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https://www.readbyqxmd.com/read/29233876/molecular-control-of-chaperone-mediated-autophagy
#1
REVIEW
Steve Catarino, Paulo Pereira, Henrique Girão
Chaperone-mediated autophagy (CMA) is a selective form of autophagy in which cytosolic proteins bearing a pentapeptide motif biochemically related to the KFERQ sequence, are recognized by the heat shock protein family A member 8 (HSPA8) chaperone, delivered to the lysomal membrane, and directly translocated across the lysosomal membrane by a protein complex containing lysosomal associated membrane protein 2a (Lamp2a). Since its discovery over two decades ago, the importance of this pathway in cell proteostasis has been made increasingly apparent...
December 12, 2017: Essays in Biochemistry
https://www.readbyqxmd.com/read/29228892/sequence-fingerprints-distinguish-erroneous-from-correct-predictions-of-intrinsically-disordered-protein-regions
#2
Konda Mani Saravanan, A Keith Dunker, Sankaran Krishnaswamy
More than sixty prediction methods for intrinsically disordered proteins (IDPs) have been developed over the years, many of which are accessible on the world-wide web. Nearly, all of these predictors give balanced accuracies in the ~65% to ~80% range. Since predictors are not perfect, further studies are required to uncover the role of amino acid residues in native IDP as compared to predicted IDP regions. In the present work, we make use of sequences of 100% predicted IDP regions, false positive disorder predictions, and experimentally determined IDP regions to distinguish the characteristics of native versus predicted IDP regions...
December 11, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29226462/spontaneous-death-of-rat-chloroleukaemia-cells-induced-by-an-endogenous-growth-inhibitor
#3
T Rytömaa, K Grip-Rytömaa
OBJECTIVES: When rat chloroleukaemia (CHL) cells are grown undisturbed in a confined space, a genomic long interspersed nuclear element (LINE) is transcriptionally activated at a relatively low population density, followed by the retrotransposition of LINE and population death. This death programme is fundamentally different from conventional cell death pathways. MATERIALS AND METHODS: This work is essentially based on the re-analysis of relevant, old experimental data...
December 10, 2017: Cell Proliferation
https://www.readbyqxmd.com/read/29178159/crystallographic-insights-into-the-self-assembly-of-klvff-amyloid-beta-peptides
#4
Andrea Pizzi, Valentina Dichiarante, Giancarlo Terraneo, Pierangelo Metrangolo
Amyloidogenic peptide fragment KLVFF (H2 N-Lys-Leu-Val-Phe-Phe-COOH, Aβ16-20 ), the core-sequence of the polypeptide Aβ40, is a well-studied model for amyloid formation. However, due to its low crystallinity, detailed atomic information of KLVFF structure is lacking. Here we report the high-resolution single-crystal X-ray structure of two monohalogenated KLVFF derivatives, KLVFF(I) and KLVFF(Br). The obtained results highlight how halogenation is a good strategy to promote crystallization and facilitate the phase determination of KLVFF(I) and KLVFF(Br) fragments...
November 27, 2017: Biopolymers
https://www.readbyqxmd.com/read/29170620/the-coordination-abilities-of-three-novel-analogues-of-saliva-peptides-the-influence-of-structural-modification-on-the-copper-binding
#5
Aleksandra Kotynia, Edward Krzyżak, Elżbieta Kamysz, Małgorzata Sobocińska, Justyna Brasuń
Three novel analogues of salivary peptides as sialorphin (QHNPR) and opiorphin (QRFSR) were synthesized by the solid-phase method. The sequences of these ligands were following: AHNPR, QANPR and QRFPR. The aim of our work was investigation in what way some structural modifications may impact on coordination abilities of studied peptides. In this work we presented the interaction of pentapeptides with copper(II) ions in wide range of pH. To determine the coordination model of ligands there were carried out several studies by spectroscopy (UV-Vis, CD) methods and potentiometric measurements...
