keyword
MENU ▼
Read by QxMD icon Read
search

Helix stabilization

keyword
https://www.readbyqxmd.com/read/28550305/dynamics-and-ligand-induced-conformational-changes-in-human-prolyl-oligopeptidase-analyzed-by-hydrogen-deuterium-exchange-mass-spectrometry
#1
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
#2
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
https://www.readbyqxmd.com/read/28546429/structural-studies-unravel-the-active-conformation-of-apo-ror%C3%AE-t-nuclear-receptor-and-a-common-inverse-agonism-of-two-diverse-classes-of-ror%C3%AE-t-inhibitors
#3
Xiang Li, Marie Anderson, Delphine Collin, Ingo Muegge, John Wan, Debra Brennan, Stanley Kugler, Donna Terenzio, Charles Kennedy, Siqi Lin, Mark E Labadia, Brian Cook, Robert Hughes, Neil A Farrow
The nuclear receptor retinoid acid-related orphan receptor γt (RORγt) is a master regulator of the Th17/IL-17 pathway that plays crucial roles in the pathogenesis of autoimmunity. RORγt has recently emerged as a highly promising target for treatment of a number of autoimmune diseases. Through high-throughput screening we previously identified several classes of inverse agonists for RORγt. Here, we report the crystal structures for the ligand binding domain of RORγt in both apo and ligand-bound states. We show that apo RORγt adopts an active conformation capable of recruiting coactivator peptides and present a detailed analysis of the structural determinants that stabilize helix 12 (H12) of RORγt in the active state in the absence of a ligand...
May 25, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28543443/structural-review-of-ppar%C3%AE-in-complex-with-ligands-cartesian-and-dihedral-angle-principal-component-analyses-of-x-ray-crystallographic-data
#4
Åsmund Kaupang, Tuomo Laitinen, Antti Poso, Trond Vidar Hansen
Two decades of research into the ligand-dependent modulation of the activity of the peroxisome proliferator-activated receptor γ (PPARγ) have demonstrated the heterogeneous modes of action of PPARγ ligands, in terms of their interaction surfaces in the ligand-binding pocket, binding stoichiometry and ability to interact with functionally important parts of the receptor, through both direct and allosteric mechanisms. These findings signal the complex mechanistic bases of the distinct biological effects of different classes of PPARγ ligands...
May 24, 2017: Proteins
https://www.readbyqxmd.com/read/28541029/homochiral-mof-as-circular-dichroism-sensor-for-enantioselective-recognition-on-nature-and-chirality-of-unmodified-amino-acids
#5
Yan-Wu Zhao, Yan Wang, Xian-Ming Zhang
Self-assembly of zinc salt with rationally designed chiral ligand, (1R,2R)-2-(pyridine-4-yl carbamoyl) cyclohexanecarboxylic acid (RR-PCCH) generated 2D homochiral metal-organic framework [Zn(RR-PCCHC)2] (HMOF-1) that is composed of DNA-like right-handed double-helix structure. HMOF-1 shows high solvent and thermal stability and is also stable in neutral, weak acidic and weak basic aqueous solution. Emulsified HMOF-1 shows strong inherent circular dichroism (CD) signal in aqueous solution, which can show regular intensity change by induction of amino acids...
