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Helix stabilization

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https://www.readbyqxmd.com/read/28815856/molecular-dynamics-insights-into-polyamine-dna-binding-modes-implications-for-cross-link-selectivity
#1
Emmanuelle Bignon, Chen-Hui Chan, Christophe Morell, Antonio Monari, Jean-Luc Ravanat, Elise Dumont
Biogenic polyamines, which play a role in DNA condensation and stabilization, are ubiquitous and are found at millimolar concentration in the nucleus of eukaryotic cells. The interaction modes of three polyamines-putrescine (Put), spermine (Spm), and spermidine (Spd)-with a self-complementary 16 base pair (bp) duplex, are investigated by all-atom explicit-solvent molecular dynamics. The length of the amine aliphatic chain leads to a change of the interaction mode from minor groove binding to major groove binding...
August 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28813589/regulation-of-stability-on-histone-h2a-h2b-dimer-by-h2a-tyr57-phosphorylation
#2
Takuma Sueoka, Gosuke Hayashi, Akimitsu Okamoto
Histone H2A and H2B form a H2A-H2B heterodimer, which is a fundamental unit of nucleosome assembly and disassembly. Several posttranslational modifications change the interface between the H2A-H2B dimer and the H3-H4 tetramer, and regulate nucleosome stability. However, posttranslational modifications associated with the interface between H2A and H2B have not been discussed. In this paper, it is shown that Tyr57 phosphorylation in H2A strongly influences H2A-H2B dimerization. Tyr57-phosphorylated H2A was chemically synthesized and utilized to reconstitute the H2A-H2B dimer and nucleosome as well as canonical H2A...
August 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28811070/evaluation-of-sequence-variability-in-hiv-1-gp41-c-peptide-helix-grafted-proteins
#3
Rachel L Tennyson, Susanne N Walker, Terumasa Ikeda, Reuben S Harris, Brian R McNaughton
Many therapeutically-relevant protein-protein interactions (PPIs) have been reported that feature a helix and helix-binding cleft at the interface. Given this, different approaches to disrupting such PPIs have been developed. While short peptides (<15 amino acids) typically do not fold into a stable helix, researchers have reported chemical approaches to constraining helix structure. However, these approaches rely on laborious, and often expensive, chemical synthesis and purification. Our premise is that protein-based solutions that stabilize a therapeutically-relevant helix offer a number of advantages...
August 1, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28805214/the-low-populated-folding-intermediate-of-a-mutant-of-the-fyn-sh3-domain-identified-by-a-simple-model
#4
Jing Wu, Guojun Chen, Zhuqing Zhang, Ping Zhang, Tao Chen
Experimental studies indicate that the A39V/N53P/V55L Fyn SH3 domain folds from the unfolded state to the native state via a low-populated on-pathway intermediate, whereas the folding of the wildtype is two-state-like. To get insights into the biophysical basis of their different folding mechanisms, we used native-centric models with and without additional transferrable, sequence-dependent nonnative hydrophobic interactions to study the folding behaviors of the Fyn SH3 domain and its mutant. The pure native-centric model predicts that both the wildtype and the mutant fold in a two-state manner, without any detectable intermediate...
August 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28802845/fluorescence-quenching-structural-and-unfolding-studies-of-a-purified-cysteine-protease-zcpg-from-zingiber-montanum-rhizome
#5
Kizukala Jamir, Kottapalli Seshagirirao
A first attempt was made to study the fluorescence quenching, structure and unfolding nature of the purified Zingiber montanum (J.Koenig) Link ex A.Dietr. cysteine protease glycoprotein (ZCPG). ATR-IR spectra showed the presences of amide groups along with carbohydrate stretch indicating the glycoprotein nature. UV-vis spectra determined the presences of peptide groups and aromatic sidechains of tyrosine, tryptophan and phenylalanine. Far UV-Circular Dichroism spectrum revealed that the secondary structure consists of 47...
August 9, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28802270/intra-molecular-salt-bridge-in-bacillus-thuringiensis-cry4ba-toxin-is-involved-in-the-stability-of-helix-%C3%AE-3-that-is-needed-for-oligomerization-and-insecticidal-activity
#6
Sabino Pacheco, Isabel Gómez, Jorge Sanchez, Blanca-Ines García-Gómez, Mario Soberón, Alejandra Bravo
Bacillus thuringiensis three domain Cry toxins kill insects by forming pores in the apical membrane of larval midgut cells. Oligomerization of the toxin is an important step for pore formation. Domain I helix α-3 participates in toxin oligomerization. Here we identify an intra-molecular salt bridge within helix α-3 of Cry4Ba (D111-K115) that is conserved in many members of the family of the three-domain Cry toxins. Single point mutations such as D111K or K115D resulted in proteins severely affected in toxicity...
