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https://www.readbyqxmd.com/read/28341845/the-trimer-interface-in-the-quaternary-structure-of-the-bifunctional-prokaryotic-fad-synthetase-from-corynebacterium-ammoniagenes
#1
Ana Serrano, María Sebastián, Sonia Arilla-Luna, Silvia Baquedano, Beatriz Herguedas, Adrián Velázquez-Campoy, Marta Martínez-Júlvez, Milagros Medina
Bifunctional FAD synthetases (FADSs) fold in two independent modules; The C-terminal riboflavin kinase (RFK) catalyzes the RFK activity, while the N-terminal FMN-adenylyltransferase (FMNAT) exhibits the FMNAT activity. The search for macromolecular interfaces in the Corynebacterium ammoniagenes FADS (CaFADS) crystal structure predicts a dimer of trimers organization. Within each trimer, a head-to-tail arrangement causes the RFK and FMNAT catalytic sites of the two neighboring protomers to approach, in agreement with active site residues of one module influencing the activity at the other...
March 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28340512/activation-mechanisms-of-%C3%AE-v%C3%AE-3-integrin-by-binding-to-fibronectin-a-computational-study
#2
Lingyun Wang, Di Pan, Qi Yan, Yuhua Song
Integrin αVβ3 plays an important role in regulating cellular activities and in human diseases. Although the structure of αVβ3 has been studied by crystallography and electron microscopy, the detailed activation mechanism of integrin αVβ3 induced by fibronectin (Fn) remains unclear. In this study, we investigated the conformational and dynamical motion changes of Mn(2+) -bound integrin αVβ3 by binding to Fn with molecular dynamics simulations. Results showed that Fn binding to integrin αVβ3 caused the changes of the conformational flexibility of αVβ3 domains, the essential mode of motion for the domains of αV subunit and β3 subunit and the degrees of correlated motion of residues between the domains of αV subunit and β3 subunit of integrin αVβ3...
March 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28338958/molecular-cloning-and-characterization-of-antimicrobial-peptides-from-skin-of-hylarana-guentheri
#3
Zhu Dong, Wenjie Luo, Hengren Zhong, Manchuriga Wang, Yanting Song, Shiming Deng, Yingxia Zhang
The cDNAs encoding antimicrobial peptides (AMPs) in the skin of Hylarana guentheri were identified, namely temporin (five peptides, termed temporin-GHa-GHd and temporin-GUa), brevinin-1 (one peptide, brevinin-1GUb), and brevinin-2 (eight peptides, brevinin-2GHd-2GHj, and brevinin-2GHb). Eleven of the 14 peptides have novel primary structures. Synthesized temporin GHa-GHd have broad-spectrum antimicrobial activities against Gram-positive bacteria (Staphylococcus aureus and Bacillus subtilis), Gram-negative bacteria (Escherichia coli, Vibrio alginolyticus, and Pseudomonas aeruginosa), as well as fungus (Candida albicans)...
March 18, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28334819/comparative-analyses-of-the-thermodynamic-rna-binding-signatures-of-different-types-of-rna-recognition-motifs
#4
Brighton Samatanga, Antoine Cléry, Pierre Barraud, Frédéric H-T Allain, Ilian Jelesarov
RNA recognition motifs (RRMs) are structurally versatile domains important in regulation of alternative splicing. Structural mechanisms of sequence-specific recognition of single-stranded RNAs (ssRNAs) by RRMs are well understood. The thermodynamic strategies are however unclear. Therefore, we utilized microcalorimetry and semi-empirical analyses to comparatively analyze the cognate ssRNA binding thermodynamics of four different RRM domains, each with a different RNA binding mode. The different binding modes are: canonical binding to the β-sheet surface; canonical binding with involvement of N- and C-termini; binding to conserved loops; and binding to an α-helix...
February 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28329249/acetylation-regulates-protein-stability-and-dna-binding-ability-of-hild-to-modulate-salmonella-typhimurium-virulence
#5
Yu Sang, Jie Ren, Ran Qin, Shuting Liu, Zhongli Cui, Sen Cheng, Xiaoyun Liu, Jie Lu, Jing Tao, Yu-Feng Yao
HilD, a dominant regulator of Salmonella pathogenicity island 1 (SPI-1), can be acetylated by acetyltransferase Pat in Salmonella Typhimurium, and the acetylation is beneficial to its stability. However, the underlying mechanism of HilD stability regulated by acetylation is not clear. We show here that lysine 297 (K297) located in the helix-turn-helix motif, can be acetylated by Pat. Acetylation of K297 increases HilD stability, but reduces its DNA-binding affinity. In turn, the deacetylated K297 enhances the DNA-binding ability, but decreases HilD stability...