May 25, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28538735/ensemble-cryo-em-elucidates-the-mechanism-of-translation-fidelity
#6
Anna B Loveland, Gabriel Demo, Nikolaus Grigorieff, Andrei A Korostelev
Gene translation depends on accurate decoding of mRNA, the structural mechanism of which remains poorly understood. Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by elongation factor Tu (EF-Tu). Here we present high-resolution structural ensembles of ribosomes with cognate or near-cognate aminoacyl-tRNAs delivered by EF-Tu. Both cognate and near-cognate tRNA anticodons explore the aminoacyl-tRNA-binding site (A site) of an open 30S subunit, while inactive EF-Tu is separated from the 50S subunit...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28538729/cryo-em-structure-of-the-activated-glp-1-receptor-in-complex-with-a-g-protein
#7
Yan Zhang, Bingfa Sun, Dan Feng, Hongli Hu, Matthew Chu, Qianhui Qu, Jeffrey T Tarrasch, Shane Li, Tong Sun Kobilka, Brian K Kobilka, Georgios Skiniotis
Glucagon-like peptide 1 (GLP-1) is a hormone with essential roles in regulating insulin secretion, carbohydrate metabolism and appetite. GLP-1 effects are mediated through binding to the GLP-1 receptor (GLP-1R), a class B G-protein-coupled receptor (GPCR) that signals primarily through the stimulatory G protein Gs. Class B GPCRs are important therapeutic targets; however, our understanding of their mechanism of action is limited by the lack of structural information on activated and full-length receptors. Here we report the cryo-electron microscopy structure of the peptide-activated GLP-1R-Gs complex at near atomic resolution...
May 24, 2017: Nature
https://www.readbyqxmd.com/read/28538145/nmr-analysis-of-amide-hydrogen-exchange-rates-in-a-pentapeptide-repeat-protein-from-a-%C3%A2-thaliana
#8
Shenyuan Xu, Shuisong Ni, Michael A Kennedy
At2g44920 from Arabidopsis thaliana is a pentapeptide-repeat protein (PRP) composed of 25 repeats capped by N- and C-terminal α-helices. PRP structures are dominated by four-sided right-handed β-helices typically consisting of mixtures of type II and type IV β-turns. PRPs adopt repeated five-residue (Rfr) folds with an Rfr consensus sequence (STAV)(D/N)(L/F)(S/T/R)(X). Unlike other PRPs, At2g44920 consists exclusively of type II β-turns. At2g44920 is predicted to be located in the thylakoid lumen although its biochemical function remains unknown...
May 23, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28538095/high-resolution-structures-of-the-amyloid-%C3%AE-1-42-dimers-from-the-comparison-of-four-atomistic-force-fields
#9
Viet Hoang Man, Phuong Hoang Nguyen, Philippe Derreumaux
The dimer of the amyloid-beta peptide Aβ of 42 residues is the smallest toxic species in Alzheimer's disease, but its equilibrium structures are unknown. Here we determined the equilibrium ensembles generated by the four atomistic OPLS-AA, CHARMM22*, AMBER99sb-ildn and AMBERsb14 force fields with the TIP3P water model. Based on 144 microsecond replica exchange molecular dynamics simulations (with 750 ns per replica), we find that the four force fields lead to random coil ensembles with calculated cross-collision sections, hydrodynamics properties and small-angle X-ray scattering profiles independent on the force field...
May 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28537738/a-peptoid-square-helix-via-synergistic-control-of-backbone-dihedral-angles
#10
Benjamin Craig Gorske, Emily M Mumford, Charles G Gerrity, Imelda Ko
The continued expansion of the fields of macromolecular chemistry and nanoscience has motivated the development of new secondary structures that can serve as architectural elements of innovative materials, molecular machines, biological probes, and even commercial medicines. Synthetic foldamers are particularly attractive systems for developing such elements because they are specifically designed to facilitate synthetic manipulation and functional diversity. However, relatively few predictive design principles exist that permit both rational and modular control of foldamer secondary structure, while maintaining the capacity for facile diversification of displayed functionality...
May 24, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28533266/non-linearity-of-the-collagen-triple-helix-in-solution-and-implications-for-collagen-function
#11
Kenneth T Walker, Ruodan Nan, David W Wright, Jayesh Gor, Anthony C Bishop, George I Makhatadze, Barbara Brodsky, Stephen J Perkins
Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly)n sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units...
May 22, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28532099/interaction-of-insulin-with-colloidal-zns-quantum-dots-functionalized-by-various-surface-capping-agents
#12
Ghader Hosseinzadeh, Ali Maghari, Seyed Morteza Famil Farniya, Amir Homayoun Keihan, Ali A Moosavi-Movahedi
Interaction of quantum dots (QDs) and proteins strongly influenced by the surface characteristics of the QDs at the protein-QD interface. For a precise control of these surface-related interactions, it is necessary to improve our understanding in this field. In this regard, in the present work, the interaction between the insulin and differently functionalized ZnS quantum dots (QDs) were studied. The ZnS QDs were functionalized with various functional groups of hydroxyl (OH), carboxyl (COOH), amine (NH2), and amino acid (COOH and NH2)...
