Literature DB >> 30712981

Biophysical and Mechanistic Models for Disease-Causing Protein Variants.

Amelie Stein1, Douglas M Fowler2, Rasmus Hartmann-Petersen3, Kresten Lindorff-Larsen4.   

Abstract

The rapid decrease in DNA sequencing cost is revolutionizing medicine and science. In medicine, genome sequencing has revealed millions of missense variants that change protein sequences, yet we only understand the molecular and phenotypic consequences of a small fraction. Within protein science, high-throughput deep mutational scanning experiments enable us to probe thousands of variants in a single, multiplexed experiment. We review efforts that bring together these topics via experimental and computational approaches to determine the consequences of missense variants in proteins. We focus on the role of changes in protein stability as a driver for disease, and how experiments, biophysical models, and computation are providing a framework for understanding and predicting how changes in protein sequence affect cellular protein stability.
Copyright © 2019 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  computational biophysics; deep mutational scanning; genomics; protein quality control; protein stability; variant classification

Mesh:

Substances:

Year:  2019        PMID: 30712981      PMCID: PMC6579676          DOI: 10.1016/j.tibs.2019.01.003

Source DB:  PubMed          Journal:  Trends Biochem Sci        ISSN: 0968-0004            Impact factor:   13.807


  79 in total

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Journal:  Protein Sci       Date:  2005-02-02       Impact factor: 6.725

4.  Identification of direct residue contacts in protein-protein interaction by message passing.

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Journal:  Cell       Date:  2005-03-25       Impact factor: 41.582

6.  Hsp70 stabilizes lysosomes and reverts Niemann-Pick disease-associated lysosomal pathology.

Authors:  Thomas Kirkegaard; Anke G Roth; Nikolaj H T Petersen; Ajay K Mahalka; Ole Dines Olsen; Irina Moilanen; Alicja Zylicz; Jens Knudsen; Konrad Sandhoff; Christoph Arenz; Paavo K J Kinnunen; Jesper Nylandsted; Marja Jäättelä
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7.  Small heat-shock proteins select deltaF508-CFTR for endoplasmic reticulum-associated degradation.

Authors:  Annette Ahner; Kunio Nakatsukasa; Hui Zhang; Raymond A Frizzell; Jeffrey L Brodsky
Journal:  Mol Biol Cell       Date:  2006-12-20       Impact factor: 4.138

8.  The Hsc70 co-chaperone CHIP targets immature CFTR for proteasomal degradation.

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Journal:  Nat Cell Biol       Date:  2001-01       Impact factor: 28.824

9.  Predicted effects of missense mutations on native-state stability account for phenotypic outcome in phenylketonuria, a paradigm of misfolding diseases.

Authors:  Angel L Pey; Francois Stricher; Luis Serrano; Aurora Martinez
Journal:  Am J Hum Genet       Date:  2007-10-02       Impact factor: 11.025

Review 10.  The roles of intracellular protein-degradation pathways in neurodegeneration.

Authors:  David C Rubinsztein
Journal:  Nature       Date:  2006-10-19       Impact factor: 49.962

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  25 in total

1.  Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation.

Authors:  Lene Clausen; Amelie Stein; Martin Grønbæk-Thygesen; Lasse Nygaard; Cecilie L Søltoft; Sofie V Nielsen; Michael Lisby; Tommer Ravid; Kresten Lindorff-Larsen; Rasmus Hartmann-Petersen
Journal:  PLoS Genet       Date:  2020-11-02       Impact factor: 5.917

2.  High-Throughput Reclassification of SCN5A Variants.

Authors:  Andrew M Glazer; Yuko Wada; Bian Li; Ayesha Muhammad; Olivia R Kalash; Matthew J O'Neill; Tiffany Shields; Lynn Hall; Laura Short; Marcia A Blair; Brett M Kroncke; John A Capra; Dan M Roden
Journal:  Am J Hum Genet       Date:  2020-06-12       Impact factor: 11.025

3.  Recent Advances in Machine Learning Variant Effect Prediction Tools for Protein Engineering.

Authors:  Jesse Horne; Diwakar Shukla
Journal:  Ind Eng Chem Res       Date:  2022-04-06       Impact factor: 4.326

4.  Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure.

Authors:  Lukas Gerasimavicius; Benjamin J Livesey; Joseph A Marsh
Journal:  Nat Commun       Date:  2022-07-06       Impact factor: 17.694

Review 5.  How Functional Genomics Can Keep Pace With VUS Identification.

Authors:  Corey L Anderson; Saba Munawar; Louise Reilly; Timothy J Kamp; Craig T January; Brian P Delisle; Lee L Eckhardt
Journal:  Front Cardiovasc Med       Date:  2022-07-04

6.  e-MutPath: computational modeling reveals the functional landscape of genetic mutations rewiring interactome networks.

Authors:  Yongsheng Li; Brandon Burgman; Ishaani S Khatri; Sairahul R Pentaparthi; Zhe Su; Daniel J McGrail; Yang Li; Erxi Wu; S Gail Eckhardt; Nidhi Sahni; S Stephen Yi
Journal:  Nucleic Acids Res       Date:  2021-01-11       Impact factor: 16.971

7.  Multiplexing mutation rate assessment: determining pathogenicity of Msh2 variants in Saccharomyces cerevisiae.

Authors:  Anja R Ollodart; Chiann-Ling C Yeh; Aaron W Miller; Brian H Shirts; Adam S Gordon; Maitreya J Dunham
Journal:  Genetics       Date:  2021-06-24       Impact factor: 4.562

8.  Computational and cellular studies reveal structural destabilization and degradation of MLH1 variants in Lynch syndrome.

Authors:  Amanda B Abildgaard; Amelie Stein; Sofie V Nielsen; Katrine Schultz-Knudsen; Elena Papaleo; Amruta Shrikhande; Eva R Hoffmann; Inge Bernstein; Anne-Marie Gerdes; Masanobu Takahashi; Chikashi Ishioka; Kresten Lindorff-Larsen; Rasmus Hartmann-Petersen
Journal:  Elife       Date:  2019-11-07       Impact factor: 8.140

9.  Genetic Variants in KIR/HLA-C Genes Are Associated With the Susceptibility to HCV Infection in a High-Risk Chinese Population.

Authors:  Chao Shen; Zhijun Ge; Chen Dong; Chunhui Wang; Jianguo Shao; Weihua Cai; Peng Huang; Haozhi Fan; Jun Li; Yun Zhang; Ming Yue
Journal:  Front Immunol       Date:  2021-06-18       Impact factor: 7.561

10.  Probing biophysical sequence constraints within the transmembrane domains of rhodopsin by deep mutational scanning.

Authors:  Wesley D Penn; Andrew G McKee; Charles P Kuntz; Hope Woods; Veronica Nash; Timothy C Gruenhagen; Francis J Roushar; Mahesh Chandak; Chris Hemmerich; Douglas B Rusch; Jens Meiler; Jonathan P Schlebach
Journal:  Sci Adv       Date:  2020-03-04       Impact factor: 14.136

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