February 24, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28328107/chiral-exploration-of-6-12-diphenyldibenzo-b-f-1-5-diazocine-with-stable-conformation
#6
Zheng-Yi Li, Yong Pan, Lin-Lin Jin, Yue Yin, Bao-Zhu Yang, Xiao-Qiang Sun
A first optical resolution of 6,12-diphenyldibenzo[b,f][1,5]diazocine with stable boat conformation was achieved by chiral supercritical fluid chromatography (SFC). The absolute configurations of enantiomers were first assigned and determined by X-ray crystal structure based on CIP-rules. The high optical rotation and circular dichroism spectrum were well explained by electronic helix theory. Owing to the high stabilization of boat conformation, the chiral configuration could be maintained at very high temperature, more than 200 °C, which was proved by Density Functional Theory calculations...
March 22, 2017: Chirality
https://www.readbyqxmd.com/read/28327546/missense-mutations-near-the-n-glycosylation-site-of-the-a2-domain-lead-to-various-intracellular-trafficking-defects-in-coagulation-factor-viii
#7
Wei Wei, Chunlei Zheng, Min Zhu, Xiaofan Zhu, Renchi Yang, Saurav Misra, Bin Zhang
Missense mutation is the most common mutation type in hemophilia. However, the majority of missense mutations remain uncharacterized. Here we characterize how hemophilia mutations near the unused N-glycosylation site of the A2 domain (N582) of FVIII affect protein conformation and intracellular trafficking. N582 is located in the middle of a short 310-helical turn (D580-S584), in which most amino acids have multiple hemophilia mutations. All 14 missense mutations found in this 310-helix reduced secretion levels of the A2 domain and full-length FVIII...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327374/discovery-and-molecular-interaction-studies-of-a-highly-stable-tarantula-peptide-modulator-of-acid-sensing-ion-channel-1
#8
REVIEW
Sing Yan Er, Ben Cristofori-Armstrong, Pierre Escoubas, Lachlan D Rash
Acute pharmacological inhibition of acid-sensing ion channel 1a (ASIC1a) is efficacious in rodent models in alleviating symptoms of neurological diseases such as stroke and multiple sclerosis. Thus, ASIC1a is a promising therapeutic target and selective ligands that modulate it are invaluable research tools and potential therapeutic leads. Spider venoms have provided an abundance of voltage-gated ion channel modulators, however, only one ASIC modulator (PcTx1) has so far been isolated from this source. Here we report the discovery, characterization, and chemical stability of a second spider venom peptide that potently modulates ASIC1a and ASIC1b, and investigate the molecular basis for its subtype selectivity...
March 18, 2017: Neuropharmacology
https://www.readbyqxmd.com/read/28321930/uncovering-allostery-and-regulation-in-samhd1-through-molecular-dynamics-simulations
#9
Kajwal Kumar Patra, Akash Bhattacharya, Swati Bhattacharya
The human sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a retroviral restriction factor in myeloid cells and non-cycling CD4+ T cells, a feature imputed to its phosphohydrolase activity - the enzyme depletes the cellular dNTP levels inhibiting reverse transcription. The functionally active form of SAMHD1 is an allosterically triggered tetramer which utilizes GTP-Mg(+2) -dNTP cross bridges to link and stabilize adjacent monomers. However, very little is known about how it assembles into a tetramer and how long the tetramer stays intact...
March 21, 2017: Proteins
https://www.readbyqxmd.com/read/28318221/crystal-structure-of-a-homogeneous-igg-fc-glycoform-with-the-n-glycan-designed-to-maximize-the-antibody-dependent-cellular-cytotoxicity
#10
Chia-Lin Chen, Jen-Chi Hsu, Chin-Wei Lin, Chia-Hung Wang, Ming-Hung Tsai, Chung-Yi Wu, Chi-Huey Wong, Che Ma
N-glycosylation on IgG modulates Fc conformation and effector functions. An IgG-Fc contains a human sialo-complex type (hSCT) glycan of biantennary structure with two α2,6-sialylations and without core-fucosylation is an optimized glycoform developed to enhance the antibody dependent cellular cytotoxicity (ADCC). hSCT modification not only enhances the binding affinity to Fc receptors in the presence of antigen, but also in some cases provides gain-of-function effector activity. We used enzymatic glyco-engineering to prepare an IgG-Fc with homogeneous hSCT attached to each CH2 domain, and solved its crystal structure...
