Plasma Proteome Database as a resource for proteomics research

Muthusamy, Babylakshmi; Hanumanthu, G.; Suresh, Shubha; Rekha, B.; Srinivas, D.; Lakshmanan, Karthick; Vrushabendra, B. M.; Sharma, Salil; Mishra, Goparani; Chatterjee, Pritam; Mangala, K. S.; Shivashankar, H N; Chandrika, K N; Deshpande, Nandan P.; Suresh, M.; Nandakumar, Kutty Selva; Niranjan, Vidya; Nalli, Anuradha; Prasad, T. S. Keshava; Arun, Kumar S.; Reddy, Raghunath; Chandran, Sreenath; Jadhav, Trafina; Julie, Ducreux; Mahesh, M. K.; John, Sally; Palvankar, Kshitish; Sudhir, D.; Bała, Piotr; Rashmi, N. S.; Vishnupriya, G.; Dhar, Kaushik; Reshma, S.; Chaerkady, Raghothama; Gandhi, Tejas; Harsha, H. C.; Mohan, S. Sujatha; Deshpande, K. S.; Sarker, Malabika; Pandey, Akhilesh

doi:10.1002/pmic.200401335

Cited by 136 publications

(126 citation statements)

References 23 publications

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“…Furthermore, the degree of the structural perturbation that proteins undergo in response to their interaction with particular nanoparticles varies across protein species. The complete plasma proteome is composed of approximately 3700 different proteins and about 50 of these have been shown to associate with nanoparticles (6,7). Therefore, there are concerns regarding the safety of nanoparticles and whether modifications that biological materials undergo upon their interaction with nanoparticles may alter their intended function (8).…”

Section: Introductionmentioning

confidence: 99%

Cysteine‐capped gold nanoparticles suppress aggregation of proteins exposed to heat stress

et al. 2013

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Gold nanoparticles show a lot of promise as potential agents for drug delivery and disease diagnosis. Because of this, it is important that the interaction between gold nanoparticles and biomolecules be well characterized to avoid undesirable consequences. In this study, gold nanoparticles were synthesized by the reduction of gold salt by sodium borohydride in the presence of cysteine as the capping agent. The physical features of the nanoparticles were analyzed using Ultraviolet-Visible spectrophotometry and transmission electron microscopy. The interaction between gold nanoparticles and the following proteins: bovine serum albumin, citrate synthase, malate dehydrogenase, and human heat shock protein 70 was investigated by UV-Vis spectrophotometry. The stability of the proteins against heat stress was assessed by monitoring their aggregation at 48 8C, either in the presence or absence of gold nanoparticles. The gold nanoparticles were capable of suppressing the heat-induced aggregation of the proteins. Furthermore, apart from possessing independent protein-aggregation suppression function, the AuNPs also augmented the chaperone function of human heat shock protein 70. Findings from this study demonstrate that cyteinecoated gold nanoparticles exhibit chaperone-like activity and have the capability to stabilize proteins to which they may be conjugated. V C 2013 IUBMB Life, 65(5): 454-461, 2013.

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Section: Introductionmentioning

confidence: 99%

Cysteine‐capped gold nanoparticles suppress aggregation of proteins exposed to heat stress

et al. 2013

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“…Plasma is a complex fluid that contains Ͼ3,700 different proteins, and the relative amounts of the proteins vary over the population (27) and also in the same individual over the day. In addition, there is a large sequence variation among individuals (28).…”

Section: Gel Filtration Reveals Preferential Binding Of Specific Plasmentioning

confidence: 99%

Understanding the nanoparticle–protein corona using methods to quantify exchange rates and affinities of proteins for nanoparticles

