29,396 results match your criteria Archives of Biochemistry and Biophysics[Journal]


Crystal structure of Plasmodium falciparum adenosine deaminase reveals a novel binding pocket for inosine.

Arch Biochem Biophys 2019 Apr 16;667:6-13. Epub 2019 Apr 16.

National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Phahonyothin Road, Klong 1, Klong Luang, Pathumthani, 12120, Thailand. Electronic address:

Plasmodium falciparum (Pf), a malarial pathogen, can only synthesize purine nucleotides employing a salvage pathway because it lacks de novo biosynthesis. Adenosine deaminase (ADA), one of the three purine salvage enzymes, catalyzes the irreversible hydrolytic deamination of adenosine to inosine, which is further converted to GMP and AMP for DNA/RNA production. In addition to adenosine conversion, Plasmodium ADA also catalyzes the conversion of 5'-methylthioadenosine, derived from polyamine biosynthesis, into 5'-methylthioinosine whereas the human enzyme is not capable of this function. Read More

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http://dx.doi.org/10.1016/j.abb.2019.04.002DOI Listing
April 2019
1 Read

Quantitative atomic force microscopy provides new insight into matrix vesicle mineralization.

Arch Biochem Biophys 2019 Apr 16;667:14-21. Epub 2019 Apr 16.

Nanoscience & Nanotechnology & Innovative Instrumentation (NAST) Centre, University of Rome Tor Vergata, Rome, Italy; Department of Experimental Medicine, University of Rome Tor Vergata, Rome, Italy; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA. Electronic address:

Matrix vesicles (MVs) are a class of extracellular vesicles that initiate mineralization in cartilage, bone, and other vertebrate tissues by accumulating calcium ions (Ca) and inorganic phosphate (P) within their lumen and forming a nucleation core (NC). After further sequestration of Ca and P, the NC transforms into crystalline complexes. Direct evidence of the existence of the NC and its maturation have been provided solely by analyses of dried samples. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00039861183104
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http://dx.doi.org/10.1016/j.abb.2019.04.003DOI Listing
April 2019
2 Reads

Vasodilatory effect of kaempferol-7-O-α-L-rhamnopyranoside via NO-cGMP-PKG signaling.

Arch Biochem Biophys 2019 Apr 11;667:1-5. Epub 2019 Apr 11.

Department of Physiology, College of Korean Medicine, Dongguk University, Gyeongju, South Korea; National Development Institute of Korean Medicine, Gyeongsan, Gyeongbuk, 712-210, South Korea. Electronic address:

Hypertension is one of the major causes of mortality. Though a host of drugs are available for the treatment of hypertension, majority have been linked to adverse side effects, necessitating the need for research into natural compounds with fewer side effects. Kaempferol-7-O-α-L-rhamnopyroside (KR) is a glycosylated flavone with neuroprotective and anti-inflammatory effects. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00039861183096
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http://dx.doi.org/10.1016/j.abb.2019.04.001DOI Listing
April 2019
2 Reads

Aroylthiourea derivatives of ciprofloxacin drug as DNA binder: Theoretical, spectroscopic and electrochemical studies along with cytotoxicity assessment.

Arch Biochem Biophys 2019 Apr 2;666:83-98. Epub 2019 Apr 2.

Healthcare Biotechnology Atta-ur-Rehman School of Applied Biosciences National University of Science and Technology (NUST), Islamabad, Pakistan.

Aroylthiourea derivatives of ciprofloxacin drug - [1-cyclopropyl-6-fluoro-7-(4-((4-methoxybenzoyl)carbamothioyl)piperazin-1-yl)-4-oxo-1,4-dihydroquinoline-3-carboxylic acid] ATU-1, [1-cyclopropyl-7-(4-((2,4-dibromobenzoyl)carbamothioyl)piperazin-1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid] ATU-2, and [1-cyclopropyl-7-(4-((3,5-dinitrobenzoyl)carbamothioyl)piperazin-1-yl)-6-fluoro-4-oxo-1,4-dihydroquinoline-3-carboxylic acid] ATU-3 were synthesized, characterized and investigated for DNA binding at stomach pH (4.7) and at 37 °C. All findings by using DFT, molecular docking, spectroscopic (UV-, fluorescence; FL-), cyclic voltammetric (CV) and viscometric techniques revealed that these compounds have the potency to bind with DNA via a mixed mode of interaction. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.021DOI Listing
April 2019
4 Reads

MiR-34s negatively regulate homologous recombination through targeting RAD51.

Arch Biochem Biophys 2019 Apr 2;666:73-82. Epub 2019 Apr 2.

Department of Radiobiology, Beijing Key Laboratory for Radiobiology, Beijing Institute of Radiation Medicine, Beijing, 100850, PR China. Electronic address:

Double-strand breaks (DSBs), the most serious lesions of DNA, often induce chromosomal aberrations and are intimately associated with oncogenesis. A normal DNA damage response (DDR) network contains two major repair pathways: homologous recombination (HR) and non-homologous end-joining (NHEJ). Studies of DSB repair-associated molecules have focused mainly on DNA repair proteins. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00039861193006
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http://dx.doi.org/10.1016/j.abb.2019.03.017DOI Listing
April 2019
5 Reads

Dauricine negatively regulates lipopolysaccharide- or cecal ligation and puncture-induced inflammatory response via NF-κB inactivation.

