Proteomics. 2008 May;8(10):1959-64.

Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits.

Source

Institute for Research in Biomedicine (IRB) and Barcelona Supercomputing Center (BSC), Barcelona, Spain.

Abstract

The last years have seen the emergence of many large-scale proteomics initiatives that have identified thousands of new protein interactions and macromolecular assemblies. However, unfortunately, only a few among the discovered complexes meet the high-quality standards required to be promptly used in structural studies. This has thus created an increasing gap between the number of known protein interactions and complexes and those for which a high-resolution 3-D structure is available. Here, we present and validate a computational strategy to distinguish those complexes found in high-throughput affinity purification experiments that will stand the best chances to successfully express, purify and crystallize with little further intervention. Our method suggests that there are some 50 complexes recently discovered in yeast that could readily enter the structural biology pipelines.

PMID:: 18491310; [PubMed - indexed for MEDLINE]

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, Non-U.S. Gov't

MeSH Terms

Substances

Proteins

LinkOut - more resources

Full Text Sources

Molecular Biology Databases

Saccharomyces Genome Database

Supplemental Content

Save items

Related citations in PubMed

Pushing structural information into the yeast interactome by high-throughput protein docking experiments. [PLoS Comput Biol. 2009]
Pushing structural information into the yeast interactome by high-throughput protein docking experiments.
Mosca R, Pons C, Fernández-Recio J, Aloy P. PLoS Comput Biol. 2009 Aug; 5(8):e1000490. Epub 2009 Aug 28.
Classification of protein complexes based on docking difficulty. [Proteins. 2005]
Classification of protein complexes based on docking difficulty.
Vajda S. Proteins. 2005 Aug 1; 60(2):176-80.
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs. [BMC Bioinformatics. 2006]
PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.
Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan N, et al. BMC Bioinformatics. 2006 Jul 27; 7:365. Epub 2006 Jul 27.
Review Ions of the interactome: the role of MS in the study of protein interactions in proteomics and structural biology. [Proteomics. 2006]
Review Ions of the interactome: the role of MS in the study of protein interactions in proteomics and structural biology.
Downard KM. Proteomics. 2006 Oct; 6(20):5374-84.
Review Genome-wide studies of protein-protein interaction. [Curr Opin Struct Biol. 2003]
Review Genome-wide studies of protein-protein interaction.
Janin J, Séraphin B. Curr Opin Struct Biol. 2003 Jun; 13(3):383-8.

See reviews... See all...

Cited by 2 PubMed Central articles

Computational approaches to selecting and optimising targets for structural biology. [Methods. 2011]
Computational approaches to selecting and optimising targets for structural biology.
Overton IM, Barton GJ. Methods. 2011 Sep; 55(1):3-11. Epub 2011 Aug 27.
Pushing structural information into the yeast interactome by high-throughput protein docking experiments. [PLoS Comput Biol. 2009]
Pushing structural information into the yeast interactome by high-throughput protein docking experiments.
Mosca R, Pons C, Fernández-Recio J, Aloy P. PLoS Comput Biol. 2009 Aug; 5(8):e1000490. Epub 2009 Aug 28.

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Incorporating high-throughput proteomics experiments into structural biology pip...
Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits.
Proteomics. 2008 May ;8(10):1959-64.

PubMed
The K/BxN arthritis model.
The K/BxN arthritis model.
Curr Protoc Immunol. 2008 May ;Chapter 15:Unit 15.22.

PubMed
Cumulative effect of five genetic variants on prostate cancer risk in multiple s...
Cumulative effect of five genetic variants on prostate cancer risk in multiple study populations.
Prostate. 2008 Sep 1 ;68(12):1257-62.

PubMed
[Acute hepatitis B: is antiviral therapy indicated? Two case reports].
[Acute hepatitis B: is antiviral therapy indicated? Two case reports].
Dtsch Med Wochenschr. 2008 May ;133(22):1178-82.

PubMed
Tips for teachers of evidence-based medicine: clinical prediction rules (CPRs) a...
Tips for teachers of evidence-based medicine: clinical prediction rules (CPRs) and estimating pretest probability.
J Gen Intern Med. 2008 Aug ;23(8):1261-8. Epub 2008 May 20 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: