1
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Waszkiewicz R, Michaś A, Białobrzewski MK, Klepka BP, Cieplak-Rotowska MK, Staszałek Z, Cichocki B, Lisicki M, Szymczak P, Niedzwiecka A. Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation. J Phys Chem Lett 2024; 15:5024-5033. [PMID: 38696815 PMCID: PMC11103702 DOI: 10.1021/acs.jpclett.4c00312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/12/2024] [Accepted: 04/26/2024] [Indexed: 05/04/2024]
Abstract
The diffusion coefficients of globular and fully unfolded proteins can be predicted with high accuracy solely from their mass or chain length. However, this approach fails for intrinsically disordered proteins (IDPs) containing structural domains. We propose a rapid predictive methodology for estimating the diffusion coefficients of IDPs. The methodology uses accelerated conformational sampling based on self-avoiding random walks and includes hydrodynamic interactions between coarse-grained protein subunits, modeled using the generalized Rotne-Prager-Yamakawa approximation. To estimate the hydrodynamic radius, we rely on the minimum dissipation approximation recently introduced by Cichocki et al. Using a large set of experimentally measured hydrodynamic radii of IDPs over a wide range of chain lengths and domain contributions, we demonstrate that our predictions are more accurate than the Kirkwood approximation and phenomenological approaches. Our technique may prove to be valuable in predicting the hydrodynamic properties of both fully unstructured and multidomain disordered proteins.
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Affiliation(s)
- Radost Waszkiewicz
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Agnieszka Michaś
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Michał K. Białobrzewski
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Barbara P. Klepka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | | | - Zuzanna Staszałek
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Bogdan Cichocki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Maciej Lisicki
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Piotr Szymczak
- Institute
of Theoretical Physics, Faculty of Physics, University of Warsaw, L. Pasteura 5, 02-093 Warsaw, Poland
| | - Anna Niedzwiecka
- Institute
of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
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2
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Baxa MC, Lin X, Mukinay CD, Chakravarthy S, Sachleben JR, Antilla S, Hartrampf N, Riback JA, Gagnon IA, Pentelute BL, Clark PL, Sosnick TR. How hydrophobicity, side chains, and salt affect the dimensions of disordered proteins. Protein Sci 2024; 33:e4986. [PMID: 38607226 PMCID: PMC11010952 DOI: 10.1002/pro.4986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/13/2024]
Abstract
Despite the generally accepted role of the hydrophobic effect as the driving force for folding, many intrinsically disordered proteins (IDPs), including those with hydrophobic content typical of foldable proteins, behave nearly as self-avoiding random walks (SARWs) under physiological conditions. Here, we tested how temperature and ionic conditions influence the dimensions of the N-terminal domain of pertactin (PNt), an IDP with an amino acid composition typical of folded proteins. While PNt contracts somewhat with temperature, it nevertheless remains expanded over 10-58°C, with a Flory exponent, ν, >0.50. Both low and high ionic strength also produce contraction in PNt, but this contraction is mitigated by reducing charge segregation. With 46% glycine and low hydrophobicity, the reduced form of snow flea anti-freeze protein (red-sfAFP) is unaffected by temperature and ionic strength and persists as a near-SARW, ν ~ 0.54, arguing that the thermal contraction of PNt is due to stronger interactions between hydrophobic side chains. Additionally, red-sfAFP is a proxy for the polypeptide backbone, which has been thought to collapse in water. Increasing the glycine segregation in red-sfAFP had minimal effect on ν. Water remained a good solvent even with 21 consecutive glycine residues (ν > 0.5), and red-sfAFP variants lacked stable backbone hydrogen bonds according to hydrogen exchange. Similarly, changing glycine segregation has little impact on ν in other glycine-rich proteins. These findings underscore the generality that many disordered states can be expanded and unstructured, and that the hydrophobic effect alone is insufficient to drive significant chain collapse for typical protein sequences.
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Affiliation(s)
- Michael C. Baxa
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Xiaoxuan Lin
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Cedrick D. Mukinay
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team (BioCAT), Center for Synchrotron Radiation Research and Instrumentation and Department of Biological and Chemical SciencesIllinois Institute of TechnologyChicagoIllinoisUSA
- Present address:
Cytiva, Fast TrakMarlboroughMAUSA
| | | | - Sarah Antilla
- Department of Materials Science and EngineeringMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Nina Hartrampf
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
- Present address:
Department of ChemistryUniversity of ZurichSwitzerland
| | - Joshua A. Riback
- Graduate Program in Biophysical ScienceUniversity of ChicagoChicagoIllinoisUSA
- Present address:
Department of Molecular and Cellular BiologyBaylor College of MedicineHoustonTXUSA
| | - Isabelle A. Gagnon
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
| | - Bradley L. Pentelute
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Patricia L. Clark
- Department of Chemistry & BiochemistryUniversity of Notre DameNotre DameIndianaUSA
| | - Tobin R. Sosnick
- Department of Biochemistry & Molecular BiologyThe University of ChicagoChicagoIllinoisUSA
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3
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Sethi V, Cohen-Gerassi D, Meir S, Ney M, Shmidov Y, Koren G, Adler-Abramovich L, Chilkoti A, Beck R. Modulating hierarchical self-assembly in thermoresponsive intrinsically disordered proteins through high-temperature incubation time. Sci Rep 2023; 13:21688. [PMID: 38066072 PMCID: PMC10709347 DOI: 10.1038/s41598-023-48483-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
The cornerstone of structural biology is the unique relationship between protein sequence and the 3D structure at equilibrium. Although intrinsically disordered proteins (IDPs) do not fold into a specific 3D structure, breaking this paradigm, some IDPs exhibit large-scale organization, such as liquid-liquid phase separation. In such cases, the structural plasticity has the potential to form numerous self-assembled structures out of thermal equilibrium. Here, we report that high-temperature incubation time is a defining parameter for micro and nanoscale self-assembly of resilin-like IDPs. Interestingly, high-resolution scanning electron microscopy micrographs reveal that an extended incubation time leads to the formation of micron-size rods and ellipsoids that depend on the amino acid sequence. More surprisingly, a prolonged incubation time also induces amino acid composition-dependent formation of short-range nanoscale order, such as periodic lamellar nanostructures. We, therefore, suggest that regulating the period of high-temperature incubation, in the one-phase regime, can serve as a unique method of controlling the hierarchical self-assembly mechanism of structurally disordered proteins.