August 11, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28799853/effect-of-combination-of-high-intensity-ultrasound-treatment-and-dextran-glycosylation-on-structural-and-interfacial-properties-of-buckwheat-protein-isolates
#7
Feng Xue, Zhoushan Wu, Jinrong Tong, Jialun Zheng, Chen Li
This study investigated the effects of high-intensity ultrasound and glycosylation on the structural and interfacial properties of the Maillard reaction conjugates of buckwheat protein isolate (BPI). The covalent attachment of dextran to BPI was confirmed by examination of the Fourier-transform infrared spectra. Emulsifying properties of the conjugates obtained by ultrasound treatment were improved as compared to those obtained by classical heating. Structural feature analyses suggested that conjugates obtained by ultrasound treatment had less α-helix and more random coil, higher surface hydrophobicity and less compact tertiary structure as compared to those obtained by classical heating...
August 11, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28798234/structural-transitions-in-conserved-ordered-beclin-1-domains-essential-to-regulating-autophagy
#8
Karen Glover, Yue Li, Shreya Mukhopadhyay, Zoe Leuthner, Srinivas Chakravarthy, Christopher L Colbert, Sangita C Sinha
Beclin 1 (BECN1) is a key regulator of autophagy, a critical catabolic homeostasis pathway that involves the sequestration of cytoplasmic components by multilayered vesicles called autophagosomes, followed by lysosomal fusion and degradation. BECN1 is a core component of class III phosphatidylinositol-3-kinase complexes responsible for autophagosome nucleation. Without heterologous binding partners, BECN1 forms an antiparallel homodimer via its coiled-coil domain (CCD). However, the last 16 CCD residues, composing an overlap helix (OH), have been crystallized in two mutually exclusive states: either as part of the CCD or packed against the C-terminal lower case β-α-repeated, autophagy-specific domain (BARAD)...
August 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28795265/the-stress-induced-scp-hlip-family-of-small-light-harvesting-like-proteins-scpabcde-protects-photosystem-ii-from-photoinhibitory-damages-in-the-cyanobacterium-synechocystis-sp-pcc-6803
#9
Tania Tibiletti, Ateeq Ur Rehman, Imre Vass, Christiane Funk
Small CAB-like proteins (SCPs) are single-helix light-harvesting-like proteins found in all organisms performing oxygenic photosynthesis. We investigated the effect of growth in moderate salt stress on these stress-induced proteins in the cyanobacterium Synechocystis sp. PCC 6803 depleted of Photosystem I (PSI), which expresses SCPs constitutively, and compared these cells with a PSI-less/ScpABCDE(-) mutant. SCPs, by stabilizing chlorophyll-binding proteins and Photosystem II (PSII) assembly, protect PSII from photoinhibitory damages, and in their absence electrons accumulate and will lead to ROS formation...
August 9, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/28794035/crystal-structure-of-the-dna-binding-domain-of-human-herpesvirus-6a-immediate-early-protein-2
#10
Mitsuhiro Nishimura, Junjie Wang, Aika Wakata, Kento Sakamoto, Yasuko Mori
Immediate early proteins of human herpesvirus 6A (HHV-6A) are expressed at the outset of lytic infection, and thereby regulate viral gene expression. Immediate early protein 2 (IE2) of HHV-6A is a trans-activator that drives a variety of promoters. The C-terminal region of HHV-6A IE2 is shared among IE2 homologs in beta-herpesviruses, and is involved in dimerization, DNA binding, and transcription factor binding. In this study, the structure of the C-terminal domain (IE2-CTD) was determined by X-ray crystallography at a resolution of 2...