August 1, 2017: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/28530710/engineering-protein-stability-with-atomic-precision-in-a-monomeric-miniprotein
#13
Emily G Baker, Christopher Williams, Kieran L Hudson, Gail J Bartlett, Jack W Heal, Kathryn L Porter Goff, Richard B Sessions, Matthew P Crump, Derek N Woolfson
Miniproteins simplify the protein-folding problem, allowing the dissection of forces that stabilize protein structures. Here we describe PPα-Tyr, a designed peptide comprising an α-helix buttressed by a polyproline II helix. PPα-Tyr is water soluble and monomeric, and it unfolds cooperatively with a midpoint unfolding temperature (TM) of 39 °C. NMR structures of PPα-Tyr reveal proline residues docked between tyrosine side chains, as designed. The stability of PPα is sensitive to modifications in the aromatic residues: replacing tyrosine with phenylalanine, i...
May 22, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28528776/structural-basis-of-tpr-mediated-oligomerization-and-activation-of-oncogenic-fusion-kinases
#14
Kuntal Pal, Abhishek Bandyopadhyay, X Edward Zhou, Qingping Xu, David P Marciano, Joseph S Brunzelle, Smitha Yerrum, Patrick R Griffin, George Vande Woude, Karsten Melcher, H Eric Xu
The nuclear pore complex subunit TPR is found in at least five different oncogenic fusion kinases, including TPR-MET, yet how TPR fusions promote activation of kinases and their oncogenic activities remains poorly understood. Here we report the crystal structure of TPR(2-142), the MET fusion partner of oncogenic TPR-MET. TPR(2-142) contains a continuous 124-residue α helix that forms an antiparallel tetramer from two leucine zipper-containing parallel coiled coils. Remarkably, single mutations cause strikingly different conformations of the coiled coil, indicating its highly dynamic nature...
May 18, 2017: Structure
https://www.readbyqxmd.com/read/28522372/effective-antimicrobial-activity-of-a-peptide-mutant-cbf-14-2-against-penicillin-resistant-bacteria-based-on-its-unnatural-amino-acids
#15
Wei Kang, Hanhan Liu, Lingman Ma, Mengxiao Wang, Shanshan Wei, Pengbo Sun, Meiling Jiang, Min Guo, Changlin Zhou, Jie Dou
Broad spectrum activities, a unique mode of actions and rare resistant variants make antimicrobial peptide (AMP) a potential alternative to antibiotics. However, AMPs still have limitations in clinical development due to their physiological stability, toxicity and manufacturing costs. Cbf-14, derived from cathelicidin-BF has been proven to be effective against drug-resistant bacteria. Herein, a series of Cbf-14 mutants were designed to overcome these limitations. Design strategies included substitutions of lysine (Lys) or leucine (Leu) with similar residues such as ornithine (Orn) and norleucine (Ile), which are unnatural amino acids, to generate AMPs with enhanced therapeutic potential...
May 15, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28521820/destabilization-of-the-twist1-e12-complex-dimerization-following-the-r154p-point-mutation-of-twist1-an-in-silico-approach
#16
Charlotte Bouard, Raphael Terreux, Agnès Tissier, Laurent Jacqueroud, Arnaud Vigneron, Stéphane Ansieau, Alain Puisieux, Léa Payen
BACKGROUND: The bHLH transcription factor TWIST1 plays a key role in the embryonic development and in tumorigenesis. Some loss-of-function mutations of the TWIST1 gene have been shown to cause an autosomal dominant craniosynostosis, known as the Saethre-Chotzen syndrome (SCS). Although the functional impacts of many TWIST1 mutations have been experimentally reported, little is known on the molecular mechanisms underlying their loss-of-function. In a previous study, we highlighted the predictive value of in silico molecular dynamics (MD) simulations in deciphering the molecular function of TWIST1 residues...
