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Helix stabilization

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https://www.readbyqxmd.com/read/28630813/mutations-in-the-sh1-helix-alter-the-thermal-properties-of-myosin-ii
#1
Kotomi Shibata, Tsubasa Koyama, Shohei Inde, Sosuke Iwai, Shigeru Chaen
The myosin II SH1 helix is a joint that links the converter subdomain to the rest of the myosin motor domain and possibly plays a key role in the arrangement of the converter/lever arm. Several point mutations within the SH1 helix in human myosin IIs have been shown to cause diseases. To reveal whether these SH1 helix mutations affect not only motile activities but also thermal properties of myosin II, here we introduced the E683K or R686C point mutation into the SH1 helix in Dictyostelium myosin II. Thermal inactivation as well as thermal aggregation rates of these mutant proteins demonstrated that these mutations decreased the thermal stability of myosin II...
2017: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28630402/exploration-of-binding-and-inhibition-mechanism-of-a-small-molecule-inhibitor-of-influenza-virus-h1n1-hemagglutinin-by-molecular-dynamics-simulation
#2
Shanshan Guan, Tianao Wang, Ziyu Kuai, Mengdan Qian, Xiaopian Tian, Xiuqi Zhang, Yongjiao Yu, Song Wang, Hao Zhang, Hao Li, Wei Kong, Yaming Shan
Influenza viruses are a major public health threat worldwide. The influenza hemagglutinin (HA) plays an essential role in the virus life cycle. Due to the high conservation of the HA stem region, it has become an especially attractive target for inhibitors for therapeutics. In this study, molecular simulation was applied to study the mechanism of a small molecule inhibitor (MBX2329) of influenza HA. Behaviors of the small molecule under neutral and acidic conditions were investigated, and an interesting dynamic binding mechanism was found...
June 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28628118/oncoppi-informed-discovery-of-mitogen-activated-protein-kinase-kinase-3-as-a-novel-binding-partner-of-c-myc
#3
A A Ivanov, V Gonzalez-Pecchi, L F Khuri, Q Niu, Y Wang, Y Xu, Y Bai, X Mo, E V Prochownik, M A Johns, Y Du, F R Khuri, H Fu
Mitogen-activated protein kinase kinase 3 (MKK3) is a dual threonine/tyrosine protein kinase that regulates inflammation, proliferation and apoptosis through specific phosphorylation and activation of the p38 mitogen-activated protein kinase. However, the role of MKK3 beyond p38-signaling remains elusive. Recently, we reported a protein-protein interaction (PPI) network of cancer-associated genes, termed OncoPPi, as a resource for the scientific community to generate new biological models. Analysis of the OncoPPi connectivity identified MKK3 as one of the major hub proteins in the network...
June 19, 2017: Oncogene
https://www.readbyqxmd.com/read/28623663/structural-mechanism-of-atp-independent-transcription-initiation-by-rna-polymerase-i
#4
Yan Han, Chunli Yan, Thi Hoang Duong Nguyen, Ashleigh J Jackobel, Ivaylo Ivanov, Bruce A Knutson, Yuan He
Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location...
June 17, 2017: ELife
https://www.readbyqxmd.com/read/28621923/capture-and-release-of-trna-by-the-t-loop-receptor-in-the-function-of-the-t-box-riboswitch
#5
Xianyang Fang, Malgorzata Michnicka, Yikan Zhang, Yun Xing Wang, Edward P Nikonowicz
In Gram-positive bacteria, the tRNA-dependent T-box riboswitch system regulates expression of amino acid biosynthetic and aminoacyl-tRNA synthetase genes through a transcription attenuation mechanism. Binding of uncharged tRNA "closes" the switch, allowing transcription read-through. Structure studies of the 100 nt stem I domain reveal tRNA utilizes base pairing and stacking interactions to bind the stem, but little is known structurally about the 180 nt riboswitch core (stem I, stem III, and antiterminator stem) in complex with tRNA and the mechanism of coupling of the intermolecular binding domains crucial to T-box function...