Arch Biochem Biophys 2019 Apr 1;666:99-106. Epub 2019 Apr 1.

Department of Vascular Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China. Electronic address:

Acute lung injury (ALI) is a challenging clinical problem worldwide characterized by severe pulmonary inflammation. Dauricine, extracted from the root of traditional Chinese medicine Menispermum dauricum DC, is employed as anti-inflammatory herbs. In this study, we explored the inhibitory effects of dauricine on lipopolysaccharide (LPS)-induced inflammation in macrophages and LPS- or cecal ligation and puncture (CLP)-induced ALI in C57BL/6 mice. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.018DOI Listing

X-ray driven reduction of Cpd I of Catalase-3 from N. crassa reveals differential sensitivity of active sites and formation of ferrous state.

Arch Biochem Biophys 2019 Mar 30;666:107-115. Epub 2019 Mar 30.

Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico. Electronic address:

Catalases are biotechnologically relevant enzymes because of their applications in food technology, bioremediation, and biomedicine. The dismutation of hydrogen peroxide occurs in two steps; in the first one, the enzyme forms an oxidized compound I (Cpd I) and in the second one, the enzyme is reduced to the ferric state. In this research work, we analyzed the reduction of Cpd I by X-ray radiation damage during diffraction experiments in crystals of CAT-3, a Large-Size Subunit Catalase (LSC) from Neurospora crassa. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.020DOI Listing
March 2019
6 Reads

Mutations of Cys and Ser residues in the α5-subunit of the 20S proteasome from Saccharomyces cerevisiae affects gating and chronological lifespan.

Arch Biochem Biophys 2019 Mar 30;666:63-72. Epub 2019 Mar 30.

Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo-SP, Brazil. Electronic address:

In addition to autophagy, proteasomes are critical for regulating intracellular protein levels and removing misfolded proteins. The 20S proteasome (20SPT), the central catalytic unit, is sometimes flanked by regulatory units at one or both ends. Additionally, proteosomal activation has been associated with increased lifespan in many organisms. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.012DOI Listing
March 2019
2 Reads

Altering the Y137K164K166 triad of mandelate racemase and its effect on the observed pK of the brønsted base catalysts.

Arch Biochem Biophys 2019 Mar 29. Epub 2019 Mar 29.

Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada; Department of Chemistry, Dalhousie University, Halifax, NS, B3H 4R2, Canada. Electronic address:

Mandelate racemase (MR) catalyzes the interconversion of the enantiomers of mandelate using a two-base mechanism with Lys 166 acting as the Brønsted base to abstract the α-proton from (S)-mandelate. The resulting intermediate is subsequently re-protonated by the conjugate acid of His 297 to yield (R)-mandelate. The roles of these amino acids are reversed when (R)-mandelate is the substrate. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.011DOI Listing
March 2019
2 Reads

The secret messages between mitochondria and nucleus in muscle cell biology.

Arch Biochem Biophys 2019 Mar 30;666:52-62. Epub 2019 Mar 30.

Department of Pathology, Johns Hopkins University, Baltimore, MD, United States. Electronic address:

Over two thousand proteins are found in the mitochondrial compartment but the mitochondrial genome codes for only 13 proteins. The majority of mitochondrial proteins are products of nuclear genes and are synthesized in the cytosol, then translocated into the mitochondria. Most of the subunits of the five respiratory chain complexes in the inner mitochondrial membrane, which generate a proton gradient across the membrane and produce ATP, are encoded by nuclear genes. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.019DOI Listing
March 2019
2 Reads

Dynamics of the mitochondrial permeability transition pore: Transient and permanent opening events.

Arch Biochem Biophys 2019 Mar 28;666:31-39. Epub 2019 Mar 28.

Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA; Department of Physiology, University of Maryland School of Medicine, 111 Penn Street, Baltimore, MD, 21201, USA. Electronic address:

A gentle optical examination of the mitochondrial permeability transition pore (mPTP) opening events was carried out in isolated quiescent ventricular myocytes by tracking the inner membrane potential (ΔΨ) using TMRM (tetramethylrhodamine methyl ester). Zeiss Airyscan 880 ″super-resolution" or "high-resolution" imaging was done with very low levels of illumination (0.009% laser power). Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.016DOI Listing
March 2019
2 Reads

Analysis of histone ubiquitylation by MSL1/MSL2 proteins in vitro.

Arch Biochem Biophys 2019 Mar 29;666:22-30. Epub 2019 Mar 29.

Shemyakin Institute of Bioorganic Chemistry, Russian Academy of Sciences, Ul. Miklukho-Maklaya, 16/10, Moscow, V-437, Russia.

Histone posttranslational modifications (PTM) control gene activity by targeting chromatin-regulatory proteins. By altering histone charges PTMs could also modulate inter- and intra-nucleosomal interactions, and thus affect chromatin high-order compaction and nucleosome stochastic folding, respectively. However, recently it has been shown that histone H2BK34- ubiquitylation (which is deposited in vivo by MOF-MSL) can destabilize one of the nucleosomal H2A-H2B dimers in symmetrically and (albeit to a lesser extend) asymmetrically modified nucleosomes, and thus promote formation of a hexasome particle. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.015DOI Listing
March 2019
2 Reads

Proton-pumping F-ATPase plays an important role in Streptococcus mutans under acidic conditions.

