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Protein and Peptide Letters

Jeong Ho Chang, Chang-Kyu Ok
The secretion systems of gram-negative bacteria have been classified into six types according to their structures and functions. Of these, the type VI secretion system (T6SS) plays a role in the export of effector proteins, which could be cytotoxic to the host cell. While the components of the T6SS complex have been largely assessed, structural data on the T6SS components from virulent bacteria are insufficient. Here, we report the crystal structure of Pseudomonas aeruginosa TagF (PaTagF), the product of the T6SS accessory gene F, at a resolution of 2...
January 19, 2019: Protein and Peptide Letters
Özlem Biçen Ünlüer, Nursenem Karaca
In recent years, precise diagnosis and efficient drug targeting have been drawing attention to cancer therapy. The potential side effects of nanocarriers have encouraged scientists to study with biocompatible materials for nanoparticles. Albumin is an ingredient of the human blood serum and many formulations have contained albumin as an excipient. Several investigations have been made on albumin-based nanomedicine, including preparation methods, nano-biomaterial synthesis, and therapeutic applications. In this study, hyaluronic acid (HA) conjugated bovine serum albumin (BSA) nanoparticles have been synthesized according to AmiNoAcid Decorated and Light Underpinning Conjugation Approach (ANADOLUCA) that provides microemulsion polymerization at room temperature, under a nitrogen atmosphere in daylight...
January 19, 2019: Protein and Peptide Letters
Guo-Ping Zhou, Siming Liao, Ge Liang, Jing Zhu, Bo Lu, Li-Xing Peng, Qing-Yang Wang, Yu-Tuo Wei, Ri-Bo Huang
A study on thermostability of α-amylase is a central requirement for its application in life science and biotechnology. In this study, we focus on the impact of Ca2+ on the thermal characteristics of moderately thermostable α-amylase from Anoxybacillus sp.GXS-BL (AGXA) by the biochemical analysis, differential scanning calorimetry (DSC), circular dichroism (CD) spectrum measurements and homology modeling. The maximum active temperature (Topt), half-inactivation temperature (T50) and half-life (t1/2) of the α-amylase with Ca2+ are higher than that of the α-amylase without Ca2+...
January 16, 2019: Protein and Peptide Letters
E N Lorenzón, J P Piccoli, N A Santos-Filho, E M Cilli
Antimicrobial resistance is a global health problem with strong social and economic impacts. The development of new antimicrobial agents is considered an urgent challenge. In this regard, antimicrobial peptides (AMPs) appear to be novel candidates to overcome this problem. The mechanism of action of AMPs involves intracellular targets and membrane disruption. Although the exact mechanism of action of AMPs remains controversial, most AMPs act through membrane disruption of the target cell. Several strategies have been used to improve AMP activity, such as peptide dimerization...
January 2, 2019: Protein and Peptide Letters
Vinita Chauhan, Ritika Chauhan, Priyanka Sonkar, Ram Kumar Dhaked
The Shiga toxins comprise a family of related protein toxins produced by bacteria Shigella dysenteriae and some strains of Escherichia coli that cause severe clinical manifestations. Severe Shiga toxin intoxication results in hemolytic-uremic syndrome (HUS), up to 50% of HUS patients manifest some degree of renal failure and ∼10% of such cases develop permanent renal failure or death. Purification of Shiga toxin from bacteria is a multistep time consuming process resulting in low yield. E. coli clones expressing recombinant A and B subunits (rStxA and rStxB) were established for in vitro reconstitution of recombinant Shiga toxin (rStx)...
December 28, 2018: Protein and Peptide Letters
Michael Brenowitz, Jessica R Chapman, Beatrix Ueberheide, Michael Khine, Jonathan Pegan, Matt Law, Mohammed El Makkaoui, Micheal Leser
BACKGROUND: For almost four decades, hydroxyl radical chemically generated by Fenton chemistry has been a mainstay for the oxidative 'footprinting' of macromolecules. OBJECTIVE: In this article, we start by reviewing the application of chemical generation of hydroxyl radical to the development of oxidative footprinting of DNA and RNA and the subsequent application of the method to oxidative footprinting of proteins. We next discuss a novel strategy for generating hydroxyl radicals by Fenton chemistry that immobilizes catalytic iron on a solid surface (Pyrite Shrink Wrap laminate) for the application of nucleic acid and protein footprinting...