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Affiliation(s)
- Vaishali Sethi
- School of Physics and Astronomy, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Dana Cohen-Gerassi
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Sagi Meir
- School of Physics and Astronomy, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Max Ney
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Yulia Shmidov
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Gil Koren
- School of Physics and Astronomy, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Lihi Adler-Abramovich
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Roy Beck
- School of Physics and Astronomy, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Center for Physics and Chemistry of Living Systems, Tel Aviv University, 6997801, Tel Aviv, Israel.
- The Center for Nanoscience and Nanotechnology, Tel Aviv University, 6997801, Tel Aviv, Israel.
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4
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Białobrzewski MK, Klepka BP, Michaś A, Cieplak-Rotowska MK, Staszałek Z, Niedźwiecka A. Diversity of hydrodynamic radii of intrinsically disordered proteins. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:607-618. [PMID: 37831084 PMCID: PMC10618399 DOI: 10.1007/s00249-023-01683-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 08/08/2023] [Accepted: 09/06/2023] [Indexed: 10/14/2023]
Abstract
Intrinsically disordered proteins (IDPs) form an important class of biomolecules regulating biological processes in higher organisms. The lack of a fixed spatial structure facilitates them to perform their regulatory functions and allows the efficiency of biochemical reactions to be controlled by temperature and the cellular environment. From the biophysical point of view, IDPs are biopolymers with a broad configuration state space and their actual conformation depends on non-covalent interactions of its amino acid side chain groups at given temperature and chemical conditions. Thus, the hydrodynamic radius (Rh) of an IDP of a given polymer length (N) is a sequence- and environment-dependent variable. We have reviewed the literature values of hydrodynamic radii of IDPs determined experimentally by SEC, AUC, PFG NMR, DLS, and FCS, and complement them with our FCS results obtained for a series of protein fragments involved in the regulation of human gene expression. The data collected herein show that the values of hydrodynamic radii of IDPs can span the full space between the folded globular and denatured proteins in the Rh(N) diagram.
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Affiliation(s)
- Michał K Białobrzewski
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Barbara P Klepka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Agnieszka Michaś
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Maja K Cieplak-Rotowska
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, PL-02093, Warsaw, Poland
- The International Institute of Molecular Mechanisms and Machines, Polish Academy of Sciences, Flisa 6, PL-02247, Warsaw, Poland
| | - Zuzanna Staszałek
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland
| | - Anna Niedźwiecka
- Laboratory of Biological Physics, Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668, Warsaw, Poland.
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5
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Wilson C, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. ParSe 2.0: A web tool to identify drivers of protein phase separation at the proteome level. Protein Sci 2023; 32:e4756. [PMID: 37574757 PMCID: PMC10464302 DOI: 10.1002/pro.4756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/09/2023] [Accepted: 08/10/2023] [Indexed: 08/15/2023]
Abstract
We have developed an algorithm, ParSe, which accurately identifies from the primary sequence those protein regions likely to exhibit physiological phase separation behavior. Originally, ParSe was designed to test the hypothesis that, for flexible proteins, phase separation potential is correlated to hydrodynamic size. While our results were consistent with that idea, we also found that many different descriptors could successfully differentiate between three classes of protein regions: folded, intrinsically disordered, and phase-separating intrinsically disordered. Consequently, numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. Built from that finding, ParSe 2.0 uses an optimal set of property scales to predict domain-level organization and compute a sequence-based prediction of phase separation potential. The algorithm is fast enough to scan the whole of the human proteome in minutes on a single computer and is equally or more accurate than other published predictors in identifying proteins and regions within proteins that drive phase separation. Here, we describe a web application for ParSe 2.0 that may be accessed through a browser by visiting https://stevewhitten.github.io/Parse_v2_FASTA to quickly identify phase-separating proteins within large sequence sets, or by visiting https://stevewhitten.github.io/Parse_v2_web to evaluate individual protein sequences.
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Affiliation(s)
- Colorado Wilson
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
- Present address:
Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular BiophysicsUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Karen A. Lewis
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
| | - Nicholas C. Fitzkee
- Department of ChemistryMississippi State UniversityMississippi StateMississippiUSA
| | - Loren E. Hough
- Department of PhysicsUniversity of Colorado BoulderBoulderColoradoUSA
- BioFrontiers InstituteUniversity of Colorado BoulderBoulderColoradoUSA
| | - Steven T. Whitten
- Department of Chemistry and BiochemistryTexas State UniversitySan MarcosTexasUSA
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6
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Devlin T, Fleming PJ, Loza N, Fleming KG. Generation of unfolded outer membrane protein ensembles defined by hydrodynamic properties. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:415-425. [PMID: 36899114 DOI: 10.1007/s00249-023-01639-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 01/23/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
Outer membrane proteins (OMPs) must exist as an unfolded ensemble while interacting with a chaperone network in the periplasm of Gram-negative bacteria. Here, we developed a method to model unfolded OMP (uOMP) conformational ensembles using the experimental properties of two well-studied OMPs. The overall sizes and shapes of the unfolded ensembles in the absence of a denaturant were experimentally defined by measuring the sedimentation coefficient as a function of urea concentration. We used these data to model a full range of unfolded conformations by parameterizing a targeted coarse-grained simulation protocol. The ensemble members were further refined by short molecular dynamics simulations to reflect proper torsion angles. The final conformational ensembles have polymer properties different from unfolded soluble and intrinsically disordered proteins and reveal inherent differences in the unfolded states that necessitate further investigation. Building these uOMP ensembles advances the understanding of OMP biogenesis and provides essential information for interpreting structures of uOMP-chaperone complexes.
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Affiliation(s)
- Taylor Devlin
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Patrick J Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Nicole Loza
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Karen G Fleming
- Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD, 21218, USA.
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7
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Thole JF, Waudby CA, Pielak GJ. Disordered proteins mitigate the temperature dependence of site-specific binding free energies. J Biol Chem 2023; 299:102984. [PMID: 36739945 PMCID: PMC10027511 DOI: 10.1016/j.jbc.2023.102984] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Biophysical characterization of protein-protein interactions involving disordered proteins is challenging. A common simplification is to measure the thermodynamics and kinetics of disordered site binding using peptides containing only the minimum residues necessary. We should not assume, however, that these few residues tell the whole story. Son of sevenless, a multidomain signaling protein from Drosophila melanogaster, is critical to the mitogen-activated protein kinase pathway, passing an external signal to Ras, which leads to cellular responses. The disordered 55 kDa C-terminal domain of Son of sevenless is an autoinhibitor that blocks guanidine exchange factor activity. Activation requires another protein, Downstream of receptor kinase (Drk), which contains two Src homology 3 domains. Here, we utilized NMR spectroscopy and isothermal titration calorimetry to quantify the thermodynamics and kinetics of the N-terminal Src homology 3 domain binding to the strongest sites incorporated into the flanking disordered sequences. Comparing these results to those for isolated peptides provides information about how the larger domain affects binding. The affinities of sites on the disordered domain are like those of the peptides at low temperatures but less sensitive to temperature. Our results, combined with observations showing that intrinsically disordered proteins become more compact with increasing temperature, suggest a mechanism for this effect.
