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Helix stabilization

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https://www.readbyqxmd.com/read/28230348/nmr-structures-of-gcn4p-are-largely-conserved-when-ion-pairs-are-disrupted-at-acidic-ph-but-show-a-relaxation-of-the-coiled-coil-superhelix
#1
Anne R Kaplan, Megan R Brady, Mark W Maciejewski, Richard A Kammerer, Andrei T Alexandrescu
To understand the roles ion pairs play in stabilizing coiled coils we determined NMR structures of GCN4p at three pH values. At pH 6.6 all acidic residues are fully charged, at pH 4.4 they are half-charged, and at pH 1.5 they are protonated and uncharged. The α-helix monomer and coiled coil structures of GCN4p are largely conserved, except for a loosening of the coiled coil quaternary structure with decreasing pH. Differences going from neutral to acidic pH include (i) an unwinding of the coiled coil superhelix due to the loss of inter-chain ion pair contacts, (ii) a small increase in the separation of the monomers in the dimer, (iii) a loosening of knobs-into-holes packing motifs, and (iv) an increased separation between oppositely charged residues that participate in ion pairs at neutral pH...
February 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28228927/computational-approaches-for-revealing-the-structure-of-membrane-transporters-case-study-on-bilitranslocase
#2
REVIEW
Katja Venko, A Roy Choudhury, Marjana Novič
The structural and functional details of transmembrane proteins are vastly underexplored, mostly due to experimental difficulties regarding their solubility and stability. Currently, the majority of transmembrane protein structures are still unknown and this present a huge experimental and computational challenge. Nowadays, thanks to X-ray crystallography or NMR spectroscopy over 3000 structures of membrane proteins have been solved, among them only a few hundred unique ones. Due to the vast biological and pharmaceutical interest in the elucidation of the structure and the functional mechanisms of transmembrane proteins, several computational methods have been developed to overcome the experimental gap...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28223511/a-signal-sequence-suppressor-mutant-that-stabilizes-an-assembled-state-of-the-twin-arginine-translocase
#3
Qi Huang, Felicity Alcock, Holger Kneuper, Justin C Deme, Sarah E Rollauer, Susan M Lea, Ben C Berks, Tracy Palmer
The twin-arginine protein translocation (Tat) system mediates transport of folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of chloroplasts. The Tat system of Escherichia coli is made up of TatA, TatB, and TatC components. TatBC comprise the substrate receptor complex, and active Tat translocases are formed by the substrate-induced association of TatA oligomers with this receptor. Proteins are targeted to TatBC by signal peptides containing an essential pair of arginine residues...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28221775/electrostatic-interactions-as-mediators-in-the-allosteric-activation-of-pka-ri%C3%AE
#4
Emilia Pecora de Barros, Robert D Malmstrom, Kimya Nourbakhsh, Jason Cruz Del Rio, Alexandr P Kornev, Susan S Taylor, Rommie E Amaro
Close-range electrostatic interactions that form salt bridges are key components of protein stability. Here we investigate the role of these charged interactions in modulating the allosteric activation of Protein Kinase A (PKA) via computational and experimental mutational studies on a conserved basic patch located in the regulatory subunit's B/C helix. Molecular dynamics simulations evidenced the presence of an extended network of fluctuating salt bridges spanning the helix and connecting the two cAMP binding domains in its extremities...
February 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28218648/expression-purification-and-monitoring-of-conformational-changes-of-hcb2-tmh67h8-in-different-membrane-mimetic-lipid-mixtures-using-circular-dichroism-and-nmr-techniques
#5
Elvis K Tiburu, Jianqin Zhuang, Heidimarie N A Fleischer, Patrick K Arthur, Gordon A Awandare
This work was intended to develop self-assembly lipids for incorporating G-protein coupled receptors (GPCRs) in order to improve the success rate for nuclear magnetic resonance spectroscopy (NMR) structural elucidation. We hereby report the expression and purification of uniformly (15)N-labeled human cannabinoid receptor-2 domain in insect cell media. The domain was refolded by screening several membrane mimetic environments. Different q ratios of isotropic bicelles were screened for solubilizing transmembrane helix 6, 7 and 8 (TMH67H8)...
