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Helix stabilization

Sethu M Madhavan, John F O'Toole, Martha Konieczkowski, Laura Barisoni, David B Thomas, Santhi Ganesan, Leslie A Bruggeman, Matthias Buck, John R Sedor
APOL1 variants in African populations mediate resistance to trypanosomal infection but increase risk for kidney diseases through unknown mechanisms. APOL1 is expressed in glomerular podocytes and does not vary with underlying kidney disease diagnoses or APOL1 genotypes, suggesting that the kidney disease-associated variants dysregulate its function rather than its localization or abundance. Structural homology searches identified vesicle-associated membrane protein 8 (VAMP8) as an APOL1 protein interactor. VAMP8 colocalizes with APOL1 in the podocyte, and the APOL1:VAMP8 interaction was confirmed biochemically and with surface plasmon resonance...
July 20, 2017: JCI Insight
Changkeun Lee, Jiangtao Guo, Weizhong Zeng, Sunghoon Kim, Ji She, Chunlei Cang, Dejian Ren, Youxing Jiang
TMEM175 is a lysosomal K(+) channel that is important for maintaining the membrane potential and pH stability in lysosomes. It contains two homologous copies of a six-transmembrane-helix (6-TM) domain, which has no sequence homology to the canonical tetrameric K(+) channels and lacks the TVGYG selectivity filter motif found in these channels. The prokaryotic TMEM175 channel, which is present in a subset of bacteria and archaea, contains only a single 6-TM domain and functions as a tetramer. Here, we present the crystal structure of a prokaryotic TMEM175 channel from Chamaesiphon minutus, CmTMEM175, the architecture of which represents a completely different fold from that of canonical K(+) channels...
July 19, 2017: Nature
Jeevan B Gc, Bernard S Gerstman, Prem P Chapagain
The Ebola virus matrix protein VP40 is a major structural protein that provides the scaffolding for new Ebola virus particles. For this, VP40 is first trafficked to the lower leaflet of the plasma membrane (PM) in its dimeric form. Once associated with the PM, the VP40 dimers undergo structural rearrangements and oligomerize into hexamers and filaments that make up the virus matrix. Therefore, association of the VP40 dimers and their stabilization at the PM is a crucial step in the Ebola life-cycle. To understand the molecular details of the VP40 dimer-PM interactions, we investigated the dimer association with the inner leaflet of the PM using detailed all-atom molecular dynamics (MD) simulations...
July 12, 2017: Biochimica et Biophysica Acta
Hajime Yamazaki, Elia Beniash, Yasuo Yamakoshi, James P Simmer, Henry C Margolis
Previously, we have shown that serine-16 phosphorylation in native full-length porcine amelogenin (P173) and the Leucine-Rich Amelogenin Peptide (LRAP(+P)), an alternative amelogenin splice product, affects protein assembly and mineralization in vitro. Notably, P173 and LRAP(+P) stabilize amorphous calcium phosphate (ACP) and inhibit hydroxyapatite (HA) formation, while non-phosphorylated counterparts (rP172, LRAP(-P)) guide the growth of ordered bundles of HA crystals. Based on these findings, we hypothesize that the phosphorylation of full-length amelogenin and LRAP induces conformational changes that critically affect its capacity to interact with forming calcium phosphate mineral phases...
2017: Frontiers in Physiology
Stephanie Bleicken, Annika Hantusch, Kushal Kumar Das, Tancred Frickey, Ana J Garcia-Saez
The Bcl-2 proteins form a complex interaction network that controls mitochondrial permeabilization and apoptosis. The relative importance of different Bcl-2 complexes and their spatio-temporal regulation is debated. Using fluorescence cross-correlation spectroscopy to quantify the interactions within a minimal Bcl-2 network, comprised by cBid, Bax, and Bcl-xL, we show that membrane insertion drastically alters the pattern of Bcl-2 complexes, and that the C-terminal helix of Bcl-xL determines its binding preferences...
July 13, 2017: Nature Communications
Zhaolong Xu, Xiaoqing Liu, Xiaolan He, Ling Xu, Yihong Huang, Hongbo Shao, Dayong Zhang, Boping Tang, Hongxiang Ma
Cadmium (Cd) is one of the most dangerous heavy metal pollutants in the environment and is toxic to animal and plant cells. On the other hand, iron (Fe) is an essential element for plant growth and development. The chlorosis of plant leaves under cadmium stress is similar to the typical symptom of iron deficiency. Recently, several Arabidopsis basic/helix-loop-helix (bHLH) transcription factors have been identified that are involved in the interactions between Cd and Fe. In the present study, over-expression the ORG3-like gene GmORG3, a bHLH transcription factor OBP3-responsive gene (ORG), enhanced Cd tolerance and stabilized Fe homeostasis...