March 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28302046/the-role-of-the-complex-usp1-wdr48-in-differentiation-and-proliferation-processes-in-cancer-stem-cells
#11
Jussara Maria Gonçalves, Mabel Mariela Rodriguez Cordeiro, Elena Riet Correa Rivero
Recently some studies identified the Basic-Helix-Loop-Helix (bHLH) transcription factor as a significant regulator for the evolution of neoplasms. The binding between bHLH proteins and DNA is restricted by heterodimerization with Inhibitors of DNA binding (ID). IDs prevent cellular differentiation, promote growth and sustain tumor development. The wide presence of stem cells in cancers suggests that genes ID are essential to cancer stem cells (CSC) progress. The enzyme Ubiquitin-specific protease 1 (USP1) is reported by deubiquitination and stabilization of IDs...
March 15, 2017: Current Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28300777/functional-contributions-of-positive-charges-in-the-pore-lining-helix-3-of-the-bordetella-pertussis-cyaa-hemolysin-to-hemolytic-activity-and-ion-channel-opening
#12
Chattip Kurehong, Chalermpol Kanchanawarin, Busaba Powthongchin, Panchika Prangkio, Gerd Katzenmeier, Chanan Angsuthanasombat
The Bordetella pertussis CyaA-hemolysin (CyaA-Hly) domain was previously demonstrated to be an important determinant for hemolysis against target erythrocytes and ion-channel formation in planar lipid bilayers (PLBs). Here, net-charge variations in the pore-lining helix of thirteen related RTX cytolysins including CyaA-Hly were revealed by amino acid sequence alignments, reflecting their different degrees of hemolytic activity. To analyze possible functional effects of net-charge alterations on hemolytic activity and channel formation of CyaA-Hly, specific mutations were made at Gln(574) or Glu(581) in its pore-lining α3 of which both residues are highly conserved Lys in the three highly active RTX cytolysins (i...
March 16, 2017: Toxins
https://www.readbyqxmd.com/read/28295503/nuclear-magnetic-resonance-structure-of-the-human-polyoma-jc-virus-agnoprotein
#13
Pascale Coric, A Sami Saribas, Magid Abou-Gharbia, Wayne Childers, Jon Condra, Martyn K White, Mahmut Safak, Serge Bouaziz
Agnoprotein is an important regulatory protein of the human polyoma JC virus (JCV) and plays critical roles during the viral replication cycle. It forms highly stable dimers and oligomers through its Leu/Ile/Phe-rich domain, which is important for the stability and function of the protein. We recently resolved the partial 3D structure of this protein by NMR using a synthetic peptide encompassing amino acids Thr17 to Gln52, where the Leu/Ile/Phe- rich domain was found to adopt a major alpha-helix conformation spanning amino acids 23 to 39...
March 10, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28289156/u7-snrnp-is-recruited-to-histone-pre-mrna-in-a-flash-dependent-manner-by-two-separate-regions-of-the-stem-loop-binding-protein
#14
Aleksandra Skrajna, Xiao-Cui Yang, Katarzyna Bucholc, Jun Zhang, Traci M Hall, Michał Dadlez, William F Marzluff, Zbigniew Dominski
Cleavage of histone pre-mRNAs at the 3' end requires Stem-Loop Binding Protein (SLBP) and U7 snRNP that consists of U7 snRNA and a unique Sm ring containing two U7-specific proteins: Lsm10 and Lsm11. Lsm11 interacts with FLASH and together they bring a subset of polyadenylation factors to U7 snRNP, including the CPSF73 endonuclease that cleaves histone pre-mRNA. SLBP binds to a conserved stem-loop structure upstream of the cleavage site and acts by promoting an interaction between the U7 snRNP and a sequence element located downstream of the cleavage site...