August 9, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28793212/intrinsically-disordered-stress-protein-cor15a-resides-at-the-membrane-surface-during-dehydration
#11
Anne Bremer, Ben Kent, Thomas Hauß, Anja Thalhammer, Nageshwar R Yepuri, Tamim A Darwish, Christopher J Garvey, Gary Bryant, Dirk K Hincha
Plants from temperate climate zones are able to increase their freezing tolerance during exposure to low, above-zero temperatures in a process termed cold acclimation. During this process, several cold-regulated (COR) proteins are accumulated in the cells. One of them is COR15A, a small, intrinsically disordered protein that contributes to leaf freezing tolerance by stabilizing cellular membranes. The isolated protein folds into amphipathic α-helices in response to increased crowding conditions, such as high concentrations of glycerol...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28792044/enzyme-assisted-peptide-folding-assembly-and-anti-cancer-properties
#12
Chunhui Liang, Debin Zheng, Fang Shi, Tengyan Xu, Cuihong Yang, Jianfeng Liu, Ling Wang, Zhimou Yang
The α-helix is the most prevalent conformation in proteins. However, formation of the α-helical conformation remains a challenge for short peptides with less than 5 amino acids. We demonstrated in this study that enzyme-instructed self-assembly (EISA) provides a unique pathway to assist the self-assembly of peptides into the α-helical conformation, while a heating-cooling process leads to a conformation more similar to a β-sheet. The same peptide with different conformations self-assembled into different nanostructures...
August 9, 2017: Nanoscale
https://www.readbyqxmd.com/read/28789896/development-of-helix-stabilized-antimicrobial-peptides-composed-of-lysine-and-hydrophobic-%C3%AE-%C3%AE-disubstituted-%C3%AE-amino-acid-residues
#13
Takashi Misawa, Mitsuyoshi Imamura, Yuto Ozawa, Kazuchika Haishima, Masaaki Kurihara, Yutaka Kikuchi, Yosuke Demizu
Lysine-based amphipathic nonapeptides, including homochiral peptides [Ac-(l-Lys-l-Lys-Xaa)3-NH2 (Xaa=Gly, Ala, Aib, Ac5c, or Ac6c) and Ac-(d-Lys-d-Lys-Aib)3-NH2], a heterochiral peptide [Ac-(l-Lys-d-Lys-Aib)3-NH2], and a racemic mixture of diastereomeric peptides [Ac-(rac-Lys-rac-Lys-Aib)3-NH2] were designed and synthesized to investigate the relationship between their preferred secondary structures and their antimicrobial activity. Peptide 5, [Ac-(l-Lys-l-Lys-Ac6c)3-NH2] formed a stable α-helical structure and exhibited strong activity against Gram-negative bacteria (Escherichia coli and Pseudomonas aeruginosa)...
July 29, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28783665/structural-basis-for-potent-antibody-mediated-neutralization-of-human-cytomegalovirus
#14
Sumana Chandramouli, Enrico Malito, TuongVi Nguyen, Kate Luisi, Danilo Donnarumma, Yi Xing, Nathalie Norais, Dong Yu, Andrea Carfi
Human cytomegalovirus (HCMV) is the leading viral cause of birth defects and organ transplant rejection. The HCMV gH/gL/UL128/UL130/UL131A complex (Pentamer) is the main target of humoral responses and thus a key vaccine candidate. We report two structures of Pentamer bound to human neutralizing antibodies, 8I21 and 9I6, at 3.0 and 5.9 Å resolution, respectively. The HCMV gH/gL architecture is similar to that of Epstein-Barr virus (EBV) except for amino-terminal extensions on both subunits. The extension of gL forms a subdomain composed of a three-helix bundle and a β hairpin that acts as a docking site for UL128/UL130/UL131A...
June 30, 2017: Science Immunology
https://www.readbyqxmd.com/read/28781166/cryo-em-structure-of-a-pre-catalytic-human-spliceosome-primed-for-activation
#15
Karl Bertram, Dmitry E Agafonov, Olexandr Dybkov, David Haselbach, Majety N Leelaram, Cindy L Will, Henning Urlaub, Berthold Kastner, Reinhard Lührmann, Holger Stark
Little is known about the spliceosome's structure before its extensive remodeling into a catalytically active complex. Here, we report a 3D cryo-EM structure of a pre-catalytic human spliceosomal B complex. The U2 snRNP-containing head domain is connected to the B complex main body via three main bridges. U4/U6.U5 tri-snRNP proteins, which are located in the main body, undergo significant rearrangements during tri-snRNP integration into the B complex. These include formation of a partially closed Prp8 conformation that creates, together with Dim1, a 5' splice site (ss) binding pocket, displacement of Sad1, and rearrangement of Brr2 such that it contacts its U4/U6 substrate and is poised for the subsequent spliceosome activation step...
