Read by QxMD icon Read

Protein chemistry

Eileen K Jaffe
Porphobilinogen synthase (PBGS), also known as 5-aminolevulinate dehydratase, is an essential enzyme in the biosynthesis of all tetrapyrroles, which function in respiration, photosynthesis, and methanogenesis. Throughout evolution, PBGS adapted to a diversity of cellular niches and evolved to use an unusual variety of metal ions both for catalytic function and to control protein multimerization. With regard to the active site, some PBGSs require Zn(2+); a subset of those, including human PBGS, contain a constellation of cysteine residues that acts as a sink for the environmental toxin Pb(2+)...
October 26, 2016: Accounts of Chemical Research
Svenja Winzen, James Ciro Schwabacher, Julius Mueller, Katharina Landfester, Kristin Mohr
Surfactants, even in miniscule amounts, are often used for the synthesis and especially the stabilization of nanomaterials, which is essential for in vivo applications. In this study, we show that the interaction between nanoparticles and proteins strongly depends on the type of stabilizing surfactants and their (small) concentration changes. The reaction between human serum albumin (HSA) and polystyrene nanoparticles (PS-NPs) stabilized by an ionic or nonionic surfactant - sodium dodecyl sulfate (SDS) or Lutensol AT50, respectively - was monitored using isothermal titration calorimetry (ITC)...
October 26, 2016: Biomacromolecules
Philip R Nicovich, Miro Janco, Tom Sobey, Mehul Gajwani, Peyman Obeidy, Renee Whan, Katharina Gaus, Peter Gunning, Adelle Cf Coster, Till Böcking
Reconstitution of actin filaments on surfaces for observation of filament-associated protein dynamics by fluorescence microscopy is currently an exciting field in biophysics. Here we examine the effects of attaching actin filaments to surfaces on the binding and dissociation kinetics of a fluorescence-labelled tropomyosin, a rod-shaped protein that forms continuous strands wrapping around the actin filament. Two attachment modalities of the actin to the surface are explored: where the actin filament is attached to the surface at multiple points along its length; and where the actin filament is attached at one end and aligned parallel to the surface by buffer flow...
October 26, 2016: Cytoskeleton
Tobias Baumann, Matthias Exner, Nediljko Budisa
To date, the two systems most extensively used for noncanonical amino acid (ncAA) incorporation via orthogonal translation are based on the Methanococcus jannaschii TyrRS/tRNA CUA(Tyr) and the Methanosarcina barkeri/Methanosarcina mazei PylRS/tRNA CUA(Pyl) pairs. Here, we summarize the development and usage of the pyrrolysine-based system for orthogonal translation, a process that allows for the recombinant production of site-specifically labeled proteins and peptides. Via stop codon suppression in Escherichia coli and mammalian cells, genetically encoded biomolecules can be equipped with a great diversity of chemical functionalities including click chemistry handles, post-translational modifications, and photocaged sidechains...
October 26, 2016: Advances in Biochemical Engineering/biotechnology
Imad Younus Hasan, Adam Mechler
Supported planar phospholipid membranes are used in a range of biophysical measurements, typically for characterizing protein-membrane interactions. Liposome deposition is the most common method to create such membranes. The ability of liposomes to fuse into a lamellar membrane during deposition is strongly dependent on the surface chemistry; some important substrate materials such as oxidized gold do not promote liposome fusion. Circumventing this determinism poses an enduring challenge to membrane biophysics...
September 22, 2016: Biointerphases
Bradley M Dickson, Parker W de Waal, Zachary H Ramjan, H Eric Xu, Scott B Rothbart
In this communication we introduce an efficient implementation of adaptive biasing that greatly improves the speed of free energy computation in molecular dynamics simulations. We investigated the use of accelerated simulations to inform on compound design using a recently reported and clinically relevant inhibitor of the chromatin regulator BRD4 (bromodomain-containing protein 4). Benchmarking on our local compute cluster, our implementation achieves up to 2.5 times more force calls per day than plumed2. Results of five 1 μs-long simulations are presented, which reveal a conformational switch in the BRD4 inhibitor between a binding competent and incompetent state...