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Affiliation(s)
- Joseph F Thole
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Gary J Pielak
- Department of Chemistry, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Molecular and Cellular Biophysics Program, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry & Biophysics, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Lineberger Cancer Center, UNC-Chapel Hill, Chapel Hill, North Carolina, USA; Integrative Program for Biological and Genome Sciences, UNC - Chapel Hill, Chapel Hill, North Carolina, USA.
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8
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Yarawsky AE, Ori AL, English LR, Whitten ST, Herr AB. Convergent behavior of extended stalk regions from staphylococcal surface proteins with widely divergent sequence patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.06.523059. [PMID: 36711672 PMCID: PMC9881980 DOI: 10.1101/2023.01.06.523059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Staphylococcus epidermidis and S. aureus are highly problematic bacteria in hospital settings. This stems, at least in part, from strong abilities to form biofilms on abiotic or biotic surfaces. Biofilms are well-organized multicellular aggregates of bacteria, which, when formed on indwelling medical devices, lead to infections that are difficult to treat. Cell wall-anchored (CWA) proteins are known to be important players in biofilm formation and infection. Many of these proteins have putative stalk-like regions or regions of low complexity near the cell wall-anchoring motif. Recent work demonstrated the strong propensity of the stalk region of the S. epidermidis accumulation-associated protein (Aap) to remain highly extended under solution conditions that typically induce compaction or other significant conformational changes. This behavior is consistent with the expected function of a stalk-like region that is covalently attached to the cell wall peptidoglycan and projects the adhesive domains of Aap away from the cell surface. In this study, we evaluate whether the ability to resist compaction is a common theme among stalk regions from various staphylococcal CWA proteins. Circular dichroism spectroscopy was used to examine secondary structure changes as a function of temperature and cosolvents along with sedimentation velocity analytical ultracentrifugation and SAXS to characterize structural characteristics in solution. All stalk regions tested are intrinsically disordered, lacking secondary structure beyond random coil and polyproline type II helix, and they all sample highly extended conformations. Remarkably, the Ser-Asp dipeptide repeat region of SdrC exhibited nearly identical behavior in solution when compared to the Aap Pro/Gly-rich region, despite highly divergent sequence patterns, indicating conservation of function by various distinct staphylococcal CWA protein stalk regions.
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Affiliation(s)
- Alexander E. Yarawsky
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Andrea L. Ori
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Medical Sciences Baccalaureate Program, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Lance R. English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Steven T. Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Andrew B. Herr
- Division of Immunobiology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Division of Infectious Diseases, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
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9
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Koulgi S, Achalere A, Sonavane U, Joshi R. Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain. J Chem Inf Model 2022; 62:6449-6461. [PMID: 35614540 DOI: 10.1021/acs.jcim.2c00380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The transcription factor p53 is one of the most widely studied cancer proteins. Its temperature-sensitive nature suggests reduction in functionality at physiological temperatures. Temperature-induced conformational variations and their impact on its functional ability still remain unexplored. A total of 20.8 μs molecular dynamics simulations of wildtype p53 in the apo and the DNA-bound states have been performed at 300 K and 310 K. Further, Markov State Modeling (MSM) analyses were performed, considering Cα-Cα distances as reaction coordinates. Filtering of these distances based on correlation with the time-independent components (tICs) resulted in 16 and 32 distances for apo and DNA-bound systems, respectively. Individual MSM analyses using these filtered distances were performed for both p53 systems. These Cα-Cα residue pairs belonged to the N-terminal, S6/7 β-turn, loop L2, loop L3, and hydrophobic core residues. At physiological temperatures, apo-p53 exhibits exposure of its hydrophobic core, where the temperature-sensitive hotspot residues were also located. This exposure was the result of the S6/7 β-turn and N-terminal moving apart. In the DNA-bound p53 system, loop L1 attains an open conformation at physiological temperatures, which weakens the DNA binding. It is already known that p53 mutants that lack DNA binding also tend to show similar conformational variations. The S6/7 β-turn along with the already known functionally important loop L2 may pose as regions to be targeted to overcome the loss in binding of temperature-sensitive wildtype p53. Rescue strategies directed toward these temperature-sensitive regions may be useful to recuperate its strong binding at physiological temperatures.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
| | - Archana Achalere
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
| | - Uddhavesh Sonavane
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
| | - Rajendra Joshi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development for Advanced Computing (C-DAC), Panchawati, Pashan, Pune 411 008, India
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10
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Ibrahim AY, Khaodeuanepheng NP, Amarasekara DL, Correia JJ, Lewis KA, Fitzkee NC, Hough LE, Whitten ST. Intrinsically disordered regions that drive phase separation form a robustly distinct protein class. J Biol Chem 2022; 299:102801. [PMID: 36528065 PMCID: PMC9860499 DOI: 10.1016/j.jbc.2022.102801] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/29/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Protein phase separation is thought to be a primary driving force for the formation of membrane-less organelles, which control a wide range of biological functions from stress response to ribosome biogenesis. Among phase-separating (PS) proteins, many have intrinsically disordered regions (IDRs) that are needed for phase separation to occur. Accurate identification of IDRs that drive phase separation is important for testing the underlying mechanisms of phase separation, identifying biological processes that rely on phase separation, and designing sequences that modulate phase separation. To identify IDRs that drive phase separation, we first curated datasets of folded, ID, and PS ID sequences. We then used these sequence sets to examine how broadly existing amino acid property scales can be used to distinguish between the three classes of protein regions. We found that there are robust property differences between the classes and, consequently, that numerous combinations of amino acid property scales can be used to make robust predictions of protein phase separation. This result indicates that multiple, redundant mechanisms contribute to the formation of phase-separated droplets from IDRs. The top-performing scales were used to further optimize our previously developed predictor of PS IDRs, ParSe. We then modified ParSe to account for interactions between amino acids and obtained reasonable predictive power for mutations that have been designed to test the role of amino acid interactions in driving protein phase separation. Collectively, our findings provide further insight into the classification of IDRs and the elements involved in protein phase separation.
