Abstract：
:NMR ligand affinity screening is a powerful technique that is routinely used in drug discovery or functional genomics to directly detect protein-ligand binding events. Binding events can be identified by monitoring differences in the 1D (1)H NMR spectrum of a compound with and without protein. Although a single NMR spectrum can be collected within a short period (2-10 min per sample), one-by-one screening of a protein against a library of hundreds or thousands of compounds requires a large amount of spectrometer time and a large quantity of protein. Therefore, compounds are usually evaluated in mixtures ranging in size from 3 to 20 compounds to improve the efficiency of these screens in both time and material. Ideally, the NMR signals from individual compounds in the mixture should not overlap so that spectral changes can be associated with a particular compound. We have developed a software tool, NMRmix, to assist in creating ideal mixtures from a large panel of compounds with known chemical shifts. Input to NMRmix consists of an (1)H NMR peak list for each compound, a user-defined overlap threshold, and additional user-defined parameters if default settings are not used. NMRmix utilizes a simulated annealing algorithm to optimize the composition of the mixtures to minimize spectral peak overlaps so that each compound in the mixture is represented by a maximum number of nonoverlapping chemical shifts. A built-in graphical user interface simplifies data import and visual evaluation of the results.
journal_name
J Proteome Resjournal_title
Journal of proteome researchauthors
Stark JL,Eghbalnia HR,Lee W,Westler WM,Markley JLdoi
10.1021/acs.jproteome.6b00121subject
Has Abstractpub_date
2016-04-01 00:00:00pages
1360-8issue
4eissn
1535-3893issn
1535-3907journal_volume
15pub_type
杂志文章abstract：:Colon cancer is the most common cancer and the third leading cause of cancer mortality in humans. Using mass spectrometry-based metabolomics, the current study revealed the accumulation of four uremic toxins (cresol sulfate, cresol glucuronide, indoxyl sulfate, and phenyl sulfate) in the serum of mice harboring adenom...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5013152
更新日期：2015-04-03 00:00:00
abstract：:Preeclampsia is a pregnancy-specific hypertensive syndrome and a major cause of maternal and fetal morbidity and mortality. At the present time, no reliable screening tests to identify women at risk are available. We have compared the amniotic fluids (AF) proteomic maps of five preeclamptic patients with those of five...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060315z
更新日期：2007-01-01 00:00:00
abstract：:Two-dimensional differential gel electrophoresis (2-D DIGE) was used to analyze human serum following the removal of albumin and five other high-abundant serum proteins. After protein removal, serum was analyzed by SDS-PAGE as a preliminary screen, and significant differences between four high-abundant protein removal...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr049921p
更新日期：2004-11-01 00:00:00
abstract：:Untargeted GC-TOF-MS analysis proved to be a suitable analytical platform to determine alterations in the metabolic profile. Several metabolic pathways were found to be altered in a first clinical study comparing smokers against nonsmokers. Subsequently, we conducted a clinical diet-controlled study to investigate alt...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00128
更新日期：2017-10-06 00:00:00
abstract：:Starting in 2007, we have grown soybean (Glycine max [L.] Merr. variety Soniachna) and flax (Linum usitatissimum, L. variety Kyivskyi) in the radio-contaminated Chernobyl area and analyzed the seed proteomes. In the second-generation flax seeds, we detected a 12% increase in oil content. To characterize the bases for ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr400528m
更新日期：2013-11-01 00:00:00
abstract：:Russell and colleagues deserve credit for being the first to use a QconCAT standard to simultaneously quantify both the wild-type and mutant peptides of a protein (i.e., CYP2B6) ( J. Proteome Res. 2013, 12 (12), 5934-5942. DOI: 10.1021/pr400279u). However, the rationale of their study was entirely different from ours ...
journal_title：Journal of proteome research
pub_type： 评论,杂志文章
doi：10.1021/acs.jproteome.8b00940
更新日期：2019-03-01 00:00:00
abstract：:Hundreds of ribosomally synthesized cyclopeptides have been isolated from all domains of life, the vast majority having been reported in the last 15 years. Studies of cyclic peptides have highlighted their exceptional potential both as stable drug scaffolds and as biomedicines in their own right. Despite this, computa...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200323a
更新日期：2011-10-07 00:00:00
abstract：:Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00873
更新日期：2017-02-03 00:00:00
abstract：:The use of matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) to acquire spectral profiles has become a common approach to detect proteomic biomarkers of disease. MALDI-MS signals may represent both intact proteins as well as proteolysis products. Liquid chromatography-tandem mass spectrometry (L...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050138m
更新日期：2005-09-01 00:00:00
abstract：:Fast (120 s) and high-throughput (more than six samples at once) in-gel trypsin digestion of proteins using sonoreactor technology has been achieved. Successful protein identification was done by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, MALDI-TOF-MS. Specific identification of the ...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060508m
更新日期：2007-02-01 00:00:00
abstract：:The energy-dissipating alternative oxidase (AOX) from Hansenula anomala was expressed in Saccharomyces cerevisiae. The recombinant AOX was functional. A comparative analysis by two-dimensional differential in-gel electrophoresis (2D-DIGE) of mitochondrial protein patterns found in wild-type and recombinant AOX strains...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr050346e
更新日期：2006-02-01 00:00:00
abstract：:The two key steps for analyzing proteomic data generated by high-resolution MS are database searching and postprocessing. While the two steps are interrelated, studies on their combinatory effects and the optimization of these procedures have not been adequately conducted. Here, we investigated the performance of thre...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b00536
更新日期：2015-11-06 00:00:00
abstract：:Activation of AMP-activated protein kinase (AMPK) upon energy depletion stimulates energy production and limits energy utilization. Erythrocytes lacking AMPK are susceptible to suicidal cell death (eryptosis). A hallmark of eryptosis is cell membrane scrambling with phosphatidylserine exposure at the erythrocyte surfa...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr101004j