October 21, 2016: Journal of Chemical Physics
Weilong Zhong, Bo Sun, Cheng Lu, Hengheng Yu, Changhua Wang, Lingfei He, Ju Gu, Shuang Chen, Yanrong Liu, Xiangyan Jing, Zhun Bi, Guang Yang, Honggang Zhou, Tao Sun, Cheng Yang
Small-molecule fluorescent probes have been widely used in target identification, but this method has many disadvantages. For example, the identified proteins are usually complex, and additional biochemical studies are needed to distinguish real targets from interference results. To address this problem, we propose a series of strategies for improving the efficiency of target identification. First, pretreatment with a lower concentration of hydrogen peroxide can shield against thiol interference. Second, the use of benzophenone as a photo-affinity group is not appropriate, and diazirines are preferred...
October 26, 2016: Scientific Reports
Yu Wu, Bin Yue, Jia Liu
Obesity is characterized by the abnormal or excessive fat accumulation that may impair health and extensive increase in body mass index (BMI). Childhood obesity may occur due to disturbances in metabolic regulation, which lead to metabolic syndrome and other diseases. Peripheral blood suspended immune cells are responsible for immune surveillance. The aim of the present study was to map the inflammatory cytokine expression pattern of isolated peripheral blood mononuclear cells (PBMCs) following lipopolysaccharide (LPS) stress in vitro and clinical chemistry parameters in the plasma of subjects...
October 20, 2016: Molecular Medicine Reports
Ji Hoon Park, Minsup Kim, Masaharu Shiratani, Art E Cho, Eun Ha Choi, Pankaj Attri
Over the last few years, the variation in liquid chemistry due to the development of radicals generated by cold atmospheric plasma (CAP) has played an important role in plasma medicine. CAP direct treatment or CAP activated media treatment in cancer cells shows promising anticancer activity for both in vivo and in vitro studies. However, the anticancer activity or antimicrobial activity varies between plasma devices due to the different abilities among plasma devices to generate the reactive oxygen and nitrogen species (RONS) at different ratios and in different concentrations...
October 25, 2016: Scientific Reports
Seah Ling Kuan, Tao Wang, Tanja Weil
The synthetic transformation of polypeptides with molecular accuracy holds great promise for providing functional and structural diversity beyond the proteome. Consequently, the last decade has seen an exponential growth of site-directed chemistry to install additional features into peptides and proteins even inside living cells. The disulfide rebridging strategy has emerged as a powerful tool for site-selective modifications since most proteins contain disulfide bonds. In this Review, we present the chemical design, advantages and limitations of the disulfide rebridging reagents, while summarizing their relevance for synthetic customization of functional protein bioconjugates, as well as the resultant impact and advancement for biomedical applications...
October 25, 2016: Chemistry: a European Journal
Yinliang Yang, Marko Fonović, Steven H L Verhelst
The discovery of the protein targets of small molecule probes is a crucial aspect of activity-based protein profiling and chemical biology. Mass spectrometry is the primary method for target identification, and in the last decade, cleavable linkers have become a popular strategy to facilitate protein enrichment and identification. In this chapter, we provide an overview of cleavable linkers used in chemical proteomics approaches, discuss their different chemistries, and describe how they aid in protein identification...
2017: Methods in Molecular Biology
Madhu Sudhan Ravindran, Markus R Wenk
This chapter provides a step-by-step protocol using activity-based protein profiling (ABPP) as a chemical-proteomic tool to survey the antibiotic properties of a small molecule. Here, we investigate the molecular mechanism behind the bactericidal activity of tetrahydrolipstatin (THL). ABPP relies on small molecule probes that target the active site of specific enzymes in complex proteomes. These probes in turn are equipped with a reporter tag that allows capturing, visualization, enrichment, identification, and quantification of its targets either in vitro or in situ...
2017: Methods in Molecular Biology
Susanne Zweerink, Tanja Pollmann, Sabrina Ninck, Farnusch Kaschani, Markus Kaiser
Bioreactive natural products represent versatile starting points for the development of structurally unique activity-based probes. In the present protocol, we describe the workflow for an activity-based protein profiling (ABPP) experiment with an alkyne-tagged natural product derivative. Our protocol includes experimental procedures for in vivo labeling, sample preparation and 2-step (click chemistry) visualization and sample preparation for mass spectrometry-based target identification.
2017: Methods in Molecular Biology
Sella Kim, Ji-Hye Lee, Jong Hyeon Seok, Yi-Ho Park, Sang Won Jung, Art E Cho, Cheolju Lee, Mi Sook Chung, Kyung Hyun Kim
Iron and oxygen chemistry is mediated by iron proteins for many biological functions. Carboxylate-bridged diiron enzymes including ferritin have in common the mechanism of oxygen activation via peroxodiferric intermediates. However, the route for iron uptake and the structural identification of intermediates still remain incomplete. The 4-fold symmetry channel of Helicobacter pylori ferritin (Hpf) was previously proposed as the iron uptake route in eubacteria, but the amino acid residues at the 4-fold channel are not highly conserved...
October 21, 2016: Journal of Molecular Biology
Peter M Fischer
Kinase inhibitor research is a comparatively recent branch of medicinal chemistry and pharmacology and the first small-molecule kinase inhibitor, imatinib, was approved for clinical use only 15 years ago. Since then, 33 more kinase inhibitor drugs have received regulatory approval for the treatment of a variety of cancers and the volume of reports on the discovery and development of kinase inhibitors has increased to an extent where it is now difficult-even for those working in the field-easily to keep an overview of the compounds that are being developed, as currently there are 231 such compounds, targeting 38 different protein and lipid kinases (not counting isoforms), in clinical use or under clinical investigation...
October 24, 2016: Medicinal Research Reviews
Søren B van Witteloostuijn, Søren L Pedersen, Knud J Jensen
Peptides and proteins constitute a vast pool of excellent drug candidates. Evolution has equipped these molecules with superior drug-like properties such as high specificity and potency. However, native peptides and proteins suffer from an inadequate pharmacokinetic profile, and their outstanding pharmacological potential can only be realized if this issue is addressed during drug development. To overcome this challenge, a variety of half-life extension techniques relying on covalent chemical modification have been developed...
October 24, 2016: ChemMedChem
Giulia Morgese, Lucca Trachsel, Matteo Romio, Mohammad Divandari, Shivaprakash N Ramakrishna, Edmondo M Benetti
The cyclic polymer topology strongly alters the interfacial, physico-chemical properties of polymer brushes, when compared to the linear counterparts. In this study, we especially concentrated on poly-2-ethyl-2-oxazoline (PEOXA) cyclic and linear grafts assembled on titanium oxide surfaces by the "grafting-to" technique. The smaller hydrodynamic radius of ring PEOXAs favors the formation of denser brushes with respect to linear analogs. Denser and more compact cyclic brushes generate a steric barrier that surpasses the typical entropic shield by a linear brush...
October 24, 2016: Angewandte Chemie
Yung-Hao Wong, Chia-Chiun Chiu, Chih-Lung Lin, Ting-Shou Chen, Bo-Ren Jheng, Yu-Ching Lee, Jeremy Chen, Bor-Sen Chen
In recent years, many systems biology approaches have been used with various cancers. The materials described here can be used to build bases to discover novel cancer therapy targets in connection with computer-aided drug design (CADD). A deeper understanding of the mechanisms of cancer will provide more choices and correct strategies in the development of multiple target drug therapies, which is quite different from the traditional cancer single target therapy. Targeted therapy is one of the most powerful strategies against cancer and can also be applied to other diseases...
October 19, 2016: Current Pharmaceutical Biotechnology
Oksana N Khokhlova, Elena A Tukhovskaya, Irina N Kravchenko, Elena S Sadovnikova, Irina A Pakhomova, Elena A Kalabina, Alexander V Lobanov, Elvira R Shaykhutdinova, Alina M Ismailova, Arkady N Murashev
INTRODUCTION: It is important that the method of anesthesia of mice does not considerably alter the animal's physiological and metabolic status before terminal blood sampling taken in order to analyze clinical pathology parameters. METHODS: Hematology, hemostasis, and clinical chemistry parameters were compared in male and female BALB/c mice exposed to either tiletamine-zolazepam-xylazine (TZX) anesthesia or euthanasia in carbon dioxide (CO2) chamber to reveal an alternative method of anesthesia vs...
October 20, 2016: Journal of Pharmacological and Toxicological Methods
Tao Peng, Howard C Hang
Over the past years, fluorescent proteins (e.g., green fluorescent proteins) have been widely utilized to visualize recombinant protein expression and localization in live cells. Although powerful, fluorescent protein tags are limited by their relatively large sizes and potential perturbation to protein function. Alternatively, site-specific labeling of proteins with small-molecule organic fluorophores using bioorthogonal chemistry may provide a more precise and less perturbing method. This approach involves site-specific incorporation of unnatural amino acids (UAAs) into proteins via genetic code expansion, followed by bioorthogonal chemical labeling with small organic fluorophores in living cells...
October 21, 2016: Journal of the American Chemical Society
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"