Article
Multidisciplinary Sciences
Gil Koren, Sagi Meir, Lennard Holschuh, Haydyn D. T. Mertens, Tamara Ehm, Nadav Yahalom, Adina Golombek, Tal Schwartz, Dmitri I. Svergun, Omar A. Saleh, Joachim Dzubiella, Roy Beck
Summary: Short-range interactions and long-range contacts drive the folding of proteins. The structure of proteins directly affects their biological function. Nearly 40% of eukaryotes proteome is composed of intrinsically disordered proteins (IDPs) and protein regions that fluctuate between ensembles of numerous conformations. Polymer physics can, to some level, relate the IDP's sequence to its ensemble conformations, but long-range contacts between distant amino acids play a crucial role in determining intramolecular structures.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Nanoscience & Nanotechnology
T. Ehm, H. Shinar, S. Meir, A. Sekhon, V Sethi, I. L. Morgan, G. Rahamim, O. A. Saleh, R. Beck
Summary: This article reviews the abundance of intrinsically disordered proteins in the human proteome and their role in biological functions. Recent evidence strongly suggests that this structural plasticity contributes to multiple biological functions.
Article
Biochemistry & Molecular Biology
Ellen Rieloff, Marie Skepo
Summary: Phosphorylation is a common post-translational modification in intrinsically disordered proteins, and computer simulations are useful tools to study its effects. In this study, CHARMM36m consistently produced more compact conformations with a higher content of bends in phosphorylated peptides compared to Amber ff99SB-ILDN+TIP4P-D. Despite a reduction in salt-bridging probability, changes in ionic strength had negligible effects on the conformational ensembles.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Physical
Florencia Klein, Exequiel E. Barrera, Sergio Pantano
Summary: The CG SIRAH force field shows a good ability to describe the dynamical behavior of IDPs and unstructured peptides, and it can effectively capture the effect of point mutations in loosely structured peptides.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Biochemistry & Molecular Biology
Ellen Rieloff, Marie Skepo
Summary: Phosphorylation plays a crucial role in regulating the function of intrinsically disordered proteins, with the distribution of phosphorylated and positively charged residues throughout the sequence impacting the formation of salt bridges. Understanding the structural implications of phosphorylation remains a challenge, as factors beyond net charge, such as specific residue interactions, can influence the global dimensions of disordered proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Meili Liu, Akshaya K. Das, James Lincoff, Sukanya Sasmal, Sara Y. Cheng, Robert M. Vernon, Julie D. Forman-Kay, Teresa Head-Gordon
Summary: This study explores the connection between protein force fields and configurational entropy, proposing a new direction for understanding protein force field development. The research finds that force fields with the largest statistical fluctuations better describe IDPs and IDRs, as well as disorder-to-order transitions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Chemistry, Medicinal
Junxi Mu, Hao Liu, Jian Zhang, Ray Luo, Hai-Feng Chen
Summary: Intrinsically disordered proteins (IDPs) play crucial roles in biological processes and are associated with various diseases. Molecular dynamics simulation is a valuable tool for quantifying IDP structures, but faces limitations. Recent force field strategies aim to improve accuracy, but further advancements are needed.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Surl-Hee Ahn, Gary A. Huber, J. Andrew McCammon
Summary: Intrinsically disordered proteins (IDPs) have attracted significant attention due to their involvement in biological processes and diseases. Computational studies using Brownian dynamics (BD) simulations with a coarse-grained force field for proteins (COFFDROP) have been conducted to complement experimental work. The researchers found that IDPs' properties, such as hydrodynamic radii and entanglement indices, are influenced by salt concentration.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Chemistry, Physical
Jared M. Lalmansingh, Alex T. Keeley, Kiersten M. Ruff, Rohit V. Pappu, Alex S. Holehouse
Summary: Conformational heterogeneity is a characteristic feature of intrinsically disordered proteins and protein regions. Simulations based on atomistic and coarse-grained models are commonly used to understand the sequence-specific interactions and functions of these proteins. In this study, a new analysis toolkit called SOURSOP is introduced, which provides a collection of easy-to-use functions to characterize the conformational ensembles of intrinsically disordered proteins.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Anas Malki, Jean-Marie Teulon, Aldo R. Camacho-Zarco, Shu-Wen W. Chen, Wiktor Adamski, Damien Maurin, Nicola Salvi, Jean-Luc Pellequer, Martin Blackledge
Summary: The study characterizes the conformational and physical behavior of CAHS-8 protein from Hypsibius exemplaris, showing its ability to form fibrous gels that may enhance the protective properties of the proteins. This unique ability of reversible formation of fibrous gels could be associated with the exceptional resistance of tardigrades to harsh stress conditions.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Biology