Cedervall¹,

Lynch²,

Lindman

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

2,710

2,532

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Due to their small size, nanoparticles have distinct properties compared with the bulk form of the same materials. These properties are rapidly revolutionizing many areas of medicine and technology. Despite the remarkable speed of development of nanoscience, relatively little is known about the interaction of nanoscale objects with living systems. In a biological fluid, proteins associate with nanoparticles, and the amount and presentation of the proteins on the surface of the particles leads to an in vivo response. Proteins compete for the nanoparticle ''surface,'' leading to a protein ''corona'' that largely defines the biological identity of the particle. Thus, knowledge of rates, affinities, and stoichiometries of protein association with, and dissociation from, nanoparticles is important for understanding the nature of the particle surface seen by the functional machinery of cells. Here we develop approaches to study these parameters and apply them to plasma and simple model systems, albumin and fibrinogen. A series of copolymer nanoparticles are used with variation of size and composition (hydrophobicity). We show that isothermal titration calorimetry is suitable for studying the affinity and stoichiometry of protein binding to nanoparticles. We determine the rates of protein association and dissociation using surface plasmon resonance technology with nanoparticles that are thiol-linked to gold, and through size exclusion chromatography of protein-nanoparticle mixtures. This method is less perturbing than centrifugation, and is developed into a systematic methodology to isolate nanoparticle-associated proteins. The kinetic and equilibrium binding properties depend on protein identity as well as particle surface characteristics and size.

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“…Putative PTMs were noted for 254, including 85 with phosphorylation and 45 with glycosylation sites. A separate analysis of nearly twice as many proteins based on EnsEMBL matches using the Human Protein Reference Database (www.hprd.org; Muthusamy et al, [58]) found 628 with a signal sequence, 405 with transmembrane domains, 153 with a total of 1169 phosphorylation events, and 112 with a total of 555 glycolysation events.…”

Section: Annotation Of the Hupo Ppp Core Dataset(s)mentioning

confidence: 99%

“…Muthusamy et al [58] utilized a Java 2 Platform literature search tool to facilitate manual curation of functional classes of proteins, starting with the PPP set of 3020 IPI proteins (2446 genes). They subjected protein and nucleotide sequences in NCBI to BLAST queries to identify splice isoforms; they report that 51% of the genes encoded more than one protein isoform (a total of 4932 products).…”

Section: Annotation Of the Hupo Ppp Core Dataset(s)mentioning

confidence: 99%

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly‐available database

et al. 2005

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HUPO initiated the Plasma Proteome Project (PPP) in 2002. Its pilot phase has (1) evaluated advantages and limitations of many depletion, fractionation, and MS technology platforms; (2) compared PPP reference specimens of human serum and EDTA, heparin, and citrate-anticoagulated plasma; and (3) created a publicly-available knowledge base (www.bioinformatics.med.umich.edu/hupo/ppp; www.ebi.ac.uk/pride). Thirty-five participating laboratories in 13 countries submitted datasets. Working groups addressed (a) specimen stability and protein concentrations; (b) protein identifications from 18 MS/MS datasets; (c) independent analyses from raw MS-MS spectra; (d) search engine performance, subproteome analyses, and biological insights; (e) antibody arrays; and (f) direct MS/SELDI analyses. MS-MS datasets had 15 710 different International Protein Index (IPI) protein IDs; our integration algorithm applied to multi- We recommend use of plasma instead of serum, with EDTA (or citrate) for anticoagulation. To improve resolution, sensitivity and reproducibility of peptide identifications and protein matches, we recommend combinations of depletion, fractionation, and MS/MS technologies, with explicit criteria for evaluation of spectra, use of search algorithms, and integration of homologous protein matches.This Special Issue of PROTEOMICS presents papers integral to the collaborative analysis plus many reports of supplementary work on various aspects of the PPP workplan. These PPP results on complexity, dynamic range, incomplete sampling, false-positive matches, and integration of diverse datasets for plasma and serum proteins lay a foundation for development and validation of circulating protein biomarkers in health and disease.

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Plasma Proteome Database as a resource for proteomics research

Cited by 136 publications

References 23 publications

Cysteine‐capped gold nanoparticles suppress aggregation of proteins exposed to heat stress

Cysteine‐capped gold nanoparticles suppress aggregation of proteins exposed to heat stress

Understanding the nanoparticle–protein corona using methods to quantify exchange rates and affinities of proteins for nanoparticles

Overview of the HUPO Plasma Proteome Project: Results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly‐available database

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