2017: Frontiers in Plant Science
Wei Liang Tan, Ka H Wong, Jian Lei, Naoki Sakai, Hong Wei Tan, Rolf Hilgenfeld, James P Tam
Cysteine-rich peptides (CRPs) of 2-6 kDa are generally thermally and proteolytically stable because of their multiple cross-bracing disulfide bonds. Here, we report the discovery and characterization of two novel cystine-stapled CRPs, designated lybatide 1 and 2 (lyba1 and lyba2), from the cortex of Lycium barbarum root. Lybatides, 32 to 33 amino acids in length, are hyperstable and display a novel disulfide connectivity with a cysteine motif of C-C-C-C-CC-CC which contains two pairs of adjacent cysteines (-CC-CC)...
July 12, 2017: Scientific Reports
Catarina A Carvalheda, Andrei V Pisliakov
Cytochrome cbb3 (or C-type) oxidases are a highly divergent group and the least studied members of the heme-copper oxidases (HCOs) superfamily. HCOs couple the reduction of oxygen at the end of the respiratory chain to the active proton translocation across the membrane, contributing to establishment of an electrochemical gradient essential for ATP synthesis. Cbb3 oxidases exhibit unique structural and functional features and have an essential role in the metabolism of many clinically relevant human pathogens...
July 7, 2017: Biochemical and Biophysical Research Communications
Garry W Buchko, Nathanial Echols, E Megan Flynn, Ho Ng, Sam Stephenson, Heung-Bok Kim, Peter J Myler, Thomas C Terwilliger, Tom Alber, Chang-Yub Kim
The 261-residue Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the responsible component for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2. It also has 36% amino acid sequence identity to Streptomyces coelicolor AfsK-binding protein A (KbpA), a component in the complex secondary metabolite pathways in the Streptomycetes genus from which many commercial antibiotics are derived...
July 10, 2017: Biochemistry
Yi-Cheng Chen
According to amyloid cascade hypothesis, the deposit of amyloid-β (Aβ) peptide is the main cause of Alzheimer's disease (AD). The aggregation ability and toxicity of Aβ peptides are highly associated with the sequence and conformation. A discordant helix is a helical segment with a tendency to form a β-strand conformation and has been found in many amyloid-like proteins or peptides. In this review, we summarize the current knowledge of the properties of a Aβ discordant helix and its impact on the Aβ structure, aggregation ability and cytotoxicity...
July 7, 2017: European Biophysics Journal: EBJ
Katherine W Pulsipher, Jose A Villegas, Benjamin W Roose, Tacey L Hicks, Jennifer Yoon, Jeffery G Saven, Ivan J Dmochowski
Protein cage self-assembly enables encapsulation and sequestration of small molecules, macromolecules, and nanomaterials for many applications in bionanotechnology. Notably, wild-type thermophilic ferritin from Archaeoglobus fulgidus (AfFtn) exists as a stable dimer of four-helix bundle proteins at a low ionic strength, and the protein forms a hollow assembly of 24 protomers at a high ionic strength (∼800 mM NaCl). This assembly process can also be initiated by highly charged gold nanoparticles (AuNPs) in solution, leading to encapsulation...
July 6, 2017: Biochemistry
Frank Seela, Xiurong Guo
α-D-Nucleosides are rare in nature but can develop fascinating properties when incorporated in DNA. This work reports on the first silver mediated base pair constructed from two anomeric nucleosides: α-dC and β-dC. The hybrid base pair was integrated in DNA and DNA/RNA double helix. A 12-mer duplex with α-dC and β-dC pair exhibits a greatly higher thermal stability (Tm = 43°C) than that incorporating the β-dC-Ag+-β-dC homo pair (Tm = 34°C). Furthermore: α-dC shows excellent mismatch discrimination for DNA single nucleotide polymorphism (SNP)...
July 6, 2017: Chemistry: a European Journal
Mason S Smith, Wendy M Billings, Frank G Whitby, McKenzie B Miller, Joshua L Price
The interaction of a positively charged amino acid residue with a negatively charged residue (i.e. a salt bridge) can contribute substantially to protein conformational stability, especially when two ionic groups are in close proximity. At longer distances, this stabilizing effect tends to drop off precipitously. However, several lines of evidence suggest that salt-bridge interaction could persist at longer distances if an aromatic amino acid residue were positioned between the anion and cation. Here we explore this possibility in the context of a peptide in which a Lys residue occupies the i + 8 position relative to an i-position Glu on the solvent-exposed surface of a helix-bundle homotrimer...
