Literature DB >> 26707199

Deciphering Complexity in Molecular Biophysics with Single-Molecule Resolution.

Ashok A Deniz1.   

Abstract

The structural features and dynamics of biological macromolecules underlie the molecular biology and correct functioning of cells. However, heterogeneity and other complexity of these molecules and their interactions often lead to loss of important information in traditional biophysical experiments. Single-molecule methods have dramatically altered the conceptual thinking and experimental tests available for such studies, leveraging their ability to avoid ensemble averaging. Here, I discuss briefly the rise of fluorescence single-molecule methods over the past two decades, a few key applications, and end with a view to challenges and future prospects.
Copyright © 2015 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  IDPs; conformational dynamics studies; proteins; single-molecule fluorescence; smFRET

Mesh:

Substances:

Year:  2015        PMID: 26707199      PMCID: PMC4744532          DOI: 10.1016/j.jmb.2015.12.011

Source DB:  PubMed          Journal:  J Mol Biol        ISSN: 0022-2836            Impact factor:   5.469


  58 in total

1.  Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Förster distance dependence and subpopulations.

Authors:  A A Deniz; M Dahan; J R Grunwell; T Ha; A E Faulhaber; D S Chemla; S Weiss; P G Schultz
Journal:  Proc Natl Acad Sci U S A       Date:  1999-03-30       Impact factor: 11.205

2.  Stepwise protein-mediated RNA folding directs assembly of telomerase ribonucleoprotein.

Authors:  Michael D Stone; Mariana Mihalusova; Catherine M O'connor; Ramadevi Prathapam; Kathleen Collins; Xiaowei Zhuang
Journal:  Nature       Date:  2007-02-25       Impact factor: 49.962

3.  From sequence and forces to structure, function, and evolution of intrinsically disordered proteins.

Authors:  Julie D Forman-Kay; Tanja Mittag
Journal:  Structure       Date:  2013-09-03       Impact factor: 5.006

Review 4.  A practical guide to single-molecule FRET.

Authors:  Rahul Roy; Sungchul Hohng; Taekjip Ha
Journal:  Nat Methods       Date:  2008-06       Impact factor: 28.547

Review 5.  Ultra-stable organic fluorophores for single-molecule research.

Authors:  Qinsi Zheng; Manuel F Juette; Steffen Jockusch; Michael R Wasserman; Zhou Zhou; Roger B Altman; Scott C Blanchard
Journal:  Chem Soc Rev       Date:  2014-02-21       Impact factor: 54.564

6.  Single-molecule fluorescence experiments determine protein folding transition path times.

Authors:  Hoi Sung Chung; Kevin McHale; John M Louis; William A Eaton
Journal:  Science       Date:  2012-02-24       Impact factor: 47.728

7.  Single-molecule lysozyme dynamics monitored by an electronic circuit.

Authors:  Yongki Choi; Issa S Moody; Patrick C Sims; Steven R Hunt; Brad L Corso; Israel Perez; Gregory A Weiss; Philip G Collins
Journal:  Science       Date:  2012-01-20       Impact factor: 47.728

8.  Continuous throughput and long-term observation of single-molecule FRET without immobilization.

Authors:  Swati Tyagi; Virginia VanDelinder; Niccolò Banterle; Gustavo Fuertes; Sigrid Milles; Morgane Agez; Edward A Lemke
Journal:  Nat Methods       Date:  2014-01-19       Impact factor: 28.547

9.  Interplay of alpha-synuclein binding and conformational switching probed by single-molecule fluorescence.

Authors:  Allan Chris M Ferreon; Yann Gambin; Edward A Lemke; Ashok A Deniz
Journal:  Proc Natl Acad Sci U S A       Date:  2009-03-17       Impact factor: 11.205

10.  Probing cellular protein complexes using single-molecule pull-down.

Authors:  Ankur Jain; Ruijie Liu; Biswarathan Ramani; Edwin Arauz; Yuji Ishitsuka; Kaushik Ragunathan; Jeehae Park; Jie Chen; Yang K Xiang; Taekjip Ha
Journal:  Nature       Date:  2011-05-26       Impact factor: 49.962

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  4 in total

1.  Ubiquitin S65 phosphorylation engenders a pH-sensitive conformational switch.

Authors:  Xu Dong; Zhou Gong; Yun-Bi Lu; Kan Liu; Ling-Yun Qin; Meng-Lin Ran; Chang-Li Zhang; Zhu Liu; Wei-Ping Zhang; Chun Tang
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-13       Impact factor: 11.205

Review 2.  FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices.

Authors:  Eitan Lerner; Anders Barth; Jelle Hendrix; Benjamin Ambrose; Victoria Birkedal; Scott C Blanchard; Richard Börner; Hoi Sung Chung; Thorben Cordes; Timothy D Craggs; Ashok A Deniz; Jiajie Diao; Jingyi Fei; Ruben L Gonzalez; Irina V Gopich; Taekjip Ha; Christian A Hanke; Gilad Haran; Nikos S Hatzakis; Sungchul Hohng; Seok-Cheol Hong; Thorsten Hugel; Antonino Ingargiola; Chirlmin Joo; Achillefs N Kapanidis; Harold D Kim; Ted Laurence; Nam Ki Lee; Tae-Hee Lee; Edward A Lemke; Emmanuel Margeat; Jens Michaelis; Xavier Michalet; Sua Myong; Daniel Nettels; Thomas-Otavio Peulen; Evelyn Ploetz; Yair Razvag; Nicole C Robb; Benjamin Schuler; Hamid Soleimaninejad; Chun Tang; Reza Vafabakhsh; Don C Lamb; Claus Am Seidel; Shimon Weiss
Journal:  Elife       Date:  2021-03-29       Impact factor: 8.140

Review 3.  Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes.

Authors:  Cibran Perez-Gonzalez; Daniel A Lafontaine; J Carlos Penedo
Journal:  Front Chem       Date:  2016-08-03       Impact factor: 5.221

4.  SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes.

Authors:  Chuankai Zhao; Diwakar Shukla
Journal:  Sci Rep       Date:  2018-12-10       Impact factor: 4.379

  4 in total

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