June 16, 2017: Biochemistry
https://www.readbyqxmd.com/read/28621532/synthesis-of-luminescent-platinum-ii-2-6-bis-n-dodecylbenzimidazol-2-yl-pyridine-foldamers-and-their-supramolecular-assembly-and-metallogel-formation
#6
Michael Ho-Yeung Chan, Maggie Ng, Sammual Yu-Lut Leung, Wai Han Lam, Vivian Wing-Wah Yam
Dinuclear alkynylplatinum(II) metallofoldamers with an oligomeric m-phenyleneethynylene backbone have been designed with the incorporation of a sterically undemanding, π-conjugated, and hydrophobic 2,6-bis(N-dodecylbenzimidazol-2'-yl)pyridine pincer ligand. The complex with the optimal chain length has been found to exhibit gelation behavior via stabilization by noncovalent Pt···Pt and π-π stacking interactions in the hierarchical architecture constructed from the single-turn helix. The chain lengths of the complexes have been found to be a critical determinant for their gelation behavior, conformations, and morphologies...
June 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28616630/experimental-and-computational-insights-on-the-recognition-mechanism-between-the-estrogen-receptor-%C3%AE-with-bisphenol-compounds
#7
Huiming Cao, Fengbang Wang, Yong Liang, Hailin Wang, Aiqian Zhang, Maoyong Song
Certain bisphenols (BPs) have been regarded as endocrine-disrupting chemicals due to their structural similarities to bisphenol A (BPA), a well-known weak estrogenic chemical. However, very limited data are currently available on the relationship between estrogenic activity and the structure of BP analogs. Therefore, we systematically investigated the estrogenic potency of 14 selected BP analogs with typical structures using experimental and computational methods. Most of the tested BP analogs exhibited weak estrogenic activities in both cell proliferation and MVLN assays with the exception of TBBPA, TCBPA and TBBPS...
June 14, 2017: Archives of Toxicology
https://www.readbyqxmd.com/read/28607368/nmr-structure-of-the-bacillus-cereus-hemolysin-ii-c-terminal-domain-reveals-a-novel-fold
#8
Anne R Kaplan, Katherine Kaus, Swastik De, Rich Olson, Andrei T Alexandrescu
In addition to multiple virulence factors, Bacillus cereus a pathogen that causes food poisoning and life-threatening wound infections, secretes the pore-forming toxin hemolysin II (HlyII). The HlyII toxin has a unique 94 amino acid C-terminal domain (HlyIIC). HlyIIC exhibits splitting of NMR resonances due to cis/trans isomerization of a single proline near the C-terminus. To overcome heterogeneity, we solved the structure of P405M-HlyIIC, a mutant that exclusively stabilizes the trans state. The NMR structure of HlyIIC reveals a novel fold, consisting of two subdomains αA-β1-β2 and β3-β4-αB-β5, that come together in a barrel-like structure...
June 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28607160/a-pria-mutant-expressed-in-two-pieces-has-almost-full-activity-in-e-coli-k-12
#9
Maxime Leroux, Niketa Jani, Steven J Sandler
The ability to restart broken DNA replication forks is essential across all domains of life. In Escherichia coli, the priA, priB, priC and dnaT genes encode the Replication Restart Proteins (RRPs) to accomplish this task. PriA plays a critical role in Replication Restart such that its absence reveals a dramatic phenotype: poor growth, high basal levels of SOS expression, poorly partitioned nucleoids (Par(-)), UV sensitivity and recombination deficiency. PriA has 733 amino acids and its structure is composed of six domains that enable it to bind to DNA replication fork-like structures, re-model the strands of DNA, interact with SSB (single-stranded DNA binding protein), PriB and DnaT, and display ATPase, helicase and translocase activities...
June 12, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28591604/g-protein-coupled-receptors-contain-two-conserved-packing-clusters
#10
Omar B Sanchez-Reyes, Aidan L G Cooke, Dale B Tranter, Dawood Rashid, Markus Eilers, Philip J Reeves, Steven O Smith
G protein-coupled receptors (GPCRs) have evolved a seven-transmembrane helix framework that is responsive to a wide range of extracellular signals. An analysis of the interior packing of family A GPCR crystal structures reveals two clusters of highly packed residues that facilitate tight transmembrane helix association. These clusters are centered on amino acid positions 2.47 and 4.53, which are highly conserved as alanine and serine, respectively. Ala2.47 mediates the interaction between helices H1 and H2, while Ser4...