2017: International Journal of Peptide Research and Therapeutics
https://www.readbyqxmd.com/read/29161266/knowledge-based-prediction-of-protein-backbone-conformation-using-a-structural-alphabet
#6
Iyanar Vetrivel, Swapnil Mahajan, Manoj Tyagi, Lionel Hoffmann, Yves-Henri Sanejouand, Narayanaswamy Srinivasan, Alexandre G de Brevern, Frédéric Cadet, Bernard Offmann
Libraries of structural prototypes that abstract protein local structures are known as structural alphabets and have proven to be very useful in various aspects of protein structure analyses and predictions. One such library, Protein Blocks, is composed of 16 standard 5-residues long structural prototypes. This form of analyzing proteins involves drafting its structure as a string of Protein Blocks. Predicting the local structure of a protein in terms of protein blocks is the general objective of this work...
2017: PloS One
https://www.readbyqxmd.com/read/29153423/uracil-amino-acid-as-a-scaffold-for-%C3%AE-sheet-peptidomimetics-study-of-photophysics-and-interaction-with-bsa-protein
#7
Subhendu Sekhar Bag, Afsana Yashmeen
We report herein the uracil-di-aza-amino acid (U(r)AA) as a new family of molecular scaffold to induce β-hairpin structure with H-bonded β-sheet conformation in a short peptide. This has been demonstrated in two conceptual fluorescent pentapeptides wherein triazolylpyrenyl alanine and/or triazolylmethoxynapthyl alanine ((TPy)AlaDo and/or (TMNap)AlaDo) are embedded into two arms of the uracil-amino acid via an intervening leucine. Conformational analysis by CD, IR, variable temperature and 2D NMR spectroscopy reveals the β-hairpin structures for both the peptides...
November 10, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/29133203/expression-and-functional-characterization-of-tachykinin-related-peptides-in-the-blood-feeding-bug-rhodnius-prolixus
#8
A N S Haddad, M S Defferrari, S Hana, S G Szeto, A B Lange
Tachykinins (tachykinin-related peptides, TRPs) are multifunctional neuropeptides that have widespread distribution in the central nervous system (CNS) and in the gastrointestinal tract of many insects, and most have been shown to stimulate contractions of visceral muscles. Invertebrate TRPs carry a characteristic conserved C-terminal pentapeptide (FXGXR-amide) and most of them share some amino acid sequence similarities (approx. 45%) with the vertebrate and mammalian tachykinin family. We have functionally characterized the tachykinins in R...
November 10, 2017: Peptides
https://www.readbyqxmd.com/read/29131507/the-disruptive-effect-of-lysozyme-on-the-bacterial-cell-wall-explored-by-an-in-silico-structural-outlook
#9
Emiliano D Primo, Lisandro H Otero, Francisco Ruiz, Sebastián Klinke, Walter Giordano
The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall and disrupt the bacterial life cycle by cleaving the linkage between the NAG and NAM carbohydrates. Lab exercises focused on the effects of lysozyme on the bacterial cell wall are frequently incorporated in biochemistry classes designed for undergraduate students in diverse fields as biology, microbiology, chemistry, agronomy, medicine, and veterinary medicine...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29124531/identification-of-peptide-aedg-in-the-polypeptide-complex-of-the-pineal-gland
#10
V Kh Khavinson, A T Kopylov, B V Vaskovsky, G A Ryzhak, N S Lin'kova
The polypeptide complex of the epiphysis and the peptide AEDG, constructed on the basis of its amino acid analysis, exert similar biological effects. Both bioregulators normalize melatonin synthesis in the pineal gland, functioning of the brain, eye retina, cardiovascular, endocrine, and immune systems; they also act as antioxidants, stress-protectors, and geroprotectors. Within the epiphysis polypeptide complex, free amino acids (3.26%), dipeptides (23.19%), tripeptides (50.72%), tetrapeptides (22.10%), and pentapeptides (0...
November 9, 2017: Bulletin of Experimental Biology and Medicine
https://www.readbyqxmd.com/read/29104984/conformational-heterogeneity-in-tails-of-dna-binding-proteins-is-augmented-by-proline-containing-repeats
#11
Harshavardhan Khare, Debayan Dey, Chilakapati Madhu, Dillip Senapati, Srinivasarao Raghothama, Thimmaiah Govindaraju, Suryanarayanarao Ramakumar
A cationic terminal extension or tail is a common feature of many DNA-binding proteins. We show that a particular type of tail rich in proline, alanine and lysine belongs to the class of 'flexible disorder' and consists of characteristic pentapeptide repeats. Our designed peptides, (AAKKA)1-4 and (PAKKA)1-4, represent the tails of several bacterial DNA-binding proteins. Enhanced conformational sampling of these representative peptides using accelerated molecular dynamic simulations supported by circular dichroism spectroscopy and nuclear magnetic resonance studies demonstrates the role of frequent and interspersed prolines in augmenting conformational heterogeneity of the peptide backbone...
