for weeks...
March 18, 2017: Solid State Nuclear Magnetic Resonance
https://www.readbyqxmd.com/read/28342718/noisy-response-to-antibiotic-stress-predicts-subsequent-single-cell-survival-in-an-acidic-environment
#6
Karin Mitosch, Georg Rieckh, Tobias Bollenbach
Antibiotics elicit drastic changes in microbial gene expression, including the induction of stress response genes. While certain stress responses are known to "cross-protect" bacteria from other stressors, it is unclear whether cellular responses to antibiotics have a similar protective role. By measuring the genome-wide transcriptional response dynamics of Escherichia coli to four antibiotics, we found that trimethoprim induces a rapid acid stress response that protects bacteria from subsequent exposure to acid...
March 21, 2017: Cell Systems
https://www.readbyqxmd.com/read/28340512/activation-mechanisms-of-%C3%AE-v%C3%AE-3-integrin-by-binding-to-fibronectin-a-computational-study
#7
Lingyun Wang, Di Pan, Qi Yan, Yuhua Song
Integrin αVβ3 plays an important role in regulating cellular activities and in human diseases. Although the structure of αVβ3 has been studied by crystallography and electron microscopy, the detailed activation mechanism of integrin αVβ3 induced by fibronectin (Fn) remains unclear. In this study, we investigated the conformational and dynamical motion changes of Mn(2+) -bound integrin αVβ3 by binding to Fn with molecular dynamics simulations. Results showed that Fn binding to integrin αVβ3 caused the changes of the conformational flexibility of αVβ3 domains, the essential mode of motion for the domains of αV subunit and β3 subunit and the degrees of correlated motion of residues between the domains of αV subunit and β3 subunit of integrin αVβ3...
March 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28340413/design-synthesis-and-biological-evaluation-of-novel-coumarin-based-benzamides-as-potent-histone-deacetylase-inhibitors-and-anticancer-agents
#8
Tooba Abdizadeh, Mohammad Reza Kalani, Khalil Abnous, Zahra Tayarani-Najaran, Bibi Zahra Khashyarmanesh, Rahman Abdizadeh, Razieh Ghodsi, Farzin Hadizadeh
Histone deacetylases (HDACs) are attractive therapeutic targets for the treatment of cancer and other diseases. It has four classes (I-IV), among them especially class I isozyme are involved in promoting tumor cells proliferation, angiogenesis, differentiation, invasion and metastasis and also viable targets for cancer therapeutics. A novel series of coumarin-based benzamides was designed and synthesized as HDAC inhibitors. The cytotoxic activity of the synthesized compounds (8a-u) was evaluated against six human cancer cell lines including HCT116, A2780, MCF7, PC3, HL60 and A549 and a single normal cell line (Huvec)...
March 18, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28340400/pharmacoinformatics-exploration-of-polyphenol-oxidases-leading-to-novel-inhibitors-by-virtual-screening-and-molecular-dynamic-simulation-study
#9
Mubashir Hassan, Qamar Abbas, Zaman Ashraf, Ahmed A Moustafa, Sung-Yum Seo
Polyphenol oxidases (PPOs)/tyrosinases are metal-dependent enzymes and known as important targets for melanogenesis. Although considerable attempts have been conducted to control the melanin-associated diseases by using various inhibitors. However, the exploration of the best anti-melanin inhibitor without side effect still remains a challenge in drug discovery. In present study, protein structure prediction, ligand-based pharmacophore modeling, virtual screening, molecular docking and dynamic simulation study were used to screen the strong novel inhibitor to cure melanogenesis...
March 15, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28340381/studying-the-adsorption-of-dna-nanostructures-on-graphene-in-the-aqueous-phase-using-molecular-dynamic-simulations
#10
Jixue Sun, Yang Li, Jianping Lin
DNA nanostructures can undergo large structural fluctuations and deviate from their intended configurations. In this work, two model DNA nanostructures (i.e., Nan and Kai) were designed based on the shape of the two Chinese characters of the name of Nankai University, and additional single-stranded DNA fragments were added to interact with graphene. During four 50-ns molecular dynamic simulations in aqueous solution, the DNA nanostructures adsorbed onto graphene demonstrated more stable conformations with lower root mean square deviations and smaller coordinate changes in the z-axis direction than the DNA nanostructures that were not adsorbed onto graphene...