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Affiliation(s)
- Ayyam Y. Ibrahim
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | | | - John J. Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Karen A. Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | | | - Loren E. Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado, USA,BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA,For correspondence: Steven T. Whitten; Loren E. Hough
| | - Steven T. Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA,For correspondence: Steven T. Whitten; Loren E. Hough
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11
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The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy. Essays Biochem 2022; 66:875-890. [PMID: 36416865 PMCID: PMC9760427 DOI: 10.1042/ebc20220065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/24/2022]
Abstract
Intrinsically disordered proteins (IDPs) and regions (IDRs) have emerged as key players across many biological functions and diseases. Differently from structured proteins, disordered proteins lack stable structure and are particularly sensitive to changes in the surrounding environment. Investigation of disordered ensembles requires new approaches and concepts for quantifying conformations, dynamics, and interactions. Here, we provide a short description of the fundamental biophysical properties of disordered proteins as understood through the lens of single-molecule fluorescence observations. Single-molecule Förster resonance energy transfer (FRET) and fluorescence correlation spectroscopy (FCS) provides an extensive and versatile toolbox for quantifying the characteristics of conformational distributions and the dynamics of disordered proteins across many different solution conditions, both in vitro and in living cells.
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12
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Bhuyan AK. Negative Thermal Expansion and Disorder-to-Order Collapse of an Intrinsically Disordered Protein under Marginally Denaturing Conditions. J Phys Chem B 2022; 126:5055-5065. [PMID: 35786899 DOI: 10.1021/acs.jpcb.2c03386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Recent work with intrinsically disordered proteins (IDPs) has projected a myriad of their survival instincts based mainly on the total charge content, the abundance of polar residues, and the paucity of hydrophobic amino acids. This work uses a plant IDP AtPP16-1 (Arabidopsis thaliana phloem protein class 16-1), whose solution NMR structure was determined by us recently, to show legitimate negative thermal expansion (NTE) of the native state. The thermal expansion continues to be negative even as the tertiary structure is perturbed by ultralow levels of urea up to 0.4 M. The NTE of these subdenatured states is called apparent NTE because they are prone to undergo conformational changes with temperature. Hydrodynamic shrinkage of the NTE IDP is also observed by dynamic light scattering (DLS) and NMR-measured global rotational correlation time (τc). The protein with denatured tertiary structure but otherwise preserved native-state secondary structure collapses to a dynamically rigid state. The data are mainly based on thermal coefficients of chemical shift and nuclear relaxation measured by heteronuclear NMR. The hydrodynamic shrinkage and collapse under marginally varying solvent compositions that may arise from unstable tertiary structure and dynamic disorder of chain segments across the backbone could be a generic property of IDPs.
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Affiliation(s)
- Abani K Bhuyan
- School of Chemistry University of Hyderabad, Hyderabad 50046, India
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13
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Expression, Purification, Characterization and Cellular Uptake of MeCP2 Variants. Protein J 2022; 41:345-359. [PMID: 35546650 PMCID: PMC9122891 DOI: 10.1007/s10930-022-10054-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2022] [Indexed: 11/05/2022]
Abstract
The transcriptional regulator Methyl-CpG-binding protein 2 (MeCP2) is an intrinsically disordered protein, mutations in which, are implicated in the onset of Rett Syndrome, a severe and debilitating neurodevelopmental disorder. Delivery of this protein fused to the cell-penetrating peptide TAT could allow for the intracellular replenishment of functional MeCP2 and hence potentially serve as a prospective Rett Syndrome therapy. This work outlines the expression, purification and characterization of various TAT-MeCP2 constructs as well as their full-length and shortened eGFP fusion variants. The latter two constructs were used for intracellular uptake studies with subsequent analysis via western blotting and live-cell imaging. All purified MeCP2 samples exhibited high degree of stability and very little aggregation propensity. Full length and minimal TAT-MeCP2-eGFP were found to efficiently transduce into human dermal and murine fibroblasts and localize to cell nuclei. These findings clearly support the utility of MeCP2-based protein replacement therapy as a potential Rett Syndrome treatment option.
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14
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15
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Paiz EA, Allen JH, Correia JJ, Fitzkee NC, Hough LE, Whitten ST. Beta turn propensity and a model polymer scaling exponent identify intrinsically disordered phase-separating proteins. J Biol Chem 2021; 297:101343. [PMID: 34710373 PMCID: PMC8592878 DOI: 10.1016/j.jbc.2021.101343] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/14/2022] Open
Abstract
The complex cellular milieu can spontaneously demix, or phase separate, in a process controlled in part by intrinsically disordered (ID) proteins. A protein's propensity to phase separate is thought to be driven by a preference for protein-protein over protein-solvent interactions. The hydrodynamic size of monomeric proteins, as quantified by the polymer scaling exponent (v), is driven by a similar balance. We hypothesized that mean v, as predicted by protein sequence, would be smaller for proteins with a strong propensity to phase separate. To test this hypothesis, we analyzed protein databases containing subsets of proteins that are folded, disordered, or disordered and known to spontaneously phase separate. We find that the phase-separating disordered proteins, on average, had lower calculated values of v compared with their non-phase-separating counterparts. Moreover, these proteins had a higher sequence-predicted propensity for β-turns. Using a simple, surface area-based model, we propose a physical mechanism for this difference: transient β-turn structures reduce the desolvation penalty of forming a protein-rich phase and increase exposure of atoms involved in π/sp2 valence electron interactions. By this mechanism, β-turns could act as energetically favored nucleation points, which may explain the increased propensity for turns in ID regions (IDRs) utilized biologically for phase separation. Phase-separating IDRs, non-phase-separating IDRs, and folded regions could be distinguished by combining v and β-turn propensity. Finally, we propose a new algorithm, ParSe (partition sequence), for predicting phase-separating protein regions, and which is able to accurately identify folded, disordered, and phase-separating protein regions based on the primary sequence.
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Affiliation(s)
- Elisia A Paiz
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA
| | - Jeffre H Allen
- Department of Biochemistry, University of Colorado Boulder, Boulder, Colorado, USA
| | - John J Correia
- Department of Cell and Molecular Biology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Nicholas C Fitzkee
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, USA
| | - Loren E Hough
- Department of Physics, University of Colorado Boulder, Boulder, Colorado, USA; BioFrontiers Institute, University of Colorado Boulder, Boulder, Colorado, USA.
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, USA.
