1
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Shadman H, Ziebarth JD, Gallops CE, Luo R, Li Z, Chen HF, Wang Y. Map conformational landscapes of intrinsically disordered proteins with polymer physics quantities. Biophys J 2024; 123:1253-1263. [PMID: 38615193 PMCID: PMC11140466 DOI: 10.1016/j.bpj.2024.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 02/20/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024] Open
Abstract
Disordered proteins are conformationally flexible proteins that are biologically important and have been implicated in devastating diseases such as Alzheimer's disease and cancer. Unlike stably folded structured proteins, disordered proteins sample a range of different conformations that needs to be accounted for. Here, we treat disordered proteins as polymer chains, and compute a dimensionless quantity called instantaneous shape ratio (Rs), as Rs = Ree2/Rg2, where Ree is end-to-end distance and Rg is radius of gyration. Extended protein conformations tend to have high Ree compared with Rg, and thus have high Rs values, whereas compact conformations have smaller Rs values. We use a scatter plot of Rs (representing shape) against Rg (representing size) as a simple map of conformational landscapes. We first examine the conformational landscape of simple polymer models such as Random Walk, Self-Avoiding Walk, and Gaussian Walk (GW), and we notice that all protein/polymer maps lie within the boundaries of the GW map. We thus use the GW map as a reference and, to assess conformational diversity, we compute the fraction of the GW conformations (fC) covered by each protein/polymer. Disordered proteins all have high fC scores, consistent with their disordered nature. Each disordered protein accesses a different region of the reference map, revealing differences in their conformational ensembles. We additionally examine the conformational maps of the nonviral gene delivery vector polyethyleneimine at various protonation states, and find that they resemble disordered proteins, with coverage of the reference map decreasing with increasing protonation state, indicating decreasing conformational diversity. We propose that our method of combining Rs and Rg in a scatter plot generates a simple, meaningful map of the conformational landscape of a disordered protein, which in turn can be used to assess conformational diversity of disordered proteins.
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Affiliation(s)
- Hossain Shadman
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Jesse D Ziebarth
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Caleb E Gallops
- Department of Chemistry, The University of Memphis, Memphis, Tennessee
| | - Ray Luo
- Chemical and Materials Physics Graduate Program, Departments of Molecular Biology and Biochemistry, Chemical and Biomolecular Engineering, Materials Science and Engineering, and Biomedical Engineering, University of California, Irvine, Irvine, California
| | - Zhengxin Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yongmei Wang
- Department of Chemistry, The University of Memphis, Memphis, Tennessee.
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2
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Chao TH, Rekhi S, Mittal J, Tabor DP. Data-Driven Models for Predicting Intrinsically Disordered Protein Polymer Physics Directly from Composition or Sequence. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2023; 8:1146-1155. [PMID: 38222029 PMCID: PMC10786636 DOI: 10.1039/d3me00053b] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The molecular-level understanding of intrinsically disordered proteins is challenging due to experimental characterization difficulties. Computational understanding of IDPs also requires fundamental advances, as the leading tools for predicting protein folding (e.g., AlphaFold), typically fail to describe the structural ensembles of IDPs. The focus of this paper is to 1) develop new representations for intrinsically disordered proteins and 2) pair these representations with classical machine learning and deep learning models to predict the radius of gyration and derived scaling exponent of IDPs. Here, we build a new physically-motivated feature called the bag of amino acid interactions representation, which encodes pairwise interactions explicitly into the representation. This feature essentially counts and weights all possible non-bonded interactions in a sequence and thus is, in principle, compatible with arbitrary sequence lengths. To see how well this new feature performs, both categorical and physically-motivated featurization techniques are tested on a computational dataset containing 10,000 sequences simulated at the coarse-grained level. The results indicate that this new feature outperforms the other purely categorical and physically-motivated features and possesses solid extrapolation capabilities. For future use, this feature can potentially provide physical insights into amino acid interactions, including their temperature dependence, and be applied to other protein spaces.
