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Helix stabilization

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https://www.readbyqxmd.com/read/27913751/new-fungal-defensin-like-peptides-provide-evidence-for-fold-change-of-proteins-in-evolution
#1
Yucheng Wu, Bin Gao, Shunyi Zhu
Defensins containing a consensus cystine framework, Cys[1]..Cys[2]X3Cys[3]..Cys[4]..Cys[5]X1Cys[6] ("X", any amino acids normally except Cys; "...", variable residue numbers), are extensively distributed in a variety of multicellular organisms (plants, fungi and invertebrates) and essentially involved in immunity as microbicidal agents. This framework is a prerequisite for forming a cystine-stabilized α-helix and β-sheet (CSαβ) fold, in which the two invariant motifs, Cys[2]X3Cys[3]/Cys[5]X1Cys[6], are key determinants of fold formation...
December 2, 2016: Bioscience Reports
https://www.readbyqxmd.com/read/27911771/stability-folding-dynamics-and-long-range-conformational-transition-of-the-synaptic-t-snare-complex
#2
Xinming Zhang, Aleksander A Rebane, Lu Ma, Feng Li, Junyi Jiao, Hong Qu, Frederic Pincet, James E Rothman, Yongli Zhang
Synaptic soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) couple their stepwise folding to fusion of synaptic vesicles with plasma membranes. In this process, three SNAREs assemble into a stable four-helix bundle. Arguably, the first and rate-limiting step of SNARE assembly is the formation of an activated binary target (t)-SNARE complex on the target plasma membrane, which then zippers with the vesicle (v)-SNARE on the vesicle to drive membrane fusion. However, the t-SNARE complex readily misfolds, and its structure, stability, and dynamics are elusive...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27907055/effect-of-glu12-his89-interaction-on-dynamic-structures-in-hiv-1-p17-matrix-protein-elucidated-by-nmr
#3
Yuta Konagaya, Rina Miyakawa, Masumi Sato, Akimasa Matsugami, Satoru Watanabe, Fumiaki Hayashi, Takanori Kigawa, Chiaki Nishimura
To test the existence of the salt bridge and stability of the HIV-1 p17 matrix protein, an E12A (mutated at helix 1) was established to abolish possible electrostatic interactions. The chemical shift perturbation from the comparison between wild type and E12A suggested the existence of an electrostatic interaction in wild type between E12 and H89 (located in helix 4). Unexpectedly, the studies using urea denaturation indicated that the E12A substitution slightly stabilized the protein. The dynamic structure of E12A was examined under physiological conditions by both amide proton exchange and relaxation studies...
2016: PloS One
https://www.readbyqxmd.com/read/27901172/conformational-states-of-hamp-domains-interacting-with-sensory-rhodopsin-membrane-systems-an-integrated-all-atom-and-coarse-grained-molecular-dynamics-simulation-approach
#4
Bikash Ranjan Sahoo, Toshimichi Fujiwara
Understanding the downstream signaling mechanism of sensory rhodopsin and its cognate transducer complex (srII-htrII) has long been a challenge in the field of photoreceptor research. Here, an integration of all-atom and coarse-grained (CG) molecular dynamics (MD) simulations in different srII-htrII complex states is carried out. It is shown that the cytoplasmic four-helix HAMP dimer gives rise to a gear-box model interaction with discrete hydrophobic packing in Natronomonas pharaonis (Np). Structural analysis in all-atom and CG-MD reveals a stable conformational state in the physiological environment (323 K and 1...
November 30, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27900727/antimicrobial-activity-and-stability-of-the-d-amino-acid-substituted-derivatives-of-antimicrobial-peptide-polybia-mpi
#5
Yanyan Zhao, Min Zhang, Shuai Qiu, Jiayi Wang, Jinxiu Peng, Ping Zhao, Ranran Zhu, Hailin Wang, Yuan Li, Kairong Wang, Wenjin Yan, Rui Wang
Antimicrobial peptide has the potential to be developed as new kind of antimicrobial agents with novel action mechanism. However, the susceptibility to protease is a drawback for potential peptides to be clinical used. D-amino acid substitution can be one way to increase the proteolytic stability of peptides. In the present study, we synthesized the D-lysines substituted analog (D-lys-MPI) and the D-enantiomer of polybia-MPI (D-MPI) to improve the proteolytic resistance of polybia-MPI. Our results showed that, the stability of its D-amino acid partially substituted analog D-lys-MPI was increased...
