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Archives of Biochemistry and Biophysics

Joshua W Jeffs, Shadi Ferdosi, Hussein N Yassine, Chad R Borges
Ex vivo protein modifications occur within plasma and serum (P/S) samples due to prolonged exposure to the thawed state-which includes temperatures above -30 °C. Herein, the ex vivo glycation of human serum albumin from healthy and diabetic subjects was monitored in P/S samples stored for hours to months at -80 °C, -20 °C, and room temperature, as well as in samples subjected to multiple freeze-thaw cycles, incubated at different surface area-to-volume ratios or under different atmospheric compositions...
July 13, 2017: Archives of Biochemistry and Biophysics
Li-Kai Liu, Donald F Becker, John J Tanner
Proline has important roles in multiple biological processes such as cellular bioenergetics, cell growth, oxidative and osmotic stress response, protein folding and stability, and redox signaling. The proline catabolic pathway, which forms glutamate, enables organisms to utilize proline as a carbon, nitrogen, and energy source. FAD-dependent proline dehydrogenase (PRODH) and NAD(+)-dependent glutamate semialdehyde dehydrogenase (GSALDH) convert proline to glutamate in two sequential oxidative steps. Depletion of PRODH and GSALDH in humans leads to hyperprolinemia, which is associated with mental disorders such as schizophrenia...
July 13, 2017: Archives of Biochemistry and Biophysics
Sajjad Ahrari, Navid Mogharrab, Leila Navapour
The Ser/Thr protein kinase MARK2, also known as Par1b, belongs to a highly-conserved group of PAR proteins which regulate cell polarity and partitioning through the animal kingdom. In the current study, inactive and active structures of human MARK2 were constructed by modeling and molecular dynamics simulation, based on available incomplete crystal structures in Protein Data Bank, to investigate local structural changes through which MARK2 switches from inactive to active state. None of the MARK2 wild type inactive crystal structures represent the position of activation segment...
July 12, 2017: Archives of Biochemistry and Biophysics
Mahdie Rahban, Najmeh Salehi, Ali Akbar Saboury, Saman Hosseinkhani, Mohammad Hossein Karimi-Jafari, Rohoullah Firouzi, Nasrollah Rezaei-Ghaleh, Ali Akbar Moosavi-Movahedi
Molecular dynamics (MD) at two temperatures of 300 and 340 K identified two histidine residues, His461 and His489, in the most flexible regions of firefly luciferase, a light emitting enzyme. We therefore designed four protein mutants H461D, H489K, H489D and H489M to investigate their enzyme kinetic and thermodynamic stability changes. Substitution of His461 by aspartate (H461D) decreased ATP binding affinity, reduced the melting temperature of protein by around 25 °C and shifted its optimum temperature of activity to 10 °C...
July 12, 2017: Archives of Biochemistry and Biophysics
B Chami, G Jeong, A Varda, A-M Maw, H-B Kim, G M Fong, M Simone, B S Rayner, X-S Wang, J M Dennis, P K Witting
After acute myocardial infarction (AMI), neutrophils are recruited to the affected myocardium. Hypochlorous acid (HOCl) produced by neutrophil myeloperoxidase (MPO) damages cardiomyocytes and potentially expands the primary infarct. Rat cardiomyocyte-like cells were incubated with isolated human neutrophils treated with chemical activators in the absence or presence of nitroxide 4-methoxy-Tempo (MetT; 25 μM) for 4, 6 or 24 h; studies with reagent HOCl served as positive control. Treating cardiomyocytes with activated neutrophils or reagent HOCl resulted in a marked increase in protein tyrosine chlorination and a decline in protein tyrosine phosphatase (PTP) activity...
July 5, 2017: Archives of Biochemistry and Biophysics
Bastian Daniel, Barbara Konrad, Marina Toplak, Majd Lahham, Julia Messenlehner, Andreas Winkler, Peter Macheroux
Biological oxidations form the basis of life on earth by utilizing organic compounds as electron donors to drive the generation of metabolic energy carriers, such as ATP. Oxidative reactions are also important for the biosynthesis of complex compounds, i.e. natural products such as alkaloids that provide vital benefits for organisms in all kingdoms of life. The vitamin B2-derived cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) enable an astonishingly diverse array of oxidative reactions that is based on the versatility of the redox-active isoalloxazine ring...