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16
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Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins. Molecules 2021; 26:molecules26030634. [PMID: 33530506 PMCID: PMC7865441 DOI: 10.3390/molecules26030634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 01/10/2023] Open
Abstract
The α and polyproline II (PPII) basins are the two most populated regions of the Ramachandran map when constructed from the protein coil library, a widely used denatured state model built from the segments of irregular structure found in the Protein Data Bank. This indicates the α and PPII conformations are dominant components of the ensembles of denatured structures that exist in solution for biological proteins, an observation supported in part by structural studies of short, and thus unfolded, peptides. Although intrinsic conformational propensities have been determined experimentally for the common amino acids in short peptides, and estimated from surveys of the protein coil library, the ability of these intrinsic conformational propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs), an increasingly important class of proteins in cell function, has thus far proven elusive to establish. Recently, we demonstrated that the sequence dependence of the mean hydrodynamic size of IDPs in water and the impact of heat on the coil dimensions, provide access to both the sequence dependence and thermodynamic energies that are associated with biases for the α and PPII backbone conformations. Here, we compare results from peptide-based studies of intrinsic conformational propensities and surveys of the protein coil library to those of the sequence-based analysis of heat effects on IDP hydrodynamic size, showing that a common structural and thermodynamic description of the protein denatured state is obtained.
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17
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Baul U, Bley M, Dzubiella J. Thermal Compaction of Disordered and Elastin-like Polypeptides: A Temperature-Dependent, Sequence-Specific Coarse-Grained Simulation Model. Biomacromolecules 2020; 21:3523-3538. [DOI: 10.1021/acs.biomac.0c00546] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Upayan Baul
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Michael Bley
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
| | - Joachim Dzubiella
- Applied Theoretical Physics—Computational Physics, Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Strasse 3, D-79104 Freiburg, Germany
- Cluster of Excellence livMatS@FIT—Freiburg Center for Interactive Materials and Bioinspired Technologies, Albert-Ludwigs-Universität Freiburg, Georges-Köhler-Allee 105, D-79110 Freiburg, Germany
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18
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Trushina NI, Mulkidjanian AY, Brandt R. The microtubule skeleton and the evolution of neuronal complexity in vertebrates. Biol Chem 2020; 400:1163-1179. [PMID: 31116700 DOI: 10.1515/hsz-2019-0149] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 04/17/2019] [Indexed: 12/21/2022]
Abstract
The evolution of a highly developed nervous system is mirrored by the ability of individual neurons to develop increased morphological complexity. As microtubules (MTs) are crucially involved in neuronal development, we tested the hypothesis that the evolution of complexity is driven by an increasing capacity of the MT system for regulated molecular interactions as it may be implemented by a higher number of molecular players and a greater ability of the individual molecules to interact. We performed bioinformatics analysis on different classes of components of the vertebrate neuronal MT cytoskeleton. We show that the number of orthologs of tubulin structure proteins, MT-binding proteins and tubulin-sequestering proteins expanded during vertebrate evolution. We observed that protein diversity of MT-binding and tubulin-sequestering proteins increased by alternative splicing. In addition, we found that regions of the MT-binding protein tau and MAP6 displayed a clear increase in disorder extent during evolution. The data provide evidence that vertebrate evolution is paralleled by gene expansions, changes in alternative splicing and evolution of coding sequences of components of the MT system. The results suggest that in particular evolutionary changes in tubulin-structure proteins, MT-binding proteins and tubulin-sequestering proteins were prominent drivers for the development of increased neuronal complexity.
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Affiliation(s)
- Nataliya I Trushina
- Department of Neurobiology, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, University of Osnabrück, Barbarastraße 7, D-49076 Osnabrück, Germany.,A.N. Belozersky Institute of Physico-Chemical Biology and School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roland Brandt
- Department of Neurobiology, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany.,Center for Cellular Nanoanalytics, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany.,Institute of Cognitive Science, University of Osnabrück, Barbarastraße 11, D-49076 Osnabrück, Germany
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19
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English LR, Voss SM, Tilton EC, Paiz EA, So S, Parra GL, Whitten ST. Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias. J Phys Chem B 2019; 123:10014-10024. [PMID: 31679343 DOI: 10.1021/acs.jpcb.9b09088] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Conformational equilibria in the protein denatured state have key roles regulating folding, stability, and function. The extent of conformational bias in the protein denatured state under folding conditions, however, has thus far proven elusive to quantify, particularly with regard to its sequence dependence and energetic character. To better understand the structural preferences of the denatured state, we analyzed both the sequence dependence to the mean hydrodynamic size of disordered proteins in water and the impact of heat on the coil dimensions, showing that the sequence dependence and thermodynamic energies associated with intrinsic biases for the α and polyproline II (PPII) backbone conformations can be obtained. Experiments that evaluate how the hydrodynamic size changes with compositional changes in the protein reveal amino acid specific preferences for PPII that are in good quantitative agreement with calorimetry-measured values from unfolded peptides and those inferred by survey of the protein coil library. At temperatures above 25 °C, the denatured state follows the predictions of a PPII-dominant ensemble. Heat effects on coil hydrodynamic size indicate the α bias is comparable to the PPII bias at cold temperatures. Though historically thought to give poor resolution to structural details, the hydrodynamic size of the unfolded state is found to be an effective reporter on the extent of the biases for the α and PPII backbone conformations.
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20
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Trushina NI, Bakota L, Mulkidjanian AY, Brandt R. The Evolution of Tau Phosphorylation and Interactions. Front Aging Neurosci 2019; 11:256. [PMID: 31619983 PMCID: PMC6759874 DOI: 10.3389/fnagi.2019.00256] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 08/28/2019] [Indexed: 12/18/2022] Open
Abstract
Tau is a neuronal microtubule-associated protein (MAP) that is involved in the regulation of axonal microtubule assembly. However, as a protein with intrinsically disordered regions (IDRs), tau also interacts with many other partners in addition to microtubules. Phosphorylation at selected sites modulates tau's various intracellular interactions and regulates the properties of IDRs. In Alzheimer's disease (AD) and other tauopathies, tau exhibits pathologically increased phosphorylation (hyperphosphorylation) at selected sites and aggregates into neurofibrillary tangles (NFTs). By bioinformatics means, we tested the hypothesis that the sequence of tau has changed during the vertebrate evolution in a way that novel interactions developed and also the phosphorylation pattern was affected, which made tau prone to the development of tauopathies. We report that distinct regions of tau show functional specialization in their molecular interactions. We found that tau's amino-terminal region, which is involved in biological processes related to "membrane organization" and "regulation of apoptosis," exhibited a strong evolutionary increase in protein disorder providing the basis for the development of novel interactions. We observed that the predicted phosphorylation sites have changed during evolution in a region-specific manner, and in some cases the overall number of phosphorylation sites increased owing to the formation of clusters of phosphorylatable residues. In contrast, disease-specific hyperphosphorylated sites remained highly conserved. The data indicate that novel, non-microtubule related tau interactions developed during evolution and suggest that the biological processes, which are mediated by these interactions, are of pathological relevance. Furthermore, the data indicate that predicted phosphorylation sites in some regions of tau, including a cluster of phosphorylatable residues in the alternatively spliced exon 2, have changed during evolution. In view of the "antagonistic pleiotropy hypothesis" it may be worth to take disease-associated phosphosites with low evolutionary conservation as relevant biomarkers into consideration.