November 21, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/29097321/the-first-tropical-sea-cucumber-caspase-8-from-holothuria-leucospilota-molecular-characterization-involvement-of-apoptosis-and-inducible-expression-by-immune-challenge
#12
Aifen Yan, Chunhua Ren, Ting Chen, Xiao Jiang, Hongyan Sun, Da Huo, Chaoqun Hu, Jing Wen
In this study, the first tropical sea cucumber caspase-8 named HLcaspase-8 was identified from Holothuria leucospilota. The full-length cDNA of HLcaspase-8 is 2293 bp in size, containing a 245 bp 5'-untranslated region (UTR), a 521 bp 3'-UTR and a 1527 bp open reading frame (ORF) encoding a protein of 508 amino acids with a deduced molecular weight of 57.47 kDa. Besides the common signatures of caspase family including conserved cysteine active site pentapeptide motif QACQG, P20 domain and P10 domain, HLcaspase-8 also contains a characteristic DED domain...
October 31, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/29065689/an-exploration-of-the-calcium-binding-mode-of-egg-white-peptide-asp-his-thr-lys-glu-and-in-vitro-calcium-absorption-studies-of-peptide-calcium-complex
#13
Na Sun, Ziqi Jin, Dongmei Li, Hongjie Yin, Songyi Lin
The binding mode between the pentapeptide (DHTKE) from egg white hydrolysates and calcium ions was elucidated upon its structural and thermodynamics characteristics. The present study demonstrated that the DHTKE peptide could spontaneously bind calcium with a 1:1 stoichiometry, and that the calcium-binding site corresponded to the carboxyl oxygen, amino nitrogen, and imidazole nitrogen atoms of the DHTKE peptide. Moreover, the effect of the DHTKE-calcium complex on improving the calcium absorption was investigated in vitro using Caco-2 cells...
October 31, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/29052787/pentapeptide-insertion-scanning-mutational-analysis-of-turkey-herpesvirus-hvt063-reveals-residues-important-for-its-rna-silencing-suppression-activity
#14
Gang Jia, Wenjing Li, Meina Fan, Ru Yu, Yang Xu, Liwei Geng, Jiedao Zhang, Changxiang Zhu, Hongmei Liu
HVT063, an RNA-binding protein encoded by turkey herpesvirus, has been shown previously to suppress RNA silencing. Here, a scanning library produced by pentapeptide-insertion scanning mutagenesis was used to identify key residues associated with its RNA silencing suppressor (RSS) activity. Forty-two in-frame insertion mutants of HVT063 protein were evaluated for their RSS activity using the dual-luciferase transient expressing assay system. Sixteen mutations resulted in a loss of RSS activity, 20 mutations resulted in decreased RSS activity, and six mutations exhibited high RSS activity similar to wild-type HVT063...
October 20, 2017: Archives of Virology
https://www.readbyqxmd.com/read/29037739/targeted-regulation-of-hygroscopicity-of-soybean-antioxidant-pentapeptide-powder-by-zinc-ions-binding-to-the-moisture-absorption-sites
#15
Peiyu Xue, Na Sun, Yong Li, Sheng Cheng, Songyi Lin
In the present study, a targeted regulation of hygroscopicity of soybean antioxidant pentapeptide (SAP) powder was explored by zinc ions binding to its moisture absorption sites. Scanning electron microscopy, X-ray diffraction analysis, Fourier transform infrared spectroscopy and an energy-dispersive X-ray spectroscope were used to confirm the formation of the SAP-zinc complex. The results showed that morphology of SAP-zinc complex belonged to crystalline nanoparticles. The moisture sorption/desorption kinetics of the SAP-zinc complex changed compared to that of the SAP...