Arch Biochem Biophys 2019 Mar 29;666:46-51. Epub 2019 Mar 29.

Division of Biochemistry, School of Pharmacy, Iwate Medical University, Yahaba, Iwate, 028-3694, Japan. Electronic address:

Streptococcus mutans, a bacterium mainly inhabiting the tooth surface, is a major pathogen of dental caries. The bacterium metabolizes sugars to produce acids, resulting in an acidic microenvironment in the dental plaque. Hence, S. Read More

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https://data.crossref.org/10.1016%2Fj.abb.2019.03.014
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http://dx.doi.org/10.1016/j.abb.2019.03.014DOI Listing
March 2019
4 Reads

Invertebrate troponin: Insights into the evolution and regulation of striated muscle contraction.

Arch Biochem Biophys 2019 Mar 27;666:40-45. Epub 2019 Mar 27.

Department of Physiology, Wayne State University School of Medicine, 540 E. Canfield, Detroit, MI, 48201, USA. Electronic address:

The troponin complex plays a central role in regulating the contraction and relaxation of striated muscles. Among the three protein subunits of troponin, the calcium receptor subunit, TnC, belongs to the calmodulin family of calcium signaling proteins whereas the inhibitory subunit, TnI, and tropomyosin-binding/thin filament-anchoring subunit, TnT, are striated muscle-specific regulatory proteins. TnI and TnT emerged early in bilateral symmetric invertebrate animals and have co-evolved during the 500-700 million years of muscle evolution. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.013DOI Listing
March 2019
3 Reads

Catalytic properties of 25-hydroxyvitamin D3 3-epimerase in rat and human liver microsomes.

Arch Biochem Biophys 2019 Mar 27;666:16-21. Epub 2019 Mar 27.

School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.

25-Hydroxyvitamin D3 3-epimerase catalyzes the 3β → 3α epimerization of 25-hydroxyvitamin D3 (25(OH)D3) producing 3-epi-25-hydroxyvitamin D3 (3-epi-25(OH)D3). 3-Epi-25(OH)D3 is one of the most abundant forms of vitamin D present in the serum. It can be converted to 3-epi-1α,25-dihydroxyvitamin D3 by CYP27B1 which generally displays lower biological activity than 1α,25-dihydroxyvitamin D3 (1,25(OH)D3). Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.010DOI Listing

Alterations of elastin in female reproductive tissues arising from advancing parity.

Arch Biochem Biophys 2019 Mar 23. Epub 2019 Mar 23.

Department of Physics, The Graduate Center of the City University of New York, NY, United States; Department of Physics, Brooklyn College of the City University of New York, Brooklyn, NY, United States; Department of Chemistry, The Graduate Center of the City University of New York, NY, United States; Department of Biochemistry, The Graduate Center of the City University of New York, NY, United States. Electronic address:

Female reproductive tissues undergo significant alterations during pregnancy, which may compromise the structural integrity of extracellular matrix proteins. Here, we report on modifications of elastic fibers, which are primarily composed of elastin and believed to provide a scaffold to the reproductive tissues, due to parity and parturition. Elastic fibers from the upper vaginal wall of virgin Sprague Dawley rats were investigated and compared to rats having undergone one, three, or more than five pregnancies. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.008DOI Listing
March 2019
7 Reads
3.017 Impact Factor

Resveratrol and dimethyl fumarate ameliorate testicular dysfunction caused by chronic unpredictable mild stress-induced depression in rats.

Arch Biochem Biophys 2019 Apr 21;665:152-165. Epub 2019 Mar 21.

Department of Biochemistry, Faculty of Pharmacy, October 6 University, Cairo, Egypt.

Chronic stress is a major factor contributing to male infertility. Increasing evidence has demonstrated that resveratrol or dimethyl fumarate (DMF) has antioxidant and anti-inflammatory functions. Our study aimed to evaluate the protective effects of resveratrol or DMF against testicular dysfunction associated with chronic unpredictable mild stress (CUMS)-induced depression in rats. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.009DOI Listing
April 2019
2 Reads

Temperature dependence of mitoflash biogenesis in cardiac mitochondria.

Arch Biochem Biophys 2019 Mar 18;666:8-15. Epub 2019 Mar 18.

State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China. Electronic address:

Mitochondrial flashes (mitoflashes) represent fundamental biochemical and biophysical dynamics of the organelle, involving sudden depolarization of mitochondrial membrane potential (ΔΨ), bursting production of reactive oxygen species (ROS), and accelerated extrusion of matrix protons. Here we investigated temperature dependence of mitoflash biogenesis as well as ΔΨ oscillations, a subset of which overlapping with mitoflashes, in both cardiac myocytes and isolated respiring cardiac mitochondria. Unexpectedly, we found that mitoflash biogenesis was essentially temperature-independent in intact cardiac myocytes, evidenced by the constancy of frequency as well as amplitude and rise speed over 5 °C-40 °C. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.002DOI Listing

Deletion analyses reveal insights into the domain specific activities of an essential GTPase CgtA in Vibrio cholerae.

