Abstract：
:In analysing the red blood cell cytoplasmic proteome, in search for low abundance proteins, 15 amino acid (AA; Arg, Asn, Asp, Gln, Gly, His, Ile, Lys, Phe, Pro, Ser, Thr, Trp, Tyr, and Val) probes, used individually, captured a total of 787 unique gene products. Of those, 76 were found to be the common catch of all AA probes, 497 were captured by more than one (but not all) probe, and 214 were captured by only one probe. By using the InterPro database, for 151 of the 214 IPIs associated with proteins captured by a single amino acid, we have found 265 annotations of motifs (231 protein domains, 3 binding sites, 3 active sites, 13 conserved sites, and 15 repeats). Among these 151 proteins annotated, there are 75 domains, 2 active sites, 5 conserved sites, and 3 repeats (a total of 85 motifs) that are at all effects amino acid strictly specific. As a result of these findings, these 85 amino acid specific motifs singled out 40 (18.69%) of the total list of 214 proteins representing the total capture of the 15 AAs here reported. If one considers that only for 151 (70.56%) of the 214 proteins data about interacting motifs could be collected, the percentage of proteins for which the 85 amino acid strictly specific motifs have been found increases to the even more relevant value of 26.49%. The identified motifs can partially explain the exclusive protein capture of the 15 amino acid probes. The unique general and specific capturing ability of two of these AA probes, Phe and Arg, is evaluated, discussed and put in perspective.
journal_name
J Proteomicsjournal_title
Journal of proteomicsauthors
Masseroli M,Bachi A,Boschetti E,Righetti PGdoi
10.1016/j.jprot.2009.04.001subject
Has Abstractpub_date
2009-07-21 00:00:00pages
791-802issue
5eissn
1874-3919issn
1876-7737pii
S1874-3919(09)00158-4journal_volume
72pub_type
杂志文章abstract：:Leishmaniasis is second most neglected disease after malaria and seems to be a worldwide concern because of increased drug resistance and non-availability of approved vaccine. The underlying molecular mechanism of drug resistance (Amp B) in Leishmania parasites still remains elusive. Herein, the present study investig...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103464
更新日期：2019-09-15 00:00:00
abstract：:A phaC knockout mutant from Bacillus thuringiensis (Bt) strain BMB171, named BMB171/PHB(-1), was constructed. A physiological and metabolic investigation and a proteomic analysis were conducted for both ΔphaC mutant and its parent strain. Grown in peptone medium with 5 gram glucose per liter as sole carbon source, BMB...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.06.002
更新日期：2012-09-18 00:00:00
abstract：UNLABELLED:Escherichia coli is a commensal microorganism of the gastrointestinal tract of animals and humans and it is an excellent model organism for the study of antibiotic resistance mechanisms. The resistance transmission and other characteristics of bacteria are based on different types of gene transfer occurring ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.03.042
更新日期：2016-08-11 00:00:00
abstract：:Increased life expectancy and broader restorative dental treatment alternatives for missing teeth have resulted in an increasing request of bone regeneration/augmentation procedures not only in healthy patients, but also in elderly and medically compromised ones. This is also combined with a growing demand for short i...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2018.01.017
更新日期：2018-09-30 00:00:00
abstract：UNLABELLED:Next generation sequencing and proteomics have helped to comprehensively characterize gene expression in tick salivary glands at both the transcriptome and the proteome level. Functional data are, however, lacking. Given that tick salivary secretions are critical to the success of the tick transmission lifec...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2015.07.005
更新日期：2015-10-14 00:00:00
abstract：:Multiple reaction monitoring (MRM), commonly employed for the mass spectrometric detection of small molecules, is rapidly gaining ground in proteomics. Its high sensitivity and specificity makes this targeted approach particularly useful when sample throughput or proteome coverage limits global studies. Existing tools...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2008.11.015
更新日期：2009-07-21 00:00:00
abstract：UNLABELLED:Inhibition of the essential chaperone Hsp90 with drugs causes a global perturbation of protein folding and the depletion of direct substrates of Hsp90, also called clients. Ubiquitination and proteasomal degradation play a key role in cellular stress responses, but the impact of Hsp90 inhibition on the ubiqu...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.02.020
更新日期：2015-04-29 00:00:00
abstract：UNLABELLED:The methylotrophic yeast Pichia pastoris is an attractive platform for a plethora of recombinant proteins. There is growing evidence that host cells producing recombinant proteins are exposed to a variety of cellular stresses resulting in the induction of the unfolded protein response (UPR) pathway. At prese...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.06.031
更新日期：2013-10-08 00:00:00
abstract：:Lung cancer, COPD and cardiovascular diseases are highlighted as some of the most common disease that cause mortality, and for that reason are the most active areas for drug development. This perspective paper overviews the urgent need to develop a health care system for a rapidly growing patient population in Japan, ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2010.12.006