更新日期：2011-04-01 00:00:00
abstract：:The intake of 3,4-methylenedioxymethamphetamine (MDMA) is known to increase several endogenous substances involved in steroid and inflammation pathways. Untargeted metabolomics screening approaches can determine biochemical changes after drug exposure and can reveal new pathways, which might be involved in the pharmac...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.8b00438
更新日期：2018-08-03 00:00:00
abstract：:Mammary tumors are a major health threat to women and female dogs. In both, metastasis of the primary tumor to distant organs is the most common cause of tumor-related death. Nevertheless, the molecular mechanisms of tumor metastasis are far from being understood, and it is still unknown why some human and canine carc...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr100671c
更新日期：2010-12-03 00:00:00
abstract：:A rate-limiting and costly step in many proteomics analyses is the cloning of all of the ORFs for an organism into technique-specific vectors. Here, we describe the generation of a Campylobacter jejuni expression clone set using a high-throughput cloning approach based on recombination in E. coli. The approach uses na...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr0341134
更新日期：2004-05-01 00:00:00
abstract：:Hepatocellular carcinoma (HCC) causes more than half a million annual deaths worldwide. Understanding the mechanisms contributing to HCC development is highly desirable for improved surveillance, diagnosis, and treatment. Liver tissue metabolomics has the potential to reflect the physiological changes behind HCC devel...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00185
更新日期：2019-08-02 00:00:00
abstract：:Nicotinamide adenine dinucleotide (NAD) is a coenzyme found in all living cells and mediates multiple cellular signaling pathways. In the present study, a 35% decrease of cellular NAD level is achieved by stable expression of the N-terminal truncated CD38, a NAD hydrolase. CD38-expressing (CD38(+)) cells have the lowe...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr4010597
更新日期：2014-02-07 00:00:00
abstract：:The field of computational proteomics is approaching the big data age, driven both by a continuous growth in the number of samples analyzed per experiment as well as by the growing amount of data obtained in each analytical run. In order to process these large amounts of data, it is increasingly necessary to use elast...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00328
更新日期：2020-01-03 00:00:00
abstract：:Beta-thalassemia results from mutations of the β-hemoglobin (Hbb) gene and reduced functional Hbb synthesis. Excess α-Hb causes globin chain aggregation, oxidation, cytoskeletal damage, and increased red blood cell clearance. These events result in anemia, altered iron homeostasis, and expansion of extramedullary eryt...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr5010778
更新日期：2015-02-06 00:00:00
abstract：:Kalirin-7 (Kal7), a multifunctional Rho GDP/GTP exchange factor (GEF) for Rac1 and RhoG, is embedded in the postsynaptic density at excitatory synapses, where it participates in the formation and maintenance of dendritic spines. Kal7 has been implicated in long-term potentiation, fear memories, and addiction-like beha...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr200088w
更新日期：2011-06-03 00:00:00
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journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00028
更新日期：2017-04-07 00:00:00
abstract：:Cytokinin hormones are crucial regulators of a large number of processes in plant development. Recently, significant progress has been made toward the elucidation of the molecular details of cytokinin that has led to a model for signal transduction involving a phosphorylation cascade. However, the current knowledge of...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr060152e
更新日期：2006-09-01 00:00:00
abstract：:Cellular functions are largely carried out by noncovalent protein complexes that may exist within the cell as stable modules or as assemblies of dynamically changing composition, whose formation and decomposition are triggered in response to extracellular stimuli. The protein constituents of complexes often exhibit po...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr1003888
更新日期：2010-10-01 00:00:00
abstract：:Chinese hamster ovary cells (CHO) are the most common cell line used in the production of therapeutic proteins. Understanding the complex pattern of secreted host cell proteins (HCP) that are released by CHO cells will facilitate the development of new recombinant protein production processes. In this study, we have a...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr300810f
更新日期：2012-12-07 00:00:00
abstract：:Yellow fever virus (YFV) replication is highly dependent on host cell factors. YFV NS4B is reported to be involved in viral replication and immune evasion. Here interactions between NS4B and human proteins were determined using a GST pull-down assay and analyzed using 1-DE and LC-MS/MS. We present a total of 207 prote...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.6b00933
更新日期：2017-04-07 00:00:00
abstract：:Cannabinoid 2 receptor (CB2R), a Class-A G-protein coupled receptor (GPCR), is a promising drug target under a wide array of pathological conditions. Rational drug design has been hindered due to our poor understanding of the structural features involved in ligand binding. Binding of a high-affinity biarylpyrazole inv...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.7b00023
更新日期：2017-07-07 00:00:00
abstract：:Transcription regulation translates static genome information to dynamic cell behaviors, making it central to understand how cells interact with and adapt to their environment. However, only a limited number of transcription regulators and their target genes have been identified in the pathogen Mycobacterium tubercul...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/pr3006233
更新日期：2012-09-07 00:00:00
abstract：:Geobacter sulfurreducens is a dissimilatory metal-reducing bacterium capable of forming thick electron-conducting biofilms on solid electrodes. Here, we employ for the first time comparative proteomics to identify key physiological changes involved in G. sulfurreducens adaptation from fumarate-respiring planktonic cel...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.5b01019
更新日期：2016-01-01 00:00:00
abstract：:Protein citrullination (or deimination), an irreversible post-translational modification, has been implicated in several physiological and pathological processes, including gene expression regulation, apoptosis, rheumatoid arthritis, and Alzheimer's disease. Several research studies have been carried out on citrullina...
journal_title：Journal of proteome research
pub_type： 杂志文章
doi：10.1021/acs.jproteome.9b00118
更新日期：2019-05-03 00:00:00