July 1, 2017: Archives of Biochemistry and Biophysics
V Satish Bollimpelli, Pankaj S Dholaniya, Anand K Kondapi
Topoisomerase IIβ is a type II DNA topoisomerase that was reported to be expressed in all mammalian cells but abundantly expressed in cells that have undergone terminal differentiation to attain a post mitotic state. Enzymatically it catalyzes ATP-dependent topological changes of double stranded DNA, while as a protein it was reported to be associated with several factors in promoting cell growth, migration, DNA repair and transcription regulation. The cellular roles of topoisomerase IIβ are very less understood compared to its counterpart topoisomerase IIα...
June 29, 2017: Archives of Biochemistry and Biophysics
Tom A Ewing, Marco W Fraaije, Andrea Mattevi, Willem J H van Berkel
The VAO/PCMH flavoprotein family consists of structurally homologous flavin-dependent enzymes that catalyze a wide range of chemical reactions. Family members share an architecture consisting of a conserved FAD-binding domain and a more variable substrate-binding domain, which enables varying interactions with a range of substrates while maintaining the same cofactor-binding fold. Here, we provide an overview of the current state of our knowledge on the members of the VAO/PCMH family. Based on a phylogenetic analysis, we divide the family into 11 subgroups...
June 29, 2017: Archives of Biochemistry and Biophysics
Fayezeh Mofidi Najjar, Fereshteh Taghavi, Rahim Ghadari, Nader Sheibani, Ali Akbar Moosavi-Movahedi
Non-enzymatic glycation of protein is a post-translational modification which is produced by a covalent binding between reducing sugars and amino groups in lysine and arginine residues. This modification is directly linked to high blood glucose concentration and therefore to pathological condition. In this paper, the effect of pathological conditions derived from hyperglycemia (16 mM glucose) on bovine liver catalase (BLC) as a model protein was considered by measurements of the enzyme activity, reactive oxygen species (ROS) generation and changes in catalase conformational properties...
June 28, 2017: Archives of Biochemistry and Biophysics
Andrew P Hinck, Jose L Neira
No abstract text is available yet for this article.
June 27, 2017: Archives of Biochemistry and Biophysics
Renata A G Reis, Felipe Antunes Calil, Patricia Rosa Feliciano, Matheus Pinto Pinheiro, M Cristina Nonato
The flavoenzyme dihydroorotate dehydrogenase catalyzes the stereoselective oxidation of (S)-dihydroorotate to orotate in the fourth of the six conserved enzymatic reactions involved in the de novo pyrimidine biosynthetic pathway. Inhibition of pyrimidine metabolism by selectively targeting DHODHs has been exploited in the development of new therapies against cancer, immunological disorders, bacterial and viral infections, and parasitic diseases. Through a chronological narrative, this review summarizes the efforts of the scientific community to achieve our current understanding of structural and biochemical properties of DHODHs...
June 27, 2017: Archives of Biochemistry and Biophysics
Emmanuel Fajardo-Sánchez, Vicente Galiano, José Villalaín
Non-structural NS2A protein of Dengue virus is essential for viral replication but poorly characterized because of its high hydrophobicity. We have previously shown experimentally that NS2A possess a segment, peptide dens25, known to insert into membranes and interact specifically with negatively-charged phospholipids. To characterize its membrane interaction we have used two types of molecular dynamics membrane model systems, a highly mobile membrane mimetic (HMMM) and an endoplasmic reticulum (ER) membrane-like model...
June 27, 2017: Archives of Biochemistry and Biophysics
Xinyi Zhao, Rui Li, Ying Liu, Xuehong Zhang, Min Zhang, Zhi Zeng, Limin Wu, Xuelin Gao, Tian Lan, Yiqing Wang
Reactive oxygen species (ROS) play a key role in chronic liver injury and fibrosis. Polydatin, a glucoside of resveratrol, has been shown to possess anti-oxidative bioactivity. It has been demonstrated that resveratrol has many therapeutic effects on liver disorders including liver fibrosis. Recent study showed that polydatin prevented acute liver injury after carbon tetrachloride (CCl4) induction. However, the protective effects of polydatin on chronic liver injury and fibrosis has not been understood. Thus, we aimed to determine the roles of polydatin in chronic liver injury and fibrosis...
June 27, 2017: Archives of Biochemistry and Biophysics
Pablo Sobrado, John J Tanner
Flavin cofactors are widely used by enzymes to catalyze a broad range of chemical reactions. Traditionally, flavins in enzymes are regarded as redox centers, which enable enzymes to catalyze the oxidation or reduction of substrates. However, a new class of flavoenzyme has emerged over the past quarter century in which the flavin functions as a catalytic center in a non-redox reaction. Here we introduce the unifying concept of flavin hot spots to understand and categorize the mechanisms and reactivities of both traditional and noncanonical flavoenzymes...