February 17, 2017: Membranes
https://www.readbyqxmd.com/read/28216225/molecular-characterization-of-myoglobin-from-sciurus-vulgaris-meridionalis-primary-structure-kinetics-and-spectroscopic-studies
#6
Antonella M A Di Giuseppe, Luigi Russo, Rosita Russo, Sara Ragucci, J Valentina Caso, Carla Isernia, Angela Chambery, Antimo Di Maro
Myoglobins (Mbs) are heme-proteins involved in dioxygen storage necessary for metabolic respiration. Mbs are intensely investigated as archetype to investigate structure/function relationship in globular proteins. In this work, the myoglobin from S. vulgaris meridionalis has been for the first time isolated and purified with a high yield and homogeneity. The primary structure characterization has been performed by applying a strategy based on high resolution tandem mass spectrometry. Proximal (position 93, α-helix F8) and distal histidinyl residues (position 64, α-helix E7) as well as most of the amino acid residues (i...
February 16, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28215712/palmitoylation-of-cysteine-415-of-cb1-receptor-affects-ligand-stimulated-internalization-and-selective-interaction-with-membrane-cholesterol-and-caveolin-1
#7
Sergio Oddi, Tomasz Maciej Stepniewski, Antonio Totaro, Jana Selent, Lucia Scipioni, Beatrice Dufrusine, Filomena Fezza, Enrico Dainese, Mauro Maccarrone
We previously demonstrated that CB1 receptor is palmitoylated at cysteine 415, and that such a post-translational modification affects its biological activity. To assess the molecular mechanisms responsible for modulation of CB1 receptor function by S-palmitoylation, in this study biochemical and morphological approaches were paralleled with computational analyses. Molecular dynamics simulations suggested that this acyl chain stabilizes helix 8 as well as the interaction of CB1 receptor with membrane cholesterol...
February 12, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28199083/shape-memory-hydrogels-evolution-of-structural-principles-to-enable-shape-switching-of-hydrophilic-polymer-networks
#8
Candy Löwenberg, Maria Balk, Christian Wischke, Marc Behl, Andreas Lendlein
The ability of hydrophilic chain segments in polymer networks to strongly interact with water allows the volumetric expansion of the material and formation of a hydrogel. When polymer chain segments undergo reversible hydration depending on environmental conditions, smart hydrogels can be realized, which are able to shrink/swell and thus alter their volume on demand. In contrast, implementing the capacity of hydrogels to switch their shape rather than volume demands more sophisticated chemical approaches and structural concepts...
February 15, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28199023/analysis-of-%C3%AE-helix-unfolding-in-the-pine-nut-peptide-lys-cys-his-lys-pro-induced-by-pulsed-electric-field
#9
Jie Xing, Sitian Zhang, Mingdi Zhang, Songyi Lin
BACKGROUND: A variety of analytical techniques were applied to explore the effects of pulsed electric field (PEF) on the α-helix structural changes in the novel antioxidant peptide Lys-Cys-His-Lys-Pro (KCHKP, 611.76 Da). RESULTS: The relative α-helix content of the KCHKP peptide was significantly altered from 100% to 89.91 ± 0.97% when the electric pulse frequency was 1800 Hz and the field intensity was 10 kV cm(-1) . Moreover, the 1,1-diphenyl-2-pycryl-hydrazyl (DPPH) and 2,2-azinobis diammonium salt (ABTS) radical-scavenging activities of PEF-treated KCHKP were increased from 56...
February 15, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28191894/open-ringed-structure-of-the-cdt1-mcm2-7-complex-as-a-precursor-of-the-mcm-double-hexamer
#10
Yuanliang Zhai, Erchao Cheng, Hao Wu, Ningning Li, Philip Yuk Kwong Yung, Ning Gao, Bik-Kwoon Tye
The minichromosome maintenance complex (MCM) hexameric complex (Mcm2-7) forms the core of the eukaryotic replicative helicase. During G1 phase, two Cdt1-Mcm2-7 heptamers are loaded onto each replication origin by the origin-recognition complex (ORC) and Cdc6 to form an inactive MCM double hexamer (DH), but the detailed loading mechanism remains unclear. Here we examine the structures of the yeast MCM hexamer and Cdt1-MCM heptamer from Saccharomyces cerevisiae. Both complexes form left-handed coil structures with a 10-15-Å gap between Mcm5 and Mcm2, and a central channel that is occluded by the C-terminal domain winged-helix motif of Mcm5...
