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Protein dynamic

Kunzhao Du, Longbin Zhang, Trevor Lee, Tao Sun
RNA modifications are involved in many aspects of biological functions. N6-methyladenosine (m6 A) is one of the most important forms of RNA methylation and plays a vital role in regulating gene expression, protein translation, cell behaviors, and physiological conditions in many species, including humans. The dynamic and reversible modification of m6 A is conducted by three elements: methyltransferases ("writers"), such as methyltransferase-like protein 3 (METTL3) and METTL14; m6 A-binding proteins ("readers"), such as the YTH domain family proteins (YTHDFs) and YTH domain-containing protein 1 (YTHDC1); and demethylases ("erasers"), such as fat mass and obesity-associated protein (FTO) and AlkB homolog 5 (ALKBH5)...
June 16, 2018: Molecular Neurobiology
David Renault, Hesham Yousef, Amr A Mohamed
Antibiotics have been increasingly used over the past decades for human medicine, food-animal agriculture, aquaculture, and plant production. A significant part of the active molecules of antibiotics can be released into the environment, in turn affecting ecosystem functioning and biogeochemical processes. At lower organizational scales, these substances affect bacterial symbionts of insects, with negative consequences on growth and development of juveniles, and population dynamics. Yet, the multiple alterations of cellular physiology and metabolic processes have remained insufficiently explored in insects...
June 7, 2018: Environmental Pollution
Nan-Peng Chen, Zhiqi Sun, Reinhard Fässler
Integrin-mediated cell adhesion plays key roles for cell movement during development and tissue homeostasis. The dynamic life cycle of various integrin adhesions structures is required for the cell movements and regulated by the coordinated actions of both actomyosin and the microtubule (MT) cytoskeleton. The evolutionarily conserved Kank family proteins have emerged as regulators of adhesion dynamics by coordinating integrin-mediated force transmission with the recruitment of microtubules to integrins. These novel functions may play important roles in vivo and in human diseases...
June 14, 2018: Current Opinion in Cell Biology
Maryam Rouhani, Farnaz Khodabakhsh, Dariush Norouzian, Reza Ahangari Cohan, Vahideh Valizadeh
Recently protein engineering has been used as a pivotal tool for designing proteins with improved characteristics. While the experimental methods might be laborious and time-consuming, in silico protein design is a time and cost-effective approach. Moreover, in some cases, protein modeling might be the only way to obtain structural information where the experimental techniques are inapplicable. Molecular dynamics (MD) simulation is a method that allows the motion of protein to be simulated in defined conditions on the basis of classical molecular dynamics...
June 9, 2018: Journal of Molecular Graphics & Modelling
Naveen K Singh, Sunil K Arya, Pedro Estrela, Pranab Goswami
A capacitive aptasensor for detecting the malaria biomarker, Plasmodium falciparum glutamate dehydrogenase (PfGDH), directly in human serum samples developed. A thiolated ssDNA aptamer (NG3) that binds specifically to PfGDH antigen with high affinity (Kd = 79 nM) was used to develop the aptasensor. The aptasensor produced capacitance response at an optimized frequency of 2 Hz in a non-Faradaic electrochemical impedance based signal transduction platform. The aptasensor exhibited a wide dynamic range of 100 fM-100 nM with a limits of detection of 0...
June 8, 2018: Biosensors & Bioelectronics
Pavlo Bielytskyi, Daniel Gräsing, Kaustubh R Mote, Karthick Babu Sai Sankar Gupta, Shimon Vega, P K Madhu, A Alia, Jörg Matysik
In the present study, we exploit the light-induced hyperpolarization occurring on 13 C nuclei due to the solid-state photochemically induced dynamic nuclear polarization (photo-CIDNP) effect to boost the NMR signal intensity of selected protons via inverse cross-polarization. Such hyperpolarization transfer is implemented into 1 H-detected two-dimensional 13 C-1 H correlation magic-angle-spinning (MAS) NMR experiment to study protons in frozen photosynthetic reaction centers (RCs). As a first trial, the performance of such an experiment is tested on selectively 13 C labeled RCs from the purple bacteria of Rhodobacter sphaeroides...