December 12, 2018: Protein and Peptide Letters
Mark Benhaim, Kelly K Lee, Miklos Guttman
Structural biology has provided a fundamental understanding of protein structure and mechanistic insight into their function. However, high-resolution structures alone are insufficient for a complete understanding of protein behavior. Higher energy conformations, conformational changes, and subtle structural fluctuations that underlie the proper function of proteins are often difficult to probe using traditional structural approaches. Solution state structural techniques are needed to interrogate the dynamic nature of proteins under native conditions...
December 12, 2018: Protein and Peptide Letters
Ksenia N Chukhontseva, Vadim V Salnikov, Oleg S Morenkov, Sergey V Kostrov, Ilya V Demidyuk
Protealysin, a zinc metalloprotease of Serratia proteamaculans, is the prototype of a new group within the peptidase family M4. Protealysin-like proteases (PLPs) are widely spread in bacteria but are also found in fungi and archaea. The biological functions of PLPs have not been well studied, but published data showed the involvement of enzymes of this group in the interaction of bacteria with higher organisms, and most likely in the pathogenesis. Such functionality requires the release of the proteases from bacterial cells; however, the data on the cellular localization of PLPs are contradictory and no direct data of this kind have been published...
December 11, 2018: Protein and Peptide Letters
M P Taraka Prabhu, Nandini Sarkar
Amyloids are highly ordered beta sheet rich stable protein aggregates, which have been found to play a significant role in the onset of several degenerative diseases such as Alzheimer's disease, Huntington's disease, Parkinson's disease, Type II diabetes mellitus and so on. Aggregation of proteins leading to amyloid fibril formation via intermediate(s), is thought to be a nucleated condensation polymerization process associated with many pathological conditions. There has been extensive research to identify inhibitors of these disease oriented aggregation processes...
December 11, 2018: Protein and Peptide Letters
Jianglong Peng, Hao Yin, Ying Zhou, Haoyuan Jia, Yubao Cui
BACKGROUND: The dust mite Dermatophagoides farinae is a common worldwide cause of indoor allergies induced by mite proteins, including the mid-tier allergen Der f 7. Objective To identify conformational epitopes in Der f 7 using mimotope mapping and computational modelling. METHODS: Here, we used standard hybridoma technology to generate 3 new monoclonal antibodies against Der f 7 and performed mimotope mapping by probing a random peptide phage display library. Computational tools, including Minox and the DiscoTope-2...
December 8, 2018: Protein and Peptide Letters
Norio Matsushima, Shintaro Takatsuka, Hiroki Miyashita, Robert H Kretsinger
Mutations in the genes encoding Leucine Rich Repeat (LRR) containing proteins are associated with over sixty human diseases; these include high myopia, mitochondrial encephalomyopathy, and Crohn's disease. These mutations occur frequently within the LRR domains and within the regions that shield the hydrophobic core of the LRR domain. The amino acid sequences of fifty-five LRR proteins have been published. They include Nod-Like Receptors (NLRs) such as NLRP1, NLRP3, NLRP14, and Nod-2, Small Leucine Rich Repeat Proteoglycans (SLRPs) such as keratocan, lumican, fibromodulin, PRELP, biglycan, and nyctalopin, and F-box/LRR-repeat proteins such as FBXL2, FBXL4, and FBXL12...
December 8, 2018: Protein and Peptide Letters
María Verónica Húmpola, María Carolina Rey, Pablo Gabriel Sponton, Arturo Carlos Simonetta, Georgina Guadalupe Tonarelli
BACKGROUND: In the last years, antimicrobial peptides (AMPs) and lipopeptides have received attention as promising candidates to treat infections caused by resistant microorganisms. OBJECTIVE: The main objective of this study was to investigate the effect of repetitive KLFK motifs and the attachment of aliphatic acids to the N-terminus of (KLFK)n peptides on therapeutic properties. METHODS: Minimal inhibitory concentration against Gram (+) and (-) bacteria and yeast of synthetic compounds were determined by broth microtiter dilution method, and the toxicity was evaluated by hemolysis assay...