Arch Biochem Biophys 2019 Apr 17;665:143-151. Epub 2019 Mar 17.

Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia, 741246, West Bengal, India. Electronic address:

CgtA is an essential bacterial GTPase protein involved in multiple cellular activities. In the presence of 50S ribosome, its GTPase activity increases significantly. Through sequential deletions of CgtA protein of Vibrio cholerae (CgtA) we found that its N terminal Obg domain is essential for ribosome binding and augmenting the ribosome mediated GTPase activity. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.007DOI Listing
April 2019
1 Read

Impaired calcium handling and mitochondrial metabolic dysfunction as early markers of hypertrophic cardiomyopathy.

Arch Biochem Biophys 2019 Apr 16;665:166-174. Epub 2019 Mar 16.

School of Human Sciences (Physiology), The University of Western Australia, Crawley, WA, Australia; Victor Chang Cardiac Research Institute, Sydney, NSW, Australia. Electronic address:

Hypertrophic cardiomyopathy (HCM) is a primary myocardial disorder, characterised by myocyte remodeling, disorganisation of sarcomeric proteins, impaired energy metabolism and altered cardiac contractility. Gene mutations encoding cardiac contractile proteins account for 60% of HCM aetiology. Current drug therapy including L-type calcium channel antagonists, are used to manage symptoms in patients with overt HCM, but no treatment exists that can reverse or prevent the cardiomyopathy. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.006DOI Listing
April 2019
1 Read

Involvement of cutaneous SR-B1 in skin lipid homeostasis.

Arch Biochem Biophys 2019 Mar 13;666:1-7. Epub 2019 Mar 13.

Department Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy; Plants for Human Health Institute, Animal Sciences Dept., NC Research Campus, NC State University, NC, USA. Electronic address:

Background: The main functions of the skin are to protect against environmental insults and prevent water loss, which are performed by the complex lipid- and protein matrix present in the outermost layers of the epithelium. The lipidome of these outer layers is mainly composed of ceramides, fatty acids, and cholesterol, which regulates keratinocyte differentiation and skin barrier function. SR-B1 is a multifunctional scavenger receptor that is best known for facilitating uptake of cholesterol from HDL particles in the liver, but it is also expressed in the skin. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.005DOI Listing

Characterization of the cellular effects of myeloperoxidase-derived oxidants on H9c2 cardiac myoblasts.

Arch Biochem Biophys 2019 Apr 11;665:132-142. Epub 2019 Mar 11.

Heart Research Institute, 7 Eliza St. Newtown, Sydney, NSW, 2042, Australia; Sydney Medical School, University of Sydney, Sydney, NSW, 2005, Australia. Electronic address:

Oxidative stress is a major hallmark of cardiac ischemia/reperfusion (I/R) injury, which is in part due to the release of the enzyme myeloperoxidase (MPO) from activated infiltrating leukocytes, and the subsequent production of the oxidants hypochlorous acid (HOCl) and hypothiocyanous acid (HOSCN). Although exposure of various cell types to either oxidant is known to cause cellular dysfunction within a variety of pathological settings, the precise role of HOCl and HOSCN in the initiation of tissue damage evident following cardiac I/R injury remains unclear. In this study, we have employed the use of the cardiac myoblast cell line H9c2 as a model for cardiac myocytes and demonstrate that exposure to either oxidant elicits a dose-dependent increase in cytosolic calcium accumulation, depletion of the cellular thiol pool, reduction of glutathione (GSH) levels and loss of mitochondrial inner trans-membrane potential, concomitant with increased necrotic cell death. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.004DOI Listing
April 2019
1 Read

Substrate-dependent and cyclophilin D-independent regulation of mitochondrial flashes in skeletal and cardiac muscle.

Arch Biochem Biophys 2019 Apr 11;665:122-131. Epub 2019 Mar 11.

Department of Pharmacology and Physiology, University of Rochester Medical Center, Rochester, NY, 14642, USA.

Mitochondrial flashes (mitoflashes) are stochastic events in the mitochondrial matrix detected by mitochondrial-targeted cpYFP (mt-cpYFP). Mitoflashes are quantal bursts of reactive oxygen species (ROS) production accompanied by modest matrix alkalinization and depolarization of the mitochondrial membrane potential. Mitoflashes are fundamental events present in a wide range of cell types. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00039861183080
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http://dx.doi.org/10.1016/j.abb.2019.03.003DOI Listing
April 2019
2 Reads

DNA minor groove binding of a well known anti-mycobacterial drug dapsone: A spectroscopic, viscometric and molecular docking study.

Arch Biochem Biophys 2019 Apr 6;665:107-113. Epub 2019 Mar 6.

School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Bhubaneswar, India. Electronic address:

Dapsone is a sulfone drug mainly used as anti-microbial and anti-inflammatory agent for the treatment of various diseases including leprosy. Recently, its interaction with protein (bovine serum albumin) is evidenced. But, the binding propensity of this anti-mycobacterial drug towards DNA is still unknown. Read More

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http://dx.doi.org/10.1016/j.abb.2019.03.001DOI Listing

An ultra-stable glucanotransferase-cum-exoamylase from the hyperthermophile archaeon Thermococcus onnurineus.