June 8, 2018: Journal of Magnetic Resonance
Sandra Peherstorfer, Hans Henning Brewitz, Ajay Abisheck Paul George, Amelie Wißbrock, Jana Maria Adam, Lutz Schmitt, Diana Imhof
BACKGROUND: Tight regulation of heme homeostasis is a critical mechanism in pathogenic bacteria since heme functions as iron source and prosthetic group, but is also toxic at elevated concentrations. Hemolysin-activating lysine-acyltransferase (HlyC) from Escherichia coli is crucial for maturation of hemolysin A, which lyses several mammalian cells including erythrocytes liberating large amounts of heme for bacterial uptake. A possible impact and functional consequences of the released heme on events employing bacterial HlyC have remained unexplored...
June 14, 2018: Biochimica et Biophysica Acta
Luyun Cai, Minjie Cao, Ailing Cao, Joe Regenstein, Jianrong Li, Rongfa Guan
Ultrasound assisted vacuum thawing (UVT) or microwave vacuum thawing (MVT) with red seabream fillets were compared to fresh, chill storage thawing, vacuum thawing, microwave thawing and ultrasound thawing. The thermal stability and gelation properties were studied with DSC and dynamic rheology, respectively. Raman spectra before and after H/D isotope exchange and intrinsic fluorescence were used to measure protein secondary and tertiary structure. Low-field NMR was done to measure water migration. The two thawing techniques both retained actin thermal stability and generally retained more stable tertiary structures than the other thawing methods...
October 2018: Ultrasonics Sonochemistry
Hai-Bo Ding, Kai-Xiong Liu, Jie-Feng Huang, Da-Wen Wu, Jun-Ying Chen, Qing-Shi Chen
BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a multicomponent disorder characterized by inflammation, representing a significant leading cause of chronic morbidity and mortality. Reports have implicated hydrogen sulfide (H2 S) in both the pathology and treatment of COPD. The present study aimed to explore the effects involved with exogenous H2 S on endoplasmic reticulum stress (ERS) and pulmonary artery endothelial cells (PAECs) in a rat model of COPD. METHODS: Rat models of COPD were successfully established by means of passive smoke exposure and intratracheal injection with lipopolysaccharide (LPS)...
June 13, 2018: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
Markus T Bohnsack, Katherine E Sloan
Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2'-O-methylated nucleotides, which are largely introduced by small Cajal body-specific-RNPs...
June 1, 2018: Biological Chemistry
Gabrielle A Pollack, Jessica L Bezek, Serena H Lee, Miranda J Scarlata, Leah T Weingast, Hadley C Bergstrom
Fear memory is a highly stable and durable form of memory, even over vast (remote) time frames. Nevertheless, some elements of fear memory can be forgotten, resulting in generalization. The purpose of this study is to determine how cued fear memory generalizes over time and measure underlying patterns of cortico-amygdala synaptic plasticity. We established generalization gradients at recent (1-d) and remote (30-d) retention intervals following auditory cued fear conditioning in adult male C57BL/6 mice. Results revealed a flattening of the generalization gradient (increased generalization) that was dissociated from contextual fear generalization, indicating a specific influence of time on cued fear memory performance...
July 2018: Learning & Memory
Waraphon Phimpraphai, Sirikachorn Tangkawattana, Suwicha Kasemsuwan, Banchob Sripa
In northeastern Thai (Isaan) culture traditional raw fish dishes and raw fish-eating habits are common. Eating and sharing meals together among the community's members, especially relatives and neighbours, are a common practice in both daily life and social gathering events. Fish are a significant protein source and are associated with variety of traditional recipes. Cyprinid fish are one of the most preferred fish by Isaan villagers for daily consumption because they are accessible and affordable. Consumption of these fish probably causes the persistence of high endemicity of human liver fluke infection, particularly with Opisthorchis viverrini, in northeast Thailand...
2018: Advances in Parasitology
Shu-An Dong, Yuan Zhang, Jian-Bo Yu, Xiang-Yun Li, Li-Rong Gong, Jia Shi, Yuan-Yuan Kang
BACKGROUND: The protective effects of carbon monoxide against the lipopolysaccharide (LPS)-induced lung injury were attributed to maintenance of mitochondrial dynamics, but the mechanisms remain unexplored. MATERIALS AND METHODS: Using a rat model of acute lung injury induced by LPS and the LPS attacking cell model, we investigated the effects of pretreatment of carbon monoxide molecule-2 (CORM-2) on the acute lung injury and expressions of mitofusin proteins that play a critical role in mitochondrial dynamics...
