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https://www.readbyqxmd.com/read/28437077/peptide-and-protein-dynamics-and-low-temperature-dnp-magic-angle-spinning-nmr
#1
Qing Zhe Ni, Evgeny Markhasin, Thach V Can, Björn Corzilius, Kong O Tan, Alexander B Barnes, Eugenio Daviso, Yongchao Su, Judith Herzfeld, Robert G Griffin
In DNP MAS NMR experiments at ~80-110 K, the structurally important -13CH3 and -15NH3+ signals in MAS spectra of biological samples disappear due to the interference of the molecular motions with the 1H decoupling. Here we investigate the effect of these dynamic processes on the NMR lineshapes and signal intensities in several typical systems: (1) microcrystalline APG, (2) membrane protein bR, (3) amyloid fibrils PI3-SH3, (4) monomeric alanine-CD3 and (5) the pro-tonated and deuterated dipeptide N-Ac-VL over 78-300 K...
April 24, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28429417/immobilization-methods-for-the-rapid-total-chemical-synthesis-of-proteins-on-microtiter-plates
#2
Robert Zitterbart, Michael Krumrey, Oliver Seitz
The chemical synthesis of proteins typically involves the solid-phase peptide synthesis of unprotected peptide fragments that are stitched together in solution by native chemical ligation (NCL). The process is slow, and throughput is limited because of the need for repeated high performance liquid chromatography purification steps after both solid-phase peptide synthesis and NCL. With an aim to provide faster access to functional proteins and to accelerate the functional analysis of synthetic proteins by parallelization, we developed a method for the high performance liquid chromatography-free synthesis of proteins on the surface of microtiter plates...
April 21, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28429360/effects-of-silencing-annexin-a5-on-proliferation-and-invasion-of-human-cholangiocarcinoma-cell-line
#3
X-M Ding, J-X Li, K Wang, Z-S Wu, A-H Yao, C-Y Jiao, J-J Qian, D-S Bai, X-C Li
OBJECTIVE: We investigated the expression of annexin A5 (ANXA5) in human cholangiocarcinoma (CCA) cell line and its effect on proliferation, migration, and apoptosis of human CCA cells. MATERIALS AND METHODS: Expression of ANXA5 was detected by fluorescent quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and western blotting method in 2 human CCA cell lines, QBC939 and RBE. 3 shRNA plasmids for ANXA5 silencing (ANXA5-sh1, ANXA5-sh2, ANXA5-sh3) and 1 negative control plasmid were constructed to infect QBC939 cells...
April 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28426660/exhaustive-search-of-linear-information-encoding-protein-peptide-recognition
#4
Abdellali Kelil, Benjamin Dubreuil, Emmanuel D Levy, Stephen W Michnick
High-throughput in vitro methods have been extensively applied to identify linear information that encodes peptide recognition. However, these methods are limited in number of peptides, sequence variation, and length of peptides that can be explored, and often produce solutions that are not found in the cell. Despite the large number of methods developed to attempt addressing these issues, the exhaustive search of linear information encoding protein-peptide recognition has been so far physically unfeasible...
April 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28426203/tyrosine-kinase-activation-and-conformational-flexibility-lessons-from-src-family-tyrosine-kinases
#5
Yilin Meng, Matthew P Pond, Benoît Roux
Protein kinases are enzymes that catalyze the covalent transfer of the γ-phosphate of an adenosine triphosphate (ATP) molecule onto a tyrosine, serine, threonine, or histidine residue in the substrate and thus send a chemical signal to networks of downstream proteins. They are important cellular signaling enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Unregulated protein kinase activity is often associated with a wide range of diseases, therefore making protein kinases major therapeutic targets...
April 20, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28414301/striatopallidal-dysfunction-underlies-repetitive-behavior-in-shank3-deficient-model-of-autism
#6
Wenting Wang, Chenchen Li, Qian Chen, Marie-Sophie van der Goes, James Hawrot, Annie Y Yao, Xian Gao, Congyi Lu, Ying Zang, Qiangge Zhang, Katherine Lyman, Dongqing Wang, Baolin Guo, Shengxi Wu, Charles R Gerfen, Zhanyan Fu, Guoping Feng
The postsynaptic scaffolding protein SH3 and multiple ankyrin repeat domains 3 (SHANK3) is critical for the development and function of glutamatergic synapses. Disruption of the SHANK3-encoding gene has been strongly implicated as a monogenic cause of autism, and Shank3 mutant mice show repetitive grooming and social interaction deficits. Although basal ganglia dysfunction has been proposed to underlie repetitive behaviors, few studies have provided direct evidence to support this notion and the exact cellular mechanisms remain largely unknown...