March 9, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28340354/mechanism-of-substrate-translocation-in-an-alternating-access-transporter
#11
Naomi R Latorraca, Nathan M Fastman, A J Venkatakrishnan, Wolf B Frommer, Ron O Dror, Liang Feng
Transporters shuttle molecules across cell membranes by alternating among distinct conformational states. Fundamental questions remain about how transporters transition between states and how such structural rearrangements regulate substrate translocation. Here, we capture the translocation process by crystallography and unguided molecular dynamics simulations, providing an atomic-level description of alternating access transport. Simulations of a SWEET-family transporter initiated from an outward-open, glucose-bound structure reported here spontaneously adopt occluded and inward-open conformations...
March 23, 2017: Cell
https://www.readbyqxmd.com/read/28339967/placental-transporter-localization-and-expression-in-the-human-the-importance-of-species-sex-and-gestational-age-differences1
#12
Natasha Walker, Panagiotis Filis, Ugo Soffientini, Michelle Bellingham, Peter J O'Shaughnessy, Paul A Fowler
The placenta is a critical organ during pregnancy, essential for the provision of an optimal intrauterine environment, with fetal survival, growth and development relying on correct placental function. It must allow nutritional compounds and relevant hormones to pass into the fetal bloodstream and metabolic waste products to be cleared. It also acts as a semi-permeable barrier to potentially harmful chemicals both endogenous and exogenous. Transporter proteins allow for bidirectional transport and are found in the syncytiotrophoblast of the placenta and endothelium of fetal capillaries...
March 7, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28339933/effect-of-heat-stress-on-amino-acid-digestibility-and-transporters-in-meat-type-chickens
#13
W S Habashy, M C Milfort, K Adomako, Y A Attia, R Rekaya, S E Aggrey
The present study was conducted to investigate the effect of heat stress (HS) on performance, digestibility, and molecular transporters of amino acids in broilers. Cobb 500 chicks were raised from hatch till 13 d in floor pens. At d 14, 48 birds were randomly and equally divided between a control group (25°C) and a HS treatment group (35°C). Birds in both treatment classes were individually caged and fed ad libitum on a diet containing 18.7% CP and 3,560 Kcal ME/Kg. Five birds per treatment at one and 12 d post treatment were euthanized and the Pectoralis major (P...
March 2, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339256/analytic-interatomic-forces-in-the-random-phase-approximation
#14
Benjamin Ramberger, Tobias Schäfer, Georg Kresse
We discuss that in the random phase approximation (RPA) the first derivative of the energy with respect to the Green's function is the self-energy in the GW approximation. This relationship allows us to derive compact equations for the RPA interatomic forces. We also show that position dependent overlap operators are elegantly incorporated in the present framework. The RPA force equations have been implemented in the projector augmented wave formalism, and we present illustrative applications, including ab initio molecular dynamics simulations, the calculation of phonon dispersion relations for diamond and graphite, as well as structural relaxations for water on boron nitride...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28339247/thermodynamic-and-kinetic-fragility-of-freon-113-the-most-fragile-plastic-crystal
#15
A Vispa, M Romanini, M A Ramos, L C Pardo, F J Bermejo, M Hassaine, A I Krivchikov, J W Taylor, J Ll Tamarit
We present a dynamic and thermodynamic study of the orientational glass former Freon 113 (1,1,2-trichloro-1,2,2-trifluoroethane, CCl_{2}F-CClF_{2}) in order to analyze its kinetic and thermodynamic fragilities. Freon 113 displays internal molecular degrees of freedom that promote a complex energy landscape. Experimental specific heat and its microscopic origin, the vibrational density of states from inelastic neutron scattering, together with the orientational dynamics obtained by means of dielectric spectroscopy have revealed the highest fragility value, both thermodynamic and kinetic, found for this orientational glass former...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28339244/terahertz-field-induced-large-macroscopic-polarization-and-domain-wall-dynamics-in-an-organic-molecular-dielectric
#16
T Morimoto, T Miyamoto, H Yamakawa, T Terashige, T Ono, N Kida, H Okamoto
A rapid polarization control in paraelectric materials is important for an ultrafast optical switching useful in the future optical communication. In this study, we applied terahertz-pump second-harmonic-generation-probe and optical-reflectivity-probe spectroscopies to the paraelectric neutral phase of an organic molecular dielectric, tetrathiafulvalene-p-chloranil and revealed that a terahertz pulse with the electric-field amplitude of ∼400  kV/cm produces in the subpicosecond time scale a large macroscopic polarization whose magnitude reaches ∼20% of that in the ferroelectric ionic phase...