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Affiliation(s)
- Tzu-Hsuan Chao
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, TX 77842-3012, USA
| | - Shiv Rekhi
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, TX 77842-3012, USA
| | - Jeetain Mittal
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, TX 77842-3012, USA
| | - Daniel P Tabor
- Department of Chemistry, Texas A&M University, PO Box 30012, College Station, TX 77842-3012, USA
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3
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Hughes MD, Cussons S, Mahmoudi N, Brockwell DJ, Dougan L. Tuning Protein Hydrogel Mechanics through Modulation of Nanoscale Unfolding and Entanglement in Postgelation Relaxation. ACS NANO 2022; 16:10667-10678. [PMID: 35731007 PMCID: PMC9331141 DOI: 10.1021/acsnano.2c02369] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Globular folded proteins are versatile nanoscale building blocks to create biomaterials with mechanical robustness and inherent biological functionality due to their specific and well-defined folded structures. Modulating the nanoscale unfolding of protein building blocks during network formation (in situ protein unfolding) provides potent opportunities to control the protein network structure and mechanics. Here, we control protein unfolding during the formation of hydrogels constructed from chemically cross-linked maltose binding protein using ligand binding and the addition of cosolutes to modulate protein kinetic and thermodynamic stability. Bulk shear rheology characterizes the storage moduli of the bound and unbound protein hydrogels and reveals a correlation between network rigidity, characterized as an increase in the storage modulus, and protein thermodynamic stability. Furthermore, analysis of the network relaxation behavior identifies a crossover from an unfolding dominated regime to an entanglement dominated regime. Control of in situ protein unfolding and entanglement provides an important route to finely tune the architecture, mechanics, and dynamic relaxation of protein hydrogels. Such predictive control will be advantageous for future smart biomaterials for applications which require responsive and dynamic modulation of mechanical properties and biological function.
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Affiliation(s)
- Matt D.
G. Hughes
- School of
Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Sophie Cussons
- Astbury Centre
for Structural Molecular Biology, University
of Leeds, Leeds LS2 9JT, U.K.
- School of
Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Najet Mahmoudi
- ISIS
Neutron
and Muon Spallation Source, STFC Rutherford
Appleton Laboratory, Oxfordshire OX11 0QX, U.K.
| | - David J. Brockwell
- Astbury Centre
for Structural Molecular Biology, University
of Leeds, Leeds LS2 9JT, U.K.
- School of
Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, U.K.
| | - Lorna Dougan
- School of
Physics and Astronomy, Faculty of Engineering and Physical Sciences, University of Leeds, Leeds LS2 9JT, U.K.
- Astbury Centre
for Structural Molecular Biology, University
of Leeds, Leeds LS2 9JT, U.K.
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4
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Arora L, Mukhopadhyay S. Conformational Characteristics and Phase Behavior of Intrinsically Disordered Proteins─Where Physical Chemistry Meets Biology. J Phys Chem B 2022; 126:5137-5139. [PMID: 35860904 DOI: 10.1021/acs.jpcb.2c04017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lisha Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, Mohali, SAS Nagar, Knowledge City, Punjab 140306, India
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5
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Stelzl L, Pietrek LM, Holla A, Oroz J, Sikora M, Köfinger J, Schuler B, Zweckstetter M, Hummer G. Global Structure of the Intrinsically Disordered Protein Tau Emerges from Its Local Structure. JACS AU 2022; 2:673-686. [PMID: 35373198 PMCID: PMC8970000 DOI: 10.1021/jacsau.1c00536] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Indexed: 05/13/2023]
Abstract
The paradigmatic disordered protein tau plays an important role in neuronal function and neurodegenerative diseases. To disentangle the factors controlling the balance between functional and disease-associated conformational states, we build a structural ensemble of the tau K18 fragment containing the four pseudorepeat domains involved in both microtubule binding and amyloid fibril formation. We assemble 129-residue-long tau K18 chains with atomic detail from an extensive fragment library constructed with molecular dynamics simulations. We introduce a reweighted hierarchical chain growth (RHCG) algorithm that integrates experimental data reporting on the local structure into the assembly process in a systematic manner. By combining Bayesian ensemble refinement with importance sampling, we obtain well-defined ensembles and overcome the problem of exponentially varying weights in the integrative modeling of long-chain polymeric molecules. The resulting tau K18 ensembles capture nuclear magnetic resonance (NMR) chemical shift and J-coupling measurements. Without further fitting, we achieve very good agreement with measurements of NMR residual dipolar couplings. The good agreement with experimental measures of global structure such as single-molecule Förster resonance energy transfer (FRET) efficiencies is improved further by ensemble refinement. By comparing wild-type and mutant ensembles, we show that pathogenic single-point P301L, P301S, and P301T mutations shift the population from the turn-like conformations of the functional microtubule-bound state to the extended conformations of disease-associated tau fibrils. RHCG thus provides us with an atomically detailed view of the population equilibrium between functional and aggregation-prone states of tau K18, and demonstrates that global structural characteristics of this intrinsically disordered protein emerge from its local structure.