July 19, 2017: Organic & Biomolecular Chemistry
Lucas Schwob, Mathieu Lalande, Jimmy Rangama, Dmitrii Egorov, Ronnie Hoekstra, Rahul Pandey, Samuel Eden, Thomas Schlathölter, Violaine Vizcaino, Jean-Christophe Poully
Cartilage and tendons owe their special mechanical properties to the fibrous collagen structure. These strong fibrils are aggregates of a sub-unit consisting of three collagen proteins wound around each other in a triple helix. Even though collagen is the most abundant protein in the human body, the response of this protein complex to ionizing radiation has never been studied. In this work, we probe the direct effects of VUV and soft X-ray photons on isolated models of the collagen triple helix, by coupling a tandem mass spectrometer to a synchrotron beamline...
July 5, 2017: Physical Chemistry Chemical Physics: PCCP
Kaori Furukawa, Makoto Oba, Kotomi Toyama, George Ouma Opiyo, Yosuke Demizu, Masaaki Kurihara, Mitsunobu Doi, Masakazu Tanaka
We developed a novel methodology using cyclic α,α-disubstituted α-amino acids (dAAs) with an acetal-side chain to control peptide secondary structures. The introduction of cyclic dAAs into peptides contributed to the stabilization of peptide secondary structures as a helix, while an acidic treatment of peptides resulted in a marked conformational change.
July 5, 2017: Organic & Biomolecular Chemistry
Yolanda Pérez, María José Gómara, Eloísa Yuste, Patricia Gómez-Gutierrez, Juan Jesús Pérez, Isabel Haro
Previous studies support the hypothesis that the envelope GB virus C E1 protein interferes HIV-1 entry and a peptide, derived from the region (139-156) of this protein, has defined as a novel HIV-1 entry inhibitor. In this work, we firstly focus on the characterization of the peptide structural features which are determinant for its anti-HIV-1 activity and secondly, on the study of its interaction of with the proposed viral target (the HIV-1 fusion peptide). We report the peptide structure determined by NMR spectroscopy in DPC micelles solved using restrained molecular dynamics calculations...
July 5, 2017: Chemistry: a European Journal
Zahra Liyaghatdar, Rahman Emamzadeh, Sayed Mohammad Mahdi Rasa, Mahboobeh Nazari
Renilla luciferase (Rluc) from Renilla reniformis is an appropriate protein reporter for the detection of specific molecular targets due to its bioluminescent feature, although its relatively low stability limits the application. To investigate the effects of trehalose and sucrose as chemical chaperones on the kinetic stability of Rluc, we assayed the activity of the enzyme in the presence of these additives at high temperatures and to comprehend the mechanism of stability, molecular dynamic (MD) simulation was carried out...
June 30, 2017: International Journal of Biological Macromolecules
Wen Xu, Haiyan Jia, Longmei Zhang, Haiyan Wang, Hui Tang, Liping Zhang
In this paper, three mutants from wild Saccharomyces cerevisiae HBU2.558, called U2.558, UN2.558, and UNA2.558, were screened by UV, sodium nitrite, Atmospheric and room temperature plasma, respectively. Glutathione production of the three mutants increased by 41.86, 72.09 and 56.76%, respectively. We detected the activity of glutathione synthetases and found that its activity was improved. Amino acid sequences of three mutant colonies were compared with HBU2.558. Four mutants: Leu51→Pro51 (L51P), Glu62→Val62 (E62V), Ala332→Glu332 (A332E) and Ser653→Gly653 (S653G) were found in the analysis of γ-glutamylcysteine ligase...
August 2017: Protein Journal
Cuifen Gan, Bingfeng Wang, Junying Huang, Aori Qileng, Zuyu He, Hongtao Lei, Weipeng Liu, Yingju Liu
A novel multiple amplified enzyme-free immunosensor was developed for competitive immunoassay of microcystin-LR (MC-LR). Classical electrochemical immunosensors usually employ enzymes as biocatalysts to afford amplified signals, but the proteolytic degradation and poor stability are still crucial problem. Herein, monodisperse core-shell mesoporous silica (SiO2@MSN)-functionalized DNAzyme concatamers were synthesized to load hemin and methylene blue (MB) as the mimic enzyme. Firstly, the surface of SiO2@MSN was conjugated with secondary antibody as the recognition of MC-LR antibody and with a DNA strand as the initiator...
June 23, 2017: Biosensors & Bioelectronics
Meritxell Granell, Mikiyoshi Namura, Sara Alvira, Shuji Kanamaru, Mark J van Raaij
Long tail fibers of bacteriophage T4 are formed by proteins gp34, gp35, gp36, and gp37, with gp34 located at the phage-proximal end and gp37 at the phage-distal, receptor-binding end. We have solved the structure of the carboxy-terminal region of gp34, consisting of amino acids 894-1289, by single-wavelength anomalous diffraction and extended the structure to amino acids 744-1289 using data collected from crystals containing longer gp34-fragments. The structure reveals three repeats of a mixed α-β fibrous domain in residues 744 to 877...
June 30, 2017: Viruses
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