Next Article in Journal
Sensitive and Selective Detection of Oxo-Form Organophosphorus Pesticides Based on CdSe/ZnS Quantum Dots
Next Article in Special Issue
Solution NMR Studies of Mycobacterium tuberculosis Proteins for Antibiotic Target Discovery
Previous Article in Journal
An Overview of LEDs’ Effects on the Production of Bioactive Compounds and Crop Quality
Previous Article in Special Issue
Solution NMR Spectroscopy in Target-Based Drug Discovery
Article Menu
Issue 9 (September) cover image

Export Article

Open AccessArticle
Molecules 2017, 22(9), 1414; doi:10.3390/molecules22091414

Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin

1
College of Pharmaceutical Sciences, Ritsumeikan University, Noji-higashi 1-1-1, Kusatsu 525-8577, Japan
2
Okazaki Institute for Integrative Bioscience and Institute for Molecular Science, National Institutes of Natural Sciences, Myodaiji-cho, Aza-higashiyama 5-1, Okazaki 444-8787, Japan
3
Graduate School of Pharmaceutical Sciences, Nagoya City University, Tanabedouri 3-1, Mizuho-ku, Nagoya 467-8603, Japan
*
Author to whom correspondence should be addressed.
Received: 11 August 2017 / Revised: 20 August 2017 / Accepted: 20 August 2017 / Published: 28 August 2017
(This article belongs to the Special Issue Recent Advances in Biomolecular NMR Spectroscopy)
View Full-Text   |   Download PDF [5778 KB, uploaded 28 August 2017]   |  

Abstract

Rational mutation of proteins based on their structural and dynamic characteristics is a useful strategy for amplifying specific fluctuations in proteins. Here, we show the effects of mutation on the conformational fluctuations and thermodynamic stability of ubiquitin. In particular, we focus on the salt bridge between K11 and E34 and the hydrogen bond between I36 and Q41, which are predicted to control the fluctuation between the basic folded state, N1, and the alternatively folded state, N2, of the protein, using high-pressure NMR spectroscopy. The E34A mutation, which disrupts the salt bridge, did not alter picosecond–to–nanosecond, microsecond–to–millisecond dynamic motions, and stability of the protein, while the Q41N mutation, which destabilizes the hydrogen bond, specifically amplified the N1–N2 conformational fluctuation and decreased stability. Based on the observed thermodynamic stabilities of the various conformational states, we showed that in the Q41N mutant, the N1 state is more significantly destabilized than the N2 state, resulting in an increase in the relative population of N2. Identifying the interactions controlling specific motions of a protein will facilitate molecular design to achieve functional dynamics beyond native state dynamics. View Full-Text
Keywords: alternatively folded state; high-pressure NMR; ubiquitin alternatively folded state; high-pressure NMR; ubiquitin
Figures

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Kitazawa, S.; Yagi-Utsumi, M.; Kato, K.; Kitahara, R. Interactions Controlling the Slow Dynamic Conformational Motions of Ubiquitin. Molecules 2017, 22, 1414.

Show more citation formats Show less citations formats

Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]

Molecules EISSN 1420-3049 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top