June 6, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28589190/cholesteric-liquid-crystals-in-living-matter
#11
REVIEW
Michel Mitov
Liquid crystals play an important role in biology because the combination of order and mobility is a basic requirement for self-organisation and structure formation in living systems. Cholesteric liquid crystals are omnipresent in living matter under both in vivo and in vitro conditions and address the major types of molecules essential to life. In the animal and plant kingdoms, the cholesteric structure is a recurring design, suggesting a convergent evolution to an optimised left-handed helix. Herein, we review the recent advances in the cholesteric organisation of DNA, chromatin, chitin, cellulose, collagen, viruses, silk and cholesterol ester deposition in atherosclerosis...
June 14, 2017: Soft Matter
https://www.readbyqxmd.com/read/28580755/crabrolin-a-natural-antimicrobial-peptide-structural-properties
#12
Massimiliano Aschi, Argante Bozzi, Carla Luzi, Nadia Bouchemal, Marco Sette
A joint application of experimental and computational approaches has revealed the exceptionally high attitude of crabrolin, a 13-residue peptide with sequence FLPLILRKIVTAL-NH2 , to adopt alpha-helix conformation not only in membrane-mimicking solvents but also in the presence of a not negligible amount of water. Our study shows that this propensity essentially resides in the intrinsic thermodynamic stability of alpha-helix conformation whose kinetic stability is drastically reduced in water solvent. Our analysis suggests that this is due to two effects enhanced by water: a more local effect consisting of the demolition of intra-peptide H-bonds, essential for the alpha-helix formation, and a bulk - electrostatic - effect favoring conformational states more polar than alpha-helix...
June 5, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28573284/is-enzymatic-hydrolysis-a-reliable-analytical-strategy-to-quantify-glucuronidated-and-sulfated-polyphenol-metabolites-in-human-fluids
#13
Paola Quifer-Rada, Miriam Martínez-Huélamo, Rosa M Lamuela-Raventos
Phenolic compounds are present in human fluids (plasma and urine) mainly as glucuronidated and sulfated metabolites. Up to now, due to the unavailability of standards, enzymatic hydrolysis has been the method of choice in analytical chemistry to quantify these phase II phenolic metabolites. Enzymatic hydrolysis procedures vary in enzyme concentration, pH and temperature; however, there is a lack of knowledge about the stability of polyphenols in their free form during the process. In this study, we evaluated the stability of 7 phenolic acids, 2 flavonoids and 3 prenylflavanoids in urine during enzymatic hydrolysis to assess the suitability of this analytical procedure, using three different concentrations of β-glucuronidase/sulfatase enzymes from Helix pomatia...
June 2, 2017: Food & Function
https://www.readbyqxmd.com/read/28572639/construction-of-novel-repeat-proteins-with-rigid-and-predictable-structures-using-a-shared-helix-method
#14
Suk-Jun Youn, Na-Young Kwon, Ji Hyun Lee, Jin Hong Kim, Jinwoo Choi, Hayyoung Lee, Jie-Oh Lee
Generating artificial protein assemblies with complex shapes requires a method for connecting protein components with stable and predictable structures. Currently available methods for creating rigid protein assemblies rely on either complicated calculations or extensive trial and error. We describe a simple and efficient method for connecting two proteins via a fused alpha helix that is formed by joining two preexisting helices into a single extended helix. Because the end-to-end ligation of helices does not guarantee the formation of a continuous helix, we superimposed 1-2 turns of pairs of connecting helices by using a molecular graphics program...
June 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28562630/the-influence-of-n-terminal-acetylation-on-micelle-induced-conformational-changes-and-aggregation-of-%C3%AE-synuclein
#15
David Ruzafa, Yuriko S Hernandez-Gomez, Giovanni Bisello, Kerensa Broersen, Bertrand Morel, Francisco Conejero-Lara
The biological function of α-Synuclein has been related to binding to lipids and membranes but these interactions can also mediate α-Synuclein aggregation, which is associated to Parkinson's disease and other neuropathologies. In brain tissue α-Synuclein is constitutively N-acetylated, a modification that plays an important role in its conformational propensity, lipid and membrane binding, and aggregation propensity. We studied the interactions of the lipid-mimetic SDS with N-acetylated and non-acetylated α-Synuclein, as well as their early-onset Parkinson's disease variants A30P, E46K and A53T...