August 2018: Journal of Surgical Research
Da Un Jeong, Ki Moo Lim
BACKGROUND AND AIMS: Although studies on the relation between arrhythmias and the action potential duration (APD) have been carried out, most of them are based only on electrophysiological factors of the heart and lack experiments that consider cardiac mechanical and electromechanical characteristics. Therefore, we conducted this study to clarify the relevance of the shortening of APD of a cell in relation to the mechanical contraction activity of the heart and the associated risk of arrhythmia...
June 15, 2018: Biomedical Engineering Online
Hao Liu, Xiang Guo, Jingcheng Han, Ray Luo, Hai-Feng Chen
Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved...
June 14, 2018: Journal of Chemical Physics
Xiaojing Teng, Qi Huang, Chamila Chathuranga Dharmawardhana, Toshiko Ichiye
The properties of aqueous solutions of ionic, zwitterionic, and polar solutes are of interest to many fields. For instance, one of the many anomalous properties of aqueous solutions is the behavior of water diffusion in different monovalent salt solutions. In addition, solutes can affect the stabilities of macromolecules such as proteins in aqueous solution. Here, the diffusivities of aqueous solutions of sodium chloride, potassium chloride, tri-methylamine oxide (TMAO), urea, and TMAO-urea are examined in molecular dynamics simulations...
June 14, 2018: Journal of Chemical Physics
A Sinelnikova, A J Niemi, Johan Nilsson, M Ulybyshev
Chiral heteropolymers such as large globular proteins can simultaneously support multiple length scales. The interplay between the different scales brings about conformational diversity, determines the phase properties of the polymer chain, and governs the structure of the energy landscape. Most importantly, multiple scales produce complex dynamics that enable proteins to sustain live matter. However, at the moment there is incomplete understanding of how to identify and distinguish the various scales that determine the structure and dynamics of a complex protein...
May 2018: Physical Review. E
H Sasimali M Soysa, Wipa Suginta, Watcharaporn Moonsap, M F Smith
The outer membrane protein channel EcChiP, associated with a silent gene in E. coli, is a monomeric chitoporin. In a glucose-deficient environment, E. coli can express the ChiP gene to exploit chitin degradation products. Single-channel small ion current measurements, which reveal the dynamics of single sugar molecules trapped in channel, are used here to study the exotic transport of chitosugars by E. coli. Molecules escape from the channel on multiple timescales. Voltage-dependent trapping rates observed for charged chitosan molecules, as well as model calculations, indicate that the rapid escape processes are those in which the molecule escapes back to the side of the membrane from which it originated...
May 2018: Physical Review. E
Anang K Singh, P S Burada, Susmita Bhattacharya, Sudipta Bag, Amitabha Bhattacharya, Swagata Dasgupta, Anushree Roy
We have investigated the nonthermal effect of 10 GHz/22 dBm microwave radiation on hen egg-white lysozyme (HEWL) over different irradiation times, ranging from 2 min to 1 h. To ensure a control over the radiation parameters, a pair of microwave rectangular waveguides is used to irradiate the samples. Optical spectroscopic measurements, which include UV-visible absorption spectroscopy, Raman spectroscopy, and far UV CD spectroscopy, reveal the exposure of the buried tryptophan (Trp) residues of the native molecule between 15 and 30 min of radiation...
May 2018: Physical Review. E
Rajesh Kumar Pathak, Ayushi Gupta, Rohit Shukla, Mamta Baunthiyal
Xanthine oxidoreductase plays an important role in formation of uric acid and its regulation during purine catabolism. Uncontrolled expression of this enzyme is responsible for overproduction and deposition of uric acid in blood that is potentially injurious because it can breakdown DNA and protein molecules, triggering many diseases. Human Xanthine oxidoreductase (HsXOR) is considered to be a pharmacological target for the treatment of hyperuricemia. Many of the HsXOR-inhibitor drugs such as Febuxostat and Allopurinol are known to have significant adverse effects...
May 28, 2018: Computational Biology and Chemistry
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