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Protein design

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https://www.readbyqxmd.com/read/29353262/preterm-human-milk-macronutrient-concentration-is-independent-of-gestational-age-at-birth
#1
Jan Maly, Iva Burianova, Veronika Vitkova, Eva Ticha, Martina Navratilova, Eva Cermakova
OBJECTIVE: To evaluate the amount of macronutrients in aggregate of human milk samples after preterm delivery during the first 2 months of lactation. METHODS: Analysis of the donated single milk samples, gained by complete emptying of the whole breast at the same daytime between 24+0 and 35+6 gestational age (GA), was designed as prospective observational cohort trial. Two milk samples were analysed every postnatal week up to the discharge from the hospital, week 9 or loss of lactation...
January 20, 2018: Archives of Disease in Childhood. Fetal and Neonatal Edition
https://www.readbyqxmd.com/read/29352946/redox-enzyme-sensitive-chondroitin-sulfate-based-self-assembled-nanoparticles-loading-docetaxel-for-the-inhibition-of-metastasis-and-growth-of-melanoma
#2
Mengrui Liu, Hongliang Du, Abdur Rauf Khan, Jianbo Ji, Aihua Yu, Guangxi Zhai
In this report, redox/enzyme responsive chondroitin sulfate-ss-deoxycholic acid (CSCD) conjugates were synthesized using cystamine as the linkage which could self-assemble to form self-assembled nanoparticles (175.6 + 5.2 nm) in the aqueous environment. Docetaxel (DTX) was loaded in nanoparticles with desired loading efficiency for the inhibition of tumor growth and metastasis of melanoma. Interestingly, nanoparticles were demonstrated to respond to hyaluronidase-1 (Hyal-1) which could degrade chondroitin sulfate (CS) backbones...
March 15, 2018: Carbohydrate Polymers
https://www.readbyqxmd.com/read/29352432/effect-of-membrane-composition-on-receptor-association-implications-of-cancer-lipidomics-on-erbb-receptors
#3
REVIEW
Aiswarya B Pawar, Durba Sengupta
The association of single transmembrane receptors, such as the ErbB receptors is a key event in initiating cell signaling networks. The interactions between these receptors have been well characterized for both ligand-driven and pre-formed dimers. However, the role of the membrane in modulating association is less well understood and assumes greater importance in light of altered membrane composition in diseased states. Here, we discuss how membrane composition has been observed to induce both structural and dynamic differences in receptor association...
January 19, 2018: Journal of Membrane Biology
https://www.readbyqxmd.com/read/29352161/the-action-of-a-negative-allosteric-modulator-at-the-dopamine-d2-receptor-is-dependent-upon-sodium-ions
#4
Christopher J Draper-Joyce, Ravi Kumar Verma, Mayako Michino, Jeremy Shonberg, Anitha Kopinathan, Carmen Klein Herenbrink, Peter J Scammells, Ben Capuano, Ara M Abramyan, David M Thal, Jonathan A Javitch, Arthur Christopoulos, Lei Shi, J Robert Lane
Sodium ions (Na+) allosterically modulate the binding of orthosteric agonists and antagonists to many class A G protein-coupled receptors, including the dopamine D2 receptor (D2R). Experimental and computational evidences have revealed that this effect is mediated by the binding of Na+ to a conserved site located beneath the orthosteric binding site (OBS). SB269652 acts as a negative allosteric modulator (NAM) of the D2R that adopts an extended bitopic pose, in which the tetrahydroisoquinoline moiety interacts with the OBS and the indole-2-carboxamide moiety occupies a secondary binding pocket (SBP)...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352125/biomolecular-regulation-composition-and-nanoarchitecture-of-bone-mineral
#5
Atharva A Poundarik, Adele Boskey, Caren Gundberg, Deepak Vashishth
Tough natural nanocomposites like bone, nacre and sea sponges contain within their hierarchy, a mineral (phosphate, silicate or carbonate) phase that interacts with an organic phase. In bone, the role of mineral ultrastructure (organization, morphology, composition) is crucial to the mechanical and biological properties of the tissue. Better understanding of mineral interaction with the organic matrix, in particular non-collagenous proteins, osteocalcin (OC) and osteopontin (OPN), can lead to better design of biomimetic materials...