December 2016: AMB Express
https://www.readbyqxmd.com/read/27897084/multi-spectroscopic-and-molecular-modeling-studies-of-interaction-between-two-different-angiotensin-i-converting-enzyme-inhibitory-peptides-from-gluten-hydrolysate-and-human-serum-albumin
#6
Reza Assaran Darban, Behzad Shareghi, Ahmad Asoodeh, Jamshidkhan Chamani
The present study was carried out to characterize ACE inhibitory peptides which are release from the trypsin hydrolysate of wheat gluten protein. The binding of two inhibitory peptide (P4 and P6) to human serum albumin (HSA) under physiological conditions has been investigated by multi- spectroscopic in combination with molecular modeling techniques. Time-resolved and quenching fluorescence spectroscopies results revealed that the quenching of HSA fluorescence by P4 and P6 in the binary and ternary systems caused HSA-peptides complexes formation...
November 29, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27881238/rational-identification-of-natural-organic-compounds-to-target-the-intermolecular-interaction-between-foxm-and-dna-in-colorectal-cancer
#7
Chunling Dong, Peng Yan, Juxun Wang, Hailian Mu, Shuli Wang, Fangchun Guo
The oncogenic transcription factor forkhead box M (Foxm) is overexpressed in human colorectal cancer (CRC). Targeting the protein interaction with its cognate DNA has been established as an attractive approach to anti-CRC chemotherapy. State-of-the-art molecular dynamics (MD) simulations revealed that the Foxm adopts considerably different conformations to interact with and without its DNA partner; the holo conformation is tightly packed as a typical globulin configuration, whereas the apo form is locally unstructured that exhibits intrinsic disorder in DNA recognition helix, indicating that DNA binding can help the Foxm refolding...
November 9, 2016: Bioorganic Chemistry
https://www.readbyqxmd.com/read/27879049/double-helix-structure-in-carrageenan-metal-hydrogels-a-general-approach-to-porous-metal-sulfides-carbon-aerogels-with-excellent-sodium-ion-storage
#8
Daohao Li, Dongjiang Yang, Xianfeng Yang, Yu Wang, Ziqi Guo, Yanzhi Xia, Shenglei Sun, Shaojun Guo
The metal sulfide-carbon nanocomposite is a new class of anode material for sodium ion batteries, but its development is restricted by its relative poor rate ability and cyclic stability. Herein, we report the use of double-helix structure of carrageenan-metal hydrogels for the synthesis of 3D metal sulfide (Mx Sy ) nanostructure/carbon aerogels (CAs) for high-performance sodium-ion storage. The method is unique, and can be used to make multiple Mx Sy /CAs (such as FeS/CA, Co9 S8 /CA, Ni3 S4 /CA, CuS/CA, ZnS/CA, and CdS/CA) with ultra-small nanoparticles and hierarchical porous structure by pyrolyzing the carrageenan-metal hydrogels...
November 23, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27875778/phytochrome-interacting-factor-from-arabidopsis-to-liverwort
#9
REVIEW
Nayoung Lee, Giltsu Choi
Phytochromes are red and far-red light photoreceptors that regulate the responses of plants to light throughout their life cycles. Phytochromes do this in part by inhibiting the function of a group of basic helix-loop-helix transcription factors called phytochrome-interacting factors (PIFs). Arabidopsis has eight PIFs that function sometimes redundantly and sometimes distinctively depending on their expression patterns and protein stability, as well as on variations in the promoters they target in vivo. PIF-like proteins exist in other seed plants and non-vascular plants where they also regulate light responses...
November 19, 2016: Current Opinion in Plant Biology
https://www.readbyqxmd.com/read/27872311/methyltransferase-like-protein-16-binds-the-3-terminal-triple-helix-of-malat1-long-noncoding-rna
#10
Jessica A Brown, Charles G Kinzig, Suzanne J DeGregorio, Joan A Steitz
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), a cancer-promoting long noncoding RNA, accumulates in cells by using a 3'-triple-helical RNA stability element for nuclear expression (ENE). The ENE, a stem-loop structure containing a U-rich internal loop, interacts with a downstream A-rich tract (ENE+A) to form a blunt-ended triple helix composed of nine U•A-U triples interrupted by a C•G-C triple and C-G doublet. This unique structure prompted us to explore the possibility of protein binding...
