SAMPLEX: automatic mapping of perturbed and unperturbed regions of proteins and complexes.

BMC Bioinformatics
Mickaël KrzeminskiAlexandre M J J Bonvin

Abstract

The activity of proteins within the cell is characterized by their motions, flexibility, interactions or even the particularly intriguing case of partially unfolded states. In the last two cases, a part of the protein is affected either by binding or unfolding and the detection of the respective perturbed and unperturbed region(s) is a fundamental part of the structural characterization of these states. This can be achieved by comparing experimental data of the same protein in two different states (bound/unbound, folded/unfolded). For instance, measurements of chemical shift perturbations (CSPs) from NMR 1H-15N HSQC experiments gives an excellent opportunity to discriminate both moieties. We describe an innovative, automatic and unbiased method to distinguish perturbed and unperturbed regions in a protein existing in two distinct states (folded/partially unfolded, bound/unbound). The SAMPLEX program takes as input a set of data and the corresponding three-dimensional structure and returns the confidence for each residue to be in a perturbed or unperturbed state. Its performance is demonstrated for different applications including the prediction of disordered regions in partially unfolded proteins and of interacting regions in p...Continue Reading

References

Sep 13, 1994·Proceedings of the National Academy of Sciences of the United States of America·M ScheffnerP M Howley
Dec 1, 1996·Nature Structural Biology·B T FarmerL Mueller
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·J L PellequerE D Getzoff
Mar 19, 1999·Antonie van Leeuwenhoek·K J HellingwerfC Avignone-Rossa
Dec 28, 1999·Journal of Biomolecular NMR·S B WhittakerG R Moore
Jan 19, 2000·Nucleic Acids Research·T K AlbertH T Timmers
May 4, 2000·Protein Science : a Publication of the Protein Society·S B WhittakerG R Moore
Feb 17, 2001·Current Opinion in Structural Biology·C E Bell, M Lewis
Jul 27, 2002·Proceedings of the National Academy of Sciences of the United States of America·Evette S Radisky, Daniel E Koshland
Feb 13, 2003·Journal of the American Chemical Society·Cyril DominguezAlexandre M J J Bonvin
Dec 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Engin OzkanJohann Deisenhofer
Jun 5, 2007·Journal of Molecular Biology·Robert DaberMitchell Lewis
Sep 7, 2007·Proteins·Sjoerd J de VriesAlexandre M J J Bonvin
Oct 24, 2007·Journal of Biomolecular NMR·Frank H SchumannHans Robert Kalbitzer
Nov 7, 2007·Nucleic Acids Research·Eldon L UlrichJohn L Markley

❮ Previous
Next ❯

Citations

Apr 10, 2013·Journal of Biomolecular NMR·Karine LothRolf Boelens
Aug 22, 2013·Progress in Nuclear Magnetic Resonance Spectroscopy·Mike P Williamson
Oct 25, 2012·The Journal of Biological Chemistry·Jesper S OeemigReinhard Wimmer
Jan 20, 2012·Journal of Pediatric Hematology/oncology·Yunyan HeJianming Luo
Nov 17, 2010·The FEBS Journal·Françoise PaquetGérard Lancelot
Jul 12, 2011·Proteins·Dirk StratmannAlexandre M J J Bonvin
Sep 2, 2014·Progress in Biophysics and Molecular Biology·David M Dias, Alessio Ciulli
Aug 5, 2016·Molecular Informatics·Mattia SturleseStefano Moro
Mar 25, 2014·Journal of Magnetic Resonance·Hugo van Ingen, Alexandre M J J Bonvin
Oct 15, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Abdul-Hamid EmwasMariusz Jaremko

❮ Previous
Next ❯

Methods Mentioned

BETA
NMR
X-ray
ubiquitination
chemical shift

Software Mentioned

SAMPLEX ( Mapping Extremes )
SAMPLEX
HADDOCK

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.