January 19, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29352085/the-expression-of-bacteriocin-production-and-self-resistance-in-lactobacillus-brevis-174a-is-mediated-by-two-regulatory-proteins
#6
Masafumi Noda, Rumi Miyauchi, Narandalai Danshiitsoodol, Yasuyuki Matoba, Takanori Kumagai, Masanori Sugiyama
We have previously shown that a lactic acid bacterium Lactobacillus (Lb.) brevis 174A isolated from a Citrus iyo fruit produces bacteriocin designated brevicin 174A, which is comprised of two antibacterial polypeptides (designated brevicin 174A-β and 174A-γ). We have also found a gene cluster, composed of eight open reading frames (ORFs), that contains genes for the biosynthesis of brevicin 174A, self-resistance to its own bacteriocin, and two transcriptional regulatory proteins.Some lactic acid bacterial strains have a system to start the production of bacteriocin at an adequate stage of the growth...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29351988/confirmation-of-intersubunit-connectivity-and-topology-of-designed-protein-complexes-by-native-ms
#7
Aniruddha Sahasrabuddhe, Yang Hsia, Florian Busch, William Sheffler, Neil P King, David Baker, Vicki H Wysocki
Computational protein design provides the tools to expand the diversity of protein complexes beyond those found in nature. Understanding the rules that drive proteins to interact with each other enables the design of protein-protein interactions to generate specific protein assemblies. In this work, we designed protein-protein interfaces between dimers and trimers to generate dodecameric protein assemblies with dihedral point group symmetry. We subsequently analyzed the designed protein complexes by native MS...
January 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29351887/synthesis-and-anti-tumor-activity-of-ef24-analogues-as-ikk%C3%AE-inhibitors
#8
Rong Jin, Qiuxiang Chen, Song Yao, Encheng Bai, Weitao Fu, Ledan Wang, Jiabing Wang, Xiaojing Du, Tao Wei, Haineng Xu, Chengxi Jiang, Peihong Qiu, Jianzhang Wu, Wulan Li, Guang Liang
EF24 is an IKKβ inhibitor (IC50: 72 μM) containing various anti-tumor activities. In this study, a series of EF24 analogs targeting IKKβ were designed and synthesized. Several IKKβ inhibitors with better activities than EF24 were screened out and B3 showed best IKKβ inhibitory (IC50: 6.6 μM). Molecular docking and dynamic simulation experiments further confirmed this inhibitory effect. B3 obviously suppressed the viability of Hela229, A549, SGC-7901 and MGC-803 cells. Then, in SGC-7901 and MGC-803 cells, B3 blocked the NF-κB signal pathway by inhibiting IKKβ phosphorylation, and followed arrested the cell cycle at G2/M phase by suppressing the Cyclin B1 and Cdc2 p34 expression, induced the cell apoptosis by down-regulating Bcl-2 protein and up-regulating cleaved-caspase3...
December 7, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29351869/allosteric-kissing-complex-based-electrochemical-biosensor-for-sensitive-regenerative-and-versatile-detection-of-proteins
#9
Mingsha Zhao, Shanshan Zhang, Zhiqiang Chen, Changzhi Zhao, Li Wang, Shufeng Liu
Herein, an allosteric kissing complex-based electrochemical biosensor was ingeniously proposed for the simple, sensitive, regenerative and versatile detection of proteins. Two hairpins (Hp1 and Hp2) were designed and the Hp1 was immobilized on the electrode surface, which could form a kissing complex with Hp2 through the apical loop-loop or kissing interaction of the RNA-RNA base sequences. The Hp2 possesses the appended single-stranded tails on each end, which hybridize with the recognition element-conjugated DNA strands to construct a protein responsive switch of Hp2 scaffold...