December 8, 2018: Protein and Peptide Letters
Sayan Gupta
Membrane proteins are crucial for cellular sensory cascades and metabolite transport, and hence are key pharmacological targets. Structural studies by traditional high-resolution techniques are limited by the requirements for high purity and stability when handled in high concentration and nonnative buffers. Hence, there is a growing requirement for the use of alternate methods in a complementary but orthogonal approach to study the dynamic and functional aspects of membrane proteins in physiologically relevant conditions...
November 28, 2018: Protein and Peptide Letters
Simon A Morton, Sayan Gupta, Christopher J Petzold, Corie Ralston
Efforts in the field of synchrotron footprinting are progressing rapidly, with two major footprinting centers in the United States, one on the east coast at the National Synchrotron Light Source II, and one on the west coast at the Advanced Light Source. This article describes recent technical advances in the technique at the Advanced Light Source, and describes the types of biological problems that can be addressed using the new methods and instrumentation.
November 28, 2018: Protein and Peptide Letters
Simin D Maleknia, Kevin M Downard
BACKGROUND: Radical Probe Mass Spectrometry (RP-MS) describes a pioneering methodology in structural biology that enables the study of protein structures, their interactions, and dynamics on fast timescales (down to sub-milliseconds). Hydroxyl radicals (•OH) generated directly from water within aqueous solutions induce the oxidation of reactive, solvent accessible amino acid side chains that are then analyzed by mass spectrometry. Introduced in 1998 at the American Society for Mass Spectrometry annual conference, RP-MS was first published on in 1999...
November 28, 2018: Protein and Peptide Letters
Liuqing Shi, Michael L Gross
Structural proteomics approaches coupled with mass spectrometry are increasingly used in biology to examine the composition and structure of macromolecules. Hydroxyl radical-mediated protein footprinting using mass spectrometry has recently been developed to define structure, assembly, and conformational changes of macromolecules in solution based on measurements of reactivity of amino-acid side chains with reagents that irreversibly modify a protein side chain. Generating the hydroxyl radicals by laser irradiation, Hambly and Gross developed fast photochemical oxidation of proteins (FPOP), which labels proteins on the millisecond or shorter time scale...
November 28, 2018: Protein and Peptide Letters
Daichao Wu, Guoqing Li, Yao Ma, Jin Liu, Yukun Li, Juan Wang, Junhui Bai, Sijie Tan, Meixiang Li, Yongheng Chen
Human interleukin 37 (IL37), a unique anti-inflammatory cytokine of IL1 family member, plays critical roles in innate and adaptive immunity and inflammation. Preparation of high purity and tag-removed recombinant IL37 protein (rIL37) is critical for its clinical application. In this study, we constructed an N-terminal cleavable GST-fused IL37 expression vector. Subsequent to transformation and optimization of the induction temperature, the soluble expression level of rIL37 was 306.5 mg/L of culture medium at 18 °C induction in Escherichia coli...
November 28, 2018: Protein and Peptide Letters
Jen Bohon
X-ray synchrotron footprinting is a rapidly growing technique ideal for the analysis of solution-state structure and dynamics of macromolecules. First developed in the 1990's at the National Synchrotron Light Source, instrumentation to expand the technology has continuously pushed the boundaries of biological systems that can be studied using the technique. Dedicated synchrotron beamlines, first X28C at NSLS, then XFP (17-BM) at NSLS-II provide an important resource for examining fundamental biological mechanisms of folding, ligand binding, catalysis, splicing, transcription, translation, and macromolecular assembly...
November 28, 2018: Protein and Peptide Letters
Natalie K Garcia, Galahad Deperalta, Aaron T Wecksler
BACKGROUND: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solution-stability are linked to the proper three-dimensional organization of the primary sequence into higher order structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures...
November 28, 2018: Protein and Peptide Letters
Ratmir Derda, Mohammad R Jafari
Peptide-derived drugs constitute a significant fraction of therapeutic agents. In 2013, The global market of peptide therapeutics was ca. $19 billion; this value does not include revenue from insulin derivatives of $28 million. The combined sales of insulin and non-insulin peptide drugs is estimated to exceed $70 billion by 2019. A significant fraction of peptide-derived drugs is composed of an amino acid sequence and additional chemical functionalities that improve biological and pharmacological properties of the drug...
November 19, 2018: Protein and Peptide Letters
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