April 17, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28414299/an-indirect-route-to-repetitive-actions
#7
David M Lovinger
It is increasingly evident that there is a genetic contribution to autism spectrum disorders (ASDs) and other neural disorders involving excessive repetition of action sequences. Among the implicated genes in these disorders are those encoding postsynaptic scaffolding proteins with roles in synaptic transmission and plasticity. Several mouse models harboring synonymous mutations have shown alterations in synaptic transmission within the striatum, which has key roles in controlling actions and action sequences...
April 17, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28408625/ets-dependent-transcriptional-upregulation-of-the-transcriptional-co-activator-taz-promotes-cell-migration-and-metastasis-in-prostate-cancer
#8
Chen-Ying Liu, Tong Yu, Yuji Huang, Long Cui, Wanjin Hong
Prostate cancer is a very common malignant disease and a leading cause of death for men in the western world. Tumorigenesis and progression of prostate cancer involves multiple signaling pathways, including Hippo pathway. Yes-associated protein (YAP) is the downstream transcriptional co-activator of Hippo pathway, is overexpressed in the prostate cancer, and plays a vital role in the tumorigenesis and cancer progression of prostate cancer. However, the role of the YAP paralog and another downstream effector of Hippo pathway, transcriptional co-activator with PDZ-binding motif (TAZ), in prostate cancer has not been fully elucidated...
April 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28407117/nnalign-a-platform-to-construct-and-evaluate-artificial-neural-network-models-of-receptor-ligand-interactions
#9
Morten Nielsen, Massimo Andreatta
Peptides are extensively used to characterize functional or (linear) structural aspects of receptor-ligand interactions in biological systems, e.g. SH2, SH3, PDZ peptide-recognition domains, the MHC membrane receptors and enzymes such as kinases and phosphatases. NNAlign is a method for the identification of such linear motifs in biological sequences. The algorithm aligns the amino acid or nucleotide sequences provided as training set, and generates a model of the sequence motif detected in the data. The webserver allows setting up cross-validation experiments to estimate the performance of the model, as well as evaluations on independent data...
April 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28406229/the-role-of-focal-adhesion-anchoring-domains-of-cas-in-mechanotransduction
#10
Jaroslav Braniš, Csilla Pataki, Marina Spörrer, Richard C Gerum, Astrid Mainka, Vladimir Cermak, Wolfgang H Goldmann, Ben Fabry, Jan Brabek, Daniel Rosel
CAS is a docking protein, which was shown to act as a mechanosensor in focal adhesions. The unique assembly of structural domains in CAS is important for its function as a mechanosensor. The tension within focal adhesions is transmitted to a stretchable substrate domain of CAS by focal adhesion-targeting of SH3 and CCH domain of CAS, which anchor the CAS protein in focal adhesions. Mechanistic models of the stretching biosensor propose equal roles for both anchoring domains. Using deletion mutants and domain replacements, we have analyzed the relative importance of the focal adhesion anchoring domains on CAS localization and dynamics in focal adhesions as well as on CAS-mediated mechanotransduction...
April 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28393279/non-equilibrium-hydrogen-exchange-for-determination-of-h-bond-strength-and-water-accessibility-in-solid-proteins
#11
Kristof Grohe, Kumar Tekwani Movellan, Suresh Kumar Vasa, Karin Giller, Stefan Becker, Rasmus Linser
We demonstrate measurement of non-equilibrium backbone amide hydrogen-deuterium exchange rates (HDX) for solid proteins. The target of this study are the slowly exchanging residues in solid samples, which are associated with stable secondary-structural elements of proteins. These hydrogen exchange processes escape methods measuring equilibrium exchange rates of faster processes. The method was applied to a micro-crystalline preparation of the SH3 domain of chicken α-spectrin. Therefore, from a 100% back-exchanged micro-crystalline protein preparation, the supernatant buffer was exchanged by a partially deuterated buffer to reach a final protonation level of approximately 20% before packing the sample in a 1...