更新日期：2011-05-16 00:00:00
abstract：:Knowledge of the accurate copy number of HLA class I presented ligands is important in fundamental and clinical immunology. Currently, the best copy number determinations are based on mass spectrometry, employing single reaction monitoring (SRM) in combination with a known amount of isotopically labeled peptide. The m...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.07.009
更新日期：2014-09-23 00:00:00
abstract：:Intrauterine growth restriction (IUGR) is an important cause of perinatal morbidity and mortality and contributes substantially to medically indicated preterm birth; preventing fetal death. Molecular profiling of the mothers' peripheral blood was desired to monitor the health conditions of the fetuses. To develop such...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.04.027
更新日期：2016-10-21 00:00:00
abstract：UNLABELLED:Label-free LC-MS/MS proteomics has proven itself to be a powerful method for evaluating protein identification and quantification from complex samples. For comparative proteomics, several methods have been used to detect the differential expression of proteins from such data. We have assessed seven methods u...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.07.012
更新日期：2015-11-03 00:00:00
abstract：UNLABELLED:The highly conserved molecular chaperones Hsp90 and Hsp70 are indispensible for folding and maturation of a significant fraction of the proteome, including many proteins involved in signal transduction and stress response. To examine the dynamics of chaperone-client interactions after DNA damage, we applied ...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2014.09.028
更新日期：2015-01-01 00:00:00
abstract：:Vav1 is a key molecule in the ATRA-induced acquisition of a mature phenotype by tumoral myeloid precursors. Since ATRA acts throughout events that require extensive changes of nuclear architecture and activity and considering that Vav1 accumulates inside the nuclear compartment of differentiating APL-derived cells, th...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.08.005
更新日期：2011-12-21 00:00:00
abstract：UNLABELLED:Despite the noxious effects inflicted by Dinoponera ant's envenomation, the information about the biological properties and composition of their venom is still very limited. Ants from the genus Dinoponera are believed to be the world's largest living ants with a body length of 3cm. Their occurrence is restri...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2013.10.017
更新日期：2013-12-06 00:00:00
abstract：:Structural mass spectrometry with its various techniques is a powerful tool for the structural elucidation of medically relevant protein assemblies. It delivers information on the composition, stoichiometries, interactions and topologies of these assemblies. Most importantly it can deal with heterogeneous mixtures and...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2017.04.019
更新日期：2018-03-20 00:00:00
abstract：:The development of type 2 diabetes (T2D) is strongly associated with obesity. In humans, T2D increases the risk for end organ complications. Among these, heart disease has been ranked as the leading cause of death. We used a proteomic methodology to test the hypothesis that a pre-diabetic state generated by high-fat d...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2011.02.018
更新日期：2011-05-01 00:00:00
abstract：:Atrazine (ATZ), the second most commonly used herbicide in the United States, is an endocrine disrupting chemical linked to cancer and a common drinking water contaminant. This study further investigates ATZ-related developmental toxicity by testing the following hypotheses in zebrafish: the effects of embryonic ATZ e...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2018.07.006
更新日期：2018-08-30 00:00:00
abstract：:The aim of the present study was to evaluate the differences in salivary proteome at rest and in response to an acute exercise in men and women. For this, unstimulated whole saliva samples in rest and after a bout resistance exercise leading to failure (ELF) of both men and women (n = 5 for each sex) were subjected to...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2019.103629
更新日期：2020-03-01 00:00:00
abstract：:For relative protein quantitation by mass spectrometry we metabolically labeled E. coli bacteria with (15)N-enriched diets. Proteins extracted from (15)N-labeled and unlabeled E. coli bacteria were mixed, separated by two-dimensional gel electrophoresis and enzymatically digested. The resulting tryptic peptides were a...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2008.10.004
更新日期：2009-01-30 00:00:00
abstract：UNLABELLED:Pluripotent stem cell-derived committed neural precursors are an important source of cells to treat neurodegenerative diseases including spinal cord injury. There remains an urgency to identify markers for monitoring of neural progenitor specificity, estimation of neural fate and follow-up correlation with t...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2015.11.008
更新日期：2016-01-30 00:00:00
abstract：UNLABELLED:Despite being ischemic stroke a leading cause of death and functional disability, there are no other accurate tools to predict outcome of patients beyond clinical variables such as age and stroke severity. In this scenario, defining protein changes associated with acute ischemic brain damage might help to id...