March 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29030637/molecular-mechanisms-of-the-binding-and-specificity-of-streptococcus-pneumoniae-sortase-c-enzymes-for-pilin-subunits
#16
Emmanuel B Naziga, Jeff Wereszczynski
Pili are elongated structures that protrude from bacteria and increase their virulence. The Streptococcus pnuenomae pilus island 1 pili are composed of three subunits, RrgA, RrgB, and RrgC, and are assembled by three class C sortase C (SrtC) enzymes: SrtC-1, SrtC-2, and SrtC-3. Pilin subunits are recognized by SrtC proteins through a pentapeptide sorting signal, and while previous studies have sought to characterize the selectivities of SrtC isoforms for these subunits, the molecular mechanisms underlying these interactions remain unclear...
October 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28950028/an-evolutionary-analysis-identifies-a-conserved-pentapeptide-stretch-containing-the-two-essential-lysine-residues-for-rice-l-myo-inositol-1-phosphate-synthase-catalytic-activity
#17
Papri Basak, Susmita Maitra-Majee, Jayanta Kumar Das, Abhishek Mukherjee, Shubhra Ghosh Dastidar, Pabitra Pal Choudhury, Arun Lahiri Majumder
A molecular evolutionary analysis of a well conserved protein helps to determine the essential amino acids in the core catalytic region. Based on the chemical properties of amino acid residues, phylogenetic analysis of a total of 172 homologous sequences of a highly conserved enzyme, L-myo-inositol 1-phosphate synthase or MIPS from evolutionarily diverse organisms was performed. This study revealed the presence of six phylogenetically conserved blocks, out of which four embrace the catalytic core of the functional protein...
2017: PloS One
https://www.readbyqxmd.com/read/28893327/new-activity-of-yamamarin-an-insect-pentapeptide-on-immune-system-of-mealworm-tenebrio-molitor
#18
K Walkowiak-Nowicka, G Nowicki, M Kuczer, G Rosiński
In insects, two types of the immune responses, cellular and humoral, constitute a defensive barrier against various parasites and pathogens. In response to pathogens, insects produce a wide range of immune agents that act on pathogens directly, such as cecropins or lysozyme, or indirectly by the stimulation of hemocyte migration or by increasing phenoloxidase (PO) activity. Recently, many new immunologically active substances from insects, such as peptides and polypeptides, have been identified. Nevertheless, in the most cases, their physiological functions are not fully known...
September 12, 2017: Bulletin of Entomological Research
https://www.readbyqxmd.com/read/28892870/effects-of-terminal-capping-on-the-fibrillation-of-short-l-glu-n-peptides
#19
Agnieszka Hernik-Magoń, Bartłomiej Fedorczyk, Robert Dec, Wojciech Puławski, Aleksandra Misicka, Wojciech Dzwolak
Several homopolypeptides including poly-l-glutamic acid (PLGA) form amyloid-like fibrils under favorable physicochemical conditions. We have shown recently that even short uncapped (Glu)n peptides (for n>3) form fibrillar β-aggregates which cross-seed with amyloid fibrils obtained from high molecular weight fractions of PLGA. Here we investigate effects of N-terminal acetylation and C-terminal amidation on the amyloidogenic tendencies of (Glu)n peptides containing 3, 4, and 5 residues. Our results based primarily on time-lapse FT-IR spectroscopy and AFM microscopy indicate that selective modifications of C-termini (and, to a lesser degree, of N-termini) decrease capacity of tetra- and pentapeptides to form fibrils...
September 1, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28861525/impacts-of-penicillin-binding-protein-2-inactivation-on-%C3%AE-lactamase-expression-and-muropeptide-profile-in-stenotrophomonas-maltophilia
#20
Yi-Wei Huang, Yu Wang, Yun Lin, Chin Lin, Yi-Tsung Lin, Cheng-Chih Hsu, Tsuey-Ching Yang
Penicillin binding proteins (PBPs) are involved in peptidoglycan synthesis, and their inactivation is linked to β-lactamase expression in ampR-β-lactamase module-harboring Gram-negative bacteria. There are seven annotated PBP genes, namely, mrcA, mrcB, pbpC, mrdA, ftsI, dacB, and dacC, in the Stenotrophomonas maltophilia genome, and these genes encode PBP1a, PBP1b, PBP1c, PBP2, PBP3, PBP4, and PBP6, respectively. In addition, S. maltophilia harbors two β-lactamase genes, L1 and L2, whose expression is induced via β-lactam challenge...
July 2017: MSystems
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