April 9, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28391287/identification-of-2-potentially-relevant-gene-mutations-involved-in-strabismus-using-whole-exome-sequencing
#12
Xiangrong Min, Haiying Fan, Guiqiu Zhao, Guixiang Liu
BACKGROUND The etiology of strabismus has a genetic component. Our study aimed to localize the candidate causative gene mutant in a Chinese family with strabismus and to describe its underlying etiology. MATERIAL AND METHODS Genomic DNA was extracted from the affected individual and his parents in a Chinese pedigree with strabismus. The resulting exomes were sequenced by whole-exome sequencing. After variant calling and filtering, the candidate causative gene mutations were selected for the rarity and predicted damaging effect, which complied with the model of recessive disease transmission...
April 9, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28380689/docking-and-molecular-dynamics-simulations-of-the-fyn-sh3-domain-with-free-and-phospholipid-bilayer-associated-18-5-kda-myelin-basic-protein-mbp-insights-into-a-non-canonical-and-fuzzy-interaction
#13
Kyrylo Bessonov, Kenrick A Vassall, George Harauz
The molecular details of the association between the human Fyn-SH3 domain, and the fragment of 18.5-kDa myelin basic protein (MBP) spanning residues S38-S107 (denoted as xα2-peptide, murine sequence numbering), were studied in silico via docking and molecular dynamics over 50-ns trajectories. The results show that interaction between the two proteins is energetically favorable and heavily-dependent on the MBP proline-rich region (P93-P98) in both aqueous and membrane environments. In aqueous conditions, the xα2-peptide/Fyn-SH3 complex adopts a "sandwich"-like structure...
April 5, 2017: Proteins
https://www.readbyqxmd.com/read/28369144/ankrd54-preferentially-selects-bruton-s-tyrosine-kinase-btk-from-a-human-src-homology-3-sh3-domain-library
#14
Manuela O Gustafsson, Dara K Mohammad, Erkko Ylösmäki, Hyunseok Choi, Subhash Shrestha, Qing Wang, Beston F Nore, Kalle Saksela, C I Edvard Smith
Bruton's Tyrosine Kinase (BTK) is a cytoplasmic protein tyrosine kinase with a fundamental role in B-lymphocyte development and activation. The nucleocytoplasmic shuttling of BTK is specifically modulated by the Ankyrin Repeat Domain 54 (ANKRD54) protein and the interaction is known to be exclusively SH3-dependent. To identify the spectrum of the ANKRD54 SH3-interactome, we applied phage-display screening of a library containing all the 296 human SH3 domains. The BTK-SH3 domain was the prime interactor. Quantitative western blotting analysis demonstrated the accuracy of the screening procedure...
2017: PloS One
https://www.readbyqxmd.com/read/28368102/the-molecular-mechanisms-underlying-the-hijack-of-host-proteins-by-the-1918-spanish-influenza-virus
#15
Qingliang Shen, Danyun Zeng, Baoyu Zhao, Veer S Bhatt, Pingwei Li, Jae-Hyun Cho
The 1918 Spanish influenza A virus (IAV) caused one of the most serious pandemics in history. The nonstructural protein 1 (NS1) of the 1918 IAV hijacks the interaction between human CrkII and JNK1. Little is, however, known about its molecular mechanism. Here, we performed X-ray crystallography, NMR relaxation dispersion experiment, and fluorescence spectroscopy to determine the structural, kinetic, and thermodynamic mechanisms underlying the hijacking of CrkII by 1918 IAV NS1. We observed that the interaction between a proline-rich motif in NS1 and the N-terminal SH3 domain of CrkII displays strikingly rapid kinetics and exceptionally high affinity with 100-fold faster kon and 3,300-fold lower Kd compared to those for the CrkII-JNK1 interaction...