February 13, 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/28190655/development-of-helix-stabilized-cell-penetrating-peptides-containing-cationic-%C3%AE-%C3%AE-disubstituted-amino-acids-as-helical-promoters
#11
Hiroko Yamashita, Takashi Misawa, Makoto Oba, Masakazu Tanaka, Mikihiko Naito, Masaaki Kurihara, Yosuke Demizu
Cell-penetrating peptides (CPP) have attracted many scientists' attention as intracellular delivery tools due to their high cargo molecule transportation efficiency and low cytotoxicity. Therefore, in many research fields CPP, such as HIV-Tat and oligoarginine (Rn), are used to deliver hydrophilic drugs and biomolecules, including proteins, DNA, and RNA. We designed four types of CPP that contained cationic α,α-disubstituted amino acids (Api(C2Gu) and Api(C4Gu)) as helical promoters; i.e., 1-4 [FAM-β-Ala-(l-Arg-l-Arg-Xaa)3-(Gly)3-NH2 (1: Xaa=Api(C2Gu), 2: Xaa=Api(C4Gu)), 3: FAM-β-Ala-(l-Arg)8-Api(C2Gu)-(Gly)3-NH2, and 4: FAM-β-Ala-(l-Arg)5-Api(C2Gu)-(l-Arg)2-Api(C2Gu)-(Gly)3-NH2], and investigated their preferred secondary structures and cell membrane-penetrating ability...
February 1, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28187530/structural-and-dynamic-characterization-of-a-freestanding-acyl-carrier-protein-involved-in-the-biosynthesis-of-cyclic-lipopeptide-antibiotics
#12
Subrata Paul, Hiroaki Ishida, Leonard T Nguyen, Zhihong Liu, Hans J Vogel
Friulimicin is a cyclic lipodecapeptide antibiotic that is produced by Actinoplanes friuliensis. Like the related lipopeptide drug daptomycin, the peptide skeleton of friulimicin is synthesized by a large multienzyme Nonribosomal Peptide Synthetase (NRPS) system. The LipD protein plays a major role in the acylation reaction of friulimicin. The attachment of the fatty acid group promotes its antibiotic activity. Phylogenetic analysis reveals that LipD is most closely related to other freestanding Acyl Carrier Proteins (ACPs), for which the genes are located near to NRPS gene clusters...
February 10, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28186717/gating-motions-and-stationary-gating-properties-of-ionotropic-glutamate-receptors-computation-meets-electrophysiology
#13
Huan-Xiang Zhou
Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels essential to all aspects of brain function, including higher order processes such as learning and memory. For decades, electrophysiology was the primary means for characterizing the function of iGluRs and gaining mechanistic insight. Since the turn of the century, structures of isolated water-soluble domains and transmembrane-domain-containing constructs have provided the basis for formulating mechanistic hypotheses. Because these structures only represent sparse, often incomplete snapshots during iGluR activation, significant gaps in knowledge remain regarding structures, energetics, and dynamics of key substates along the functional processes...
February 10, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28185933/binding-of-%C3%AE-carrageenan-a-food-additive-to-almond-cystatin-an-insight-involving-spectroscopic-and-thermodynamic-approach
#14
Azad Alam Siddiqui, Anna Feroz, Peerzada Shariq Shaheen Khaki, Bilqees Bano
Carrageenan is a high molecular weight linear sulphated polysaccharide, primarily used in food industry as gelling, thickening, and stabilizing agent. Almond milk prepared from almonds is low in fat, but high in antioxidants, energy, proteins, lipids and fibre. Purified almond cystatin was incubated with increasing concentrations of carrageenan at 25°C for different time interval and significant loss in inhibitory activity was observed. Interaction between carrageenan and cystatin resulted in complex formation as depicted by the decrease in fluorescence intensity with increase in the concentration of carrageenan...
February 7, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28185014/recent-advances-on-polyproline-ii
#15
REVIEW
Tarun Jairaj Narwani, Hubert Santuz, Nicolas Shinada, Akhila Melarkode Vattekatte, Yassine Ghouzam, Narayanasamy Srinivasan, Jean-Christophe Gelly, Alexandre G de Brevern
About half of the globular proteins are composed of regular secondary structures, α-helices, and β-sheets, while the rest are constituted of irregular secondary structures, such as turns or coil conformations. Other regular secondary structures are often ignored, despite their importance in biological processes. Among such structures, the polyproline II helix (PPII) has interesting behaviours. PPIIs are not usually associated with conventional stabilizing interactions, and recent studies have observed that PPIIs are more frequent than anticipated...