November 21, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27872215/intramolecular-interactions-that-control-voltage-sensitivity-in-the-jshak1-potassium-channel-from-polyorchis-penicillatus
#11
Nazlee Sharmin, Warren J Gallin
Voltage-gated potassium ion (Kv) channel proteins respond to changes in membrane potential by changing the probability of K(+) flux through an ion-selective pore. Kv channels from different paralogous and orthologous families have widely varying V50 values. The voltage-sensing transmembrane helices (S4) of different channels contain 4-7 basic residues that are responsible for transducing changes in transmembrane potential into the energy required to shift the equilibrium between the open- and closed-channel conformations...
November 21, 2016: Journal of Experimental Biology
https://www.readbyqxmd.com/read/27865489/effects-of-heating-on-the-secondary-structure-of-proteins-in-milk-powders-using-mid-infrared-spectroscopy
#12
M P Ye, R Zhou, Y R Shi, H C Chen, Y Du
Milk powder is an important source of protein for adults and children. Protein is very sensitive to heat, which may influence people's usage of nutrients in milk powder. In this study, we describe the temperature-induced secondary structure of protein in milk powders. In this study, whole milk powder containing 24% protein and infant formula containing 11% protein were heated from 25 to 100°C. Attenuated total reflectance (ATR) spectra in the mid-infrared range 400-4,000 cm(-1) were used to evaluate the heat effect on the secondary structure of protein in these 2 milk powders...
November 16, 2016: Journal of Dairy Science
https://www.readbyqxmd.com/read/27864365/nmr-investigation-of-structures-of-g-protein-coupled-receptor-folding-intermediates
#13
Martin Poms, Philipp Ansorge, Luis Martinez-Gil, Simon Jurt, Daniel Gottstein, Katrina E Fracchiolla, Leah S Cohen, Peter Guentert, Ismael Mingarro, Fred Naider, Oliver Zerbe
Folding of G-protein coupled receptors (GPCRs) according to the two-stage model (Popot et al., Biochemistry 29(1990), 4031) is postulated to proceed in 2 steps: Partitioning of the polypeptide into the membrane followed by diffusion until native contacts are formed. Herein we investigate conformational preferences of fragments of the yeast Ste2p receptor using NMR. Constructs comprising the first, the first two and the first three transmembrane (TM) segments, as well as a construct comprising TM1-TM2 covalently linked to TM7 were examined...
November 18, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27860073/oligomerization-of-hmo1-mediated-by-box-a-is-essential-for-dna-binding-in%C3%A2-vitro-and-in%C3%A2-vivo
#14
Koji Kasahara, Ayako Higashino, Satoru Unzai, Hirofumi Yoshikawa, Tetsuro Kokubo
Hmo1, a member of HMGB family proteins in Saccharomyces cerevisiae, binds to and regulates the transcription of genes encoding ribosomal RNA and ribosomal proteins. The functional motifs of Hmo1 include two HMG-like motifs, box A and box B, and a C-terminal tail. To elucidate the molecular roles of the HMG-like boxes in DNA binding in vivo, we analyzed the DNA-binding activity of various Hmo1 mutants using ChIP or reporter assays that enabled us to conveniently detect Hmo1 binding to the promoter of RPS5, a major target gene of Hmo1...
November 15, 2016: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/27851939/-2-h-nmr-and-md-simulations-reveal-membrane-bound-conformation-of-magainin-2-and-its-synergy-with-pgla
#15
Erik Strandberg, Diana Horn, Sabine Reißer, Jonathan Zerweck, Parvesh Wadhwani, Anne S Ulrich
Magainin 2 (MAG2) and PGLa are two α-helical antimicrobial peptides found in the skin of the African frog Xenopus laevis. They act by permeabilizing bacterial membranes and exhibit an exemplary synergism. Here, we determined the detailed molecular alignment and dynamical behavior of MAG2 in oriented lipid bilayers by using (2)H-NMR on Ala-d3-labeled peptides, which yielded orientation-dependent quadrupolar splittings of the labels. The amphiphilic MAG2 helix was found to lie flat on the membrane surface in 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC)/1,2-dimyristoyl-sn-glycero-3-phosphatidylglycerol (DMPG) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC)/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylglycerol (POPG), as expected, with a tilt angle close to 90°...