April 3, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28366933/a-novel-ahi-1-bcr-abl-dnm2-complex-regulates-leukemic-properties-of-primitive-cml-cells-through-enhanced-cellular-endocytosis-and-ros-mediated-autophagy
#16
X Liu, K Rothe, R Yen, C Fruhstorfer, T Maetzig, M Chen, D L Forrest, K Humphries, X Jiang
Tyrosine kinase inhibitor (TKI) therapies induce clinical remission with remarkable effects on chronic myeloid leukemia (CML). However, very few TKIs completely eradicate the leukemic clone and persistence of leukemic stem cells (LSCs) remains challenging, warranting new, distinct targets for improved treatments. We demonstrated that the scaffold protein AHI-1 is highly deregulated in LSCs and interacts with multiple proteins, including Dynamin-2 (DNM2), to mediate TKI-resistance of LSCs. We have now demonstrated that the SH3 domain of AHI-1 and the proline rich domain of DNM2 are mainly responsible for this interaction...
April 3, 2017: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/28351836/structural-and-biophysical-analyses-of-the-skeletal-dihydropyridine-receptor-beta-subunit-%C3%AE-1a-reveal-critical-roles-of-domain-interactions-for-stability
#17
Nicole C Norris, Soumya Joseph, Shouvik Aditya, Yamuna Karunasekara, Philip G Board, Angela F Dulhunty, Aaron J Oakley, Marco G Casarotto
Excitation-contraction (EC) coupling in skeletal muscle requires a physical interaction between the voltage-gated calcium channel dihydropyridine receptor (DHPR) and the ryanodine receptor (RyR1) Ca2+ release channel. Although the exact molecular mechanism that initiates skeletal EC coupling is unresolved, it is clear that both the α1s and β subunits of DHPR are essential for this process. Here, we employed a series of techniques, including size-exclusion chromatography-multi-angle light scattering, differential scanning fluorimetry and isothermal calorimetry, to characterize various biophysical properties of the skeletal DHPR beta subunit β1a...
March 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28348716/understanding-protein-structure-deformation-on-the-surface-of-gold-nanoparticles-of-varying-size
#18
Karen E Woods, Y Randika Perera, Mackenzie B Davidson, Chloe A Wilks, Dinesh K Yadav, Nicholas C Fitzkee
Gold nanoparticles (AuNPs) have been of recent interest due to their unique optical properties and their biocompatibility. Biomolecules spontaneously adsorb to their surface, a trait that could potentially be exploited for drug targeting. Currently, it is unclear whether protein-AuNP interactions at the nanoparticle surface are dependent on nanoparticle size. In this work, we investigate whether varying surface curvature can induce protein unfolding and multilayer binding in citrate-coated AuNPs of various sizes...
December 15, 2016: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
https://www.readbyqxmd.com/read/28347234/clinical-value-of-mir-145-5p-in-nsclc-and-potential-molecular-mechanism-exploration-a-retrospective-study-based-on-geo-qrt-pcr-and-tcga-data
#19
Ting-Qing Gan, Zu-Cheng Xie, Rui-Xue Tang, Tong-Tong Zhang, Dong-Yao Li, Zu-Yun Li, Gang Chen
MicroRNAs have been reported to be involved in various biological processes. Here, we performed a systematic analysis to explore the clinical value and potential molecular mechanism of miR-145-5p in non-small cell lung cancer. First, a meta-analysis was performed with eligible literature, followed by microRNA microarrays in the Gene Expression Omnibus database, to verify the diagnostic and prognostic values of miR-145-5p. A cohort of 125 clinical paired non-small cell lung cancer samples was next used to detect the level of miR-145-5p and to explore the relationship of miR-145-5p with clinicopathological parameters...
March 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28345935/targeting-self-binding-peptides-as-a-novel-strategy-to-regulate-protein-activity-and-function-a-case-study-on-the-proto-oncogene-tyrosine-protein-kinase-c-src
#20
Zhengya Bai, Shasha Hou, Shilei Zhang, Zhongyan Li, Peng Zhou
Previously, we have reported a new biomolecular phenomenon spanning between protein folding and binding, termed as self-binding peptides (SBPs), where a short peptide segment in monomeric protein functions as a molecular switch by dynamically binding to/unbinding from its cognate domain in the monomer (Yang et al. J. Chem. Inf. MODEL: 2015, 55, 329-342). Here, we attempt to raise the SBP as a new class of druggable targets to regulate the biological activity and function of proteins. A case study was performed on the proto-oncogene nonreceptor tyrosine kinase, c-Src, which contains two SBPs that bind separately to SH3 and SH2 domains of the kinase...
April 24, 2017: Journal of Chemical Information and Modeling
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