March 13, 2017: RNA
https://www.readbyqxmd.com/read/28287151/characterization-of-long-and-stable-de-novo-single-alpha-helix-domains-provides-novel-insight-into-their-stability
#15
Marcin Wolny, Matthew Batchelor, Gail J Bartlett, Emily G Baker, Marta Kurzawa, Peter J Knight, Lorna Dougan, Derek N Woolfson, Emanuele Paci, Michelle Peckham
Naturally-occurring single α-helices (SAHs), are rich in Arg (R), Glu (E) and Lys (K) residues, and stabilized by multiple salt bridges. Understanding how salt bridges promote their stability is challenging as SAHs are long and their sequences highly variable. Thus, we designed and tested simple de novo 98-residue polypeptides containing 7-residue repeats (AEEEXXX, where X is K or R) expected to promote salt-bridge formation between Glu and Lys/Arg. Lys-rich sequences (EK3 (AEEEKKK) and EK2R1 (AEEEKRK)) both form SAHs, of which EK2R1 is more helical and thermo-stable suggesting Arg increases stability...
March 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28285521/exploring-covalent-allosteric-inhibition-of-antigen-85c-from-mycobacterium-tuberculosis-by-ebselen-derivatives
#16
Christopher M Goins, Steven J Dajnowicz, Sandeep Thanna, Steven J Sucheck, Jerry Matthew Parks, Donald R Ronning
Previous studies identified ebselen as a potent in vitro and in vivo inhibitor of the Mycobacterium tuberculosis (Mtb) antigen 85 (Ag85) complex, comprising three homologous enzymes required for the biosynthesis of the mycobacterial cell wall. In this study, the Mtb Ag85C enzyme was co-crystallized with azido and adamantyl ebselen derivatives, resulting in two crystallographic structures of 2.01 and 1.30 Å resolution, respectively. Both structures displayed the anticipated covalent modification of the solvent accessible, non-catalytic Cys209 residue forming a selenenylsulfide bond...
March 13, 2017: ACS Infectious Diseases
https://www.readbyqxmd.com/read/28284276/zinc-binding-site-of-human-immunodeficiency-virus-2-vpx-prevents-instability-and-dysfunction-of-the-protein
#17
Minami Yamamoto, Ryoko Koga, Haruna Fujino, Kazunori Shimagaki, Halil Ibrahim Ciftci, Masahiro Kamo, Hiroshi Tateishi, Masami Otsuka, Mikako Fujita
Human immunodeficiency virus 2 Vpx coordinates zinc through residues H39, H82, C87 and C89. We reported previously that H39, H82 and C87 mutants maintain Vpx activity to facilitate the degradation of SAMHD1. Herein, the expression of Vpx mutants in cells was examined in detail. We demonstrated that the zinc-binding site stabilizes the protein to keep its function in virus growth when low levels of Vpx are expressed. At higher levels of expression, Vpx aggregation could occur, and zinc binding would suppress such aggregation...
February 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28283568/nanostructure-and-stability-of-calcitonin-amyloids
#18
Federica Rigoldi, Pierangelo Metrangolo, Alberto Redaelli, Alfonso Gautieri
Calcitonin is a 32 amino acid thyroid hormone that can form amyloid fibrils. The structural basis of the fibril formation and stabilization is still debated and poorly understood. The reason is that NMR data strongly suggest antiparallel β-sheets calcitonin assembly, while modelling studies on the short DFNKF peptide (corresponding to sequence from Asp15 to Phe19 of human calcitonin and reported as the minimal amyloidogenic module) show that it assembles with parallel β-sheets. In this work, we first predict the structure of human calcitonin through two complementary molecular dynamics (MD) methods, finding that human calcitonin forms an alpha helix...
March 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28282142/interplay-between-conformational-heterogeneity-and-hydration-in-the-folding-landscape-of-a-designed-three-helix-bundle
#19
Gregory S Custer, Payel Das, Silvina Matysiak
Water is known to play a critical role in protein folding and stability. Here we develop and employ a coarse-grained (CG) model to directly explore the role of water in shaping the conformational landscape explored during protein folding. For this purpose, we simulate a designed sequence with binary patterning of neutral and hydrophobic residues, which is capable of folding to a three-helix bundle in explicit water. We find two folded states of this sequence, with rotation of the helices occurring to trade between hydrophobic packing and water expulsion from the core...
March 23, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28282118/control-of-collagen-triple-helix-stability-by-phosphorylation
#20
Amanda M Acevedo-Jake, Daniel H Ngo, Jeffrey D Hartgerink
The phosphorylation of the collagen triple helix plays an important role in collagen synthesis, assembly, signaling, and immune response, although no reports detailing the effect this modification has on the structure and stability of the triple helix exist. Here we investigate the changes in stability and structure resulting from the phosphorylation of collagen. Additionally, the formation of pairwise interactions between phosphorylated residues and lysine is examined. In all tested cases, phosphorylation increases helix stability...
March 10, 2017: Biomacromolecules
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