January 9, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/29351812/a-hybrid-protein-containing-msp1a-repeats-and-omp7-omp8-and-omp9-epitopes-protect-immunized-balb-c-mice-against-anaplasmosis
#10
Alex Sander R Cangussu, Luis André M Mariúba, Pritesh Lalwani, Keila Dayane E S Pereira, Spartaco Astolphi-Filho, Patricia P Orlandi, Sabrina Epiphanio, Kelvison F Viana, Mucio Flavio B Ribeiro, Hidelberto M Silva, Claudio R F Marinho, Paulo A Nogueira
Anaplasma marginale (A. marginale) has a remarkable impact on livestock production, and an effective vaccine is not currently available due to the inexistence of a small animal model. Recently, BALB/c mice were successfully infected with A. marginale, resulting in an acute and persistent anaplasmosis infection. Here, we designed a hybrid protein containing repeats of polypeptide 1a from major surface protein-1 complex (MSP1a) repeats and common epitopes of outer membrane proteins (OMPs) OMP7, OMP8 and OMP9 expressed in Escherichia coli...
January 19, 2018: Veterinary Research
https://www.readbyqxmd.com/read/29351717/prediction-of-protein-configurational-entropy-popcoen
#11
Martin Goethe, Jan Gleixner, Ignacio Fita, J Miguel Rubi
A knowledge-based method for configurational entropy prediction of proteins is presented which is extremely fast compared to previous approaches because it does not involve any kind of configurational sampling. Instead, the configurational entropy of a query fold is estimated by evaluating an artificial neural network which was trained on molecular-dynamics simulations of about 1000 proteins. The predicted entropy can be incorporated into a large class of protein software based on cost-function minimization/evaluation in which configurational entropy is currently neglected for performance reasons...
January 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29351412/expression-of-ctgf-ccn2-in-response-to-lpa-is-stimulated-by-fibrotic-extracellular-matrix-via-the-integrin-fak-axis
#12
Camilo Riquelme-Guzman, Osvaldo Contreras, Enrique Brandan
Fibrosis is a common feature of several chronic diseases, and is characterized by exacerbated accumulation of extracellular matrix (ECM). Understanding the cellular and molecular mechanisms involved in the development of this condition is crucial for designing efficient treatments for those pathologies. Connective tissue growth factor (CTGF/CCN2) is a pleiotropic protein with strong pro-fibrotic activity. In this report, we present experimental evidence showing that ECM stimulates the synthesis of CTGF in response to lysophosphatidic acid (LPA)...
December 27, 2017: American Journal of Physiology. Cell Physiology
https://www.readbyqxmd.com/read/29351374/fast-dynamic-docking-guided-by-adaptive-electrostatic-bias-the-md-binding-approach
#13
Andrea Spitaleri, Sergio Decherchi, Andrea Cavalli, Walter Rocchia
Engineering chemical entities to modify how pharmaceutical targets function, as it is done in drug design, requires a good understanding of molecular recognition and binding. In this context, the limitations of statically describing bimolecular recognition, as done in docking/scoring, call for insightful and efficient dynamical investigations. On the experimental side, the characterization of dynamical binding processes is still in its infancy. Thus, computer simulations, particularly molecular dynamics (MD), are compelled to play a prominent role, allowing a deeper comprehension of the binding process and its causes and thus a more informed compound selection, making more significant the computational contribution to drug discovery1...
January 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29351266/from-extraction-of-local-structures-of-protein-energy-landscapes-to-improved-decoy-selection-in-template-free-protein-structure-prediction
#14
Nasrin Akhter, Amarda Shehu
Due to the essential role that the three-dimensional conformation of a protein plays in regulating interactions with molecular partners, wet and dry laboratories seek biologically-active conformations of a protein to decode its function. Computational approaches are gaining prominence due to the labor and cost demands of wet laboratory investigations. Template-free methods can now compute thousands of conformations known as decoys, but selecting native conformations from the generated decoys remains challenging...
January 19, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29351230/comparison-of-antioxidative-effects-of-insect-tea-and-its-raw-tea-kuding-tea-polyphenols-in-kunming-mice
#15
Xin Zhao, Jia-Le Song, Ruokun Yi, Guijie Li, Peng Sun, Kun-Young Park, Huayi Suo
Kudingcha is a traditional Chinese tea, and insect tea is a special drink produced by the metabolism of insect larvae using the raw Kuding tea. Insect tea polyphenols (ITP) and its raw tea (Kuding tea) polyphenols (KTP) are high-purity polyphenols extracted by centrifuge precipitation. The present study was designed to compare the antioxidative effects of insect tea polyphenols (ITP) and its raw tea (Kuding tea) polyphenols (KTP) on d-galactose-induced oxidation in Kunming (KM) mice. KM mice were treated with ITP (200 mg/kg) and KTP (200 mg/kg) by gavage, and vitamin C (VC, 200 mg/kg) was also used as a positive control by gavage...
