Structural Dynamics from NMR Relaxation by SRLS Analysis: Local Geometry, Potential Energy Landscapes, and Spectral Densities.

The Journal of Physical Chemistry. B
Netanel Mendelman, Eva Meirovitch

Abstract

We have developed the two-body coupled-rotator slowly relaxing local structure (SRLS) approach for elucidating protein dynamics by nuclear magnetic resonance (NMR) relaxation. The rotators are represented by diffusion tensors D1 for overall protein tumbling and D2 for locally ordered probe motion. D1 and D2 are coupled dynamically by a potential, u, typically given by linear combinations of the Wigner functions D002 and (D022 + D0-22). Until now, our SRLS analyses provided the tensors, D1 and D2, the potential, u, and the geometric link between SRLS and NMR. Here we enhance this description by also examining the SRLS spectral densities obtained by solving the SRLS Smoluchowski equation. In addition, we show that the form of u specified above complies with two NMR-detected potential energy landscapes representing preferential ordering along N-H or Cα-Cα. Pictorial illustrations thereof are provided. The extended SRLS analysis is applied to 15N-H relaxation from the carbohydrate recognition domain of galectin-3 (Gal3C) in complex with two diastereomeric ligands, S and R. We find that D2 is isotropic with a principal value, D2, of 1010 s-1 on average, and it is faster in the strands β3, β5, and β8. The potential, u, is strong (∼20...Continue Reading

References

Jul 18, 2001·Journal of the American Chemical Society·V TugarinovE Meirovitch
Jan 5, 2005·Nature Reviews. Cancer·Fu-Tong Liu, Gabriel A Rabinovich
Feb 16, 2006·Biochimica Et Biophysica Acta·Jerka DumicMirna Flögel
Jul 11, 2006·The Journal of Physical Chemistry. a·Eva MeirovitchJack H Freed
Sep 25, 2009·The Journal of Physical Chemistry. B·Mirco ZerbettoEva Meirovitch
Feb 12, 2010·Annals of the New York Academy of Sciences·Fu-Tong Liu, Gabriel A Rabinovich
Jul 14, 2010·Progress in Nuclear Magnetic Resonance Spectroscopy·Eva MeirovitchJack H Freed
Aug 19, 2011·Biochemistry·Santiago Di LellaGabriel A Rabinovich
Mar 9, 2012·The Journal of Physical Chemistry. B·Yury E Shapiro, Eva Meirovitch
Aug 12, 2014·Expert Opinion on Therapeutic Patents·Helen BlanchardKhuchtumur Bum-Erdene
Feb 24, 2016·Journal of Magnetic Resonance·Arthur G Palmer
Mar 5, 2016·The Journal of Physical Chemistry. B·Oren TchaicheeyanEva Meirovitch
Jun 30, 2016·Chembiochem : a European Journal of Chemical Biology·Tamara DelaineUlf J Nilsson
Sep 1, 2017·Angewandte Chemie·Albert A SmithBeat H Meier
May 3, 2018·Journal of Cell Science·Ludger JohannesHakon Leffler
Jan 9, 2019·Journal of the American Chemical Society·Maria Luisa VerteramoMikael Akke
Aug 28, 2020·Frontiers in Chemistry·Sara BertuzziJesús Jiménez-Barbero
Nov 13, 2020·The International Journal of Biochemistry & Cell Biology·R J SlackA C Mackinnon
Nov 27, 2020·Emerging Topics in Life Sciences·Fa-An Chao, R Andrew Byrd

❮ Previous
Next ❯

Citations

Nov 12, 2021·Frontiers in Molecular Biosciences·Kai Zumpfe, Albert A Smith

❮ 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.