journal_title：Journal of proteomics
pub_type： 临床试验,杂志文章
doi：10.1016/j.jprot.2013.09.005
更新日期：2013-12-06 00:00:00
abstract：:There is a wide range of pathological conditions proved to be associated with inflammation. The inflammatory process offers protection against harmful stimuli such as induced cell injury and tissues damage by means of specialized mediators and cells. Alarmins, also known as endogenous danger signals or damage-associat...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2016.11.006
更新日期：2017-02-05 00:00:00
abstract：:Neuropeptides are critical signaling molecules, involved in the regulation of diverse physiological processes including energy metabolism, pain perception and brain cognitive state. Prolonged general anesthesia has an impact on many of these processes, but the regulation of peptides by general anesthetics is poorly un...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2012.11.002
更新日期：2013-03-27 00:00:00
abstract：UNLABELLED:The need for biomarkers that illuminate the pathophysiology of type 1 diabetes (T1D), enhance early diagnosis and provide additional avenues for therapeutic intervention is well recognized in the scientific community. We conducted a proteome-scale, two-stage serological AAb screening followed by an independe...
journal_title：Journal of proteomics
pub_type： 杂志文章,多中心研究,随机对照试验
doi：10.1016/j.jprot.2013.10.018
更新日期：2013-12-06 00:00:00
abstract：:Ubiquitylation is an elaborate post-translational modification involved in all biological processes. Its pleotropic effect is driven by the ability to form complex polyubiquitin chain architectures that can influence biological functions. In this study, we optimised sample preparation and chromatographic separation of...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2020.103963
更新日期：2020-10-30 00:00:00
abstract：:Dufour's gland is associated with the venom apparatuses of social wasps and bees. This location and its evolutionary adaptations indicate that it could be involved in the production of alarm pheromones in the social wasp Polybia paulista. To investigate this hypothesis, the volatile composition of this gland was analy...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.01.009
更新日期：2017-01-16 00:00:00
abstract：:The application of proteomics to respiratory diseases, such as asthma and COPD, has been limited compared to other fields, like cancer. Both asthma and COPD are recognised to be multi-factorial and complex diseases, both consisting of clusters of multiple disease phenotypes. The complexity of these diseases combined w...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2011.10.008
更新日期：2011-12-10 00:00:00
abstract：:Top-down proteomics (TDP) has great potential for high throughput proteoform characterization. With significant advances in mass spectrometry (MS) instrumentation permitting tandem MS of large intact proteins, a limitation to the widespread adoption of TDP still resides on front-end sample preparation protocols (e.g. ...
journal_title：Journal of proteomics
pub_type： 杂志文章,评审
doi：10.1016/j.jprot.2017.03.002
更新日期：2018-03-20 00:00:00
abstract：UNLABELLED:Phyllomedusine frogs are an extraordinary source of biologically active peptides. At least 8 families of antimicrobial peptides have been reported in this frog clade, the dermaseptins being the most diverse. By a peptidomic approach, integrating molecular cloning, Edman degradation sequencing and tandem mass...
journal_title：Journal of proteomics
pub_type： 杂志文章
doi：10.1016/j.jprot.2016.06.017
更新日期：2016-09-02 00:00:00
