Atomic displacement parameters in structural biology

Amino Acids
Oliviero Carugo

Abstract

Atomic displacement parameters (ADPs, also known as B-factors), which depend on structural heterogeneity, provide a wide spectrum of information on protein structure and dynamics and find several applications, from protein conformational disorder prediction to protein thermostabilization, and from protein folding kinetics prediction to protein binding sites prediction. A crucial aspect is the standardization of the ADPs when comparisons between two or more protein crystal structures are made, since ADPs are differently affected by several factors, from crystallographic resolution to refinement protocols. A potential limitation to ADP analysis is the modern tendency to let ADPs to inflate up to extremely large values that have little physico-chemical meaning.

References

May 1, 1985·Biophysical Journal·P Läuger
Feb 5, 1985·Journal of Molecular Biology·M LevittP S Stern
May 1, 1989·Protein Engineering·R RagoneG Colonna
Sep 9, 1986·Biochemistry·J L SmithS Sheriff
Jan 1, 1986·Methods in Enzymology·D Ringe, G A Petsko
Jan 13, 1987·Biochemistry·H FrauenfelderM L Connolly
Aug 1, 1982·Proceedings of the National Academy of Sciences of the United States of America·H HartmannH Frauenfelder
Oct 1, 1980·Biophysical Journal·H Frauenfelder, G A Petsko
Jun 1, 1994·Proteins·M VihinenP Riikonen
Dec 1, 1995·Proteins·J Janin, F Rodier
Apr 1, 1997·Protein Engineering·J Higo, H Umeyama
Oct 23, 1997·Protein Science : a Publication of the Protein Society·O Carugo, P Argos
Nov 5, 1997·Current Opinion in Structural Biology·Z DauterK S Wilson
Jan 7, 1998·Protein Science : a Publication of the Protein Society·S Parthasarathy, M R Murthy
Mar 25, 1999·Acta Crystallographica. Section D, Biological Crystallography·O Carugo, P Argos
Feb 19, 2000·Protein Engineering·S Parthasarathy, M R Murthy
Jun 8, 2001·Proteins·D J JacobsM F Thorpe
Aug 24, 2001·Journal of Molecular Biology·D H Juers, B W Matthews
Jan 31, 2002·Proceedings of the National Academy of Sciences of the United States of America·Bertil Halle
Jul 19, 2002·Biophysical Journal·Sibsankar KunduGeorge N Phillips
Apr 30, 2003·Protein Science : a Publication of the Protein Society·David K SmithGuang Zhu
Oct 22, 2003·Current Opinion in Structural Biology·Elspeth Garman
Nov 8, 2003·Structure·Rune LindingRobert B Russell
Mar 31, 2004·Proceedings of the National Academy of Sciences of the United States of America·Bertil Halle
Jan 13, 2005·Proteins·Zheng YuanRohan D Teasdale
Apr 9, 2005·Trends in Biochemical Sciences·Oliviero Carugo, Kristina Djinović Carugo
Jun 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·D L Stein
Oct 6, 2006·Journal of Molecular Evolution·Sandra MaguidJulián Echave
Aug 8, 2007·Journal of Molecular Biology·Evgeny Krissinel, Kim Henrick
Oct 13, 2007·Proteins·Pascal BenkertDietmar Schomburg
Apr 23, 2008·Bioinformatics·Takashi Ishida, Kengo Kinoshita
Oct 10, 2008·BMC Genomics·Philippe LieutaudSonia Longhi
Feb 26, 2009·Journal of Synchrotron Radiation·James M Holton
Oct 3, 2009·Journal of Applied Crystallography·Matthew Warkentin, Robert E Thorne

❮ Previous
Next ❯

Citations

Jun 12, 2019·Amino Acids·Pierrick CraveurAlexandre G de Brevern
Mar 1, 2019·Scientific Reports·Adam H BarczewskiMaria Pellegrini
Jan 25, 2020·Journal of Structural Biology·Melarkode Vattekatte AkhilaAlexandre G de Brevern
May 12, 2021·Journal of Molecular Biology·Yann Vander MeerscheTatiana Galochkina
Sep 27, 2019·The Journal of Physical Chemistry. B·Haotian Lei, Bruce E Bowler
Sep 19, 2021·Nature Communications·Nicholas M Pearce, Piet Gros
Sep 30, 2021·BMC Bioinformatics·Oliviero Carugo
Jan 5, 2022·Acta Crystallographica. Section D, Structural Biology·Oliviero Carugo

❮ Previous
Next ❯

Methods Mentioned

BETA
X-ray
protein folding

Software Mentioned

MobiDB
DisMeta
REDO
GeneSilico MetaDisorder MD2
DisEMBL
TNT
REFMAC
lite
mathord
MetaPrDOS

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.

© 2022 Meta ULC. All rights reserved