May 18, 2017: BMC Structural Biology
https://www.readbyqxmd.com/read/28515089/the-n-terminus-regulates-voltage-dependent-gating-of-calhm-ion-channels
#17
Jessica E Tanis, Zhongming Ma, J Kevin Foskett
CALHM1 and its C. elegans (ce) homolog, CLHM-1, belong to a new family of physiologically important ion channels that are regulated by voltage and extracellular Ca(2+) (Ca(2+)o), but lack a canonical voltage-sensing domain. Consequently, the intrinsic voltage-dependent gating mechanisms for CALHM channels are unknown. Here, we performed voltage-clamp experiments on ceCLHM-1 chimeric, deletion, insertion and point mutants to assess the role of the N-terminus (NT) in CALHM channel gating. Analyses of chimeric channels in which the ceCLHM-1 and human (h)CALHM1 N-termini were interchanged showed that the hCALHM1 NT destabilized channel-closed states, whereas the ceCLHM-1 NT had a stabilizing effect...
May 17, 2017: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/28514686/glycine-substitution-at-helix-to-coil-transitions-facilitates-the-structural-determination-of-a-stabilized-subtype-c-hiv-envelope-glycoprotein
#18
Javier Guenaga, Fernando Garces, Natalia de Val, Robyn L Stanfield, Viktoriya Dubrovskaya, Brett Higgins, Barbara Carrette, Andrew B Ward, Ian A Wilson, Richard T Wyatt
Advances in HIV-1 envelope glycoprotein (Env) design generate native-like trimers and high-resolution clade A, B, and G structures and elicit neutralizing antibodies. However, a high-resolution clade C structure is critical, as this subtype accounts for the majority of HIV infections worldwide, but well-ordered clade C Env trimers are more challenging to produce due to their instability. Based on targeted glycine substitutions in the Env fusion machinery, we defined a general approach that disfavors helical transitions leading to post-fusion conformations, thereby favoring the pre-fusion state...
May 16, 2017: Immunity
https://www.readbyqxmd.com/read/28513578/crystal-structure-of-a-multi-domain-human-smoothened-receptor-in-complex-with-a-super-stabilizing-ligand
#19
Xianjun Zhang, Fei Zhao, Yiran Wu, Jun Yang, Gye Won Han, Suwen Zhao, Andrii Ishchenko, Lintao Ye, Xi Lin, Kang Ding, Venkatasubramanian Dharmarajan, Patrick R Griffin, Cornelius Gati, Garrett Nelson, Mark S Hunter, Michael A Hanson, Vadim Cherezov, Raymond C Stevens, Wenfu Tan, Houchao Tao, Fei Xu
The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD)...
May 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28512990/luminescence-circular-dichroism-and-in-silico-studies-of-binding-interaction-of-synthesized-naphthylchalcone-derivatives-with-bovine-serum-albumin
#20
Sharda Pasricha, Deepti Sharma, Himanshu Ojha, Pragya Gahlot, Mallika Pathak, Mitra Basu, Raman Chawla, Sugandha Singhal, Anju Singh, Rajeev Goel, Shrikant Kukreti, Shefali Shukla
Chalcones possess various biological properties, for example, antimicrobial, anti-inflammatory, analgesic, antimalarial, anticancer, antiprotozoal and antitubercular activity. In this study, naphthylchalcone derivatives were synthesized and characterized using (1) H NMR (13) C NMR, Fourier transform infrared and mass techniques. Yields for all derivatives were found to be >90%. Protein-drug interactions influence the absorption, distribution, metabolism and excretion (ADME) properties of a drug. Therefore, to establish whether the synthesized naphthylchalcone derivatives can be used as drugs, their binding interaction toward a serum protein (bovine serum albumin) was investigated using fluorescence, circular dichroism and molecular docking techniques under physiological conditions...
May 16, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
keyword
keyword
33594
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"