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Affiliation(s)
- Lukas
S. Stelzl
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Faculty
of Biology, Johannes Gutenberg University
Mainz, Gresemundweg 2, 55128 Mainz, Germany
- KOMET 1, Institute of Physics, Johannes
Gutenberg University Mainz, 55099 Mainz, Germany
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Lisa M. Pietrek
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Andrea Holla
- Department
of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Javier Oroz
- German
Center for Neurodegenerative Diseases (DZNE), von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Rocasolano
Institute for Physical Chemistry, CSIC, Serrano 119, 28006 Madrid, Spain
| | - Mateusz Sikora
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Faculty
of Physics, University of Vienna, Kolingasse 14-16, 1090 Vienna, Austria
| | - Jürgen Köfinger
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Benjamin Schuler
- Department
of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
- Department
of Physics, University of Zurich, 8057 Zurich, Switzerland
| | - Markus Zweckstetter
- German
Center for Neurodegenerative Diseases (DZNE), von-Siebold-Str. 3a, 37075 Göttingen, Germany
- Department
for NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, Am Faßberg 11, 37077 Göttingen, Germany
| | - Gerhard Hummer
- Department
of Theoretical Biophysics, Max Planck Institute
of Biophysics, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
- Institute
for Biophysics, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt am Main, Germany
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6
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Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. BIOPHYSICS REVIEWS 2022; 3:011306. [PMID: 38505224 PMCID: PMC10903413 DOI: 10.1063/5.0080512] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/17/2022] [Indexed: 03/21/2024]
Abstract
Intrinsically disordered proteins (IDPs) are proteins that lack rigid 3D structure. Hence, they are often misconceived to present a challenge to Anfinsen's dogma. However, IDPs exist as ensembles that sample a quasi-continuum of rapidly interconverting conformations and, as such, may represent proteins at the extreme limit of the Anfinsen postulate. IDPs play important biological roles and are key components of the cellular protein interaction network (PIN). Many IDPs can interconvert between disordered and ordered states as they bind to appropriate partners. Conformational dynamics of IDPs contribute to conformational noise in the cell. Thus, the dysregulation of IDPs contributes to increased noise and "promiscuous" interactions. This leads to PIN rewiring to output an appropriate response underscoring the critical role of IDPs in cellular decision making. Nonetheless, IDPs are not easily tractable experimentally. Furthermore, in the absence of a reference conformation, discerning the energy landscape representation of the weakly funneled IDPs in terms of reaction coordinates is challenging. To understand conformational dynamics in real time and decipher how IDPs recognize multiple binding partners with high specificity, several sophisticated knowledge-based and physics-based in silico sampling techniques have been developed. Here, using specific examples, we highlight recent advances in energy landscape visualization and molecular dynamics simulations to discern conformational dynamics and discuss how the conformational preferences of IDPs modulate their function, especially in phenotypic switching. Finally, we discuss recent progress in identifying small molecules targeting IDPs underscoring the potential therapeutic value of IDPs. Understanding structure and function of IDPs can not only provide new insight on cellular decision making but may also help to refine and extend Anfinsen's structure/function paradigm.
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Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Vitor B. P. Leite
- Departamento de Física, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista (UNESP), São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Susmita Roy
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Supriyo Bhattacharyya
- Translational Bioinformatics, Center for Informatics, Department of Computational and Quantitative Medicine, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Atish Mohanty
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Srisairam Achuthan
- Center for Informatics, Division of Research Informatics, City of Hope National Medical Center, Duarte, California 91010, USA
| | - Divyoj Singh
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Rajeswari Appadurai
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Govindan Rangarajan
- Department of Mathematics, Indian Institute of Science, Bangalore 560012, India
| | - Keith Weninger
- Department of Physics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | - Anand Srivastava
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mohit Kumar Jolly
- Center for BioSystems Science and Engineering, Indian Institute of Science, Bangalore 560012, India
| | - Jose N. Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005-1892, USA
| | | | - Ravi Salgia
- Department of Medical Oncology and Therapeutics Research, City of Hope National Medical Center, Duarte, California 91010, USA
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7
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Zhao Y, Kremer K. Proline Isomerization Regulates the Phase Behavior of Elastin-Like Polypeptides in Water. J Phys Chem B 2021; 125:9751-9756. [PMID: 34424695 PMCID: PMC8419842 DOI: 10.1021/acs.jpcb.1c04779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Responsiveness of polypeptides and polymers in aqueous solution plays an important role in biomedical applications and in designing advanced functional materials. Elastin-like polypeptides (ELPs) are a well-known class of synthetic intrinsically disordered proteins (IDPs), which exhibit a lower critical solution temperature (LCST) in pure water and in aqueous solutions. Here, we compare the influence of cis/trans proline isomerization on the phase behavior of single ELPs in pure water. Our results reveal that proline isomerization tunes the conformational behavior of ELPs while keeping the transition temperature unchanged. We find that the presence of the cis isomers facilitates compact structures by preventing peptide-water hydrogen bonding while promoting intramolecular interactions. In other words, the LCST transition of ELPs with all proline residues in the cis state occurs with almost no noticeable conformational change.