November 15, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27851930/biophysical-characterization-of-the-interaction-between-m2-1-protein-of-hrsv-and-quercetin
#16
Thiago Salem Pançonato Teixeira, Ícaro Putinhon Caruso, Bruno Rafael Pereira Lopes, Luis Octávio Regasini, Karina Alves de Toledo, Marcelo Andrés Fossey, Fátima Pereira de Souza
hRSV is the major causative agent of acute respiratory infections. Among its eleven proteins, M2-1 is a transcription antiterminator, making it an interesting target for antivirals. Quercetin is a flavonol which inhibits some virus infectivity and replication. In the present work, the M2-1 gene was cloned, expressed and the protein was purified. Thermal stability and secondary structure were analyzed by circular dichroism and the interaction with Quercetin was evaluated by fluorescence spectroscopy. Molecular docking experiments were performed to understand this mechanism of interaction...
November 13, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27849570/the-werner-syndrome-helicase-coordinates-sequential-strand-displacement-and-fen1-mediated-flap-cleavage-during-polymerase-%C3%AE-elongation
#17
Baomin Li, Sita Reddy, Lucio Comai
The Werner syndrome protein (WRN) suppresses the loss of telomeres replicated by lagging strand synthesis by a yet to be defined mechanism. Here we show that whereas either WRN or the Bloom syndrome helicase (BLM) stimulate DNA polymerase δ progression across telomeric G-rich repeats, only WRN promotes sequential strand displacement synthesis and FEN1 cleavage, a critical step in Okazaki fragment maturation, at these sequences. Helicase activity as well as the conserved winged-helix (WH) motif and the Helicase-and-RNaseD C-terminal (HRDC) domain play important but distinct roles in this process...
November 14, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27845397/intrinsic-k-ras-dynamics-a-novel-molecular-dynamics-data-analysis-method-shows-causality-between-residue-pair-motions
#18
Sezen Vatansever, Zeynep H Gümüş, Burak Erman
K-Ras is the most frequently mutated oncogene in human cancers, but there are still no drugs that directly target it in the clinic. Recent studies utilizing dynamics information show promising results for selectively targeting mutant K-Ras. However, despite extensive characterization, the mechanisms by which K-Ras residue fluctuations transfer allosteric regulatory information remain unknown. Understanding the direction of information flow can provide new mechanistic insights for K-Ras targeting. Here, we present a novel approach -conditional time-delayed correlations (CTC) - using the motions of all residue pairs of a protein to predict directionality in the allosteric regulation of the protein fluctuations...
November 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27832722/folic-acid-delivery-by-serum-proteins-loading-efficacy-and-protein-morphology
#19
P Bourassa, P Chanphai, H A Tajmir-Riahi
The loading efficacy of folic acid with serum proteins human serum albumin (HSA), bovine serum albumin (BSA) and beta-lactoglobulin (b-LG) was analysed and the effect of acid conjugation on protein morphology was determined. Structural analysis showed that folic acid binds HSA, BSA and b-LG via hydrophilic, hydrophobic and H-bonding contacts with BSA forming more stable conjugates than HSA and b-LG. Molecular modeling showed the presence of several H-bonding systems, stabilizing acid-protein conjugates. Folic acid conjugation alters protein conformation by major alterations of alpha-helix and beta-sheet...
November 10, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27830006/mutation-near-the-binding-interfaces-at-%C3%AE-hemoglobin-stabilizing-protein-is-highly-pathogenic
#20
Jesu Francis Borgio, Mohammed S Al-Madan, Sayed AbdulAzeez
Aggregation of free alpha-hemoglobin proteins forms harmful reactive oxygen radicals during the development of normal erythroid cell, which can be prevented by a chaperone, alpha hemoglobin stabilizing protein (AHSP). Mutations at the AHSP gene may affect its interacting ability with other globin proteins. Various state-of-the-art tools have been extensively used to identify the most deleterious nsSNPs at the AHSP and their pathogenic effect during AHSP-globin interaction. Comprehensive analysis revealed that the V56G of the AHS protein is the most pathogenic amino acid substitution, agreed consistently and significantly (P=1...
2016: American Journal of Translational Research
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