Literature DB >> 33243857

Protein storytelling through physics.

Emiliano Brini1, Carlos Simmerling1,2, Ken Dill3,2,4.   

Abstract

Every protein has a story-how it folds, what it binds, its biological actions, and how it misbehaves in aging or disease. Stories are often inferred from a protein's shape (i.e., its structure). But increasingly, stories are told using computational molecular physics (CMP). CMP is rooted in the principled physics of driving forces and reveals granular detail of conformational populations in space and time. Recent advances are accessing longer time scales, larger actions, and blind testing, enabling more of biology's stories to be told in the language of atomistic physics.
Copyright © 2020, American Association for the Advancement of Science.

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Year:  2020        PMID: 33243857     DOI: 10.1126/science.aaz3041

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  15 in total

Review 1.  Computational Studies of Lipid Droplets.

Authors:  Siyoung Kim; Jessica M J Swanson; Gregory A Voth
Journal:  J Phys Chem B       Date:  2022-03-09       Impact factor: 2.991

2.  Biomolecular modeling thrives in the age of technology.

Authors:  Tamar Schlick; Stephanie Portillo-Ledesma
Journal:  Nat Comput Sci       Date:  2021-05-20

Review 3.  The Proteome Folding Problem and Cellular Proteostasis.

Authors:  Evan T Powers; Lila M Gierasch
Journal:  J Mol Biol       Date:  2021-08-13       Impact factor: 6.151

4.  Dissecting the stability determinants of a challenging de novo protein fold using massively parallel design and experimentation.

Authors:  Tae-Eun Kim; Kotaro Tsuboyama; Scott Houliston; Cydney M Martell; Claire M Phoumyvong; Alexander Lemak; Hugh K Haddox; Cheryl H Arrowsmith; Gabriel J Rocklin
Journal:  Proc Natl Acad Sci U S A       Date:  2022-10-03       Impact factor: 12.779

5.  Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis.

Authors:  Siyoung Kim; Gregory A Voth
Journal:  J Phys Chem B       Date:  2021-06-17       Impact factor: 2.991

Review 6.  Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.

Authors:  Phuong H Nguyen; Ayyalusamy Ramamoorthy; Bikash R Sahoo; Jie Zheng; Peter Faller; John E Straub; Laura Dominguez; Joan-Emma Shea; Nikolay V Dokholyan; Alfonso De Simone; Buyong Ma; Ruth Nussinov; Saeed Najafi; Son Tung Ngo; Antoine Loquet; Mara Chiricotto; Pritam Ganguly; James McCarty; Mai Suan Li; Carol Hall; Yiming Wang; Yifat Miller; Simone Melchionna; Birgit Habenstein; Stepan Timr; Jiaxing Chen; Brianna Hnath; Birgit Strodel; Rakez Kayed; Sylvain Lesné; Guanghong Wei; Fabio Sterpone; Andrew J Doig; Philippe Derreumaux
Journal:  Chem Rev       Date:  2021-02-05       Impact factor: 60.622

7.  An empirical energy landscape reveals mechanism of proteasome in polypeptide translocation.

Authors:  Rui Fang; Jason Hon; Mengying Zhou; Ying Lu
Journal:  Elife       Date:  2022-01-20       Impact factor: 8.140

Review 8.  The Protein Folding Problem: The Role of Theory.

Authors:  Roy Nassar; Gregory L Dignon; Rostam M Razban; Ken A Dill
Journal:  J Mol Biol       Date:  2021-07-03       Impact factor: 6.151

9.  A synergy between the catalytic and structural Zn(II) ions and the enzyme and substrate dynamics underlies the structure-function relationships of matrix metalloproteinase collagenolysis.

Authors:  Ann Varghese; Shobhit S Chaturvedi; Gregg B Fields; Tatyana G Karabencheva-Christova
Journal:  J Biol Inorg Chem       Date:  2021-07-06       Impact factor: 3.862

10.  Highly accurate protein structure prediction with AlphaFold.

Authors:  John Jumper; Richard Evans; Alexander Pritzel; Tim Green; Michael Figurnov; Olaf Ronneberger; Kathryn Tunyasuvunakool; Russ Bates; Augustin Žídek; Anna Potapenko; Alex Bridgland; Clemens Meyer; Simon A A Kohl; Andrew J Ballard; Andrew Cowie; Bernardino Romera-Paredes; Stanislav Nikolov; Rishub Jain; Demis Hassabis; Jonas Adler; Trevor Back; Stig Petersen; David Reiman; Ellen Clancy; Michal Zielinski; Martin Steinegger; Michalina Pacholska; Tamas Berghammer; Sebastian Bodenstein; David Silver; Oriol Vinyals; Andrew W Senior; Koray Kavukcuoglu; Pushmeet Kohli
Journal:  Nature       Date:  2021-07-15       Impact factor: 49.962

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