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Affiliation(s)
- Yani Zhao
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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8
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Alston JJ, Soranno A, Holehouse AS. Integrating single-molecule spectroscopy and simulations for the study of intrinsically disordered proteins. Methods 2021; 193:116-135. [PMID: 33831596 PMCID: PMC8713295 DOI: 10.1016/j.ymeth.2021.03.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/25/2021] [Accepted: 03/31/2021] [Indexed: 12/21/2022] Open
Abstract
Over the last two decades, intrinsically disordered proteins and protein regions (IDRs) have emerged from a niche corner of biophysics to be recognized as essential drivers of cellular function. Various techniques have provided fundamental insight into the function and dysfunction of IDRs. Among these techniques, single-molecule fluorescence spectroscopy and molecular simulations have played a major role in shaping our modern understanding of the sequence-encoded conformational behavior of disordered proteins. While both techniques are frequently used in isolation, when combined they offer synergistic and complementary information that can help uncover complex molecular details. Here we offer an overview of single-molecule fluorescence spectroscopy and molecular simulations in the context of studying disordered proteins. We discuss the various means in which simulations and single-molecule spectroscopy can be integrated, and consider a number of studies in which this integration has uncovered biological and biophysical mechanisms.
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Affiliation(s)
- Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis 63110, MO, USA; Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis 63130, MO, USA.
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9
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Michael E, Simonson T. How much can physics do for protein design? Curr Opin Struct Biol 2021; 72:46-54. [PMID: 34461593 DOI: 10.1016/j.sbi.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/22/2021] [Accepted: 07/25/2021] [Indexed: 01/03/2023]
Abstract
Physics and physical chemistry are an important thread in computational protein design, complementary to knowledge-based tools. They provide molecular mechanics scoring functions that need little or no ad hoc parameter readjustment, methods to thoroughly sample equilibrium ensembles, and different levels of approximation for conformational flexibility. They led recently to the successful redesign of a small protein using a physics-based folded state energy. Adaptive Monte Carlo or molecular dynamics schemes were discovered where protein variants are populated as per their ligand-binding free energy or catalytic efficiency. Molecular dynamics have been used for backbone flexibility. Implicit solvent models have been refined, polarizable force fields applied, and many physical insights obtained.
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Affiliation(s)
- Eleni Michael
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, 91128, Palaiseau, France
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole Polytechnique, 91128, Palaiseau, France.
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10
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Shea JE, Best RB, Mittal J. Physics-based computational and theoretical approaches to intrinsically disordered proteins. Curr Opin Struct Biol 2021; 67:219-225. [PMID: 33545530 PMCID: PMC8150118 DOI: 10.1016/j.sbi.2020.12.012] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 02/06/2023]
Abstract
Intrinsically disordered proteins (IDPs) are an important class of proteins that do not fold to a well-defined three-dimensional shape but rather adopt an ensemble of inter-converting conformations. This feature makes their experimental characterization challenging and invites a theoretical and computational approach to complement experimental studies. In this review, we highlight the recent progress in developing new computational and theoretical approaches to study the structure and dynamics of monomeric and order higher assemblies of IDPs, with a particular emphasis on their phase separation into protein-rich condensates.
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Affiliation(s)
- Joan-Emma Shea
- Department of Chemistry & Biochemistry, University of California, Santa Barbara, CA 93106, United States; Department of Physics, University of California, Santa Barbara, CA 93106, United States.
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University, 111 Research Drive, Bethlehem, PA 18015, United States.
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