2017: PloS One
https://www.readbyqxmd.com/read/28561588/protein-domain-mimics-as-modulators-of-protein-protein-interactions
#16
Nicholas Sawyer, Andrew M Watkins, Paramjit S Arora
Protein-protein interactions (PPIs) are ubiquitous in biological systems and often misregulated in disease. As such, specific PPI modulators are desirable to unravel complex PPI pathways and expand the number of druggable targets available for therapeutic intervention. However, the large size and relative flatness of PPI interfaces make them challenging molecular targets. This Account describes our systematic approach using secondary and tertiary protein domain mimics (PDMs) to specifically modulate PPIs. Our strategy focuses on mimicry of regular secondary and tertiary structure elements from one of the PPI partners to inspire rational PDM design...
May 31, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28554535/a-phosphorylation-motif-for-tuneable-helix-stabilisation-in-intrinsically-disordered-proteins-lessons-from-the-sodium-proton-exchanger-1-nhe1
#17
Ruth Hendus-Altenburger, Matteo Lambrughi, Thilde Terkelsen, Stine F Pedersen, Elena Papaleo, Kresten Lindorff-Larsen, Birthe B Kragelund
Intrinsically disordered proteins (IDPs) are involved in many pivotal cellular processes including phosphorylation and signalling. The structural and functional effects of phosphorylation of IDPs remain poorly understood and difficult to predict. Thus, a need exists to identify motifs that confer phosphorylation-dependent perturbation of the local preferences for forming e.g. helical structures as well as motifs that do not. The disordered distal tail of the Na(+)/H(+) exchanger 1 (NHE1) is six-times phosphorylated (S693, S723, S726, S771, T779, S785) by the mitogen activated protein kinase 2 (MAPK1, ERK2)...
May 26, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28553525/the-effects-of-thioamide-backbone-substitution-on-protein-stability-a-study-in-%C3%AE-helical-%C3%AE-sheet-and-polyproline-ii-helical-contexts
#18
Christopher R Walters, D Miklos Szantai-Kis, Yitao Zhang, Zachary E Reinert, W Seth Horne, David M Chenoweth, E James Petersson
Thioamides are single atom substitutions of the peptide bond that serve as versatile probes of protein structure. Effective use of thioamides requires a robust understanding of the impact that the substitution has on a protein of interest. However, the thermodynamic effects of thioamide incorporation have only been studied in small structural motifs, and their influence on secondary structure in the context of full-length proteins is not known. Here we describe a comprehensive survey of thioamide substitutions in three benchmark protein systems (calmodulin, the B1 domain of protein G, and collagen) featuring the most prevalent secondary structure motifs: α-helix, β-sheet, and polyproline type II helix...
April 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28550305/dynamics-and-ligand-induced-conformational-changes-in-human-prolyl-oligopeptidase-analyzed-by-hydrogen-deuterium-exchange-mass-spectrometry
#19
Alexandra Tsirigotaki, Roos Van Elzen, Pieter Van Der Veken, Anne-Marie Lambeir, Anastassios Economou
Prolyl oligopeptidase (PREP) is conserved in many organisms across life. It is involved in numerous processes including brain function and neuropathology, that require more than its strict proteolytic role. It consists of a seven-bladed β-propeller juxtaposed to a catalytic α/β-hydrolase domain. The conformational dynamics of PREP involved in domain motions and the gating mechanism that allows substrate accessibility remain elusive. Here we used Hydrogen Deuterium eXchange Mass Spectrometry (HDX-MS) to derive the first near-residue resolution analysis of global PREP dynamics in the presence or absence of inhibitor bound in the active site...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28547390/mono-substitution-effects-on-antimicrobial-activity-of-stapled-heptapeptides
#20
Huy X Luong, Do-Hee Kim, Ngoan T Mai, Bong-Jin Lee, Young-Woo Kim
We previously reported a de novo design of antimicrobial heptapeptide helices using Verdine's all-hydrocarbon peptide stapling system. One of the important structure-activity relationships we found from these previous studies was that extending of the hydrophobic face by replacing of alanine with leucine in positon 5 increases antimicrobial activity. In this study, to further improve the activity profile of this peptide series, we investigated the substitution effects of position 5 on conformational and proteolytic stability as well as antimicrobial and hemolytic activity...
May 25, 2017: Archives of Pharmacal Research
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