Arch Biochem Biophys 2019 Apr 4;665:114-121. Epub 2019 Mar 4.

Centre for Protein Science, Design and Engineering (CPSDE), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Knowledge City, Sector-81, SAS Nagar, Mohali, Punjab, 140306, India. Electronic address:

The genome of the hyperthermophile archaeon Thermococcus onnurineus (strain NA1) encodes a 652 residues-long putative 4-α-glucanotransferase of the GH 57 family which we have expressed in Escherichia coli. The enzyme (TonAmyGT) appears to remove glucose from the reducing end of a donor glucan and transfers it to the non-reducing end of an acceptor glucan, creating a pool of oligosaccharides through disproportionation of any substrate maltooligosaccharide, with maltose acting substantively as the smallest donor glucan as well as the smallest acceptor glucan. Additionally, glucose is also cleaved from maltooligosaccharides and released into solution without being transferred to an acceptor, causing the enzyme to function as an exo-amylase (which can digest starch) in addition to its activity as a glucanotransferase. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.017DOI Listing

Effects of phosphorylation on the NLRP3 inflammasome.

Arch Biochem Biophys 2019 Mar 5. Epub 2019 Mar 5.

Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB, T2N 4Z6, Canada. Electronic address:

The pyrin domain containing Nod-like receptors (NLRPs) are a family of pattern recognition receptors known to regulate an array of immune signaling pathways. Emergent studies demonstrate the potential for regulatory control of inflammasome assembly by phosphorylation, notably NLRP3. Over a dozen phosphorylation sites have been identified for NLRP3 with many more suggested by phosphoproteomic studies of the NLRP family. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.020DOI Listing
March 2019
10 Reads

Major yolk protein and HSC70 are essential for the activation of the TLR pathway via interacting with MyD88 in Apostichopus japonicus.

Arch Biochem Biophys 2019 Apr 2;665:57-68. Epub 2019 Mar 2.

School of Marine Sciences, Ningbo University, Ningbo, Zhejiang Province, 315211, China.

The Toll cascade plays important functions in innate immunity against infectious pathogens in animals. Toll cascade as an ancient immune defender were conserved among different species. The activation of the TLR pathway between different species often involves different interacting proteins. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.019DOI Listing
April 2019
1 Read

Characterization of the kinetics and activation thermodynamics of intra- and inter-organism hybrid tetramers of pyruvate carboxylase.

Arch Biochem Biophys 2019 Apr 1;665:87-95. Epub 2019 Mar 1.

School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Perth, WA6009, Australia. Electronic address:

In sedimentation velocity experiments, we have been able to detect hybrid Rhizobium etli pyruvate carboxylase tetramers formed between subunits that contain covalently bound biotin and mutant subunits that do not. This was performed by forming complexes of the tetramers with the biotin-binding protein avidin. In addition, we have shown that it is possible to form hybrid tetramers of pyruvate carboxylase subunits from two different organisms (bacteria - Rhizobium etli and fungi - Aspergillus nidulans). Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.018DOI Listing
April 2019
4 Reads

Crystallographic structure of a complex between trypsin and a nonapeptide derived from a Bowman-Birk inhibitor found in Vigna unguiculata seeds.

Arch Biochem Biophys 2019 Apr 25;665:79-86. Epub 2019 Feb 25.

Laboratory of Biophysics, Department of Cell Biology, University of Brasilia, Campus Darcy Ribeiro, Asa Norte, Brasília, DF, 70910-900, Brazil. Electronic address:

Natural inhibitors of proteases have been classified into different families, among them is the Bowman-Birk Inhibitor (BBI) family. Members of BBI have two structurally reactive loops that simultaneously inhibit trypsin and chymotrypsin. Here, we have investigated the binding of bovine trypsin by a cyclic nonapeptide, named PTRY9 (CTKSIPPQC), derived of the black-eyed pea trypsin/chymotrypsin inhibitor (BTCI) from Vigna unguiculata seeds. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.013DOI Listing
April 2019
2 Reads

The alkaline transition of cytochrome c revisited: Effects of electrostatic interactions and tyrosine nitration on the reaction dynamics.

Arch Biochem Biophys 2019 Apr 25;665:96-106. Epub 2019 Feb 25.

Departamento de Química Inorgánica, Analítica y Química Física and INQUIMAE (CONICET-UBA), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. 2, piso 1, Buenos Aires, C1428EHA, Argentina. Electronic address:

Here we investigated the effect of electrostatic interactions and of protein tyrosine nitration of mammalian cytochrome c on the dynamics of the so-called alkaline transition, a pH- and redox-triggered conformational change that implies replacement of the axial ligand Met80 by a Lys residue. Using a combination of electrochemical, time-resolved SERR spectroelectrochemical experiments and molecular dynamics simulations we showed that in all cases the reaction can be described in terms of a two steps minimal reaction mechanism consisting of deprotonation of a triggering group followed by ligand exchange. The pK values of the transition are strongly modulated by these perturbations, with a drastic downshift upon nitration and an important upshift upon establishing electrostatic interactions with a negatively charged model surface. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.016DOI Listing
April 2019
1 Read

The role of lysosomal cysteine cathepsins in NLRP3 inflammasome activation.