August 10, 2017: Cell
https://www.readbyqxmd.com/read/28777919/binding-profiles-of-cholesterol-ester-transfer-protein-with-current-inhibitors-a-look-at-mechanism-and-drawback
#16
Zhiwei Yang, Yang Cao, Dongxiao Hao, Xiaohui Yuan, Lei Zhang, Shengli Zhang
Although the pharmacological inhibition of cholesterol ester transport protein (CETP) has been proposed as a method of preventing and treating cardiovascular disease (CVD), the adverse effects of currentinhibitors have cast doubton theinteraction mechanisms of inhibitors and CETP.In response,a molecular dynamicssimulation was used to investigate their interaction and shed light onthe lipid exchange mechanism of CETP.Results showed that torcetrapib, anacetrapib, and evacetrapib can induce the incremental rigidityof CETP, yet decrease the stability of Helix X and the hydrophobic tunnel of CETP, withpassable binding abilities (ΔGbind, -61...
August 4, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28772159/structure-based-design-of-competitive-ligands-to-target-spon2-in-gastric-cancer-an-integration-of-molecular-modeling-and-in-vitro-assay
#17
Zhenglei Xu, Zhichao Yu, Shumei Nai, Ruiyue Shi, Qinhong Tang, Haiyang Zhang, Lijuan Ye, Lisheng Wang, Yincai Hong
Spon2 is a proto-oncogene matrix protein that plays an essential role in the tumorigenesis and metastasis of gastric cancer. The protein has recently been found to function as a guanine nucleotide exchange factor through the activation of RhoGTPase. Here, computational modeling and bioinformatics analysis were employed to investigate the molecular mechanism and biological implication underlying Spon2 autoinhibition. It is revealed that the binding of PxxP motif to SH domain can stabilize the intramolecular interaction between the N-terminal helix and DH domain of Spon2, thus shifting the protein into an autoinhibitory state...
July 18, 2017: Bioorganic Chemistry
https://www.readbyqxmd.com/read/28771005/inhibition-mechanisms-of-a-pyridazine-based-amyloid-inhibitor-as-a-%C3%AE-sheet-destabilizer-and-a-helix-bridge-maker
#18
Hamid R Kalhor, M Parsa Jabbari
Conformational diseases have been investigated extensively in recent years; as a result, a number of drug candidates have been introduced as amyloid inhibitors; however, no effective therapies have been put forward. RS-0406 with pyridazine as its core chemical structure has so far shown promising results in inhibiting amyloid formation. In the present work, using molecular dynamics, we undertook the investigation of RS-0406 interactions with U-shaped Aβ1-42 and Aβ1-40 pentamers, Aβ1-42 monomers, and double-horseshoe-like Aβ1-42...
August 3, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28758877/the-effects-of-metal-ion-contaminants-on-the-double-stranded-dna-helix-and-diseases
#19
T Theophanides, J Anastassopoulou
Mineral metal ions are essential for the maintenance of the reactions that regulate homeostasis and the functions of our body. It is known that the regulation of the neurodegenerative system depends directly on life metal ions, such as Na, K, Mg, Ca, Fe, Mo, Cu, Co, Zn, Cr, Mn, while the toxic metals Cd, Pb, Hg, etc disturb homeostasis, leading to diseases. Particularly significant is the effect of toxic metals on the double stranded forms of DNA and conformations. It was found that the toxic metal ions by reacting specifically with the nucleic bases and electrostatically with the negatively phosphate groups of the DNA backbone cause changes in the structure of the DNA double helix, leading to breaks of single or double strands...
July 31, 2017: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
https://www.readbyqxmd.com/read/28758396/impact-of-lca-associated-e14l-lrat-mutation-on-protein-stability-and-retinoid-homeostasis
#20
Sylwia Chelstowska, Made Airanthi K Widjaja-Adhi, Josie A Silvaroli, Marcin Golczak
Vitamin A (all-trans-retinol) is metabolized to the visual chromophore (11-cis-retinal) in the eyes and to all-trans-retinoic acid, a hormone like compound, in most tissues. A key enzyme in retinoid metabolism is lecithin:retinol acyltransferase (LRAT), which catalyzes the esterification of vitamin A. The importance of LRAT is indicated by pathogenic missense and nonsense mutations, which cause devastating blinding diseases. Retinoid-based chromophore replacement therapy has been proposed as treatment for these types of blindness based on studies in LRAT null mice...
August 15, 2017: Biochemistry
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