Aayush Gupta, Souvik Dey, Alan Hicks, Huan-Xiang Zhou
Summary: This study developed generative autoencoders that can learn from short molecular dynamics simulations and generate full conformational ensembles of intrinsically disordered proteins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Chemistry, Physical
Kari Gaalswyk, Austin Haider, Kingshuk Ghosh
Summary: This study introduces different criteria for self-consistency checks (SCCs) for Intrinsically Disordered Proteins (IDP) and validates them using the N terminal domain of HIV Integrase and the linker region of SARS-CoV-2 Nucleoprotein as model IDPs. The findings suggest that generating multiple short molecular dynamics (MD) simulation trajectories starting from the most representative Monte Carlo (MC) generated conformation and merging them is the optimal protocol, as it satisfies multiple SCCs, consistently reproduces experimental data, and utilizes parallel computing efficiently. Running one long trajectory can also meet the SCC criteria but is less desirable due to longer computation time.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Review
Biochemistry & Molecular Biology
Rakesh Trivedi, Hampapathalu Adimurthy Nagarajaram
Summary: This review discusses different aspects of disordered proteins and protein regions, as well as the experimental and computational methods used to characterize them. Additionally, the role of disordered proteins in diseases and their potential as drug targets are explored.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Multidisciplinary
Guy Jacoby, Merav Segal Asher, Tamara Ehm, Inbal Abutbul Ionita, Hila Shinar, Salome Azoulay-Ginsburg, Ido Zemach, Gil Koren, Dganit Danino, Michael M. Kozlov, Roey J. Amir, Roy Beck
Summary: This study introduces a new type of peptide amphiphiles, intrinsically disordered peptide amphiphiles (IDPA), that exhibit a sharp pH-induced micellar phase-transition. The shape transition can serve as a mechanism for the design of cargo hold-and-release applications, demonstrating the potential of tailoring interactions between disordered peptides for various stimuli-responsive biomedical applications.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Chandan Thapa, Pekka Roivas, Tatu Haataja, Perttu Permi, Ulla Pentikainen
Summary: PP2A activity is crucial for cellular functions, but can be inhibited in pathological conditions. ARPP-19 protein is connected to various cancer types, and understanding its interaction with PP2A is important for disease development and treatment. The structural characterization and interaction mechanism of ARPP-19 with PP2A provide insights for future therapeutic development.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Polymer Science
Peter J. Chung, Chaeyeon Song, Joanna Deek, Herbert P. Miller, Youli Li, Myung Chul Choi, Leslie Wilson, Stuart C. Feinstein, Cyrus R. Safinye
Article
Chemistry, Multidisciplinary
Peter J. Chung, Hyeondo Luke Hwang, Kinjal Dasbiswas, Alessandra Leong, Ka Yee C. Lee
Meeting Abstract
Biophysics
Christine Tchounwou, Bretton Fletcher, Chaeyeon Song, Phillip A. Kohl, Peter J. Chung, Herb P. Miller, Youli Li, Myung-Chul Choi, Leslie Wilson, Stuart C. Feinstein, Cyrus R. Safinya
BIOPHYSICAL JOURNAL
(2019)
Meeting Abstract
Biophysics
Bretton Fletcher, Chaeyeon Song, Phillip Kohl, Peter J. Chung, Herbert Miller, Youli Li, Myung Chul Choi, Leslie Wilson, Stuart C. Feinstein, Cyrus R. Safinya
BIOPHYSICAL JOURNAL
(2019)
Meeting Abstract
Biophysics
Peter J. Chung, Qingteng Zhang, Hyeondo Luke Hwang, Alessandra Leong, Eric Dufresne, Suresh Narayan, Erin J. Adams, Ka Yee C. Lee
BIOPHYSICAL JOURNAL
(2019)
Review
Chemistry, Multidisciplinary
Cyrus R. Safinya, Peter J. Chung, Chaeyeon Song, Youli Li, Herbert P. Miller, Myung Chul Choi, Uri Raviv, Kai K. Ewert, Leslie Wilson, Stuart C. Feinstein
Article
Chemistry, Multidisciplinary
Peter J. Chung, Hyeondo Luke Hwang, Benjamin R. Slaw, Alessandra Leong, Erin J. Adams, Ka Yee C. Lee
ADVANCED MATERIALS INTERFACES
(2020)
Meeting Abstract
Biophysics
Bretton Fletcher, Phillip A. Kohl, Chaeyeon Song, Peter J. Chung, Herbert P. Miller, Youli Li, Myung Chul Choi, Leslie Wilson, Stuart C. Feinstein, Cyrus R. Safinya
BIOPHYSICAL JOURNAL
(2022)
Meeting Abstract
Biophysics
Bretton Fletcher, Phillip A. Kohl, Chaeyeon Song, Christine Tchounwou, Peter J. Chung, Herbert P. Miller, Youli Li, Myung Chul Choi, Leslie Wilson, Stuart C. Feinstein, Cyrus R. Safinya
BIOPHYSICAL JOURNAL
(2021)
Meeting Abstract
Biophysics
Benjamin R. Slaw, Peter J. Chung, Hyeondo (Luke) Hwang, Ka Yee C. Lee
BIOPHYSICAL JOURNAL
(2020)
Meeting Abstract
Biophysics
Hyeondo (Luke) Hwang, Peter J. Chung, Benjamin R. Slaw, Alessandra Leong, Ka Yee C. Lee
BIOPHYSICAL JOURNAL
(2020)
Meeting Abstract
Biophysics
Phillip A. Kohl, Bretton Fletcher, Chaeyeon Song, Peter J. Chung, Herbert P. Miller, Leslie Wilson, Stuart C. Feinstein, Cyrus R. Safinya
BIOPHYSICAL JOURNAL
(2020)
Meeting Abstract
Biophysics
Peter J. Chung
BIOPHYSICAL JOURNAL
(2020)
Article
Nanoscience & Nanotechnology
Peter J. Chung, Qingteng Zhang, Hyeondo Luke Hwang, Alessandra Leong, Piotr Maj, Robert Szczygiel, Eric M. Dufresne, Suresh Narayanan, Erin J. Adams, Ka Yee C. Lee
ACS APPLIED BIO MATERIALS
(2019)
Meeting Abstract
Biophysics
Hyeondo (Luke) Hwang, Peter J. Chung, Alessandra Leong, Ka Yee C. Lee
BIOPHYSICAL JOURNAL
(2019)