Arch Biochem Biophys 2019 Feb 23. Epub 2019 Feb 23.

Institute for Immunology, Department of Basic Medical Sciences, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.

Lysosomal cysteine cathepsins are a family of proteases that are involved in a myriad of cellular processes from proteolytic degradation in the lysosome to bone resorption. These proteins mature following the cleavage of a pro-domain in the lysosome to become either exo- or endo-peptidases. The cathepsins B, C, L, S and Z have been implicated in NLRP3 inflammasome activation following their activation with ATP, monosodium urate, silica crystals, or bacterial components, among others. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.015DOI Listing
February 2019

PRMT7 as a unique member of the protein arginine methyltransferase family: A review.

Arch Biochem Biophys 2019 Apr 22;665:36-45. Epub 2019 Feb 22.

Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, CA, 90095, USA. Electronic address:

Protein arginine methyltransferases (PRMTs) are found in a wide variety of eukaryotic organisms and can regulate gene expression, DNA repair, RNA splicing, and stem cell biology. In mammalian cells, nine genes encode a family of sequence-related enzymes; six of these PRMTs catalyze the formation of ω-asymmetric dimethyl derivatives, two catalyze ω-symmetric dimethyl derivatives, and only one (PRMT7) solely catalyzes ω-monomethylarginine formation. Purified recombinant PRMT7 displays a number of unique enzymatic properties including a substrate preference for arginine residues in R-X-R motifs with additional flanking basic amino acid residues and a temperature optimum well below 37 °C. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6461449PMC
April 2019
1 Read

Solution structure of a unicellular microalgae-derived translationally controlled tumor protein revealed both conserved features and structural diversity.

Arch Biochem Biophys 2019 Apr 22;665:23-29. Epub 2019 Feb 22.

CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China. Electronic address:

Translationally controlled tumor proteins (TCTPs) are eukaryote-conserved multifunctional proteins, but their primary functions are not well understood yet. Study on TCTP from unicellular species may provide insight into the primary function of the TCTP family. Bioinformatic analysis indicated that the TCTP from Nannochloropsis oceanica (NoTCTP), a model unicellular microalga for biodiesel and polyunsaturated fatty acid production, has low sequence homology to other structure-known TCTPs and two TCTP signature patterns are not detected in NoTCTP. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.012DOI Listing
April 2019
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Effect of a high sucrose and high fat diet in BDNF (+/-) mice on oxidative stress markers in adipose tissues.

Arch Biochem Biophys 2019 Apr 21;665:46-56. Epub 2019 Feb 21.

Department of Medical Biochemistry, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey. Electronic address:

The purpose of this study was to investigate the effects of a high fat and a high sucrosediet in wild type and BDNF (+/-) mice on oxidative stress in epididymal and subcutaneousadipose tissues by measuring different markers of oxidative stress and antioxidant enzymes. Wild type (WT) and BDNF (+/-) male mice were divided into six groups receiving fed control diet (CD), high sucrose diet (HSD), or high fat diet (HFD) for four months. Levels of 3-nitrotyrosine (3-NT) increased in the HFD-fed BDNF (+/-) mice, while 4-hydroxynonenal (4-HNE) levels increased in the CD and HFD-fed BDNF (+/-) groups. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.004DOI Listing
April 2019
2 Reads

Antioxidant effect of resveratrol in single red blood cells measured by thermal fluctuation spectroscopy.

Arch Biochem Biophys 2019 Apr 20;665:30-35. Epub 2019 Feb 20.

Centro de Óptica y Fotónica, Universidad de Concepción, Concepción, Chile; Departmento de Física, Universidad de Concepción, Concepción, Chile.

The human red blood cell (RBC) membrane has significant elastic capabilities which can be described measuring typical membrane edge fluctuations and mechanical properties by optical techniques. The RBC elastic properties can be affected by changes in the surrounding media. In an attempt to elucidate the molecular mechanisms of the interaction of resveratrol with the red cell membrane and of its antioxidant capacity the changes in mechanical properties of the RBC membrane were analyzed. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.011DOI Listing
April 2019
2 Reads

Peptides in biology and biomedicine: Walking towards the future.

Arch Biochem Biophys 2019 Apr 19;665:20-22. Epub 2019 Feb 19.

Instituto de Química Médica (IQM-CSIC), Madrid, 28006, Spain. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00039861193012
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http://dx.doi.org/10.1016/j.abb.2019.02.010DOI Listing
April 2019
6 Reads

Simvastatin promotes restoration of chondrocyte morphology and phenotype.

Arch Biochem Biophys 2019 Apr 15;665:1-11. Epub 2019 Feb 15.