January 19, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29350911/a-programmable-dna-origami-platform-for-organizing-intrinsically-disordered-nucleoporins-within-nanopore-confinement
#16
Patrick D Ellis Fisher, Qi Shen, Bernice Akpinar, Luke K Davis, Kenny Kwok Hin Chung, David Baddeley, Andela Saric, Thomas J Melia, Bart W Hoogenboom, Chenxiang Lin, C Patrick Lusk
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated, but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ~40 nm diameter transport channel contributes to their collective properties and function...
January 19, 2018: ACS Nano
https://www.readbyqxmd.com/read/29350381/macrophage-migration-inhibitory-factor-knockout-attenuates-endotoxin-induced-cardiac-dysfunction-in-mice
#17
Jie Zhang, Xin Zhang, Yuqi Cui, Lianqun Cui, Peng Zhao
BACKGROUND: The accumulated evidence suggests that macrophage migration inhibitory factor (MIF) plays a key role not only in acute and chronic inflammatory diseases but also in cardiovascular disease. The cardiac dysfunction is related to lipopolysaccharide (LPS) in sepsis. AIM: This study was designed to examine whether MIF mediates LPS-induced cardiac dysfunction and address the mechanisms. METHODS: Echocardiography, immunohistochemical analysis, cell shortening/relengthening and intracellular Ca2+ fluorescence evaluation were performed in whole hearts and isolated cardiomyocytes from C57 and MIF knockout mice treated with or without LPS...
January 19, 2018: Kardiologia Polska
https://www.readbyqxmd.com/read/29350052/protective-mechanisms-of-6-gingerol-in-dextran-sulfate-sodium-induced-chronic-ulcerative-colitis-in-mice
#18
B O Ajayi, I A Adedara, E O Farombi
Ulcerative colitis (UC) is a relapsing and remitting inflammatory disease of the colon, with an increasing incidence worldwide. 6-Gingerol (6G) is a bioactive constituent of Zingiber officinale, which has been reported to possess various biological activities. This study was designed to evaluate the role of 6G in chronic UC. Chronic UC was induced in mice by three cycles of 2.5% dextran sulfate sodium (DSS) in drinking water. Each cycle consisted of 7 days of 2.5% DSS followed by 14 days of normal drinking water...
January 1, 2018: Human & Experimental Toxicology
https://www.readbyqxmd.com/read/29349888/distal-amyloid-%C3%AE-protein-fragments-template-amyloid-assembly
#19
Thanh D Do, Smriti Sangwan, Natália E C de Almeida, Alexandre I Ilitchev, Maxwell Giammona, Michael R Sawaya, Steven K Buratto, David S Eisenberg, Michael T Bowers
Amyloid formation is associated with devastating diseases such as Alzheimer's, Parkinson's and Type-2 diabetes. The large amyloid deposits found in patients suffering from these diseases have remained difficult to probe by structural means. Recent NMR models also predict heterotypic interactions from distinct peptide fragments but limited evidence of heterotypic packed sheets is observed in solution. Here we characterize two segments of the protein amyloid β (Aβ) known to form fibrils in Alzheimer's disease patients...
January 19, 2018: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29349513/3d-qsar-study-of-steroidal-and-azaheterocyclic-human-aromatase-inhibitors-using-quantitative-profile-of-protein-ligand-interactions
#20
Sehan Lee, Mace G Barron
Aromatase is a member of the cytochrome P450 superfamily responsible for a key step in the biosynthesis of estrogens. As estrogens are involved in the control of important reproduction-related processes, including sexual differentiation and maturation, aromatase is a potential target for endocrine disrupting chemicals as well as breast cancer therapy. In this work, 3D-QSAR combined with quantitative profile of protein-ligand interactions was employed in the identification and characterization of critical steric and electronic features of aromatase-inhibitor complexes and the estimation of their quantitative contribution to inhibition potency...
January 18, 2018: Journal of Cheminformatics
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