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Affiliation(s)
| | - Lidia Bakota
- Department of Neurobiology, University of Osnabrück, Osnabrück, Germany
| | - Armen Y Mulkidjanian
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,School of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Roland Brandt
- Department of Neurobiology, University of Osnabrück, Osnabrück, Germany.,Center for Cellular Nanoanalytics, University of Osnabrück, Osnabrück, Germany.,Institute of Cognitive Science, University of Osnabrück, Osnabrück, Germany
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21
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Sequence Reversal Prevents Chain Collapse and Yields Heat-Sensitive Intrinsic Disorder. Biophys J 2019; 115:328-340. [PMID: 30021108 DOI: 10.1016/j.bpj.2018.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 05/15/2018] [Accepted: 06/04/2018] [Indexed: 11/20/2022] Open
Abstract
Sequence patterns of charge, hydrophobicity, hydrogen bonding, and other amino acid physicochemical properties contribute to mechanisms of protein folding, but how sequence composition and patterns influence the conformational dynamics of the denatured state ensemble is not fully understood. To investigate structure-sequence relationships in the denatured state, we reversed the sequence of staphylococcal nuclease and characterized its structure, thermodynamic character, and hydrodynamic radius using circular dichroism spectroscopy, dynamic light scattering, analytical ultracentrifugation, and size-exclusion chromatography as a function of temperature. The macromolecular size of "Retro-nuclease" is highly expanded in solution with characteristics similar to biological intrinsically disordered proteins. In contradistinction to a disordered state, Retro-nuclease exhibits a broad sigmoid transition of its hydrodynamic dimensions as temperature is increased, indicating a thermodynamically controlled compaction. Counterintuitively, the magnitude of these temperature-induced hydrodynamic changes exceed that observed from thermal denaturation of folded unaltered staphylococcal nuclease. Undetectable by calorimetry and intrinsic tryptophan fluorescence, the lack of heat capacity or fluorescence changes throughout the thermal transition indicate canonical hydrophobic collapse did not drive the Retro-nuclease structural transitions. Temperature-dependent circular dichroism spectroscopy performed on Retro-nuclease and computer simulations correlate to temperature sensitivity in the intrinsic sampling of backbone conformations for polyproline II and α-helix. The experimental results indicate a role for sequence direction in mediating the collapse of the polypeptide chain, whereas the simulation trends illustrate the generality of the observed heat effects on disordered protein structure.
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22
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Hermosilla J, Sánchez-Martín R, Pérez-Robles R, Salmerón-García A, Casares S, Cabeza J, Cuadros-Rodríguez L, Navas N. Comparative Stability Studies of Different Infliximab and Biosimilar CT-P13 Clinical Solutions by Combined Use of Physicochemical Analytical Techniques and Enzyme-Linked Immunosorbent Assay (ELISA). BioDrugs 2019; 33:193-205. [DOI: 10.1007/s40259-019-00342-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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23
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Falahati H, Haji-Akbari A. Thermodynamically driven assemblies and liquid-liquid phase separations in biology. SOFT MATTER 2019; 15:1135-1154. [PMID: 30672955 DOI: 10.1039/c8sm02285b] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The sustenance of life depends on the high degree of organization that prevails through different levels of living organisms, from subcellular structures such as biomolecular complexes and organelles to tissues and organs. The physical origin of such organization is not fully understood, and even though it is clear that cells and organisms cannot maintain their integrity without consuming energy, there is growing evidence that individual assembly processes can be thermodynamically driven and occur spontaneously due to changes in thermodynamic variables such as intermolecular interactions and concentration. Understanding the phase separation in vivo requires a multidisciplinary approach, integrating the theory and physics of phase separation with experimental and computational techniques. This paper aims at providing a brief overview of the physics of phase separation and its biological implications, with a particular focus on the assembly of membraneless organelles. We discuss the underlying physical principles of phase separation from its thermodynamics to its kinetics. We also overview the wide range of methods utilized for experimental verification and characterization of phase separation of membraneless organelles, as well as the utility of molecular simulations rooted in thermodynamics and statistical physics in understanding the governing principles of thermodynamically driven biological self-assembly processes.
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Affiliation(s)
- Hanieh Falahati
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA.
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24
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Greenland KN, Carvajal MFCA, Preston JM, Ekblad S, Dean WL, Chiang JY, Koder RL, Wittebort RJ. Order, Disorder, and Temperature-Driven Compaction in a Designed Elastin Protein. J Phys Chem B 2018; 122:2725-2736. [PMID: 29461832 DOI: 10.1021/acs.jpcb.7b11596] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Artificial minielastin constructs have been designed that replicate the structure and function of natural elastins in a simpler context, allowing the NMR observation of structure and dynamics of elastin-like proteins with complete residue-specific resolution. We find that the alanine-rich cross-linking domains of elastin have a partially helical structure, but only when capped by proline-rich hydrophobic domains. We also find that the hydrophobic domains, composed of prominent 6-residue repeats VPGVGG and APGVGV found in natural elastins, appear random coil by both NMR chemical shift analysis and circular dichroism. However, these elastin hydrophobic domains exhibit structural bias for a dynamically disordered conformation that is neither helical nor β sheet with a degree of nonrandom structural bias which is dependent on residue type and position in the sequence. Another nonrandom-coil aspect of hydrophobic domain structure lies in the fact that, in contrast to other intrinsically disordered proteins, these hydrophobic domains retain a relatively condensed conformation whether attached to cross-linking domains or not. Importantly, these domains and the proteins containing them constrict with increasing temperature by up to 30% in volume without becoming more ordered. This property is often observed in nonbiological polymers and suggests that temperature-driven constriction is a new type of protein structural change that is linked to elastin's biological functions of coacervation-driven assembly and elastic recoil.