Department of Anatomy and Cell Biology, East Carolina University, 600 Moye Blvd., Greenville, NC, 27834, USA. Electronic address:

In this study we examined whether the action of simvastatin affects re-differentiation of passaged chondrocytes and if so, whether this was mediated via changes in cholesterol or cholesterol intermediates. Bovine articular chondrocytes, of varying passage number, human knee chondrocytes and rat chondrosarcoma chondrocytes were treated with simvastatin and examined for changes in mRNA and protein expression of markers of the chondrocyte phenotype as well as changes in cell shape, proliferation and proteoglycan production. In all three models, while still in monolayer culture, simvastatin treatment alone promoted changes in phenotype and morphology indicative of re-differentiation most prominent being an increase in SOX9 mRNA and protein expression. Read More

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http://dx.doi.org/10.1016/j.abb.2019.01.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450767PMC
April 2019
1 Read

Protein phosphatase PPP3CA (calcineurin A) down-regulates hypoxia-inducible factor transcriptional activity.

Arch Biochem Biophys 2019 Mar 15;664:174-182. Epub 2019 Feb 15.

Laboratory of Biochemistry, Faculty of Medicine, University of Thessaly, Larissa, Greece. Electronic address:

Hypoxia-inducible factors (HIF) are master regulators of the response to hypoxia. Although several kinases are known to modify their oxygen sensitive HIF-α subunits or affect indirectly their function, little is known about the role of phosphatases in HIF control. To address this issue, a library containing siRNAs for the 25 known catalytic subunits of human phosphatases was used to screen for their effect on HIF transcriptional activity in HeLa cells. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.007DOI Listing

Purification and biophysical characterization of a mannose/N-acetyl-d-glucosamine-specific lectin from Machaerium acutifolium and its effect on inhibition of orofacial pain via TRPV1 receptor.

Arch Biochem Biophys 2019 Mar 14;664:149-156. Epub 2019 Feb 14.

Centro de Ciências Agrárias e Ambientais, Universidade Federal do Maranhão, Chapadinha, Maranhão, Brazil. Electronic address:

A new mannose/N-acetyl-dglucosamine-specific lectin, named MaL, was purified from seeds of Machaerium acutifolium by precipitation with ammonium sulfate, followed by affinity and ion-exchange chromatography. MaL haemagglutinates either native rabbit erythrocytes or those treated with proteolytic enzymes. MaL is highly stable by the ability to maintain its haemagglutinating activity after exposure to temperatures up to 50 °C. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.009DOI Listing
March 2019
2 Reads

NOD-like receptors and inflammasomes: A review of their canonical and non-canonical signaling pathways.

Arch Biochem Biophys 2019 Feb 14. Epub 2019 Feb 14.

Department of Medicine, University of Calgary, Calgary, AB, Canada; Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada. Electronic address:

The NOD-like receptor (NLR) family of proteins is a group of pattern recognition receptors (PRRs) known to mediate the initial innate immune response to cellular injury and stress. The NLRP proteins represent a fourteen-member subset of the NLR family that contains an N-terminal pyrin domain. Some NLRs are known to form multi-protein complexes known as inflammasomes. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.008DOI Listing
February 2019

Glabridin inhibits dexamethasone-induced muscle atrophy.

Arch Biochem Biophys 2019 Mar 13;664:157-166. Epub 2019 Feb 13.

Graduate School of Agricultural Science, Kobe University, Kobe, Hyogo, 651-8501, Japan. Electronic address:

Prevention of muscle wasting is known to contribute to improving the quality of life and extending a healthy life. Recently, we have reported that licorice flavonoid oil containing glabridin, which is a prenylated isoflavone, enhances muscle mass in mice. In this study, we investigated the prevention effect of glabridin on dexamethasone-induced muscle atrophy and clarified its mechanism in cultured myotubes and in muscle of mice. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00039861183087
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http://dx.doi.org/10.1016/j.abb.2019.02.006DOI Listing
March 2019
10 Reads

Biochemical characterization of TyrA dehydrogenases from Saccharomyces cerevisiae (Ascomycota) and Pleurotus ostreatus (Basidiomycota).

Arch Biochem Biophys 2019 Apr 13;665:12-19. Epub 2019 Feb 13.

Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA.

L-Tyrosine is an aromatic amino acid necessary for protein synthesis in all living organisms and a precursor of secondary (specialized) metabolites. In fungi, tyrosine-derived compounds are associated with virulence and defense (i.e. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.005DOI Listing
April 2019
4 Reads

The effect of the branched chain polypeptide carrier on biodistribution of covalently attached B-cell epitope peptide (APDTRPAPG) derived from mucin 1 glycoprotein.

Arch Biochem Biophys 2019 Mar 8;664:127-133. Epub 2019 Feb 8.

MTA-ELTE Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Eötvös L. University, Budapest 112, P.O. Box 32, H-1518, Hungary; Department of Organic Chemistry, Eötvös Loránd University, Budapest 112, P.O. Box 32, H-1518, Hungary.

In order to establish structure-function relationship for the design of a new group of oligopeptide antigen-macromolecule conjugate, multiple copies of mucin-1 B-cell epitope peptide, APDTRPAPG were conjugated with branched chain polymeric polypeptides possessing poly[L-Lys] backbone. By the synthesis, radiolabeling (I) and in vivo treatment of BALB/c mice with epitope conjugates containing XK/XAK type carrier, where X = Glu (EK or EAK) or Leu (LAK), the influence of the polypeptide structure on the blood clearance profile and on tissue distribution profile concerning the epitope delivery to relevant organs (e.g. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.003DOI Listing
March 2019
6 Reads

Atomic force microscopy for single molecule characterisation of protein aggregation.

