The rate of cis-trans conformation errors is increasing in low-resolution crystal structures

Acta Crystallographica. Section D, Biological Crystallography
Tristan Ian Croll

Abstract

Cis-peptide bonds (with the exception of X-Pro) are exceedingly rare in native protein structures, yet a check for these is not currently included in the standard workflow for some common crystallography packages nor in the automated quality checks that are applied during submission to the Protein Data Bank. This appears to be leading to a growing rate of inclusion of spurious cis-peptide bonds in low-resolution structures both in absolute terms and as a fraction of solved residues. Most concerningly, it is possible for structures to contain very large numbers (>1%) of spurious cis-peptide bonds while still achieving excellent quality reports from MolProbity, leading to concerns that ignoring such errors is allowing software to overfit maps without producing telltale errors in, for example, the Ramachandran plot.

References

Jul 5, 1990·Journal of Molecular Biology·D E StewartJ E Wampler
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jan 9, 2010·Acta Crystallographica. Section D, Biological Crystallography·Vincent B ChenDavid C Richardson
Feb 4, 2010·Acta Crystallographica. Section D, Biological Crystallography·Paul D AdamsPeter H Zwart
Jul 21, 2010·Journal of Molecular Biology·Sarah HelfmannSusana L A Andrade
Jan 5, 2011·Proceedings of the National Academy of Sciences of the United States of America·Shu-Hong HuJennifer L Martin
Jun 4, 2013·Amino Acids·Pierrick CraveurJoseph Rebehmed
Aug 6, 2013·Nature Structural & Molecular Biology·Glen LiszczakRonen Marmorstein
Jun 2, 2014·Nature Structural & Molecular Biology·Ingmar B SchäferElena Conti

❮ Previous
Next ❯

Citations

Aug 8, 2015·Acta Crystallographica. Section D, Biological Crystallography·Wouter G TouwGert Vriend
Mar 14, 2018·Acta Crystallographica. Section D, Structural Biology·Jane S RichardsonDavid C Richardson
Oct 11, 2017·Acta Crystallographica. Section D, Structural Biology·Bradley J HintzeDavid C Richardson
Oct 8, 2019·Acta Crystallographica. Section D, Structural Biology·Dorothee LiebschnerPaul D Adams
Jun 7, 2018·Acta Crystallographica. Section D, Structural Biology·Tristan Ian Croll
Jan 19, 2021·Biophysical Journal·Tristan I CrollJane S Richardson

❮ Previous
Next ❯

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

Journal of Pharmacology & Pharmacotherapeutics
S Parasuraman
Methods of Biochemical Analysis
Methods in Enzymology
John WestbrookHelen M Berman
Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme
Takanori Matsuura, Atsushi Nakagawa
Nursing Standard
R Brooks-Shaverin
© 2021 Meta ULC. All rights reserved