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Affiliation(s)
- Kelly N Greenland
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | | | - Jonathan M Preston
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | - Siri Ekblad
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | - William L Dean
- Department of Biochemistry and Molecular Genetics and the James Brown Cancer Center , University of Louisville School of Medicine , Louisville , Kentucky 40292 , United States
| | - Jeff Y Chiang
- Department of Physics , The City College of New York , New York , New York 10031 , United States
| | - Ronald L Koder
- Department of Physics , The City College of New York , New York , New York 10031 , United States.,Graduate Programs of Physics, Chemistry and Biochemistry , The Graduate Center of CUNY , New York , New York 10016 , United States
| | - Richard J Wittebort
- Department of Chemistry , University of Louisville , Louisville , Kentucky 40292 , United States
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25
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Development of a nutraceutical nano-delivery system through emulsification/internal gelation of alginate. Food Chem 2017; 229:286-295. [DOI: 10.1016/j.foodchem.2017.02.071] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/05/2017] [Accepted: 02/15/2017] [Indexed: 01/22/2023]
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26
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DeForte S, Uversky VN. Quarterly intrinsic disorder digest (April-May-June, 2014). INTRINSICALLY DISORDERED PROTEINS 2017; 5:e1287505. [PMID: 28321370 DOI: 10.1080/21690707.2017.1287505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This is the 6th issue of the Digested Disorder series that continues to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the second quarter of 2014; i.e., during the period of April, May, and June of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.
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Affiliation(s)
- Shelly DeForte
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Département De Biochimie and Centre Robert-Cedergren, Bio-Informatique et Génomique, Université de Montréal, Succursale Centre-Ville, Montreal, Quebec, Canada
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA; Laboratory of New Methods in Biology, Institute of Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow Region, Russia; Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, Russia
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27
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Yarawsky AE, English LR, Whitten ST, Herr AB. The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction. J Mol Biol 2017; 429:261-279. [PMID: 27890783 PMCID: PMC5363081 DOI: 10.1016/j.jmb.2016.11.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Revised: 11/22/2016] [Accepted: 11/22/2016] [Indexed: 12/11/2022]
Abstract
Staphylococcus epidermidis is one of the primary bacterial species responsible for healthcare-associated infections. The most significant virulence factor for S. epidermidis is its ability to form a biofilm, which renders the bacteria highly resistant to host immune responses and antibiotic action. Intercellular adhesion within the biofilm is mediated by the accumulation-associated protein (Aap), a cell wall-anchored protein that self-assembles in a zinc-dependent manner. The C-terminal portion of Aap contains a 135-aa-long, proline/glycine-rich region (PGR) that has not yet been characterized. The region contains a set of 18 nearly identical AEPGKP repeats. Analysis of the PGR using biophysical techniques demonstrated the region is a highly extended, intrinsically disordered polypeptide with unusually high polyproline type II helix propensity. In contrast to many intrinsically disordered polypeptides, there was a minimal temperature dependence of the global conformational state of PGR in solution as measured by analytical ultracentrifugation and dynamic light scattering. Furthermore, PGR was resistant to conformational collapse or α-helix formation upon the addition of the osmolyte trimethylamine N-oxide or the cosolvent 2,2,2-trifluoroethanol. Collectively, these results suggest PGR functions as a resilient, extended stalk that projects the rest of Aap outward from the bacterial cell wall, promoting intercellular adhesion between cells in the biofilm. This work sheds light on regions of low complexity often found near the attachment point of bacterial cell wall-anchored proteins.
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Affiliation(s)
- Alexander E Yarawsky
- Graduate Program in Molecular Genetics, Biochemistry & Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lance R English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Andrew B Herr
- Division of Immunobiology and Center for Systems Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Division of Infectious Diseases, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
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28
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English LR, Tilton EC, Ricard BJ, Whitten ST. Intrinsic α helix propensities compact hydrodynamic radii in intrinsically disordered proteins. Proteins 2017; 85:296-311. [PMID: 27936491 DOI: 10.1002/prot.25222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Revised: 10/31/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022]
Abstract
Proteins that lack tertiary stability under normal conditions, known as intrinsically disordered, exhibit a wide range of biological activities. Molecular descriptions for the biology of intrinsically disordered proteins (IDPs) consequently rely on disordered structural models, which in turn require experiments that assess the origins to structural features observed. For example, while hydrodynamic size is mostly insensitive to sequence composition in chemically denatured proteins, IDPs show strong sequence-specific effects in the hydrodynamic radius (Rh ) when measured under normal conditions. To investigate sequence-modulation of IDP Rh , disordered ensembles generated by a hard sphere collision model modified with a structure-based parameterization of the solution energetics were used to parse the contributions of net charge, main chain dihedral angle bias, and excluded volume on hydrodynamic size. Ensembles for polypeptides 10-35 residues in length were then used to establish power-law scaling relationships for comparison to experimental Rh from 26 IDPs. Results showed the expected outcomes of increased hydrodynamic size from increases in excluded volume and net charge, and compaction from chain-solvent interactions. Chain bias representing intrinsic preferences for α helix and polyproline II (PPII ), however, modulated Rh with intricate dependence on the simulated propensities. PPII propensities at levels expected in IDPs correlated with heightened Rh sensitivity to even weak α helix propensities, indicating bias for common (φ, ψ) are important determinants of hydrodynamic size. Moreover, data show that IDP Rh can be predicted from sequence with good accuracy from a small set of physicochemical properties, namely intrinsic conformational propensities and net charge. Proteins 2017; 85:296-311. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Lance R English
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Erin C Tilton
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Benjamin J Ricard
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Steven T Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
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Laity PR, Holland C. The Rheology behind Stress-Induced Solidification in Native Silk Feedstocks. Int J Mol Sci 2016; 17:E1812. [PMID: 27801879 PMCID: PMC5133813 DOI: 10.3390/ijms17111812] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/21/2016] [Accepted: 10/25/2016] [Indexed: 01/24/2023] Open
Abstract
The mechanism by which native silk feedstocks are converted to solid fibres in nature has attracted much interest. To address this question, the present work used rheology to investigate the gelation of Bombyx mori native silk feedstock. Exceeding a critical shear stress appeared to be more important than shear rate, during flow-induced initiation. Compositional changes (salts, pH etc.,) were not required, although their possible role in vivo is not excluded. Moreover, after successful initiation, gel strength continued to increase over a considerable time under effectively quiescent conditions, without requiring further application of the initial stimulus. Gelation by elevated temperature or freezing was also observed. Prior to gelation, literature suggests that silk protein adopts a random coil configuration, which argued against the conventional explanation of gelation, based on hydrophilic and hydrophobic interactions. Instead, a new hypothesis is presented, based on entropically-driven loss of hydration, which appears to explain the apparently diverse methods by which silk feedstocks can be gelled.
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Affiliation(s)
- Peter R Laity
- Department of Materials Science and Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, UK.
| | - Chris Holland
- Department of Materials Science and Engineering, The University of Sheffield, Sir Robert Hadfield Building, Mappin Street, Sheffield S1 3JD, UK.