Arch Biochem Biophys 2019 Mar 8;664:134-148. Epub 2019 Feb 8.

Centre for Misfolding Disease, Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, United Kingdom; Cavendish Laboratory, University of Cambridge, Cambridge, CB3 0HE, United Kingdom. Electronic address:

The development of atomic force microscopy (AFM) has opened up a wide range of novel opportunities in nanoscience and new modalities of observation in complex biological systems. AFM imaging has been widely employed to resolve the complex and heterogeneous conformational states involved in protein aggregation at the single molecule scale and shed light onto the molecular basis of a variety of human pathologies, including neurodegenerative disorders. The study of individual macromolecules at nanoscale, however, remains challenging, especially when fully quantitative information is required. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6420408PMC
March 2019
1 Read

The impact of water molecules on binding affinity of the anti-diabetic thiazolidinediones for catalase: Kinetic and mechanistic approaches.

Arch Biochem Biophys 2019 Mar 7;664:110-116. Epub 2019 Feb 7.

Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Center of Excellence in Biothermodynamics, University of Tehran, Tehran, Iran.

Water molecules play a vital role in efficient drug binding to its target. Thiazolidinediones (TZDs), a class of anti-diabetic drugs, are widely used for treatment of type 2 diabetes mellitus. In the present study, the possible contribution of water molecules to the binding of TZDs to catalase, a potential target in the liver, was investigated by different experimental and theoretical methods. Read More

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http://dx.doi.org/10.1016/j.abb.2019.02.002DOI Listing

Transport of cystine across xC antiporter.

Arch Biochem Biophys 2019 Mar 6;664:117-126. Epub 2019 Feb 6.

Research Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610, Antwerp, Belgium.

Extracellular cystine (CYC) uptake by xC antiporter is important for the cell viability. Especially in cancer cells, the upregulation of xC activity is observed, which protects these cells from intracellular oxidative stress. Hence, inhibition of the CYC uptake may eventually lead to cancer cell death. Read More

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http://dx.doi.org/10.1016/j.abb.2019.01.039DOI Listing
March 2019
6 Reads

Skeletal muscle excitation-metabolism coupling.

Arch Biochem Biophys 2019 Mar 1;664:89-94. Epub 2019 Feb 1.

Center for Studies of Exercise, Metabolism and Cancer (CEMC), ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile. Electronic address:

Mitochondria represent the main source of ATP in skeletal muscle and mitochondria activity increases after muscle fiber depolarization. The regulation of mitochondrial function during contraction in skeletal muscle, however, is poorly understood. Skeletal muscle has a particular distribution of mitochondria where three distinct populations can be recognized. Read More

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http://dx.doi.org/10.1016/j.abb.2019.01.037DOI Listing
March 2019
5 Reads

Energy-dissipating hub in muscle mitochondria: Potassium channels and uncoupling proteins.

Arch Biochem Biophys 2019 Mar 1;664:102-109. Epub 2019 Feb 1.

Laboratory of Intracellular Ion Channels, Nencki Institute of Experimental Biology, Pasteur St. 3, Warsaw, Poland. Electronic address:

Energy homeostasis in mitochondria is vital for proper muscle cell function. In this review we will focus on cardiac and skeletal muscle energy-dissipating systems, i.e. Read More

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http://dx.doi.org/10.1016/j.abb.2019.01.036DOI Listing
March 2019
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Molecular simulation of peptides coming of age: Accurate prediction of folding, dynamics and structures.

Arch Biochem Biophys 2019 Mar 1;664:76-88. Epub 2019 Feb 1.

Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Alexandroupolis, 68100, Greece. Electronic address:

The application of molecular dynamics simulations to study the folding and dynamics of peptides has attracted a lot of interest in the last couple of decades. Following the successful prediction of the folding of several proteins using molecular simulation, foldable peptides emerged as a favourable system mainly due to their application in improving protein structure prediction methods and in drug design studies. However, their performance is inherently linked to the accuracy of the empirical force fields used in the simulations, whose optimisation and validation is of paramount importance. Read More

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http://dx.doi.org/10.1016/j.abb.2019.01.033DOI Listing
March 2019
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Mitochondrial Rieske iron-sulfur protein in pulmonary artery smooth muscle: A key primary signaling molecule in pulmonary hypertension.

Arch Biochem Biophys 2019 Mar 30;664:68-75. Epub 2019 Jan 30.

Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, 12208, USA. Electronic address:

Rieske iron-sulfur protein (RISP) is a catalytic subunit of the complex III in the mitochondrial electron transport chain. Studies for years have revealed that RISP is essential for the generation of intracellular reactive oxygen species (ROS) via delicate signaling pathways associated with many important molecules such as protein kinase C-ε, NADPH oxidase, and ryanodine receptors. More significantly, mitochondrial RISP-mediated ROS production has been implicated in the development of hypoxic pulmonary vasoconstriction, leading to pulmonary hypertension, right heart failure, and death. Read More

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http://dx.doi.org/10.1016/j.abb.2019.01.029DOI Listing
March 2019
1 Read