Molecular-replacement phasing using predicted protein structures from AWSEM-Suite

IUCrJ
Shikai JinPeter G. Wolynes

Abstract

The phase problem in X-ray crystallography arises from the fact that only the intensities, and not the phases, of the diffracting electromagnetic waves are measured directly. Molecular replacement can often estimate the relative phases of reflections starting with those derived from a template structure, which is usually a previously solved structure of a similar protein. The key factor in the success of molecular replacement is finding a good template structure. When no good solved template exists, predicted structures based partially on templates can sometimes be used to generate models for molecular replacement, thereby extending the lower bound of structural and sequence similarity required for successful structure determination. Here, the effectiveness is examined of structures predicted by a state-of-the-art prediction algorithm, the Associative memory, Water-mediated, Structure and Energy Model Suite (AWSEM-Suite), which has been shown to perform well in predicting protein structures in CASP13 when there is no significant sequence similarity to a solved protein or only very low sequence similarity to known templates. The performance of AWSEM-Suite structures in molecular replacement is discussed and the results show that...Continue Reading

References

Aug 25, 2006·Acta Crystallographica. Section D, Biological Crystallography·Kevin Cowtan
Dec 21, 2007·Acta Crystallographica. Section D, Biological Crystallography·Andrey A LebedevGarib N Murshudov
Dec 21, 2007·Acta Crystallographica. Section D, Biological Crystallography·Thomas C TerwilligerPaul D Adams
Jan 1, 1997·Methods in Enzymology·G J Kleywegt, T A Jones
Jul 5, 2008·Nature Protocols·Gerrit LangerAnastassis Perrakis
Apr 23, 2009·Biophysical Journal·Da-Wei Li, Rafael Brüschweiler
Aug 1, 2007·Journal of Applied Crystallography·Airlie J McCoyRandy J Read
Mar 4, 2010·Biophysical Journal·Antonija Kuzmanic, Bojan Zagrovic
Nov 7, 2012·Proceedings of the National Academy of Sciences of the United States of America·Weihua ZhengPeter G Wolynes
Nov 16, 2012·Acta Crystallographica. Section D, Biological Crystallography·Jaclyn BibbyDaniel J Rigden
Sep 7, 2013·Proceedings of the National Academy of Sciences of the United States of America·Hetunandan KamisettyDavid Baker
Nov 6, 2013·Acta Crystallographica. Section D, Biological Crystallography·Chantal Abergel
Nov 6, 2013·Acta Crystallographica. Section D, Biological Crystallography·Andrea Thorn, George M Sheldrick
Nov 6, 2013·Acta Crystallographica. Section D, Biological Crystallography·Giovanna Scapin
Oct 14, 2014·Israel Journal of Chemistry·N P SchaferP G Wolynes
Feb 11, 2015·Acta Crystallographica. Section D, Biological Crystallography·Ronan M KeeganDaniel J Rigden
Nov 1, 2016·The Journal of Physical Chemistry. B·Mingchen ChenPeter G Wolynes
Jan 6, 2017·PLoS Computational Biology·Sheng WangJinbo Xu
Nov 5, 2017·Current Opinion in Structural Biology·Diego U FerreiroPeter G Wolynes
Dec 21, 2017·Journal of Molecular Biology·Lukas ZimmermannVikram Alva
Sep 22, 2018·Journal of Chemical Theory and Computation·Mingchen ChenPeter G Wolynes
Apr 20, 2019·Proceedings of the National Academy of Sciences of the United States of America·Xingcheng LinPeter G Wolynes
May 8, 2019·The Journal of Physical Chemistry. B·Justin ChenCecilia Clementi
Aug 1, 2019·Proteins·Randy J ReadTristan I Croll
Aug 11, 2019·Proceedings of the National Academy of Sciences of the United States of America·Jinbo Xu
Aug 14, 2019·Proteins·Tristan I CrollRandy J Read
Oct 8, 2019·Acta Crystallographica. Section D, Structural Biology·Dorothee LiebschnerPaul D Adams
May 13, 2020·Journal of Chemical Theory and Computation·Shikai JinPeter G Wolynes

❮ Previous
Next ❯

Citations

Jul 6, 2021·Journal of Molecular Biology·Gal MasratiJan Kosinski

❮ Previous
Next ❯

Methods Mentioned

BETA
X-ray
NMR

Software Mentioned

RaptorX
MR
Phenix collective
autobuild
PyMOL
TASSER
phenix
wARP
QUARK
DSSP

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.