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30
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Smeller L. Folding superfunnel to describe cooperative folding of interacting proteins. Proteins 2016; 84:1009-16. [DOI: 10.1002/prot.25051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 12/18/2022]
Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology; Semmelweis University; Budapest Hungary
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31
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Tomasso ME, Tarver MJ, Devarajan D, Whitten ST. Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities. PLoS Comput Biol 2016; 12:e1004686. [PMID: 26727467 PMCID: PMC4699819 DOI: 10.1371/journal.pcbi.1004686] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/01/2015] [Indexed: 11/18/2022] Open
Abstract
The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II (PPII) structure. While intrinsic PPII propensities have been measured for the common biological amino acids in short peptides, the ability of these experimentally determined propensities to quantitatively reproduce structural behavior in intrinsically disordered proteins (IDPs) has not been established. Presented here are results from molecular simulations of disordered proteins showing that the hydrodynamic radius (Rh) can be predicted from experimental PPII propensities with good agreement, even when charge-based considerations are omitted. The simulations demonstrate that Rh and chain propensity for PPII structure are linked via a simple power-law scaling relationship, which was tested using the experimental Rh of 22 IDPs covering a wide range of peptide lengths, net charge, and sequence composition. Charge effects on Rh were found to be generally weak when compared to PPII effects on Rh. Results from this study indicate that the hydrodynamic dimensions of IDPs are evidence of considerable sequence-dependent backbone propensities for PPII structure that qualitatively, if not quantitatively, match conformational propensities measured in peptides. Molecular models of disordered protein structures are needed to elucidate the functional mechanisms of intrinsically disordered proteins, a class of proteins implicated in many disease pathologies and human health issues. Several studies have measured intrinsic conformational propensities for polyproline II helix, a key structural motif of disordered proteins, in short peptides. Whether or not these experimental polyproline II propensities, which vary by amino acid type, reproduce structural behavior in intrinsically disordered proteins has yet to be demonstrated. Presented here are simulation results showing that polyproline II propensities from short peptides accurately describe sequence-dependent variability in the hydrodynamic dimensions of intrinsically disordered proteins. Good agreement was observed from a simple molecular model even when charge-based considerations were ignored, predicting that global organization of disordered protein structure is strongly dependent on intrinsic conformational propensities and, for many intrinsically disordered proteins, modulated only weakly by coulombic effects.
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Affiliation(s)
- Maria E. Tomasso
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America
| | - Micheal J. Tarver
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America
| | - Deepa Devarajan
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America
| | - Steven T. Whitten
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas, United States of America
- * E-mail:
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32
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Zerze GH, Best RB, Mittal J. Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations. J Phys Chem B 2015; 119:14622-30. [PMID: 26498157 DOI: 10.1021/acs.jpcb.5b08619] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use all-atom molecular simulation with explicit solvent to study the properties of selected intrinsically disordered proteins and unfolded states of foldable proteins, which include chain dimensions and shape, secondary structure propensity, solvent accessible surface area, and contact formation. We find that the qualitative scaling behavior of the chains matches expectations from theory under ambient conditions. In particular, unfolded globular proteins tend to be more collapsed under the same conditions than charged disordered sequences of the same length. However, inclusion of explicit solvent in addition naturally captures temperature-dependent solvation effects, which results in an initial collapse of the chains as temperature is increased, in qualitative agreement with experiment. There is a universal origin to the collapse, revealed in the change of hydration of individual residues as a function of temperature: namely, that the initial collapse is driven by unfavorable solvation free energy of individual residues, which in turn has a strong temperature dependence. We also observe that in unfolded globular proteins, increased temperature also initially favors formation of native-like (rather than non-native-like) structure. Our results help to establish how sequence encodes the degree of intrinsic disorder or order as well as its response to changes in environmental conditions.
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Affiliation(s)
- Gül H Zerze
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
| | - Robert B Best
- Laboratory of Chemical Physics, NIDDK, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Jeetain Mittal
- Department of Chemical and Biomolecular Engineering, Lehigh University , Bethlehem, Pennsylvania 18015, United States
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33
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Hackl EV. Effect of Temperature on the Conformation of Natively Unfolded Protein 4E-BP1 in Aqueous and Mixed Solutions Containing Trifluoroethanol and Hexafluoroisopropanol. Protein J 2014; 34:18-28. [DOI: 10.1007/s10930-014-9595-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Perez RB, Tischer A, Auton M, Whitten ST. Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins. Proteins 2014; 82:3373-84. [PMID: 25244701 DOI: 10.1002/prot.24692] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 08/26/2014] [Accepted: 09/16/2014] [Indexed: 01/12/2023]
Abstract
Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins (IDPs), mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline (PRO) and alanine (ALA) to glycine (GLY) substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (R(h)) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the GLY substitutions decreased polyproline II (PP(II)) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in R(h) were not associated with folding. The experiments showed that changes in local PP(II) structure cause changes in R(h) that are variable and that depend on the intrinsic chain propensities of PRO and ALA residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed PRO and alanine effects on the structures of IDPs.
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Affiliation(s)
- Romel B Perez
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
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35
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Wuttke R, Hofmann H, Nettels D, Borgia MB, Mittal J, Best RB, Schuler B. Temperature-dependent solvation modulates the dimensions of disordered proteins. Proc Natl Acad Sci U S A 2014; 111:5213-8. [PMID: 24706910 PMCID: PMC3986154 DOI: 10.1073/pnas.1313006111] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
For disordered proteins, the dimensions of the chain are an important property that is sensitive to environmental conditions. We have used single-molecule Förster resonance energy transfer to probe the temperature-induced chain collapse of five unfolded or intrinsically disordered proteins. Because this behavior is sensitive to the details of intrachain and chain-solvent interactions, the collapse allows us to probe the physical interactions governing the dimensions of disordered proteins. We find that each of the proteins undergoes a collapse with increasing temperature, with the most hydrophobic one, λ-repressor, undergoing a reexpansion at the highest temperatures. Although such a collapse might be expected due to the temperature dependence of the classical "hydrophobic effect," remarkably we find that the largest collapse occurs for the most hydrophilic, charged sequences. Using a combination of theory and simulation, we show that this result can be rationalized in terms of the temperature-dependent solvation free energies of the constituent amino acids, with the solvation properties of the most hydrophilic residues playing a large part in determining the collapse.
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Affiliation(s)
- René Wuttke
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Hagen Hofmann
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | - Daniel Nettels
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
| | | | - Jeetain Mittal
- Department of Chemical Engineering, Lehigh University, Bethlehem, PA 18015; and
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Digestive and Diabetes and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
| | - Benjamin Schuler
- Department of Biochemistry, University of Zurich, 8057 Zurich, Switzerland
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