June 23, 2017: Archives of Biochemistry and Biophysics
Takanori Kigawa
Stable-isotope (SI) labeling of proteins is an essential technique to investigate their structures, interactions or dynamics by nuclear magnetic resonance (NMR) spectroscopy. The assignment of the main-chain signals, which is the fundamental first step in these analyses, is usually achieved by a sequential assignment method based on triple resonance experiments. Independently of the triple resonance experiment-based sequential assignment, amino acid-selective SI labeling is beneficial for discriminating the amino acid type of each signal; therefore, it is especially useful for the signal assignment of difficult targets...
June 20, 2017: Archives of Biochemistry and Biophysics
Daniel Ouedraogo, Jacob Ball, Archana Iyer, Renata A G Reis, Maria Vodovoz, Giovanni Gadda
d-Arginine dehydrogenase from Pseudomonas aeruginosa (PaDADH) is a flavin-dependent oxidoreductase, which is part of a novel two-enzyme racemization system that functions to convert d-arginine to l-arginine. PaDADH contains a noncovalently linked FAD that shows the highest activity with d-arginine. The enzyme exhibits broad substrate specificity towards d-amino acids, particularly with cationic and hydrophobic d-amino acids. Biochemical studies have established the structure and the mechanistic properties of the enzyme...
June 15, 2017: Archives of Biochemistry and Biophysics
Lombard Murielle, Hamdane Djemel
RNAs molecules fulfill key roles in the expression and regulation of the genetic information stored within the DNA chromosomes. In addition to the four canonical bases, U, C, A and G, RNAs harbor various chemically modified derivatives which are generated post-transcriptionally by specific enzymes acting directly at the polymer level. More than one hundred naturally occurring modified nucleosides have been identified to date, the largest number of which is found in tRNAs and rRNA. This remarkable biochemical process produces widely diversified RNAs further expanding the functional repertoires of these nucleic acids...
June 15, 2017: Archives of Biochemistry and Biophysics
Ertugrul Filiz, Recep Vatansever, Ibrahim Ilker Ozyigit, Mehmet Emin Uras, Ugur Sen, Naser A Anjum, Eduarda Pereira
This study aimed to improve current understanding on ethylene-insensitive 3-like (EIL) members, least explored in woody plants such as poplar (Populus trichocarpa Torr. & Grey). Herein, seven putative EIL members were identified in P. trichocarpa genome and were roughly annotated either as EIN3-like sequence associated with ethylene pathway or EIL3-like sequences related with sulfur (S)-pathway. Motif-distribution pattern of proteins also corroborated this annotation. They were distributed on six chromosomes (chr1, 3, 4 and 8-10), and were revealed to encode a protein of 509-662 residues with nuclear localization...
June 15, 2017: Archives of Biochemistry and Biophysics
Federica Piccirilli, Nicoletta Plotegher, Francesco Spinozzi, Luigi Bubacco, Paolo Mariani, Mariano Beltramini, Isabella Tessari, Valeria Militello, Andrea Perucchi, Heinz Amenitsch, Enrico Baldassarri, Milos Steinhart, Stefano Lupi, Maria Grazia Ortore
α-synuclein amyloid fibrils are found in surviving neurons of Parkinson's disease affected patients, but the role they play in the disease development is still under debate. A growing number of evidences points to soluble oligomers as the major cytotoxic species, while insoluble fibrillar aggregates could even play a protection role. In this work, we investigate α-synuclein fibrils dissociation induced at high pressure by means of Small Angle X-ray Scattering and Fourier Transform Infrared Spectroscopy. Fibrils were produced from wild type α-synuclein and two familial mutants, A30P and A53T...
June 15, 2017: Archives of Biochemistry and Biophysics
K M Abdullah, Faizan Abul Qais, Iqbal Ahmad, Imrana Naseem
Hyperglycaemia is a key factor for the formation of advanced glycated endproducts (AGEs). Inhibition of glycation may play key role in minimizing the diabetes related complications. We have tried to explore the glucose and methyl glyoxal mediated glycation and antiglycation activity of niacin using human serum albumin as model protein. Protein was incubated with glucose for 28 days at physiological temperature to achieve glycation. Antiglycation activity was evaluated by assessing free lysine, carbonyl content, AGE specific fluorescence...
June 15, 2017: Archives of Biochemistry and Biophysics
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