SEQUENCE SLIDER: expanding polyalanine fragments for phasing with multiple side-chain hypotheses

Acta Crystallographica. Section D, Structural Biology
Rafael Junqueira BorgesIsabel Usón

Abstract

Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force a...Continue Reading

References

Nov 5, 1997·Proteins·B L de GrootH J Berendsen
Oct 6, 1999·Current Opinion in Structural Biology·I Usón, G M Sheldrick
Sep 22, 2001·Acta Crystallographica. Section D, Biological Crystallography·R J Read
Sep 22, 2001·Acta Crystallographica. Section D, Biological Crystallography·A PerrakisV S Lamzin
Mar 27, 2003·Acta Crystallographica. Section D, Biological Crystallography·Nicholas M Glykos, Michael Kokkinidis
Dec 4, 2003·Journal of Synchrotron Radiation·Thomas Terwilliger
Mar 3, 2004·Acta Crystallographica. Section D, Biological Crystallography·Laurent C StoroniRandy J Read
Jun 24, 2004·Acta Crystallographica. Section D, Biological Crystallography·Robert SchwarzenbacherLukasz Jaroszewski
Nov 1, 1993·Acta Crystallographica. Section D, Biological Crystallography·V Y Lunin, M M Woolfson
Apr 5, 2005·Acta Crystallographica. Section D, Biological Crystallography·Airlie J McCoyRandy J Read
Apr 29, 2005·Acta Crystallographica. Section D, Biological Crystallography·Rocco CaliandroDritan Siliqi
Jun 28, 2005·Nucleic Acids Research·Johannes SödingAndrei N Lupas
Jul 26, 2005·Acta Crystallographica. Section D, Biological Crystallography·Rocco CaliandroDritan Siliqi
Aug 25, 2006·Acta Crystallographica. Section D, Biological Crystallography·Kevin Cowtan
Sep 21, 2007·Acta Crystallographica. Section D, Biological Crystallography·Isabel UsónGeorge M Sheldrick
Dec 21, 2007·Acta Crystallographica. Section D, Biological Crystallography·Andrey A LebedevGarib N Murshudov
Jun 21, 2008·Acta Crystallographica. Section D, Biological Crystallography·Michael P Robertson, William G Scott
Jul 5, 2008·Nature Protocols·Gerrit LangerAnastassis Perrakis
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Jul 16, 2009·Proteins·Georgii G KrivovRoland L Dunbrack
Aug 18, 2009·Nature Methods·Dayté D RodríguezIsabel Usón
Aug 20, 2009·Acta Crystallographica. Section D, Biological Crystallography·E J Dodson, M M Woolfson
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·George M Sheldrick
Apr 13, 2010·Acta Crystallographica. Section D, Biological Crystallography·P EmsleyK Cowtan
Jun 15, 2010·Methods : a Companion to Methods in Enzymology·Michael P RobertsonWilliam G Scott
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Martyn D WinnKeith S Wilson
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Gábor Bunkóczi, Randy J Read
Apr 5, 2011·Acta Crystallographica. Section D, Biological Crystallography·Garib N MurshudovAlexei A Vagin
Aug 17, 2011·Acta Crystallographica. Section A, Foundations of Crystallography·Maria Cristina BurlaGiampiero Polidori
Apr 17, 2012·Acta Crystallographica. Section D, Biological Crystallography·Dayté RodríguezIsabel Usón
Apr 17, 2012·Acta Crystallographica. Section D, Biological Crystallography·Pavel V AfoninePaul D Adams
Nov 16, 2012·Acta Crystallographica. Section D, Biological Crystallography·Jaclyn BibbyDaniel J Rigden
Feb 7, 2013·Acta Crystallographica. Section D, Biological Crystallography·Randy J ReadAirlie J McCoy
Sep 17, 2013·Nature Methods·Massimo SammitoIsabel Usón
Nov 6, 2013·Acta Crystallographica. Section D, Biological Crystallography·Robert D OeffnerRandy J Read
Nov 6, 2013·Acta Crystallographica. Section D, Biological Crystallography·Andrea Thorn, George M Sheldrick
Jul 1, 2014·The FEBS Journal·Massimo SammitoIsabel Usón
Jul 6, 2014·ACS Chemical Biology·Cecilia Artola-RecolonsJuan A Hermoso
Jul 10, 2014·Acta Crystallographica. Section D, Biological Crystallography·Rocco CaliandroAnnamaria Mazzone
Feb 11, 2015·Acta Crystallographica. Section D, Biological Crystallography·Rojan Shrestha, Kam Y J Zhang
Feb 11, 2015·Acta Crystallographica. Section D, Biological Crystallography·Ronan M KeeganDaniel J Rigden
Mar 10, 2016·Acta Crystallographica. Section D, Structural Biology·Randy J Read, Airlie J McCoy
Jul 31, 2016·The Journal of Biological Chemistry·Deenah OsmanEhmke Pohl
Jun 3, 2017·Methods in Molecular Biology·Airlie J McCoy

❮ Previous
Next ❯

Software Mentioned

ARCIMBOLDO
ACORN
ARP
refine
MOLREP
AMPLE
SHELXE
Phaser
wARP
PolyAla

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.

Related Papers

Acta Crystallographica. Section D, Biological Crystallography
Claudia MillánIsabel Usón
Journal of Applied Crystallography
Airlie J McCoyRandy J Read
Acta Crystallographica. Section D, Structural Biology
Iracema CaballeroIsabel Usón
© 2021 Meta ULC. All rights reserved