Literature DB >> 27771543

Protein folding, binding, and droplet formation in cell-like conditions.

Sanbo Qin1, Huan-Xiang Zhou2.   

Abstract

The many bystander macromolecules in the crowded cellular environments present both steric repulsion and weak attraction to proteins undergoing folding or binding and hence impact the thermodynamic and kinetic properties of these processes. The weak but nonrandom binding with bystander macromolecules may facilitate subcellular localization and biological function. Weak binding also leads to the emergence of a protein-rich droplet phase, which has been implicated in regulating a variety of cellular functions. All these important problems can now be addressed by realistic modeling of intermolecular interactions. Configurational sampling of concentrated protein solutions is an ongoing challenge.
Copyright © 2016 Elsevier Ltd. All rights reserved.

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Year:  2016        PMID: 27771543      PMCID: PMC5397379          DOI: 10.1016/j.sbi.2016.10.006

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  107 in total

1.  Binary-liquid phase separation of lens protein solutions.

Authors:  M L Broide; C R Berland; J Pande; O O Ogun; G B Benedek
Journal:  Proc Natl Acad Sci U S A       Date:  1991-07-01       Impact factor: 11.205

2.  Quinary structure modulates protein stability in cells.

Authors:  William B Monteith; Rachel D Cohen; Austin E Smith; Emilio Guzman-Cisneros; Gary J Pielak
Journal:  Proc Natl Acad Sci U S A       Date:  2015-01-26       Impact factor: 11.205

3.  Effects of macromolecular crowding on the collapse of biopolymers.

Authors:  Hongsuk Kang; Philip A Pincus; Changbong Hyeon; D Thirumalai
Journal:  Phys Rev Lett       Date:  2015-02-13       Impact factor: 9.161

4.  Unexpected effects of macromolecular crowding on protein stability.

Authors:  Laura A Benton; Austin E Smith; Gregory B Young; Gary J Pielak
Journal:  Biochemistry       Date:  2012-11-27       Impact factor: 3.162

5.  Exploring weak, transient protein--protein interactions in crowded in vivo environments by in-cell nuclear magnetic resonance spectroscopy.

Authors:  Qinghua Wang; Anastasia Zhuravleva; Lila M Gierasch
Journal:  Biochemistry       Date:  2011-10-05       Impact factor: 3.162

6.  Peptide folding in the presence of interacting protein crowders.

Authors:  Anna Bille; Sandipan Mohanty; Anders Irbäck
Journal:  J Chem Phys       Date:  2016-05-07       Impact factor: 3.488

7.  15N NMR spin relaxation dispersion study of the molecular crowding effects on protein folding under native conditions.

Authors:  Xuanjun Ai; Zheng Zhou; Yawen Bai; Wing-Yiu Choy
Journal:  J Am Chem Soc       Date:  2006-03-29       Impact factor: 15.419

8.  In-cell NMR characterization of the secondary structure populations of a disordered conformation of α-synuclein within E. coli cells.

Authors:  Christopher A Waudby; Carlo Camilloni; Anthony W P Fitzpatrick; Lisa D Cabrita; Christopher M Dobson; Michele Vendruscolo; John Christodoulou
Journal:  PLoS One       Date:  2013-08-26       Impact factor: 3.240

9.  ALS/FTD Mutation-Induced Phase Transition of FUS Liquid Droplets and Reversible Hydrogels into Irreversible Hydrogels Impairs RNP Granule Function.

Authors:  Tetsuro Murakami; Seema Qamar; Julie Qiaojin Lin; Gabriele S Kaminski Schierle; Eric Rees; Akinori Miyashita; Ana R Costa; Roger B Dodd; Fiona T S Chan; Claire H Michel; Deborah Kronenberg-Versteeg; Yi Li; Seung-Pil Yang; Yosuke Wakutani; William Meadows; Rodylyn Rose Ferry; Liang Dong; Gian Gaetano Tartaglia; Giorgio Favrin; Wen-Lang Lin; Dennis W Dickson; Mei Zhen; David Ron; Gerold Schmitt-Ulms; Paul E Fraser; Neil A Shneider; Christine Holt; Michele Vendruscolo; Clemens F Kaminski; Peter St George-Hyslop
Journal:  Neuron       Date:  2015-10-29       Impact factor: 17.173

Review 10.  Formation of protein complexes in crowded environments--from in vitro to in vivo.

Authors:  Yael Phillip; Gideon Schreiber
Journal:  FEBS Lett       Date:  2013-01-18       Impact factor: 4.124

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  16 in total

Review 1.  Whole-Cell Models and Simulations in Molecular Detail.

Authors:  Michael Feig; Yuji Sugita
Journal:  Annu Rev Cell Dev Biol       Date:  2019-07-12       Impact factor: 13.827

2.  Fatty Acids Compete with Aβ in Binding to Serum Albumin by Quenching Its Conformational Flexibility.

Authors:  Cong Guo; Huan-Xiang Zhou
Journal:  Biophys J       Date:  2018-12-06       Impact factor: 4.033

3.  Intrinsically Disordered Protein Exhibits Both Compaction and Expansion under Macromolecular Crowding.

Authors:  Anthony Banks; Sanbo Qin; Kevin L Weiss; Christopher B Stanley; Huan-Xiang Zhou
Journal:  Biophys J       Date:  2018-03-13       Impact factor: 4.033

Review 4.  Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation.

Authors:  Huan-Xiang Zhou; Xiaodong Pang
Journal:  Chem Rev       Date:  2018-01-10       Impact factor: 60.622

Review 5.  Computational approaches to macromolecular interactions in the cell.

Authors:  Ilya A Vakser; Eric J Deeds
Journal:  Curr Opin Struct Biol       Date:  2019-04-15       Impact factor: 6.809

6.  Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.

Authors:  Sanbo Qin; Huan-Xiang Zhou
Journal:  J Phys Chem B       Date:  2019-09-19       Impact factor: 2.991

7.  In-cell destabilization of a homodimeric protein complex detected by DEER spectroscopy.

Authors:  Yin Yang; Shen-Na Chen; Feng Yang; Xia-Yan Li; Akiva Feintuch; Xun-Cheng Su; Daniella Goldfarb
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-11       Impact factor: 11.205

Review 8.  Why Do Disordered and Structured Proteins Behave Differently in Phase Separation?

Authors:  Huan-Xiang Zhou; Valery Nguemaha; Konstantinos Mazarakos; Sanbo Qin
Journal:  Trends Biochem Sci       Date:  2018-04-30       Impact factor: 13.807

9.  Charge-driven condensation of RNA and proteins suggests broad role of phase separation in cytoplasmic environments.

Authors:  Bercem Dutagaci; Grzegorz Nawrocki; Joyce Goodluck; Ali Akbar Ashkarran; Charles G Hoogstraten; Lisa J Lapidus; Michael Feig
Journal:  Elife       Date:  2021-01-26       Impact factor: 8.140

10.  Preferential Interactions of a Crowder Protein with the Specific Binding Site of a Native Protein Complex.

Authors:  Xu Dong; Ling-Yun Qin; Zhou Gong; Sanbo Qin; Huan-Xiang Zhou; Chun Tang
Journal:  J Phys Chem Lett       Date:  2022-01-19       Impact factor: 6.475

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