February 9, 2017: Amino Acids
https://www.readbyqxmd.com/read/28181556/structural-variability-of-e-coli-thioredoxin-captured-in-the-crystal-structures-of-single-point-mutants
#16
Martín E Noguera, Diego S Vazquez, Gerardo Ferrer-Sueta, William A Agudelo, Eduardo Howard, Rodolfo M Rasia, Bruno Manta, Alexandra Cousido-Siah, André Mitschler, Alberto Podjarny, Javier Santos
Thioredoxin is a ubiquitous small protein that catalyzes redox reactions of protein thiols. Additionally, thioredoxin from E. coli (EcTRX) is a widely-used model for structure-function studies. In a previous paper, we characterized several single-point mutants of the C-terminal helix (CTH) that alter global stability of EcTRX. However, spectroscopic signatures and enzymatic activity for some of these mutants were found essentially unaffected. A comprehensive structural characterization at the atomic level of these near-invariant mutants can provide detailed information about structural variability of EcTRX...
February 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28177253/submolecular-structure-and-orientation-of-oligonucleotide-duplexes-tethered-to-gold-electrodes-probed-by-infrared-reflection-absorption-spectroscopy-effect-of-the-electrode-potentials
#17
László Kékedy-Nagy, Elena E Ferapontova, Izabella Brand
Unique electronic and ligand recognition properties of the DNA double helix provide basis for DNA applications in biomolecular electronic and biosensor devices. However, the relation between the structure of DNA at electrified interfaces and its electronic properties is still not well understood. Here, potential-driven changes in the submolecular structure of DNA double helices composed of either adenine-thymine (dAdT)25 or cytosine-guanine (dGdC)20 base pairs tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) performed under the electrochemical control...
February 8, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28177216/bacterioferritin-structure-dynamics-and-protein-protein-interactions-at-play-in-iron-storage-and-mobilization
#18
Mario Rivera
Despite its essentiality to life, iron presents significant challenges to cells: the exceedingly low solubility of Fe(3+) limits its bioavailability, and the reactivity of Fe(2+) toward H2O2 is a source of the toxic hydroxyl radical (HO(•)). Consequently, cellular levels of free iron are highly regulated to ensure sufficiency while preventing iron-induced toxicity. Relatively little is known about the fate of iron in the bacterial cytosol or how cells balance the need for relatively high cytosolic iron concentrations with the potential toxicity of the nutrient...
February 8, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28167950/small-one-helix-proteins-are-essential-for-photosynthesis-in-arabidopsis
#19
Jochen Beck, Jens N Lohscheider, Susanne Albert, Ulrica Andersson, Kurt W Mendgen, Marc C Rojas-Stütz, Iwona Adamska, Dietmar Funck
The extended superfamily of chlorophyll a/b binding proteins comprises the Light-Harvesting Complex Proteins (LHCs), the Early Light-Induced Proteins (ELIPs) and the Photosystem II Subunit S (PSBS). The proteins of the ELIP family were proposed to function in photoprotection or assembly of thylakoid pigment-protein complexes and are further divided into subgroups with one to three transmembrane helices. Two small One-Helix Proteins (OHPs) are expressed constitutively in green plant tissues and their levels increase in response to light stress...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28167524/gas-sensing-and-signaling-in-the-pas-heme-domain-of-the-pseudomonas-aeruginosa-aer2-receptor
#20
Darysbel Garcia, Emilie Orillard, Mark S Johnson, Kylie J Watts
: The Aer2 chemoreceptor from Pseudomonas aeruginosa contains a PAS sensing domain that coordinates b-type heme and signals in response to the binding of O2, CO or NO. PAS-heme structures suggest that Aer2 uniquely coordinates heme via a His residue on a 310 helix (H234 on Eη), stabilizes O2 binding via a Trp residue (W283), and signals via both W283 and an adjacent Leu residue (L264). Ligand binding may displace L264 and reorient W283 for hydrogen-bonding to the ligand. Here we clarified the mechanisms by which Aer2-PAS binds heme, regulates ligand-binding, and initiates conformational signaling...
February 6, 2017: Journal of Bacteriology
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