March 10, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28339205/ultrafast-non-f%C3%A3-rster-intramolecular-donor-acceptor-excitation-energy-transfer
#17
Stavros Athanasopoulos, Laura Alfonso Hernández, David Beljonne, Sebastian Fernandez-Alberti, Sergei Tretiak
Ultrafast intramolecular electronic energy transfer in a conjugated donor-acceptor system is simulated using non-adiabatic excited-state molecular dynamics. After initial site selective photoexcitation of the donor, transition density localization is monitored throughout the S2→S1 internal conversion process revealing an efficient unidirectional donor→acceptor energy transfer process. Detailed analysis of the excited state trajectories uncovers several salient features of the energy transfer dynamics. While a weak temperature dependence is observed during the entire electronic energy relaxation, an ultrafast initially temperature independent process allows the molecular system to approach the S2-S1 potential energy crossing seam within the first ten femtoseconds...
March 24, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28339071/direct-interaction-between-caffeic-acid-phenethyl-ester-and-human-neutrophil-elastase-inhibits-the-growth-and-migration-of-panc-1-cells
#18
Jianhui Duan, Yilixiati Xiaokaiti, Shengjun Fan, Yan Pan, Xin Li, Xuejun Li
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal malignant tumors of the digestive system, but the mechanisms of its development and progression are unclear. Inflammation is thought to be fundamental to pancreatic cancer development and caffeic acid phenethyl ester (CAPE) is an active component of honey bee resin or propolis with anti-inflammatory and anticancer activities. We investigated the inhibitory effects of CAPE on cell growth and migration induced by human neutrophil elastase (HNE) and report that HNE induced cancer cell migration at low doses and growth at higher doses...
March 21, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28339004/cyclocurcumin-a-curcumin-derivative-exhibits-immune-modulating-ability-and-is-a-potential-compound-for-the-treatment-of-rheumatoid-arthritis-as-predicted-by-the-mm-pbsa-method
#19
Min Fu, Lihui Chen, Limin Zhang, Xiao Yu, Qingrui Yang
The control and treatment of rheumatoid arthritis is a challenge in today's world. Therefore, the pursuit of natural disease-modifying antirheumatic drugs (DMRDs) remains a top priority in rheumatology. The present study focused on curcumin and its derivatives in the search for new DMRDs. We focused on prominent p38 mitogen-activated protein (MAP) kinase p38α which is a prime regulator of tumor necrosis factor-α (TNF-α), a key mediator of rheumatoid arthritis. In the present study, we used the X-ray crystallographic structure of p38α for molecular docking simulations and molecular dynamic simulations to study the binding modes of curcumin and its derivatives with the active site of p38α...
March 20, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28338681/dynamics-of-the-triplet-pair-state-reveals-the-likely-coexistence-of-coherent-and-incoherent-singlet-fission-in-crystalline-hexacene
#20
Nicholas R Monahan, Dezheng Sun, Hiroyuki Tamura, Kristopher W Williams, Bolei Xu, Yu Zhong, Bharat Kumar, Colin Nuckolls, Avetik R Harutyunyan, Gugang Chen, Hai-Lung Dai, David Beljonne, Yi Rao, X-Y Zhu
The absorption of a photon usually creates a singlet exciton (S1) in molecular systems, but in some cases S1 may split into two triplets (2×T1) in a process called singlet fission. Singlet fission is believed to proceed through the correlated triplet-pair (1)(TT) state. Here, we probe the (1)(TT) state in crystalline hexacene using time-resolved photoemission and transient absorption spectroscopies. We find a distinctive (1)(TT) state, which decays to 2×T1 with a time constant of 270 fs. However, the decay of S1 and the formation of (1)(TT) occur on different timescales of 180 fs and <50 fs, respectively...
April 2017: Nature Chemistry
keyword
keyword
115191
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"