On the relationship between NMR-derived amide order parameters and protein backbone entropy changes

Proteins
Kim A SharpA Joshua Wand

Abstract

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements.

References

Dec 1, 1987·Biophysical Journal·M KarplusB M Pettitt
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Dec 1, 1996·Protein Science : a Publication of the Protein Society·Z LiA J Wand
Nov 23, 2000·Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics·H Matsuda
Aug 1, 2002·Proceedings of the National Academy of Sciences of the United States of America·Hengbin Luo, Kim Sharp
Nov 13, 2002·Biochemistry·Andrew L LeeA Joshua Wand
Jun 24, 2004·Journal of the American Chemical Society·Robert B BestMartin Karplus
Jun 24, 2004·Journal of Biomolecular NMR·Dengming Ming, Rafael Brüschweiler
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Jan 16, 2007·Biophysical Journal·Xiang-jin SongA Joshua Wand
Jul 20, 2007·Nature·Kendra King FrederickA Joshua Wand
Jul 21, 2007·The Journal of Chemical Physics·Benjamin J KillianMichael K Gilson
Dec 25, 2008·Journal of the American Chemical Society·Nikola TrbovicArthur G Palmer
May 16, 2009·Journal of Computational Chemistry·B R BrooksM Karplus
Sep 29, 2009·Journal of the American Chemical Society·Da-Wei LiRafael Brüschweiler
Apr 13, 2010·Nature Chemical Biology·Michael S MarlowA Joshua Wand
Nov 17, 2010·The Journal of Physical Chemistry. B·Da-Wei LiRafael Brüschweiler
Jan 11, 2012·The Journal of Physical Chemistry. B·Bracken M KingBruce Tidor
Mar 29, 2012·Journal of the American Chemical Society·Yinan FuA Joshua Wand
Jul 18, 2012·Nature·Shiou-Ru Tzeng, Charalampos G Kalodimos
Sep 7, 2013·Journal of the American Chemical Society·Vignesh KasinathA Joshua Wand
Apr 8, 2014·The Journal of Physical Chemistry. B·Andrew T FenleyMichael K Gilson
Oct 15, 2014·Proceedings of the National Academy of Sciences of the United States of America·Michael C BaxaTobin R Sosnick

❮ Previous
Next ❯

Citations

Feb 24, 2016·Journal of Magnetic Resonance·Arthur G Palmer
Apr 26, 2016·Chemical Reviews·Stephen Boulton, Giuseppe Melacini
Mar 19, 2016·Protein Science : a Publication of the Protein Society·Evan S O'BrienKim A Sharp
Oct 28, 2015·PLoS Computational Biology·Daniel A KeedyHenry van den Bedem
Dec 9, 2016·Physical Chemistry Chemical Physics : PCCP·Antonello MerlinoGiuseppe Graziano
Apr 5, 2017·The Journal of Physical Chemistry. B·Clare-Louise TowseValerie Daggett
Mar 22, 2018·Physical Chemistry Chemical Physics : PCCP·Tomohiko HayashiMasahiro Kinoshita
Oct 27, 2017·Biopolymers·Andrea Pica, Giuseppe Graziano
Jan 19, 2018·Annual Review of Biophysics·A Joshua Wand, Kim A Sharp
Sep 19, 2018·Physical Chemistry Chemical Physics : PCCP·Falk HoffmannFrans A A Mulder
Nov 10, 2018·Nature Reviews. Drug Discovery·Ichio ShimadaKurt Wüthrich
Jul 10, 2020·Physical Chemistry Chemical Physics : PCCP·Giuseppe Graziano
Jun 7, 2017·Proceedings of the National Academy of Sciences of the United States of America·José A CaroA Joshua Wand
Sep 20, 2017·The Journal of Biological Chemistry·Jun ZhaoBuyong Ma
Jun 21, 2018·Biophysical Journal·Justin A Drake, B Montgomery Pettitt
May 26, 2018·Journal of Chemical Theory and Computation·Markus FleckBojan Zagrovic
May 1, 2020·The Journal of Physical Chemistry. B·Justin A Drake, B Montgomery Pettitt
Mar 13, 2019·The Journal of Physical Chemistry. B·Ida NyqvistJakob Dogan
Sep 15, 2017·The Journal of Physical Chemistry Letters·Ferruccio PalazzesiMichele Parrinello
Nov 10, 2018·The Journal of Physical Chemistry. B·Yulian GavrilovYaakov Levy
Dec 23, 2021·The Journal of Physical Chemistry. B·Falk HoffmannLars V Schäfer
Dec 24, 2021·The Journal of Physical Chemistry. B·Priti RoyNeelanjana Sengupta

❮ 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.